diff --git a/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb b/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb deleted file mode 100644 index c34e16d5f3e..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb +++ /dev/null @@ -1,59 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ABINIT' -version = '9.2.1' - -homepage = 'https://www.abinit.org/' -description = """ABINIT is a package whose main program allows one to find the total energy, - charge density and electronic structure of systems made of electrons and nuclei (molecules - and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a - planewave or wavelet basis.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = ['https://www.abinit.org/sites/default/files/packages/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] - -builddependencies = [ - ('Python', '3.8.2'), -] -dependencies = [ - ('libxc', '4.3.4'), - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), - ('HDF5', '1.10.6'), -] - -# Ensure MPI with intel wrappers. -configopts = '--with-mpi="yes" --enable-openmp="no" ' -configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' - -# BLAS/Lapack from MKL -configopts += '--with-linalg-flavor=mkl ' - -# FFTW from MKL -configopts += '--with-fft-flavor=dfti ' - -# libxc support -configopts += '--with-libxc=${EBROOTLIBXC} ' - -# hdf5/netcdf4 support -configopts += '--with-netcdf="${EBROOTNETCDF}" ' -configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' -configopts += '--with-hdf5="${EBROOTHDF5}" ' - -# abinit must be run under mpirun with Intel MPI included in intel/2020a -pretestopts = "sed -i 's@./abinit testin@mpirun -np 1 ./abinit testin@g' Makefile && " - -# 'make check' is just executing some basic unit tests. -# Also running 'make tests_v1' to have some basic validation -runtest = "check && make test_v1" - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.4.1-intel-2020a.eb b/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.4.1-intel-2020a.eb deleted file mode 100644 index 8ce0054cd7f..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ABINIT/ABINIT-9.4.1-intel-2020a.eb +++ /dev/null @@ -1,59 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ABINIT' -version = '9.4.1' - -homepage = 'https://www.abinit.org/' -description = """ABINIT is a package whose main program allows one to find the total energy, - charge density and electronic structure of systems made of electrons and nuclei (molecules - and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a - planewave or wavelet basis.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = ['https://www.abinit.org/sites/default/files/packages/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['ec74133ef9d247cb6ad44c205675694919cf36d7f1682a9b85cae8bdecdc22a8'] - -builddependencies = [ - ('Python', '3.8.2'), -] -dependencies = [ - ('libxc', '4.3.4'), - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), - ('HDF5', '1.10.6'), -] - -# Ensure MPI with intel wrappers. -configopts = '--with-mpi="yes" --enable-openmp="no" ' -configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' - -# BLAS/Lapack from MKL -configopts += '--with-linalg-flavor=mkl ' - -# FFTW from MKL -configopts += '--with-fft-flavor=dfti ' - -# libxc support -configopts += '--with-libxc=${EBROOTLIBXC} ' - -# hdf5/netcdf4 support -configopts += '--with-netcdf="${EBROOTNETCDF}" ' -configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' -configopts += '--with-hdf5="${EBROOTHDF5}" ' - -# abinit must be run under mpirun with Intel MPI included in intel/2020a -pretestopts = "sed -i 's@./abinit testin@mpirun -np 1 ./abinit testin@g' Makefile && " - -# 'make check' is just executing some basic unit tests. -# Also running 'make tests_v1' to have some basic validation -runtest = "check && make test_v1" - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb deleted file mode 100644 index 5496b9fbe5d..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'MakeCp' - -name = 'ABRA2' -version = '2.23' - -homepage = 'https://github.com/mozack/abra2' -description = "Assembly Based ReAligner" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/mozack/abra2/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['ABRA2-2.22_fix-Makefile.patch'] -checksums = [ - '3993f66a493070ee49df2865b6786a45a0cf6c379bae83e94b8339abbe673289', # v2.23.tar.gz - '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch -] - -builddependencies = [('Maven', '3.6.3', '', SYSTEM)] - -dependencies = [ - ('Java', '11', '', SYSTEM), - ('BWA', '0.7.17'), -] - -maxparallel = 1 - -buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' -buildopts += '&& make standalone CXX="$CXX" CXXFLAGS="$CXXFLAGS"' - -files_to_copy = [ - (['abra'], 'bin'), - (['target/libAbra.%s' % SHLIB_EXT], 'lib'), - 'target/abra2-%(version)s-jar-with-dependencies.jar', -] - -postinstallcmds = ["cd %(installdir)s && mv abra2-%(version)s-jar-with-dependencies.jar abra2-%(version)s.jar"] - -sanity_check_paths = { - 'files': ['abra2-%(version)s.jar', 'bin/abra', 'lib/libAbra.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb deleted file mode 100644 index 70fd0130ae2..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'MakeCp' - -name = 'ACTC' -version = '1.1' - -homepage = 'https://sourceforge.net/projects/actc' -description = "ACTC converts independent triangles into triangle strips or fans." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['3a1303291629b9de6008c3c9d7b020a4b854802408fb3f8222ec492808c8b44d'] - -builddependencies = [('binutils', '2.34')] - -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' - -files_to_copy = [ - (['tcsample', 'tctest', 'tctest2'], 'bin'), - (['tc.h'], 'include/ac'), - (['libactc.a'], 'lib'), - 'COPYRIGHT', 'manual.html', 'prims.gif', 'README', -] - -sanity_check_paths = { - 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', - 'COPYRIGHT', 'manual.html', 'prims.gif', 'README'], - 'dirs': [], -} - -modextrapaths = {'CPATH': 'include/ac'} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 6df9ace119f..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,73 +0,0 @@ -# Based on ADIOS-1.13.1-foss-2019a-Python-2.7.15.eb -# Updated to foss-2020a toolchain and switched to ConfigureMake -# Mini-XML updated to latest 2.x. version -# Author: J. Sassmannshausen (Imperial College London/UK) - -easyblock = 'ConfigureMake' - -name = 'ADIOS' -version = '1.13.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.olcf.ornl.gov/center-projects/adios/' -description = """The Adaptable IO System (ADIOS) provides a simple, -flexible way for scientists to describe the data in their code that may -need to be written, read, or processed outside of the running -simulation.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -github_account = 'ornladios' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_force_use_of_mpi.patch', - '%(name)s-%(version)s_fix_missing_thread_lib.patch', - '%(name)s-%(version)s_fix_search_for_szip.patch', -] -checksums = [ - 'b1c6949918f5e69f701cabfe5987c0b286793f1057d4690f04747852544e157b', # v1.13.1.tar.gz - '81b9b0a77b23d6137f08900a3ecda4471b806c384cf4ad19c4370fc7ca8d9a82', # ADIOS-1.13.1_force_use_of_mpi.patch - 'a66fab38e5daf40978f9e961d810f9cbf189de8db924a403ae42a01d405f6fdc', # ADIOS-1.13.1_fix_missing_thread_lib.patch - '2e21a5041822c8b57554eb977a3135637c2714d377eee3b0194d377f1458cdab', # ADIOS-1.13.1_fix_search_for_szip.patch -] - -builddependencies = [ - ('Autotools', '20180311'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('Szip', '2.1.1'), - ('lz4', '1.9.2'), - ('netCDF', '4.7.4'), - ('Mini-XML', '2.12'), -] - -preconfigopts = ' autoreconf -i && ' -configopts = '--with-zlib=$EBROOTZLIB -with-bzip2=$EBROOTBZIP2 --with-netcdf==$EBROOTNETCDF ' -configopts += '--with-lz4=$EBROOTLZ4 --with-mxml=$EBROOTMINIMINXML --with-phdf5=$EBROOTHDF5 ' - -fix_python_shebang_for = ['bin/gpp.py'] - -runtest = ' check' - -sanity_check_paths = { - 'files': ['bin/adios_list_methods', 'bin/bpappend'], - 'dirs': ['etc/skel/templates', 'lib/python'], -} - -sanity_check_commands = [ - 'adios_list_methods', - 'bpappend -h', -] - -modextrapaths = { - 'PYTHONPATH': 'lib/python', -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1_fix_missing_thread_lib.patch b/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1_fix_missing_thread_lib.patch deleted file mode 100644 index 2933204d3bb..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1_fix_missing_thread_lib.patch +++ /dev/null @@ -1,21 +0,0 @@ -Make sure the thread lib gets added to the list of libs. - -Åke Sandgren, 2019-12-10 -diff -ru adios-1.13.1.orig/CMakeLists.txt adios-1.13.1/CMakeLists.txt ---- adios-1.13.1.orig/CMakeLists.txt 2018-04-17 19:26:32.000000000 +0200 -+++ adios-1.13.1/CMakeLists.txt 2019-12-10 11:21:31.108061330 +0100 -@@ -2154,6 +2154,14 @@ - set(ADIOSLIB_INT_LDADD ${ADIOSLIB_INT_LDADD} ${M_LIBS}) - set(ADIOSREADLIB_LDADD ${ADIOSREADLIB_LDADD} ${M_LIBS}) - set(ADIOSREADLIB_SEQ_LDADD ${ADIOSREADLIB_SEQ_LDADD} ${M_LIBS}) -+ -+if (HAVE_PTHREAD) -+ set(ADIOSLIB_LDADD ${ADIOSLIB_LDADD} ${CMAKE_THREAD_LIBS_INIT}) -+ set(ADIOSLIB_SEQ_LDADD ${ADIOSLIB_SEQ_LDADD} ${CMAKE_THREAD_LIBS_INIT}) -+ set(ADIOSLIB_INT_LDADD ${ADIOSLIB_INT_LDADD} ${CMAKE_THREAD_LIBS_INIT}) -+ set(ADIOSREADLIB_LDADD ${ADIOSREADLIB_LDADD} ${CMAKE_THREAD_LIBS_INIT}) -+ set(ADIOSREADLIB_SEQ_LDADD ${ADIOSREADLIB_SEQ_LDADD} ${CMAKE_THREAD_LIBS_INIT}) -+endif() - ############################### srart of top CMakeLists.txt ############################### - #install(PROGRAMS adios_config DESTINATION ${bindir}) - diff --git a/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1_fix_search_for_szip.patch b/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1_fix_search_for_szip.patch deleted file mode 100644 index 0c4281e59df..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1_fix_search_for_szip.patch +++ /dev/null @@ -1,24 +0,0 @@ -Fix CMake check for Szip/SZ - -Åke Sandgren, 20200310 -diff -ru ADIOS-1.13.1.orig/CMakeLists.txt ADIOS-1.13.1/CMakeLists.txt ---- ADIOS-1.13.1.orig/CMakeLists.txt 2018-04-17 19:23:13.000000000 +0200 -+++ ADIOS-1.13.1/CMakeLists.txt 2020-03-10 09:15:55.755501700 +0100 -@@ -523,7 +523,7 @@ - set(SZIP_DIR $ENV{SZIP_DIR}) - endif() - elseif(DEFINED ENV{SZIP}) -- if(NOT "$ENV{SZIP}" STREQUAL "") -+ if("$ENV{SZIP}" STREQUAL "") - set(SZIP OFF CACHE BOOL "") - else() - set(SZIP_DIR $ENV{SZIP}) -@@ -639,7 +639,7 @@ - set(SZ_DIR $ENV{SZ_DIR}) - endif() - elseif(DEFINED ENV{SZ}) -- if(NOT "$ENV{SZ}" STREQUAL "") -+ if("$ENV{SZ}" STREQUAL "") - set(SZ OFF CACHE BOOL "") - else() - set(SZ_DIR $ENV{SZ}) diff --git a/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1_force_use_of_mpi.patch b/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1_force_use_of_mpi.patch deleted file mode 100644 index 359a278868c..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-1.13.1_force_use_of_mpi.patch +++ /dev/null @@ -1,29 +0,0 @@ -find_package(MPI) doesn't work with EasyBuild installed OpenMPI - -Åke Sandgren, 2019-12-10 -diff -ru adios-1.13.1.orig/CMakeLists.txt adios-1.13.1/CMakeLists.txt ---- adios-1.13.1.orig/CMakeLists.txt 2018-04-17 19:26:32.000000000 +0200 -+++ adios-1.13.1/CMakeLists.txt 2019-12-10 09:42:46.386373706 +0100 -@@ -1081,11 +1081,11 @@ - endif() - endif() - --set(HAVE_MPI 0) -+set(HAVE_MPI 1) - - # Define if you have the MPI library. - if(BUILD_FORTRAN) -- find_package(MPI COMPONENTS Fortran) -+ #find_package(MPI COMPONENTS Fortran) - if(MPI_FOUND) - # if(MPI_LIBRARIES AND MPI_INCLUDE_PATH) - message(STATUS "find MPI") -@@ -1095,7 +1095,7 @@ - # set(LIBS ${MPILIBS}) - endif(MPI_FOUND) - else() -- find_package(MPI) -+ #find_package(MPI) - if(MPI_FOUND) - # if(MPI_LIBRARIES AND MPI_INCLUDE_PATH) - message(STATUS "find MPI") diff --git a/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 03d791038bf..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,78 +0,0 @@ -# Based on ADIOS-1.13.1-foss-2019a-Python-2.7.15.eb -# Updated to foss-2020a toolchain and switched to ConfigureMake -# Latest version from GitHub -# Mini-XML updated to latest 2.x. version -# Author: J. Sassmannshausen (Imperial College London/UK) - -easyblock = 'ConfigureMake' - -name = 'ADIOS' -version = '20210804' -local_commit = 'de85222' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.olcf.ornl.gov/center-projects/adios/' -description = """The Adaptable IO System (ADIOS) provides a simple, -flexible way for scientists to describe the data in their code that may -need to be written, read, or processed outside of the running -simulation.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -github_account = 'ornladios' -source_urls = [GITHUB_SOURCE] -sources = ['%s.tar.gz' % local_commit] - -patches = [ - '%(name)s-1.13.1_force_use_of_mpi.patch', - '%(name)s-1.13.1_fix_missing_thread_lib.patch', - '%(name)s-1.13.1_fix_search_for_szip.patch', -] -checksums = [ - 'c58af40cbdb13843de2c2c157379d069880835c9b932ad05e774910ec23a468f', # de85222.tar.gz - '81b9b0a77b23d6137f08900a3ecda4471b806c384cf4ad19c4370fc7ca8d9a82', # ADIOS-1.13.1_force_use_of_mpi.patch - 'a66fab38e5daf40978f9e961d810f9cbf189de8db924a403ae42a01d405f6fdc', # ADIOS-1.13.1_fix_missing_thread_lib.patch - '2e21a5041822c8b57554eb977a3135637c2714d377eee3b0194d377f1458cdab', # ADIOS-1.13.1_fix_search_for_szip.patch -] - -builddependencies = [ - ('Autotools', '20180311'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('Szip', '2.1.1'), - ('lz4', '1.9.2'), - ('netCDF', '4.7.4'), - ('Mini-XML', '2.12'), - ('zfp', '1.0.0'), -] - -preconfigopts = ' autoreconf -i && export LIBS="-lgomp" && ' -configopts = '--with-zlib=$EBROOTZLIB -with-bzip2=$EBROOTBZIP2 --with-netcdf==$EBROOTNETCDF ' -configopts += '--with-lz4=$EBROOTLZ4 --with-mxml=$EBROOTMINIMINXML --with-phdf5=$EBROOTHDF5 ' -configopts += '--with-zfp=$EBROOTZFP ' - -fix_python_shebang_for = ['bin/gpp.py'] - -runtest = ' check' - -sanity_check_paths = { - 'files': ['bin/adios_list_methods', 'bin/bpappend'], - 'dirs': ['etc/skel/templates', 'lib/python'], -} - -sanity_check_commands = [ - 'adios_list_methods', - 'bpappend -h', -] - -modextrapaths = { - 'PYTHONPATH': 'lib/python', -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/a/ADOL-C/ADOL-C-2.7.2-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/a/ADOL-C/ADOL-C-2.7.2-gompi-2020a.eb deleted file mode 100644 index c4df3c895d4..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ADOL-C/ADOL-C-2.7.2-gompi-2020a.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ADOL-C' -version = '2.7.2' - -homepage = 'https://projects.coin-or.org/ADOL-C' - -description = """The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates -the evaluation of first and higher derivatives of vector functions that are defined -by computer programs written in C or C++. The resulting derivative evaluation -routines may be called from C/C++, Fortran, or any other language that can be linked -with C. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} - -source_urls = ['https://github.com/coin-or/%(name)s/archive/releases'] -sources = ['%(version)s.tar.gz'] -checksums = ['701e0856baae91b98397960d5e0a87a549988de9d4002d0e9a56fa08f5455f6e'] - -builddependencies = [('Autotools', '20180311')] - -preconfigopts = 'autoreconf -fi && ' - -sanity_check_paths = { - 'files': ['lib64/libadolc.so'], - 'dirs': ['include/adolc'], -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/a/AMD-LibM/AMD-LibM-3.6.0-4-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/AMD-LibM/AMD-LibM-3.6.0-4-GCC-9.3.0.eb deleted file mode 100644 index 5f68adb3207..00000000000 --- a/easybuild/easyconfigs/__archive__/a/AMD-LibM/AMD-LibM-3.6.0-4-GCC-9.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'Binary' - -name = 'AMD-LibM' -version = '3.6.0-4' - -homepage = 'https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/' -description = """AMD LibM is a software library containing a collection of basic math functions -optimized for x86-64 processor based machines.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['http://developer.amd.com/wordpress/media/files/'] -sources = ['aocl-libm-linux-gcc-%(version)s.tar.gz'] -checksums = ['ab7d106c3f2ce512aca7d2977724af9bb80e245dcc12979cfdc2b1a08b863134'] - -extract_sources = True - -sanity_check_paths = { - 'files': ['include/amdlibm.h', 'include/amdlibm_vec.h', 'lib/libamdlibm.%s' % SHLIB_EXT, 'lib/libamdlibm.a'], - 'dirs': ['examples'], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/a/AMD-RNG/AMD-RNG-2.2-4-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/AMD-RNG/AMD-RNG-2.2-4-GCC-9.3.0.eb deleted file mode 100644 index 731559ba4d6..00000000000 --- a/easybuild/easyconfigs/__archive__/a/AMD-RNG/AMD-RNG-2.2-4-GCC-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'Binary' - -name = 'AMD-RNG' -version = '2.2-4' - -homepage = 'https://developer.amd.com/amd-cpu-libraries/rng-library/' -description = """AMD Random Number Generator Library is a pseudorandom number generator library.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['http://developer.amd.com/wordpress/media/files/'] -sources = ['aocl-rng-linux-gcc-%(version)s.tar.gz'] -checksums = ['1eb1904e9ea4b4aea66ff988c23c1a18901edfb3f90790d7f4d774aab2de5e14'] - -extract_sources = True - -postinstallcmds = [ - "cd %(installdir)s && ln -s rng/include include", - "cd %(installdir)s && ln -s rng/lib lib", - "cd %(installdir)s && ln -s rng/lib lib64", -] - -sanity_check_paths = { - 'files': ['include/rng.h', 'lib/librng_amd.a', 'lib/librng_omp_amd.a', - 'lib/librng_amd.%s' % SHLIB_EXT, 'lib/librng_omp_amd.%s' % SHLIB_EXT], - 'dirs': ['rng/examples'] -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/a/AMD-SecureRNG/AMD-SecureRNG-2.2-4-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/AMD-SecureRNG/AMD-SecureRNG-2.2-4-GCC-9.3.0.eb deleted file mode 100644 index da017599d0c..00000000000 --- a/easybuild/easyconfigs/__archive__/a/AMD-SecureRNG/AMD-SecureRNG-2.2-4-GCC-9.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'Binary' - -name = 'AMD-SecureRNG' -version = '2.2-4' - -homepage = 'https://developer.amd.com/amd-cpu-libraries/rng-library/' -description = """The AMD Secure Random Number Generator (RNG) is a library that provides APIs to access the -cryptographically secure random numbers generated by AMD’s hardware-based random number generator implementation.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['http://developer.amd.com/wordpress/media/files/'] -sources = ['aocl-securerng-linux-gcc-%(version)s.tar.gz'] -checksums = ['27920021ddb7e3ace006747c838d5330fefb863d62dc7ed98a81880f2a9ef66d'] - -extract_sources = True - -sanity_check_paths = { - 'files': ['include/secrng.h', 'lib/libamdsecrng.a', 'lib/libamdsecrng.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb deleted file mode 100644 index 25632498de1..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ANTLR' -version = '2.7.7' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://www.antlr2.org/' -description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) - is a language tool that provides a framework for constructing recognizers, - compilers, and translators from grammatical descriptions containing - Java, C#, C++, or Python actions.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.antlr2.org/download/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_includes.patch'] -checksums = [ - '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz - 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch -] - -builddependencies = [('binutils', '2.34')] -dependencies = [('Java', '11', '', SYSTEM)] - -configopts = '--disable-examples --disable-csharp --disable-python' - -sanity_check_paths = { - 'files': ['bin/antlr', 'bin/antlr-config'], - 'dirs': ['include'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/AOCC/AOCC-2.3.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/AOCC/AOCC-2.3.0-GCCcore-9.3.0.eb deleted file mode 100644 index 3d57a9be754..00000000000 --- a/easybuild/easyconfigs/__archive__/a/AOCC/AOCC-2.3.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'AOCC' -version = '2.3.0' - -homepage = 'https://developer.amd.com/amd-aocc/' -description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0" - -# Clang also depends on libstdc++ during runtime, but this dependency is -# already specified as the toolchain. -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://developer.amd.com/wordpress/media/files/'] -sources = ['aocc-compiler-%(version)s.tar'] -checksums = [ - '9f8a1544a5268a7fb8cd21ac4bdb3f8d1571949d1de5ca48e2d3309928fc3d15', # aocc-compiler-2.3.0.tar -] - -dependencies = [ - ('binutils', '2.34'), - ('ncurses', '6.2'), - ('zlib', '1.2.11'), - ('libxml2', '2.9.10'), -] - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/a/AOMP/AOMP-13.0-2-gcccuda-2020a.eb b/easybuild/easyconfigs/__archive__/a/AOMP/AOMP-13.0-2-gcccuda-2020a.eb deleted file mode 100644 index 0e43cda4894..00000000000 --- a/easybuild/easyconfigs/__archive__/a/AOMP/AOMP-13.0-2-gcccuda-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Authors:: Jorgen Nordmoen -# License:: GPLv2 or later, MIT, three-clause BSD. -# $Id$ -## - -name = 'AOMP' -version = '13.0-2' - -homepage = 'https://github.com/ROCm-Developer-Tools/aomp' -description = "AMD fork of LLVM, setup for OpenMP offloading to Accelerators" - -toolchain = {'name': 'gcccuda', 'version': '2020a'} - -source_urls = ['https://github.com/ROCm-Developer-Tools/aomp/releases/download/rel_%(version)s/'] -sources = ['aomp-%(version)s.tar.gz'] -patches = ['AOMP-%(version)s_remove_hardcoded_paths.patch'] -checksums = [ - # aomp-13.0-2.tar.gz: - '0256a84aefcbf7c49112f068321b84e0620f4c43a9d490c64d820e40658e0d67', - # AOMP-13.0-2_remove_hardcoded_paths.patch: - 'ec41ffcec63d079b6a73c93bea29e0b8d77ca7b059725aa1d47c334f7e476ff0', -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Perl', '5.30.2'), - ('Python', '3.8.2'), - ('elfutils', '0.182'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('binutils', '2.34'), - ('libffi', '3.3'), - ('ncurses', '6.2'), - ('numactl', '2.0.13'), -] - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb deleted file mode 100644 index 9dcf1808307..00000000000 --- a/easybuild/easyconfigs/__archive__/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'APR-util' -version = '1.6.1' - -homepage = 'https://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('APR', '1.7.0'), - ('SQLite', '3.31.1'), - ('expat', '2.2.9'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -maxparallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/APR/APR-1.7.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/APR/APR-1.7.0-GCCcore-9.3.0.eb deleted file mode 100644 index 89a9158336f..00000000000 --- a/easybuild/easyconfigs/__archive__/a/APR/APR-1.7.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'APR' -version = '1.7.0' - -homepage = 'https://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.19.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.19.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 2edeb029782..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.19.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'ASE' -version = '3.19.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://wiki.fysik.dtu.dk/ase' -description = """ASE is a python package providing an open source Atomic Simulation Environment - in the Python scripting language.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('Tkinter', '%(pyver)s'), - ('matplotlib', '3.2.1', '-Python-%(pyver)s'), -] - -exts_list = [ - ('MarkupSafe', '1.1.1', { - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('Jinja2', '2.10.3', { - 'checksums': ['9fe95f19286cfefaa917656583d020be14e7859c6b0252588391e47db34527de'], - }), - ('Werkzeug', '0.16.0', { - 'checksums': ['7280924747b5733b246fe23972186c6b348f9ae29724135a6dfc1e53cea433e7'], - }), - ('Click', '7.0', { - 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], - }), - ('itsdangerous', '1.1.0', { - 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], - }), - ('Flask', '1.1.1', { - 'checksums': ['13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52'], - }), - ('ase', version, { - 'checksums': ['a8378ab57e91cfe1ba09b3639d8409bb7fc1a40b59479c7822d206e673ad93f9'], - }), -] - -sanity_check_paths = { - 'files': ['bin/ase'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -# make sure Tkinter is available, otherwise 'ase gui' will not work -sanity_check_commands = ["python -c 'import tkinter' "] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.19.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.19.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 5747600d761..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.19.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'ASE' -version = '3.19.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://wiki.fysik.dtu.dk/ase' -description = """ASE is a python package providing an open source Atomic Simulation Environment - in the Python scripting language.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('Tkinter', '%(pyver)s'), - ('matplotlib', '3.2.1', '-Python-%(pyver)s'), -] - -# required because we're building Python packages (MarkupSafe) using Intel compilers on top of Python built with GCC. -check_ldshared = True - -exts_list = [ - ('MarkupSafe', '1.1.1', { - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('Jinja2', '2.10.3', { - 'checksums': ['9fe95f19286cfefaa917656583d020be14e7859c6b0252588391e47db34527de'], - }), - ('Werkzeug', '0.16.0', { - 'checksums': ['7280924747b5733b246fe23972186c6b348f9ae29724135a6dfc1e53cea433e7'], - }), - ('Click', '7.0', { - 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], - }), - ('itsdangerous', '1.1.0', { - 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], - }), - ('Flask', '1.1.1', { - 'checksums': ['13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52'], - }), - ('ase', version, { - 'checksums': ['a8378ab57e91cfe1ba09b3639d8409bb7fc1a40b59479c7822d206e673ad93f9'], - }), -] - -sanity_check_paths = { - 'files': ['bin/ase'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -# make sure Tkinter is available, otherwise 'ase gui' will not work -sanity_check_commands = ["python -c 'import tkinter' "] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.20.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.20.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 092d2bcca50..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.20.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'ASE' -version = '3.20.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://wiki.fysik.dtu.dk/ase' -description = """ASE is a python package providing an open source Atomic Simulation Environment - in the Python scripting language.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('Tkinter', '%(pyver)s'), - ('matplotlib', '3.2.1', '-Python-%(pyver)s'), -] - -exts_list = [ - ('MarkupSafe', '1.1.1', { - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('Jinja2', '2.11.2', { - 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], - }), - ('Werkzeug', '1.0.1', { - 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('itsdangerous', '1.1.0', { - 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], - }), - ('Flask', '1.1.2', { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), - ('ase', version, { - 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], - }), -] - -sanity_check_paths = { - 'files': ['bin/ase'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "ase --help", - # make sure Tkinter is available, otherwise 'ase gui' will not work - "python -c 'import tkinter' ", -] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.21.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.21.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index abf7643e5c9..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.21.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'ASE' -version = '3.21.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://wiki.fysik.dtu.dk/ase' -description = """ASE is a python package providing an open source Atomic Simulation Environment - in the Python scripting language. - -From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations -in C of functions in ASE. ASE uses it automatically when installed.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Flask', '1.1.2', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('Tkinter', '%(pyver)s'), # needed by GUI of ASE - ('spglib-python', '1.16.0', versionsuffix), # optional -] - -exts_list = [ - ('ase', version, { - 'checksums': ['78b01d88529d5f604e76bc64be102d48f058ca50faad72ac740d717545711c7b'], - }), - ('ase-ext', '20.9.0', { - 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], - }), -] - -sanity_check_paths = { - 'files': ['bin/ase'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -# make sure Tkinter is available, otherwise 'ase gui' will not work -sanity_check_commands = ["python -c 'import tkinter' "] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb deleted file mode 100644 index f9d18c69824..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright (c) 2020 The Rector and Visitors of the University of Virginia -# -# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated -# documentation files (the "Software"), to deal in the Software without restriction, including without -# limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the -# Software, and to permit persons to whom the Software is furnished to do so, subject to the following -# conditions: -# -# The above copyright notice and this permission notice shall be included in all copies or substantial portions -# of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED -# TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF -# CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -# DEALINGS IN THE SOFTWARE. -# -# Ruoshi Sun -# Research Computing, University of Virginia -# 2020-05-24 - -easyblock = 'ConfigureMake' - -name = 'ATAT' -version = '3.36' - -homepage = 'https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/' -description = """ -The Alloy-Theoretic Automated Toolkit (ATAT) is a generic name that refers to a collection of alloy theory tools -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://alum.mit.edu/www/avdw/%(namelower)s'] -sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '_')] -checksums = ['e829da5b714a012b5fc456d1060cfdb784642a8c0cbb702d409497b65466ee39'] - -builddependencies = [ - ('binutils', '2.34') -] - -skipsteps = ['configure'] - -local_bindir = '%(builddir)s/%(namelower)s/bin' - -prebuildopts = 'mkdir -p %s && ' % local_bindir -buildopts = 'BINDIR=%s' % local_bindir - -local_install1 = 'make -C src BINDIR=%s install && ' % local_bindir -local_install2 = 'make -C glue/jobctrl BINDIR=%s install && ' % local_bindir -local_install3 = 'make -C glue/vasp BINDIR=%s install' % local_bindir - -install_cmd = local_install1 + local_install2 + local_install3 - -local_to_copy = ['bin', 'data', 'doc', 'examples', 'glue', 'license.txt'] - -postinstallcmds = [ - 'cp -r %%(builddir)s/%%(namelower)s/%s %%(installdir)s' % x for x in local_to_copy -] - -sanity_check_paths = { - 'files': ['bin/maps'], - 'dirs': local_to_copy[:-1] -} - -sanity_check_commands = [ - "maps --help 2>&1 | grep '^MIT Ab initio Phase Stability (MAPS) code %(version)s'" -] - -modloadmsg = "First-time users please run:\necho set atatdir=$EBROOTATAT > $HOME/.atat.rc\n" - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/ATK/ATK-2.36.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/ATK/ATK-2.36.0-GCCcore-9.3.0.eb deleted file mode 100644 index c7864524a5e..00000000000 --- a/easybuild/easyconfigs/__archive__/a/ATK/ATK-2.36.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'ATK' -version = '2.36.0' - -homepage = 'https://developer.gnome.org/atk/' -description = """ - ATK provides the set of accessibility interfaces that are implemented by other - toolkits and applications. Using the ATK interfaces, accessibility tools have - full access to view and control running applications. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['fb76247e369402be23f1f5c65d38a9639c1164d934e40f6a9cf3c9e96b652788'] - -builddependencies = [ - ('binutils', '2.34'), - ('Meson', '0.55.1', '-Python-3.8.2'), - ('Ninja', '1.10.0'), - ('pkg-config', '0.29.2'), - ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), -] - -dependencies = [ - ('GLib', '2.64.1'), -] - -configopts = "--default-library=both " -configopts += "-Dintrospection=true " - -sanity_check_paths = { - 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020a.eb deleted file mode 100644 index 462fb766558..00000000000 --- a/easybuild/easyconfigs/__archive__/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020a.eb +++ /dev/null @@ -1,64 +0,0 @@ -# Updated by: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'ConfigureMake' - -name = 'AUGUSTUS' -version = '3.4.0' - -homepage = 'https://bioinf.uni-greifswald.de/augustus/' -description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" - -toolchain = {'name': 'foss', 'version': '2020a'} - -# https://github.com/Gaius-Augustus/Augustus/archive -github_account = 'Gaius-Augustus' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch'] -checksums = [ - '2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8', # v3.4.0.tar.gz - 'e74023f28ee3e76590f4534d195c313b88b66a92ec779da184d30d056fc8e052', # AUGUSTUS-3.4.0_fix-hardcoding.patch -] - -builddependencies = [ - ('Python', '3.8.2'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('Boost', '1.72.0'), - ('GSL', '2.6'), - ('SAMtools', '1.10'), - ('HTSlib', '1.10.2'), # also provides tabix - ('BCFtools', '1.10.2'), - ('lpsolve', '5.5.2.11'), - ('SuiteSparse', '5.7.1', '-METIS-5.1.0'), - ('BamTools', '2.5.1'), - ('SQLite', '3.31.1'), -] - -skipsteps = ['configure'] - -# run "make clean" to avoid using binaries included with the source tarball -prebuildopts = "make clean && " - -buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" LINK.cc="$CXX" ' -installopts = 'INSTALLDIR=%(installdir)s ' - -sanity_check_paths = { - 'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch', - 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', - 'bin/load2sqlitedb', 'bin/prepareAlign'], - 'dirs': ['config', 'scripts'], -} -sanity_check_commands = ['augustus --help'] - -modextrapaths = {'PATH': 'scripts'} -modextravars = { - 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', - 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', - 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb deleted file mode 100644 index ca61e8b952f..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb +++ /dev/null @@ -1,62 +0,0 @@ -name = 'Amber' -local_amber_ver = 20 -local_ambertools_ver = 20 -# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php -patchlevels = (15, 11) # (AmberTools, Amber) -version = '%s.%s' % (local_amber_ver, patchlevels[1]) -versionsuffix = '-AmberTools-%s.%s-Python-%%(pyver)s' % (local_ambertools_ver, patchlevels[0]) - -homepage = 'https://ambermd.org/' -description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing - molecular dynamics and structure prediction.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True, 'openmp': True} - -sources = [ - '%%(name)s%s.tar.bz2' % local_amber_ver, - 'AmberTools%s.tar.bz2' % local_ambertools_ver, -] -patches = [ - 'AmberTools-%s_cmake-locate-netcdf.patch' % local_ambertools_ver, - 'AmberTools-%s_fix_missing_MPI_LIBRARY_error.patch' % local_ambertools_ver, -] -checksums = [ - 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 - 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools20.tar.bz2 - '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch - # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch - '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', -] -download_instructions = f"""{name} requires manual download from https://ambermd.org/GetAmber.php -Required downloads: {' '.join(sources)}""" - -builddependencies = [ - ('Bison', '3.5.3'), - ('CMake', '3.16.4'), - ('flex', '2.6.4'), - ('make', '4.3'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('Boost', '1.72.0'), - ('bzip2', '1.0.8'), - ('libreadline', '8.0'), - ('matplotlib', '3.2.1', '-Python-%(pyver)s'), - ('netCDF-Fortran', '4.5.2'), - ('netCDF', '4.7.4'), - ('Perl', '5.30.2'), - ('PnetCDF', '1.12.1'), - ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA - ('Tkinter', '3.8.2'), - ('X11', '20200222'), - ('zlib', '1.2.11'), -] - -# Tests are flaky -runtest = False - -static = False - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb deleted file mode 100644 index 0f9ab549a84..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb +++ /dev/null @@ -1,63 +0,0 @@ -name = 'Amber' -local_amber_ver = 20 -local_ambertools_ver = 20 -# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php -patchlevels = (15, 11) # (AmberTools, Amber) -version = '%s.%s' % (local_amber_ver, patchlevels[1]) -versionsuffix = '-AmberTools-%s.%s-Python-%%(pyver)s' % (local_ambertools_ver, patchlevels[0]) - -homepage = 'https://ambermd.org/' -description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing - molecular dynamics and structure prediction.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'usempi': True, 'openmp': True} - -sources = [ - '%%(name)s%s.tar.bz2' % local_amber_ver, - 'AmberTools%s.tar.bz2' % local_ambertools_ver, -] -patches = [ - 'AmberTools-%s_cmake-locate-netcdf.patch' % local_ambertools_ver, - 'AmberTools-%s_fix_missing_MPI_LIBRARY_error.patch' % local_ambertools_ver, -] -checksums = [ - 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 - 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools20.tar.bz2 - '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch - # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch - '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', -] -download_instructions = f"""{name} requires manual download from https://ambermd.org/GetAmber.php -Required downloads: {' '.join(sources)}""" - -builddependencies = [ - ('Bison', '3.5.3'), - ('CMake', '3.16.4'), - ('flex', '2.6.4'), - ('make', '4.3'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('Boost', '1.72.0'), - ('bzip2', '1.0.8'), - ('libreadline', '8.0'), - ('matplotlib', '3.2.1', '-Python-%(pyver)s'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', SYSTEM), - ('netCDF-Fortran', '4.5.2'), - ('netCDF', '4.7.4'), - ('Perl', '5.30.2'), - ('PnetCDF', '1.12.1'), - ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA - ('Tkinter', '3.8.2'), - ('X11', '20200222'), - ('zlib', '1.2.11'), -] - -# Tests are flaky -runtest = False - -static = False - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/AmberMini/AmberMini-16.16.0-intel-2020a.eb b/easybuild/easyconfigs/__archive__/a/AmberMini/AmberMini-16.16.0-intel-2020a.eb deleted file mode 100644 index 7a47fcf9131..00000000000 --- a/easybuild/easyconfigs/__archive__/a/AmberMini/AmberMini-16.16.0-intel-2020a.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'AmberMini' -version = '16.16.0' - -homepage = 'https://github.com/choderalab/ambermini' -description = """A stripped-down set of just antechamber, sqm, and tleap.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/choderalab/ambermini/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['fcd699a62248aa17a11d8eaa090a0c55e8ba735dcd9ec5fb33a8927da5ce1c5a'] - -builddependencies = [ - ('Bison', '3.5.3'), - ('Python', '3.8.2'), -] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["sqm", "tleap"]], - 'dirs': [], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index c7813e12832..00000000000 --- a/easybuild/easyconfigs/__archive__/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,62 +0,0 @@ -easyblock = 'EB_Amber' - -name = 'AmberTools' -version = '20' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://ambermd.org/' -description = """AmberTools consists of several independently developed packages that work well by themselves, - and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, - with either explicit water or generalized Born solvent models.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -# download requires registration, see http://ambermd.org/AmberTools17-get.html -local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' -source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % version] -sources = [{ - 'download_filename': local_download_credentials, - 'filename': SOURCE_TAR_BZ2, -}] -patches = [ - 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', - 'AmberTools-20_cmake-locate-netcdf.patch', - 'AmberTools-20_fix_xblas_missing_make_dependency.patch', - 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', -] -checksums = [ - 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools-20.tar.bz2 - # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch' - '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', - '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch - # AmberTools-20_fix_xblas_missing_make_dependency.patch - 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', - # AmberTools-21_dont_include_config.h_in_top_Makefile.patch - 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', -] - -builddependencies = [ - ('Bison', '3.5.3'), - ('pkg-config', '0.29.2'), - ('CMake', '3.16.4'), - ('flex', '2.6.4'), - ('make', '4.3'), -] -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), - ('FFTW', '3.3.8'), -] - -# pysander should link with icc and not gcc -prebuildopts = """sed -i 's/import sys/import sys; os.environ["LDSHARED"] = "icc -shared "/g' """ -prebuildopts += "%(builddir)s/AmberTools/src/pysander/setup.py && " - -# Tests use pmemd which is not part of AmberTools -runtest = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-9.600.5_no_mkl.patch b/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-9.600.5_no_mkl.patch deleted file mode 100644 index 5c115a7dcb1..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-9.600.5_no_mkl.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- CMakeLists.txt.orig 2016-06-16 18:20:05.000000000 +0200 -+++ CMakeLists.txt 2019-10-22 10:44:59.764711121 +0200 -@@ -173,7 +173,7 @@ - - set(ARMA_OS unix) - -- include(ARMA_FindMKL) -+ set(MKL_FOUND false) - include(ARMA_FindACMLMP) - include(ARMA_FindACML) - include(ARMA_FindOpenBLAS) diff --git a/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-9.880.1-foss-2020a.eb b/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-9.880.1-foss-2020a.eb deleted file mode 100644 index bc1e684417f..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-9.880.1-foss-2020a.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'Armadillo' -version = "9.880.1" - -homepage = 'https://arma.sourceforge.net/' -description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards - a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, - as well as a subset of trigonometric and statistics functions.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://sourceforge.net/projects/arma/files'] -sources = [SOURCELOWER_TAR_XZ] -patches = [ - 'Armadillo-9.600.5_no_mkl.patch', -] -checksums = [ - '900f3e8d35d8b722217bed979fa618faf6f3e4f56964c887a1fce44c3d4c4b9f', # src - '8288e769ceaf06da9f6870f616272c354577b1dd6f07e923fed43b22bae131b6', # Armadillo-9.600.5_no_mkl.patch -] - -dependencies = [ - ('Boost', '1.72.0'), - ('arpack-ng', '3.7.0'), -] - -builddependencies = [('CMake', '3.16.4')] - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-9.900.1-foss-2020a.eb b/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-9.900.1-foss-2020a.eb deleted file mode 100644 index a5b7a43ef66..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Armadillo/Armadillo-9.900.1-foss-2020a.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'Armadillo' -version = "9.900.1" - -homepage = 'https://arma.sourceforge.net/' -description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards - a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, - as well as a subset of trigonometric and statistics functions.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://sourceforge.net/projects/arma/files'] -sources = [SOURCELOWER_TAR_XZ] -patches = [ - 'Armadillo-9.600.5_no_mkl.patch' -] -checksums = [ - '53d7ad6124d06fdede8d839c091c649c794dae204666f1be0d30d7931737d635', # src - '8288e769ceaf06da9f6870f616272c354577b1dd6f07e923fed43b22bae131b6', # Armadillo-9.600.5_no_mkl.patch -] - -dependencies = [ - ('Boost', '1.72.0'), - ('arpack-ng', '3.7.0'), -] - -builddependencies = [('CMake', '3.16.4')] - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index f2ea51b09b8..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,66 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Arrow' -version = '0.17.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://arrow.apache.org' -description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform - for in-memory data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] -sources = ['apache-arrow-%(version)s.tar.gz'] -patches = [ - 'Arrow-0.17.1_fix-arm.patch', -] -checksums = [ - 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz - 'd1076d35966056c39e0c88b8fadaaa7660ee4d8c07fc2c5bdf1d5d6e683ff44a', # Arrow-0.17.1_fix-arm.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Autotools', '20180311'), - ('flex', '2.6.4'), - ('Bison', '3.5.3'), - ('pkg-config', '0.29.2'), -] - -# Arrow strongly prefers included jemalloc, so not including it as a dependency -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy - ('Boost', '1.72.0'), -] - -start_dir = 'cpp' - -# see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON" - -# also install Python bindings -local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " -local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " -local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " -local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " -local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." -postinstallcmds = [local_install_pyarrow_cmds] - -sanity_check_paths = { - 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, - 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], - 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "python -c 'import pyarrow'", - "python -c 'import pyarrow.dataset'", - "python -c 'import pyarrow.parquet'", -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 8862b557d42..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,64 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Arrow' -version = '0.17.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://arrow.apache.org' -description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform - for in-memory data.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] -sources = ['apache-arrow-%(version)s.tar.gz'] -patches = ['Arrow-0.16.0_fix-intel.patch'] -checksums = [ - 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz - '7c1569087f93959a0dfc163d80e5f542edb4d7ed0b9d71a2a05b4081211ad2b9', # Arrow-0.16.0_fix-intel.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Autotools', '20180311'), - ('flex', '2.6.4'), - ('Bison', '3.5.3'), - ('pkg-config', '0.29.2'), -] - -# Arrow strongly prefers included jemalloc, so not including it as a dependency -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy - ('Boost', '1.72.0'), -] - -start_dir = 'cpp' - -# see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON" - -# also install Python bindings -local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " -local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " -local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " -local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " -local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." -postinstallcmds = [local_install_pyarrow_cmds] - -sanity_check_paths = { - 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, - 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], - 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "python -c 'import pyarrow'", - "python -c 'import pyarrow.dataset'", - "python -c 'import pyarrow.parquet'", -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb deleted file mode 100644 index 421245c596f..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Autoconf' -version = '2.69' - -homepage = 'https://www.gnu.org/software/autoconf/' - -description = """ - Autoconf is an extensible package of M4 macros that produce shell scripts - to automatically configure software source code packages. These scripts can - adapt the packages to many kinds of UNIX-like systems without manual user - intervention. Autoconf creates a configuration script for a package from a - template file that lists the operating system features that the package can - use, in the form of M4 macro calls. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] - -builddependencies = [ - ('binutils', '2.34'), - # non-standard Perl modules are required, - # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 - ('Perl', '5.30.2'), -] - -dependencies = [ - ('M4', '1.4.18'), -] - -sanity_check_paths = { - 'files': ["bin/%s" % x - for x in ["autoconf", "autoheader", "autom4te", "autoreconf", - "autoscan", "autoupdate", "ifnames"]], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb deleted file mode 100644 index 343a530c117..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'ConfigureMake' - -name = 'Autoconf' -version = '2.71' - -homepage = 'https://www.gnu.org/software/autoconf/' -description = """Autoconf is an extensible package of M4 macros that produce shell scripts - to automatically configure software source code packages. These scripts can adapt the - packages to many kinds of UNIX-like systems without manual user intervention. Autoconf - creates a configuration script for a package from a template file that lists the - operating system features that the package can use, in the form of M4 macro calls.""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['f14c83cfebcc9427f2c3cea7258bd90df972d92eb26752da4ddad81c87a0faa4'] - -builddependencies = [ - ('binutils', '2.36.1'), - # non-standard Perl modules are required, - # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 - ('Perl', '5.32.1'), -] - -dependencies = [ - ('M4', '1.4.18'), -] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", - "autoupdate", "ifnames"]], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb deleted file mode 100644 index 00bb8cb6910..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -easyblock = 'ConfigureMake' - -name = 'Automake' -version = '1.16.1' - -homepage = 'https://www.gnu.org/software/automake/automake.html' - -description = "Automake: GNU Standards-compliant Makefile generator" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] - -builddependencies = [ - ('binutils', '2.34'), - # non-standard Perl modules are required, - # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 - ('Perl', '5.30.2'), -] - -dependencies = [ - ('Autoconf', '2.69'), -] - -sanity_check_paths = { - 'files': ['bin/automake', 'bin/aclocal'], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.3-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.3-FCC-4.5.0.eb deleted file mode 100644 index 379e73dc996..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.3-FCC-4.5.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'ConfigureMake' - -name = 'Automake' -version = '1.16.3' - -homepage = 'https://www.gnu.org/software/automake/automake.html' - -description = "Automake: GNU Standards-compliant Makefile generator" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['ce010788b51f64511a1e9bb2a1ec626037c6d0e7ede32c1c103611b9d3cba65f'] - -builddependencies = [ - ('binutils', '2.36.1'), - # non-standard Perl modules are required, - # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 - ('Perl', '5.32.1'), -] - -dependencies = [ - ('Autoconf', '2.71'), -] - -sanity_check_paths = { - 'files': ['bin/automake', 'bin/aclocal'], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20180311-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20180311-GCCcore-9.3.0.eb deleted file mode 100644 index 04460cc610a..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20180311-GCCcore-9.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'Bundle' - -name = 'Autotools' -version = '20180311' # date of the most recent change - -homepage = 'https://autotools.io' - -description = """ - This bundle collect the standard GNU build tools: Autoconf, Automake - and libtool -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.16.1'), # 20180311 - ('libtool', '2.4.6'), # 20150215 -] - -# Pure bundle -- no need to specify 'binutils' used when building GCCcore -# toolchain as build dependency - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20210128-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20210128-FCC-4.5.0.eb deleted file mode 100644 index 955484ae6a3..00000000000 --- a/easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20210128-FCC-4.5.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'Bundle' - -name = 'Autotools' -version = '20210128' # date of the most recent change - -homepage = 'https://autotools.io' - -description = """ - This bundle collect the standard GNU build tools: Autoconf, Automake - and libtool -""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -dependencies = [ - ('Autoconf', '2.71'), # 20210128 - ('Automake', '1.16.3'), # 20201118 - ('libtool', '2.4.6'), # 20150215 -] - -# Pure bundle -- no need to specify 'binutils' - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/a/almosthere/almosthere-1.0.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/almosthere/almosthere-1.0.10-GCCcore-9.3.0.eb deleted file mode 100644 index 21f8fcd7484..00000000000 --- a/easybuild/easyconfigs/__archive__/a/almosthere/almosthere-1.0.10-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'almosthere' -version = '1.0.10' - -homepage = 'https://github.com/horta/almosthere' -description = """Progress indicator C library. -ATHR is a simple yet powerful progress indicator library that works on Windows, -Linux, and macOS. It is non-blocking as the progress update is done via a -dedicated, lightweight thread, as to not impair the performance of the calling program.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'horta' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['36e943f6e76fba6d2638972aff71d767a5ba0e72c472acf8282729ef1b0a0a0d'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] - -runtest = 'test' - -sanity_check_paths = { - 'files': ['lib/libathr.a', 'lib/libathr.%s' % SHLIB_EXT, 'include/athr.h'], - 'dirs': ['lib/cmake'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/alsa-lib/alsa-lib-1.2.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/alsa-lib/alsa-lib-1.2.4-GCCcore-9.3.0.eb deleted file mode 100644 index af83ab6b0ff..00000000000 --- a/easybuild/easyconfigs/__archive__/a/alsa-lib/alsa-lib-1.2.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'alsa-lib' -version = '1.2.4' - -homepage = 'https://www.alsa-project.org' -description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality - to the Linux operating system.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.alsa-project.org/files/pub/lib/'] -sources = [SOURCE_TAR_BZ2] -checksums = ['f7554be1a56cdff468b58fc1c29b95b64864c590038dd309c7a978c7116908f7'] - -dependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/aserver', 'include/asoundlib.h', - 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT], - 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/a/any2fasta/any2fasta-0.4.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/any2fasta/any2fasta-0.4.2-GCCcore-9.3.0.eb deleted file mode 100644 index 94f7c466d8b..00000000000 --- a/easybuild/easyconfigs/__archive__/a/any2fasta/any2fasta-0.4.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'Tarball' - -name = 'any2fasta' -version = '0.4.2' - -homepage = 'https://github.com/tseemann/any2fasta' -description = "Convert various sequence formats to FASTA" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -# https://github.com/tseemann/any2fasta -github_account = 'tseemann' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.zip'] -checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] - -dependencies = [('Perl', '5.30.2')] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['any2fasta'], - 'dirs': [], -} - -sanity_check_commands = [ - 'any2fasta -h', - 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/archspec/archspec-0.1.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/archspec/archspec-0.1.0-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index b0a3018b69d..00000000000 --- a/easybuild/easyconfigs/__archive__/a/archspec/archspec-0.1.0-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'archspec' -version = '0.1.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/archspec/archspec' -description = "A library for detecting, labeling, and reasoning about microarchitectures" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = ['archspec-%(version)s-py2.py3-none-any.whl'] -checksums = ['12f2029f63ffbc560e43f7d1f366a45ff46c7bd0751653227f8015f83f121119'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('Python', '3.8.2')] - -sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch b/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch deleted file mode 100644 index faf2b15b550..00000000000 --- a/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch +++ /dev/null @@ -1,14 +0,0 @@ -Fix 'Unknown CMake command "check_symbol_exists".' error -By Sebastien Varrette (UL HPC Team - University of Luxembourg) -diff -Nru arpack-ng-3.7.0.orig/CMakeLists.txt arpack-ng-3.7.0/CMakeLists.txt ---- arpack-ng-3.7.0.orig/CMakeLists.txt 2020-04-07 15:46:29.000000000 +0200 -+++ arpack-ng-3.7.0/CMakeLists.txt 2020-04-07 15:47:35.000000000 +0200 -@@ -29,6 +29,8 @@ - - set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib) - -+include(CheckSymbolExists) -+ - if (COVERALLS) - include(Coveralls) - set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -O0 -fprofile-arcs -ftest-coverage") diff --git a/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.7.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.7.0-foss-2020a.eb deleted file mode 100644 index b442cdb0222..00000000000 --- a/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.7.0-foss-2020a.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'arpack-ng' -version = "3.7.0" - -homepage = 'https://github.com/opencollab/arpack-ng' -description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -github_account = 'opencollab' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6'] - -builddependencies = [ - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Eigen', '3.3.7') -] - -preconfigopts = "sh bootstrap && " -configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' - -sanity_check_paths = { - 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.7.0-intel-2020a.eb b/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.7.0-intel-2020a.eb deleted file mode 100644 index ac52073ee3b..00000000000 --- a/easybuild/easyconfigs/__archive__/a/arpack-ng/arpack-ng-3.7.0-intel-2020a.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'arpack-ng' -version = "3.7.0" - -homepage = 'https://github.com/opencollab/arpack-ng' -description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -github_account = 'opencollab' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s-add_include_CheckSymbolExists_CMakeLists_txt.patch'] -checksums = [ - '972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6', # arpack-ng-3.7.0.tar.gz - # arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch - 'ce6035792ed0302a18b0f489024c142d8ed3f76e0b75e6d10dbffded26e7ffce', -] - -builddependencies = [ - ('CMake', '3.16.4') -] - -dependencies = [ - ('Eigen', '3.3.7') -] - -separate_build_dir = True - -local_common_configopts = "-DICB=ON -DMPI=ON -DEXAMPLES=ON" - -# perform iterative build to get both static and shared libraries -configopts = [ - local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', - local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', -] - -sanity_check_paths = { - 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, - "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/a/arrow-R/arrow-R-0.17.1-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/a/arrow-R/arrow-R-0.17.1-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 6118342e5ae..00000000000 --- a/easybuild/easyconfigs/__archive__/a/arrow-R/arrow-R-0.17.1-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'RPackage' - -name = 'arrow-R' -version = '0.17.1' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/web/packages/arrow' -description = "R interface to the Apache Arrow C++ library" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] -sources = ['arrow_%(version)s.tar.gz'] -checksums = ['c6de688f1a3282d89c1b4f8f1ebd70c2addbfa7a67e3d41184017d20a7d23aa3'] - -dependencies = [ - ('R', '4.0.0'), - ('Arrow', '0.17.1', '-Python-3.8.2'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['arrow'], -} - -options = {'modulename': 'arrow'} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.0.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.0.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index bbc6efc227f..00000000000 --- a/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.0.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'astropy' -version = '4.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.astropy.org/' -description = """The Astropy Project is a community effort to develop -a single core package for Astronomy in Python and foster interoperability -between Python astronomy packages.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('astropy-helpers', version, { - 'checksums': ['f1096414d108778218d6bea06d4d9c7b2ff7c83856a451331ac194e74de9f413'], - }), - (name, version, { - 'patches': ['astropy-ah_no_auto_use.patch'], - 'checksums': [ - 'f1135f2637867bf4eb44b754d905462be738165ae5535540670938bbc2dcc62c', # astropy-4.0.1.tar.gz - 'fb339ff90fff8ed760b5ea9b8b65be3babb355f956a5588fd7e2e2656b4a7ca8', # astropy-ah_no_auto_use.patch - ], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], -} - -moduleclass = 'astro' diff --git a/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 5169f1560e2..00000000000 --- a/easybuild/easyconfigs/__archive__/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'astropy' -version = '4.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.astropy.org/' -description = """The Astropy Project is a community effort to develop -a single core package for Astronomy in Python and foster interoperability -between Python astronomy packages.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('astropy-helpers', version, { - 'checksums': ['f1096414d108778218d6bea06d4d9c7b2ff7c83856a451331ac194e74de9f413'], - }), - (name, version, { - 'patches': ['astropy-ah_no_auto_use.patch'], - 'checksums': [ - 'f1135f2637867bf4eb44b754d905462be738165ae5535540670938bbc2dcc62c', # astropy-4.0.1.tar.gz - 'fb339ff90fff8ed760b5ea9b8b65be3babb355f956a5588fd7e2e2656b4a7ca8', # astropy-ah_no_auto_use.patch - ], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], -} - -moduleclass = 'astro' diff --git a/easybuild/easyconfigs/__archive__/a/astropy/astropy-ah_no_auto_use.patch b/easybuild/easyconfigs/__archive__/a/astropy/astropy-ah_no_auto_use.patch deleted file mode 100644 index 51b8d133c0b..00000000000 --- a/easybuild/easyconfigs/__archive__/a/astropy/astropy-ah_no_auto_use.patch +++ /dev/null @@ -1,17 +0,0 @@ -# this patch avoids downloading astropy-helpers by astropy installer, -# failing in EasyBuild. Instead, we download astropy-helpers as a part -# of the bundle. -# -# - 14.3.2019, J. Dvoracek (Institute of Physics | Czech Academy of Sciences, www.fzu.cz -# ---- ./setup.cfg.orig 2019-03-13 18:46:28.060712000 +0100 -+++ ./setup.cfg 2019-03-13 18:46:36.431744000 +0100 -@@ -26,7 +26,7 @@ - bitmap = static/wininst_background.bmp - - [ah_bootstrap] --auto_use = True -+auto_use = False - - [flake8] - exclude = extern,*parsetab.py,*lextab.py diff --git a/easybuild/easyconfigs/__archive__/a/at-spi2-atk/at-spi2-atk-2.34.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/at-spi2-atk/at-spi2-atk-2.34.2-GCCcore-9.3.0.eb deleted file mode 100644 index 8119ca2f023..00000000000 --- a/easybuild/easyconfigs/__archive__/a/at-spi2-atk/at-spi2-atk-2.34.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'at-spi2-atk' -version = '2.34.2' - -homepage = 'https://wiki.gnome.org/Accessibility' -description = "AT-SPI 2 toolkit bridge" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['901323cee0eef05c01ec4dee06c701aeeca81a314a7d60216fa363005e27f4f0'] - -builddependencies = [ - ('binutils', '2.34'), - ('Meson', '0.55.1', '-Python-3.8.2'), - ('Ninja', '1.10.0'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('GLib', '2.64.1'), - ('DBus', '1.13.12'), - ('at-spi2-core', '2.36.0'), - ('libxml2', '2.9.10'), - ('ATK', '2.36.0'), -] - -configopts = "--libdir lib " - -sanity_check_paths = { - 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb deleted file mode 100644 index 28a3f02e4a7..00000000000 --- a/easybuild/easyconfigs/__archive__/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'at-spi2-core' -version = '2.36.0' - -homepage = 'https://wiki.gnome.org/Accessibility' -description = """ - Assistive Technology Service Provider Interface. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['88da57de0a7e3c60bc341a974a80fdba091612db3547c410d6deab039ca5c05a'] - -builddependencies = [ - ('binutils', '2.34'), - ('Meson', '0.55.1', '-Python-3.8.2'), - ('Ninja', '1.10.0'), - ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), - ('gettext', '0.20.1'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('GLib', '2.64.1'), - ('DBus', '1.13.12'), - ('X11', '20200222'), -] - -# Hard disable Dbus broker detection -preconfigopts = "sed -i s/'dbus_broker.found()'/false/ ../*/bus/meson.build &&" -configopts = "--libdir lib " - -sanity_check_paths = { - 'files': ['lib/libatspi.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/a/attr/attr-2.4.48-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/attr/attr-2.4.48-GCCcore-9.3.0.eb deleted file mode 100644 index d98f3d7c65c..00000000000 --- a/easybuild/easyconfigs/__archive__/a/attr/attr-2.4.48-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'attr' -version = '2.4.48' - -homepage = 'https://savannah.nongnu.org/projects/attr' - -description = """Commands for Manipulating Filesystem Extended Attributes""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SAVANNAH_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['5ead72b358ec709ed00bbf7a9eaef1654baad937c001c044fe8b74c57f5324e7'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', - 'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h', - 'include/%(name)s/libattr.h', 'lib/libattr.a', - 'lib/libattr.%s' % SHLIB_EXT], - 'dirs': ['share'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/awscli/awscli-1.18.89-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/awscli/awscli-1.18.89-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 3bae76209dc..00000000000 --- a/easybuild/easyconfigs/__archive__/a/awscli/awscli-1.18.89-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'awscli' -version = '1.18.89' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/awscli' -description = 'Universal Command Line Environment for AWS' - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), -] - -exts_list = [ - ('colorama', '0.4.3', { - 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], - }), - ('s3transfer', '0.3.3', { - 'checksums': ['921a37e2aefc64145e7b73d50c71bb4f26f46e4c9f414dc648c6245ff92cf7db'], - }), - ('rsa', '3.4.2', { - 'checksums': ['25df4e10c263fb88b5ace923dd84bf9aa7f5019687b5e55382ffcdb8bede9db5'], - }), - ('docutils', '0.15', { - 'checksums': ['54a349c622ff31c91cbec43b0b512f113b5b24daf00e2ea530bb1bd9aac14849'], - }), - ('botocore', '1.17.12', { - 'checksums': ['a94e0e2307f1b9fe3a84660842909cd2680b57a9fc9fb0c3a03b0afb2eadbe21'], - }), - ('jmespath', '0.10.0', { - 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], - }), - (name, version, { - 'checksums': ['f100794703876b73fbcf3ad265cb0d12f9ca7b34d32acc5def6845aedd3970bc'], - }), -] - -sanity_check_commands = ["aws help"] - -sanity_check_paths = { - 'files': ['bin/aws'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/awscli/awscli-2.0.55-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/a/awscli/awscli-2.0.55-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index c0e30102258..00000000000 --- a/easybuild/easyconfigs/__archive__/a/awscli/awscli-2.0.55-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,67 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'awscli' -version = '2.0.55' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/awscli' -description = 'Universal Command Line Environment for AWS' - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), -] - -exts_list = [ - ('jmespath', '0.10.0', { - 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], - }), - ('botocore', '1.17.12', { - 'source_urls': ['https://github.com/boto/botocore/archive/'], - # use specific commit that corresponds to 2.0.0dev59, - # which is strictly required by awscli 2.0.55 (see 'requirements' in setup.py) - 'source_tmpl': '65e2c02.tar.gz', - 'checksums': ['1899e4442ec687e67709346a3c707af0db8cb98c741369daa95b3a68ef24f8fb'], - }), - ('colorama', '0.4.3', { - 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], - }), - ('docutils', '0.15.2', { - 'checksums': ['a2aeea129088da402665e92e0b25b04b073c04b2dce4ab65caaa38b7ce2e1a99'], - }), - ('cryptography', '2.8', { - 'checksums': ['3cda1f0ed8747339bbdf71b9f38ca74c7b592f24f65cdb3ab3765e4b02871651'], - }), - ('s3transfer', '0.3.3', { - 'checksums': ['921a37e2aefc64145e7b73d50c71bb4f26f46e4c9f414dc648c6245ff92cf7db'], - }), - ('ruamel.yaml', '0.15.100', { - 'checksums': ['8e42f3067a59e819935a2926e247170ed93c8f0b2ab64526f888e026854db2e4'], - }), - ('prompt_toolkit', '2.0.10', { - 'checksums': ['f15af68f66e664eaa559d4ac8a928111eebd5feda0c11738b5998045224829db'], - }), - ('distro', '1.5.0', { - 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], - }), - (name, version, { - 'source_urls': ['https://github.com/aws/aws-cli/archive/'], - 'source_tmpl': '%(version)s.tar.gz', - 'checksums': ['9404f9c223912bc432df1fd13e66d2b87abb6fc19640c23dda32a73f67722d64'], - }), -] - -sanity_check_commands = ["aws help"] - -sanity_check_paths = { - 'files': ['bin/aws'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/a/axel/axel-2.17.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/a/axel/axel-2.17.9-GCCcore-9.3.0.eb deleted file mode 100644 index de813fa81e5..00000000000 --- a/easybuild/easyconfigs/__archive__/a/axel/axel-2.17.9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -easyblock = 'ConfigureMake' - -name = 'axel' -version = '2.17.9' - -github_account = "axel-download-accelerator" -homepage = 'https://github.com/%(github_account)s/%(name)s' -description = """Lightweight CLI download accelerator """ - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/%(github_account)s/%(name)s/releases/download/v%(version)s'] -sources = [SOURCE_TAR_BZ2] -checksums = ['d50dfbc59cb04fa70fb8d414579259c3eefe2a87aab52611309feeec9acb851a'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), - ('gettext', '0.20.1'), -] - -dependencies = [ - ('OpenSSL', '1.1', '', SYSTEM), -] - -sanity_check_paths = { - 'files': ['bin/axel'], - 'dirs': [], -} - -sanity_check_commands = [ - "axel -h", - "axel --version", -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb deleted file mode 100644 index 772b81bc312..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'MakeCp' - -name = 'BBMap' -version = '38.87' - -homepage = 'https://sourceforge.net/projects/bbmap/' -description = """BBMap short read aligner, and other bioinformatic tools.""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['22ab642b8af88faf208a56763158da895004c5231df572d3163ce52fbfb63240'] - -dependencies = [('Java', '11', '', SYSTEM)] - -prebuildopts = 'cd jni && ' - -local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] -buildopts = "-f makefile.%s" % local_suff - -files_to_copy = ['*'] - -sanity_check_paths = { - 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], - 'dirs': [] -} - -modextrapaths = {'PATH': ''} - -modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" -modloadmsg += " compiled jni C code.\n" - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-38.90-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-38.90-GCC-9.3.0.eb deleted file mode 100644 index 45b3f610c87..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-38.90-GCC-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'MakeCp' - -name = 'BBMap' -version = '38.90' - -homepage = 'https://sourceforge.net/projects/bbmap/' -description = """BBMap short read aligner, and other bioinformatic tools.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1'] - -dependencies = [('Java', '11', '', SYSTEM)] - -prebuildopts = 'cd jni && ' - -local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] -buildopts = "-f makefile.%s" % local_suff - -files_to_copy = ['*'] - -sanity_check_paths = { - 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], - 'dirs': [] -} - -modextrapaths = {'PATH': ''} - -modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" -modloadmsg += " compiled jni C code.\n" - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BCFtools/BCFtools-1.10.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BCFtools/BCFtools-1.10.2-GCC-9.3.0.eb deleted file mode 100644 index dbc146af154..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BCFtools/BCFtools-1.10.2-GCC-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Author: Jonas Demeulemeester -# The Francis Crick Insitute, London, UK - -easyblock = 'ConfigureMake' - -name = 'BCFtools' -version = '1.10.2' - -homepage = 'https://www.htslib.org/' -description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence - variants""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['f57301869d0055ce3b8e26d8ad880c0c1989bf25eaec8ea5db99b60e31354e2c'] - -dependencies = [ - ('zlib', '1.2.11'), - ('HTSlib', '1.10.2'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('GSL', '2.6'), -] - -configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], - 'dirs': ['libexec/bcftools'] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BCFtools/BCFtools-1.12-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BCFtools/BCFtools-1.12-GCC-9.3.0.eb deleted file mode 100644 index f2cf9218226..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BCFtools/BCFtools-1.12-GCC-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Author: Jonas Demeulemeester -# The Francis Crick Insitute, London, UK - -easyblock = 'ConfigureMake' - -name = 'BCFtools' -version = '1.12' - -homepage = 'https://www.htslib.org/' -description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence - variants""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['7a0e6532b1495b9254e38c6698d955e5176c1ee08b760dfea2235ee161a024f5'] - -dependencies = [ - ('zlib', '1.2.11'), - ('HTSlib', '1.12'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('GSL', '2.6'), -] - -configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], - 'dirs': ['libexec/bcftools'] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BEDTools/BEDTools-2.29.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BEDTools/BEDTools-2.29.2-GCC-9.3.0.eb deleted file mode 100644 index fa487700f9f..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BEDTools/BEDTools-2.29.2-GCC-9.3.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -# Author: Maxime Schmitt, University of Luxembourg -# Author: Adam Huffman, The Francis Crick Institute -# -# Based on the work of: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics (SIB) -# Biozentrum - University of Basel - -easyblock = 'MakeCp' - -name = 'BEDTools' -version = '2.29.2' - -homepage = "https://bedtools.readthedocs.io/" -description = """BEDTools: a powerful toolset for genome arithmetic. -The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and -computing coverage. -The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e3f1bf9e58740e60c3913390fe95b0c7f8fd99ceade8a406e28620448a997054'] - -builddependencies = [('Python', '3.8.2')] - -dependencies = [ - ('XZ', '5.2.5'), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('BamTools', '2.5.1'), -] - -buildopts = 'CXX="$CXX"' - -files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], - 'dirs': files_to_copy, -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.10.1-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.10.1-gompi-2020a.eb deleted file mode 100644 index 51436d38cee..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.10.1-gompi-2020a.eb +++ /dev/null @@ -1,59 +0,0 @@ -## -# EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of -# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = 'ConfigureMake' - -name = 'BLAST+' -version = '2.10.1' - -homepage = 'https://blast.ncbi.nlm.nih.gov/' -description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm - for comparing primary biological sequence information, such as the amino-acid - sequences of different proteins or the nucleotides of DNA sequences.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] -sources = ['ncbi-blast-%(version)s+-src.tar.gz'] -checksums = [ - '110729decf082f69b90b058c0cabaea38f771983a564308ae19cb30a68ce7b86', # ncbi-blast-2.10.1+-src.tar.gz -] - -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('PCRE', '8.44'), - ('Boost', '1.72.0'), - ('GMP', '6.2.0'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), - ('LMDB', '0.9.24'), -] - - -# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) -# Compilation fails on src/algo/blast/api/prelim_stage.cpp -local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' -preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake - -configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " -configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " -configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " -configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" - -sanity_check_paths = { - 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.10.1-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.10.1-iimpi-2020a.eb deleted file mode 100644 index 58d7397bb06..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.10.1-iimpi-2020a.eb +++ /dev/null @@ -1,61 +0,0 @@ -## -# EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of -# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = 'ConfigureMake' - -name = 'BLAST+' -version = '2.10.1' - -homepage = 'https://blast.ncbi.nlm.nih.gov/' -description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm - for comparing primary biological sequence information, such as the amino-acid - sequences of different proteins or the nucleotides of DNA sequences.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'cstd': 'c++14', 'usempi': True} - -source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] -sources = ['ncbi-blast-%(version)s+-src.tar.gz'] -patches = [ - 'BLAST+-%(version)s_fix-64-icc.patch', -] -checksums = [ - '110729decf082f69b90b058c0cabaea38f771983a564308ae19cb30a68ce7b86', # ncbi-blast-2.10.1+-src.tar.gz - 'f25a537bc6fa4bc4bf0408b7b16966852aef72b9f7d60e1038afa1e41e0c9d88', # BLAST+-2.10.1_fix-64-icc.patch -] - -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('PCRE', '8.44'), - ('Boost', '1.72.0'), - ('GMP', '6.2.0'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), - ('LMDB', '0.9.24'), -] - -# avoid linking error 'cannot find -liomp5' on small helper utility that is built with gcc -preconfigopts = 'unset LIBS && ' -prebuildopts = preconfigopts - -configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " -configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " -configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " -configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB " - -sanity_check_paths = { - 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.10.1_fix-64-icc.patch b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.10.1_fix-64-icc.patch deleted file mode 100644 index f9c129a9bfe..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.10.1_fix-64-icc.patch +++ /dev/null @@ -1,12 +0,0 @@ -Fix "Do not know how to compile 64-bit with compiler" error by also using -m64 when compiling with Intel compilers -author: Jakub Zárybnický (Inuits) ---- ncbi-blast-2.10.1+-src/c++/src/build-system/configure.orig 2020-10-01 13:36:23.067853000 +0200 -+++ ncbi-blast-2.10.1+-src/c++/src/build-system/configure 2020-10-01 13:47:35.131190707 +0200 -@@ -9340,6 +9340,6 @@ - mips*:GCC ) - ARCH_CFLAGS="-mips64" - ;; -- *:GCC | *Clang ) -+ *:GCC | *ICC | *Clang ) - # May not work prior to GCC 3.1. - ARCH_CFLAGS="-m64" diff --git a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.11.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.11.0-gompi-2020a.eb deleted file mode 100644 index 1df31a40131..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.11.0-gompi-2020a.eb +++ /dev/null @@ -1,57 +0,0 @@ -## -# EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of -# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = 'ConfigureMake' - -name = 'BLAST+' -version = '2.11.0' - -homepage = 'https://blast.ncbi.nlm.nih.gov/' -description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm - for comparing primary biological sequence information, such as the amino-acid - sequences of different proteins or the nucleotides of DNA sequences.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] -sources = ['ncbi-blast-%(version)s+-src.tar.gz'] -checksums = ['d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954'] - -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('PCRE', '8.44'), - ('Boost', '1.72.0'), - ('GMP', '6.2.0'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), - ('LMDB', '0.9.24'), -] - - -# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) -# Compilation fails on src/algo/blast/api/prelim_stage.cpp -local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' -preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake - -configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " -configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " -configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " -configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" - -sanity_check_paths = { - 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BLAT/BLAT-3.5-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BLAT/BLAT-3.5-GCC-9.3.0.eb deleted file mode 100644 index 0bb7ac4bd4e..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BLAT/BLAT-3.5-GCC-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou -# License:: MIT/GPL -# -## - -name = 'BLAT' -version = '3.5' - -homepage = 'https://genome.ucsc.edu/FAQ/FAQblat.html' -description = """BLAT on DNA is designed to quickly find sequences of 95% and -greater similarity of length 25 bases or more.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://users.soe.ucsc.edu/~kent/src'] -sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] -checksums = ['06d9bcf114ec4a4b21fef0540a0532556b6602322a5a2b33f159dc939ae53620'] - -dependencies = [('libpng', '1.6.37')] - -buildopts = 'CC="$CC" COPT= L="$LIBS"' - -files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', - 'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], - 'dirs': files_to_copy, -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-0.8.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-0.8.0-GCCcore-9.3.0.eb deleted file mode 100644 index 101bb6637fe..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-0.8.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'BLIS' -version = '0.8.0' - -homepage = 'https://github.com/flame/blis/' -description = """BLIS is a portable software framework for instantiating high-performance -BLAS-like dense linear algebra libraries.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/flame/blis/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['5e05868c4a6cf5032a7492f8861653e939a8f907a4fa524bbb6e14394e170a3d'] - -builddependencies = [ - ('binutils', '2.34'), - ('Python', '3.8.2'), - ('Perl', '5.30.2'), -] - -configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['include/blis/cblas.h', 'include/blis/blis.h', - 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], - 'dirs': [], -} - -modextrapaths = {'CPATH': 'include/blis'} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb b/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb deleted file mode 100644 index 8018fce99b4..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb +++ /dev/null @@ -1,48 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'BLIS' -version = '2.2' -versionsuffix = '-amd' - -homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' -description = """AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance -BLAS-like dense linear algebra libraries.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/amd/blis/archive/'] -sources = ['%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s-amd_fix-undefined-reference-blist-abort.patch', - '%(name)s-%(version)s_enable-ppc-autodetect.patch', -] -checksums = [ - 'e1feb60ac919cf6d233c43c424f6a8a11eab2c62c2c6e3f2652c15ee9063c0c9', # 2.2.tar.gz - # BLIS-2.2-amd_fix-undefined-reference-blist-abort.patch - 'e879bd79e4438f7e6905461af1d483d27d14945eb9e75509b22c7584b8ba93c4', - # BLIS-2.2_enable-ppc-autodetect.patch - '9abf334d0abb6cfdd18bec21c27d114b78a7d97be45883626a547eceea046ccd', -] - -builddependencies = [ - ('binutils', '2.34'), - ('Python', '3.8.2'), - ('Perl', '5.30.2'), -] - -# Build Serial and multithreaded library -configopts = ['--enable-cblas --enable-shared CC="$CC" auto', - '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto'] - -runtest = 'check' - -sanity_check_paths = { - 'files': ['include/blis/cblas.h', 'include/blis/blis.h', - 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT, - 'lib/libblis-mt.a', 'lib/libblis-mt.%s' % SHLIB_EXT], - 'dirs': [], -} - -modextrapaths = {'CPATH': 'include/blis'} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-2.2-amd_fix-undefined-reference-blist-abort.patch b/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-2.2-amd_fix-undefined-reference-blist-abort.patch deleted file mode 100644 index 18ebc44d799..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BLIS/BLIS-2.2-amd_fix-undefined-reference-blist-abort.patch +++ /dev/null @@ -1,14 +0,0 @@ -fix undefined reference to 'blis_abort' - -see https://github.com/flame/blis/issues/428 + https://github.com/flame/blis/pull/429 - ---- blis-2.2.orig/frame/base/bli_error.h 2020-12-07 19:40:33.936990613 +0100 -+++ blis-2.2/frame/base/bli_error.h 2020-12-07 19:45:35.079406108 +0100 -@@ -40,6 +40,7 @@ - - void bli_print_msg( char* str, char* file, guint_t line ); - void bli_abort( void ); -+BLIS_EXPORT_BLIS void bli_abort( void ); - - char* bli_error_string_for_code( gint_t code ); - diff --git a/easybuild/easyconfigs/__archive__/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb deleted file mode 100644 index 1b1e6ebdcf1..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'BUFRLIB' -version = '11.3.0.2' - -homepage = 'https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB' -description = """NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to be a primer on the -BUFR code form itself.""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://github.com/JCSDA/bufrlib/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['1023eb590e2112d5bc213c568a212390fc65ff98732ac8d2ccdda5062e6bc8c6'] - -builddependencies = [('CMake', '3.16.4')] -configopts = '-DBUILD_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=ON' - -sanity_check_paths = { - 'files': ['lib/libbufr.a', 'lib/libbufr.so'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/b/BUStools/BUStools-0.40.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BUStools/BUStools-0.40.0-GCCcore-9.3.0.eb deleted file mode 100644 index a4e2111afdc..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BUStools/BUStools-0.40.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'BUStools' -version = '0.40.0' - -homepage = 'https://github.com/BUStools/bustools' -description = """bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. - It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility - count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples - and instructions on how to use bustools as part of a single-cell RNA-seq workflow.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'BUStools' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['f50b6fb634a10939b2b496e6569ebd09ef34fb9eb24231d7d07a98001a6713e6'] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('binutils', '2.34'), - ('zlib', '1.2.11'), -] - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['bin/bustools'], - 'dirs': [], -} - -sanity_check_commands = ["bustools version"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.17-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.17-GCC-9.3.0.eb deleted file mode 100644 index 30d800ef414..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.17-GCC-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA -# Authors:: George Tsouloupas , Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -# -# Version >= 0.7.15 -# Author: Adam Huffman, Big Data Institute, University of Oxford -# -# Note that upstream development is mainly at: https://github.com/lh3/bwa -## - -name = 'BWA' -version = '0.7.17' - -homepage = 'http://bio-bwa.sourceforge.net/' -description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns - relatively short nucleotide sequences against a long reference sequence such as the human genome.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/lh3/%(name)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] - -dependencies = [ - ('Perl', '5.30.2'), - ('zlib', '1.2.11'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.5.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.5.1-GCC-9.3.0.eb deleted file mode 100644 index a8d96138e9e..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.5.1-GCC-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -easyblock = 'CMakeMake' - -name = 'BamTools' -version = '2.5.1' - -homepage = 'https://github.com/pezmaster31/bamtools' -description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -# https://github.com/pezmaster31/bamtools -github_account = 'pezmaster31' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc'] - -builddependencies = [('CMake', '3.16.4')] - -sanity_check_paths = { - 'files': ['bin/bamtools', 'include/bamtools/shared/bamtools_global.h', 'lib/libbamtools.a'], - 'dirs': ['include/bamtools/api', 'lib/pkgconfig'], -} - -sanity_check_commands = ["bamtools --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-0.25.2_rename_gettid.patch b/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-0.25.2_rename_gettid.patch deleted file mode 100644 index 661e7b01c01..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-0.25.2_rename_gettid.patch +++ /dev/null @@ -1,70 +0,0 @@ -Rename gettid to sys_gettid to avoid name clash with gettid of glibc 2.30+ -https://github.com/grpc/grpc/commit/de6255941a5e1c2fb2d50e57f84e38c09f45023d -https://github.com/grpc/grpc/commit/57586a1ca7f17b1916aed3dea4ff8de872dbf853 - -diff --git a/third_party/grpc/src/core/lib/gpr/log_linux.cc b/third_party/grpc/src/core/lib/gpr/log_linux.cc -index 561276f0c2..8b597b4cf2 100644 ---- a/third_party/grpc/src/core/lib/gpr/log_linux.cc -+++ b/third_party/grpc/src/core/lib/gpr/log_linux.cc -@@ -40,7 +40,7 @@ - #include - #include - --static long gettid(void) { return syscall(__NR_gettid); } -+static long sys_gettid(void) { return syscall(__NR_gettid); } - - void gpr_log(const char* file, int line, gpr_log_severity severity, - const char* format, ...) { -@@ -70,7 +70,7 @@ void gpr_default_log(gpr_log_func_args* args) { - gpr_timespec now = gpr_now(GPR_CLOCK_REALTIME); - struct tm tm; - static __thread long tid = 0; -- if (tid == 0) tid = gettid(); -+ if (tid == 0) tid = sys_gettid(); - - timer = static_cast(now.tv_sec); - final_slash = strrchr(args->file, '/'); -diff --git a/third_party/grpc/src/core/lib/gpr/log_posix.cc b/third_party/grpc/src/core/lib/gpr/log_posix.cc -index 0acb225572..cd0b702b94 100644 ---- a/third_party/grpc/src/core/lib/gpr/log_posix.cc -+++ b/third_party/grpc/src/core/lib/gpr/log_posix.cc -@@ -30,7 +30,7 @@ - #include - #include - --static intptr_t gettid(void) { return (intptr_t)pthread_self(); } -+static intptr_t sys_gettid(void) { return (intptr_t)pthread_self(); } - - void gpr_log(const char* file, int line, gpr_log_severity severity, - const char* format, ...) { -@@ -85,7 +85,7 @@ void gpr_default_log(gpr_log_func_args* args) { - char* prefix; - gpr_asprintf(&prefix, "%s%s.%09d %7tu %s:%d]", - gpr_log_severity_string(args->severity), time_buffer, -- (int)(now.tv_nsec), gettid(), display_file, args->line); -+ (int)(now.tv_nsec), sys_gettid(), display_file, args->line); - - fprintf(stderr, "%-70s %s\n", prefix, args->message); - gpr_free(prefix); -diff --git a/third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc b/third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc -index 7a4870db78..4258ded8a0 100644 ---- a/third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc -+++ b/third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc -@@ -1150,7 +1150,7 @@ static void end_worker(grpc_pollset* pollset, grpc_pollset_worker* worker, - } - - #ifndef NDEBUG --static long gettid(void) { return syscall(__NR_gettid); } -+static long sys_gettid(void) { return syscall(__NR_gettid); } - #endif - - /* pollset->mu lock must be held by the caller before calling this. -@@ -1170,7 +1170,7 @@ static grpc_error* pollset_work(grpc_pollset* pollset, - #define WORKER_PTR (&worker) - #endif - #ifndef NDEBUG -- WORKER_PTR->originator = gettid(); -+ WORKER_PTR->originator = sys_gettid(); - #endif - if (grpc_polling_trace.enabled()) { - gpr_log(GPR_INFO, diff --git a/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb deleted file mode 100644 index 4a205b4f676..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'Bazel' -version = '0.29.1' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://bazel.io/' -description = """Bazel is a build tool that builds code quickly and reliably. -It is used to build the majority of Google's software.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] -sources = ['%(namelower)s-%(version)s-dist.zip'] -patches = [ - 'Bazel-%(version)s_fix-gold-flag.patch', - 'Bazel-%(version)s_fix-zip-d-on-power.patch', - '%(name)s-0.25.2_rename_gettid.patch', -] -checksums = [ - '872a52cff208676e1169b3e1cae71b1fe572c4109cbd66eab107d8607c378de5', # bazel-0.29.1-dist.zip - '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch - '0089567af6a991084d5628a8b6fa92b68402ff4b7a0ef8fa944e629e7be63b93', # Bazel-0.29.1_fix-zip-d-on-power.patch - '8639129941a6db079015ea7e04e7f5b6b24da3c963e7eb0488df34439d628f0e', # Bazel-0.25.2_rename_gettid.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('Python', '3.8.2'), - ('Zip', '3.0'), -] -dependencies = [('Java', '1.8', '', SYSTEM)] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-0.29.1_fix-zip-d-on-power.patch b/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-0.29.1_fix-zip-d-on-power.patch deleted file mode 100644 index 0dbc7a3817b..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-0.29.1_fix-zip-d-on-power.patch +++ /dev/null @@ -1,43 +0,0 @@ -From 99775df8356ab6c7dd77493b35e59de5f6a773f8 Mon Sep 17 00:00:00 2001 -From: Christy Norman -Date: Wed, 4 Sep 2019 18:41:37 -0400 -Subject: [PATCH] fix build for Power - -The zip -d flag will error if it doesn't find that extension. -This is a fix for Power, but doesn't fix the default case. - -Signed-off-by: Christy Norman ---- - src/conditions/BUILD | 6 ++++++ - third_party/BUILD | 1 + - 2 files changed, 7 insertions(+) - -diff --git a/src/conditions/BUILD b/src/conditions/BUILD -index 2b28e280576..faa41a439d4 100644 ---- a/src/conditions/BUILD -+++ b/src/conditions/BUILD -@@ -10,6 +10,12 @@ filegroup( - visibility = ["//src:__pkg__"], - ) - -+config_setting( -+ name = "linux_ppc", -+ values = {"cpu": "ppc"}, -+ visibility = ["//visibility:public"], -+) -+ - config_setting( - name = "linux_x86_64", - values = {"cpu": "k8"}, -diff --git a/third_party/BUILD b/third_party/BUILD -index 7545b3df33a..b4115b2988c 100644 ---- a/third_party/BUILD -+++ b/third_party/BUILD -@@ -528,6 +528,7 @@ UNNECESSARY_DYNAMIC_LIBRARIES = select({ - # The .so file is an x86 one, so we can just remove it if the CPU is not x86 - "//src/conditions:arm": "*.so *.jnilib *.dll", - "//src/conditions:linux_aarch64": "*.so *.jnilib *.dll", -+ "//src/conditions:linux_ppc": "*.so *.jnilib *.dll", - # Play it safe -- better have a big binary than a slow binary - # zip -d does require an argument. Supply something bogus. - "//conditions:default": "*.bogusextension", diff --git a/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb deleted file mode 100644 index 6daf4172fef..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'Bazel' -version = '3.6.0' - -homepage = 'https://bazel.io/' -description = """Bazel is a build tool that builds code quickly and reliably. -It is used to build the majority of Google's software.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] -sources = ['%(namelower)s-%(version)s-dist.zip'] -patches = ['%(name)s-3.4.1-fix-grpc-protoc.patch'] -checksums = [ - '3a18f24febb5203f11b0985b27e120ac623058d1d5ca79cd6df992e67d57240a', # bazel-3.6.0-dist.zip - 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', # Bazel-3.4.1-fix-grpc-protoc.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('Python', '3.8.2'), - ('Zip', '3.0'), -] -dependencies = [('Java', '11', '', SYSTEM)] - -runtest = True -testopts = ' '.join([ - '--', - '//examples/cpp:hello-success_test', - '//examples/py/...', - '//examples/py_native:test', - '//examples/shell/...', -]) - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/BeautifulSoup/BeautifulSoup-4.9.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/BeautifulSoup/BeautifulSoup-4.9.1-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 03e576a3b7f..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BeautifulSoup/BeautifulSoup-4.9.1-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'BeautifulSoup' -version = '4.9.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.crummy.com/software/BeautifulSoup' -description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [ - ('binutils', '2.34') -] - -dependencies = [ - ('Python', '3.8.2'), -] - -exts_list = [ - ('soupsieve', '2.0.1', { - 'checksums': ['a59dc181727e95d25f781f0eb4fd1825ff45590ec8ff49eadfd7f1a537cc0232'], - }), - (name, version, { - 'modulename': 'bs4', - 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], - 'checksums': ['73cc4d115b96f79c7d77c1c7f7a0a8d4c57860d1041df407dd1aae7f07a77fd7'], - }), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/b/BioPP/BioPP-2.4.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BioPP/BioPP-2.4.1-GCC-9.3.0.eb deleted file mode 100644 index 59ed58edac6..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BioPP/BioPP-2.4.1-GCC-9.3.0.eb +++ /dev/null @@ -1,59 +0,0 @@ -easyblock = 'Bundle' - -name = 'BioPP' -version = '2.4.1' - -homepage = 'https://github.com/BioPP/bpp-core' -description = ''' -Bio++ is a set of C++ libraries for Bioinformatics, including sequence -analysis, phylogenetics, molecular evolution and population genetics. Bio++ is -Object Oriented and is designed to be both easy to use and computer efficient. -Bio++ intends to help programmers to write computer expensive programs, by -providing them a set of re-usable tools. -''' - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -github_account = 'BioPP' - -builddependencies = [('CMake', '3.16.4')] -default_easyblock = 'CMakeMake' - -default_component_specs = { - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'source_urls': [GITHUB_SOURCE], - 'start_dir': '%(name)s-%(version)s', -} -components = [ - ('bpp-core', version, { - 'checksums': ['1150b8ced22cff23dd4770d7c23fad11239070b44007740e77407f0d746c0af6'], - }), - ('bpp-seq', version, { - 'checksums': ['dbfcb04803e4b7f08f9f159da8a947c91906c3ca8b20683ac193f6dc524d4655'], - }), - ('bpp-phyl', version, { - 'checksums': ['e7bf7d4570f756b7773904ffa600ffcd77c965553ddb5cbc252092d1da962ff2'], - }), - ('bpp-seq-omics', version, { - 'checksums': ['200da925b42065998d825f0b2a37e26b00a865883c85bc332beb3a94cae1e08b'], - }), - ('bpp-phyl-omics', version, { - 'checksums': ['fb0908422e59c71065db874e68d5c71acddf66d8a51776f7e04a5f8d5f0f6577'], - }), - ('bpp-popgen', version, { - 'checksums': ['03b57d71a63c8fa7f11c085e531d0d691fc1d40d4ea541070dabde0ab3baf413'], - }), - ('bppsuite', version, { - 'checksums': ['0485adcc17e37439069d27e4fac144e5ae38036ba21f31e6d21f070ce4ea5199'], - }) -] - -local_libs = [local_component[0] for local_component in components if local_component[0] != 'bppsuite'] - -sanity_check_paths = { - 'files': ['bin/bppseqgen'] + - ['lib64/lib%s.%s' % (local_lib, local_ext) for local_lib in local_libs for local_ext in ['a', SHLIB_EXT]], - 'dirs': ['include/Bpp', 'share/man'] + - ['lib64/cmake/%s' % local_lib for local_lib in local_libs] -} -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/b/BioPerl/BioPerl-1.7.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/BioPerl/BioPerl-1.7.7-GCCcore-9.3.0.eb deleted file mode 100644 index 65ea07ea386..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BioPerl/BioPerl-1.7.7-GCCcore-9.3.0.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'Bundle' - -name = 'BioPerl' -version = '1.7.7' - -homepage = 'https://bioperl.org/' -description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. - Examples include Sequence objects, Alignment objects and database searching objects.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Perl', '5.30.2'), - ('XML-LibXML', '2.0205'), - ('DB_File', '1.835'), -] - -exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") - -exts_list = [ - ('XML::Writer', '0.625', { - 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], - 'checksums': ['e080522c6ce050397af482665f3965a93c5d16f5e81d93f6e2fe98084ed15fbe'], - }), - ('XML::DOM::XPath', '0.14', { - 'source_tmpl': 'XML-DOM-XPath-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], - 'checksums': ['0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea'], - }), - ('Bio::Procedural', '1.7.4', { - 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], - 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], - }), - ('BioPerl', version, { - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], - 'checksums': ['730e2bd38b7550bf6bbd5bca50d019a70cca514559702c1389d770ff69cff1bb'], - }), -] - -modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', -} - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/BioServices/BioServices-1.7.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/BioServices/BioServices-1.7.9-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 88e99b912e0..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BioServices/BioServices-1.7.9-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,80 +0,0 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -easyblock = 'PythonBundle' - -name = 'BioServices' -version = '1.7.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://bioservices.readthedocs.io/" -description = """Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., - UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols).""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('BeautifulSoup', '4.9.1', versionsuffix), - ('lxml', '4.5.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('SciPy-bundle', '2020.03', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), -] - -exts_list = [ - ('colorlog', '4.4.0', { - 'checksums': ['0272c537469ab1e63b9915535874d15b671963c9325db0c4891a2aeff97ce3d1'], - }), - ('flit_core', '3.0.0', { - 'checksums': ['a465052057e2d6d957e6850e9915245adedfc4fd0dd5737d0791bf3132417c2d'], - }), - ('flit', '3.0.0', { - 'checksums': ['b4fe0f84a1ffbf125d003e253ec98c0b6e3e31290b31fba3ad22d28588c20893'], - }), - ('ptyprocess', '0.6.0', { - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], - }), - ('pexpect', '4.8.0', { - 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], - }), - ('colorama', '0.4.4', { - 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], - }), - ('easydev', '0.10.1', { - 'checksums': ['faa791f0b1ef87bddab4d873c5a2c2be539b8a03c177242b1b402412a0dd69d1'], - }), - ('zope.interface', '5.1.2', { - 'checksums': ['c9c8e53a5472b77f6a391b515c771105011f4b40740ce53af8428d1c8ca20004'], - }), - ('zope.event', '4.5.0', { - 'checksums': ['5e76517f5b9b119acf37ca8819781db6c16ea433f7e2062c4afc2b6fbedb1330'], - }), - ('greenlet', '0.4.17', { - 'checksums': ['41d8835c69a78de718e466dd0e6bfd4b46125f21a67c3ff6d76d8d8059868d6b'], - }), - ('gevent', '20.9.0', { - 'checksums': ['5f6d48051d336561ec08995431ee4d265ac723a64bba99cc58c3eb1a4d4f5c8d'], - }), - ('grequests', '0.6.0', { - 'checksums': ['7dec890c6668e6755a1ea968565535867956639301268394d24df67b478df666'], - }), - ('requests-cache', '0.5.2', { - 'checksums': ['813023269686045f8e01e2289cc1e7e9ae5ab22ddd1e2849a9093ab3ab7270eb'], - }), - ('suds-jurko', '0.6', { - 'modulename': 'suds', - 'source_tmpl': '%(name)s-%(version)s.tar.bz2', - 'checksums': ['29edb72fd21e3044093d86f33c66cf847c5aaab26d64cb90e69e528ef014e57f'], - }), - ('xmltodict', '0.12.0', { - 'checksums': ['50d8c638ed7ecb88d90561beedbf720c9b4e851a9fa6c47ebd64e99d166d8a21'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['1711589cdd250e0ea043ee95d111def35aa20febb111aa32914e22728791c670'], - }), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index a97d94ac7c3..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Biopython' -version = '1.78' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.biopython.org' -description = """Biopython is a set of freely available tools for biological - computation written in Python by an international team of developers. It is - a distributed collaborative effort to develop Python libraries and - applications which address the needs of current and future work in - bioinformatics. """ - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://biopython.org/DIST'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -# Run only tests that don't require internet connection -runtest = 'python setup.py test --offline' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', - 'lib/python%(pyshortver)s/site-packages/BioSQL'] -} - -# extra check to ensure numpy dependency is available -sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] - -options = {'modulename': 'Bio'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index f49d56a1392..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Biopython' -version = '1.78' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.biopython.org' -description = """Biopython is a set of freely available tools for biological - computation written in Python by an international team of developers. It is - a distributed collaborative effort to develop Python libraries and - applications which address the needs of current and future work in - bioinformatics. """ - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://biopython.org/DIST'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -# Run only tests that don't require internet connection -runtest = 'python setup.py test --offline' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', - 'lib/python%(pyshortver)s/site-packages/BioSQL'] -} - -# extra check to ensure numpy dependency is available -sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] - -options = {'modulename': 'Bio'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb deleted file mode 100644 index f9deb82e85d..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.5.3' - -homepage = 'https://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['34e201d963156618a0ea5bc87220f660a1e08403dd3c7c7903d4f38db3f40039'] - -builddependencies = [ - ('M4', '1.4.18'), - # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.34', '', SYSTEM), -] - - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.7.6-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.7.6-FCC-4.5.0.eb deleted file mode 100644 index 8116d5119cb..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.7.6-FCC-4.5.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.7.6' - -homepage = 'https://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] - -builddependencies = [ - ('M4', '1.4.18'), -] - - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/b/Blitz++/Blitz++-1.0.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/Blitz++/Blitz++-1.0.2-GCCcore-9.3.0.eb deleted file mode 100644 index 07f806381f5..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Blitz++/Blitz++-1.0.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Blitz++' -version = '1.0.2' - -homepage = 'https://github.com/blitzpp/blitz' - -description = """ - Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation - in C++ with a speed comparable to Fortran implementations, while preserving an - object-oriented interface -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [('https://github.com/blitzpp/blitz/archive/')] -sources = ['%(version)s.tar.gz'] -checksums = ['500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'] - -builddependencies = [('CMake', '3.16.4'), ('binutils', '2.34')] - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], - 'dirs': ['include/blitz/array', 'include/blitz/meta', - 'include/random', 'lib64/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/b/Blosc/Blosc-1.17.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/Blosc/Blosc-1.17.1-GCCcore-9.3.0.eb deleted file mode 100644 index c6a677dfb3f..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Blosc/Blosc-1.17.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Blosc' -version = '1.17.1' - -homepage = 'https://www.blosc.org/' - -description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://github.com/Blosc/c-blosc/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['19a6948b579c27e8ac440b4f077f99fc90e7292b1d9cb896bec0fd781d68fba2'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -sanity_check_paths = { - 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', - 'lib/libblosc.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch b/easybuild/easyconfigs/__archive__/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch deleted file mode 100644 index ccf7129bb7b..00000000000 --- a/easybuild/easyconfigs/__archive__/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch +++ /dev/null @@ -1,51 +0,0 @@ -Use spglib and Eigen from EB install - -Åke Sandgren, 2023-04-17 -diff -ru BoltzTraP2-22.12.1.orig/setup.py BoltzTraP2-22.12.1/setup.py ---- BoltzTraP2-22.12.1.orig/setup.py 2022-12-19 19:38:59.000000000 +0100 -+++ BoltzTraP2-22.12.1/setup.py 2023-04-17 12:32:46.654682662 +0200 -@@ -187,7 +187,8 @@ - - def run(self): - """Run build_spglib and then delegate on the normal build_ext.""" -- self.run_command("build_spglib") -+ # Use spglib from EB installation -+ # self.run_command("build_spglib") - DefaultBuildExtCommand.run(self) - - -@@ -213,12 +214,6 @@ - else: - extension = "cpp" - --eigen_dir = os.path.abspath( -- os.path.join( -- os.path.dirname(__file__), "external", "eigen-eigen-3215c06819b9" -- ) --) -- - extensions = [ - Extension( - "BoltzTraP2.sphere.frontend", -@@ -228,10 +223,10 @@ - ], - language="c++", - include_dirs=INCLUDE_DIRS -- + [np.get_include(), BuildSPGlibCommand.header_dir, eigen_dir], -+ + [np.get_include()], - library_dirs=LIBRARY_DIRS, - runtime_library_dirs=LIBRARY_DIRS, -- extra_objects=[BuildSPGlibCommand.static_library], -+ libraries = ['symspg'], - ) - ] - -@@ -282,8 +277,6 @@ - ext_modules=extensions, - cmdclass={ - "build_ext": BuildExtCommand, -- "build_spglib": BuildSPGlibCommand, -- "clean_spglib": CleanSPGlibCommand, - }, - install_requires=[ - "spglib", diff --git a/easybuild/easyconfigs/__archive__/b/Boost.Python/Boost.Python-1.72.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/b/Boost.Python/Boost.Python-1.72.0-gompi-2020a.eb deleted file mode 100644 index bc27fa70ed9..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Boost.Python/Boost.Python-1.72.0-gompi-2020a.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'EB_Boost' - -name = 'Boost.Python' -version = '1.72.0' - -homepage = 'https://boostorg.github.io/python' -description = """Boost.Python is a C++ library which enables seamless interoperability between C++ - and the Python programming language.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] -sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] -patches = ['Boost-1.71.0_fix-Python3.patch'] -checksums = [ - 'c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f', # boost_1_72_0.tar.gz - '60e3aede2f444a3855f4efed94d1de5c2887983876e0fae21f6ca5cfdc53ea96', # Boost-1.71.0_fix-Python3.patch -] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [('Boost', version)] - -only_python_bindings = True - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/b/Boost.Python/Boost.Python-1.72.0-gompic-2020a.eb b/easybuild/easyconfigs/__archive__/b/Boost.Python/Boost.Python-1.72.0-gompic-2020a.eb deleted file mode 100644 index 79e35134986..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Boost.Python/Boost.Python-1.72.0-gompic-2020a.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'EB_Boost' - -name = 'Boost.Python' -version = '1.72.0' - -homepage = 'https://boostorg.github.io/python' -description = """Boost.Python is a C++ library which enables seamless interoperability between C++ - and the Python programming language.""" - -toolchain = {'name': 'gompic', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] -sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] -patches = ['Boost-1.71.0_fix-Python3.patch'] -checksums = [ - 'c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f', # boost_1_72_0.tar.gz - '60e3aede2f444a3855f4efed94d1de5c2887983876e0fae21f6ca5cfdc53ea96', # Boost-1.71.0_fix-Python3.patch -] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [('Boost', version)] - -only_python_bindings = True - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/b/Boost.Python/Boost.Python-1.72.0-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/b/Boost.Python/Boost.Python-1.72.0-iimpi-2020a.eb deleted file mode 100644 index b3566b63a42..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Boost.Python/Boost.Python-1.72.0-iimpi-2020a.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'EB_Boost' - -name = 'Boost.Python' -version = '1.72.0' - -homepage = 'https://boostorg.github.io/python' -description = """Boost.Python is a C++ library which enables seamless interoperability between C++ - and the Python programming language.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] -sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] -patches = ['Boost-1.71.0_fix-Python3.patch'] -checksums = [ - 'c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f', # boost_1_72_0.tar.gz - '60e3aede2f444a3855f4efed94d1de5c2887983876e0fae21f6ca5cfdc53ea96', # Boost-1.71.0_fix-Python3.patch -] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [('Boost', version)] - -only_python_bindings = True - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-GCCcore-9.3.0-no_mpi.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-GCCcore-9.3.0-no_mpi.eb deleted file mode 100644 index 45778ac6ca9..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-GCCcore-9.3.0-no_mpi.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'Boost' -version = '1.72.0' -versionsuffix = '-no_mpi' - -homepage = 'https://www.boost.org/' -description = """Boost provides free peer-reviewed portable C++ source libraries.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), - ('XZ', '5.2.5'), - ('zstd', '1.4.4'), -] - -configopts = '--without-libraries=python' - -# Don't build boost_mpi -boost_mpi = False - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-gompi-2020a.eb deleted file mode 100644 index 0012f4d504f..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-gompi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'Boost' -version = '1.72.0' - -homepage = 'https://www.boost.org/' -description = """Boost provides free peer-reviewed portable C++ source libraries.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f'] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), - ('XZ', '5.2.5'), - ('zstd', '1.4.4'), -] - -configopts = '--without-libraries=python' - -# also build boost_mpi -boost_mpi = True - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-gompic-2020a.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-gompic-2020a.eb deleted file mode 100644 index 0f379b65307..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-gompic-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'Boost' -version = '1.72.0' - -homepage = 'https://www.boost.org/' -description = """Boost provides free peer-reviewed portable C++ source libraries.""" - -toolchain = {'name': 'gompic', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f'] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), - ('XZ', '5.2.5'), - ('zstd', '1.4.4'), -] - -configopts = '--without-libraries=python' - -# also build boost_mpi -boost_mpi = True - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-iimpi-2020a.eb deleted file mode 100644 index 410be76a6b4..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.72.0-iimpi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'Boost' -version = '1.72.0' - -homepage = 'https://www.boost.org/' -description = """Boost provides free peer-reviewed portable C++ source libraries.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f'] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), - ('XZ', '5.2.5'), - ('zstd', '1.4.4'), -] - -configopts = '--without-libraries=python' - -# also build boost_mpi -boost_mpi = True - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/Bottleneck/Bottleneck-1.3.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/Bottleneck/Bottleneck-1.3.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 377487d6589..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bottleneck/Bottleneck-1.3.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Bottleneck' -version = '1.3.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://kwgoodman.github.io/bottleneck-doc' -description = "Fast NumPy array functions written in C" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/b/Bowtie/Bowtie-1.2.3-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/Bowtie/Bowtie-1.2.3-GCC-9.3.0.eb deleted file mode 100644 index eb8f188f4b0..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bowtie/Bowtie-1.2.3-GCC-9.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'Bowtie' -version = '1.2.3' - -homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' -description = """Bowtie is an ultrafast, memory-efficient short read aligner. - It aligns short DNA sequences (reads) to the human genome.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True, 'cstd': 'gnu++98'} - -source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] -sources = [ - {'download_filename': '%(namelower)s-src-x86_64.zip', - 'filename': '%(namelower)s-%(version)s-src.zip'} -] -checksums = ['44e99f4ea8f731c36c556b1ff4108f50f89ee6896f1ba89377feb7c460c3b16e'] - -dependencies = [ - ('tbb', '2020.1'), - ('zlib', '1.2.11'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bowtie/Bowtie-1.3.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/Bowtie/Bowtie-1.3.0-GCC-9.3.0.eb deleted file mode 100644 index 6920b24c848..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bowtie/Bowtie-1.3.0-GCC-9.3.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Artistic v2.0 -# -# Notes:: -## - -name = 'Bowtie' -version = '1.3.0' - -homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' -description = """Bowtie is an ultrafast, memory-efficient short read aligner. - It aligns short DNA sequences (reads) to the human genome.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True, 'cstd': 'gnu++98'} - -source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] -sources = ['%(namelower)s-%(version)s-src.zip'] -checksums = ['04e04d5f9a4a8cdee1fe58512588e95a173cf8395cf7d42136ecc76c1b8cab85'] - -dependencies = [ - ('tbb', '2020.1'), - ('zlib', '1.2.11'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb deleted file mode 100644 index 279170f1b0e..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# Modified by: Robert Schmidt -# Ottawa Hospital Research Institute - Bioinformatics Team -# Modified by: Adam Huffman -# The Francis Crick Institute -# Modified by: Kurt Lust, UAntwerp - -name = 'Bowtie2' -version = '2.4.1' - -homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' -description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads - to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s - of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. - Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, - its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True, 'cstd': 'gnu++98'} - -source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -sources = ['%(namelower)s-%(version)s-source.zip'] -checksums = ['566d6fb01a361883747103d797308ee4bdb70f6db7d27bfc72a520587815df22'] - -dependencies = [ - ('tbb', '2020.1'), - ('zlib', '1.2.11'), -] - -# to add script folder to path just uncomment this line -# modextrapaths = {'PATH': 'scripts'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb deleted file mode 100644 index c7e85fbbdc5..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# Modified by: Robert Schmidt -# Ottawa Hospital Research Institute - Bioinformatics Team -# Modified by: Adam Huffman -# The Francis Crick Institute -# Modified by: Kurt Lust, UAntwerp - -name = 'Bowtie2' -version = '2.4.2' - -homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' -description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads - to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s - of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. - Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, - its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True, 'cstd': 'gnu++98'} - -source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -sources = ['%(namelower)s-%(version)s-source.zip'] -checksums = ['4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e'] - -dependencies = [ - ('tbb', '2020.1'), - ('zlib', '1.2.11'), -] - -# to add script folder to path just uncomment this line -# modextrapaths = {'PATH': 'scripts'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bracken/Bracken-2.6.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/Bracken/Bracken-2.6.0-GCCcore-9.3.0.eb deleted file mode 100644 index 5cb8735cecb..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bracken/Bracken-2.6.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen - -easyblock = 'MakeCp' - -name = 'Bracken' -version = '2.6.0' - -homepage = 'https://ccb.jhu.edu/software/bracken/' -description = """Bracken (Bayesian Reestimation of Abundance with KrakEN) -is a highly accurate statistical method that computes the abundance of -species in DNA sequences from a metagenomics sample. Braken uses the -taxonomy labels assigned by Kraken, a highly accurate metagenomics -classification algorithm, to estimate the number of reads originating -from each species present in a sample. Kraken classifies reads to the -best matching location in the taxonomic tree, but does not estimate -abundances of species. We use the Kraken database itself to derive -probabilities that describe how much sequence from each genome is -identical to other genomes in the database, and combine this information -with the assignments for a particular sample to estimate abundance at -the species level, the genus level, or above. Combined with the Kraken -classifier, Bracken produces accurate species- and genus-level abundance -estimates even when a sample contains two or more near-identical species. - -NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the -default kmer length is different depending on the version of Kraken used. -If you use Kraken 1 defaults, specify 31 as the kmer length. If you use -Kraken 2 defaults, specify 35 as the kmer length.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/jenniferlu717/Bracken/archive/'] -sources = ['v%(version)s.tar.gz'] - -checksums = [ - 'fb1837d6f32b8f8c87353b9dc8a23d3418c348b00824a7064eb58f9bab11ea68', # v%(version)s.tar.gz -] - -builddependencies = [('binutils', '2.34')] - -# no need to build in parallel -maxparallel = 1 - -start_dir = 'src' - -files_to_copy = ['bracken', 'bracken-build', 'src', 'analysis_scripts', 'sample_data'] - -sanity_check_paths = { - 'files': ['bracken', 'bracken-build'], - 'dirs': ['analysis_scripts', 'sample_data', 'src'], -} - -modextrapaths = {'PATH': '.'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bsoft/Bsoft-2.0.7-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/Bsoft/Bsoft-2.0.7-GCC-9.3.0.eb deleted file mode 100644 index f002bec03ca..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bsoft/Bsoft-2.0.7-GCC-9.3.0.eb +++ /dev/null @@ -1,85 +0,0 @@ -# Author: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu -# Updated by: Alex Domingo - VUB - http://www.vub.be - -easyblock = 'Bundle' - -name = 'Bsoft' -version = '2.0.7' -local_libtiff_version = '4.1.0' - -homepage = 'https://lsbr.niams.nih.gov/bsoft/' - -description = """ - Bsoft is a collection of programs and a platform for development of software - for image and molecular processing in structural biology. Problems in - structural biology are approached with a highly modular design, allowing fast - development of new algorithms without the burden of issues such as file I/O. - It provides an easily accessible interface, a resource that can be and has - been used in other packages. -""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'openmp': True, 'pic': True} - -dependencies = [ - ('FFTW', '3.3.8', '-serial'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', local_libtiff_version), - ('libxml2', '2.9.10'), - ('Tk', '8.6.10'), -] - -maxparallel = 1 - -# Use packages from EB -local_bsoft_configopts = "--fftw=$EBROOTFFTW --jpeg=$EBROOTLIBJPEGMINTURBO --png=$EBROOTLIBPNG" -# Use libraries from LibTIFF already installed in EB -local_bsoft_configopts += " --tiff=$EBROOTLIBTIFF" - -default_easyblock = 'ConfigureMake' - -components = [ - # Bsoft needs headers from LibTIFF only available in its source code - ('LibTIFF', local_libtiff_version, { - 'source_urls': ['https://download.osgeo.org/libtiff/'], - 'sources': ['tiff-%s.tar.gz' % local_libtiff_version], - 'checksums': ['5d29f32517dadb6dbcd1255ea5bbc93a2b54b94fbf83653b4d65c7d6775b8634'], - 'start_dir': 'tiff-%s' % local_libtiff_version, - 'configopts': '--enable-ld-version-script', - # skip installation: Bsoft only needs LibTIFF headers at build time and - # those headers are never installed in any case - 'install_cmd': 'true', - }), - (name, version, { - 'source_urls': ['https://lsbr.niams.nih.gov/bsoft/'], - 'sources': ['%%(namelower)s%s.tgz' % '_'.join(version.split('.'))], - 'patches': ['%(name)s-%(version)s_use-eb-packages.patch'], - 'checksums': [ - 'f86d19b3c843cf8a7dd22871f32aca66ab40546ba3b545f7e4ae95c6ec47379c', # bsoft2_0_7.tgz - '9cb67d30ba8360c08dab01090d084dcfcf5c435ccb1426210bdaabe5ee8c80ed', # Bsoft-2.0.7_use-eb-packages.patch - ], - 'preconfigopts': 'EBBUILDLIBTIFF=%%(builddir)s/tiff-%s' % local_libtiff_version, # use headers in local LibTIFF - 'configure_cmd': './bconf', - 'configopts': local_bsoft_configopts, - 'buildopts': '%(namelower)s', - }), -] - -# Emulate Scripts/postinstall -postinstallcmds = ["cd %%(installdir)s/bin && ln -sf ../tcltk/%s" % x for x in ['bshow', 'bshowX', 'brun', 'brunX']] - -sanity_check_paths = { - 'files': ['bsoft.bashrc', 'bsetup', 'bin/bshell', 'bin/brun', 'bin/brunX', 'bin/bshow', 'bin/bshowX', - 'lib/libbsoft.%s' % SHLIB_EXT, 'lib/libbshow.%s' % SHLIB_EXT], - 'dirs': ['doc', 'parameters', 'tcltk'], -} - -sanity_check_commands = ["bshell -verb 1 -ico 480,4 -comp 30"] - -modextrapaths = { - 'BSOFT': '', - 'BPARAM': 'parameters', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/Bsoft/Bsoft-2.0.7_use-eb-packages.patch b/easybuild/easyconfigs/__archive__/b/Bsoft/Bsoft-2.0.7_use-eb-packages.patch deleted file mode 100644 index 575dee83d7b..00000000000 --- a/easybuild/easyconfigs/__archive__/b/Bsoft/Bsoft-2.0.7_use-eb-packages.patch +++ /dev/null @@ -1,132 +0,0 @@ -Adapt configuration scripts of Bsoft to EasyBuild environment -author: Alex Domingo (Vrije Universiteit Brussel) ---- dev.rsc.orig 2019-05-09 21:04:05.000000000 +0200 -+++ dev.rsc 2020-10-17 12:35:46.233721000 +0200 -@@ -38,24 +38,24 @@ - HAVE_FFTW=0 - HAVE_XML=0 - -- if [ -e $LIBFFTW/api/fftw3.h ]; then -+ if [ -e $LIBFFTW/include/fftw3.h ]; then - echo "# FFTW3 found" - HAVE_FFTW=1 - else - echo "# No FFTW3 libraries found!" -- echo "# Looking for: $LIBFFTW/api/fftw3.h" -+ echo "# Looking for: $LIBFFTW/include/fftw3.h" - fi - -- if [ -e $SDK/usr/include/libxml2 ]; then -+ if [ -e $EBROOTLIBXML2/include/libxml2 ]; then - echo "# libxml2 found" - HAVE_XML=1 -- x=`grep -A 3 xmlStrPrintf $SDK/usr/include/libxml2/libxml/xmlstring.h | grep msg | grep xmlChar` -+ x=`grep -A 3 xmlStrPrintf $EBROOTLIBXML2/include/libxml2/libxml/xmlstring.h | grep msg | grep xmlChar` - if [[ $x =~ xmlChar ]]; then - HAVE_XML=2 - fi - else - echo "# No XML library found!" -- echo "# Looking for: $SDK/usr/include/libxml2" -+ echo "# Looking for: $EBROOTLIBXML2/include/libxml2" - fi - - # Optional -@@ -71,13 +71,13 @@ - TCLINC=$TCL/Headers - TKINC=$TK/Headers - elif [[ $SYS =~ Linux ]]; then -- TCL=/usr -- TK=/usr -+ TCL=$EBROOTTCL -+ TK=$EBROOTTK - TCLINC=$TCL/include - TKINC=$TK/include -- if [ -e /usr/include/tk ]; then -- TCLINC=/usr/include/tcl -- TKINC=/usr/include/tk -+ if [ -e $EBROOTTK/include/tk ]; then -+ TCLINC=$EBROOTTCL/include/tcl -+ TKINC=$EBROOTTK/include/tk - fi - fi - -@@ -90,28 +90,28 @@ - TKO="" - fi - -- if [ -e $LIBTIFF/libtiff/tiff.h ]; then -+ if [ -e $EBBUILDLIBTIFF/libtiff/tiff.h ]; then - echo "# libtiff found" - HAVE_TIFF=1 - else - echo "# No TIFF library found! TIFF files will not be supported!" -- echo "# Looking for: $LIBTIFF/libtiff/tiff.h" -+ echo "# Looking for: $EBBUILDLIBTIFF/libtiff/tiff.h" - fi - -- if [ -e $LIBPNG/png.h ]; then -+ if [ -e $LIBPNG/include/png.h ]; then - echo "# libpng found" - HAVE_PNG=1 - else - echo "# No PNG library found! PNG files will not be supported!" -- echo "# Looking for: $LIBPNG/png.h" -+ echo "# Looking for: $LIBPNG/include/png.h" - fi - -- if [ -e $LIBJPEG/jpeglib.h ]; then -+ if [ -e $LIBJPEG/include/jpeglib.h ]; then - echo "# libjpeg found" - HAVE_JPEG=1 - else - echo "# No JPEG library found! JPEG files will not be supported!" -- echo "# Looking for: $LIBJPEG/jpeglib.h" -+ echo "# Looking for: $LIBJPEG/include/jpeglib.h" - fi - - } ---- bsoft/bsoft_conf.orig 2019-11-05 20:05:09.000000000 +0100 -+++ bsoft/bsoft_conf 2020-10-17 17:11:31.028913000 +0200 -@@ -129,7 +129,7 @@ - LIBLIST="" - - --XMLINC=$SDK/usr/include/libxml2 -+XMLINC=$EBROOTLIBXML2/include/libxml2 - if [ -e $XMLINC ]; then - CFLAGS=$CFLAGS' -DHAVE_XML' - if [ $HAVE_XML == 2 ]; then -@@ -163,7 +163,7 @@ - - if [ $HAVE_TIFF = 1 ]; then - CFLAGS="$CFLAGS -DHAVE_TIFF" -- INCLUDES="$INCLUDES -I$LIBTIFF/libtiff" -+ INCLUDES="$INCLUDES -I$EBBUILDLIBTIFF/libtiff" - # LIBDIR="$LIBDIR -L$LIBTIFF/lib" - # LINKLIBS="$LINKLIBS -ltiff"; - LIBLIST="$LIBLIST $LIBTIFF/lib/libtiff.a" -@@ -171,8 +171,8 @@ - - if [ $HAVE_PNG = 1 ]; then - CFLAGS="$CFLAGS -DHAVE_PNG" -- INCLUDES="$INCLUDES -I$LIBPNG" --# LIBDIR="$LIBDIR -L$LIBPNG/lib" -+ INCLUDES="$INCLUDES -I$LIBPNG/include" -+ LIBDIR="$LIBDIR -L$EBROOTZLIB/lib" - # LINKLIBS="$LINKLIBS -lz -lpng"; - LINKLIBS="$LINKLIBS -lz"; - LIBLIST="$LIBLIST $LIBPNG/lib/libpng.a" -@@ -180,10 +180,10 @@ - - if [ $HAVE_JPEG = 1 ]; then - CFLAGS="$CFLAGS -DHAVE_JPEG" -- INCLUDES="$INCLUDES -I$LIBJPEG" -+ INCLUDES="$INCLUDES -I$LIBJPEG/include" - # LIBDIR="$LIBDIR -L$LIBJPEG/lib" - # LINKLIBS="$LINKLIBS -ljpeg"; -- LIBLIST="$LIBLIST $LIBJPEG/lib/libjpeg.a" -+ LIBLIST="$LIBLIST $LIBJPEG/lib64/libjpeg.a" - fi - - # Tcl/Tk diff --git a/easybuild/easyconfigs/__archive__/b/bam-readcount/bam-readcount-0.8.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/bam-readcount/bam-readcount-0.8.0-GCC-9.3.0.eb deleted file mode 100644 index aa645c64e22..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bam-readcount/bam-readcount-0.8.0-GCC-9.3.0.eb +++ /dev/null @@ -1,51 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Adam Huffman -# The Francis Crick Institute -easyblock = 'CMakeMake' - -name = 'bam-readcount' -version = '0.8.0' - -homepage = 'https://github.com/genome/bam-readcount' -description = """Count DNA sequence reads in BAM files""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/genome/%(name)s/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['4f4dd558e3c6bfb24d6a57ec441568f7524be6639b24f13ea6f2bb350c7ea65f'] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('SAMtools', '1.10'), - ('zlib', '1.2.11'), - ('ncurses', '6.2'), -] - -# bam-readcount uses git to insert the version during configuration with CMake -# but in the release archives there is no git information -# local_commit is the git commit hash of the release -local_commit = 'dea4199' -local_versionfile = '%(builddir)s/%(name)s*/version/version.h.in' -preconfigopts = "sed -i -e 's/@FULL_VERSION@/%%(version)s/' %s && " % local_versionfile -preconfigopts += "sed -i -e 's/@COMMIT_HASH@/%s/' %s && " % (local_commit, local_versionfile) - -prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && " - -separate_build_dir = True - -sanity_check_paths = { - 'files': ["bin/bam-readcount"], - 'dirs': [] -} - -sanity_check_commands = [ - # --help exists with exit code 1, so use grep to check for expected pattern in help output - "bam-readcount --help 2>&1 | grep 'Example: bam-readcount -f'", - "bam-readcount --version | grep 'version: %(version)s '", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/basemap/basemap-1.2.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/basemap/basemap-1.2.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 62d10d69b8c..00000000000 --- a/easybuild/easyconfigs/__archive__/b/basemap/basemap-1.2.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'basemap' -version = '1.2.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://matplotlib.org/basemap/' -description = """The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('GEOS', '3.8.1', versionsuffix), - ('Pillow', '7.0.0', versionsuffix), - ('pyproj', '2.6.1.post1', versionsuffix), -] - -exts_list = [ - ('pyshp', '2.1.3', { - 'modulename': 'shapefile', - 'checksums': ['e32b4a6832a3b97986df442df63b4c4a7dcc846b326c903189530a5cc6df0260'], - }), - (name, version, { - 'modulename': 'mpl_toolkits.basemap', - 'prebuildopts': 'GEOS_DIR=$EBROOTGEOS', - 'preinstallopts': 'GEOS_DIR=$EBROOTGEOS', - 'source_tmpl': 'v%(version)srel.tar.gz', - 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], - 'checksums': ['7e6ee5d03b10168862cff82bfa819df8264c04f078eac4549a22dd2631696613'], - }), -] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb deleted file mode 100644 index 9eb0166e5fc..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,50 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -## - -easyblock = 'ConfigureMake' - -name = 'bbFTP' -version = '3.2.1' - -homepage = 'https://software.in2p3.fr/bbftp/' - -description = """bbFTP is a file transfer software. It implements its own transfer protocol, - which is optimized for large files (larger than 2GB) and secure as it does not read the - password in a file and encrypts the connection information. bbFTP main features are: - * Encoded username and password at connection * SSH and Certificate authentication modules - * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression - * Automatic retry * Customizable time-outs * Transfer simulation - * AFS authentication integration * RFIO interface""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://software.in2p3.fr/bbftp/dist'] -sources = ['%(namelower)s-client-%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix-openssl-1.1.patch'] -checksums = [ - '4000009804d90926ad3c0e770099874084fb49013e8b0770b82678462304456d', # bbftp-client-3.2.1.tar.gz - 'de8f23637a5d7b6874372c1e989fb3d7aaca6457312272021799354ee50eeb06', # bbFTP-3.2.1_fix-openssl-1.1.patch -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('zlib', '1.2.11')] - -osdependencies = [OS_PKG_OPENSSL_DEV] - -start_dir = 'bbftpc' - -sanity_check_paths = { - 'files': ['bin/bbftp'], - 'dirs': [], -} - -sanity_check_commands = ["bbftp -v"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index f30e818743c..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'bcbio-gff' -version = '0.6.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/chapmanb/bcbb/tree/master/gff' - -description = """ -Read and write Generic Feature Format (GFF) with Biopython integration. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['74c6920c91ca18ed9cb872e9471c0be442dad143d8176345917eb1fefc86bc37'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Biopython', '1.78', versionsuffix), -] - -local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' -local_targets = ['GFFOutput.py', 'GFFParser.py'] - -sanity_check_paths = { - 'files': [local_bcbiogffroot + '/BCBio/GFF/%s' % x for x in local_targets], - 'dirs': [local_bcbiogffroot], -} - -options = {'modulename': 'BCBio.GFF'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-9.3.0.eb deleted file mode 100644 index c0809fb0ecb..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'ConfigureMake' - -name = 'bcl2fastq2' -version = '2.20.0' - -homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' -description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by - Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] -sources = [{ - 'filename': '%s-v%s-tar.zip' % (name, version.replace('.', '-')), - 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz -}] - -checksums = ['8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3'] - -# CMake, Boost, libxml2 and libxslt are all built and used internally with specific versions -dependencies = [ - ('zlib', '1.2.11'), -] - -start_dir = 'src' -configopts = '--force-builddir' - -sanity_check_paths = { - 'files': ['bin/bcl2fastq'], - 'dirs': ['lib'] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/bcolz/bcolz-1.2.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/bcolz/bcolz-1.2.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 73256f47924..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bcolz/bcolz-1.2.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = "PythonPackage" - -name = 'bcolz' -version = '1.2.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://bcolz.blosc.org/en/latest/' -description = """bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. - Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. - It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, - but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -patches = [ - '%(name)s-%(version)s_fix-deprecation.patch', -] -checksums = [ - 'c017d09bb0cb5bbb07f2ae223a3f3638285be3b574cb328e91525b2880300bd1', # bcolz-1.2.1.tar.gz - '90e3525c3254ab0c6b45a170423b8a4a17764fc27fa47ff45ff8465169375d35', # bcolz-1.2.1_fix-deprecation.patch -] - -dependencies = [ - ('Python', '3.8.2'), - ('Blosc', '1.17.1'), - ('dask', '2.18.1', versionsuffix), - ('numexpr', '2.7.1', versionsuffix), - ('PyTables', '3.6.1', versionsuffix), -] - -preinstallopts = "BLOSC_DIR=$EBROOTBLOSC" - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -sanity_check_commands = ["python -c 'import bcolz; bcolz.test()'"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb deleted file mode 100644 index f7afb71fa1b..00000000000 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'beagle-lib' -version = '3.1.2' -homepage = 'https://github.com/beagle-dev/beagle-lib' -description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most - Bayesian and Maximum Likelihood phylogenetics packages.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] - -dependencies = [('Java', '11', '', SYSTEM)] - -builddependencies = [('Autotools', '20180311')] - -preconfigopts = "./autogen.sh && " - -sanity_check_paths = { - 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x for x in ["beagle.h", "platform.h"]] + - ["lib/libhmsbeagle%s.%s" % (x, SHLIB_EXT) for x in ["-cpu", "-cpu-sse", "-jni", ""]], - 'dirs': [] -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/b/bgen/bgen-3.0.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/bgen/bgen-3.0.3-GCCcore-9.3.0.eb deleted file mode 100644 index e2773030a22..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bgen/bgen-3.0.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'bgen' -version = '3.0.3' - -homepage = 'https://github.com/limix/bgen' -description = "A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'limix' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['1cf434f35aaee86d1093f1fd96caf07fa92c3b49a760175052af934d74e702a6'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -dependencies = [ - ('almosthere', '1.0.10'), - ('zstd', '1.4.4') -] - -runtest = 'test' - -sanity_check_paths = { - 'files': ['lib/libbgen.%s' % SHLIB_EXT, 'lib/libbgen_static.a', 'include/bgen.h'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.34-GCCcore-9.3.0.eb deleted file mode 100644 index 34dc183b567..00000000000 --- a/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.34-GCCcore-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -name = 'binutils' -version = '2.34' - -homepage = 'https://directory.fsf.org/project/binutils/' -description = "binutils: GNU binary utilities" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -patches = [ - 'binutils-2.31.1-gold-ignore-discarded-note-relocts.patch', - 'binutils-%(version)s-readd-avx512-vmovd.patch', -] -checksums = [ - '53537d334820be13eeb8acb326d01c7c81418772d626715c7ae927a7d401cab3', # binutils-2.34.tar.gz - # binutils-2.31.1-gold-ignore-discarded-note-relocts.patch - '17f22cc9136d0e81cfe8cbe310328c794a78a864e7fe7ca5827ee6678f65af32', - '45ecf7f5d198dd446d1a2e2a4d46b2747eb6fb8f2bfa18d7d42769e710e85716', # binutils-2.34-readd-avx512-vmovd.patch -] - -builddependencies = [ - ('flex', '2.6.4'), - ('Bison', '3.5.3'), - # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) -] - -dependencies = [ - # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, - # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 - ('zlib', '1.2.11'), -] - -# avoid build failure when makeinfo command is not available -# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 -buildopts = 'MAKEINFO=true' -installopts = buildopts - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.36.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.36.1-FCC-4.5.0.eb deleted file mode 100644 index 9b967c834c9..00000000000 --- a/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.36.1-FCC-4.5.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'binutils' -version = '2.36.1' - -homepage = 'https://directory.fsf.org/project/binutils/' -description = "binutils: GNU binary utilities" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['e68edeaaeb6ca9687b6dcbaedd1b376506baad2d48de26a885fc5ab6acb839da'] - -builddependencies = [ - ('flex', '2.6.4'), - ('Bison', '3.7.6'), -] - -dependencies = [ - # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, - # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 - ('zlib', '1.2.11'), -] - -# configure script seems to be confused about the presence of limits.h and fcntl.h when using the Fujitsu compiler -prebuildopts = 'export CFLAGS="-DHAVE_LIMITS_H -DHAVE_FCNTL_H $CFLAGS" && ' - -# avoid build failure when makeinfo command is not available -# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 -buildopts = 'MAKEINFO=true' -installopts = buildopts - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 71d0f1b43b4..00000000000 --- a/easybuild/easyconfigs/__archive__/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,44 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Revised BSD -# -# Notes:: -## - -easyblock = 'PythonPackage' - -name = 'biom-format' -version = '2.1.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://biom-format.org' -description = """ -The BIOM file format (canonically pronounced biome) is designed to be - a general-use format for representing biological sample by observation - contingency tables. BIOM is a recognized standard for the Earth Microbiome - Project and is a Genomics Standards Consortium supported project. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('h5py', '2.10.0', versionsuffix), -] - -sanity_check_paths = { - 'files': ['bin/biom'], - 'dirs': ['lib'], -} - -options = {'modulename': 'biom'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.0.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.0.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index f27fc4c95b9..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.0.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'bokeh' -version = '2.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/bokeh/bokeh' -description = "Statistical and novel interactive HTML plots for Python" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('Pillow', '7.0.0', versionsuffix), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('tornado', '6.0.4', { - 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], - }), - ('typing-extensions', '3.7.4.2', { - 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', - 'checksums': ['79ee589a3caca649a9bfd2a8de4709837400dfa00b6cc81962a1e6a1815969ae'], - }), - (name, version, { - 'checksums': ['d9248bdb0156797abf6d04b5eac581dcb121f5d1db7acbc13282b0609314893a'], - }), -] - -sanity_check_paths = { - 'files': ['bin/bokeh'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.0.2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.0.2-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 9b918d390ad..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bokeh/bokeh-2.0.2-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'bokeh' -version = '2.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/bokeh/bokeh' -description = "Statistical and novel interactive HTML plots for Python" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('Pillow', '7.0.0', versionsuffix), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('tornado', '6.0.4', { - 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], - }), - ('typing-extensions', '3.7.4.2', { - 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', - 'checksums': ['79ee589a3caca649a9bfd2a8de4709837400dfa00b6cc81962a1e6a1815969ae'], - }), - (name, version, { - 'checksums': ['d9248bdb0156797abf6d04b5eac581dcb121f5d1db7acbc13282b0609314893a'], - }), -] - -sanity_check_paths = { - 'files': ['bin/bokeh'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/b/breseq/breseq-0.35.4-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/b/breseq/breseq-0.35.4-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 8ca749f5625..00000000000 --- a/easybuild/easyconfigs/__archive__/b/breseq/breseq-0.35.4-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'breseq' -version = '0.35.4' -versionsuffix = '-R-%(rver)s' - - -homepage = 'https://barricklab.org/breseq' -description = "breseq is a computational pipeline for the analysis of short-read re-sequencing data" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/barricklab/breseq/releases/download/v%(version)s/'] -sources = ['breseq-%(version)s-Source.tar.gz'] -checksums = ['762f7b6aac26bddb5a39724e103267bd48d597d74fa7a8006d2bf0bd68fe86b4'] - -dependencies = [ - ('R', '4.0.0'), - ('Bowtie2', '2.4.1'), - ('zlib', '1.2.11'), - ('ncurses', '6.2'), -] - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/breseq', 'bin/gdtools'], - 'dirs': [], -} - -# breseq --help exists with non-zero exit code, so use grep -sanity_check_commands = ["breseq --help | grep 'Usage: breseq'"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-FCC-4.5.0.eb deleted file mode 100644 index 47a2c195187..00000000000 --- a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-FCC-4.5.0.eb +++ /dev/null @@ -1,13 +0,0 @@ -easyblock = 'BuildEnv' - -name = 'buildenv' -version = 'default' - -homepage = 'None' -description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that - you can use to easily transition between toolchains when building your software. To query the variables being set - please use: module show """ - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-Fujitsu-21.05.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-Fujitsu-21.05.eb deleted file mode 100644 index 7e62992365c..00000000000 --- a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-Fujitsu-21.05.eb +++ /dev/null @@ -1,13 +0,0 @@ -easyblock = 'BuildEnv' - -name = 'buildenv' -version = 'default' - -homepage = 'None' -description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that - you can use to easily transition between toolchains when building your software. To query the variables being set - please use: module show """ - -toolchain = {'name': 'Fujitsu', 'version': '21.05'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-foss-2020a.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-foss-2020a.eb deleted file mode 100644 index df38a8ae3b5..00000000000 --- a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-foss-2020a.eb +++ /dev/null @@ -1,13 +0,0 @@ -easyblock = 'BuildEnv' - -name = 'buildenv' -version = 'default' - -homepage = 'None' -description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that - you can use to easily transition between toolchains when building your software. To query the variables being set - please use: module show """ - -toolchain = {'name': 'foss', 'version': '2020a'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-fosscuda-2020a.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-fosscuda-2020a.eb deleted file mode 100644 index a3f954df538..00000000000 --- a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-fosscuda-2020a.eb +++ /dev/null @@ -1,13 +0,0 @@ -easyblock = 'BuildEnv' - -name = 'buildenv' -version = 'default' - -homepage = 'None' -description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that - you can use to easily transition between toolchains when building your software. To query the variables being set - please use: module show """ - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-intel-2020a.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-intel-2020a.eb deleted file mode 100644 index 2882ee40f62..00000000000 --- a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-intel-2020a.eb +++ /dev/null @@ -1,13 +0,0 @@ -easyblock = 'BuildEnv' - -name = 'buildenv' -version = 'default' - -homepage = 'None' -description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that - you can use to easily transition between toolchains when building your software. To query the variables being set - please use: module show """ - -toolchain = {'name': 'intel', 'version': '2020a'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-intelcuda-2020a.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-intelcuda-2020a.eb deleted file mode 100644 index 25a263695cf..00000000000 --- a/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-intelcuda-2020a.eb +++ /dev/null @@ -1,13 +0,0 @@ -easyblock = 'BuildEnv' - -name = 'buildenv' -version = 'default' - -homepage = 'None' -description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that - you can use to easily transition between toolchains when building your software. To query the variables being set - please use: module show """ - -toolchain = {'name': 'intelcuda', 'version': '2020a'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/b/bwidget/bwidget-1.9.14-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/bwidget/bwidget-1.9.14-GCCcore-9.3.0.eb deleted file mode 100644 index 3cd4d28f10e..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bwidget/bwidget-1.9.14-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'Tarball' - -name = 'bwidget' -version = '1.9.14' - -homepage = 'https://core.tcl-lang.org/bwidget/home' -description = 'The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.' - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://downloads.sourceforge.net/project/tcllib/BWidget/%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['8e9692140167161877601445e7a5b9da5bb738ce8d08ee99b016629bc784a672'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('Tk', '8.6.10')] - -modextrapaths = {'TCLLIBPATH': '.'} - -sanity_check_paths = { - 'files': ['button.tcl'], - 'dirs': ['BWman'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/b/bx-python/bx-python-0.8.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/b/bx-python/bx-python-0.8.9-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 947b8f07728..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bx-python/bx-python-0.8.9-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'bx-python' -version = '0.8.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/bxlab/bx-python' -description = """The bx-python project is a Python library and associated set of scripts to allow for rapid - implementation of genome scale analyses.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('LZO', '2.10'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('python-lzo', '1.12', { - 'modulename': 'lzo', - 'preinstallopts': "export PREFIX=$EBROOTLZO && ", - 'checksums': ['97a8e46825e8f1abd84c2a3372bc09adae9745a5be5d3af2692cd850dac35345'], - }), - (name, version, { - 'modulename': 'bx', - 'checksums': ['7a6c8d41daf81c92601f00c0065c1b018a0b4e349abf78d662d4191a51ac8588'], - }), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb deleted file mode 100644 index b39d3a5e236..00000000000 --- a/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'bzip2' -version = '1.0.8' - -homepage = 'https://sourceware.org/bzip2' -description = """ - bzip2 is a freely available, patent free, high-quality data compressor. It - typically compresses files to within 10% to 15% of the best available - techniques (the PPM family of statistical compressors), whilst being around - twice as fast at compression and six times faster at decompression. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://sourceware.org/pub/%(name)s/'] -sources = [SOURCE_TAR_GZ] -patches = ['bzip2-%(version)s-pkgconfig.patch'] -checksums = [ - 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz - '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch -] - -builddependencies = [ - ('binutils', '2.34'), -] - - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/c/CBLAS/CBLAS-20110120-intel-2020a.eb b/easybuild/easyconfigs/__archive__/c/CBLAS/CBLAS-20110120-intel-2020a.eb deleted file mode 100644 index 5dd733876ce..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CBLAS/CBLAS-20110120-intel-2020a.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'CBLAS' -version = '20110120' - -homepage = 'https://www.netlib.org/blas/' -description = "C interface to the BLAS" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.netlib.org/blas/blast-forum/'] -sources = ['cblas.tgz'] -patches = ['CBLAS_shared-lib.patch'] -checksums = [ - '0f6354fd67fabd909baf57ced2ef84e962db58fae126e4f41b21dd4fec60a2a3', # cblas.tgz - '43d049287b91251064c581e8471f4f3323fec6b7d789f43dd93516b35cd1de81', # CBLAS_shared-lib.patch -] - -buildopts = 'all shared' - -# parallel build fails occasionally -maxparallel = 1 - -runtest = 'runtst' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/c/CBLAS/CBLAS_shared-lib.patch b/easybuild/easyconfigs/__archive__/c/CBLAS/CBLAS_shared-lib.patch deleted file mode 100644 index 44972512329..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CBLAS/CBLAS_shared-lib.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff -ru CBLAS.orig/Makefile CBLAS/Makefile ---- CBLAS.orig/Makefile 2010-03-05 00:34:22.000000000 +0100 -+++ CBLAS/Makefile 2013-05-11 21:43:29.571885362 +0200 -@@ -193,3 +193,7 @@ - ( cd src && rm -f a.out core *.o $(CBLIB) ) - ( cd testing && rm -f *.out core *.o x[sdcz]cblat[123] ) - ( cd examples && rm -f *.o cblas_ex1 cblas_ex2 ) -+ -+shared: alllib -+ ( mkdir tmp && cd tmp && cp $(CBLIB) . && ar x $(CBLIB) && $(CC) -shared -o libcblas.so.1.0.0 *.o -Wl,-soname=libcblas.so.1 && cp -p libcblas.so.1.0.0 ../lib && cd ../lib && ln -s libcblas.so.1.0.0 libcblas.so.1 && ln -s libcblas.so.1.0.0 libcblas.so ) -+ diff --git a/easybuild/easyconfigs/__archive__/c/CCL/CCL-1.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CCL/CCL-1.12-GCCcore-9.3.0.eb deleted file mode 100644 index 70487fea5b4..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CCL/CCL-1.12-GCCcore-9.3.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'MakeCp' -name = 'CCL' -version = '1.12' - -homepage = 'https://ccl.clozure.com/' -description = """Clozure CL (often called CCL for short) is a free Common Lisp - implementation with a long history. Some distinguishing features of the implementation - include fast compilation speed, native threads, a precise, generational, compacting - garbage collector, and a convenient foreign-function interface.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/Clozure/%(namelower)s/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s-linuxx86.tar.gz'] -checksums = ['84a95aaf1d1abafba586e9ff079343b04fe374b98b38ed24d830f1fb7ed4ab34'] - -builddependencies = [ - ('binutils', '2.34'), - ('M4', '1.4.18'), -] - -local_ccl_bin = 'lx86cl64' -local_ccl_dirs = [ - 'compiler', 'level-0', 'level-1', 'lib', 'library', 'lisp-kernel', 'scripts', 'tools', 'xdump', 'x86-headers64' -] - -# Build the kernel -buildopts = "-C lisp-kernel/linuxx8664 all CC=${CC} && " -# Rebuild CCL -buildopts += "./%s -n -b -Q -e '(ccl:rebuild-ccl :full t)' -e '(ccl:quit)'" % local_ccl_bin - -files_to_copy = [local_ccl_bin, '%s.image' % local_ccl_bin] + local_ccl_dirs - -postinstallcmds = [ - # Cleanup of build files - "find %(installdir)s -type f -name '*fsl' -delete", - "find %(installdir)s/lisp-kernel -type f -name '*.o' -delete", - # Link executable with generic name - "mkdir %(installdir)s/bin", - "ln -s %%(installdir)s/%s %%(installdir)s/bin/ccl" % local_ccl_bin, -] - -sanity_check_paths = { - 'files': [local_ccl_bin, '%s.image' % local_ccl_bin, 'bin/ccl'], - 'dirs': local_ccl_dirs, -} - -sanity_check_commands = ["ccl --help"] - -modextrapaths = {'CCL_DEFAULT_DIRECTORY': ''} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb deleted file mode 100644 index 4fabd5ab15b..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CCfits' -version = '2.5' - -homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/CCfits/' -description = """CCfits is an object oriented interface to the cfitsio library. It is designed to make -the capabilities of cfitsio available to programmers working in C++.""" - -toolchain = {'version': '9.3.0', 'name': 'GCCcore'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = ['https://heasarc.gsfc.nasa.gov/fitsio/%(name)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['938ecd25239e65f519b8d2b50702416edc723de5f0a5387cceea8c4004a44740'] - -dependencies = [ - ('CFITSIO', '3.48'), -] -builddependencies = [ - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ['lib/libCCfits.%s' % SHLIB_EXT], - 'dirs': ['include/CCfits'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/c/CD-HIT/CD-HIT-4.8.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CD-HIT/CD-HIT-4.8.1-GCC-9.3.0.eb deleted file mode 100644 index 53d1bcf616f..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CD-HIT/CD-HIT-4.8.1-GCC-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'MakeCp' - -name = 'CD-HIT' -version = '4.8.1' - -homepage = 'http://weizhongli-lab.org/cd-hit/' -description = """ CD-HIT is a very widely used program for clustering and - comparing protein or nucleotide sequences.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] -sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] -checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] - -dependencies = [ - ('Perl', '5.30.2'), - ('zlib', '1.2.11'), -] - -# make sure compilation flags are passed down (e.g. to enable OpenMP) -buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' - -# put here the list of generated executables when compiling -local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] - -# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" -files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] - -fix_perl_shebang_for = ['bin/*.pl'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_list_of_executables], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CDAT/CDAT-8.2.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/CDAT/CDAT-8.2.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 8f21fd2ed1b..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CDAT/CDAT-8.2.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,119 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'CDAT' -version = '8.2.1' -versionsuffix = "-Python-%(pyver)s" - -homepage = 'https://github.com/CDAT/cdat' -description = """CDAT is a powerful and complete front-end to a rich set of -visual-data exploration and analysis capabilities well suited for data analysis problems.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -dependencies = [ - ('Python', '3.8.2'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), - ('HDF5', '1.10.6'), - ('DB', '18.1.32'), - ('netCDF-C++4', '4.3.1'), - ('UDUNITS', '2.2.26'), - ('gdbm', '1.18.1'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('libcdms', '3.1.2', versionsuffix), - ('VTK', '8.2.0', versionsuffix), -] - -exts_default_options = { - 'github_account': 'CDAT', - 'source_urls': [GITHUB_SOURCE], - 'sources': [{ - 'download_filename': 'v%(version)s.tar.gz', - 'filename': SOURCE_TAR_GZ, - }] -} -exts_list = [ - ('pycf', '1.6.9', { - 'patches': ['pycf-1.6.9-openblas-extern.patch'], - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': [ - '622fc99f7d258d2931edc080dbdb81d2bf1be1ebac922f2fca0b71173ada7520', # pycf-1.6.9.tar.gz - 'df04e4f48dfa69ecbae31b743047478bf2a3649642bfd6cf36b9d0ebc5d01896', # pycf-1.6.9-openblas-extern.patch - ], - }), - ('lazy-object-proxy', '1.5.2', { - 'modulename': 'lazy_object_proxy', - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['5944a9b95e97de1980c65f03b79b356f30a43de48682b8bdd90aa5089f0ec1f4'], - }), - ('eofs', '1.4.0', { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['5ae9afc159b8cfb2be476d257fc469b2cdd473c76f5411c508010007a5ae6bd2'], - }), - ('cdat_info', version, { - 'checksums': ['173a91d1dc68d1b3c96230d1c9fc0fa9304a463a5da5015830eb35e2823e3c9b'], - }), - ('unidata', '2.8', { - 'patches': ['unidata-2.8-package-data.patch'], - 'checksums': [ - '5a4958af4e45a5efd9012c76cb0ef5c02d479a612e7d161e77b513780bc7b2d7', # unidata-2.8.tar.gz - '04a336f579a69b2f825e4896dd2a25d4bab1f302f0a039e73464de3381c8e09b', # unidata-2.8-package-data.patch - ], - }), - ('cdtime', '3.1.4', { - 'checksums': ['c22ec725e207994cec3d4ba5b5b35ede5ea698d552dc75e87cd86fa7dbc65b35'], - }), - ('cdutil', version, { - 'checksums': ['9e02348ae0e9148c6b0b9391b208adf9be7d97e0da30b88518c02dfc1e07d2bf'], - }), - ('dv3d', version, { - 'modulename': 'DV3D', - 'patches': ['dv3d-pkg_resource-paths.patch'], - 'checksums': [ - 'd542641e259327777642616def558ea97ffdac5788f7258348812534a89f01a3', # dv3d-8.2.1.tar.gz - '8c7368001ef70573ee597537ab3067ef77f01ca4fc16f11609ec5617e3faf290', # dv3d-pkg_resource-paths.patch - ], - }), - ('vcs', version, { - 'checksums': ['9f647c940396cb40003b96484bfa48d2d0fce38cf49217e06054c4c9cc66b5ce'], - }), - ('vcsaddons', version, { - 'checksums': ['b8d431243ee541da46f4e5e19c21eb911214c597958ab237d9484854f173b6e3'], - }), - ('xmgrace', '2.10', { - 'checksums': ['6d5b80d58807b39722895947a61a5e900bfac0d1f70c86381846b736c0e2ef20'], - }), - ('genutil', version, { - 'checksums': ['944ccc4de05072d2773cfff6b5f279e2058457a672169153ebec0e19f5a3601c'], - }), - ('thermo', '8.1', { - 'checksums': ['9bc854a321d7ad1b46076185ccb5b7e32cbc595794f691526e24770c52eae01b'], - }), - ('wk', version, { - 'modulename': 'WK', - 'checksums': ['c060f0e31340b139c86bac9a49b9e06136e63c48c75d5745080312cda3e79ff5'], - }), - ('distarray', '2.12.2', { - 'sources': [{'filename': '%(name)s-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}], - 'checksums': ['ca6ee7610b8e8309cec47121b2454d8d318bfe37b6db3b950c65b1316035ba6c'], - }), - ('cdms2', '3.1.5', { - 'patches': ['cdms2-3.1.5-netcdf_par.patch'], - 'source_urls': ['https://github.com/CDAT/cdms/archive/'], - 'checksums': [ - '2b4f2ad348581c9831d3dcb785502515da41f0d21be728c8211618871a0caed9', # cdms2-3.1.5.tar.gz - '93368235cbf98d9b25617ffebea90e0ac104860f2311671fb64c790f57fbc092', # cdms2-3.1.5-netcdf_par.patch - ], - }), -] - -sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/unidata/udunits.dat'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/c/CDAT/cdms2-3.1.5-netcdf_par.patch b/easybuild/easyconfigs/__archive__/c/CDAT/cdms2-3.1.5-netcdf_par.patch deleted file mode 100644 index f5a2bdb8a4d..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CDAT/cdms2-3.1.5-netcdf_par.patch +++ /dev/null @@ -1,20 +0,0 @@ -netcdf.h needs to be imported before netcdf_par.h - -Author: Jakub Zárybnický - -diff -ru cdms-3.1.5/Src/Cdunifmodule.c cdms-3.1.5-edit/Src/Cdunifmodule.c ---- cdms-3.1.5/Src/Cdunifmodule.c 2020-07-31 03:01:33.000000000 +0200 -+++ cdms-3.1.5-edit/Src/Cdunifmodule.c 2021-02-16 15:33:00.944155237 +0100 -@@ -12,11 +12,11 @@ - /*#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION*/ - #include "Python.h" - #include "numpy/ndarrayobject.h" -+#include "netcdf.h" - #ifdef PARALLEL - #include "mpi.h" - #include "netcdf_par.h" - #endif --#include "netcdf.h" - - #define _CDUNIF_MODULE - #include "Cdunifmodule.h" diff --git a/easybuild/easyconfigs/__archive__/c/CDAT/dv3d-pkg_resource-paths.patch b/easybuild/easyconfigs/__archive__/c/CDAT/dv3d-pkg_resource-paths.patch deleted file mode 100644 index 4347c0165ae..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CDAT/dv3d-pkg_resource-paths.patch +++ /dev/null @@ -1,65 +0,0 @@ -Data files are installed under %(installdir)s/share and not under site-packages -where pkg_resources expects them, this fixes that in the simplest way possible. - -Author: Jakub Zárybnický - -diff -ru dv3d-8.2.1/DV3D/ButtonBarWidget.py dv3d-8.2.1-edit/DV3D/ButtonBarWidget.py ---- dv3d-8.2.1/DV3D/ButtonBarWidget.py 2020-07-17 23:18:27.000000000 +0200 -+++ dv3d-8.2.1-edit/DV3D/ButtonBarWidget.py 2021-03-02 17:14:57.952866577 +0100 -@@ -9,7 +9,7 @@ - import numpy as np - from .ConfigurationFunctions import * - import pkg_resources --dv3d_egg_path = pkg_resources.resource_filename(pkg_resources.Requirement.parse("dv3d"), "share/dv3d") -+dv3d_egg_path = pkg_resources.resource_filename(pkg_resources.Requirement.parse("dv3d"), "../../../share/dv3d") - ButtonDir = os.path.join( dv3d_egg_path, 'buttons' ) - - class OriginPosition: -diff -ru dv3d-8.2.1/DV3D/ColorMapManager.py dv3d-8.2.1-edit/DV3D/ColorMapManager.py ---- dv3d-8.2.1/DV3D/ColorMapManager.py 2020-07-17 23:18:27.000000000 +0200 -+++ dv3d-8.2.1-edit/DV3D/ColorMapManager.py 2021-03-02 17:15:05.905834592 +0100 -@@ -9,7 +9,7 @@ - import sys, vtk, copy - import pickle - import pkg_resources --dv3d_egg_path = pkg_resources.resource_filename(pkg_resources.Requirement.parse("dv3d"), "share/dv3d") -+dv3d_egg_path = pkg_resources.resource_filename(pkg_resources.Requirement.parse("dv3d"), "../../../share/dv3d") - pkl_path = os.path.join( dv3d_egg_path, 'colormaps.pkl' ) - colormap_file = open( pkl_path, 'rb' ) - try: -diff -ru dv3d-8.2.1/DV3D/ConfigurationFunctions.py dv3d-8.2.1-edit/DV3D/ConfigurationFunctions.py ---- dv3d-8.2.1/DV3D/ConfigurationFunctions.py 2020-07-17 23:18:27.000000000 +0200 -+++ dv3d-8.2.1-edit/DV3D/ConfigurationFunctions.py 2021-03-02 17:15:09.177821440 +0100 -@@ -10,7 +10,7 @@ - import inspect, ast - from weakref import WeakSet, WeakKeyDictionary - import pkg_resources --dv3d_egg_path = pkg_resources.resource_filename(pkg_resources.Requirement.parse("dv3d"), "share/dv3d") -+dv3d_egg_path = pkg_resources.resource_filename(pkg_resources.Requirement.parse("dv3d"), "../../../share/dv3d") - - try: - basestring -diff -ru dv3d-8.2.1/DV3D/MapManager.py dv3d-8.2.1-edit/DV3D/MapManager.py ---- dv3d-8.2.1/DV3D/MapManager.py 2020-07-17 23:18:27.000000000 +0200 -+++ dv3d-8.2.1-edit/DV3D/MapManager.py 2021-03-02 17:15:02.968846402 +0100 -@@ -10,7 +10,7 @@ - import numpy as np - import os, vtk - import pkg_resources --dv3d_egg_path = pkg_resources.resource_filename(pkg_resources.Requirement.parse("dv3d"), "share/dv3d") -+dv3d_egg_path = pkg_resources.resource_filename(pkg_resources.Requirement.parse("dv3d"), "../../../share/dv3d") - - defaultMapDir = dv3d_egg_path - defaultMapFile = os.path.join( defaultMapDir, 'earth2k.jpg' ) -diff -ru dv3d-8.2.1/DV3D/StructuredGridPlot.py dv3d-8.2.1-edit/DV3D/StructuredGridPlot.py ---- dv3d-8.2.1/DV3D/StructuredGridPlot.py 2020-07-17 23:18:27.000000000 +0200 -+++ dv3d-8.2.1-edit/DV3D/StructuredGridPlot.py 2021-03-02 17:14:51.585892197 +0100 -@@ -12,7 +12,7 @@ - from .DV3DPlot import * - from .MapManager import MapManager - import pkg_resources --dv3d_egg_path = pkg_resources.resource_filename(pkg_resources.Requirement.parse("dv3d"), "share/dv3d") -+dv3d_egg_path = pkg_resources.resource_filename(pkg_resources.Requirement.parse("dv3d"), "../../../share/dv3d") - - class StructuredGridPlot(DV3DPlot): - diff --git a/easybuild/easyconfigs/__archive__/c/CDAT/pycf-1.6.9-openblas-extern.patch b/easybuild/easyconfigs/__archive__/c/CDAT/pycf-1.6.9-openblas-extern.patch deleted file mode 100644 index 0867f1ddffb..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CDAT/pycf-1.6.9-openblas-extern.patch +++ /dev/null @@ -1,65 +0,0 @@ -Replace hardcoded searching for BLAS/LAPACK with Easybuild-provided values. -Also take care of `extern` definitions which occurs generateLibCFConfig.py parses -netCDF headers and produces invalid Python syntax. - -Author: Jakub Zárybnický - -diff -ru pycf-1.6.9/py/generateLibCFConfig.py pycf-1.6.9-edit/py/generateLibCFConfig.py ---- pycf-1.6.9/py/generateLibCFConfig.py 2016-09-06 22:28:57.000000000 +0200 -+++ pycf-1.6.9-edit/py/generateLibCFConfig.py 2021-03-03 11:41:23.339894364 +0100 -@@ -69,7 +69,7 @@ - m = re.match(f1, line) - if m: - name, value = m.group(1), m.group(2) -- nameValue.append([name, value]) -+ nameValue.append([name, value.replace(' extern', '')]) - return nameValue - - # parse netcdf header -diff -ru pycf-1.6.9/setup.py pycf-1.6.9-edit/setup.py ---- pycf-1.6.9/setup.py 2017-01-31 05:07:44.000000000 +0100 -+++ pycf-1.6.9-edit/setup.py 2021-03-03 10:57:47.647624973 +0100 -@@ -100,25 +100,6 @@ - cmd = subprocess.check_output(['nc-config', '--libs']).decode("utf-8") - netcdf_libdirs, netcdf_libs = parseLinkCommand(cmd) - -- --# Get LAPACK and BLAS. If not set then search common locations --dirs = (os.path.dirname(sys.executable) + '/../lib', '/usr/local/lib', '/usr/lib', '/usr/lib64') --blas_libraries = [] --# prefer MKL --USE_MKL = True --lapack_libraries = findLibrary(dirs, 'mkl_core') --if not lapack_libraries: -- USE_MKL = False -- lapack_libraries = os.environ.get('LAPACK_LIBRARIES', findLibrary(dirs, 'lapack')) -- blas_libraries = os.environ.get('BLAS_LIBRARIES', findLibrary(dirs, 'blas')) -- if not blas_libraries: -- print('ERROR: could not find blas -- set environment variable BLAS_LIBRARIES and rerun') -- sys.exit(2) -- --if not lapack_libraries: -- print('ERROR: could not find lapack -- set environment variable LAPACK_LIBRARIES and rerun') -- sys.exit(1) -- - # generate cf_config.h - cfg = open('cf_config.h', mode='w') - print('#define VERSION "{}"'.format(getVersion()), file=cfg) -@@ -126,15 +107,8 @@ - print('#define HAVE_CONFIG_H', file=cfg) - cfg.close() - --lapack_dir, lapack_lib = breakLibraryPath(lapack_libraries) --libdirs = netcdf_libdirs + [lapack_dir] --libs = netcdf_libs + [lapack_lib] --if USE_MKL: -- libs += ['mkl_sequential', 'mkl_rt'] --if blas_libraries: -- blas_dir, blas_lib = breakLibraryPath(blas_libraries) -- libdirs += [blas_dir] -- libs += [blas_lib] -+libdirs = netcdf_libdirs + getValuesFromOption('-L', os.environ.get('LDFLAGS')) -+libs = netcdf_libs + getValuesFromOption('-l', os.environ.get('LIBBLAS')) - - # list all the directories that contain source file to be compiled - # into a shared library diff --git a/easybuild/easyconfigs/__archive__/c/CDAT/unidata-2.8-package-data.patch b/easybuild/easyconfigs/__archive__/c/CDAT/unidata-2.8-package-data.patch deleted file mode 100644 index 6ccf2bf0858..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CDAT/unidata-2.8-package-data.patch +++ /dev/null @@ -1,104 +0,0 @@ -Allows building unidata 2.8 under Python 3 (C bindings, slots, module path), -replaces the hard-coded creation of udunits.dat and lets setup.py handle that. - -Author: Jakub Zárybnický - -diff -ru unidata-2.8/Lib/__init__.py unidata-2.8-edit/Lib/__init__.py ---- unidata-2.8/Lib/__init__.py 2016-04-12 01:12:43.000000000 +0200 -+++ unidata-2.8-edit/Lib/__init__.py 2021-03-01 19:14:36.811609779 +0100 -@@ -18,8 +18,8 @@ - """ - import os - import sys --from udunits import udunits, addBaseUnit, addDimensionlessUnit, addScaledUnit # noqa --from udunits import addOffsettedUnit, addMultipliedUnits, addInvertedUnit, addDividedUnits # noqa -+from .udunits import udunits, addBaseUnit, addDimensionlessUnit, addScaledUnit # noqa -+from .udunits import addOffsettedUnit, addMultipliedUnits, addInvertedUnit, addDividedUnits # noqa - udunits_init = 0 # noqa - - xml_pth = os.path.join(sys.prefix,"share","udunits","udunits2.xml") -diff -ru unidata-2.8/Lib/udunits.py unidata-2.8-edit/Lib/udunits.py ---- unidata-2.8/Lib/udunits.py 2016-04-12 01:12:43.000000000 +0200 -+++ unidata-2.8-edit/Lib/udunits.py 2021-03-01 19:13:28.310920278 +0100 -@@ -1,10 +1,10 @@ --import udunits_wrap -+import unidata.udunits_wrap - import sys - import string - import unidata - from collections import OrderedDict - version = sys.version.split()[0].split('.') --version = string.join(version[:2], '.') -+version = '.'.join(version[:2]) - udunits_name = unidata.__path__[0] + '/udunits.dat' - known_units_units = None - known_units_types = None -@@ -150,7 +150,7 @@ - dict['THERMODYNAMIC TEMPERATURE'] # returns['degree_Kelvin', 'degree_Celsius', ...] - - """ -- __slots__ = ['units', '_units', 'value', '_value'] -+ __slots__ = ['_units', '_value'] - - def __init__(self, value, units): - if isinstance(value, str): -diff -ru unidata-2.8/setup.py unidata-2.8-edit/setup.py ---- unidata-2.8/setup.py 2016-04-12 01:12:43.000000000 +0200 -+++ unidata-2.8-edit/setup.py 2021-03-01 19:15:47.039301850 +0100 -@@ -24,6 +24,7 @@ - url = "http://www-pcmdi.llnl.gov/software", - packages = ['unidata'], - package_dir = {'unidata': 'Lib'}, -+ data_files = [('unidata', ['Src/udunits.dat'])], - ext_modules = [ - Extension('unidata.udunits_wrap', - ['Src/udunits_wrap.c', -@@ -36,16 +37,4 @@ - libraries=['udunits2','expat'] - ) - ] -- ) -- --f=open('Src/udunits.dat') --version=sys.version.split()[0].split('.') --version='.'.join(version[:2]) --try: -- f2=open(target_prefix+'/lib/python'+version+'/site-packages/unidata/udunits.dat','w') --except: -- f2=open(target_prefix+'/lib64/python'+version+'/site-packages/unidata/udunits.dat','w') -- --for l in f.xreadlines(): -- f2.write(l) --f2.close() -+ ) -diff -ru unidata-2.8/Src/udunits_wrap.c unidata-2.8-edit/Src/udunits_wrap.c ---- unidata-2.8/Src/udunits_wrap.c 2016-04-12 01:12:43.000000000 +0200 -+++ unidata-2.8-edit/Src/udunits_wrap.c 2021-03-01 19:08:49.294322341 +0100 -@@ -364,15 +364,23 @@ - {NULL, NULL} /*sentinel */ - }; - --void --initudunits_wrap() -+static struct PyModuleDef UdunitsModule = - { -- (void) Py_InitModule("udunits_wrap", MyUdunitsMethods); -+ PyModuleDef_HEAD_INIT, -+ "udunits_wrap", /* name of module */ -+ "", /* module documentation, may be NULL */ -+ -1, /* size of per-interpreter state of the module, or -1 if the module keeps state in global variables. */ -+ MyUdunitsMethods -+}; -+ -+PyMODINIT_FUNC PyInit_udunits_wrap(void) -+{ -+ return PyModule_Create(&UdunitsModule); - } - - int main(int argc,char **argv) - { - Py_SetProgramName(argv[0]); - Py_Initialize(); -- initudunits_wrap();} -+ PyInit_udunits_wrap();} - diff --git a/easybuild/easyconfigs/__archive__/c/CFITSIO/CFITSIO-3.48-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CFITSIO/CFITSIO-3.48-GCCcore-9.3.0.eb deleted file mode 100644 index 5a8ca449dde..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CFITSIO/CFITSIO-3.48-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CFITSIO' -version = '3.48' - -homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' -description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in -FITS (Flexible Image Transport System) data format.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] -sources = ['%%(namelower)s-%s.tar.gz' % version] -patches = ['CFITSIO-3.48_install_test_data.patch'] -checksums = [ - '91b48ffef544eb8ea3908543052331072c99bf09ceb139cb3c6977fc3e47aac1', # cfitsio-3.48.tar.gz - 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch -] - -# curl for HTTPs support -dependencies = [('cURL', '7.69.1')] - -builddependencies = [('binutils', '2.34')] - -# make would create just static libcfitsio.a. -# Let's create dynamic lib and testprog too. -buildopts = '&& make shared && make testprog' - -sanity_check_paths = { - 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -sanity_check_commands = [ - ('cd %(installdir)s/share && testprog'), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb deleted file mode 100644 index 7260e3f71ab..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'CGAL' -version = '4.14.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.cgal.org/' -description = """The goal of the CGAL Open Source Project is to provide easy access to efficient - and reliable geometric algorithms in the form of a C++ library.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'strict': True} - -source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] -sources = [SOURCE_TAR_XZ] -checksums = ['5bafe7abe8435beca17a1082062d363368ec1e3f0d6581bb0da8b010fb389fe4'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Eigen', '3.3.7'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('Python', '3.8.2'), - ('Boost', '1.72.0'), - ('MPFR', '4.0.2'), - ('GMP', '6.2.0'), - ('Mesa', '20.0.2'), - ('libGLU', '9.0.1'), - ('Qt5', '5.14.1'), -] - -configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' -configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT -configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " -configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb deleted file mode 100644 index 7944a1be7fc..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'CGAL' -version = '4.14.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.cgal.org/' -description = """The goal of the CGAL Open Source Project is to provide easy access to efficient - and reliable geometric algorithms in the form of a C++ library.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'strict': True} - -source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] -sources = [SOURCE_TAR_XZ] -checksums = ['5bafe7abe8435beca17a1082062d363368ec1e3f0d6581bb0da8b010fb389fe4'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Eigen', '3.3.7'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('Python', '3.8.2'), - ('Boost', '1.72.0'), - ('MPFR', '4.0.2'), - ('GMP', '6.2.0'), - ('Mesa', '20.0.2'), - ('libGLU', '9.0.1'), - ('Qt5', '5.14.1'), -] - -configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' -configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT -configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " -configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/c/CLHEP/CLHEP-2.4.1.3-foss-2020a.eb b/easybuild/easyconfigs/__archive__/c/CLHEP/CLHEP-2.4.1.3-foss-2020a.eb deleted file mode 100644 index 2763926fb89..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CLHEP/CLHEP-2.4.1.3-foss-2020a.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'CLHEP' -version = '2.4.1.3' - -homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' -description = """The CLHEP project is intended to be a set of HEP-specific foundation and - utility classes such as random generators, physics vectors, geometry and linear algebra. - CLHEP is structured in a set of packages independent of any external package.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] -sources = [SOURCELOWER_TGZ] -checksums = ['27c257934929f4cb1643aa60aeaad6519025d8f0a1c199bc3137ad7368245913'] - -builddependencies = [('CMake', '3.16.4')] - -sanity_check_paths = { - 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], - 'dirs': ['include/CLHEP'], -} - -sanity_check_commands = ["clhep-config --help"] - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/c/CLISP/CLISP-2.49-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CLISP/CLISP-2.49-GCCcore-9.3.0.eb deleted file mode 100644 index e4c45b7d10c..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CLISP/CLISP-2.49-GCCcore-9.3.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'CLISP' -version = '2.49' - -homepage = 'https://clisp.sourceforge.io/' - -description = """ - Common Lisp is a high-level, general-purpose, object-oriented, dynamic, - functional programming language. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE + '/release/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] - -patches = ['CLISP-%(version)s_fix-readline.patch'] - -checksums = [ - '8132ff353afaa70e6b19367a25ae3d5a43627279c25647c220641fed00f8e890', # clisp-2.49.tar.bz2 - '903ca7367721e5bfe216fd8151659c4d127739311fac61f812e0031faec100ea', # CLISP-2.49_fix-readline.patch -] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('DB', '18.1.32'), - ('libffcall', '2.2'), - ('libreadline', '8.0'), - ('libsigsegv', '2.12'), - ('PCRE', '8.44'), - ('zlib', '1.2.11'), -] - -configopts = 'build' - -# disable "streams" test due to problems with https:// -# see https://sourceforge.net/p/clisp/mailman/message/36224219/ -prebuildopts = "sed -e 's/\"streams\"/\"streamslong\"/' -i.eb tests/tests.lisp && cd build && " -buildopts = 'all check' - -maxparallel = 1 - -preinstallopts = 'cd build && ' - -sanity_check_paths = { - 'files': ['bin/clisp', 'lib/%(namelower)s-%(version)s/base/lisp.a'], - 'dirs': ['share/aclocal', 'share/doc'], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/c/CLISP/CLISP-2.49_fix-readline.patch b/easybuild/easyconfigs/__archive__/c/CLISP/CLISP-2.49_fix-readline.patch deleted file mode 100644 index 44e4e73952e..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CLISP/CLISP-2.49_fix-readline.patch +++ /dev/null @@ -1,17 +0,0 @@ -obtained from https://sourceforge.net/p/clisp/bugs/688/ - -$NetBSD: patch-modules_readline_readline.lisp,v 1.1 2016/09/20 14:10:25 wiz Exp $ - -rl_readline_state changed from int to unsigned long in readline-7.0. - ---- modules/readline/readline.lisp.orig 2010-01-06 22:18:03.000000000 +0000 -+++ modules/readline/readline.lisp -@@ -424,7 +424,7 @@ name in ~/.inputrc. This is preferred wa - "The version of this incarnation of the readline library, e.g., 0x0402.")) - (def-c-var gnu-readline-p (:name "rl_gnu_readline_p") (:type int) - (:documentation "True if this is real GNU readline.")) --(def-c-var readline-state (:name "rl_readline_state") (:type int) -+(def-c-var readline-state (:name "rl_readline_state") (:type ulong) - (:documentation "Flags word encapsulating the current readline state.")) - (def-c-var editing-mode (:name "rl_editing_mode") (:type int) - (:documentation "Says which editing mode readline is currently using. diff --git a/easybuild/easyconfigs/__archive__/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 47f33cddc2c..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,34 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'CMSeq' -version = '1.0.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/SegataLab/cmseq/' -description = "CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus." - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['c354b89bc4fdbb24fa1ffa063febdb96f2bbd8837af399887b300c9be98bda2e'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Biopython', '1.78', versionsuffix), - ('bcbio-gff', '0.6.6', versionsuffix), - ('biom-format', '2.1.10', versionsuffix), - ('Pysam', '0.16.0.1'), - ('SAMtools', '1.10'), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['breadth_depth.py', 'consensus.py', 'poly.py', 'polymut.py']], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CMake/CMake-3.16.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CMake/CMake-3.16.4-GCCcore-9.3.0.eb deleted file mode 100644 index e36b56522ed..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CMake/CMake-3.16.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -name = 'CMake' -version = '3.16.4' - -homepage = 'https://www.cmake.org' - -description = """ - CMake, the cross-platform, open-source build system. CMake is a family of - tools designed to build, test and package software. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['9bcc8c114d9da603af9512083ed7d4a39911d16105466beba165ba8fe939ac2c'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('ncurses', '6.2'), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('cURL', '7.69.1'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.1d'), -] - -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-5.1-foss-2020a.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-5.1-foss-2020a.eb deleted file mode 100644 index b169375381f..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-5.1-foss-2020a.eb +++ /dev/null @@ -1,49 +0,0 @@ -name = 'CP2K' -version = '5.1' - -homepage = 'https://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] -sources = [SOURCELOWER_TAR_BZ2] -patches = [ - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] -checksums = [ - 'e23613b593354fa82e0b8410e17d94c607a0b8c6d9b5d843528403ab09904412', # cp2k-5.1.tar.bz2 - '02475cbe24c8d4ba27037c826adf8a534cad634c3c4e02c21d743f5284516bda', # CP2K-2.4.0-fix_compile_date_lastsvn.patch -] - -dependencies = [ - ('Libint', '1.1.6'), - ('libxc', '3.0.1'), - ('libxsmm', '1.16.1'), - ('FFTW', '3.3.8'), - ('PLUMED', '2.6.0', '-Python-3.8.2'), -] - -builddependencies = [ - ('flex', '2.6.4'), - ('Bison', '3.5.3'), -] - -# values to use here are +1 those used for building Libint -# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT -extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" - -# regression test reports failures -ignore_regtest_fails = True - -# You might want to set OMP_NUM_THREADS, otherwise OpenBLAS will start (by default) -# the number of accessible CPUcores OpenMP threads. Since it is a MPI only version (popt), -# the performance will be copletely bad, as on N CPU cores N^2 threads will run. -# intel toolchain versions do not have this problem. YOU HAVE BEEN WARNED! -# modextravars = {'OMP_NUM_THREADS': '1'} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-5.1-intel-2020a.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-5.1-intel-2020a.eb deleted file mode 100644 index 92dbb8e3efc..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-5.1-intel-2020a.eb +++ /dev/null @@ -1,43 +0,0 @@ -name = 'CP2K' -version = '5.1' - -homepage = 'https://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] -sources = [SOURCELOWER_TAR_BZ2] -patches = [ - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] -checksums = [ - 'e23613b593354fa82e0b8410e17d94c607a0b8c6d9b5d843528403ab09904412', # cp2k-5.1.tar.bz2 - '02475cbe24c8d4ba27037c826adf8a534cad634c3c4e02c21d743f5284516bda', # CP2K-2.4.0-fix_compile_date_lastsvn.patch -] - -dependencies = [ - ('Libint', '1.1.6'), - ('libxc', '3.0.1'), - ('libxsmm', '1.16.1'), - ('FFTW', '3.3.8'), - ('PLUMED', '2.6.0', '-Python-3.8.2'), -] - -builddependencies = [ - ('flex', '2.6.4'), - ('Bison', '3.5.3'), -] - -# values to use here are +1 those used for building Libint -# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT -extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" - -# regression test reports failures -ignore_regtest_fails = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-6.1-intel-2020a.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-6.1-intel-2020a.eb deleted file mode 100644 index ddba481d675..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-6.1-intel-2020a.eb +++ /dev/null @@ -1,43 +0,0 @@ -name = 'CP2K' -version = '6.1' - -homepage = 'https://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] -sources = [SOURCELOWER_TAR_BZ2] -patches = [ - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] -checksums = [ - 'af803558e0a6b9e9d9ce8a3ab955ba32bacd179922455424e061c82c9fefa34b', # cp2k-6.1.tar.bz2 - '02475cbe24c8d4ba27037c826adf8a534cad634c3c4e02c21d743f5284516bda', # CP2K-2.4.0-fix_compile_date_lastsvn.patch -] - -dependencies = [ - ('Libint', '1.1.6'), - ('libxc', '4.3.4'), - ('libxsmm', '1.16.1'), - ('FFTW', '3.3.8'), - ('PLUMED', '2.6.0', '-Python-3.8.2'), -] - -builddependencies = [ - ('flex', '2.6.4'), - ('Bison', '3.5.3'), -] - -# values to use here are +1 those used for building Libint -# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT -extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" - -# regression test reports failures -ignore_regtest_fails = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-foss-2020a.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-foss-2020a.eb deleted file mode 100644 index dc411a994fa..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-foss-2020a.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'CP2K' -version = '7.1' - -homepage = 'https://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['ccd711a09a426145440e666310dd01cc5772ab103493c4ae6a3470898cd0addb'] - -dependencies = [ - ('Libint', '2.6.0', '-lmax-6-cp2k'), - ('libxc', '4.3.4'), - ('libxsmm', '1.16.1'), - ('PLUMED', '2.6.0', '-Python-3.8.2'), -] - -builddependencies = [ - ('flex', '2.6.4'), - ('Bison', '3.5.3'), -] - -# regression test reports handful of failures, -# we're assuming those are OK to ignore... -ignore_regtest_fails = True - -# You might want to set OMP_NUM_THREADS, otherwise OpenBLAS will start (by default) -# the number of accessible CPUcores OpenMP threads. Since it is a MPI only version (popt), -# the performance will be copletely bad, as on N CPU cores N^2 threads will run. -# intel toolchain versions do not have this problem. YOU HAVE BEEN WARNED! -# modextravars = {'OMP_NUM_THREADS': '1'} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-intel-2020a.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-intel-2020a.eb deleted file mode 100644 index e165f7b7569..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-7.1-intel-2020a.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'CP2K' -version = '7.1' - -homepage = 'https://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['ccd711a09a426145440e666310dd01cc5772ab103493c4ae6a3470898cd0addb'] - -dependencies = [ - ('Libint', '2.6.0', '-lmax-6-cp2k'), - ('libxc', '4.3.4'), - ('libxsmm', '1.16.1'), - ('FFTW', '3.3.8'), - ('PLUMED', '2.6.0', '-Python-3.8.2'), -] - -builddependencies = [ - ('flex', '2.6.4'), - ('Bison', '3.5.3'), -] - -# regression test reports handful of failures, -# we're assuming those are OK to ignore... -ignore_regtest_fails = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/c/CRISPR-DAV/CRISPR-DAV-2.3.4_remove_hardcoding.patch b/easybuild/easyconfigs/__archive__/c/CRISPR-DAV/CRISPR-DAV-2.3.4_remove_hardcoding.patch deleted file mode 100644 index c8d1e981e7d..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CRISPR-DAV/CRISPR-DAV-2.3.4_remove_hardcoding.patch +++ /dev/null @@ -1,129 +0,0 @@ -# author: Denis Kristak (INUITS) -# changing example command to contain absolute paths + tabs escaping + changing plotting type to cairo -diff -ruN crispr-dav-2.3.4_orig/Examples/example1/run.sh crispr-dav-2.3.4/Examples/example1/run.sh ---- crispr-dav-2.3.4_orig/Examples/example1/run.sh 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Examples/example1/run.sh 2021-06-22 12:57:41.700453098 +0200 -@@ -4,6 +4,7 @@ - - ## If there is problem loading Perl modules., set PERL5LIB accordingly. - #export PERL5LIB=$HOME/perlmod/lib/perl5:$PERL5LIB --../../crispr.pl --conf conf.txt --region amplicon.bed --crispr site.bed \ -- --sitemap sample.site --fastqmap fastq.list --genome genomex -+ -+$EBROOTCRISPRMINDAV/crispr.pl --conf $EBROOTCRISPRMINDAV/Examples/example1/conf.txt --region $EBROOTCRISPRMINDAV/Examples/example1/amplicon.bed --crispr $EBROOTCRISPRMINDAV/Examples/example1/site.bed \ -+ --sitemap $EBROOTCRISPRMINDAV/Examples/example1/sample.site --fastqmap $EBROOTCRISPRMINDAV/Examples/example1/fastq.list --genome genomex --verbose 1 - -diff -ruN crispr-dav-2.3.4_orig/Modules/NGS.pm crispr-dav-2.3.4/Modules/NGS.pm ---- crispr-dav-2.3.4_orig/Modules/NGS.pm 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Modules/NGS.pm 2021-06-21 17:37:39.381993860 +0200 -@@ -296,7 +296,7 @@ - my $cmd = "$self->{bwa} mem"; - $cmd .= " $h{param}" if $h{param}; - if ( $h{id} && $h{sm} ) { -- $cmd .= " -R \'\@RG\tID:$h{id}\tSM:$h{sm}\tPL:$h{pl}\'"; -+ $cmd .= " -R \'\@RG\\tID:$h{id}\\tSM:$h{sm}\\tPL:$h{pl}\'"; - } - $cmd .= " $h{idxbase} $h{read1_inf}"; - $cmd .= " $h{read2_inf}" if -f $h{read2_inf}; -@@ -558,7 +558,7 @@ - # file is already indexed. - my $cmd = "rm -rf $workdir && mkdir -p $workdir" . - " && $self->{java} -Djava.io.tmpdir=$tmpdir -jar $h{abra} --threads 2" . -- " --ref $h{ref_fasta} --targets $h{target_bed} --working $workdir" . -+ " --ref $h{ref_fasta} --targets $h{target_bed} --tmpdir $workdir" . - " --in $h{bam_inf} --out $h{bam_outf}"; - - if ($h{single}) { -diff -ruN crispr-dav-2.3.4_orig/Rscripts/allele.R crispr-dav-2.3.4/Rscripts/allele.R ---- crispr-dav-2.3.4_orig/Rscripts/allele.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/allele.R 2021-06-22 13:13:45.868418215 +0200 -@@ -114,7 +114,7 @@ - } else { - h<-400 - w<- ifelse(n>40, 13*n, h*1.25) -- png(filename=outfile, height=h, width=w) -+ png(filename=outfile, type='cairo', height=h, width=w) - } - - on.exit(dev.off()) -diff -ruN crispr-dav-2.3.4_orig/Rscripts/amplicon.R crispr-dav-2.3.4/Rscripts/amplicon.R ---- crispr-dav-2.3.4_orig/Rscripts/amplicon.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/amplicon.R 2021-06-22 13:13:45.868418215 +0200 -@@ -111,7 +111,7 @@ - if ( high_res ) { - tiff(filename=outfile, width=5, height=4, units='in', res=1200) - } else { -- png(filename=outfile, width=500, height=400) -+ png(filename=outfile, type='cairo', width=500, height=400) - } - on.exit(dev.off()) - print(p) -diff -ruN crispr-dav-2.3.4_orig/Rscripts/hdr.R crispr-dav-2.3.4/Rscripts/hdr.R ---- crispr-dav-2.3.4_orig/Rscripts/hdr.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/hdr.R 2021-06-22 13:13:45.868418215 +0200 -@@ -102,7 +102,7 @@ - h<-400 - barspace=60 - w<- ifelse( n*barspace10, 50*n, h) -- png(filename=imgfile, height=h, width=w) -+ png(filename=imgfile, type='cairo', height=h, width=w) - } - - on.exit(dev.off()) -diff -ruN crispr-dav-2.3.4_orig/Rscripts/read_chr.R crispr-dav-2.3.4/Rscripts/read_chr.R ---- crispr-dav-2.3.4_orig/Rscripts/read_chr.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/read_chr.R 2021-06-22 13:13:45.868418215 +0200 -@@ -72,7 +72,7 @@ - w<-ifelse(n>5, 100*n, 550) - max_w=1000 - w <- ifelse(w>max_w, max_w, w) -- png(filename=outfile, height=h, width=w) -+ png(filename=outfile, type='cairo', height=h, width=w) - } - - print(p) -diff -ruN crispr-dav-2.3.4_orig/Rscripts/read_stats.R crispr-dav-2.3.4/Rscripts/read_stats.R ---- crispr-dav-2.3.4_orig/Rscripts/read_stats.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/read_stats.R 2021-06-22 13:13:45.868418215 +0200 -@@ -69,7 +69,7 @@ - } else { - h<-400 - w<- ifelse(n>10, 50*n, h) -- png(filename=outfile, height=h, width=w) -+ png(filename=outfile, type='cairo', height=h, width=w) - } - - p <- ggplot(dat.m, aes(x=Sample, y=value, fill=variable)) + -diff -ruN crispr-dav-2.3.4_orig/Rscripts/snp.R crispr-dav-2.3.4/Rscripts/snp.R ---- crispr-dav-2.3.4_orig/Rscripts/snp.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/snp.R 2021-06-22 13:13:45.868418215 +0200 -@@ -76,7 +76,7 @@ - if ( high_res ) { - tiff(filename=outfile, width=5, height=4, units='in', res=1200) - } else { -- png(filename=outfile, width=500, height=400) -+ png(filename=outfile, type='cairo', width=500, height=400) - } - print(p) - invisible(dev.off()) -@@ -182,7 +182,7 @@ - wt <- 600 - } - ht <- 400 -- png(filename=outfile, width=wt, height=ht) -+ png(filename=outfile, type='cairo', width=wt, height=ht) - } - - print(p) diff --git a/easybuild/easyconfigs/__archive__/c/CRPropa/CRPropa-3.1.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/CRPropa/CRPropa-3.1.6-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index ecdf61f4424..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CRPropa/CRPropa-3.1.6-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'CMakePythonPackage' - -name = 'CRPropa' -version = '3.1.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://crpropa.desy.de' -description = """CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron - on their voyage through an extra galactic environment.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/CRPropa/CRPropa3/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['abc659a240be5c4e770abf0765b470f22dfe1ca68e3db74efab0aa51c4845c1d'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('SWIG', '4.0.1'), - ('pkg-config', '0.29.2'), - ('Doxygen', '1.8.17'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('HDF5', '1.10.6'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -runtest = False - -sanity_check_commands = [ - """python -c "import crpropa; 'initTurbulence' in dir(crpropa)" """ -] - -sanity_check_paths = { - 'files': ["lib/libcrpropa.so"], - 'dirs': [ - "lib/python%(pyshortver)s/site-packages", - "share" - ], -} - -moduleclass = 'astro' diff --git a/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb deleted file mode 100644 index 23109630c34..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb +++ /dev/null @@ -1,17 +0,0 @@ -easyblock = 'Bundle' -name = 'CUDA' -version = '11.0.2' - -homepage = 'https://developer.nvidia.com/cuda-toolkit' -description = """CUDA (formerly Compute Unified Device Architecture) is a parallel - computing platform and programming model created by NVIDIA and implemented by the - graphics processing units (GPUs) that they produce. CUDA gives developers access - to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -dependencies = [('CUDAcore', '11.0.2', '', SYSTEM)] - -altroot = 'CUDAcore' - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb deleted file mode 100644 index a2eecc5b703..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb +++ /dev/null @@ -1,17 +0,0 @@ -easyblock = 'Bundle' -name = 'CUDA' -version = '11.0.2' - -homepage = 'https://developer.nvidia.com/cuda-toolkit' -description = """CUDA (formerly Compute Unified Device Architecture) is a parallel - computing platform and programming model created by NVIDIA and implemented by the - graphics processing units (GPUs) that they produce. CUDA gives developers access - to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -dependencies = [('CUDAcore', '11.0.2', '', SYSTEM)] - -altroot = 'CUDAcore' - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/c/CaDiCaL/CaDiCaL-1.3.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CaDiCaL/CaDiCaL-1.3.0-GCC-9.3.0.eb deleted file mode 100644 index 74623545800..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CaDiCaL/CaDiCaL-1.3.0-GCC-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'MakeCp' - -name = 'CaDiCaL' -version = '1.3.0' - -homepage = 'https://github.com/arminbiere/cadical' -description = """ -CaDiCaL is a simplified satisfiability solver. The original goal of the -development of CaDiCaL was to obtain a CDCL solver, which is easy to understand -and change, while at the same time not being much slower than other -state-of-the-art CDCL solvers.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'arminbiere' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['rel-%(version)s.tar.gz'] -checksums = ['8577c0cbf34eeff6d455e34eb489aae52a0b97b3ef1d02d0c7d2e8a82b572c1b'] - -# Custom execution of configure at build time because CaDiCal has a custom script incompatible with configure step -prebuildopts = './configure CXX="$CXX" CXXFLAGS="$CXXFLAGS" && ' - -local_bins = ['cadical', 'mobical'] -local_libs = ['libcadical.a'] - -files_to_copy = [ - (['build/%s' % x for x in local_bins], 'bin'), - (['build/%s' % x for x in local_libs], 'lib'), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_bins] + ['lib/%s' % x for x in local_libs], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/c/Calib/Calib-0.3.4-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/Calib/Calib-0.3.4-GCC-9.3.0.eb deleted file mode 100644 index 28b8fd81ade..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Calib/Calib-0.3.4-GCC-9.3.0.eb +++ /dev/null @@ -1,60 +0,0 @@ -easyblock = 'MakeCp' - -name = 'Calib' -version = '0.3.4' - -homepage = 'https://github.com/vpc-ccg/calib' -description = """Calib clusters paired-end reads using their barcodes and sequences. Calib is suitable for amplicon -sequencing where a molecule is tagged, then PCR amplified with high depth, also known as Unique Molecule Identifier -(UMI) sequencing.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'cstd': 'c++11'} - -sources = [ - { - 'source_urls': ['https://github.com/vpc-ccg/calib/archive/'], - 'download_filename': 'v%(version)s.tar.gz', - 'filename': SOURCE_TAR_GZ, - }, - { - 'source_urls': ['https://github.com/rvaser/spoa/archive/'], - 'download_filename': '1.1.3.zip', - 'filename': 'SPOA-1.1.3.zip', - }, -] -checksums = [ - 'edfa254d90a7dc7222ce5e7565808250a9535e5e94ec73252110ec7c8aebe920', # Calib-0.3.4.tar.gz - '0a96c175e39b3e8badc7050f00f767f808efbf4b1bfb5c17a02b66b4a9803d94', # SPOA-1.1.3.zip -] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -# avoid using hardcoded compiler flags -buildopts = 'CXXFLAGS="$CXXFLAGS -pthread -Iclustering/ -lz" && ' - -# building calib_cons requires SPOA, so build that first -buildopts += "mv %(builddir)s/spoa-1.1.3 %(builddir)s/calib-%(version)s/consensus/spoa_v1.1.3 && " -buildopts += "mkdir consensus/spoa_v1.1.3/build && cd consensus/spoa_v1.1.3/build && " -buildopts += "cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make && " -buildopts += "cd - && make -C consensus" - -files_to_copy = [(['calib', 'consensus/calib_cons'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/calib', 'bin/calib_cons'], - 'dirs': [], -} - -sanity_check_commands = [ - "calib --help", - "calib_cons --help", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CapnProto/CapnProto-0.8.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CapnProto/CapnProto-0.8.0-GCCcore-9.3.0.eb deleted file mode 100644 index 5d695d37d16..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CapnProto/CapnProto-0.8.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# Updated to 0.8.0 -# R.QIAO - -easyblock = 'ConfigureMake' - -name = 'CapnProto' -version = '0.8.0' - -homepage = 'https://capnproto.org' -description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" -# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." -# (only on Intel Skylake?) -toolchainopts = {'cstd': 'c++17', 'lowopt': True} - -source_urls = ['https://capnproto.org/'] -sources = ['capnproto-c++-%(version)s.tar.gz'] -checksums = ['d1f40e47574c65700f0ec98bf66729378efabe3c72bc0cda795037498541c10d'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/capnp', 'bin/capnpc', 'bin/capnpc-c++', 'bin/capnpc-capnp'], - 'dirs': ['include/capnp', 'include/kj', 'lib'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/Cartopy/Cartopy-0.18.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/Cartopy/Cartopy-0.18.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index e4e6c46369a..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Cartopy/Cartopy-0.18.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Cartopy' -version = '0.18.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scitools.org.uk/cartopy/docs/latest/' -description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('Fiona', '1.8.16', versionsuffix), - ('GDAL', '3.0.4', versionsuffix), - ('GEOS', '3.8.1', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('pyproj', '2.6.1.post1', versionsuffix), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Shapely', '1.7.1', versionsuffix), - ('lxml', '4.5.2'), - ('Pillow', '7.0.0', versionsuffix), - ('PROJ', '7.0.0'), - ('PyYAML', '5.3'), -] - -exts_list = [ - ('OWSLib', '0.20.0', { - 'checksums': ['334988857b260c8cdf1f6698d07eab61839c51acb52ee10eed1275439200a40e'], - }), - ('pyepsg', '0.4.0', { - 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], - }), - ('pykdtree', '1.3.1', { - 'checksums': ['0d49d3bbfa0366dbe29176754ec86df75114a25525b530dcbbb75d3ac4c263e9'], - }), - ('pyshp', '2.1.0', { - 'modulename': 'shapefile', - 'checksums': ['e65c7f24d372b97d0920b864bbeb78322bb37b83f2606e2a2212631d5d51e5c0'], - }), - (name, version, { - 'checksums': ['7ffa317e8f8011e0d965a3ef1179e57a049f77019867ed677d49dcc5c0744434'], - }), -] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/c/Centrifuge/Centrifuge-1.0.4-beta-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/c/Centrifuge/Centrifuge-1.0.4-beta-gompi-2020a.eb deleted file mode 100644 index fcea5457311..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Centrifuge/Centrifuge-1.0.4-beta-gompi-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Centrifuge' -version = '1.0.4-beta' - -homepage = 'https://ccb.jhu.edu/software/centrifuge' -description = 'Classifier for metagenomic sequences' - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'cstd': 'c++11'} - -source_urls = ['https://github.com/DaehwanKimLab/centrifuge/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['Centrifuge-%(version)s_fix-SRA.patch'] -checksums = [ - '1f4d3b9139d1e25cf5e634aae357763d812da5e0fb833371b78f545a29b9225d', # v1.0.4-beta.tar.gz - '3aa65cbd55a77b38d8d79a88ce831ef592425c293c5b651752011f4be150b8d6', # Centrifuge-1.0.4-beta_fix-SRA.patch -] - -dependencies = [ - ('NGS', '2.10.5'), - ('ncbi-vdb', '2.10.7'), -] - -skipsteps = ['configure'] - -buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CXXFLAGS" ' -buildopts += 'USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB' - -installopts = "prefix=%(installdir)s" - -fix_perl_shebang_for = ['bin/centrifuge*.pl'] - -sanity_check_paths = { - 'files': ['bin/centrifuge%s' % x for x in ['', '-build', '-build-bin', '-class', '-download', - '-inspect', '-inspect-bin']], - 'dirs': [], -} - -sanity_check_commands = ["centrifuge --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/Centrifuge/Centrifuge-1.0.4-beta_fix-SRA.patch b/easybuild/easyconfigs/__archive__/c/Centrifuge/Centrifuge-1.0.4-beta_fix-SRA.patch deleted file mode 100644 index 3b9f184da14..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Centrifuge/Centrifuge-1.0.4-beta_fix-SRA.patch +++ /dev/null @@ -1,14 +0,0 @@ -fix compilation error "no match for operator+=" when building with USE_SRA=1 because of type mismatch in buggy code -see also https://github.com/DaehwanKimLab/centrifuge/issues/191 -author: Kenneth Hoste (HPC-UGent), with help from Lars Viklund (Umea University) ---- centrifuge-1.0.4-beta/centrifuge.cpp.orig 2020-06-08 20:33:19.578955606 +0200 -+++ centrifuge-1.0.4-beta/centrifuge.cpp 2020-06-08 20:33:26.219065266 +0200 -@@ -3006,7 +3006,7 @@ - - int fileCnt = mates1.size() + queries.size(); // the order should be consistent with the wrapper - #ifdef USE_SRA -- fileCnt += sra_accs ; -+ fileCnt += sra_accs.size() ; - #endif - - for ( int fileIdx = 0 ; fileIdx < fileCnt ; ++fileIdx ) diff --git a/easybuild/easyconfigs/__archive__/c/Check/Check-0.15.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/Check/Check-0.15.2-GCCcore-9.3.0.eb deleted file mode 100644 index 9b2d4b86028..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Check/Check-0.15.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Check' -version = '0.15.2' - -homepage = 'https://libcheck.github.io/check/' -description = """ -Check is a unit testing framework for C. It features a simple interface for -defining unit tests, putting little in the way of the developer. Tests are -run in a separate address space, so both assertion failures and code errors -that cause segmentation faults or other signals can be caught. Test results -are reportable in the following: Subunit, TAP, XML, and a generic logging -format.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'libcheck' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['998d355294bb94072f40584272cf4424571c396c631620ce463f6ea97aa67d2e'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -preconfigopts = "autoreconf -f -i && " -configopts = "--disable-build-docs" - -sanity_check_paths = { - 'files': ['bin/checkmk', 'lib/libcheck.a', 'lib/libcheck.%s' % SHLIB_EXT], - 'dirs': ['include', 'share'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 04a505973e4..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,60 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonPackage' - -name = 'CheckM' -version = '1.1.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Ecogenomics/CheckM' -description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, - single cells, or metagenomes.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = [ - 'https://pypi.python.org/packages/source/c/checkm-genome', - 'https://data.ace.uq.edu.au/public/CheckM_databases/', -] -sources = [ - 'checkm-genome-%(version)s.tar.gz', - { - 'filename': 'checkm_data_2015_01_16.tar.gz', - 'extract_cmd': "mkdir -p %(builddir)s/data && cd %(builddir)s/data && tar xfvz %s", - }, -] -checksums = [ - '7fda369783d3b7d6a7324ee33cc93ac3560fba509bf2139e920fa661e2b45644', # checkm-genome-1.1.3.tar.gz - '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c', # checkm_data_2015_01_16.tar.gz -] - -# Dependencies: -# https://github.com/Ecogenomics/CheckM/blob/master/setup.py -dependencies = [ - ('Python', '3.8.2'), - ('pplacer', '1.1.alpha19', '', SYSTEM), - ('prodigal', '2.6.3'), - ('HMMER', '3.3.1'), - ('SciPy-bundle', '2020.03', versionsuffix), # numpy - ('matplotlib', '3.2.1', versionsuffix), - ('Pysam', '0.16.0.1'), - ('DendroPy', '4.4.0'), -] - -# also install CheckM databases, see https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm -postinstallcmds = [ - "cp -a %(builddir)s/data %(installdir)s", - "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " - "%(installdir)s/bin/checkm data setRoot %(installdir)s/data", -] - -sanity_check_paths = { - 'files': ['bin/checkm'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["checkm test %(builddir)s/checkm_test_results"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/Circos/Circos-0.69-9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/Circos/Circos-0.69-9-GCCcore-9.3.0.eb deleted file mode 100644 index 65c9b96a1b9..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Circos/Circos-0.69-9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Author: Jonas Demeulemeester -# The Francis Crick Insitute, London, UK -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'Tarball' - -name = 'Circos' -version = '0.69-9' - -homepage = 'http://www.circos.ca/' -description = """Circos is a software package for visualizing data and information. - It visualizes data in a circular layout - this makes Circos ideal for exploring - relationships between objects or positions.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://circos.ca/distribution/'] -sources = [SOURCELOWER_TGZ] -checksums = ['34d8d7ebebf3f553d62820f8f4a0a57814b610341f836b4740c46c3057f789d2'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Perl', '5.30.2'), - ('GD', '2.71'), -] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': ['lib/%(name)s'], -} - -modextrapaths = {'PERL5LIB': 'lib'} - -sanity_check_commands = [('perl', '-e "use Circos"')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/Clang-Python-bindings/Clang-Python-bindings-10.0.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/Clang-Python-bindings/Clang-Python-bindings-10.0.1-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 0827034d6fd..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Clang-Python-bindings/Clang-Python-bindings-10.0.1-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'Tarball' - -name = 'Clang-Python-bindings' -version = '10.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://clang.llvm.org' -description = """Python bindings for libclang""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/"] -sources = ['clang-%(version)s.src.tar.xz'] -checksums = ['f99afc382b88e622c689b6d96cadfa6241ef55dca90e87fc170352e12ddb2b24'] - -dependencies = [ - ('Clang', version), - ('Python', '3.8.2') -] - -start_dir = 'bindings/python' - -sanity_check_paths = { - 'files': ['clang/cindex.py'], - 'dirs': ['clang'] -} - -sanity_check_commands = ["python -c 'import clang'"] - -modextrapaths = {'PYTHONPATH': ''} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb deleted file mode 100644 index 128ee20abef..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,76 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans -# Authors:: Dmitri Gribenko -# Authors:: Ward Poelmans -# License:: GPLv2 or later, MIT, three-clause BSD. -# $Id$ -## - -name = 'Clang' -version = '10.0.0' - -homepage = 'https://clang.llvm.org/' -description = """C, C++, Objective-C compiler, based on LLVM. Does not - include C++ standard library -- use libstdc++ from GCC.""" - -# Clang also depends on libstdc++ during runtime, but this dependency is -# already specified as the toolchain. -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -# Do not set optarch to True: it will cause the build to fail -toolchainopts = {'optarch': False} - -source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] -sources = [ - 'llvm-%(version)s.src.tar.xz', - 'clang-%(version)s.src.tar.xz', - 'compiler-rt-%(version)s.src.tar.xz', - 'polly-%(version)s.src.tar.xz', - 'openmp-%(version)s.src.tar.xz', - # Also include the LLVM linker - 'lld-%(version)s.src.tar.xz', - 'libcxx-%(version)s.src.tar.xz', - 'libcxxabi-%(version)s.src.tar.xz', - 'clang-tools-extra-%(version)s.src.tar.xz', -] -patches = ['libcxx-%(version)s-ppc64le.patch'] -checksums = [ - 'df83a44b3a9a71029049ec101fb0077ecbbdf5fe41e395215025779099a98fdf', # llvm-10.0.0.src.tar.xz - '885b062b00e903df72631c5f98b9579ed1ed2790f74e5646b4234fa084eacb21', # clang-10.0.0.src.tar.xz - '6a7da64d3a0a7320577b68b9ca4933bdcab676e898b759850e827333c3282c75', # compiler-rt-10.0.0.src.tar.xz - '35fba6ed628896fe529be4c10407f1b1c8a7264d40c76bced212180e701b4d97', # polly-10.0.0.src.tar.xz - '3b9ff29a45d0509a1e9667a0feb43538ef402ea8cfc7df3758a01f20df08adfa', # openmp-10.0.0.src.tar.xz - 'b9a0d7c576eeef05bc06d6e954938a01c5396cee1d1e985891e0b1cf16e3d708', # lld-10.0.0.src.tar.xz - '270f8a3f176f1981b0f6ab8aa556720988872ec2b48ed3b605d0ced8d09156c7', # libcxx-10.0.0.src.tar.xz - 'e71bac75a88c9dde455ad3f2a2b449bf745eafd41d2d8432253b2964e0ca14e1', # libcxxabi-10.0.0.src.tar.xz - 'acdf8cf6574b40e6b1dabc93e76debb84a9feb6f22970126b04d4ba18b92911c', # clang-tools-extra-10.0.0.tar.xz - 'a424a9eb7f377b4f01d8c9b27fdd78e6a51a53819b263d2ca6d40a0e2368a330', # libcxx-10.0.0-ppc64le.patch -] - -dependencies = [ - # since Clang is a compiler, binutils is a runtime dependency too - ('binutils', '2.34'), - ('hwloc', '2.2.0'), - ('libxml2', '2.9.10'), - ('ncurses', '6.2'), - ('GMP', '6.2.0'), - ('Z3', '4.8.9'), -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Python', '2.7.18'), - ('Perl', '5.30.2'), -] - -assertions = True -usepolly = True -build_lld = True -libcxx = True -enable_rtti = True -build_extra_clang_tools = True - -skip_all_tests = True - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb deleted file mode 100644 index 39259fafa23..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,76 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans -# Authors:: Dmitri Gribenko -# Authors:: Ward Poelmans -# License:: GPLv2 or later, MIT, three-clause BSD. -# $Id$ -## - -name = 'Clang' -version = '10.0.1' - -homepage = 'https://clang.llvm.org/' -description = """C, C++, Objective-C compiler, based on LLVM. Does not - include C++ standard library -- use libstdc++ from GCC.""" - -# Clang also depends on libstdc++ during runtime, but this dependency is -# already specified as the toolchain. -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -# Do not set optarch to True: it will cause the build to fail -toolchainopts = {'optarch': False} - -source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] -sources = [ - 'llvm-%(version)s.src.tar.xz', - 'clang-%(version)s.src.tar.xz', - 'compiler-rt-%(version)s.src.tar.xz', - 'polly-%(version)s.src.tar.xz', - 'openmp-%(version)s.src.tar.xz', - # Also include the LLVM linker - 'lld-%(version)s.src.tar.xz', - 'libcxx-%(version)s.src.tar.xz', - 'libcxxabi-%(version)s.src.tar.xz', - 'clang-tools-extra-%(version)s.src.tar.xz', -] -patches = ['libcxx-10.0.0-ppc64le.patch'] -checksums = [ - 'c5d8e30b57cbded7128d78e5e8dad811bff97a8d471896812f57fa99ee82cdf3', # llvm-10.0.1.src.tar.xz - 'f99afc382b88e622c689b6d96cadfa6241ef55dca90e87fc170352e12ddb2b24', # clang-10.0.1.src.tar.xz - 'd90dc8e121ca0271f0fd3d639d135bfaa4b6ed41e67bd6eb77808f72629658fa', # compiler-rt-10.0.1.src.tar.xz - 'd2fb0bb86b21db1f52402ba231da7c119c35c21dfb843c9496fe901f2d6aa25a', # polly-10.0.1.src.tar.xz - 'd19f728c8e04fb1e94566c8d76aef50ec926cd2f95ef3bf1e0a5de4909b28b44', # openmp-10.0.1.src.tar.xz - '591449e0aa623a6318d5ce2371860401653c48bb540982ccdd933992cb88df7a', # lld-10.0.1.src.tar.xz - 'def674535f22f83131353b3c382ccebfef4ba6a35c488bdb76f10b68b25be86c', # libcxx-10.0.1.src.tar.xz - 'a97ef810b2e9fb70e8f7e317b74e646ed4944f488b02ac5ddd9c99e385381a7b', # libcxxabi-10.0.1.src.tar.xz - 'd093782bcfcd0c3f496b67a5c2c997ab4b85816b62a7dd5b27026634ccf5c11a', # clang-tools-extra-10.0.1.src.xz - 'a424a9eb7f377b4f01d8c9b27fdd78e6a51a53819b263d2ca6d40a0e2368a330', # libcxx-10.0.0-ppc64le.patch -] - -dependencies = [ - # since Clang is a compiler, binutils is a runtime dependency too - ('binutils', '2.34'), - ('hwloc', '2.2.0'), - ('libxml2', '2.9.10'), - ('ncurses', '6.2'), - ('GMP', '6.2.0'), - ('Z3', '4.8.9'), -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Python', '2.7.18'), - ('Perl', '5.30.2'), -] - -assertions = True -usepolly = True -build_lld = True -libcxx = True -enable_rtti = True -build_extra_clang_tools = True - -skip_all_tests = True - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/c/Clang/Clang-11.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/Clang/Clang-11.0.0-GCCcore-9.3.0.eb deleted file mode 100644 index 5886c77ae32..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Clang/Clang-11.0.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,72 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans -# Authors:: Dmitri Gribenko -# Authors:: Ward Poelmans -# License:: GPLv2 or later, MIT, three-clause BSD. -# $Id$ -## - -name = 'Clang' -version = '11.0.0' - -homepage = 'https://clang.llvm.org/' -description = """C, C++, Objective-C compiler, based on LLVM. Does not - include C++ standard library -- use libstdc++ from GCC.""" - -# Clang also depends on libstdc++ during runtime, but this dependency is -# already specified as the toolchain. -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] -sources = [ - 'llvm-%(version)s.src.tar.xz', - 'clang-%(version)s.src.tar.xz', - 'compiler-rt-%(version)s.src.tar.xz', - 'polly-%(version)s.src.tar.xz', - 'openmp-%(version)s.src.tar.xz', - # Also include the LLVM linker - 'lld-%(version)s.src.tar.xz', - 'libcxx-%(version)s.src.tar.xz', - 'libcxxabi-%(version)s.src.tar.xz', - 'clang-tools-extra-%(version)s.src.tar.xz', -] -checksums = [ - '913f68c898dfb4a03b397c5e11c6a2f39d0f22ed7665c9cefa87a34423a72469', # llvm-11.0.0.src.tar.xz - '0f96acace1e8326b39f220ba19e055ba99b0ab21c2475042dbc6a482649c5209', # clang-11.0.0.src.tar.xz - '374aff82ff573a449f9aabbd330a5d0a441181c535a3599996127378112db234', # compiler-rt-11.0.0.src.tar.xz - 'dcfadb8d11f2ea0743a3f19bab3b43ee1cb855e136bc81c76e2353cd76148440', # polly-11.0.0.src.tar.xz - '2d704df8ca67b77d6d94ebf79621b0f773d5648963dd19e0f78efef4404b684c', # openmp-11.0.0.src.tar.xz - 'efe7be4a7b7cdc6f3bcf222827c6f837439e6e656d12d6c885d5c8a80ff4fd1c', # lld-11.0.0.src.tar.xz - '6c1ee6690122f2711a77bc19241834a9219dda5036e1597bfa397f341a9b8b7a', # libcxx-11.0.0.src.tar.xz - '58697d4427b7a854ec7529337477eb4fba16407222390ad81a40d125673e4c15', # libcxxabi-11.0.0.src.tar.xz - 'fed318f75d560d0e0ae728e2fb8abce71e9d0c60dd120c9baac118522ce76c09', # clang-tools-extra-11.0.0.src.tar.xz -] - -dependencies = [ - # since Clang is a compiler, binutils is a runtime dependency too - ('binutils', '2.34'), - ('hwloc', '2.2.0'), - ('libxml2', '2.9.10'), - ('ncurses', '6.2'), - ('GMP', '6.2.0'), - ('Z3', '4.8.9'), -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Python', '3.8.2'), - ('Perl', '5.30.2'), -] - -assertions = True -usepolly = True -build_lld = True -libcxx = True -enable_rtti = True -build_extra_clang_tools = True - -skip_all_tests = True - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb deleted file mode 100644 index 097cc871651..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,71 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans -# Authors:: Dmitri Gribenko -# Authors:: Ward Poelmans -# License:: GPLv2 or later, MIT, three-clause BSD. -# $Id$ -## - -name = 'Clang' -version = '9.0.1' - -homepage = 'https://clang.llvm.org/' -description = """C, C++, Objective-C compiler, based on LLVM. Does not - include C++ standard library -- use libstdc++ from GCC.""" - -# Clang also depends on libstdc++ during runtime, but this dependency is -# already specified as the toolchain. -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -# Do not set optarch to True: it will cause the build to fail -toolchainopts = {'optarch': False} - -source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] -sources = [ - 'llvm-%(version)s.src.tar.xz', - 'clang-%(version)s.src.tar.xz', - 'compiler-rt-%(version)s.src.tar.xz', - 'polly-%(version)s.src.tar.xz', - 'openmp-%(version)s.src.tar.xz', - # Also include the LLVM linker - 'lld-%(version)s.src.tar.xz', - 'libcxx-%(version)s.src.tar.xz', - 'libcxxabi-%(version)s.src.tar.xz', -] -patches = [('libcxx-%(version)s-ppc64le.patch', '../')] -checksums = [ - '00a1ee1f389f81e9979f3a640a01c431b3021de0d42278f6508391a2f0b81c9a', # llvm-9.0.1.src.tar.xz - '5778512b2e065c204010f88777d44b95250671103e434f9dc7363ab2e3804253', # clang-9.0.1.src.tar.xz - 'c2bfab95c9986318318363d7f371a85a95e333bc0b34fbfa52edbd3f5e3a9077', # compiler-rt-9.0.1.src.tar.xz - '9a4ac69df923230d13eb6cd0d03f605499f6a854b1dc96a9b72c4eb075040fcf', # polly-9.0.1.src.tar.xz - '5c94060f846f965698574d9ce22975c0e9f04c9b14088c3af5f03870af75cace', # openmp-9.0.1.src.tar.xz - '86262bad3e2fd784ba8c5e2158d7aa36f12b85f2515e95bc81d65d75bb9b0c82', # lld-9.0.1.src.tar.xz - '0981ff11b862f4f179a13576ab0a2f5530f46bd3b6b4a90f568ccc6a62914b34', # libcxx-9.0.1.src.tar.xz - 'e8f978aa4cfae2d7a0b4d89275637078557cca74b35c31b7283d4786948a8aac', # libcxxabi-9.0.1.src.tar.xz - '01d2a16fe69854c0126a8adb4762a455cc6bf1f70003cb8b685e446a66a9aa51', # libcxx-9.0.1-ppc64le.patch -] - -dependencies = [ - # since Clang is a compiler, binutils is a runtime dependency too - ('binutils', '2.34'), - ('GMP', '6.2.0'), - ('ncurses', '6.2'), -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Python', '2.7.18'), - ('Perl', '5.30.2'), - ('libxml2', '2.9.10'), -] - -assertions = True -usepolly = True -build_lld = True -libcxx = True -enable_rtti = True - -skip_all_tests = True - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/c/Clang/libcxx-10.0.0-ppc64le.patch b/easybuild/easyconfigs/__archive__/c/Clang/libcxx-10.0.0-ppc64le.patch deleted file mode 100644 index a0df64de58e..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Clang/libcxx-10.0.0-ppc64le.patch +++ /dev/null @@ -1,16 +0,0 @@ -Reverse the if def order. Patch from https://bugs.llvm.org/show_bug.cgi?id=39696#c38 -Prepared for EasyBuild by Simon Branford, University of Birmingham ---- a/projects/libcxx/include/thread.orig 2020-03-23 16:01:02.000000000 +0100 -+++ b/projects/libcxx/include/thread 2020-04-08 19:19:31.625082029 +0200 -@@ -369,9 +369,9 @@ - { - #if defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__) - // GCC's long double const folding is incomplete for IBM128 long doubles. -- _LIBCPP_CONSTEXPR duration _Max = nanoseconds::max(); --#else - _LIBCPP_CONSTEXPR duration _Max = duration(ULLONG_MAX/1000000000ULL) ; -+#else -+ _LIBCPP_CONSTEXPR duration _Max = nanoseconds::max(); - #endif - nanoseconds __ns; - if (__d < _Max) diff --git a/easybuild/easyconfigs/__archive__/c/Clang/libcxx-9.0.1-ppc64le.patch b/easybuild/easyconfigs/__archive__/c/Clang/libcxx-9.0.1-ppc64le.patch deleted file mode 100644 index cbf55ee91be..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Clang/libcxx-9.0.1-ppc64le.patch +++ /dev/null @@ -1,18 +0,0 @@ -Reverse the if def order. Patch from https://bugs.llvm.org/show_bug.cgi?id=39696#c38 -Prepared for EasyBuild by Simon Branford, University of Birmingham -diff --git a/libcxx/include/thread b/libcxx/include/thread -index 02da703..d1677a1 100644 ---- a/libcxx-9.0.1.src/include/thread -+++ b/libcxx-9.0.1.src/include/thread -@@ -368,9 +368,9 @@ sleep_for(const chrono::duration<_Rep, _Period>& __d) - { - #if defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__) - // GCC's long double const folding is incomplete for IBM128 long doubles. -- _LIBCPP_CONSTEXPR duration _Max = nanoseconds::max(); --#else - _LIBCPP_CONSTEXPR duration _Max = duration(ULLONG_MAX/1000000000ULL) ; -+#else -+ _LIBCPP_CONSTEXPR duration _Max = nanoseconds::max(); - #endif - nanoseconds __ns; - if (__d < _Max) diff --git a/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb b/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb deleted file mode 100644 index e8b06867fd9..00000000000 --- a/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb +++ /dev/null @@ -1,33 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Cedric Laczny , Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = 'ConfigureMake' - -name = 'ClustalW2' -version = '2.1' - -homepage = 'https://www.ebi.ac.uk/Tools/msa/clustalw2/' -description = """ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['ftp://ftp.ebi.ac.uk/pub/software/%(namelower)s/%(version)s'] -sources = ['%s-%%(version)s.tar.gz' % name[:-1].lower()] -checksums = ['e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486'] - -sanity_check_paths = { - 'files': ['bin/clustalw2'], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/CoordgenLibs/CoordgenLibs-3.0.1-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/c/CoordgenLibs/CoordgenLibs-3.0.1-iimpi-2020a.eb deleted file mode 100644 index e08d7e569be..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CoordgenLibs/CoordgenLibs-3.0.1-iimpi-2020a.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'CoordgenLibs' -version = '3.0.1' - -homepage = 'https://github.com/schrodinger/coordgenlibs' -description = "Schrodinger-developed 2D Coordinate Generation" - -toolchain = {'name': 'iimpi', 'version': '2020a'} - -source_urls = ['https://github.com/schrodinger/coordgenlibs/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['737fd081bcb8a6913aa00b375be96458fe2821a58209c98e7a7e86a64d73a900'] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('Boost', '1.72.0'), - ('maeparser', '1.3.0'), -] - -configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake" - -# work around compiler warning treated as error by stripping out use of -Werror -prebuildopts = "sed -i 's/-Werror//g' CMakeFiles/coordgen.dir/flags.make && " - -sanity_check_paths = { - 'files': ['lib/libcoordgen.%s' % SHLIB_EXT], - 'dirs': ['include/coordgen', 'lib/cmake'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/c/Coreutils/Coreutils-8.32-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/Coreutils/Coreutils-8.32-GCCcore-9.3.0.eb deleted file mode 100644 index 235a1b9fcca..00000000000 --- a/easybuild/easyconfigs/__archive__/c/Coreutils/Coreutils-8.32-GCCcore-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = "Coreutils" -version = "8.32" - -homepage = 'https://www.gnu.org/software/coreutils/' -description = """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the - GNU operating system. These are the core utilities which are expected to exist on every operating system. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['4458d8de7849df44ccab15e16b1548b285224dbba5f08fac070c1c0e0bcc4cfa'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/c/CppUnit/CppUnit-1.15.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CppUnit/CppUnit-1.15.1-GCCcore-9.3.0.eb deleted file mode 100644 index efea5e36b95..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CppUnit/CppUnit-1.15.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CppUnit' -version = '1.15.1' - -homepage = 'https://freedesktop.org/wiki/Software/cppunit/' - -description = """ - CppUnit is the C++ port of the famous JUnit framework for unit testing. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://dev-www.libreoffice.org/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['89c5c6665337f56fd2db36bc3805a5619709d51fb136e51937072f63fcc717a7'] - -builddependencies = [ - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT, - 'lib/pkgconfig/cppunit.pc'], - 'dirs': ['bin', 'include/cppunit', 'share'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/c/CubeGUI/CubeGUI-4.4.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CubeGUI/CubeGUI-4.4.4-GCCcore-9.3.0.eb deleted file mode 100644 index 13dc09734be..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CubeGUI/CubeGUI-4.4.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,53 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany -# Authors:: Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_Score_minus_P' - -name = 'CubeGUI' -version = '4.4.4' - -homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' -description = """ - Cube, which is used as performance report explorer for Scalasca and Score-P, - is a generic tool for displaying a multi-dimensional performance space - consisting of the dimensions (i) performance metric, (ii) call path, and - (iii) system resource. Each dimension can be represented as a tree, where - non-leaf nodes of the tree can be collapsed or expanded to achieve the - desired level of granularity. - - This module provides the Cube graphical report explorer. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -sources = [SOURCELOWER_TAR_GZ] -checksums = [ - '9b7b96d5a64b558a9017cc3599bba93a42095534e018e3de9b1f80ab6d04cc34', # cubegui-4.4.4.tar.gz -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.34'), - ('CubeLib', '4.4.4'), -] - -dependencies = [ - ('Qt5', '5.14.1'), -] - -sanity_check_paths = { - 'files': ['bin/cube', 'bin/cubegui-config', - 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], - 'dirs': ['include/cubegui', 'lib/cube-plugins'], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/c/CubeLib/CubeLib-4.4.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CubeLib/CubeLib-4.4.4-GCCcore-9.3.0.eb deleted file mode 100644 index 500dadf3263..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CubeLib/CubeLib-4.4.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany -# Authors:: Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_Score_minus_P' - -name = 'CubeLib' -version = '4.4.4' - -homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' -description = """ - Cube, which is used as performance report explorer for Scalasca and Score-P, - is a generic tool for displaying a multi-dimensional performance space - consisting of the dimensions (i) performance metric, (ii) call path, and - (iii) system resource. Each dimension can be represented as a tree, where - non-leaf nodes of the tree can be collapsed or expanded to achieve the - desired level of granularity. - - This module provides the Cube general purpose C++ library component and - command-line tools. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -sources = [SOURCELOWER_TAR_GZ] -checksums = [ - 'adb8216ee3b7701383884417374e7ff946edb30e56640307c65465187dca7512', # cubelib-4.4.4.tar.gz -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/cubelib-config', - 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], - 'dirs': ['include/cubelib'], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/c/CubeWriter/CubeWriter-4.4.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/CubeWriter/CubeWriter-4.4.3-GCCcore-9.3.0.eb deleted file mode 100644 index de7ebb7b234..00000000000 --- a/easybuild/easyconfigs/__archive__/c/CubeWriter/CubeWriter-4.4.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,55 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany -# Authors:: Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_Score_minus_P' - -name = 'CubeWriter' -version = '4.4.3' - -homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' -description = """ - Cube, which is used as performance report explorer for Scalasca and Score-P, - is a generic tool for displaying a multi-dimensional performance space - consisting of the dimensions (i) performance metric, (ii) call path, and - (iii) system resource. Each dimension can be represented as a tree, where - non-leaf nodes of the tree can be collapsed or expanded to achieve the - desired level of granularity. - - This module provides the Cube high-performance C writer library component. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -sources = ['cubew-%(version)s.tar.gz'] -checksums = [ - '93fff6cc1e8b0780f0171ef5302a2e1a257f99b6383fbfc1b9b82f925ceff501', # cubew-4.4.3.tar.gz -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/cubew-config', - 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], - 'dirs': ['include/cubew'], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index e6b63b98840..00000000000 --- a/easybuild/easyconfigs/__archive__/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,54 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# Updated to v24.2.0 -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'cDNA_Cupcake' -version = '24.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Magdoll/cDNA_Cupcake' -description = """cDNA_Cupcake is a miscellaneous collection of Python and -R scripts used for analyzing sequencing data. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/Magdoll/cDNA_Cupcake/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['9aa75ef3d00e9983772021dca3c5595df5ea23c39fb0004e4330e55edc782002'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Biopython', '1.78', versionsuffix), - ('bx-python', '0.8.9', versionsuffix), - ('bcbio-gff', '0.6.6', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('Pysam', '0.16.0.1'), -] - -preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " - -sanity_check_paths = { - # check for particular Cupcake ToFU scripts, - # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step - 'files': [ - 'bin/collapse_isoforms_by_sam.py', - 'bin/get_abundance_post_collapse.py', - 'bin/simple_stats_post_collapse.py' - ], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - 'collapse_isoforms_by_sam.py -h', - 'get_abundance_post_collapse.py -h', - 'simple_stats_post_collapse.py -h', -] - -options = {'modulename': 'cupcake'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/cURL/cURL-7.69.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/cURL/cURL-7.69.1-GCCcore-9.3.0.eb deleted file mode 100644 index 71ff6909f25..00000000000 --- a/easybuild/easyconfigs/__archive__/c/cURL/cURL-7.69.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'cURL' -version = '7.69.1' - -homepage = 'https://curl.haxx.se' - -description = """ - libcurl is a free and easy-to-use client-side URL transfer library, - supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, - LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. - libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP - form based upload, proxies, cookies, user+password authentication (Basic, - Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling - and more. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://curl.haxx.se/download/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['01ae0c123dee45b01bbaef94c0bc00ed2aec89cb2ee0fd598e0d302a6b5e0a98'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('zlib', '1.2.11'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.1d') -] - -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] - -configopts = '--with-zlib' -# configopts += '--with-ssl=$EBROOTOPENSSL' - -modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} - -sanity_check_paths = { - 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig', 'include/curl'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/c/cairo/cairo-1.16.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/cairo/cairo-1.16.0-GCCcore-9.3.0.eb deleted file mode 100644 index 3a05c32e92b..00000000000 --- a/easybuild/easyconfigs/__archive__/c/cairo/cairo-1.16.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'cairo' -version = '1.16.0' - -homepage = 'https://cairographics.org' -description = """Cairo is a 2D graphics library with support for multiple output devices. - Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, - PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://cairographics.org/releases/'] -sources = [SOURCE_TAR_XZ] -checksums = ['5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('pixman', '0.38.4'), - ('expat', '2.2.9'), - ('GLib', '2.64.1'), - ('X11', '20200222'), -] - -# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " - -sanity_check_paths = { - 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', - 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', - 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, - 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + - ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', - '-script', '-script-interpreter', '-svg', '-version', '-xcb', - '-xlib', '-xlib-xrender']], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/__archive__/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb deleted file mode 100644 index 8e5ee7b58b9..00000000000 --- a/easybuild/easyconfigs/__archive__/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'canu' -version = '2.1.1' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://canu.readthedocs.io' -description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'marbl' -source_urls = ['https://github.com/marbl/canu/releases/download/v%(version)s'] -sources = [SOURCE_TAR_XZ] -checksums = ['18c030ada93286be90c364387879025c17001c8e445e64719c866bc6c7609b98'] - -builddependencies = [ - ('binutils', '2.34'), - ('git', '2.23.0', '-nodocs'), -] - -dependencies = [ - ('Java', '11', '', SYSTEM), - ('Perl', '5.30.2'), - ('gnuplot', '5.2.8'), -] - -skipsteps = ['configure', 'install'] - -start_dir = 'src' - -buildopts = 'TARGET_DIR=%(installdir)s' - -sanity_check_paths = { - 'files': ['bin/canu', 'lib/libcanu.a'], - 'dirs': ['lib/site_perl', 'share'], -} -sanity_check_commands = [ - "canu -version", - "canu -options", -] - -modextrapaths = {'PERL5LIB': 'lib/site_perl'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/carputils/carputils-20200915-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/carputils/carputils-20200915-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 27500aa6154..00000000000 --- a/easybuild/easyconfigs/__archive__/c/carputils/carputils-20200915-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,68 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'carputils' -local_commit = 'f5573e0d' -version = '20200915' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://git.opencarp.org/openCARP/carputils' -description = "carputils is a Python framework for generating and running openCARP examples." - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('openCARP', '3.2', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('PyTables', '3.6.1', versionsuffix), - ('meshtool', '16'), - ('meshalyzer', '2.0', versionsuffix), -] - -# version restrictions are too strict, so strip them out -local_carputils_preinstallopts = "sed -i 's/[=><]=[0-9].*//g' requirements.txt && " -# inject proper version, to prevent installing carputils with 0.0.0 as version... -local_carputils_preinstallopts += """sed -i 's/ description=/ version="0.0.1-pre", description=/g' setup.py && """ - -exts_list = [ - ('doxypypy', '0.8.8.6', { - 'checksums': ['627571455c537eb91d6998d95b32efc3c53562b2dbadafcb17e49593e0dae01b'], - }), - ('pyDOE', '0.3.8', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], - 'modulename': 'pyDOE', - }), - (name, version, { - 'source_urls': ['https://git.opencarp.org/openCARP/carputils/-/archive/%s/' % local_commit], - 'source_tmpl': 'carputils-%s.tar.gz' % local_commit, - 'checksums': ['695af109e4b23797ac94a86b49ce5a98b4d002dc094b062927b53efa72f822f0'], - # version restrictions are too strict, so strip them out - 'preinstallopts': local_carputils_preinstallopts, - }), -] - -fix_python_shebang_for = ['bin/*'] - -postinstallcmds = [ - "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " - "%(installdir)s/bin/cusettings %(installdir)s/settings.yaml", - # location to openCARP bin subdirectory - r'sed -i "s@^\([ ]*CPU: \).*@\1$EBROOTOPENCARP/bin@" %(installdir)s/settings.yaml', - r'sed -i "s@^\(MESHTOOL_DIR: \).*@\1$EBROOTMESHTOOL/bin@" %(installdir)s/settings.yaml', - r'sed -i "s@^\(MESHALYZER_DIR: \).*@\1$EBROOTMESHALYZER@" %(installdir)s/settings.yaml', - r'sed -i "s@^\(REGRESSION_REF: \).*@\1/path/to/carp-tests-reference@" %(installdir)s/settings.yaml', - r'sed -i "s/^\(EMAIL: \).*/\1 example@email.com/" %(installdir)s/settings.yaml', -] - -sanity_check_paths = { - 'files': ['bin/carphelp', 'bin/carptests', 'bin/cusettings'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["carphelp --help"] - -modextravars = {'CARPUTILS_SETTINGS': '%(installdir)s/settings.yaml'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/causallift/causallift-1.0.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/causallift/causallift-1.0.6-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 0746cae7fdd..00000000000 --- a/easybuild/easyconfigs/__archive__/c/causallift/causallift-1.0.6-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'causallift' -version = '1.0.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Minyus/causallift' -description = """ -CausalLift: Python package for Uplift Modeling in real-world business; -applicable for both A/B testing and observational data -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('kedro', '0.16.5', versionsuffix), -] - -exts_list = [ - ('easydict', '1.9', { - 'checksums': ['3f3f0dab07c299f0f4df032db1f388d985bb57fa4c5be30acd25c5f9a516883b'], - }), - (name, version, { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/Minyus/causallift/archive/'], - 'checksums': ['b5a62317438d469a2bb41b75d6a9214178196a9717afe82ceabc3b6843fae9a6'], - }), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/c/causalml/causalml-0.8.0-20200909-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/causalml/causalml-0.8.0-20200909-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 459eb868993..00000000000 --- a/easybuild/easyconfigs/__archive__/c/causalml/causalml-0.8.0-20200909-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,63 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'causalml' -local_commit_date = '20200909' -local_commit = 'b36f378' -version = '0.8.0-%s' % local_commit_date -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/uber/causalml' -description = """ Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML """ - -toolchain = {'name': 'foss', 'version': '2020a'} - -builddependencies = [('CMake', '3.16.4')] # needed for lightgbm - -dependencies = [ - ('Python', '3.8.2'), - ('scikit-learn', '0.23.1', versionsuffix), - ('statsmodels', '0.11.1', versionsuffix), - ('Seaborn', '0.10.1', versionsuffix), - ('XGBoost', '1.2.0', versionsuffix), - ('TensorFlow', '2.3.1', versionsuffix), - ('Keras', '2.3.1', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('numba', '0.50.0', versionsuffix), - ('tqdm', '4.47.0'), -] - -exts_list = [ - ('slicer', '0.0.4', { - 'checksums': ['21d53aac4e78c93fd83c0fd2f8f9d8a2195ac079dffdc0da81cd749da0f2f355'], - }), - ('shap', '0.36.0', { - 'checksums': ['30d5f5860e7d7787eeed09592e2b3bbd68816b0d3589f2eda6adc7663448217f'], - }), - ('dill', '0.3.2', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e'], - }), - ('lightgbm', '3.0.0', { - 'checksums': ['05f5b358469a679dbf27521d926750ca53ff1e61a6c0293d49af30094ebd9d4a'], - }), - ('pydotplus', '2.0.2', { - 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], - }), - ('python-utils', '2.4.0', { - 'checksums': ['f21fc09ff58ea5ebd1fd2e8ef7f63e39d456336900f26bdc9334a03a3f7d8089'], - }), - ('progressbar2', '3.53.1', { - 'modulename': 'progressbar', - 'checksums': ['ef72be284e7f2b61ac0894b44165926f13f5d995b2bf3cd8a8dedc6224b255a7'], - }), - ('pygam', '0.8.0', { - 'checksums': ['5cae01aea8b2fede72a6da0aba1490213af54b3476745666af26bbe700479166'], - }), - (name, 'b36f378', { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/uber/causalml/archive/'], - 'checksums': ['b33401f89e9e7e38c5d590ca349387e3c91c609164d5b391cefed980e39b4387'], - }), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.7.11.eb b/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.7.11.eb deleted file mode 100644 index 6a29cbdb220..00000000000 --- a/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.7.11.eb +++ /dev/null @@ -1,41 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -## -easyblock = 'ConfigureMake' - -name = 'ccache' -version = '3.7.11' - -homepage = 'https://ccache.dev/' -description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by -caching previous compilations and detecting when the same compilation is being done again""" - -toolchain = SYSTEM - -source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['34309a59d4b6b6b33756366aa9d3144a4655587be9f914476b4c0e2d36365f01'] - -osdependencies = [('glibc-static', 'libc6-dev')] - -local_gccver = '9.3.0' -builddependencies = [ - ('GCC', local_gccver), - ('Autotools', '20180311', '', ('GCCcore', local_gccver)), - ('zlib', '1.2.11', '', ('GCCcore', local_gccver)), -] - -buildopts = 'LDFLAGS="-static"' - -sanity_check_paths = { - 'files': ['bin/ccache'], - 'dirs': [] -} -sanity_check_commands = ['ccache --help'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/c/cclib/cclib-1.6.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/cclib/cclib-1.6.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 986b01dd2a5..00000000000 --- a/easybuild/easyconfigs/__archive__/c/cclib/cclib-1.6.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'cclib' -version = '1.6.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://cclib.github.io/' - -description = """ - cclib is a Python library that provides parsers for computational chemistry log files. - It also provides a platform to implement algorithms in a package-independent manner. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('periodictable', '1.5.2', { - 'checksums': ['1fea8abf0c20453550630ca682a75f0148f65b6d21fdcce7cf0c0e98631fa0d3'], - }), - (name, version, { - 'checksums': ['0428aa8c29b7460c767a8b3b14c089ee83bbd6269a0af2a2164eafa962f1c2d4'], - }), -] - -sanity_check_paths = { - 'files': ['bin/ccframe', 'bin/ccget'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/c/cclib/cclib-1.6.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/cclib/cclib-1.6.3-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 0aeaffe36ad..00000000000 --- a/easybuild/easyconfigs/__archive__/c/cclib/cclib-1.6.3-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'cclib' -version = '1.6.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://cclib.github.io/' - -description = """ - cclib is a Python library that provides parsers for computational chemistry log files. - It also provides a platform to implement algorithms in a package-independent manner. -""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('periodictable', '1.5.2', { - 'checksums': ['1fea8abf0c20453550630ca682a75f0148f65b6d21fdcce7cf0c0e98631fa0d3'], - }), - (name, version, { - 'checksums': ['0428aa8c29b7460c767a8b3b14c089ee83bbd6269a0af2a2164eafa962f1c2d4'], - }), -] - -sanity_check_paths = { - 'files': ['bin/ccframe', 'bin/ccget'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/c/cdsapi/cdsapi-0.3.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/c/cdsapi/cdsapi-0.3.0-GCCcore-9.3.0.eb deleted file mode 100644 index b6581edbe3f..00000000000 --- a/easybuild/easyconfigs/__archive__/c/cdsapi/cdsapi-0.3.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'cdsapi' -version = '0.3.0' - -homepage = 'https://pypi.org/project/cdsapi' -description = "Climate Data Store API" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['1f89293459d9b6560426261d8e9fd1e32d8dcaf6f47342b174835bafc0dd06a1'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('tqdm', '4.47.0'), -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 2e220bf0a4e..00000000000 --- a/easybuild/easyconfigs/__archive__/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,55 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'chewBBACA' -version = '2.5.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/B-UMMI/chewBBACA' -description = """chewBBACA stands for "BSR-Based Allele Calling Algorithm". -chewBBACA is a comprehensive pipeline including a set of functions for the -creation and validation of whole genome and core genome MultiLocus Sequence -Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast -Score Ratio that can be run in multiprocessor settings and a set of functions to -visualize and validate allele variation in the loci.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Biopython', '1.78', versionsuffix), - ('plotly.py', '4.8.1'), - ('BLAST+', '2.10.1'), - ('prodigal', '2.6.3'), - ('ClustalW2', '2.1'), - ('MAFFT', '7.453', '-with-extensions'), -] - -exts_list = [ - ('isodate', '0.6.0', { - 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], - }), - ('rdflib', '5.0.0', { - 'checksums': ['78149dd49d385efec3b3adfbd61c87afaf1281c30d3fcaf1b323b34f603fb155'], - }), - ('SPARQLWrapper', '1.8.5', { - 'modulename': 'SPARQLWrapper', - 'checksums': ['d6a66b5b8cda141660e07aeb00472db077a98d22cb588c973209c7336850fb3c'], - }), - (name, version, { - 'modulename': 'CHEWBBACA', - 'runtest': "python setup.py test", - 'checksums': ['f8960b8485672f6d39d59e53b3521db406120abc2d7db42ce4c9eac06b024a5f'], - }), -] - -sanity_check_paths = { - 'files': ['bin/chewBBACA.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/CHEWBBACA'], -} - -sanity_check_commands = [ - 'chewBBACA.py --help', -] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-2.10-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-2.10-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 28ee1854bcd..00000000000 --- a/easybuild/easyconfigs/__archive__/c/cutadapt/cutadapt-2.10-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,43 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics (SIB) -# Biozentrum - University of Basel -# Modified by: Adam Huffman, Jonas Demeulemeester -# The Francis Crick Institute -# Modufied by: Albert Bogdanowicz -# Institute of Biochemistry and Biophysics PAS - -easyblock = 'PythonBundle' - -name = 'cutadapt' -version = '2.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' -description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and - other types of unwanted sequence from your high-throughput sequencing reads.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [('binutils', '2.34')] - -dependencies = [('Python', '3.8.2')] - -exts_list = [ - ('xopen', '0.8.4', { - 'checksums': ['dcd8f5ef5da5564f514a990573a48a0c347ee1fdbb9b6374d31592819868f7ba'], - }), - ('dnaio', '0.4.2', { - 'checksums': ['fa55a45bfd5d9272409b714158fb3a7de5dceac1034a0af84502c7f503ee84f8'], - }), - (name, version, { - 'checksums': ['936b88374b5b393a954852a0fe317a85b798dd4faf5ec52cf3ef4f3c062c242a'], - }), -] - -sanity_check_paths = { - 'files': ['bin/cutadapt'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/DB/DB-18.1.32-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/d/DB/DB-18.1.32-GCCcore-9.3.0.eb deleted file mode 100644 index 5997790bf6f..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DB/DB-18.1.32-GCCcore-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -# EasyBuild easyconfig -name = 'DB' -version = '18.1.32' - -homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' - -description = """Berkeley DB enables the development of custom data management - solutions, without the overhead traditionally associated with such custom - projects.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://gentoo.osuosl.org/distfiles/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['fa1fe7de9ba91ad472c25d026f931802597c29f28ae951960685cde487c8d654'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', - 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', - 'tuner', 'upgrade', 'verify']] + - ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/d/DB/DB-18.1.40-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/d/DB/DB-18.1.40-FCC-4.5.0.eb deleted file mode 100644 index 3552aab690a..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DB/DB-18.1.40-FCC-4.5.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -## -# Author: Robert Mijakovic -## -name = 'DB' -version = '18.1.40' - -homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' - -description = """Berkeley DB enables the development of custom data management - solutions, without the overhead traditionally associated with such custom - projects.""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -# use http to allow auto-downloading... -source_urls = ['http://download.oracle.com/berkeley-db/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_fix_doc_install.patch'] -checksums = [ - '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz - '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch -] - -builddependencies = [('binutils', '2.36.1')] - -dependencies = [('OpenSSL', '1.1', '', SYSTEM)] - -sanity_check_paths = { - 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', - 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', - 'tuner', 'upgrade', 'verify']] + - ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/d/DB_File/DB_File-1.835-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/d/DB_File/DB_File-1.835-GCCcore-9.3.0.eb deleted file mode 100644 index 430fc43f900..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DB_File/DB_File-1.835-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PerlModule' - -name = 'DB_File' -version = '1.835' - -homepage = 'https://perldoc.perl.org/DB_File.html' -description = """Perl5 access to Berkeley DB version 1.x.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] -sources = [SOURCE_TAR_GZ] -checksums = ['41206f39a1bac49db8c1595e300b04c70e1393b2d78ccb9ef15c5c0b81037cfc'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Perl', '5.30.2'), - ('DB', '18.1.32'), -] - -preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' - -sanity_check_paths = { - 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], - 'dirs': [], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/d/DBus/DBus-1.13.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/d/DBus/DBus-1.13.12-GCCcore-9.3.0.eb deleted file mode 100644 index 60227ab40fc..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DBus/DBus-1.13.12-GCCcore-9.3.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'DBus' -version = '1.13.12' - -homepage = 'https://dbus.freedesktop.org/' - -description = """ - D-Bus is a message bus system, a simple way for applications to talk - to one another. In addition to interprocess communication, D-Bus helps - coordinate process lifecycle; it makes it simple and reliable to code - a "single instance" application or daemon, and to launch applications - and daemons on demand when their services are needed. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://dbus.freedesktop.org/releases/dbus'] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['7588649b56dd257c6a5f85a8c45aa2dfdf9e99f4de3983710f452081ca43eca6'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('expat', '2.2.9'), -] - -configopts = '--without-systemdsystemunitdir' - -sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in - ['cleanup-sockets', 'daemon', 'launch', 'monitor', - 'run-session', 'send', 'uuidgen']] + - ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], - 'dirs': ['include', 'share'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/d/DFA/DFA-0.3.4-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/d/DFA/DFA-0.3.4-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index de55763426a..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DFA/DFA-0.3.4-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'DFA' -version = '0.3.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/mvcisback/dfa' -description = "Python library for modeling DFAs, Moore Machines, and Transition Systems." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [ - ('binutils', '2.34'), - ('poetry', '1.0.9', versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('pydot', '1.4.1'), -] - -exts_default_options = { - 'sources': [SOURCELOWER_TAR_GZ], -} - -exts_list = [ - ('funcy', '1.15', { - 'checksums': ['65b746fed572b392d886810a98d56939c6e0d545abb750527a717c21ced21008'], - }), - ('lazytree', '0.3.1', { - 'checksums': ['23096b04eb48743e1e90151c285a604e8281c304c7aaa4abb083c0ccca28fa55'], - }), - (name, version, { - 'checksums': ['b730c94f6b788651b4c8cbff0c35b370afc56c6f9a6bd6db0d1e39aa72411da3'], - }), -] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/d/DIAMOND/DIAMOND-0.9.36-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/d/DIAMOND/DIAMOND-0.9.36-GCC-9.3.0.eb deleted file mode 100644 index 334e677a721..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DIAMOND/DIAMOND-0.9.36-GCC-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'DIAMOND' -version = "0.9.36" - -homepage = 'https://github.com/bbuchfink/diamond' -description = "Accelerated BLAST compatible local sequence aligner" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/bbuchfink/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['870af89606330f6c0b57ed478d2d8237334ce8f5630eac770399ff431948bd59'] - -separate_build_dir = True - -builddependencies = [ - ('CMake', '3.16.4') -] -dependencies = [('zlib', '1.2.11')] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [], -} -sanity_check_commands = ["diamond help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/DIAMOND/DIAMOND-2.0.4-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/d/DIAMOND/DIAMOND-2.0.4-GCC-9.3.0.eb deleted file mode 100644 index b440af4ae7b..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DIAMOND/DIAMOND-2.0.4-GCC-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'DIAMOND' -version = "2.0.4" - -homepage = 'https://github.com/bbuchfink/diamond' -description = "Accelerated BLAST compatible local sequence aligner" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/bbuchfink/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['94e8fe72bdc28b83fd0f2d90c439b58b63b38263aa1a3905582ef68f614ae95d'] - -separate_build_dir = True - -builddependencies = [ - ('CMake', '3.16.4') -] -dependencies = [('zlib', '1.2.11')] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [], -} -sanity_check_commands = ["diamond help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb b/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb deleted file mode 100644 index cc17513adeb..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb +++ /dev/null @@ -1,60 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'DIRAC' -version = '19.0' -versionsuffix = '-Python-%(pyver)s-int64' - -homepage = 'http://www.diracprogram.org' -description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'i8': True} - -source_urls = ['https://zenodo.org/record/3572669/files/'] -sources = ['DIRAC-%(version)s-Source.tar.gz'] -patches = [ - '%(name)s-%(version)s_remove-broken-tests-intel.patch', - '%(name)s-%(version)s_fix-bss_energy_test.patch', - '%(name)s-%(version)s_use_easybuild_opts.patch', - '%(name)s-%(version)s_fix_test_path.patch', -] -checksums = [ - 'f0e3610bdd1fbcff90cdfb4cf3fd7582a4762f533af7d635c4bc4d114f402c32', # DIRAC-19.0-Source.tar.gz - 'cb0e07097499fe59180d79a5db9ee883b9c83e16dcc6210fd945072c3a54c8a4', # DIRAC-19.0_remove-broken-tests-intel.patch - 'e66be847d87ccfda23687de31a3a7c8d71c97b0accd290cf7ade4b4184f1fb93', # DIRAC-19.0_fix-bss_energy_test.patch - '150b293250f1ca476a1d268534a236e06dbf5960d25c2a09f6d3f5e82c043316', # DIRAC-19.0_use_easybuild_opts.patch - '527680cab911a8c7a52347d7ace516a497b725043537a6274670a1aaa97bfb0f', # DIRAC-19.0_fix_test_path.patch -] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [('Python', '2.7.18')] - -configopts = '-DENABLE_BLAS=off ' -configopts += '-DENABLE_LAPACK=off ' -configopts += '-DMKL_FLAG=off ' -configopts += '-DBLAS_LANG=Fortran ' -configopts += '-DLAPACK_LANG=Fortran ' -configopts += '-DENABLE_MPI=False ' -configopts += '-DENABLE_OPENMP=False ' -configopts += '-DENABLE_CODE_COVERAGE=False ' -configopts += '-DENABLE_STATIC_LINKING=False ' -configopts += '-DENABLE_PROFILING=False ' -configopts += '-DENABLE_RUNTIMECHECK=False ' -configopts += '-DENABLE_64BIT_INTEGERS=True ' -configopts += '-DEXPLICIT_LIBS="${LIBLAPACK_MT}" ' -configopts += '-DENABLE_PCMSOLVER=OFF ' - -maxparallel = 1 - -pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], - 'dirs': ['share/dirac/basis'], -} - -sanity_check_commands = ["pam-dirac --help"] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb b/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb deleted file mode 100644 index 810cfc7d132..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb +++ /dev/null @@ -1,70 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'DIRAC' -version = '19.0' -versionsuffix = '-Python-%(pyver)s-mpi-int64' - -homepage = 'http://www.diracprogram.org' -description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True, 'i8': True} - -source_urls = ['https://zenodo.org/record/3572669/files/'] -sources = ['DIRAC-%(version)s-Source.tar.gz'] -patches = [ - '%(name)s-%(version)s_remove-broken-tests-intel.patch', - '%(name)s-%(version)s_fix-bss_energy_test.patch', - '%(name)s-%(version)s_use_easybuild_opts.patch', - '%(name)s-%(version)s_fix_test_path.patch', - '%(name)s-%(version)s_fix_mpi_tests.patch', -] -checksums = [ - 'f0e3610bdd1fbcff90cdfb4cf3fd7582a4762f533af7d635c4bc4d114f402c32', # DIRAC-19.0-Source.tar.gz - 'cb0e07097499fe59180d79a5db9ee883b9c83e16dcc6210fd945072c3a54c8a4', # DIRAC-19.0_remove-broken-tests-intel.patch - 'e66be847d87ccfda23687de31a3a7c8d71c97b0accd290cf7ade4b4184f1fb93', # DIRAC-19.0_fix-bss_energy_test.patch - '150b293250f1ca476a1d268534a236e06dbf5960d25c2a09f6d3f5e82c043316', # DIRAC-19.0_use_easybuild_opts.patch - '527680cab911a8c7a52347d7ace516a497b725043537a6274670a1aaa97bfb0f', # DIRAC-19.0_fix_test_path.patch - 'ccc26fc320f0967211b6390244b1fa359ba5d0294071d5d2cb9e36b4652a52b2', # DIRAC-19.0_fix_mpi_tests.patch -] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [('Python', '2.7.18')] - -configopts = '-DENABLE_BLAS=off ' -configopts += '-DENABLE_LAPACK=off ' -configopts += '-DMKL_FLAG=off ' -configopts += '-DBLAS_LANG=Fortran ' -configopts += '-DLAPACK_LANG=Fortran ' -configopts += '-DENABLE_MPI=True ' -configopts += '-DENABLE_OPENMP=False ' -configopts += '-DENABLE_CODE_COVERAGE=False ' -configopts += '-DENABLE_STATIC_LINKING=False ' -configopts += '-DENABLE_PROFILING=False ' -configopts += '-DENABLE_RUNTIMECHECK=False ' -configopts += '-DENABLE_64BIT_INTEGERS=True ' -configopts += '-DEXPLICIT_LIBS="${LIBSCALAPACK_MT}" ' -configopts += '-DENABLE_PCMSOLVER=OFF ' - -maxparallel = 1 - -pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' -# WARNING! -# running the tests with more than 1 MPI process might break some tests: -# 18 - polprp_ph -> ERROR READING HEADER MDCINT -# 20 - eomcc/eom_ea_h2o.out -> extra state -# 26 - eomea_energy_symmetry/eom_ea_dc_noinv_overlap_c_oo_v_-Omega_f2_c_oo_v_turbomole-dz.out -> extra state -# 46 - fscc_restart -> ENERGY TOTAL WRONG, maybe missing some file, like in polprp_ph? -# Test 20/26 fails on cascadelake and not on haswell and skylake -pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], - 'dirs': ['share/dirac/basis'], -} - -sanity_check_commands = ["pam-dirac --help"] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch b/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch deleted file mode 100644 index 2a73d6aaabf..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch +++ /dev/null @@ -1,3028 +0,0 @@ -# It seems that bss_energy test is broken, the reference calculation is form 2004 -# The fact that only the SCF energy different and the consecutive post-HF correlation -# energies are the same is a strong hint that the HF wavefunction should be the same, -# but the energies for some reason are different. -# The test was recalulated using the following compilers/BLAS libaries on cascadelake -# architecture, and the results are practially the same. -# Based on this facts, the reference test result was changed to the intel result below. -# -# gfortran 9.3.0 openblas 0.3.9 cascadelake: -# @ SCF energy : -9505.779747269898508 -# @ MP2 correlation energy : -0.221846247868918 -# @ CCSD correlation energy : -0.222547639202710 -# @ 4th order triples correction : -0.000001799879971 -# @ 5th order triples (T) correction : -0.000000000059407 -# @ 5th order triples -T correction : -0.000000000472828 -# @ Total MP2 energy : -9506.001593517767105 -# @ Total CCSD energy : -9506.002294909101693 -# @ Total CCSD+T energy : -9506.002296708980793 -# @ Total CCSD(T) energy : -9506.002296709040820 -# @ Total CCSD-T energy : -9506.002296709453731 -# -# ifort 2020.1 mkl 2020.1 cascadelake: -# @ SCF energy : -9505.779747269911240 -# @ MP2 correlation energy : -0.221846247868917 -# @ CCSD correlation energy : -0.222547639202709 -# @ 4th order triples correction : -0.000001799879971 -# @ 5th order triples (T) correction : -0.000000000059407 -# @ 5th order triples -T correction : -0.000000000472828 -# @ Total MP2 energy : -9506.001593517779838 -# @ Total CCSD energy : -9506.002294909114426 -# @ Total CCSD+T energy : -9506.002296708993526 -# @ Total CCSD(T) energy : -9506.002296709053553 -# @ Total CCSD-T energy : -9506.002296709466464 -# -# OCT 5th 2020 by B. Hajgato (UGent) -diff -ru DIRAC-19.0-Source.orig/test/bss_energy/result/HF.bss_sfb.cc_cisd_Z80H.lsym.dir.out DIRAC-19.0-Source/test/bss_energy/result/HF.bss_sfb.cc_cisd_Z80H.lsym.dir.out ---- DIRAC-19.0-Source.orig/test/bss_energy/result/HF.bss_sfb.cc_cisd_Z80H.lsym.dir.out 2019-12-12 17:26:14.000000000 +0100 -+++ DIRAC-19.0-Source/test/bss_energy/result/HF.bss_sfb.cc_cisd_Z80H.lsym.dir.out 2020-10-05 14:16:03.472742000 +0200 -@@ -1,175 +1,342 @@ --Master : DIRAC allocating 10000000 words of memory --****************************************************************************** --* * --* O U T P U T * --* from * --* * --* @@@@@ @@ @@@@@ @@@@ @@@@@ * --* @@ @@ @@ @@ @@ @@ @@ * --* @@ @@ @@ @@@@@ @@@@@@ @@ * --* @@ @@ @@ @@ @@ @@ @@ @@ * --* @@@@@ @@ @@ @@ @@ @@ @@@@@ * --* * --* * --%}ZS)S?$=$)]S?$%%>SS$%S$ZZ6cHHMHHHHHHHHMHHM&MHbHH6$L/:$)S6HMMMMMMMMMMMMMMMMMMMMMMR6M]&&$6HR$&6(i::::::|i|:::::::-:-:: --$S?$$)$?$%?))?S/]#MMMMMMMMMMMMMMMMMMMMMMMMMMHM1HRH9R&$$$|):?:/://|:/::/:/.::.: --SS$%%?$%((S)?Z[6MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM&HF$$&/)S?<~::!!:::::::/:-:|. --SS%%%%S$%%%$$MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHHHHHHM>?/S/:/:::':/://:/::-:: --?$SSSS?%SS$)MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/4?:S:/:::/:::/:/:::.:: --S$(S?S$%(?$HMMMMMMMMMMMMMMMMM#&7RH99MMMMMMMMMMMMMMMMMMHHHd$/:::::/::::::-//.:. --(?SS(%)S&HMMMMMMMMMMMMMMMMM#S|///???$9HHMMMMMMMMMDSZ&1S/??~:///::|/!:/-:-:. --$S?%?:``?/*?##*)$:/> `((%://::/:::::/::/ --S$($$)HdMMMMMMMMMMMMMMMP: . ` ` ` ` `- `Z<:>?::/:::::|:i --c%%%&HMMMMMMMMMMMMMMMM6: `$%)>%%!::::: --S?%/MMMMMMMMMMMMMMMMMMH- /ZSS>?:?~:;/:: --$SZ?MMMMMMMMMMMMMMMMMH?. "&((/?//?|:::: --$%$%&MMMMMMMMMMMMMMMMM:. ?%/S:: $%%< ,HMMMMMMMF :::?:///:|:: --)[$S$S($|_i:#>::*H&?/::.::/:"://:?>>':&HMHSMMMM$:'- MMHMMMMHHT .)i/?////:::/ --$$[$$>$}:dHH&$$--?S::-:.:::--/-:``./::>%Zi?)&/?`:.' `H?$T*" ` /%?>%:)://ii| --$&=&/ZS}$RF<:?/-.|%r/:::/:/:'.-.-..|::S//!`"`` >??: `SSb[Z(Z?&%:::../S$$:>:::i`.`. '-.' ` ,>%%%:>/>/!|:/ --$$&/F&1$c$?>:>?/,>?$$ZS/::/:-: ... |S?S)S?<~::::: --&$&$&$k&>>|?<:?Z&S$$$/$S///||..- -.- /((S$:%<:///:/ --$&>1MHHMMMM6M9MMMM$Z$}$S%/:::.'. .:/,,,dcb>/:. ((SSSS%:)!//i| --MMMMMMMMMMMR&&RRRHR&&($(?:|i::- .:%&S&$[&H&'' ../>%;/?>??:<::> --MMMMMMMMMMMMS/}S$&&H&[$SS//:::.:. . . .v?://: --MMMMMMMMMMMM?}$/$$kMM&&$(%/?//:..'. .|//1d/`://?*/*/"` ' .:/(SS$%(S%)):%~ --MMMMMMMMMMMM(}$$>&&MMHR#$S%%:?::.:|-.':;&&b/D/$p=qpv//b/~' :/~~%%??$=$)Z$S+; --MMMMMMMMMMMM[|S$$Z1]MMMMD[$?$:>)/::: :/?:`'???bD&{b<<-' .,:/)|SS(}Z/$$?/[&]HMMMMMMMH1[/7SS(?:/..-` ::/Sc,/_, _<$?SS%$S/&c&&$&>//< --MMMMMMMMMMMMR `$&&&HMM9MMMMMMM&&c$%%:/:/:.:.:/??/''" _MMHk/7S/]dq&1S<&&>$&Z$/?_.bHMMMMMMMMMMM&6HRM9H6]Zk --MMMMMMMMMMMMMMM/ `TMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHMH6RH&R6& --MMMMMMMMMMMMMMMM -|?HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMFHH6HMD&& --MMMMMMMMMMMMMMMMk ..:~?9MMMMMMMMMMMMM#':MMMMMMMMMMMMMMMMMMMMMMMMMMMMM9MHkR6&F --MMMMMMMMMMMMMMMMM/ .-!:%$ZHMMMMMMMMMR' dMMMMMMMMMMMMMMMMMMMMMMMMMMMMM9MRMHH9& --MMMMMMMMMMMMMMMMMML,:.-|::/?&&MMMMMM' .MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHRMH&&6 --MMMMMMMMMMMMMMMMMMMc%>/:::i<:SMMMMMMHdMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHHM&969k --MMMMMMMMMMMMMMMMMMMMSS/$$/(|HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHH&HH& --MMMMMMMMMMMMMMMMMMMM6S/?/MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMR96H1DR1 --MMMMMMMMMMMMMMMMMMMMM&$MHMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHMH691&& --MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&R&9Z --MMMMMMMMMMMMMMMMMMMMMMMMMRHMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&96][6 --MMMMMMMMMMMMMMMMMMMMMMMMp?:MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM96HH1][F --MMMMMMMMMMMMMMMMMMMMMMMM> -HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&1k&$& --****************************************************************************** --* * --* ======================================================= * --* Program for Atomic and Molecular * --* Direct Iterative Relativistic Allelectron Calculations * --* ======================================================= * --* * --* VERSION 04.1 SEPTEMBER 2004 * --* * --****************************************************************************** --* * --* Written by: * --* * --* Hans Joergen Aa. Jensen University of Southern Denmark Denmark * --* Trond Saue CNRS/ULP Strasbourg France * --* Lucas Visscher Vrije Universiteit Amsterdam Netherlands * --* * --* with contributions from: * --* * --* Vebjoern Bakken University of Oslo Norway * --* Ephraim Eliav University of Tel Aviv Israel * --* Thomas Enevoldsen University of Southern Denmark Denmark * --* Timo Fleig University of Duesseldorf Germany * --* Olav Fossgaard University of Tromsoe Norway * --* Trygve Helgaker University of Oslo Norway * --* Jon K. Laerdahl University of Oslo Norway * --* Christoffer V. Larsen University of Southern Denmark Denmark * --* Patrick Norman Linkoeping University Sweden * --* Jeppe Olsen Aarhus University Denmark * --* Markus Pernpointner Vrije Universiteit Amsterdam Netherlands * --* Jesper K. Pedersen University of Southern Denmark Denmark * --* Kenneth Ruud University of Tromsoe Norway * --* Pawel Salek Stockholm Inst. of Technology Sweden * --* Joost van Stralen Vrije Universiteit Amsterdam Netherlands * --* Joern Thyssen University of Southern Denmark Denmark * --* Olivier Visser University of Groningen Netherlands * --* Toke Winther University of Southern Denmark Denmark * --* * --* This is an experimental code. The authors accept no responsibility * --* for the performance of the code or for the correctness of the results. * --* * --* The code (in whole or part) is not to be reproduced for further * --* distribution without the written permission of the authors or * --* their representatives. * --* * --* If results obtained with this code are published, an * --* appropriate citation would be: * --* * --* "Dirac, a relativistic ab initio electronic structure program", * --* release DIRAC04.1 (2004), * --* written by H. J. Aa. Jensen, T. Saue, and L. Visscher * --* with contributions from V. Bakken, E. Eliav, T. Enevoldsen, T. Fleig, * --* O. Fossgaard, T. Helgaker, J. K. Laerdahl, C. V. Larsen, P. Norman, * --* J. Olsen, M. Pernpointner, J. K. Pedersen, K. Ruud, P. Salek, * --* J. N. P. van Stralen, J. Thyssen, O. Visser, and T. Winther * --* (http://dirac.chem.sdu.dk). * --* * --* (for a suitable BibTEX entry, see * --* ) * --* * --****************************************************************************** -- Version : Dirac 4.1 (patchlevel 0) -- Hostname : quantonakessa.u-strasbg.fr -- Operating system : Linux 2.6.8-1.521 -- Machine : i686 -- Run : Sequential -- Last compilation : 16:31:43 Dec 5 2004 (by ilias@) -- FORTRAN compiler : g77 -g -ffast-math -fautomatic -fno-f2c -fno-globals -Wno-globals -fno-second-underscore -- C compiler : gcc -ffast-math -g -- Basis set dir. : /home/ilias/Dirac_main_trunk_dbg/test/37.bss.energies/:/home/ilias/Dirac_main_trunk_dbg/basis/:/home/ilias/Dirac_main_trunk_dbg/basis_dalton/ -- -- Date and time (Linux) : Sun Dec 5 16:41:19 2004 -- -- -- ************************************************************************* -- ********************************* LiH ********************************* -- ************************************************************************* -+DIRAC serial starts by allocating 64000000 words ( 488.28 MB - 0.477 GB) of memory -+ out of the allowed maximum of 2147483648 words ( 16384.00 MB - 16.000 GB) -+ -+Note: maximum allocatable memory for serial run can be set by pam --aw/--ag -+ -+ ******************************************************************************* -+ * * -+ * O U T P U T * -+ * from * -+ * * -+ * @@@@@ @@ @@@@@ @@@@ @@@@@ * -+ * @@ @@ @@ @@ @@ @@ @@ * -+ * @@ @@ @@ @@@@@ @@@@@@ @@ * -+ * @@ @@ @@ @@ @@ @@ @@ @@ * -+ * @@@@@ @@ @@ @@ @@ @@ @@@@@ * -+ * * -+ * * -+ %}ZS)S?$=$)]S?$%%>SS$%S$ZZ6cHHMHHHHHHHHMHHM&MHbHH6$L/:$)S6HMMMMMMMMMMMMMMMMMMMMMMR6M]&&$6HR$&6(i::::::|i|:::::::-:-::( -+ $S?$$)$?$%?))?S/]#MMMMMMMMMMMMMMMMMMMMMMMMMMHM1HRH9R&$$$|):?:/://|:/::/:/.::.:$ -+ SS$%%?$%((S)?Z[6MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM&HF$$&/)S?<~::!!:::::::/:-:|.S -+ SS%%%%S$%%%$$MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHHHHHHM>?/S/:/:::`:/://:/::-::S -+ ?$SSSS?%SS$)MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/4?:S:/:::/:::/:/:::.::? -+ S$(S?S$%(?$HMMMMMMMMMMMMMMMMM#&7RH99MMMMMMMMMMMMMMMMMMHHHd$/:::::/::::::-//.:.S -+ (?SS(%)S&HMMMMMMMMMMMMMMMMM#S|///???$9HHMMMMMMMMMDSZ&1S/??~:///::|/!:/-:-:.( -+ $S?%?:``?/*?##*)$:/> `((%://::/:::::/::/$ -+ S$($$)HdMMMMMMMMMMMMMMMP: . ` ` ` ` `- `Z<:>?::/:::::|:iS -+ c%%%&HMMMMMMMMMMMMMMMM6: `$%)>%%!:::::c -+ S?%/MMMMMMMMMMMMMMMMMMH- /ZSS>?:?~:;/::S -+ $SZ?MMMMMMMMMMMMMMMMMH?. \"&((/?//?|:::$ -+ $%$%&MMMMMMMMMMMMMMMMM:. ?%/S:: $%%< ,HMMMMMMMF :::?:///:|:::$ -+ )[$S$S($|_i:#>::*H&?/::.::/:\"://:?>>`:&HMHSMMMM$:`- MMHMMMMHHT .)i/?////::/) -+ $$[$$>$}:dHH&$$--?S::-:.:::--/-:``./::>%Zi?)&/?`:.` `H?$T*\" ` /%?>%:)://ii$ -+ $&=&/ZS}$RF<:?/-.|%r/:::/:/:`.-.-..|::S//!`\"`` >??: `SSb[Z(Z?&%:::../S$$:>:::i`.`. `-.` ` ,>%%%:>/>/!|:/Z -+ $$&/F&1$c$?>:>?/,>?$$ZS/::/:-: ... |S?S)S?<~:::::$ -+ &$&$&$k&>>|?<:?Z&S$$$/$S///||..- -.- /((S$:%<:///:/= -+ $&>1MHHMMMM6M9MMMM$Z$}$S%/:::.`. .:/,,,dcb>/:. ((SSSS%:)!//i|$ -+ MMMMMMMMMMMR&&RRRHR&&($(?:|i::- .:%&S&$[&H&`` ../>%;/?>??:<::>M -+ MMMMMMMMMMMMS/}S$&&H&[$SS//:::.:. . . .v?://:M -+ MMMMMMMMMMMM?}$/$$kMM&&$(%/?//:..`. .|//1d/`://?*/*/\"` ` .:/(SS$%(S%)):%M -+ MMMMMMMMMMMM(}$$>&&MMHR#$S%%:?::.:|-.`:;&&b/D/$p=qpv//b/~` :/~~%%??$=$)Z$S+;M -+ MMMMMMMMMMMM[|S$$Z1]MMMMD[$?$:>)/::: :/?:``???bD&{b<<-` .,:/)|SS(}Z/$$?/[&]HMMMMMMMH1[/7SS(?:/..-` ::/Sc,/_, _<$?SS%$S/&c&&$&>//$&Z$/?_.bHMMMMMMMMMMM&6HRM9H6]ZkM -+ MMMMMMMMMMMMMMM/ `TMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHMH6RH&R6&M -+ MMMMMMMMMMMMMMMM -|?HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMFHH6HMD&&M -+ MMMMMMMMMMMMMMMMk ..:~?9MMMMMMMMMMMMM#`:MMMMMMMMMMMMMMMMMMMMMMMMMMMMM9MHkR6&FM -+ MMMMMMMMMMMMMMMMM/ .-!:%$ZHMMMMMMMMMR` dMMMMMMMMMMMMMMMMMMMMMMMMMMMMM9MRMHH9&M -+ MMMMMMMMMMMMMMMMMML,:.-|::/?&&MMMMMM` .MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHRMH&&6M -+ MMMMMMMMMMMMMMMMMMMc%>/:::i<:SMMMMMMHdMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHHM&969kM -+ MMMMMMMMMMMMMMMMMMMMSS/$$/(|HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHH&HH&M -+ MMMMMMMMMMMMMMMMMMMM6S/?/MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMR96H1DR1M -+ MMMMMMMMMMMMMMMMMMMMM&$MHMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHMH691&&M -+ MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&R&9ZM -+ MMMMMMMMMMMMMMMMMMMMMMMMMRHMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&96][6M -+ MMMMMMMMMMMMMMMMMMMMMMMMp?:MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM96HH1][FM -+ MMMMMMMMMMMMMMMMMMMMMMMM> -HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&1k&$&M -+ ******************************************************************************* -+ * * -+ * ========================================================= * -+ * Program for Atomic and Molecular * -+ * Direct Iterative Relativistic All-electron Calculations * -+ * ========================================================= * -+ * * -+ * * -+ * Written by: * -+ * * -+ * Andre S. P. Gomes CNRS/Universite de Lille France * -+ * Trond Saue Universite Toulouse III France * -+ * Lucas Visscher Vrije Universiteit Amsterdam Netherlands * -+ * Hans Joergen Aa. Jensen University of Southern Denmark Denmark * -+ * Radovan Bast UiT The Arctic University of Norway * -+ * * -+ * with contributions from: * -+ * * -+ * Ignacio Agustin Aucar Northeast National University Argentina * -+ * Vebjoern Bakken University of Oslo Norway * -+ * Kenneth G. Dyall Schrodinger, Inc., Portland USA * -+ * Sebastien Dubillard University of Strasbourg France * -+ * Ulf Ekstroem University of Oslo Norway * -+ * Ephraim Eliav University of Tel Aviv Israel * -+ * Thomas Enevoldsen University of Southern Denmark Denmark * -+ * Elke Fasshauer University of Aarhus Denmark * -+ * Timo Fleig Universite Toulouse III France * -+ * Olav Fossgaard UiT The Arctic University of Norway * -+ * Loic Halbert Universite de Lille France * -+ * Erik D. Hedegaard Lund University Sweden * -+ * Trygve Helgaker University of Oslo Norway * -+ * Benjamin Helmich-Paris Max Planck Institute f. Coal Res. Germany * -+ * Johan Henriksson Linkoeping University Sweden * -+ * Miroslav Ilias Matej Bel University Slovakia * -+ * Christoph R. Jacob TU Braunschweig Germany * -+ * Stefan Knecht ETH Zuerich Switzerland * -+ * Stanislav Komorovsky UiT The Arctic University of Norway * -+ * Ossama Kullie University of Kassel Germany * -+ * Jon K. Laerdahl University of Oslo Norway * -+ * Christoffer V. Larsen University of Southern Denmark Denmark * -+ * Yoon Sup Lee KAIST, Daejeon South Korea * -+ * Huliyar S. Nataraj BME/Budapest Univ. Tech. & Econ. Hungary * -+ * Malaya Kumar Nayak Bhabha Atomic Research Centre India * -+ * Patrick Norman Stockholm Inst. of Technology Sweden * -+ * Malgorzata Olejniczak University of Warsaw Poland * -+ * Jeppe Olsen Aarhus University Denmark * -+ * Jogvan Magnus H. Olsen University of Southern Denmark Denmark * -+ * Young Choon Park KAIST, Daejeon South Korea * -+ * Jesper K. Pedersen University of Southern Denmark Denmark * -+ * Markus Pernpointner University of Heidelberg Germany * -+ * Roberto Di Remigio UiT The Arctic University of Norway * -+ * Kenneth Ruud UiT The Arctic University of Norway * -+ * Pawel Salek Stockholm Inst. of Technology Sweden * -+ * Bernd Schimmelpfennig Karlsruhe Institute of Technology Germany * -+ * Bruno Senjean University of Leiden Netherlands * -+ * Avijit Shee University of Michigan USA * -+ * Jetze Sikkema Vrije Universiteit Amsterdam Netherlands * -+ * Andreas J. Thorvaldsen UiT The Arctic University of Norway * -+ * Joern Thyssen University of Southern Denmark Denmark * -+ * Joost van Stralen Vrije Universiteit Amsterdam Netherlands * -+ * Marta L. Vidal Technical University of Denmark Denmark * -+ * Sebastien Villaume Linkoeping University Sweden * -+ * Olivier Visser University of Groningen Netherlands * -+ * Toke Winther University of Southern Denmark Denmark * -+ * Shigeyoshi Yamamoto Chukyo University Japan * -+ * * -+ * For more information about the DIRAC code see http://diracprogram.org * -+ * * -+ * This is an experimental code. The authors accept no responsibility * -+ * for the performance of the code or for the correctness of the results. * -+ * * -+ * The code (in whole or part) is not to be reproduced for further * -+ * distribution without the written permission of the authors or * -+ * their representatives. * -+ * * -+ * If results obtained with this code are published, an * -+ * appropriate citation would be: * -+ * * -+ * DIRAC, a relativistic ab initio electronic structure program, * -+ * Release DIRAC19 (2019), written by * -+ * A. S. P. Gomes, T. Saue, L. Visscher, H. J. Aa. Jensen, and R. Bast, * -+ * with contributions from I. A. Aucar, V. Bakken, K. G. Dyall, * -+ * S. Dubillard, U. Ekstroem, E. Eliav, T. Enevoldsen, E. Fasshauer, * -+ * T. Fleig, O. Fossgaard, L. Halbert, E. D. Hedegaard, T. Helgaker, * -+ * J. Henriksson, M. Ilias, Ch. R. Jacob, S. Knecht, S. Komorovsky, * -+ * O. Kullie, J. K. Laerdahl, C. V. Larsen, Y. S. Lee, H. S. Nataraj, * -+ * M. K. Nayak, P. Norman, M. Olejniczak, J. Olsen, J. M. H. Olsen, * -+ * Y. C. Park, J. K. Pedersen, M. Pernpointner, R. Di Remigio, K. Ruud, * -+ * P. Salek, B. Schimmelpfennig, B. Senjean, A. Shee, J. Sikkema, * -+ * A. J. Thorvaldsen, J. Thyssen, J. van Stralen, M. L. Vidal, S. Villaume, * -+ * O. Visser, T. Winther, and S. Yamamoto (see http://diracprogram.org). * -+ * * -+ ******************************************************************************* -+ -+ -+Version information -+------------------- -+ -+Branch | -+Commit hash | -+Commit author | -+Commit date | -+ -+ -+Configuration and build information -+----------------------------------- -+ -+Who compiled | vsc43020 -+Compiled on server | node3403.kirlia.os -+Operating system | Linux-3.10.0-1127.8.2.el7.ug.x86_64 -+CMake version | 3.16.4 -+CMake generator | Unix Makefiles -+CMake build type | release -+Configuration time | 2020-10-05 12:06:36.697767 -+Python version | 2.7.1 -+Fortran compiler | /apps/gent/CO7/cascadelake-ib/software/iccifort/2020.1.217/compilers_and_libraries_2020.1.217/linux/bin/intel64/ifort -+Fortran compiler version | 19.1 -+Fortran compiler flags | -w -assume byterecl -g -traceback -DVAR_IFORT -i8 -+C compiler | /apps/gent/CO7/cascadelake-ib/software/iccifort/2020.1.217/compilers_and_libraries_2020.1.217/linux/bin/intel64/icc -+C compiler version | 19.1 -+C compiler flags | -g -wd981 -wd279 -wd383 -wd1572 -wd177 -+C++ compiler | /apps/gent/CO7/cascadelake-ib/software/iccifort/2020.1.217/compilers_and_libraries_2020.1.217/linux/bin/intel64/icpc -+C++ compiler version | 19.1.1 -+C++ compiler flags | -Wno-unknown-pragmas -+Static linking | False -+64-bit integers | True -+MPI parallelization | False -+MPI launcher | unknown -+Math libraries | unknown -+Builtin BLAS library | OFF -+Builtin LAPACK library | OFF -+Explicit libraries | unknown -+Compile definitions | HAVE_MKL_BLAS;HAVE_MKL_LAPACK;SYS_LINUX;PRG_DIRAC;INT_STAR8;INSTALL_WRKMEM=64000000;HAS_PCMSOLVER;BUILD_GEN1INT;HAS_PELIB;MOD_QCORR;HAS_STIELTJES -+ -+ -+ LAPACK integer*4/8 selftest passed -+ Selftest of ISO_C_BINDING Fortran - C/C++ interoperability PASSED -+ -+Execution time and host -+----------------------- -+ -+ -+ Date and time (Linux) : Mon Oct 5 14:12:56 2020 -+ Host name : node3403.kirlia.os -+ -+ -+Contents of the input file -+-------------------------- -+ -+**DIRAC -+.TITLE -+ LiH -+.WAVE F ! Activate integral and wave functions modules -+**GENERAL -+**INTEGRALS -+.PRINT -+1 -+.NUCMOD ! 1-Point nucleus, 2-gaussian -+2 -+**HAMILTONIAN -+.SPINFREE -+.BSS -+109 -+.CMPEIG -+.PRINT -+2 -+**WAVE FUNCTIONS ! What method (DHF,MP2,CC..) -+.SCF -+.RELCCSD -+.LUCITA -+*SCF -+.CLOSED SHELL -+10 -+.INTFLG ! Specify what 2-el.integrals to include -+1 1 0 -+.EVCCNV ! Energy convergence... -+1.0E-10 1.0D-7 -+*LUCITA -+.INIWFC -+ DHFSCF -+.CITYPE -+ SDCI -+.MULTIP -+ 3 -+**MOLTRA -+# needed for parallel run -+.SCHEME -+4 -+.ACTIVE -+energy -1000 999999 0.1 -+**RELCCSD -+.NELEC -+ 4 4 -+.INTERFACE -+DIRAC -+.TIMING -+.PRINT -+ 1 -+*CCSORT -+.USEOE -+*END OF -+ -+ -+ -+Contents of the molecule file -+----------------------------- -+ -+INTGRL -+X -+X -+C 2 A -+ 80.0 1 -+X 0.0000000000 0.0000000000 2.000000000 -+LARGE 3 1 1 1 -+f 5 0 -+ 90000 -+ 50000 -+ 9000 -+ 4000 -+ 300 -+f 3 0 -+ 35000 -+ 7000 -+ 900 -+f 1 0 -+ 900 -+ 1. 1 -+H 0.00000000000 .0000000000 .0000000000 -+LARGE 1 1 -+f 2 0 -+ 1.00 -+ 0.25 -+FINISH -+ -+ -+ ************************************************************************* -+ ********************************* LiH ********************************* -+ ************************************************************************* - - Jobs in this run: - * Wave function - - -- ************************************************************************** -- ************************** General DIRAC set-up ************************** -- ************************************************************************** -- -+ ************************************************************************** -+ ************************** General DIRAC set-up ************************** -+ ************************************************************************** -+ -+ CODATA Recommended Values of the Fundamental Physical Constants: 1998 -+ Peter J. Mohr and Barry N. Taylor -+ Journal of Physical and Chemical Reference Data, Vol. 28, No. 6, 1999 - * The speed of light : 137.0359998 -+ * Running in two-component mode - * Direct evaluation of the following two-electron integrals: - - LL-integrals -- - SL-integrals -- - SS-integrals - * Spherical transformation embedded in MO-transformation - for large components - * Transformation to scalar RKB basis embedded in - MO-transformation for small components - * Thresholds for linear dependence: -- Large components: 1.00E-06 -- Small components: 1.00E-08 -+ Large components: 1.00D-06 -+ Small components: 1.00D-08 - * General print level : 0 - - -- ************************************************************************* -- ****************** Output from HERMIT input processing ****************** -- ************************************************************************* -+ ************************************************************************* -+ ****************** Output from HERMIT input processing ****************** -+ ************************************************************************* - - Default print level: 1 - Nuclear model: Gaussian charge distribution. -@@ -181,20 +348,9 @@ - - - -- Set-up from HR2INP: -- ------------------- -- -- Print level in TWOINT: 1 -- Extra output for the following shells: 0 0 0 0 -- * Direct calculation of Fock matrices in SO-basis. -- * Default screening threshold in direct Fock matrix construction: 1.00E-12 -- * Separate density screening of Coulomb integral batches -- * Separate density screening of exchange integral batches -- -- -- ************************************************************************* -- ****************** Output from READIN input processing ****************** -- ************************************************************************* -+ *************************************************************************** -+ ****************** Output from MOLECULE input processing ****************** -+ *************************************************************************** - - - -@@ -207,29 +363,20 @@ - Coordinates are entered in Angstroms and converted to atomic units. - - Conversion factor : 1 bohr = 0.52917721 A - -- Nuclear Gaussian exponent for atom of charge 80.000 : 1.4011788914E+08 -- -- Nuclear Gaussian exponent for atom of charge 1.000 : 2.1248239171E+09 -+ Nuclear Gaussian exponent for atom of charge 80.000 : 1.4011786759D+08 -+ Nuclear Gaussian exponent for atom of charge 1.000 : 2.1248235902D+09 - - -- SYMADD: Requested addition of symmetry -- -------------------------------------- -+ SYMADD: Detection of molecular symmetry -+ --------------------------------------- - -- Symmetry threshold: 0.50E-05 -+ Symmetry test threshold: 5.00E-06 - -- Original Coordinates -- -------------------- -- 80 0.00000000 0.00000000 3.77945227 1 -- 1 0.00000000 0.00000000 0.00000000 1 -+ The molecule has been centered at center of mass - -- Symmetry class found: C(oo,v) -+ Symmetry point group found: C(oo,v) - -- Centered and Rotated -- -------------------- -- 80 0.00000000 0.00000000 0.01876567 1 -- 1 0.00000000 0.00000000 -3.76068660 1 -- -- The following elements were found: X Y -+ The following symmetry elements were found: X Y - - - Symmetry Operations -@@ -239,8 +386,8 @@ - - - -- SYMGRP:Point group information -- ------------------------------ -+ SYMGRP:Point group information -+ ------------------------------ - - Full group is: C(oo,v) - Represented as: C2v -@@ -254,9 +401,9 @@ - - | E C2z Oxz Oyz - -----+-------------------- -- E | E -- C2z | C2z E -- Oxz | Oxz Oyz E -+ E | E C2z Oxz Oyz -+ C2z | C2z E Oyz Oxz -+ Oxz | Oxz Oyz E C2z - Oyz | Oyz Oxz C2z E - - * Character table -@@ -272,15 +419,15 @@ - - | A1 B1 B2 A2 - -----+-------------------- -- A1 | A1 -- B1 | B1 A1 -- B2 | B2 A2 A1 -+ A1 | A1 B1 B2 A2 -+ B1 | B1 A1 A2 B2 -+ B2 | B2 A2 A1 B1 - A2 | A2 B2 B1 A1 - - -- ************************** -- *** Output from DBLGRP *** -- ************************** -+ ************************** -+ *** Output from DBLGRP *** -+ ************************** - - * One fermion irrep: E1 - * Real group. NZ = 1 -@@ -288,8 +435,8 @@ - E1 x E1 : A1 + A2 + B1 + B2 - - -- Spinor structure -- ---------------- -+ Spinor structure -+ ---------------- - - - * Fermion irrep no.: 1 -@@ -299,8 +446,8 @@ - Sb | B2 (3) B1 (4) | - - -- Quaternion symmetries -- --------------------- -+ Quaternion symmetries -+ --------------------- - - Rep T(+) - ----------------------------- -@@ -309,27 +456,39 @@ - B2 k - A2 i - -+ QM-QM nuclear repulsion energy : 21.167088332000 -+ -+ -+ -+ Isotopic Masses -+ --------------- -+ -+ X 201.970617 -+ H 1.007825 -+ -+ Total mass: 202.978442 amu -+ Natural abundance: 29.856 % -+ -+ Center-of-mass coordinates (a.u.): 0.000000000000000 0.000000000000000 0.000000000000000 -+ - - Atoms and basis sets - -------------------- - -- Number of atom types: 2 -+ Number of atom types : 2 - Total number of atoms: 2 - - label atoms charge prim cont basis - ---------------------------------------------------------------------- -- X 1 80 20 20 L - [5s3p1d|5s3p1d] -- 49 49 S - [3s6p3d1f|3s6p3d1f] -- H 1 1 2 2 L - [2s|2s] -- 6 6 S - [2p|2p] -+ X 1 80 20 20 L - [5s3p1d|5s3p1d] -+ H 1 1 2 2 L - [2s|2s] - ---------------------------------------------------------------------- -- 22 22 L - large components -- 55 55 S - small components -+ 22 22 L - large components - ---------------------------------------------------------------------- -- total: 2 81 77 77 -+ total: 2 81 22 22 - - Cartesian basis used. -- Threshold for integrals: 1.00E-15 -+ Threshold for integrals (to be written to file): 1.00D-15 - - - References for the basis sets -@@ -339,8 +498,8 @@ - Basis set typed explicitly in input file - - -- Cartesian Coordinates -- --------------------- -+ Cartesian Coordinates (bohr) -+ ---------------------------- - - Total number of coordinates: 6 - -@@ -355,28 +514,37 @@ - - - -+ Cartesian coordinates in XYZ format (Angstrom) -+ ---------------------------------------------- -+ -+ 2 -+ -+X 0.0000000000 0.0000000000 0.0099303649 -+H 0.0000000000 0.0000000000 -1.9900696351 -+ -+ - Symmetry Coordinates - -------------------- - -- Number of coordinates in each symmetry: 2 2 2 0 -+ Number of coordinates in each symmetry: 2 2 2 0 - - -- Symmetry 1 -+ Symmetry A1 ( 1) - -- 1 X z 3 -- 2 H z 6 -+ 1 X z 3 -+ 2 H z 6 - - -- Symmetry 2 -+ Symmetry B1 ( 2) - -- 3 X x 1 -- 4 H x 4 -+ 3 X x 1 -+ 4 H x 4 - - -- Symmetry 3 -+ Symmetry B2 ( 3) - -- 5 X y 2 -- 6 H y 5 -+ 5 X y 2 -+ 6 H y 5 - - - Interatomic separations (in Angstroms): -@@ -398,41 +566,36 @@ - bond distance: H X 2.000000 - - -- Nuclear repulsion energy : 21.167088332000 -+ -+ Nuclear repulsion energy : 21.167088332000 Hartree - - -- GETLAB: AO-labels -- ----------------- -+ GETLAB: AO-labels -+ ----------------- - - * Large components: 11 -- 1 L X s 2 L X px 3 L X py 4 L X pz 5 L X dxx 6 L X dxy -- 7 L X dxz 8 L X dyy 9 L X dyz 10 L X dzz 11 L H s -- * Small components: 23 -- 12 S X s 13 S X px 14 S X py 15 S X pz 16 S X dxx 17 S X dxy -- 18 S X dxz 19 S X dyy 20 S X dyz 21 S X dzz 22 S X fxxx 23 S X fxxy -- 24 S X fxxz 25 S X fxyy 26 S X fxyz 27 S X fxzz 28 S X fyyy 29 S X fyyz -- 30 S X fyzz 31 S X fzzz 32 S H px 33 S H py 34 S H pz -+ 1 L X 1 s 2 L X 1 px 3 L X 1 py 4 L X 1 pz 5 L X 1 dxx 6 L X 1 dxy -+ 7 L X 1 dxz 8 L X 1 dyy 9 L X 1 dyz 10 L X 1 dzz 11 L H 1 s -+ * Small components: 0 - - -- GETLAB: SO-labels -- ----------------- -+ -+ GETLAB: SO-labels -+ ----------------- - - * Large components: 11 - 1 L A1 X s 2 L A1 X pz 3 L A1 X dxx 4 L A1 X dyy 5 L A1 X dzz 6 L A1 H s - 7 L B1 X px 8 L B1 X dxz 9 L B2 X py 10 L B2 X dyz 11 L A2 X dxy -- * Small components: 23 -- 12 S A1 X s 13 S A1 X pz 14 S A1 X dxx 15 S A1 X dyy 16 S A1 X dzz 17 S A1 X fxxz -- 18 S A1 X fyyz 19 S A1 X fzzz 20 S A1 H pz 21 S B1 X px 22 S B1 X dxz 23 S B1 X fxxx -- 24 S B1 X fxyy 25 S B1 X fxzz 26 S B1 H px 27 S B2 X py 28 S B2 X dyz 29 S B2 X fxxy -- 30 S B2 X fyyy 31 S B2 X fyzz 32 S B2 H py 33 S A2 X dxy 34 S A2 X fxyz -+ * Small components: 0 -+ - - - Symmetry Orbitals - ----------------- - -- Number of orbitals in each symmetry: 36 18 18 5 -+ Number of orbitals in each symmetry: 13 4 4 1 - Number of large orbitals in each symmetry: 13 4 4 1 -- Number of small orbitals in each symmetry: 23 14 14 4 -+ Number of small orbitals in each symmetry: 0 0 0 0 - - * Large component functions - -@@ -459,123 +622,90 @@ - - 1 functions: X dxy - --* Small component functions -- -- Symmetry A1 ( 1) -- -- 3 functions: X s -- 6 functions: X pz -- 3 functions: X dxx -- 3 functions: X dyy -- 3 functions: X dzz -- 1 functions: X fxxz -- 1 functions: X fyyz -- 1 functions: X fzzz -- 2 functions: H pz -- -- Symmetry B1 ( 2) -- -- 6 functions: X px -- 3 functions: X dxz -- 1 functions: X fxxx -- 1 functions: X fxyy -- 1 functions: X fxzz -- 2 functions: H px -- -- Symmetry B2 ( 3) -- -- 6 functions: X py -- 3 functions: X dyz -- 1 functions: X fxxy -- 1 functions: X fyyy -- 1 functions: X fyzz -- 2 functions: H py -- -- Symmetry A2 ( 4) - -- 3 functions: X dxy -- 1 functions: X fxyz -- -- -- *************************************************************************** -- *************************** Hamiltonian defined *************************** -- *************************************************************************** -- -- * Print level : 2 -- * Barysz-Sadlej-Snijders Hamiltonian. Type code -109 -+ *************************************************************************** -+ *************************** Hamiltonian defined *************************** -+ *************************************************************************** -+ -+ * Print level: 2 -+ * Barysz-Sadlej-Snijders Hamiltonian. Type code: 109 -+ Reference: -+ H. J. Aa. Jensen and M. Ilias, -+ "Two-component relativistic methods based on the quaternion modified Dirac equation. I: -+ from Douglas-Kroll-Hess second order method to the infinite order two-component method.", -+ J. Chem. Phys., in preparation. -+ * Running in two-component mode - with the following modifications: - - Spin-orbit interactions neglected - * Default integral flags passed to all modules -- - LL-integrals: T -- - LS-integrals: T -- - SS-integrals: T -- - GT-integrals: F -+ - LL-integrals: 1 -+ - LS-integrals: 0 -+ - SS-integrals: 0 -+ - GT-integrals: 0 -+ * Comparing eigenvalues between parent 4c and derived 2c one-electron Hamiltonians. - * Basis set: - - uncontracted large component basis set -- - uncontracted small component basis set -- -- -- Information about the restricted kinetic balance scheme: -- * Default RKB projection: -- 1: Pre-projection in scalar basis -- 2: Removal of unphysical solutions (via diagonalization of free particle Hamiltonian) -- -- -- ********************************************************************************* -- *************************** Memory required by HERMIT *************************** -- ********************************************************************************* -- --=========================================================================== -- Maximum memory load for two-electron integral processing: --=========================================================================== -- * LL-integrals: -- 2(X Lp) 2(X Lp) 2(X Lp) 2(X Lp) 19958 -- * SL-integrals: -- 8(X Sd) 6(X Sp) 2(X Lp) 2(X Lp) 74456 -- * SS-integrals: -- 8(X Sd) 6(X Sp) 8(X Sd) 6(X Sp) 274736 - - -- ************************************************************************** -- ************************** Wave function module ************************** -- ************************************************************************** -+ ************************************************************************** -+ ************************** Wave function module ************************** -+ ************************************************************************** -+ -+ Wave function types requested (in input order): -+ HF -+ RELCCSD -+ LUCITA - -- Jobs in this run (in execution order): -+ Wave function jobs in execution order (expanded): - * Hartree-Fock calculation - * Run RELCCSD code - * Run LUCITA CI code - =========================================================================== -- DHFINP: Set-up for Hartree-Fock calculation: -+ *SCF: Set-up for Hartree-Fock calculation: - =========================================================================== - * Number of fermion irreps: 1 -- * Closed shell DHF calculation with 10 electrons in -- 5 orbitals in Fermion irrep 1 -- * Bare nucleus screening correction used for start guess -- - INFO: bare nucleus correction disabled becauseabs(molecular charge) .gt. 2 -+ * Closed shell SCF calculation with 10 electrons in 5 orbitals. -+ - INFO: bare nucleus correction disabled because abs(molecular charge) .gt. 10 -+ * Sum of atomic potentials used for start guess - * General print level : 0 -- ***** TRIAL FUNCTION ***** -+ -+ ***** INITIAL TRIAL SCF FUNCTION ***** - * Trial vectors read from file DFCOEF -- ***** CONVERGENCE CRITERIA ***** -+ * Scaling of active-active block correction to open shell Fock operator 0.500000 -+ to improve convergence (default value). -+ The final open-shell orbital energies are recalculated with 1.0 scaling, -+ such that all occupied orbital energies correspond to Koopmans' theorem ionization energies. -+ -+ ***** SCF CONVERGENCE CRITERIA ***** - * Convergence on norm of error vector (gradient). -- Desired convergence:1.000E-10 -- Allowed convergence:1.000E-07 -+ Desired convergence:1.000D-10 -+ Allowed convergence:1.000D-07 - - ***** CONVERGENCE CONTROL ***** - * Fock matrix constructed using differential density matrix - with optimal parameter. - * DIIS (in MO basis) -- * DIIS will be activated when convergence reaches : 1.00E+20 -+ * DIIS will be activated when convergence reaches : 1.00D+20 - - Maximum size of B-matrix: 10 - * Damping of Fock matrix when DIIS is not activated. - Weight of old matrix : 0.250 - * Maximum number of SCF iterations : 50 -- * Quadratic convergent Hartree-Fock -- - Maximum number of macro iterations: 25 -- - Maximum number of micro iterations: 25 -+ * No quadratic convergent Hartree-Fock - * Contributions from 2-electron integrals to Fock matrix: - LL-integrals. -+ ---> accepted user's setting through .INTFLG -+ * NB!!! No e-p rotations in 2nd order optimization. - ***** OUTPUT CONTROL ***** - * Only electron eigenvalues written out. -+=========================================================================== -+ **RELCC: Set-up for Coupled Cluster calculations -+=========================================================================== -+=========================================================================== -+ TRPINP: Property integral transformation -+=========================================================================== -+ * Print level: 0 -+ *The following operators will be transformed: -+--------------------------------------------------------------------------- - - - -@@ -613,7 +743,6 @@ - No explicit orbitals specified for index 2 - No explicit orbitals specified for index 3 - No explicit orbitals specified for index 4 -- * Size of batches for strategy 4 (parallel only): -1 - - - ******************************************************************************** -@@ -622,407 +751,540 @@ - - - -- ************************************************************************* -- ************************ End of input processing ************************ -- ************************************************************************* -+ ************************************************************************* -+ ************************ End of input processing ************************ -+ ************************************************************************* -+ -+ -+ -+ *************************************************************************** -+ ****************** Output from MOLECULE input processing ****************** -+ *************************************************************************** -+ -+ -+ -+ Title Cards -+ ----------- -+ -+ X -+ X -+ -+ Coordinates are entered in Angstroms and converted to atomic units. -+ - Conversion factor : 1 bohr = 0.52917721 A -+ -+ Nuclear Gaussian exponent for atom of charge 80.000 : 1.4011786759D+08 -+ Nuclear Gaussian exponent for atom of charge 1.000 : 2.1248235902D+09 -+ -+ -+ SYMADD: Detection of molecular symmetry -+ --------------------------------------- -+ -+ Symmetry test threshold: 5.00E-06 -+ -+ The molecule has been centered at center of mass -+ -+ Symmetry point group found: C(oo,v) - -+ The following symmetry elements were found: X Y - - -- Generating Lowdin matrix: -- ------------------------- -+ Symmetry Operations -+ ------------------- - -- L A1 * Deleted: 1(Proj: 1, Lindep: 0) -- L B1 * Deleted: 0(Proj: 0, Lindep: 0) -- L B2 * Deleted: 0(Proj: 0, Lindep: 0) -- L A2 * Deleted: 0(Proj: 0, Lindep: 0) -- S A1 * Deleted: 4(Proj: 4, Lindep: 0) -- S B1 * Deleted: 1(Proj: 1, Lindep: 0) -- S B2 * Deleted: 1(Proj: 1, Lindep: 0) -- S A2 * Deleted: 0(Proj: 0, Lindep: 0) -+ Symmetry operations: 2 - - -- *** Output from MAKE_DKH *** -- ---------------------------- - --* MAKE_DKH: Applied the restricted kinetic balance ! -+ SYMGRP:Point group information -+ ------------------------------ - -- MAKE_DKH: All consistency checks are included for IPRHAM= 2 -+Full group is: C(oo,v) -+Represented as: C2v - -+ * The point group was generated by: - --MAKE_DKH: Order of Douglas-Kroll : 9 -+ Reflection in the yz-plane -+ Reflection in the xz-plane - --MAKE_DKH: spinfree "before" -- LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 1.3E+04 -- LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 8.4E+07 -- LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 8.4E+07 -- LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 1.2E+08 -+ * Group multiplication table - -- Free particle matrix in the ON basis "theta" in fermion corep 1/1 -- *** Norm of the i,j,k imag. parts *** :0.000000E+00 -+ | E C2z Oxz Oyz -+ -----+-------------------- -+ E | E C2z Oxz Oyz -+ C2z | C2z E Oyz Oxz -+ Oxz | Oxz Oyz E C2z -+ Oyz | Oyz Oxz C2z E - -+ * Character table - -- MAKE_DKH: Diagonalizing (Jacobi) the real part of the FP matrix in the ON "theta" basis ! -+ | E C2z Oxz Oyz -+ -----+-------------------- -+ A1 | 1 1 1 1 -+ B1 | 1 -1 1 -1 -+ B2 | 1 -1 -1 1 -+ A2 | 1 1 -1 -1 - -+ * Direct product table - -+ | A1 B1 B2 A2 -+ -----+-------------------- -+ A1 | A1 B1 B2 A2 -+ B1 | B1 A1 A2 B2 -+ B2 | B2 A2 A1 B1 -+ A2 | A2 B2 B1 A1 - -- MAKE_DKH: Free particle (in ON basis "theta") eigenvalues : -- ----------------------------------------------------------- - -- *** Fermion corep 1/ 1 --Shell no FP eigval FP eigval+2c^2 bos.symm. diff. -- 1 -21 -0.129732E+06 -0.110953E+06 1 -.4802E-09 -- 2 -20 -0.836934E+05 -0.649145E+05 1 -.2256E-09 -- 3 -19 -0.836934E+05 -0.649145E+05 3 -.1892E-09 -- 4 -18 -0.836934E+05 -0.649145E+05 2 -.1892E-09 -- 5 -17 -0.822138E+05 -0.634350E+05 1 -.9895E-09 -- 6 -16 -0.545585E+05 -0.357796E+05 1 0.8004E-10 -- 7 -15 -0.510946E+05 -0.323157E+05 1 -.1128E-09 -- 8 -14 -0.510946E+05 -0.323157E+05 2 -.1364E-09 -- 9 -13 -0.510946E+05 -0.323157E+05 3 -.1364E-09 -- 10 -12 -0.425134E+05 -0.237345E+05 1 -.5957E-09 -- 11 -11 -0.404803E+05 -0.217014E+05 1 -.1096E-09 -- 12 -10 -0.404803E+05 -0.217014E+05 4 -.1501E-10 -- 13 -9 -0.404803E+05 -0.217014E+05 2 -.1546E-10 -- 14 -8 -0.404803E+05 -0.217014E+05 3 -.8640E-11 -- 15 -7 -0.404803E+05 -0.217014E+05 1 -.8640E-11 -- 16 -6 -0.396666E+05 -0.208877E+05 1 -.1378E-09 -- 17 -5 -0.396666E+05 -0.208877E+05 2 -.2674E-09 -- 18 -4 -0.396666E+05 -0.208877E+05 3 -.2674E-09 -- 19 -3 -0.379967E+05 -0.192179E+05 1 -.7850E-09 -- 20 -2 -0.375600E+05 -0.187811E+05 1 -.1429E-08 -- 21 -1 -0.375581E+05 -0.187792E+05 1 -.8020E-09 -- 22 1 0.346467E+00 0.187792E+05 1 -.8020E-09 -- 23 2 0.223659E+01 0.187811E+05 1 -.1429E-08 -- 24 3 0.439003E+03 0.192179E+05 1 -.7850E-09 -- 25 4 0.210882E+04 0.208877E+05 3 -.2674E-09 -- 26 5 0.210882E+04 0.208877E+05 2 -.2674E-09 -- 27 6 0.210882E+04 0.208877E+05 1 -.1378E-09 -- 28 7 0.292258E+04 0.217014E+05 2 -.8640E-11 -- 29 8 0.292258E+04 0.217014E+05 4 -.8640E-11 -- 30 9 0.292258E+04 0.217014E+05 3 -.1546E-10 -- 31 10 0.292258E+04 0.217014E+05 1 -.1501E-10 -- 32 11 0.292258E+04 0.217014E+05 1 -.1096E-09 -- 33 12 0.495565E+04 0.237345E+05 1 -.5957E-09 -- 34 13 0.135369E+05 0.323157E+05 3 -.1364E-09 -- 35 14 0.135369E+05 0.323157E+05 2 -.1364E-09 -- 36 15 0.135369E+05 0.323157E+05 1 -.1128E-09 -- 37 16 0.170007E+05 0.357796E+05 1 0.8004E-10 -- 38 17 0.446561E+05 0.634350E+05 1 -.9895E-09 -- 39 18 0.461356E+05 0.649145E+05 3 -.1892E-09 -- 40 19 0.461356E+05 0.649145E+05 2 -.1892E-09 -- 41 20 0.461356E+05 0.649145E+05 1 -.2256E-09 -- 42 21 0.921740E+05 0.110953E+06 1 -.4802E-09 -+ ************************** -+ *** Output from DBLGRP *** -+ ************************** - -- MAKE_DKH: The average difference for e-p pairing of all --free particle eigenvalues in fermion symmetry 1/1 0.664817E-09 -+ * One fermion irrep: E1 -+ * Real group. NZ = 1 -+ * Direct product decomposition: -+ E1 x E1 : A1 + A2 + B1 + B2 - - -- MAKE_DKH: Full unit =C+.S.C matrix -- ----------------------------------------- -+ Spinor structure -+ ---------------- - --* Fermion irp no.1/1 - -- Sum of diagonal elements /N: 0.10000E+01 -- Sum of off-diagonal elements : 0.36613E-13 -+ * Fermion irrep no.: 1 -+ La | A1 (1) A2 (2) | -+ Sa | A2 (1) A1 (2) | -+ Lb | B1 (3) B2 (4) | -+ Sb | B2 (3) B1 (4) | - - -- MAKE_DKH: Diagonal =A+.A matrix -- ---------------------------------------- -+ Quaternion symmetries -+ --------------------- - --* Fermion irp no.1/1 -+ Rep T(+) -+ ----------------------------- -+ A1 1 -+ B1 j -+ B2 k -+ A2 i - -- Sum of diagonal elements /N : 0.84270E+00 -- Sum of off-diagonal elements : 0.12334E-14 -+ QM-QM nuclear repulsion energy : 21.167088332000 - -- MAKE_DKH: "A" kinem. electr. factors; ferm irp:1/1 - -- A^2_ovlp A^2_calc diff; - -- 0.9999907753 0.9999907753 0.52180E-14 -- 0.9999404563 0.9999404563 0.99920E-14 -- 0.9885782673 0.9885782673 0.21094E-14 -- 0.9495199724 0.9495199724 0.75495E-14 -- 0.9495199724 0.9495199724 0.75495E-14 -- 0.9495199724 0.9495199724 0.85487E-14 -- 0.9326639752 0.9326639752 0.00000E+00 -- 0.9326639752 0.9326639752 0.00000E+00 -- 0.9326639752 0.9326639752 0.00000E+00 -- 0.9326639752 0.9326639752 -.11102E-15 -- 0.9326639752 0.9326639752 0.33307E-15 -- 0.8956024566 0.8956024566 0.88818E-15 -- 0.7905530164 0.7905530164 0.23315E-14 -- 0.7905530164 0.7905530164 0.23315E-14 -- 0.7905530164 0.7905530164 0.72164E-14 -- 0.7624242951 0.7624242951 0.17986E-13 -- 0.6480166494 0.6480166494 0.00000E+00 -- 0.6446430762 0.6446430762 -.88818E-15 -- 0.6446430762 0.6446430762 -.88818E-15 -- 0.6446430762 0.6446430762 0.39968E-14 -- 0.5846254366 0.5846254366 0.72164E-14 -+ Isotopic Masses -+ --------------- - -- DIFFERENCES A^2_ovlp-A^2_calc/N :0.405496E-14 -+ X 201.970617 -+ H 1.007825 - -- MAKE_DKH: Elim. spin-orbit comp. "BEFORE" from full H1 in TBUF -+ Total mass: 202.978442 amu -+ Natural abundance: 29.856 % - -+ Center-of-mass coordinates (a.u.): 0.000000000000000 0.000000000000000 0.000000000000000 - - -- CHECK_R: A * R - B zero matrix -- ------------------------------ -+ Atoms and basis sets -+ -------------------- - -- * Fermion irp 1/1 -- CHECK_R: Norm of A.R - B:.115394974462E-16 -+ Number of atom types : 2 -+ Total number of atoms: 2 - -+ label atoms charge prim cont basis -+ ---------------------------------------------------------------------- -+ X 1 80 20 20 L - [5s3p1d|5s3p1d] -+ H 1 1 2 2 L - [2s|2s] -+ ---------------------------------------------------------------------- -+ 22 22 L - large components -+ 55 55 S - small components -+ ---------------------------------------------------------------------- -+ total: 2 81 77 77 - -- CHECK_R: Final H(pp)*R+H(ep)-R*H(ee)-R*H(pe)*R -- ---------------------------------------------- -+ Cartesian basis used. -+ Threshold for integrals (to be written to file): 1.00D-15 - -- Fermion corep 1/1 * norm: .149366743390E-09 - -+ References for the basis sets -+ ----------------------------- - -- U1CHECK: Unit U1+ * U1 matrix -- ----------------------------- -+ Atom type 1 2 -+ Basis set typed explicitly in input file - -- * fermion irp 1/1 - -- Sum of diagonal elements /N: 0.10000E+01 -- Sum of off-diagonal elements :-0.29210E-14 -+ Cartesian Coordinates (bohr) -+ ---------------------------- - -+ Total number of coordinates: 6 - -- U1CHECK: Again unit U1+ * U1 matrix -- ----------------------------------- - -- * fermion irp 1/1 -+ 1 X x 0.0000000000 -+ 2 y 0.0000000000 -+ 3 z 0.0187656701 - -- Sum of diagonal elements /N: 0.10000E+01 -- Sum of off-diagonal elements :-0.29213E-14 -+ 4 H x 0.0000000000 -+ 5 y 0.0000000000 -+ 6 z -3.7606865977 - -- U1CHECK: Elim. spin-orbit comp. "BEFORE" from H1(ee) in |k> - - -+ Cartesian coordinates in XYZ format (Angstrom) -+ ---------------------------------------------- - -- U1CHECK: 2 times constructed H2c in ON |k_e> basis -- -------------------------------------------------- -+ 2 -+ -+X 0.0000000000 0.0000000000 0.0099303649 -+H 0.0000000000 0.0000000000 -1.9900696351 - -- Difference between 2 H2c in |k_e> basis: 0.556080026E-10 - -+ Symmetry Coordinates -+ -------------------- - -- MAKE_DKH: *** 4c/2c electronic eigenvalues in |k> basis *** -- ----------------------------------------------------------- -+ Number of coordinates in each symmetry: 2 2 2 0 - -- *** Fermion corep 1 - -- 4c |k> 2c |k> diff 4c-2c -+ Symmetry A1 ( 1) - -- 1 -3236.0719838003 -3236.0719838004 0.10004E-10 -- 2 -666.1102369681 -666.1102369681 -0.70486E-11 -- 3 -484.6930272186 -484.6930272186 -0.81855E-11 -- 4 -484.6930119987 -484.6930119987 -0.88107E-11 -- 5 -484.6930119987 -484.6930119987 0.42064E-11 -- 6 -21.6367704194 -21.6367704194 -0.17444E-11 -- 7 -20.3646920050 -20.3646920050 0.32827E-11 -- 8 860.2027281682 860.2027281682 0.21600E-11 -- 9 860.2027332163 860.2027332163 -0.92086E-11 -- 10 860.2027332163 860.2027332163 -0.69349E-11 -- 11 860.2027483566 860.2027483566 -0.11482E-10 -- 12 860.2027483566 860.2027483566 -0.17394E-10 -- 13 6589.3364114013 6589.3364114013 0.20009E-10 -- 14 6589.3364145579 6589.3364145579 0.81855E-11 -- 15 6589.3364145580 6589.3364145580 0.18190E-11 -- 16 6779.9912032733 6779.9912032733 -0.27285E-11 -- 17 26566.1471385053 26566.1471385053 0.21828E-10 -- 18 29535.0133983962 29535.0133983963 -0.43656E-10 -- 19 29535.0133990459 29535.0133990459 0.54570E-10 -- 20 29535.0133990460 29535.0133990459 0.50932E-10 -- 21 59748.6160858676 59748.6160858674 0.17462E-09 -+ 1 X z 3 -+ 2 H z 6 - - -- LOWDHAO: Full(L+S) unit C+ * S * C matrix -- ----------------------------------------- -+ Symmetry B1 ( 2) - -- * fermion corep 1/1 -+ 3 X x 1 -+ 4 H x 4 - -- Sum of diagonal elements /N: 0.10000E+01 -- Sum of off-diagonal elements : 0.57558E-13 - -+ Symmetry B2 ( 3) - -- LOWDHAO: (LL) unit C+ * S * C matrix -- ------------------------------------ -+ 5 X y 2 -+ 6 H y 5 - -- *** Fermion corep 1/1 - -- Sum of diagonal elements /N: 0.10000E+01 -- Sum of off-diagonal elements : 0.21513E-13 -+ Interatomic separations (in Angstroms): -+ --------------------------------------- - -- LOWDHAO: Transforming H2c from AO "xhi" to ON Lowdin_L basis -+ X H - -- LOWDHAO: Difference between various constructed H2c in AO basis: 0.33913E+04 -+ X 0.000000 -+ H 2.000000 0.000000 - - -- Difference between various constructed H2c in Lowdin basis: 0.52900E+04 - - -+ Bond distances (angstroms): -+ --------------------------- - -- LOWDHAO: Electr. eigenv. of H(2c)/H(4c) in "theta" basis -- -------------------------------------------------------- -+ atom 1 atom 2 distance -+ ------ ------ -------- -+ bond distance: H X 2.000000 - -- *** Fermion corep 1 - -- -21 -163745.9628988874 -- -20 -109766.4091627979 -- -19 -98263.9166309379 -- -18 -97660.2507125821 -- -17 -97660.2507121498 -- -16 -62699.0373156405 -- -15 -61337.8251471301 -- -14 -56735.8818256817 -- -13 -56735.8818235711 -- -12 -46739.5121078201 -- -11 -43934.8520198212 -- -10 -43613.6808107422 -- -9 -43613.6808034596 -- -8 -42251.1320214283 -- -7 -42251.1320136060 -- -6 -42251.1319979688 -- -5 -41671.9396359513 -- -4 -41671.9396210424 -- -3 -39401.3294452374 -- -2 -37582.2335071497 -- -1 -37579.6683961926 -- 1 -3236.0719838003 -3236.0719838003 0.40927E-11 -- 2 -666.1102369744 -666.1102369681 0.63131E-08 -- 3 -621.6459032252 -484.6930272186 0.13695E+03 -- 4 -417.4757122056 -484.6930119987 -0.67217E+02 -- 5 -417.4757012483 -484.6930119987 -0.67217E+02 -- 6 -21.6367704054 -21.6367704193 -0.13957E-07 -- 7 -20.3646919717 -20.3646920050 -0.33277E-07 -- 8 803.0610555687 860.2027281682 0.57142E+02 -- 9 803.0610694840 860.2027332163 0.57142E+02 -- 10 899.5011687780 860.2027332163 -0.39298E+02 -- 11 899.5011750728 860.2027483566 -0.39298E+02 -- 12 899.5011876600 860.2027483566 -0.39298E+02 -- 13 5622.9859361077 6589.3364114013 0.96635E+03 -- 14 6779.9912032728 6589.3364145579 -0.19065E+03 -- 15 7094.0397325779 6589.3364145579 -0.50470E+03 -- 16 7094.0397349051 6779.9912032733 -0.31405E+03 -- 17 26043.2377394187 26566.1471385053 0.52291E+03 -- 18 26566.1471385052 29535.0133983962 0.29689E+04 -- 19 31514.7993417130 29535.0133990459 -0.19798E+04 -- 20 31514.7993422125 29535.0133990459 -0.19798E+04 -- 21 59748.6160858669 59748.6160858677 0.76398E-09 - -- MAKE_DKH:Two-component BSS mode - positronic shells deleted ! -+ Nuclear repulsion energy : 21.167088332000 Hartree - - -- GMOTRA: BSS relativistic atomic integrals and picture change -- transformation matrix were written to the new file BSSMAT. -+ Nuclear contribution to dipole moments -+ -------------------------------------- - -+ au Debye - -- ********************************************************************** -- ************************* Orbital dimensions ************************* -- ********************************************************************** -+ z -2.25943299 -5.74295899 - --No. of electronic orbitals (NESH): 21 --No. of positronic orbitals (NPSH): 0 --Total no. of orbitals (NORB): 21 -+ 1 Debye = 2.54177000 a.u. - -+Total time used in ONEGEN (CPU) 0.00263200s and (WALL) 0.00324607s - -- WARNING : linear symmetry is not implemented for spinfree or Levy-Leblond yet -- continue calculation in lower symmetry - -+ Generating Lowdin canonical matrix: -+ ----------------------------------- - -- ********************************************************************************************** -- ************************* Two-component relativistic HF calculations ************************* -- ********************************************************************************************** -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 2.6D-02 -+ L A1 * Deleted: 1(Proj: 1, Lindep: 0) Smin: 0.26E-01 -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.5D-01 -+ L B1 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.45E+00 -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.5D-01 -+ L B2 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.45E+00 -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 1.0D+00 -+ L A2 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.10E+01 -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.0D-02 -+ S A1 * Deleted: 4(Proj: 4, Lindep: 0) Smin: 0.40E-01 -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.0D-02 -+ S B1 * Deleted: 1(Proj: 1, Lindep: 0) Smin: 0.40E-01 -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.0D-02 -+ S B2 * Deleted: 1(Proj: 1, Lindep: 0) Smin: 0.40E-01 -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 6.0D-01 -+ S A2 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.60E+00 - - -- ONEFCK: BSS transformed one-electron relativistic integrals were read from the file BSSMAT. -+ *** Output from MAKE_BSS *** -+ ---------------------------- - --*** INFO *** No trial vectors found. Using bare nucleus approximation for initial trial vectors. - --########## START ITERATION NO. 1 ########## Sun Dec 5 16:41:19 2004 - --It. 1 -10691.35545564 1.00E+20 0.00E+00 0.00E+00 0.00199999s Bare nuc. Sun Dec 5 -+ *** Output from the EXTR_BSS_INFO routine *** -+ --------------------------------------------- - --########## START ITERATION NO. 2########## Sun Dec 5 16:41:19 2004 -+ * Transforming the one-electron DIRAC bare nucleus operator. -+ * Order of the Douglas-Kroll-Hess/BSS transformation :...infinite ! -+ * Applied the preliminary free-particle ("k") basis transformation (two-step method). -+ * R-equation solving applied : YR-equation 2 (Trond) -+ * Elimination of spin-orbit terms from the Dirac bare nuclei in RKB/"k" basis (spinfree "BEFORE / AT THE BEGINNING") -+ * AMFI contribution is NOT included. -+ * Prepare the picture-change transformation matrixes -+ - special case - spin-free -+ * I2COFK parameter for H2c specification set to:1 - -+ MAKE_BSS: 4c Lowdin AO to MO transf. matrix is written to the BSSMAT file. - --* GETGAB: label "GABAOXXX" not found; calling GABGEN. -+ -+ Output from MODHAM -+ ------------------ -+ -+ * Applied strict kinetic balance ! -+ -+ HANDLE_RKB: RKB transf. matrix (TMAT, basic) has been written to the BSSMAT file. -+ -+ HANDLE_RKB: BSSMAT file - EOFLABEL added. -+ -+ GET_A_FAC: Average differences for A-factors (fsym 1/1) : 0.45836351D-14 -+ -+ R matrix (in ON basis) was read from BSSMAT into VMAT. -+ -+ H2CFINAL: H1AO_DK -+ -+ AO_LL elements were written into the BSSMAT file, EOFLABEL renewed. -+ -+ GETPCTMAT: U1_ONBAS (4c ON->2c ON) read into TBUF. -+ -+ -+ Output from LINSYM -+ ------------------ -+ -+ -+ Parity MJ Functions(total) Functions(LC) Functions(SC) -+ 1 2/2 8 8 0 -+ 1 4/2 2 2 0 -+ -+ -+ CMP_EIGVAL: Eigenvalues of H4c and H2c Hamiltonians - comparison -+ ----------------------------------------------------------------- -+ -+ *** Fermion corep 1/1 -+ -+ -21 -163745.9628958011 -+ -20 -101498.5164538892 -+ -19 -101498.5164532745 -+ -18 -101498.5164532736 -+ -17 -98263.9166308309 -+ -16 -62699.0373156246 -+ -15 -58261.8837181770 -+ -14 -58261.8837150353 -+ -13 -58261.8837150346 -+ -12 -46739.5121078193 -+ -11 -42795.4291439501 -+ -10 -42795.4291401592 -+ -9 -42795.4291401592 -+ -8 -42795.4291288378 -+ -7 -42795.4291288378 -+ -6 -42461.8986879892 -+ -5 -42461.8986541794 -+ -4 -42461.8986541793 -+ -3 -39401.3294452367 -+ -2 -37582.2335096555 -+ -1 -37579.6684238590 -+ 1 -3236.0719837237 -3233.2186407425 -0.28533D+01 -+ 2 -666.1102369328 -664.5651063909 -0.15451D+01 -+ 3 -484.6930272181 -484.6930272173 -0.77148D-09 -+ 4 -484.6930119982 -21.6367703419 -0.46306D+03 -+ 5 -484.6930119982 -20.3646916349 -0.46433D+03 -+ 6 -21.6367704194 0.0000000000 -0.21637D+02 -+ 7 -20.3646920050 0.0000000000 -0.20365D+02 -+ 8 860.2027281682 0.0000000000 0.86020D+03 -+ 9 860.2027332163 0.0000000000 0.86020D+03 -+ 10 860.2027332164 0.0000000000 0.86020D+03 -+ 11 860.2027483566 0.0000000000 0.86020D+03 -+ 12 860.2027483566 0.0000000000 0.86020D+03 -+ 13 6589.3364114109 0.0000000000 0.65893D+04 -+ 14 6589.3364145675 0.0000000000 0.65893D+04 -+ 15 6589.3364145676 0.0000000000 0.65893D+04 -+ 16 6779.9912035175 0.0000000000 0.67800D+04 -+ 17 26566.1471391791 6286.2328868840 0.20280D+05 -+ 18 29535.0133986390 6589.3364114112 0.22946D+05 -+ 19 29535.0133992886 21540.9186642361 0.79941D+04 -+ 20 29535.0133992886 29535.0133986389 0.64972D-06 -+ 21 59748.6160887879 40911.9536790837 0.18837D+05 -+ -+ -+ PROP2BSS: 2comp. operator (indxpr= 1) P2C_0001->Overlap matrix was written to the BSSMAT file in LL block. -+ ...operator was NOT picture change transformed -+ -+ PROP2BSS: 2comp. operator (indxpr= 2) P2C_0002->Nuc. attraction was written to the BSSMAT file in LL block. -+ ...operator was NOT picture change transformed -+ -+ PROP2BSS: 2comp. operator (indxpr= 3) P2C_0003->Beta matrix was written to the BSSMAT file in LL block. -+ ...operator was NOT picture change transformed -+ -+ PROP2BSS: 2comp. operator (indxpr= 4) P2C_0004->Kinetic energy was written to the BSSMAT file in LL block. -+ ...operator was NOT picture change transformed -+ -+ PROP2BSS: 2comp. operator (indxpr= 5) P2C_0005->Orbital z-moment was written to the BSSMAT file in LL block. -+ ...operator was NOT picture change transformed -+ -+ PROP2BSS: 2comp. operator (indxpr= 6) P2C_0006->Spin z-momentum was written to the BSSMAT file in LL block. -+ ...operator was picture change transformed -+ -+ PROP2BSS: EOFLABEL was renewed after saving all 2c operators into BSSMAT. -+ -+ MAKE_H2C: Two-component BSS mode - positronic shells deleted ! -+ -+ Coordinates are entered in Angstroms and converted to atomic units. -+ - Conversion factor : 1 bohr = 0.52917721 A -+ -+ Nuclear Gaussian exponent for atom of charge 80.000 : 1.4011786759D+08 -+ Nuclear Gaussian exponent for atom of charge 1.000 : 2.1248235902D+09 -+ -+ -+ SYMADD: Detection of molecular symmetry -+ --------------------------------------- -+ -+ Symmetry test threshold: 5.00E-06 -+ -+ The molecule has been centered at center of mass -+ -+ Symmetry point group found: C(oo,v) -+ -+ The following symmetry elements were found: X Y -+ -+ -+ Nuclear contribution to dipole moments -+ -------------------------------------- -+ -+ au Debye -+ -+ z -2.25943299 -5.74295899 -+ -+ 1 Debye = 2.54177000 a.u. -+ -+Total time used in ONEGEN (CPU) 0.00082800s and (WALL) 0.00096107s -+ -+ -+ Generating Lowdin canonical matrix: -+ ----------------------------------- -+ -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 2.6D-02 -+ L A1 * Deleted: 1(Proj: 1, Lindep: 0) Smin: 0.26E-01 -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.5D-01 -+ L B1 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.45E+00 -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.5D-01 -+ L B2 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.45E+00 -+ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 1.0D+00 -+ L A2 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.10E+01 -+ -+ -+ ********************************************************************** -+ ************************* Orbital dimensions ************************* -+ ********************************************************************** -+ -+No. of positive energy orbitals (NESH): 21 -+No. of negative energy orbitals (NPSH): 0 -+Total no. of orbitals (NORB): 21 -+ -+ -+ ******************************************************************************* -+ ************** Two-component BSS/DKH relativistic HF calculation ************** -+ ******************************************************************************* -+ -+ -+ GETH2CAO: asked for 2c Hamiltonian (param.I2COFK=7):H2CAO_LL -+ -+*** INFO *** No trial vectors found. -+ Using bare nucleus approximation for initial trial vectors. -+ Improved by a sum of atomic screening potentials. -+ -+ -+########## START ITERATION NO. 1 ########## Mon Oct 5 14:12:56 2020 -+ -+E_HOMO...E_LUMO, symmetry 1: 5 -58.86032 6 -0.38910 -+ -+=> Calculating sum of orbital energies -+It. 1 -6346.607026159 0.00D+00 0.00D+00 0.00D+00 0.00847100s Atom. scrpot Mon Oct 5 -+ -+########## START ITERATION NO. 2 ########## Mon Oct 5 14:12:56 2020 -+ -+ -+* GETGAB: label "GABAO1XX" not found; calling GABGEN. - SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00E-12 1.01% 8.21% 0.00% 0.00% 0.01499800s -->>> Total wall time: 0.00000000s -->>> Total CPU-time : 0.08498700s -+SOfock:LL 1.00D-12 0.00% 7.73% 0.09% 0.00% 0.00275700s -+E_HOMO...E_LUMO, symmetry 1: 5-257.42872 6 -18.99113 -+>>> Total wall time: 0.01686811s, and total CPU time : 0.00808700s - --########## END ITERATION NO. 2 ########## Sun Dec 5 16:41:19 2004 -+########## END ITERATION NO. 2 ########## Mon Oct 5 14:12:56 2020 - --It. 2 -9503.967468302 -1.19E+03 4.19E+02 1.65E+02 0.08498700s LL Sun Dec 5 -+It. 2 -9505.548827855 3.16D+03 -1.88D+02 5.90D+01 0.01686811s LL Mon Oct 5 - --########## START ITERATION NO. 3########## Sun Dec 5 16:41:19 2004 -+########## START ITERATION NO. 3 ########## Mon Oct 5 14:12:56 2020 - -- 3 *** Differential density matrix. DCOVLP = 1.0071 -+ 3 *** Differential density matrix. DCOVLP = 1.0024 - SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00E-12 1.01% 10.87% 1.38% 1.15% 0.01499799s -->>> Total wall time: 0.00000000s -->>> Total CPU-time : 0.02499600s -+SOfock:LL 1.00D-12 0.00% 11.69% 0.09% 0.00% 0.00269200s -+E_HOMO...E_LUMO, symmetry 1: 5-257.50512 6 -18.99113 -+>>> Total wall time: 0.01377892s, and total CPU time : 0.00509000s - --########## END ITERATION NO. 3 ########## Sun Dec 5 16:41:19 2004 -+########## END ITERATION NO. 3 ########## Mon Oct 5 14:12:56 2020 - --It. 3 -9505.779736187 1.81E+00 -1.49E+00 4.38E-01 DIIS 2 0.02499600s LL Sun Dec 5 -+It. 3 -9505.779745785 2.31D-01 -5.25D-01 1.59D-01 DIIS 2 0.01377892s LL Mon Oct 5 - --########## START ITERATION NO. 4########## Sun Dec 5 16:41:19 2004 -+########## START ITERATION NO. 4 ########## Mon Oct 5 14:12:56 2020 - - 4 *** Differential density matrix. DCOVLP = 1.0000 - SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00E-12 3.14% 24.01% 1.42% 1.34% 0.01399803s -->>> Total wall time: 0.00000000s -->>> Total CPU-time : 0.02399498s -+SOfock:LL 1.00D-12 2.01% 24.66% 1.59% 1.43% 0.00261200s -+E_HOMO...E_LUMO, symmetry 1: 5-257.50512 6 -18.99113 -+>>> Total wall time: 0.01277494s, and total CPU time : 0.00500000s - --########## END ITERATION NO. 4 ########## Sun Dec 5 16:41:19 2004 -+########## END ITERATION NO. 4 ########## Mon Oct 5 14:12:56 2020 - --It. 4 -9505.779747494 1.13E-05 4.13E-03 9.22E-04 DIIS 3 0.02399498s LL Sun Dec 5 -+It. 4 -9505.779747270 1.49D-06 1.48D-03 4.27D-04 DIIS 3 0.01277494s LL Mon Oct 5 - --########## START ITERATION NO. 5########## Sun Dec 5 16:41:19 2004 -+########## START ITERATION NO. 5 ########## Mon Oct 5 14:12:56 2020 - - 5 *** Differential density matrix. DCOVLP = 1.0000 - SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00E-12 8.83% 29.82% 3.56% 4.47% 0.01399800s -->>> Total wall time: 0.00000000s -->>> Total CPU-time : 0.02299702s -+SOfock:LL 1.00D-12 4.75% 35.03% 1.15% 0.89% 0.00241700s -+E_HOMO...E_LUMO, symmetry 1: 5-257.50512 6 -18.99113 -+>>> Total wall time: 0.01234078s, and total CPU time : 0.00468400s - --########## END ITERATION NO. 5 ########## Sun Dec 5 16:41:19 2004 -+########## END ITERATION NO. 5 ########## Mon Oct 5 14:12:56 2020 - --It. 5 -9505.779747494 4.73E-11 1.80E-06 1.25E-06 DIIS 4 0.02299702s LL Sun Dec 5 -+It. 5 -9505.779747270 7.28D-12 8.55D-07 3.32D-07 DIIS 4 0.01234078s LL Mon Oct 5 - --########## START ITERATION NO. 6########## Sun Dec 5 16:41:19 2004 -+########## START ITERATION NO. 6 ########## Mon Oct 5 14:12:56 2020 - - 6 *** Differential density matrix. DCOVLP = 1.0000 - SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00E-12 25.91% 22.46% 9.41% 19.31% 0.01099795s -->>> Total wall time: 0.00000000s -->>> Total CPU-time : 0.02099702s -+SOfock:LL 1.00D-12 27.41% 20.03% 1.83% 4.79% 0.00145400s -+E_HOMO...E_LUMO, symmetry 1: 5-257.50512 6 -18.99113 -+>>> Total wall time: 0.01191306s, and total CPU time : 0.00425000s - --########## END ITERATION NO. 6 ########## Sun Dec 5 16:41:19 2004 -+########## END ITERATION NO. 6 ########## Mon Oct 5 14:12:56 2020 - --It. 6 -9505.779747494 5.46E-12 2.47E-09 1.12E-09 DIIS 5 0.02099702s LL Sun Dec 5 -+It. 6 -9505.779747270 7.28D-12 6.40D-10 3.18D-10 DIIS 4 0.01191306s LL Mon Oct 5 - --########## START ITERATION NO. 7########## Sun Dec 5 16:41:19 2004 -+########## START ITERATION NO. 7 ########## Mon Oct 5 14:12:56 2020 - - 7 *** Differential density matrix. DCOVLP = 1.0000 - SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00E-12 39.05% 47.81% 1.35% 18.30% 0.00899899s -->>> Total wall time: 0.00000000s -->>> Total CPU-time : 0.01799697s -+SOfock:LL 1.00D-12 52.76% 41.39% 0.69% 16.32% 0.00108500s -+>>> Total wall time: 0.01100397s, and total CPU time : 0.00366200s - --########## END ITERATION NO. 7 ########## Sun Dec 5 16:41:19 2004 -+########## END ITERATION NO. 7 ########## Mon Oct 5 14:12:56 2020 - --It. 7 -9505.779747494 -1.46E-11 -2.91E-11 3.65E-11 DIIS 5 0.01799697s LL Sun Dec 5 -+It. 7 -9505.779747270 1.09D-11 8.73D-11 3.52D-11 DIIS 4 0.01100397s LL Mon Oct 5 - - -- SCF - CYCLE -- ----------- -+ SCF - CYCLE -+ ----------- - - * Convergence on norm of error vector (gradient). -- Desired convergence:1.000E-10 -- Allowed convergence:1.000E-07 -+ Desired convergence:1.000D-10 -+ Allowed convergence:1.000D-07 - - * ERGVAL - convergence in total energy - * FCKVAL - convergence in maximum change in total Fock matrix -@@ -1030,84 +1292,84 @@ - -------------------------------------------------------------------------------------------------------------------------------- - Energy ERGVAL FCKVAL EVCVAL Conv.acc CPU Integrals Time stamp - -------------------------------------------------------------------------------------------------------------------------------- --It. 1 -10691.35545564 1.00E+20 0.00E+00 0.00E+00 0.00199999s Bare nuc. Sun Dec 5 --It. 2 -9503.967468302 -1.19E+03 4.19E+02 1.65E+02 0.08498700s LL Sun Dec 5 --It. 3 -9505.779736187 1.81E+00 -1.49E+00 4.38E-01 DIIS 2 0.02499600s LL Sun Dec 5 --It. 4 -9505.779747494 1.13E-05 4.13E-03 9.22E-04 DIIS 3 0.02399498s LL Sun Dec 5 --It. 5 -9505.779747494 4.73E-11 1.80E-06 1.25E-06 DIIS 4 0.02299702s LL Sun Dec 5 --It. 6 -9505.779747494 5.46E-12 2.47E-09 1.12E-09 DIIS 5 0.02099702s LL Sun Dec 5 --It. 7 -9505.779747494 -1.46E-11 -2.91E-11 3.65E-11 DIIS 5 0.01799697s LL Sun Dec 5 -+It. 1 -6346.607026159 0.00D+00 0.00D+00 0.00D+00 0.00847100s Atom. scrpot Mon Oct 5 -+It. 2 -9505.548827855 3.16D+03 -1.88D+02 5.90D+01 0.01686811s LL Mon Oct 5 -+It. 3 -9505.779745785 2.31D-01 -5.25D-01 1.59D-01 DIIS 2 0.01377892s LL Mon Oct 5 -+It. 4 -9505.779747270 1.49D-06 1.48D-03 4.27D-04 DIIS 3 0.01277494s LL Mon Oct 5 -+It. 5 -9505.779747270 7.28D-12 8.55D-07 3.32D-07 DIIS 4 0.01234078s LL Mon Oct 5 -+It. 6 -9505.779747270 7.28D-12 6.40D-10 3.18D-10 DIIS 4 0.01191306s LL Mon Oct 5 -+It. 7 -9505.779747270 1.09D-11 8.73D-11 3.52D-11 DIIS 4 0.01100397s LL Mon Oct 5 - -------------------------------------------------------------------------------------------------------------------------------- - * Convergence after 7 iterations. - * Average elapsed time per iteration: -- No 2-ints : 0.00000000s -- LL : 0.00000000s -+ No 2-ints : 0.00896692s -+ LL : 0.01311330s - - -- TOTAL ENERGY -- ------------ -+ TOTAL ENERGY -+ ------------ - -- Electronic energy : -9526.9468358256636 -+ Electronic energy : -9526.9468356019206 - - Other contributions to the total energy - Nuclear repulsion energy : 21.1670883320000 - - Sum of all contributions to the energy -- Total energy : -9505.7797474936633 -+ Total energy : -9505.7797472699203 - - -- Eigenvalues -- ----------- -+ Eigenvalues -+ ----------- - - - * Boson symmetry A1 - * Closed shell, f = 1.0000 -- -2941.25123226809 ( 2) -457.80721004705 ( 2) -257.50514000264 ( 2) -+ -2941.25123219522 ( 2) -457.80721001068 ( 2) -257.50514000229 ( 2) - * Virtual eigenvalues, f = 0.0000 -- -18.99112858231 ( 2) -17.71939273124 ( 2) 1077.52561948054 ( 4) 6952.39415603238 ( 2) 7144.19342453015 ( 2) -- 27000.48461267307 ( 2) 29976.56904017511 ( 2) 60216.83941698664 ( 2) -+ -18.99112858231 ( 2) -17.71939273125 ( 2) 1077.52561948049 ( 4) 6952.39415604068 ( 2) 7144.19342477336 ( 2) -+ 27000.48461334186 ( 2) 29976.56904041467 ( 2) 60216.83941990400 ( 2) - - * Boson symmetry B1 - * Closed shell, f = 1.0000 -- -257.50512395633 ( 2) -+ -257.50512395597 ( 2) - * Virtual eigenvalues, f = 0.0000 -- 1077.52562451694 ( 2) 6952.39415911992 ( 2) 29976.56904082861 ( 2) -+ 1077.52562451688 ( 2) 6952.39415912822 ( 2) 29976.56904106820 ( 2) - - * Boson symmetry B2 - * Closed shell, f = 1.0000 -- -257.50512395632 ( 2) -+ -257.50512395597 ( 2) - * Virtual eigenvalues, f = 0.0000 -- 1077.52562451694 ( 2) 6952.39415911992 ( 2) 29976.56904082861 ( 2) -+ 1077.52562451688 ( 2) 6952.39415912824 ( 2) 29976.56904106813 ( 2) - - * Boson symmetry A2 - * Virtual eigenvalues, f = 0.0000 -- 1077.52563962093 ( 2) -+ 1077.52563962086 ( 2) - - * Occupation in fermion symmetry E1 - * Inactive orbitals -- A1 A1 A1 B1 B2 -+ A1 A1 A1 B2 B1 - * Virtual orbitals -- A1 A1 A1 B1 B2 A1 A2 A1 B1 B2 A1 A1 A1 B2 B1 A1 -+ A1 A1 A1 B2 B1 A2 A1 A1 B1 B2 A1 A1 A1 B2 B1 A1 - -- Occupation of subblocks -- E1 : A1 B1 B2 A2 -+* Occupation of subblocks -+ E1 : A1 B1 B2 A2 - closed shells (f=1.0000): 3 1 1 0 - virtual shells (f=0.0000): 9 3 3 1 --tot.num. of electr. shells: 12 4 4 1 -+tot.num. of pos.erg shells: 12 4 4 1 - - - * HOMO - LUMO gap: - - E(LUMO) : -18.99112858 au (symmetry A1 ) -- - E(HOMO) : -257.50512396 au (symmetry B2 ) -+ - E(HOMO) : -257.50512396 au (symmetry B1 ) - ------------------------------------------ - gap : 238.51399537 au - - - -- ************************************************************************** -- **************** Transformation to Molecular Spinor Basis **************** -- ************************************************************************** -+ ************************************************************************** -+ **************** Transformation to Molecular Spinor Basis **************** -+ ************************************************************************** - - - Written by Luuk Visscher, Jon Laerdahl & Trond Saue -@@ -1116,19 +1378,19 @@ - - - -- ************************************************************************ -- **************** Transformation of 2-electron integrals **************** -- ************************************************************************ -+ ************************************************************************ -+ **************** Transformation of 2-electron integrals **************** -+ ************************************************************************ - - -- Transformation started at : Sun Dec 5 16:41:19 2004 -- --* REACMO: Coefficients read from file DFCOEF - Total energy: -9505.77974749367786 --* Heading : LiH Sun Dec 5 16:41:19 2004 -- Energy selection of active orbitals : -1000.00 < Eps. < ******** with a mininum gap of 0.1000 au. -- Energy selection of active orbitals : -1000.00 < Eps. < ******** with a mininum gap of 0.1000 au. -- Energy selection of active orbitals : -1000.00 < Eps. < ******** with a mininum gap of 0.1000 au. -- Energy selection of active orbitals : -1000.00 < Eps. < ******** with a mininum gap of 0.1000 au. -+ Transformation started at : Mon Oct 5 14:12:56 2020 -+ -+* REACMO: Coefficients read from file DFCOEF - Total energy: -9505.77974726990942 -+* Heading : LiH Mon Oct 5 14:12:56 2020 -+ Energy selection of active orbitals : -1000.00 < Eps. < 999999.00 with a mininum gap of 0.1000 au. -+ Energy selection of active orbitals : -1000.00 < Eps. < 999999.00 with a mininum gap of 0.1000 au. -+ Energy selection of active orbitals : -1000.00 < Eps. < 999999.00 with a mininum gap of 0.1000 au. -+ Energy selection of active orbitals : -1000.00 < Eps. < 999999.00 with a mininum gap of 0.1000 au. - - * Orbital ranges for 4-index transformation: - -@@ -1151,6 +1413,8 @@ - 2 3 4 5 6 7 8 9 10 11 12 13 - 14 15 16 17 18 19 20 21 - -+ (PAMTRA) Orbitals read from DFCOEF -+ - * Core orbital ranges for 2-index transformation: - - -@@ -1160,9 +1424,9 @@ - 1 - - -- ************************************************************************** -- **************** Transformation to Molecular Spinor Basis **************** -- ************************************************************************** -+ ************************************************************************** -+ **************** Transformation to Molecular Spinor Basis **************** -+ ************************************************************************** - - - Written by Luuk Visscher, Jon Laerdahl & Trond Saue -@@ -1171,90 +1435,95 @@ - - - -- ******************************************************************** -- **************** Transformation of core Fock matrix **************** -- ******************************************************************** -+ ******************************************************************** -+ **************** Transformation of core Fock matrix **************** -+ ******************************************************************** - - -- Transformation started at : Sun Dec 5 16:41:19 2004 -+ Transformation started at : Mon Oct 5 14:12:56 2020 - --* REACMO: Coefficients read from file DFCOEF - Total energy: -9505.77974749367786 --* Heading : LiH Sun Dec 5 16:41:19 2004 -+* REACMO: Coefficients read from file DFCOEF - Total energy: -9505.77974726990942 -+* Heading : LiH Mon Oct 5 14:12:56 2020 - SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00E-12 15.59% 20.70% 0.75% 2.21% 0.01499799s -+SOfock:LL 1.00D-12 15.59% 20.70% 0.75% 2.21% 0.00235999s - --* REAFCK: Fock matrix read from file DFFCK1 --* Heading : LiH Sun Dec 5 16:41:19 2004 -+* REAFCK: Fock matrix read from file /kyukon/home/gent/430/vsc43020/DIRAC_scratch_directory/vsc43 -+* Heading : LiH Mon Oct 5 14:12:56 2020 - - -- Core energy (includes nuclear repulsion) : -6388.2074957273 -- - Electronic part : -6409.3745840593 -- - One-electron terms : -6469.3406420395 -- - Two-electron terms : 59.9660579802 -+ Core energy (includes nuclear repulsion) : -6388.2074955762 -+ - Electronic part : -6409.3745839082 -+ - One-electron terms : -6469.3406418861 -+ - Two-electron terms : 59.9660579779 - - - MOLFDIR file MRCONEE is written - - Integral class 1 : (LL|??) -- - Beginning with task 1 of 4 after 0.00 seconds -- and after 0.00 CPU-seconds -- - Beginning with task 2 of 4 after 0.00 seconds -- and after 0.05 CPU-seconds -- - Beginning with task 3 of 4 after 0.00 seconds -- and after 0.19 CPU-seconds -- - Beginning with task 4 of 4 after 0.00 seconds -- and after 0.35 CPU-seconds -- - Integral class 2 : (SS|??) -- - Integral class 3 : (LS|??) -+ - Beginning task 1 of 4 after 0. seconds and 0. CPU-seconds -+ - Beginning task 2 of 4 after 0. seconds and 0. CPU-seconds -+ - Beginning task 3 of 4 after 0. seconds and 0. CPU-seconds -+ - Beginning task 4 of 4 after 0. seconds and 0. CPU-seconds - * Screening statistics: - (LL|LL)ints : 0.00% - Total : 0.00% -- - Starting symmetrization after 0.00 seconds -- - Finished symmetrization after 0.00 seconds -- - MOLFDIR file MDCINT was written. - -------- Timing report (in CPU seconds) of module integral transformation -+ - Starting symmetrization after 0.03 seconds -+ - Finished symmetrization after 0.04 seconds -+ -+ - Binary file MDCINT was written. - -- Time in Initializing MS4IND fi 0.025 seconds -- Time in Computing+transform. i 0.431 seconds -- Time in Symmetrizing MO integr 0.038 seconds -+------ Timing report (in CPU seconds) of module integral transformation - -+ Time in Initializing MS4IND file 0.004 seconds -+ Time in Computing+transform. integral 0.029 seconds -+ Time in Symmetrizing MO integrals 0.004 seconds - -- Total wall time used in PAMTRA : 00:00:01 -- Total CPU time used in PAMTRA (master only) : 00:00:01 - -+ Total wall time used in PAMTRA : 00:00:00 -+ Total CPU time used in PAMTRA (master only) : 00:00:00 - -+ Transformation ended at : Mon Oct 5 14:12:56 2020 - -- Transformation ended at : Sun Dec 5 16:41:20 2004 - - ---< Process 1 of 1----< - - - - Relativistic Coupled Cluster program RELCCSD -- Version number 2.3 -- Version date September 2002 - - Written by : -- Lucas (Luuk) Visscher -+ Lucas Visscher - -- NASA Ames Research Center (1994) -- Rijks Universiteit Groningen (1995) -- Odense Universitet (1996-1997) -- Vrije Universiteit Amsterdam (1998-2002) -+ NASA Ames Research Center (1994) -+ Rijks Universiteit Groningen (1995) -+ Odense Universitet (1996-1997) -+ VU University Amsterdam (1998-present) - - - This module is documented in - - Initial implementation : L. Visscher, T.J. Lee and K.G. Dyall, J. Chem. Phys. 105 (1996) 8769. -- - Fock space formalism : L. Visscher, E. Eliav and U. Kaldor, J. Chem. Phys. 115 (2002) 9720. -+ - Fock Space (FSCC): L. Visscher, E. Eliav and U. Kaldor, J. Chem. Phys. 115 (2002) 9720. -+ - Intermediate Hamiltonian E. Eliav, M. J. Vilkas, Y. Ishikawa, and U. Kaldor, J. Chem. Phys. 122 (2005) 224113. - - Parallelization : M. Pernpointner and L. Visscher, J. Comp. Chem. 24 (2003) 754. -+ - MP2 expectation values : J.N.P. van Stralen, L. Visscher, C.V. Larsen and H.J.Aa. Jensen," Chem. Phys. 311 (2005) 81. -+ - CC expectation values : A. Shee, L. Visscher, and T. Saue, J. Chem. Phys. 145 (2016) 184107. -+ - EOM-IP/EA/EE energies : A. Shee, T. Saue, L. Visscher, and A.S.P. Gomes, J. Chem. Phys. 149 (2018) 174113. - - -- Today is : 5 Dec 04 -- The time is : 16:41:20 -+ Today is : 5 Oct 20 -+ The time is : 14:12:56 - - Initializing word-addressable I/O : the FORTRAN-interface is used with 16 KB records -+=========================================================================== -+ **RELCC: Set-up for Coupled Cluster calculations -+=========================================================================== -+ * General print level : 1 -+ NEL_F1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - -- Total memory available : 76 MB -+ Total memory available : 16384.00 MB 16.000 GB -+ -+ INFO: No old restart file(s) found! -+ - - Configuration in highest pointgroup - -@@ -1262,7 +1531,6 @@ - Spinor class : occupied 4 4 - Spinor class : virtual 16 16 - -- - Configuration in abelian subgroup - - A1 a B1 a B2 a A2 a A1 b B1 b B2 b A2 b -@@ -1271,6 +1539,7 @@ - - - Number of electrons : 8 -+ Total charge of the system : 71 - Number of virtual spinors : 32 - Complex arithmetic mode : F - Do integral sorting : T -@@ -1280,39 +1549,48 @@ - Debug information : F - Timing information : T - Print level : 1 -- Memory limit (MWord) : 10 -+ Memory limit (MWord) : 2048 - Interface used : DIRAC - - -- Memory for reading and sorting integrals : 157514 8-byte words -- Core used for calculating amplitudes : 34890 8-byte words -- Core used for in core evaluation of triples : 31100 8-byte words -- Core used for Gradient calculation : 9999998 8-byte words -- Core used for RPA calculation : 19533 8-byte words -- Memory for reading and sorting integrals : 1511114 8-byte words -- Core used for Fock space CCSD energies : 1511114 8-byte words -- Memory used for active modules : 157514 8-byte words -+ Leave after calculating the total memory demand : F -+ Memory for reading and sorting integrals : 256030 8-byte words -+ Core used for calculating amplitudes : 34680 8-byte words -+ Core used for in core evaluation of triples : 32644 8-byte words -+ Memory used for active modules : 256030 8-byte words - -- Expanding and sorting integrals to unique types : -- Type OOOO : 92 integrals -- Type VOOO : 768 integrals -- Type VVOO : 1512 integrals -- Type VOVO : 6912 integrals -- Type VOVV : 13440 integrals -- Type VVVV : 26272 integrals -+ Predicted RelCC memory demand: 1.95 MB -+ Predicted RelCC memory demand: 0.002 GB - -- Sorting of first 4 classes done. -+ Expanding and sorting integrals to unique types : -+ Type OOOO : 92 integrals -+ Type VOOO : 768 integrals -+ Type VVOO : 1512 integrals -+ Type VOVO : 6912 integrals -+ Type VOVV : 13440 integrals -+ Type VVVV : 26272 integrals -+ -+ Start sorting of integral classes at 5 Oct 20 14:12:56 -+ -+ -+ Sorting of first 4 classes done at 5 Oct 20 14:12:56 - - Need 1 passes to sort VOVV integrals -- VOVV sorting done. -+ -+ Pass 1 ended at 5 Oct 20 14:12:56 -+ -+ VOVV sorting done at 5 Oct 20 14:12:56 - - Need 1 passes to sort VVVV integrals -- VVVV sorting done. -+ -+ Pass 1 ended at 5 Oct 20 14:12:56 -+ -+ VVVV sorting done at 5 Oct 20 14:12:56 - - Reading Coulomb integrals : -- File date : 5Dec04 -- File time : 16:41:20 -- # of integrals 22964 -+ File date : 5 Oct 20 -+ File time : 14:12:56 -+ # of integrals 23323 - - Finished sorting of integrals - -@@ -1322,16 +1600,16 @@ - are given if above a treshold or if iprnt > 1 - - Spinor Abelian Rep. Energy Recalc. Energy -- O 1 1 A1 a -457.8072100470 -457.8072100470 -- O 2 2 A1 a -257.5051400026 -257.5051400026 -- O 1 3 B1 a -257.5051239563 -257.5051239563 -- O 1 4 B2 a -257.5051239563 -257.5051239563 -- O 1 5 A1 b -457.8072100470 -457.8072100470 -- O 2 6 A1 b -257.5051400026 -257.5051400026 -- O 1 7 B1 b -257.5051239563 -257.5051239563 -- O 1 8 B2 b -257.5051239563 -257.5051239563 -+ O 1 1 A1 a -457.8072100107 -457.8072100107 -+ O 2 2 A1 a -257.5051400023 -257.5051400023 -+ O 1 3 B1 a -257.5051239560 -257.5051239560 -+ O 1 4 B2 a -257.5051239560 -257.5051239560 -+ O 1 5 A1 b -457.8072100107 -457.8072100107 -+ O 2 6 A1 b -257.5051400023 -257.5051400023 -+ O 1 7 B1 b -257.5051239560 -257.5051239560 -+ O 1 8 B2 b -257.5051239560 -257.5051239560 - -- The diagonal elements of the recomputed Fock matrix (right column) are used in perturbation expressions. -+ The original energies (left column) are used in perturbation expressions. - - Use the perturbative values (MP2, CCSD[T]/(T)/-T) with care, especially - in open shell calculations because the orbitals need not always be -@@ -1339,11 +1617,11 @@ - The missing terms may be important ! - - -- Nuclear repulsion + core energy : -6388.207495727295282 -- Zero order electronic energy : -2460.645195924678774 -- First order electronic energy : -656.927055841711194 -- Electronic energy : -3117.572251766389854 -- SCF energy : -9505.779747493685136 -+ Nuclear repulsion + core energy : -6388.207495576216388 -+ Zero order electronic energy : -2460.645195849844640 -+ First order electronic energy : -656.927055843850439 -+ Electronic energy : -3117.572251693694852 -+ SCF energy : -9505.779747269911240 - - - Energy calculations -@@ -1354,10 +1632,10 @@ - - MP2 results - -- SCF energy : -9505.779747493685136 -- MP2 correlation energy : -0.221846247868006 -- Total MP2 energy : -9506.001593741553734 -- T1 diagnostic : 0.000000000000017 -+ SCF energy : -9505.779747269911240 -+ MP2 correlation energy : -0.221846247868917 -+ Total MP2 energy : -9506.001593517779838 -+ T1 diagnostic : 0.000000000000010 - - - CCSD options : -@@ -1367,49 +1645,48 @@ - - - NIT ENERGY RMS T1-DIAGN -- 0 -0.221846247868006 1.000000000000000 0.00000 -- 1 -0.222543090352100 0.000169723714323 0.00000 -- 2 -0.222547639799351 0.000001146914982 0.00000 -- 3 -0.222547639196545 0.000000002916755 0.00000 -- 4 -0.222547639201801 0.000000000004730 0.00000 -- 5 -0.222547639201729 0.000000000000043 0.00000 -+ 0 -0.221846247868917 1.000000000000000 0.00000 -+ 1 -0.222543090353008 0.000001024031689 0.00000 -+ 2 -0.222547639800258 0.000000012409001 0.00000 -+ 3 -0.222547639197452 0.000000000073854 0.00000 -+ 4 -0.222547639202709 0.000000000000097 0.00000 - - - CCSD results - -- SCF energy : -9505.779747493685136 -- CCSD correlation energy : -0.222547639201729 -- Total CCSD energy : -9506.002295132886502 -- T1 diagnostic : 0.000000727335985 -- Convergence : 0.000000000000043 -- Number or iterations used : 5 -+ SCF energy : -9505.779747269911240 -+ CCSD correlation energy : -0.222547639202709 -+ Total CCSD energy : -9506.002294909114426 -+ T1 diagnostic : 0.000000727335984 -+ Convergence : 0.000000000000097 -+ Number or iterations used : 4 - - - Performance of BLAS GEMM in the largest contractions - - Contraction type Performance -- VVVV+VOVV (in B: includes I/O) 79.87 Mflop/s -- VOVO (in H: only XGEMM) 321.9 Mflop/s -- VOVO (in T2EQN: includes sort) 173.3 Mflop/s -+ VVVV+VOVV (in B: includes I/O) 942.4 Mflop/s -+ VOVO (in H: only XGEMM) 15.67 Gflop/s -+ VOVO (in T2EQN: includes sort) 3.129 Gflop/s - - - Perturbative treatment of triple excitations - -- SCF energy : -9505.779747493685136 -- CCSD correlation energy : -0.222547639201729 -+ SCF energy : -9505.779747269911240 -+ CCSD correlation energy : -0.222547639202709 - 4th order triples correction : -0.000001799879971 - 5th order triples (T) correction : -0.000000000059407 - 5th order triples -T correction : -0.000000000472828 -- Total CCSD+T energy : -9506.002296932767422 -- Total CCSD(T) energy : -9506.002296932825629 -- Total CCSD-T energy : -9506.002296933240359 -+ Total CCSD+T energy : -9506.002296708993526 -+ Total CCSD(T) energy : -9506.002296709053553 -+ Total CCSD-T energy : -9506.002296709466464 - - - -------------------------------------------------------------------------------- - - -- Today is : 5 Dec 04 -- The time is : 16:41:20 -+ Today is : 5 Oct 20 -+ The time is : 14:12:56 - - Status of the calculations - Integral sort # 1 : Completed, restartable -@@ -1418,166 +1695,196 @@ - MP2 energy calculation : Completed, restartable - CCSD energy calculation : Completed, restartable - CCSD(T) energy calculation : Completed, restartable -+ CCSD(T) energy calculation : Completed, restartable - - Overview of calculated energies --@ SCF energy : -9505.779747493685136 --@ MP2 correlation energy : -0.221846247868006 --@ CCSD correlation energy : -0.222547639201729 -+@ SCF energy : -9505.779747269911240 -+@ MP2 correlation energy : -0.221846247868917 -+@ CCSD correlation energy : -0.222547639202709 - @ 4th order triples correction : -0.000001799879971 - @ 5th order triples (T) correction : -0.000000000059407 - @ 5th order triples -T correction : -0.000000000472828 --@ Total MP2 energy : -9506.001593741553734 --@ Total CCSD energy : -9506.002295132886502 --@ Total CCSD+T energy : -9506.002296932767422 --@ Total CCSD(T) energy : -9506.002296932825629 --@ Total CCSD-T energy : -9506.002296933240359 -+@ Total MP2 energy : -9506.001593517779838 -+@ Total CCSD energy : -9506.002294909114426 -+@ Total CCSD+T energy : -9506.002296708993526 -+@ Total CCSD(T) energy : -9506.002296709053553 -+@ Total CCSD-T energy : -9506.002296709466464 - - - -------------------------------------------------------------------------------- - - ------ Timing report (in CPU seconds) of module RELCCSD - -- Time in Sorting of integrals 0.234 seconds -- Time in CCSD equations 0.123 seconds -- Time in - T1 equations 0.020 seconds -- Time in --- T1EQNS HOV*T2(A,C,I 0.001 seconds -- Time in --- T1EQNS VOVV contrib 0.005 seconds -- Time in --- T1EQNS VOVO * T(C,K 0.004 seconds -- Time in - T2 equations 0.090 seconds -- Time in -- GVINTM 0.010 seconds -- Time in -- AINTM 0.003 seconds -- Time in -- HINTM 0.029 seconds -- Time in --- HINTM: VOVV*T 0.011 seconds -- Time in --- HINTM: VVOO contrib 0.007 seconds -- Time in -- T2 EQNS 0.028 seconds -- Time in --- T2EQNS: TAU*AINTM c 0.002 seconds -- Time in --- T2EQNS: VOVV*T1 0.005 seconds -- Time in --- T2EQNS: HINTM*T2 0.013 seconds -- Time in -- BINTM 0.020 seconds -- Time in - DIIS extrapolation 0.010 seconds -- Time in CCSD(T) evaluation 0.043 seconds -- Time in -- T3CORR: Integral res 0.002 seconds -- Time in -- T3CORR: VOVV contrac 0.020 seconds -- Time in -- T3CORR: energy calcu 0.019 seconds -+ Time in Sorting of integrals 0.053 seconds -+ Time in CCSD equations 0.010 seconds -+ Time in - T1 equations 0.002 seconds -+ Time in --- T1EQNS T*[HOV - F]*T 0.000 seconds -+ Time in --- T1EQNS HOV*T2(A,C,I,K 0.000 seconds -+ Time in --- T1EQNS HV*T / T*HO 0.000 seconds -+ Time in --- T1EQNS VOOO*TAU 0.000 seconds -+ Time in --- T1EQNS VOVV contribution 0.001 seconds -+ Time in --- T1EQNS VOVO * T(C,K) 0.000 seconds -+ Time in -- GOINTM 0.000 seconds -+ Time in -- GVINTM 0.001 seconds -+ Time in -- AINTM 0.000 seconds -+ Time in -- HINTM 0.002 seconds -+ Time in --- HINTM: VOVV*T 0.001 seconds -+ Time in --- HINTM: VVOO contribution 0.000 seconds -+ Time in -- T2 EQNS 0.003 seconds -+ Time in --- T2EQNS: TAU*AINTM contract 0.000 seconds -+ Time in --- T2EQNS: VOVV*T1 0.001 seconds -+ Time in --- T2EQNS: HINTM*T2 0.001 seconds -+ Time in -- BINTM 0.001 seconds -+ Time in - adding partial T1/T2 amplitu 0.000 seconds -+ Time in - DIIS extrapolation 0.001 seconds -+ Time in - synchronizing T1 & T2 amplit 0.000 seconds -+ Time in CCSD(T) evaluation 0.003 seconds -+ Time in -- T3CORR: Integral resorting 0.000 seconds -+ Time in -- T3CORR: VOVV contraction 0.001 seconds -+ Time in -- T3CORR: energy calculation 0.002 seconds - - - Timing of main modules : Wallclock (s) CPU on master (s) -- Before CC driver : 2.00 0.89 -- Initialization : 0.00 0.00 -- Integral sorting : 0.00 0.23 -- Energy calculation : 0.00 0.17 -+ Before CC driver : ************ 0.21 -+ Initialization : 0.10 0.10 -+ Integral sorting : 0.05 0.05 -+ Energy calculation : 0.08 0.07 - First order properties : 0.00 0.00 - Second order properties : 0.00 0.00 - Fock space energies : 0.00 0.00 -+ EOMCC energies : 0.00 0.00 - Untimed parts : 0.00 0.00 -- Total time in CC driver : 0. 0.41 -+ Total time in CC driver : 0. 0.23 - - Statistics for the word-addressable I/O -- Number of write calls 519. -- Number of read calls 538. -- Megabytes written 0.566 -- Megabytes read 5.543 -- Seconds spent in reads 0.000 -- Seconds spent in writes 0.000 -- average I/O speed for write (Mb/s) 0.000 -- average I/O speed for read (Mb/s) 0.000 -+ Number of write calls 409. -+ Number of read calls 428. -+ Megabytes written 0.265 -+ Megabytes read 2.215 -+ Seconds spent in reads 0.004 -+ Seconds spent in writes 0.004 -+ average I/O speed for write (Mb/s) 74.410 -+ average I/O speed for read (Mb/s) 598.620 - - -- CPU time (seconds) used in RELCCSD: 0.4089 -- CPU time (seconds) used before RELCCSD: 0.8869 -- CPU time (seconds) used in total sofar: 1.2958 -+ CPU time (seconds) used in RELCCSD: 0.2306 -+ CPU time (seconds) used before RELCCSD: 0.2148 -+ CPU time (seconds) used in total sofar: 0.4454 - - --- Normal end of RELCCSD Run --- - - - ################################################################################ -- -- -- ******************************************************************************** -- -- -- -- D I R L U C -- An interface section for LUCIA under DIRAC -- -- author: -- T. Fleig -- Theoretische Chemie und Computerchemie, -- Heinrich-Heine-Universitaet Duesseldorf -- -- Calling LUCIA version 1999 -- author: J. Olsen, Lund/Aarhus -- -- Traditional sigma vector and density modules. -- -- ******************************************************************************** -- -- -+ -+ -+ ********************************************************************** -+ ********************************************************************** -+ -+ -+ D I R L U C -+ An interface section for LUCIA under DIRAC -+ -+ author: -+ T. Fleig -+ Theoretische Chemie und Computerchemie, -+ Heinrich-Heine-Universitaet Duesseldorf -+ -+ Calling LUCIA version 1999 -+ author: J. Olsen, Lund/Aarhus -+ -+ Traditional sigma vector and density modules. -+ -+ Citation: -+ J. Olsen, P. Joergensen, J. Simons, -+ Chem. Phys. Lett. 169 (1990) 463 -+ T. Fleig, L. Visscher, -+ Chem. Phys. 311 (2005) 113 -+ -+ -+ Parallelization of LUCIA, Duesseldorf/Odense: -+ S. Knecht -+ Theoretische Chemie und Computerchemie, -+ Heinrich-Heine-Universitaet Duesseldorf -+ -+ Citation: -+ S. Knecht, H. J. Aa. Jensen and T. Fleig, -+ J. Chem. Phys., 128 (2008) 014108 -+ -+ ********************************************************************** -+ ********************************************************************** -+ -+ - ******************************************************************************** - * * - * Title: * - * Running LUCIA under DIRAC. No title supplied. * - * * - ******************************************************************************** -- -+ - Orbitals as initial wave function .... HF_SCF -- -+ - Type of calculation .................. SDCI -- -+ - Number of roots to be obtained ....... 1 -- -+ - Calculation carried out in irrep ..... 1 -- -+ - Spin multiplicity .................... 3 -- -+ - Global print level is ................ NON -- -+ - Local print level is ................. 0 -- -+ - Approximate size of CI calculation ... NOR -+ -+ Running the CI calculation ........... sequenti -+ -+ Using MPI-FILE I/O ................... No -+ - -+ Truncation Factor ..................... 0.00D+00 -+ - Number of active electrons ........... 8 -- -- Dimension of R*8 workspace : 10000000 -- -+ -+ Dimension of R*8 workspace : 64000000 - Integral import from DIRAC. - No checking of environment dims. -- -+ - ************************************* - * Symmetry and spin of CI vectors * - ************************************* -- -- Point group ............ D2H -- Using subgroup ......... D2 -- (D2 equiv. C2v, C2 eq. Cs) -- Spatial symmetry ....... 1 -- 2 times spinprojection 2 -- Spin multiplicity .... 3 -- Active electrons ..... 8 -- -+ -+ Point group ............ D2h -+ Using subgroup ......... D2 -+ (D2 equiv. C2v, C2 eq. Cs) -+ Spatial symmetry ....... 1 -+ 2 times spinprojection 2 -+ Spin multiplicity .... 3 -+ Active electrons ..... 8 -+ - ********************************************* - * Shell spaces and occupation constraints * - ********************************************* -- -- -+ -+ - ************************* - Generalized active space - ************************* -- -+ - Orbital subspaces: - ================== -- -- Irrep 1 2 3 4 -- ===== ================ -+ -+ Irrep 1 2 3 4 -+ ===== ================ - GAS 1 2 1 1 0 - GAS 2 9 3 3 1 -- -+ - ******************* - Occupation spaces - ******************* -- -+ - Number of Occupation spaces : 1 -- -+ - Bounds on accumulated occupations for space : 1 - ====================================================== - -@@ -1585,180 +1892,259 @@ - ======== ======== - GAS 1 6 8 - GAS 2 8 8 -- -+ - ************************************************** - Specification of CI Spaces (combinations of above) - ************************************************** -- -- -+ -+ - Number of CI spaces included : 1 -- -- -+ -+ - Information about CI space 1 - ================================== -- Number of occupation spaces included 1 -+ Number of occupation spaces included 1 - Occupation spaces included 1 -- -+ - ****************************************** - Specification of Sequence of calculations - ****************************************** -- -- -+ -+ - CI space 1 - ============== -- -+ - Normal CI with max. iterations = 100 -- -- -+ -+ - *********** - * Roots * - *********** -- -- Number of roots to be obtained 1 -- Roots to be obtained 1 -- -+ -+ Number of roots to be obtained 1 -+ Roots to be obtained 1 -+ - ************************** - * Run time definitions * - ************************** -- -+ - Program environment... DIRAC -- All integrals stored in core -- -- CI optimization performed with SD's -- -- Initial vectors obtained from diagonal -- No combination of degenerate initial vectors -- -+ All integrals stored in core -+ -+ CI optimization performed with SD's -+ -+ Initial vectors obtained from diagonal -+ No combination of degenerate initial vectors -+ - 3 symmetry-occ-occ blocks will be held in core - Smallest allowed size of sigma- and C-batch 100000 -- Dimension of block of resolution strings 1000 -- Particle-hole separation used -- Advice routine call to optimize sigma generation -- Strings not divided into active and passive parts -- -- No calculation of density matrices -- -- CI diagonalization : -- ==================== -- No subspace Hamiltonian -- Diagonalizer : MICDV* -- No root homing -- Initial energy evaluations skipped after first calc -- (Only active in connection with TERACI ) -- Allowed Dimension of CI subspace 3 -- Convergence threshold for energy 0.10000E-09 -- No multispace method in use -- -- -- -+ Dimension of block of resolution strings 1000 -+ Particle-hole separation not used -+ Strings not divided into active and passive parts -+ -+ No calculation of density matrices -+ -+ CI diagonalization : -+ ==================== -+ No subspace Hamiltonian -+ Diagonalizer : MICDV* -+ No root homing -+ Initial energy evaluations skipped after first calc -+ (Only active in connection with TERACI ) -+ Allowed Dimension of CI subspace 3 -+ Convergence threshold for energy 1.00000E-08 -+ No multispace method in use -+ -+ -+ - Final orbitals : - ================ -- -+ - Natural orbitals -- -- Print levels : -- Raised print level for string information = 0 -- Raised print level for CI space information = 0 -- Raised print level for orbital information = 0 -- Raised print level for density matrix = 0 -- Raised print level for iterative information = 0 -- Raised print level for External blocks = 0 -- -- -+ -+ Print levels : -+ Raised print level for string information = 0 -+ Raised print level for CI space information = 0 -+ Raised print level for orbital information = 0 -+ Raised print level for density matrix = 0 -+ Raised print level for iterative information = 0 -+ Raised print level for External blocks = 0 -+ -+ - Integrals imported from DIRAC files -- -+ - Using spinfree Dirac Hamiltonian! --DIRAC core energy = -6388.2074957273 -+ DIRAC core energy = -6388.2074955762 - Integrals have been calculated on the -- 5Dec04 -- at 16:41:20 -+ 5Oct20 -+ at 14:12:56 - End of file MDCINT. - Only or last 2-el. integral file. -- Complete real list of 2-el. ints processed. -- Updated core energy -9505.77975 -- - -+ Complete real list of 2-el. ints processed. -+ Updated core energy -6388.20749557622 -+ -+ - Number of internal combinations per symmetry - =========================================== -- CI space 1 -+ CI space 1 - 0.928000000000000E+03 0.888000000000000E+03 0.888000000000000E+03 0.816000000000000E+03 -- -- -- -+ -+ -+ - ******************************** - ****************************** -- -+ - Calculations in space 1 -- -+ - ****************************** - ******************************** -- -- -- -- -- -- Number of determinants/combinations 928 -- Number of blocks 12 -- Min/Max taken zero length vector set to zero -- -- ::::::::::::::::::: -- Entering MICDV6 -- ::::::::::::::::::: -- Min/Max taken zero length vector set to zero -- -+ -+ -+ -+ -+ -+ Number of determinants/combinations 928 -+ Number of blocks 12 -+ -+ ============================================================== -+ ==> allocation of two CI vectors and one resolution vector <== -+ -+ current available free memory in double words: 63987889 -+ allocate two CI vectors each of length: 928 -+ allocate resolution vector of length: 2704 -+ ============================================================== -+ -+ -+ ************************************************** -+ entering MICDV6 (sequential solver routine) -+ ************************************************** -+ -+ - Info from iteration 1 - _______________________ -- Iter RNORM EIGAPR 1 .9601356084203E+01 -9267.5303112690 -- Min/Max taken zero length vector set to zero -- >>> CPU (WALL) TIME IN ITERATION: 0.15697587s( 1.00000000s) -- -+ Iter RNORM EIGAPR 1 .9601356084089E+01 -9267.5303110455 -+ >>> CPU (WALL) TIME IN SIGMA VECTOR CALL : 0.02180900s( 0.02197480s) -+ >>> CPU (WALL) TIME IN STEP3 OF ILOOP: 0.00572800s( 0.00975108s) -+ >>> CPU (WALL) TIME IN ITERATION: 0.03027800s( 0.03653908s) -+ - Info from iteration 2 - _______________________ -- Iter RNORM EIGAPR 2 .3840924503079E-01 -9267.5598590200 -- Min/Max taken zero length vector set to zero -- >>> CPU (WALL) TIME IN ITERATION: 0.17197502s( 0.00000000s) -- -+ Iter RNORM EIGAPR 2 .3840924503134E-01 -9267.5598587966 -+ >>> CPU (WALL) TIME IN SIGMA VECTOR CALL : 0.02152600s( 0.02168798s) -+ >>> CPU (WALL) TIME IN STEP3 OF ILOOP: 0.00608100s( 0.00920391s) -+ >>> CPU (WALL) TIME IN ITERATION: 0.03194600s( 0.03669691s) -+ - Info from iteration 3 - _______________________ -- Iter RNORM EIGAPR 3 .1079759854168E-03 -9267.5598595541 -- Min/Max taken zero length vector set to zero -- >>> CPU (WALL) TIME IN ITERATION: 0.17197394s( 0.00000000s) -- -+ Iter RNORM EIGAPR 3 .1079759854208E-03 -9267.5598593307 -+ >>> CPU (WALL) TIME IN SIGMA VECTOR CALL : 0.02164600s( 0.02180982s) -+ >>> CPU (WALL) TIME IN STEP3 OF ILOOP: 0.00616400s( 0.00909591s) -+ >>> CPU (WALL) TIME IN ITERATION: 0.03213400s( 0.03650999s) -+ - Info from iteration 4 - _______________________ -- Iter RNORM EIGAPR 4 .6150758055566E-05 -9267.5598595541 -- -+ Iter RNORM EIGAPR 4 .6150758097328E-05 -9267.5598593307 -+ - ------------------------ -- Root number 1 -+ Root number 1 - ------------------------ -- 1 -9267.5303112689671 0.96014E+01 -- 2 -9267.5598590199970 0.38409E-01 -- 3 -9267.5598595541269 0.10798E-03 -- 4 -9267.5598595541305 0.61508E-05 -- -+ 1 -9267.5303110455370 0.96014E+01 -+ 2 -9267.5598587965669 0.38409E-01 -+ 3 -9267.5598593306968 0.10798E-03 -+ 4 -9267.5598593307004 0.61508E-05 -+ - ************************************************************ - Iter Root Energy RESIDUAL RESRATIO - ************************************************************ -+ -+ 4 1 -9267.5598593307 0.615E-05 0.156E+07 -+ Final energy -9267.5598593307 -+ -+ ************************************************** -+ Analysis of Density and occupation for ROOT = 1 -+ ************************************************** -+ -+ -+ Natural occupation numbers for symmetry = 1 -+ __________________________________________________ -+ -+ 1.999985601 1.000008650 1.000000000 0.000005735 0.000000015 -+ 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 -+ 0.000000000 -+ -+ Sum = 4.000000001 -+ -+ Natural occupation numbers for symmetry = 2 -+ __________________________________________________ -+ -+ 1.999995682 0.000004317 0.000000001 0.000000000 -+ -+ Sum = 1.999999999 -+ -+ Natural occupation numbers for symmetry = 3 -+ __________________________________________________ -+ -+ 1.999995682 0.000004317 0.000000001 0.000000000 -+ -+ Sum = 1.999999999 -+ -+ Natural occupation numbers for symmetry = 4 -+ __________________________________________________ - -- 4 1 -9267.5598595541 0.615E-05 0.156E+07 -- Final energy -9267.5598595541 -- Min/Max taken zero length vector set to zero -+ 0.000000000 - -+ Sum = 0.000000000 -+ - Information about MATML7 calls : - ================================ -- -- Number of calls 24093. -- Number of flops executed 1643840. -- Average row length of C 2.2880225 -- Average column length of C 3.41733405 -- Average number of operations per element of C 8.56077492 -- Average number of operations per per call 68.2289462 -- Number of seconds spent in MATML7 0.0569934845 -- Average MFLOPS 28.8425952 -+ -+ Number of calls 31997.0000000000 -+ Number of flops executed 5577024.00000000 -+ Average row length of C 12.3634401503225 -+ Average column length of C 1.93440695103564 -+ Average number of operations per element of C 5.72710860818613 -+ Average number of operations per per call 174.298340469419 -+ Number of seconds spent in MATML7 7.342338562011719E-003 -+ Average MFLOPS 759.570530955189 -+ Lucita says: - I am home from the loops - -- Date and time (Linux) : Sun Dec 5 16:41:21 2004 - ***************************************************** -->>>> Total CPU time used in DIRAC: 1.86471600s -->>>> Total WALL time used in DIRAC: 3.00000000s - ********** E N D of D I R A C output ********** -+***************************************************** -+ -+ -+ -+ Date and time (Linux) : Mon Oct 5 14:12:56 2020 -+ Host name : node3403.kirlia.os -+ -+ -+ Dynamical Memory Usage Summary for Master -+ -+ Mean allocation size (Mb) : 28.77 -+ -+ Largest 10 allocations -+ -+ 488.28 Mb at subroutine pamlu_+0x8b for WRK in PAMLU -+ 488.28 Mb at subroutine pamtra_+0x16b for WORK in PAMTRA -+ 488.28 Mb at subroutine psiscf_+0xa9 for WORK in PSISCF -+ 488.28 Mb at subroutine pamset_+0x1867 for WORK in PAMSET - 2 -+ 488.28 Mb at subroutine gmotra_+0x4ddb for WORK in GMOTRA -+ 488.28 Mb at subroutine pamset_+0x97 for WORK in PAMSET - 1 -+ 488.28 Mb at subroutine MAIN__+0x2b8 for test allocation of work array in DIRAC mai -+ 1.37 Mb at subroutine ccseti_+0x718 for ibuf -+ 1.37 Mb at subroutine ccseti_+0x718 for ibuf -+ 0.76 Mb at subroutine paminp_+0x8a for PAMINP WORK array -+ -+ Peak memory usage: 488.29 MB -+ Peak memory usage: 0.477 GB -+ reached at subroutine : mdscri_+0xb8 -+ for variable : unnamed variable -+ -+ MEMGET high-water mark: 0.00 MB -+ -+***************************************************** -+>>>> Node 0, utime: 0, stime: 0, minflt: 6800, majflt: 0, nvcsw: 871, nivcsw: 3, maxrss: 121080 -+>>>> Total WALL time used in DIRAC: 0s -+DIRAC pam run in /tmp/DIRAC-19.0-Source/build/test/bss_energy diff --git a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_fix_mpi_tests.patch b/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_fix_mpi_tests.patch deleted file mode 100644 index 2e121e7687e..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_fix_mpi_tests.patch +++ /dev/null @@ -1,1398 +0,0 @@ -# pam_test mpi part is designed for pre-2020 Intel MPI and OpenMPI -# eedm_mhyp_ensps_krci gives different result with sequantial and mpi parallel. -# although GNU 9.3.0/OpenBLAS 0.3.9 and Intel 2020.1/MKL 2020.1 gives the same result on cascadelake: -# GNU 9.3.0/OpenBLAS 0.3.9 cascadelake: -# EEDM state 1(1 ) state 1(1 ) -0.000110451220 -0.000567963004 -# MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 -# MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 -# MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 -# MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 -# MHYP state 1(1 ) state 1(1 ) -0.006752216685 0.000000010532 -# MHYP state 1(1 ) state 1(1 ) -0.001232901004 -0.000000013685 -# ENSPS state 1(1 ) state 1(1 ) 0.001238395771 0.001238395771 -# ENSPS state 1(1 ) state 1(1 ) -0.000041690709 0.000041690709 -# Intel 2020.1/MKL 2020.1 cascadelake: -# EEDM state 1(1 ) state 1(1 ) -0.000110451220 -0.000567963004 -# MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 -# MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 -# MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 -# MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 -# MHYP state 1(1 ) state 1(1 ) -0.006752216685 0.000000010532 -# MHYP state 1(1 ) state 1(1 ) -0.001232901004 -0.000000013685 -# ENSPS state 1(1 ) state 1(1 ) 0.001238395771 0.001238395771 -# ENSPS state 1(1 ) state 1(1 ) -0.000041690709 0.000041690709 -# OCT 9th 2020 by B. Hajgato (UGent) -diff -ru DIRAC-19.0-Source.orig/cmake/custom/test.cmake DIRAC-19.0-Source/cmake/custom/test.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/test.cmake 2019-12-12 17:26:15.000000000 +0100 -+++ DIRAC-19.0-Source/cmake/custom/test.cmake 2020-10-09 14:32:56.939227043 +0200 -@@ -103,7 +103,7 @@ - dirac_test(basis_input_scripted "basis;long" "3600") - dirac_test(bsse "basis;short" "") - dirac_test(bss_energy "short" "") --dirac_test(pam_test "short;pam" "") -+#dirac_test(pam_test "short;pam" "") - dirac_test(cc_essential "short;cc" "") - dirac_test(cc_linear "short;cc" "") - dirac_test(cc_gradient "cc_gradient" "") -diff -ru DIRAC-19.0-Source.orig/test/eedm_mhyp_ensps_krci/result/BeH_BeH.out DIRAC-19.0-Source/test/eedm_mhyp_ensps_krci/result/BeH_BeH.out ---- DIRAC-19.0-Source.orig/test/eedm_mhyp_ensps_krci/result/BeH_BeH.out 2019-12-12 17:26:14.000000000 +0100 -+++ DIRAC-19.0-Source/test/eedm_mhyp_ensps_krci/result/BeH_BeH.out 2020-10-09 14:34:08.021942896 +0200 -@@ -1,8 +1,12 @@ --DIRAC serial starts by allocating 2000000000 words ( 15258.79 MB - 14.901 GB) -- of memory out of the allowed maximum of 2147483648 words ( 16384.00 MB - 16.000 GB) -- --Note: maximum allocatable memory for serial run can be set by pam --aw/--ag -+ ** interface to 64-bit integer MPI enabled ** - -+DIRAC master (node3414.kirlia.os) starts by allocating 64000000 r*8 words ( 0.477 GB) of memory -+DIRAC nodes 1 to 1 starts by allocating 64000000 r*8 words ( 0.477 GB) of memory -+DIRAC master (node3414.kirlia.os) to allocate at most 2147483648 r*8 words ( 16.000 GB) of memory -+DIRAC nodes 1 to 1 to allocate at most 2147483648 r*8 words ( 16.000 GB) of memory -+ -+Note: maximum allocatable memory for master+nodes can be set by -aw (MW)/-ag (GB) flags in pam -+ - ******************************************************************************* - * * - * O U T P U T * -@@ -168,52 +172,53 @@ - Version information - ------------------- - --Branch | genp_krci --Commit hash | c8f8cf4 --Commit author | mknayak72 --Commit date | Sat Dec 7 14:19:33 2019 +0530 -+Branch | -+Commit hash | -+Commit author | -+Commit date | - - - Configuration and build information - ----------------------------------- - --Who compiled | mknayak --Compiled on server | malaya.tcs --Operating system | Linux-3.10.0-1062.7.1.el7.x86_64 --CMake version | 3.12.1 -+Who compiled | vsc43020 -+Compiled on server | node3414.kirlia.os -+Operating system | Linux-3.10.0-1127.8.2.el7.ug.x86_64 -+CMake version | 3.16.4 - CMake generator | Unix Makefiles --CMake build type | release --Configuration time | 2019-12-07 08:51:29.918953 --Python version | 2.7.5 --Fortran compiler | /usr/bin/gfortran --Fortran compiler version | 4.8.5 --Fortran compiler flags | -g -fcray-pointer -fbacktrace -fno-range-check -DVAR_GFORTRAN -DVAR_MFDS -fdefault-integer-8 -g -fcray-pointer -fbacktrace -fno-range-check -DVAR_GFORTRAN -DVAR_MFDS -fdefault-integer-8 --C compiler | /usr/bin/gcc --C compiler version | 4.8.5 --C compiler flags | -g -g --C++ compiler | /usr/bin/g++ --C++ compiler version | 4.8.5 --C++ compiler flags | -g -Wall -Wno-unknown-pragmas -Wno-sign-compare -Woverloaded-virtual -Wwrite-strings -Wno-unused -g -Wall -Wno-unknown-pragmas -Wno-sign-compare -Woverloaded-virtual -Wwrite-strings -Wno-unused -+CMake build type | RELEASE -+Configuration time | 2020-10-09 11:26:21.998545 -+Python version | 2.7.1 -+Fortran compiler | /apps/gent/CO7/cascadelake-ib/software/impi/2019.7.217-iccifort-2020.1.217/intel64/bin/mpiifort -+Fortran compiler version | 19.1 -+Fortran compiler flags | -O2 -ftz -fp-speculation=safe -fp-model source -i8 -w -assume byterecl -DVAR_IFORT -i8 -+C compiler | /apps/gent/CO7/cascadelake-ib/software/impi/2019.7.217-iccifort-2020.1.217/intel64/bin/mpiicc -+C compiler version | 19.1 -+C compiler flags | -O2 -ftz -fp-speculation=safe -fp-model source -DMKL_ILP64 -wd981 -wd279 -wd383 -wd1572 -wd177 -+C++ compiler | /apps/gent/CO7/cascadelake-ib/software/impi/2019.7.217-iccifort-2020.1.217/intel64/bin/mpiicpc -+C++ compiler version | 19.1.1 -+C++ compiler flags | -O2 -ftz -fp-speculation=safe -fp-model source -Wno-unknown-pragmas - Static linking | False - 64-bit integers | True --MPI parallelization | False --MPI launcher | unknown --Math libraries | -Wl,--start-group;/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_lapack95_ilp64.a;/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_gf_ilp64.so;-fopenmp;-Wl,--end-group;-Wl,--start-group;/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_gf_ilp64.so;/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_gnu_thread.so;/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_core.so;/usr/lib64/libpthread.so;/usr/lib64/libm.so;-fopenmp;-Wl,--end-group -+MPI parallelization | True -+MPI launcher | /apps/gent/CO7/cascadelake-ib/software/impi/2019.7.217-iccifort-2020.1.217/intel64/bin/mpiexec -+Math libraries | unknown - Builtin BLAS library | OFF - Builtin LAPACK library | OFF --Explicit libraries | unknown --Compile definitions | MOD_UNRELEASED;SYS_LINUX;PRG_DIRAC;INT_STAR8;INSTALL_WRKMEM=64000000;HAS_PCMSOLVER;BUILD_GEN1INT;HAS_PELIB;MOD_QCORR;HAS_STIELTJES;MOD_INTEREST;MOD_LAO_REARRANGED;MOD_MCSCF_spinfree;MOD_AOOSOC;MOD_ESR;MOD_KRCC;MOD_SRDFT -+Explicit libraries | -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread -+Compile definitions | HAVE_MPI;VAR_MPI;VAR_MPI2;USE_MPI_MOD_F90;SYS_LINUX;PRG_DIRAC;INT_STAR8;INSTALL_WRKMEM=64000000;BUILD_GEN1INT;HAS_PELIB;MOD_QCORR;HAS_STIELTJES - - - LAPACK integer*4/8 selftest passed - Selftest of ISO_C_BINDING Fortran - C/C++ interoperability PASSED -+ MPI selftest passed with MPI_INTEGER of the size 8 bytes - - Execution time and host - ----------------------- - - -- Date and time (Linux) : Sat Dec 7 14:42:42 2019 -- Host name : malaya.tcs -+ Date and time (Linux) : Fri Oct 9 13:31:22 2020 -+ Host name : node3414.kirlia.os - - - Contents of the input file -@@ -325,6 +330,7 @@ - Journal of Physical and Chemical Reference Data, Vol. 28, No. 6, 1999 - * The speed of light : 137.0359998 - * Running in four-component mode -+ * Parallel run with 1 slaves. - * Direct evaluation of the following two-electron integrals: - - LL-integrals - - SL-integrals -@@ -523,7 +529,7 @@ - ---------------------------------------------- - - 2 -- -+ - Be 0.0000000000 0.0000000000 -0.0922128491 - H 0.0000000000 0.0000000000 0.8245866800 - -@@ -719,10 +725,10 @@ - * Hartree-Fock calculation - * Kramers restricted CI calculation - evaluating active dbg irrep... -- # dbg irreps : 128 -- # active MJ value (doubled): 1 -- # active fermion sym : 1 -- # active double group irrep: 65 -+ # dbg irreps : 128 -+ # active MJ value (doubled): 1 -+ # active fermion sym : 1 -+ # active double group irrep: 65 - =========================================================================== - *KRCICALC: General set-up for KR-CI calculation: - =========================================================================== -@@ -753,6 +759,7 @@ - =========================================================================== - * Energy convergence threshold: 8.00D-13 - * Maximum number of CI iterations for each symmetry: 50 -+ * Integrals on slave nodes provided by the MASTER - * Property calculation for the following one-electron operators: - - i*BETA*GAMMA5 operator, setting IATIM=-1 -@@ -898,7 +905,7 @@ - - 1 Debye = 2.54177000 a.u. - --Total time used in ONEGEN (CPU) 0.03528100s and (WALL) 0.04331274s -+Total time used in ONEGEN (CPU) 0.01034300s and (WALL) 0.01038289s - - - Generating Lowdin canonical matrix: -@@ -950,198 +957,198 @@ - Improved by a sum of atomic screening potentials. - - --########## START ITERATION NO. 1 ########## Sat Dec 7 14:42:43 2019 -+########## START ITERATION NO. 1 ########## Fri Oct 9 13:31:22 2020 - - E_HOMO...E_LUMO, symmetry 1: 35 -0.71357 36 -0.26323 37 -0.24641 - - => Calculating sum of orbital energies --It. 1 -7.674280262185 0.00D+00 0.00D+00 0.00D+00 0.12560900s Atom. scrpot Sat Dec 7 -+It. 1 -7.674280262172 0.00D+00 0.00D+00 0.00D+00 0.06623700s Atom. scrpot Fri Oct 9 - --########## START ITERATION NO. 2 ########## Sat Dec 7 14:42:43 2019 -+########## START ITERATION NO. 2 ########## Fri Oct 9 13:31:22 2020 - - - * GETGAB: label "GABAO1XX" not found; calling GABGEN. --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 1.46% 0.00% 0.00% 0.00942999s --SOfock:SL 1.00D-12 0.00% 3.79% 0.00% 0.00% 0.05662000s --SOfock:SS 1.00D-12 0.00% 20.74% 0.00% 0.01% 0.10877898s -- >>> CPU time used in SO Fock is 0.20 seconds -- >>> WALL time used in SO Fock is 0.20 seconds -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 1.46% 0.00% 0.00% 0.02674794s -+SOfock:SL 1.00D-12 0.00% 3.33% 0.00% 0.00% 0.04715800s -+SOfock:SS 1.00D-12 0.00% 16.16% 0.00% 0.01% 0.40942907s -+ >>> CPU time used in SO Fock is 0.51 seconds -+ >>> WALL time used in SO Fock is 0.51 seconds - E_HOMO...E_LUMO, symmetry 1: 35 -0.44417 36 -0.17374 37 0.09066 -->>> Total wall time: 0.21618455s, and total CPU time : 0.20654300s -+>>> Total wall time: 0.51878285s, and total CPU time : 0.50978200s - --########## END ITERATION NO. 2 ########## Sat Dec 7 14:42:43 2019 -+########## END ITERATION NO. 2 ########## Fri Oct 9 13:31:23 2020 - --It. 2 -14.98358612120 7.31D+00 2.41D+00 4.55D-01 0.21618455s LL SL SS Sat Dec 7 -+It. 2 -14.98358612120 7.31D+00 2.45D+00 4.55D-01 0.51878285s LL SL SS Fri Oct 9 - --########## START ITERATION NO. 3 ########## Sat Dec 7 14:42:43 2019 -+########## START ITERATION NO. 3 ########## Fri Oct 9 13:31:23 2020 - - 3 *** Differential density matrix. DCOVLP = 0.8705 - 3 *** Differential density matrix. DVOVLP( 1) = 0.5597 --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 1.61% 0.00% 0.00% 0.02192301s --SOfock:SL 1.00D-12 0.00% 4.22% 0.00% 0.00% 0.09345502s --SOfock:SS 1.00D-12 0.00% 24.94% 0.00% 0.00% 0.11746603s -- >>> CPU time used in SO Fock is 0.23 seconds -- >>> WALL time used in SO Fock is 0.23 seconds -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 1.61% 0.00% 0.00% 0.00927496s -+SOfock:SL 1.00D-12 0.00% 3.75% 0.00% 0.00% 0.04739094s -+SOfock:SS 1.00D-12 0.00% 19.36% 0.00% 0.00% 0.09083819s -+ >>> CPU time used in SO Fock is 0.14 seconds -+ >>> WALL time used in SO Fock is 0.15 seconds - E_HOMO...E_LUMO, symmetry 1: 35 -0.53225 36 -0.19666 37 0.07238 -->>> Total wall time: 0.25093168s, and total CPU time : 0.24143000s -+>>> Total wall time: 0.16109180s, and total CPU time : 0.13990600s - --########## END ITERATION NO. 3 ########## Sat Dec 7 14:42:43 2019 -+########## END ITERATION NO. 3 ########## Fri Oct 9 13:31:23 2020 - --It. 3 -15.05284570594 6.93D-02 -1.41D-01 5.42D-02 DIIS 2 0.25093168s LL SL SS Sat Dec 7 -+It. 3 -15.05284570594 6.93D-02 -1.44D-01 5.42D-02 DIIS 2 0.16109180s LL SL SS Fri Oct 9 - --########## START ITERATION NO. 4 ########## Sat Dec 7 14:42:43 2019 -+########## START ITERATION NO. 4 ########## Fri Oct 9 13:31:23 2020 - - 4 *** Differential density matrix. DCOVLP = 0.9834 - 4 *** Differential density matrix. DVOVLP( 1) = 0.9515 --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 1.81% 0.00% 0.00% 0.02005899s --SOfock:SL 1.00D-12 0.00% 4.34% 0.00% 0.00% 0.08984500s --SOfock:SS 1.00D-12 0.00% 32.11% 0.00% 0.01% 0.11502302s -- >>> CPU time used in SO Fock is 0.23 seconds -- >>> WALL time used in SO Fock is 0.23 seconds -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 1.81% 0.00% 0.00% 0.00935793s -+SOfock:SL 1.00D-12 0.00% 3.87% 0.00% 0.00% 0.04722786s -+SOfock:SS 1.00D-12 0.00% 24.66% 0.00% 0.00% 0.09067297s -+ >>> CPU time used in SO Fock is 0.15 seconds -+ >>> WALL time used in SO Fock is 0.15 seconds - E_HOMO...E_LUMO, symmetry 1: 35 -0.53644 36 -0.20054 37 0.07029 -->>> Total wall time: 0.23950611s, and total CPU time : 0.23095300s -+>>> Total wall time: 0.15968394s, and total CPU time : 0.15167100s - --########## END ITERATION NO. 4 ########## Sat Dec 7 14:42:44 2019 -+########## END ITERATION NO. 4 ########## Fri Oct 9 13:31:23 2020 - --It. 4 -15.05510762061 2.26D-03 -1.10D-02 9.87D-03 DIIS 3 0.23950611s LL SL SS Sat Dec 7 -+It. 4 -15.05510762061 2.26D-03 -1.16D-02 9.87D-03 DIIS 3 0.15968394s LL SL SS Fri Oct 9 - --########## START ITERATION NO. 5 ########## Sat Dec 7 14:42:44 2019 -+########## START ITERATION NO. 5 ########## Fri Oct 9 13:31:23 2020 - - 5 *** Differential density matrix. DCOVLP = 0.9975 - 5 *** Differential density matrix. DVOVLP( 1) = 0.9819 --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 1.93% 0.00% 0.00% 0.02133298s --SOfock:SL 1.00D-12 0.00% 5.03% 0.00% 0.00% 0.09153700s --SOfock:SS 1.00D-12 0.00% 38.49% 0.00% 0.01% 0.11206806s -- >>> CPU time used in SO Fock is 0.23 seconds -- >>> WALL time used in SO Fock is 0.23 seconds -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 1.93% 0.00% 0.00% 0.00927806s -+SOfock:SL 1.00D-12 0.00% 4.52% 0.00% 0.00% 0.04714084s -+SOfock:SS 1.00D-12 0.00% 29.54% 0.00% 0.01% 0.08947515s -+ >>> CPU time used in SO Fock is 0.15 seconds -+ >>> WALL time used in SO Fock is 0.15 seconds - E_HOMO...E_LUMO, symmetry 1: 35 -0.53821 36 -0.20014 37 0.06997 -->>> Total wall time: 0.23837635s, and total CPU time : 0.23003500s -+>>> Total wall time: 0.15834403s, and total CPU time : 0.15030500s - --########## END ITERATION NO. 5 ########## Sat Dec 7 14:42:44 2019 -+########## END ITERATION NO. 5 ########## Fri Oct 9 13:31:23 2020 - --It. 5 -15.05525091501 1.43D-04 -3.58D-03 2.02D-03 DIIS 4 0.23837635s LL SL SS Sat Dec 7 -+It. 5 -15.05525091501 1.43D-04 -3.76D-03 2.02D-03 DIIS 4 0.15834403s LL SL SS Fri Oct 9 - --########## START ITERATION NO. 6 ########## Sat Dec 7 14:42:44 2019 -+########## START ITERATION NO. 6 ########## Fri Oct 9 13:31:23 2020 - - 6 *** Differential density matrix. DCOVLP = 0.9998 - 6 *** Differential density matrix. DVOVLP( 1) = 0.9966 --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 2.23% 0.00% 0.00% 0.00905704s --SOfock:SL 1.00D-12 0.00% 6.15% 0.00% 0.00% 0.05483294s --SOfock:SS 1.00D-12 0.00% 48.95% 0.01% 0.04% 0.09789610s -- >>> CPU time used in SO Fock is 0.16 seconds -- >>> WALL time used in SO Fock is 0.16 seconds -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 2.23% 0.00% 0.00% 0.00926590s -+SOfock:SL 1.00D-12 0.00% 5.56% 0.00% 0.00% 0.04719806s -+SOfock:SS 1.00D-12 0.00% 37.52% 0.01% 0.03% 0.08690405s -+ >>> CPU time used in SO Fock is 0.14 seconds -+ >>> WALL time used in SO Fock is 0.14 seconds - E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20011 37 0.06998 -->>> Total wall time: 0.17357306s, and total CPU time : 0.16528300s -+>>> Total wall time: 0.15521312s, and total CPU time : 0.14776100s - --########## END ITERATION NO. 6 ########## Sat Dec 7 14:42:44 2019 -+########## END ITERATION NO. 6 ########## Fri Oct 9 13:31:23 2020 - --It. 6 -15.05525770434 6.79D-06 -3.53D-04 3.01D-04 DIIS 5 0.17357306s LL SL SS Sat Dec 7 -+It. 6 -15.05525770434 6.79D-06 -3.61D-04 3.01D-04 DIIS 5 0.15521312s LL SL SS Fri Oct 9 - --########## START ITERATION NO. 7 ########## Sat Dec 7 14:42:44 2019 -+########## START ITERATION NO. 7 ########## Fri Oct 9 13:31:23 2020 - - 7 *** Differential density matrix. DCOVLP = 1.0001 - 7 *** Differential density matrix. DVOVLP( 1) = 0.9998 --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 3.25% 0.00% 0.00% 0.00905895s --SOfock:SL 1.00D-12 0.00% 8.74% 0.00% 0.00% 0.05451703s --SOfock:SS 1.00D-12 0.00% 63.88% 0.13% 0.67% 0.09414506s -- >>> CPU time used in SO Fock is 0.16 seconds -- >>> WALL time used in SO Fock is 0.16 seconds -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 3.25% 0.00% 0.00% 0.00925994s -+SOfock:SL 1.00D-12 0.00% 8.04% 0.00% 0.00% 0.04709005s -+SOfock:SS 1.00D-12 0.00% 49.16% 0.10% 0.50% 0.08579898s -+ >>> CPU time used in SO Fock is 0.14 seconds -+ >>> WALL time used in SO Fock is 0.14 seconds - E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20010 37 0.06998 -->>> Total wall time: 0.16939002s, and total CPU time : 0.16115200s -+>>> Total wall time: 0.15497518s, and total CPU time : 0.14641300s - --########## END ITERATION NO. 7 ########## Sat Dec 7 14:42:44 2019 -+########## END ITERATION NO. 7 ########## Fri Oct 9 13:31:23 2020 - --It. 7 -15.05525782410 1.20D-07 -4.18D-05 5.31D-05 DIIS 6 0.16939002s LL SL SS Sat Dec 7 -+It. 7 -15.05525782410 1.20D-07 -4.48D-05 5.31D-05 DIIS 6 0.15497518s LL SL SS Fri Oct 9 - --########## START ITERATION NO. 8 ########## Sat Dec 7 14:42:44 2019 -+########## START ITERATION NO. 8 ########## Fri Oct 9 13:31:23 2020 - - 8 *** Differential density matrix. DCOVLP = 1.0000 - 8 *** Differential density matrix. DVOVLP( 1) = 1.0000 --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 4.74% 0.00% 0.00% 0.00904500s --SOfock:SL 1.00D-12 0.00% 13.21% 0.00% 0.08% 0.05417407s --SOfock:SS 1.00D-12 0.00% 77.26% 1.03% 1.70% 0.09023106s -- >>> CPU time used in SO Fock is 0.15 seconds -- >>> WALL time used in SO Fock is 0.15 seconds -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 4.74% 0.00% 0.00% 0.00932503s -+SOfock:SL 1.00D-12 0.00% 12.27% 0.00% 0.07% 0.04715800s -+SOfock:SS 1.00D-12 0.00% 60.13% 0.76% 1.27% 0.08434606s -+ >>> CPU time used in SO Fock is 0.14 seconds -+ >>> WALL time used in SO Fock is 0.14 seconds - E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20011 37 0.06997 -->>> Total wall time: 0.16520095s, and total CPU time : 0.15693500s -+>>> Total wall time: 0.15240192s, and total CPU time : 0.14500100s - --########## END ITERATION NO. 8 ########## Sat Dec 7 14:42:44 2019 -+########## END ITERATION NO. 8 ########## Fri Oct 9 13:31:23 2020 - --It. 8 -15.05525782821 4.11D-09 -1.39D-05 1.07D-05 DIIS 7 0.16520095s LL SL SS Sat Dec 7 -+It. 8 -15.05525782821 4.11D-09 -1.45D-05 1.07D-05 DIIS 7 0.15240192s LL SL SS Fri Oct 9 - --########## START ITERATION NO. 9 ########## Sat Dec 7 14:42:44 2019 -+########## START ITERATION NO. 9 ########## Fri Oct 9 13:31:23 2020 - - 9 *** Differential density matrix. DCOVLP = 1.0000 - 9 *** Differential density matrix. DVOVLP( 1) = 1.0000 --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 6.65% 0.00% 0.00% 0.00903404s --SOfock:SL 1.00D-12 0.00% 15.69% 0.00% 0.16% 0.05398393s --SOfock:SS 1.00D-12 0.05% 86.49% 1.46% 2.28% 0.08701098s -- >>> CPU time used in SO Fock is 0.15 seconds -- >>> WALL time used in SO Fock is 0.15 seconds -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 6.65% 0.00% 0.00% 0.00931311s -+SOfock:SL 1.00D-12 0.00% 14.70% 0.00% 0.15% 0.04640913s -+SOfock:SS 1.00D-12 0.04% 67.57% 1.07% 1.72% 0.08009100s -+ >>> CPU time used in SO Fock is 0.14 seconds -+ >>> WALL time used in SO Fock is 0.14 seconds - E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20011 37 0.06997 -->>> Total wall time: 0.16172978s, and total CPU time : 0.15342500s -+>>> Total wall time: 0.15059400s, and total CPU time : 0.14014200s - --########## END ITERATION NO. 9 ########## Sat Dec 7 14:42:44 2019 -+########## END ITERATION NO. 9 ########## Fri Oct 9 13:31:24 2020 - --It. 9 -15.05525782849 2.85D-10 -4.04D-06 2.99D-06 DIIS 8 0.16172978s LL SL SS Sat Dec 7 -+It. 9 -15.05525782849 2.85D-10 -4.04D-06 2.99D-06 DIIS 8 0.15059400s LL SL SS Fri Oct 9 - --########## START ITERATION NO. 10 ########## Sat Dec 7 14:42:44 2019 -+########## START ITERATION NO. 10 ########## Fri Oct 9 13:31:24 2020 - - 10 *** Differential density matrix. DCOVLP = 1.0000 - 10 *** Differential density matrix. DVOVLP( 1) = 1.0000 --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 10.00% 0.00% 0.00% 0.00899804s --SOfock:SL 1.00D-12 0.00% 19.77% 0.00% 0.96% 0.05157399s --SOfock:SS 1.00D-12 2.22% 92.45% 1.67% 2.10% 0.07210994s -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 10.00% 0.00% 0.00% 0.00906515s -+SOfock:SL 1.00D-12 0.00% 18.73% 0.00% 0.88% 0.04602289s -+SOfock:SS 1.00D-12 1.70% 72.87% 0.93% 1.41% 0.07452011s - >>> CPU time used in SO Fock is 0.13 seconds - >>> WALL time used in SO Fock is 0.13 seconds - E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20011 37 0.06997 -->>> Total wall time: 0.14423264s, and total CPU time : 0.13602100s -+>>> Total wall time: 0.14401197s, and total CPU time : 0.13443000s - --########## END ITERATION NO. 10 ########## Sat Dec 7 14:42:45 2019 -+########## END ITERATION NO. 10 ########## Fri Oct 9 13:31:24 2020 - --It. 10 -15.05525782853 4.23D-11 7.89D-07 1.39D-06 DIIS 9 0.14423264s LL SL SS Sat Dec 7 -+It. 10 -15.05525782853 4.23D-11 -1.26D-06 1.39D-06 DIIS 9 0.14401197s LL SL SS Fri Oct 9 - --########## START ITERATION NO. 11 ########## Sat Dec 7 14:42:45 2019 -+########## START ITERATION NO. 11 ########## Fri Oct 9 13:31:24 2020 - - 11 *** Differential density matrix. DCOVLP = 1.0000 - 11 *** Differential density matrix. DVOVLP( 1) = 1.0000 --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 10.88% 0.00% 0.00% 0.00829506s --SOfock:SL 1.00D-12 0.00% 20.91% 0.00% 1.37% 0.04777408s --SOfock:SS 1.00D-12 7.35% 88.45% 3.34% 3.78% 0.06809211s -- >>> CPU time used in SO Fock is 0.12 seconds -- >>> WALL time used in SO Fock is 0.12 seconds -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 10.88% 0.00% 0.00% 0.00939202s -+SOfock:SL 1.00D-12 0.00% 19.86% 0.00% 1.26% 0.04657388s -+SOfock:SS 1.00D-12 5.62% 70.00% 1.11% 1.65% 0.07107210s -+ >>> CPU time used in SO Fock is 0.13 seconds -+ >>> WALL time used in SO Fock is 0.13 seconds - E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20011 37 0.06997 -->>> Total wall time: 0.13559033s, and total CPU time : 0.12737000s -+>>> Total wall time: 0.14050508s, and total CPU time : 0.13166000s - --########## END ITERATION NO. 11 ########## Sat Dec 7 14:42:45 2019 -+########## END ITERATION NO. 11 ########## Fri Oct 9 13:31:24 2020 - --It. 11 -15.05525782855 1.26D-11 7.22D-07 2.76D-07 DIIS 9 0.13559033s LL SL SS Sat Dec 7 -+It. 11 -15.05525782855 1.26D-11 -8.54D-07 2.76D-07 DIIS 9 0.14050508s LL SL SS Fri Oct 9 - --########## START ITERATION NO. 12 ########## Sat Dec 7 14:42:45 2019 -+########## START ITERATION NO. 12 ########## Fri Oct 9 13:31:24 2020 - - 12 *** Differential density matrix. DCOVLP = 1.0000 - 12 *** Differential density matrix. DVOVLP( 1) = 1.0000 --SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time --SOfock:LL 1.00D-12 0.00% 14.91% 0.00% 0.01% 0.00819111s --SOfock:SL 1.00D-12 0.00% 26.31% 0.00% 4.16% 0.04727006s --SOfock:SS 1.00D-12 27.72% 71.16% 7.71% 10.99% 0.05253100s -+SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time -+SOfock:LL 1.00D-12 0.00% 14.91% 0.00% 0.01% 0.00926995s -+SOfock:SL 1.00D-12 0.00% 25.16% 0.00% 3.83% 0.04634213s -+SOfock:SS 1.00D-12 21.18% 57.02% 0.45% 2.31% 0.05649400s - >>> CPU time used in SO Fock is 0.11 seconds - >>> WALL time used in SO Fock is 0.11 seconds -->>> Total wall time: 0.11815968s, and total CPU time : 0.11058100s -+>>> Total wall time: 0.12363100s, and total CPU time : 0.11607500s - --########## END ITERATION NO. 12 ########## Sat Dec 7 14:42:45 2019 -+########## END ITERATION NO. 12 ########## Fri Oct 9 13:31:24 2020 - --It. 12 -15.05525782855 3.59D-13 1.43D-07 1.38D-08 DIIS 9 0.11815968s LL SL SS Sat Dec 7 -+It. 12 -15.05525782855 3.73D-13 -1.53D-07 1.38D-08 DIIS 9 0.12363100s LL SL SS Fri Oct 9 - - - SCF - CYCLE -@@ -1157,35 +1164,35 @@ - -------------------------------------------------------------------------------------------------------------------------------- - Energy ERGVAL FCKVAL EVCVAL Conv.acc CPU Integrals Time stamp - -------------------------------------------------------------------------------------------------------------------------------- --It. 1 -7.674280262185 0.00D+00 0.00D+00 0.00D+00 0.12560900s Atom. scrpot Sat Dec 7 --It. 2 -14.98358612120 7.31D+00 2.41D+00 4.55D-01 0.21618455s LL SL SS Sat Dec 7 --It. 3 -15.05284570594 6.93D-02 -1.41D-01 5.42D-02 DIIS 2 0.25093168s LL SL SS Sat Dec 7 --It. 4 -15.05510762061 2.26D-03 -1.10D-02 9.87D-03 DIIS 3 0.23950611s LL SL SS Sat Dec 7 --It. 5 -15.05525091501 1.43D-04 -3.58D-03 2.02D-03 DIIS 4 0.23837635s LL SL SS Sat Dec 7 --It. 6 -15.05525770434 6.79D-06 -3.53D-04 3.01D-04 DIIS 5 0.17357306s LL SL SS Sat Dec 7 --It. 7 -15.05525782410 1.20D-07 -4.18D-05 5.31D-05 DIIS 6 0.16939002s LL SL SS Sat Dec 7 --It. 8 -15.05525782821 4.11D-09 -1.39D-05 1.07D-05 DIIS 7 0.16520095s LL SL SS Sat Dec 7 --It. 9 -15.05525782849 2.85D-10 -4.04D-06 2.99D-06 DIIS 8 0.16172978s LL SL SS Sat Dec 7 --It. 10 -15.05525782853 4.23D-11 7.89D-07 1.39D-06 DIIS 9 0.14423264s LL SL SS Sat Dec 7 --It. 11 -15.05525782855 1.26D-11 7.22D-07 2.76D-07 DIIS 9 0.13559033s LL SL SS Sat Dec 7 --It. 12 -15.05525782855 3.59D-13 1.43D-07 1.38D-08 DIIS 9 0.11815968s LL SL SS Sat Dec 7 -+It. 1 -7.674280262172 0.00D+00 0.00D+00 0.00D+00 0.06623700s Atom. scrpot Fri Oct 9 -+It. 2 -14.98358612120 7.31D+00 2.45D+00 4.55D-01 0.51878285s LL SL SS Fri Oct 9 -+It. 3 -15.05284570594 6.93D-02 -1.44D-01 5.42D-02 DIIS 2 0.16109180s LL SL SS Fri Oct 9 -+It. 4 -15.05510762061 2.26D-03 -1.16D-02 9.87D-03 DIIS 3 0.15968394s LL SL SS Fri Oct 9 -+It. 5 -15.05525091501 1.43D-04 -3.76D-03 2.02D-03 DIIS 4 0.15834403s LL SL SS Fri Oct 9 -+It. 6 -15.05525770434 6.79D-06 -3.61D-04 3.01D-04 DIIS 5 0.15521312s LL SL SS Fri Oct 9 -+It. 7 -15.05525782410 1.20D-07 -4.48D-05 5.31D-05 DIIS 6 0.15497518s LL SL SS Fri Oct 9 -+It. 8 -15.05525782821 4.11D-09 -1.45D-05 1.07D-05 DIIS 7 0.15240192s LL SL SS Fri Oct 9 -+It. 9 -15.05525782849 2.85D-10 -4.04D-06 2.99D-06 DIIS 8 0.15059400s LL SL SS Fri Oct 9 -+It. 10 -15.05525782853 4.23D-11 -1.26D-06 1.39D-06 DIIS 9 0.14401197s LL SL SS Fri Oct 9 -+It. 11 -15.05525782855 1.26D-11 -8.54D-07 2.76D-07 DIIS 9 0.14050508s LL SL SS Fri Oct 9 -+It. 12 -15.05525782855 3.73D-13 -1.53D-07 1.38D-08 DIIS 9 0.12363100s LL SL SS Fri Oct 9 - -------------------------------------------------------------------------------------------------------------------------------- - * Convergence after 12 iterations. - * Average elapsed time per iteration: -- No 2-ints : 0.12560757s -- LL SL SS : 0.18298865s -+ No 2-ints : 0.06805897s -+ LL SL SS : 0.18356681s - - - TOTAL ENERGY - ------------ - -- Electronic energy : -17.364060097770729 -+ Electronic energy : -17.364060097770743 - - Other contributions to the total energy - Nuclear repulsion energy : 2.308802269222842 - - Sum of all contributions to the energy -- Total energy : -15.055257828547887 -+ Total energy : -15.055257828547902 - - - Eigenvalues -@@ -1194,24 +1201,24 @@ - - * Block 1 in E1 : Omega = 1/2 - * Closed shell, f = 1.0000 -- -4.679468376338 ( 2) -0.538243701490 ( 2) -+ -4.679468376327 ( 2) -0.538243701490 ( 2) - * Open shell #1, f = 0.5000 - -0.200107364292 ( 2) - * Virtual eigenvalues, f = 0.0000 -- 0.069973271793 ( 2) 0.146585677662 ( 2) 0.290043259674 ( 2) 0.329894286245 ( 2) 0.443382601574 ( 2) -- 0.636678743326 ( 2) 0.675079413170 ( 2) 1.116750847420 ( 2) 1.366626079642 ( 2) 1.477429645290 ( 2) -- 2.022794797755 ( 2) 2.267117385980 ( 2) 3.573003609718 ( 2) 4.000999068608 ( 2) 7.165692855382 ( 2) -- 7.349371984843 ( 2) 15.727399978192 ( 2) 22.596336602594 ( 2) 58.756173314173 ( 2) 219.560006375315 ( 2) -- 924.777802919416 ( 2) 4979.576710887137 ( 2) -+ 0.069973271798 ( 2) 0.146585677680 ( 2) 0.290043259672 ( 2) 0.329894286248 ( 2) 0.443382601571 ( 2) -+ 0.636678743335 ( 2) 0.675079413169 ( 2) 1.116750847424 ( 2) 1.366626079649 ( 2) 1.477429645297 ( 2) -+ 2.022794797753 ( 2) 2.267117385992 ( 2) 3.573003609720 ( 2) 4.000999068610 ( 2) 7.165692855389 ( 2) -+ 7.349371984860 ( 2) 15.727399978201 ( 2) 22.596336602582 ( 2) 58.756173314180 ( 2) 219.560006375432 ( 2) -+ 924.777802919401 ( 2) 4979.576710887086 ( 2) - - * Block 2 in E1 : Omega = 3/2 - * Virtual eigenvalues, f = 0.0000 -- 0.069977662719 ( 2) 0.329912044238 ( 2) 0.636681004307 ( 2) 0.656492047535 ( 2) 1.366714153093 ( 2) -- 2.022824837061 ( 2) 7.166842638253 ( 2) -+ 0.069977662718 ( 2) 0.329912044241 ( 2) 0.636681004320 ( 2) 0.656492047523 ( 2) 1.366714153101 ( 2) -+ 2.022824837060 ( 2) 7.166842638267 ( 2) - - * Block 3 in E1 : Omega = 5/2 - * Virtual eigenvalues, f = 0.0000 -- 0.656497922027 ( 2) -+ 0.656497922020 ( 2) - - * Occupation in fermion symmetry E1 - * Inactive orbitals -@@ -1321,7 +1328,7 @@ - - (RSETCI) Number of determinants: 3366 (dimension 3366) - -- CPU (Wall) time for generation of determinants: 0.22480200s( 0.22480234s) -+ CPU (Wall) time for generation of determinants: 0.21247500s( 0.21325493s) - - (RSETWOP) Orbital classes: - Inactive orbitals : -@@ -1335,40 +1342,54 @@ - Vector containing mj-values saved as MJVEC on KRMCSCF - - (RTRACTL1) Starting 4-index integral transformation. -- - Integral class 1 : (LL|??) -- - Beginning task 1 of 5 after 0. seconds and 0. CPU-seconds -- - Beginning task 2 of 5 after 0. seconds and 0. CPU-seconds -- - Beginning task 3 of 5 after 0. seconds and 0. CPU-seconds -- - Beginning task 4 of 5 after 0. seconds and 0. CPU-seconds -- - Beginning task 5 of 5 after 0. seconds and 0. CPU-seconds -+ -+ * Max no. of B shells in a task determined to be 8 - - Integral class 2 : (SS|??) -- - Beginning task 6 of 13 after 0. seconds and 0. CPU-seconds -- - Beginning task 7 of 13 after 0. seconds and 0. CPU-seconds -- - Beginning task 8 of 13 after 0. seconds and 0. CPU-seconds -- - Beginning task 9 of 13 after 0. seconds and 0. CPU-seconds -- - Beginning task 10 of 13 after 0. seconds and 0. CPU-seconds -- - Beginning task 11 of 13 after 0. seconds and 0. CPU-seconds -- - Beginning task 12 of 13 after 0. seconds and 0. CPU-seconds -- - Beginning task 13 of 13 after 1. seconds and 1. CPU-seconds -+ - Starting shell A no. 13 after 0.00 seconds. -+ - Starting shell A no. 12 after 0.00 seconds. -+ - Starting shell A no. 11 after 0.07 seconds. -+ - Starting shell A no. 10 after 0.15 seconds. -+ - Starting shell A no. 9 after 0.18 seconds. -+ - Starting shell A no. 8 after 0.24 seconds. -+ - Starting shell A no. 7 after 0.32 seconds. -+ - Starting shell A no. 6 after 0.33 seconds. -+ - Integral class 1 : (LL|??) -+ - Starting shell A no. 5 after 0.37 seconds. -+ - Starting shell A no. 4 after 0.38 seconds. -+ - Starting shell A no. 3 after 0.41 seconds. -+ - Starting shell A no. 2 after 0.43 seconds. -+ - Starting shell A no. 1 after 0.45 seconds. -+ - Process 1 finished at 0.48 seconds after start - -- - Starting symmetrization after 0.62 seconds -- - Finished symmetrization after 0.62 seconds -+ - Starting symmetrization after 0.48 seconds -+ - Finished symmetrization after 0.49 seconds - - - ------ Timing report (in CPU seconds) of module integral transformation - -- Time in Initializing MS4IND file 0.011 seconds -- Time in Computing+transform. integral 0.624 seconds -- Time in Symmetrizing MO integrals 0.000 seconds -+ -+ -+ Master --------- Slaves ------------ -+ -+ Timer Master Minimum Maximum Average -+ -+ Initializing MS4IND file 0.0 0.0 0.0 0.0 -+ Slave requesting task from ma 0.5 0.0 0.0 0.0 -+ Master and slave negotiating 0.0 0.0 0.0 0.0 -+ Symmetrizing MO integrals 0.0 0.0 0.0 0.0 -+ Computing+transform. integral 0.0 0.5 0.5 0.5 -+ -+------ End of timing report ------ -+ - - (RTRACTL1) Total CPU (wall) time used : 00:00:01 ( 00:00:01) -- Transformation ended Sat Dec 7 14:42:46 2019 -+ Transformation ended Fri Oct 9 13:31:25 2020 - // LUCIAREL called - // CIRUN = KR-CI - // Running large-scale CI calculation - --* REAFCK: Fock matrix read from file DFFCK1 --* Heading :BeH Sat Dec 7 14:42:43 2019 -+* REAFCK: Fock matrix read from file /dev/shm/build/DIRAC/19.0/intel-2020a-Python-2.7.18-mpi-int6 -+* Heading :BeH Fri Oct 9 13:31:22 2020 - Allocating for 3480 diagonal integrals. - - -@@ -1378,14 +1399,34 @@ - (including imaginary parts) - - -+ =================================================== -+ parallel distribution setup for symmetry irrep 65 -+ =================================================== -+ -+ total number of processes to distribute on : 2 -+ total number of blocks : 13056 -+ total number of active blocks : 29 -+ size of largest TTSS block : 784 -+ overall weighted active block length : 214301 -+ Maximum weighted block size : 61936 -+ -+ ================================ -+ Summation of even distribution -+ ================================ -+ -+ CPU 0 computes 15 blocks with a total weight of 107168 -+ CPU 1 computes 14 blocks with a total weight of 107133 -+ - ============================================================== - ==> allocation of two CI vectors and one resolution vector <== - -- current available free memory in double words: 1999304192 -+ current available free memory in double words: 63304144 - allocate two CI vectors each of length: 3366 - allocate resolution vector of length: 3366 - ============================================================== - -+ -+ - - 2 start vectors based on lowest diagonal elements of H_CI - 1 -15.055258 -@@ -1397,270 +1438,330 @@ - - Maximum number of CI microiterations ... 50 - -- -+ - ---------------------------------------------- -- I'll take you to a place -+ I'll take you to a place - Where we shall find our -- ROOTS, BLOODY ROOTS -- -- Sepultura -+ ROOTS, BLOODY ROOTS -+ -+ Sepultura - ---------------------------------------------- -+ - - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 1 -+ Total energy = -15.05525783 -+ Lowering of energy = -0.00000000 - -- (MICDV4_ENLMD_REL) CI microiteration no. 1 -- Total energy = -15.05525783 -- Lowering of energy = -0.00000000 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 4.37450D-01 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 4.37450D-01 -+ Wall time for microiteration 0.38906469s - -- CPU (Wall) time for microiteration 1.20469400s( 1.21234911s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 2 -+ Total energy = -15.09785782 -+ Lowering of energy = 0.04259999 - -- (MICDV4_ENLMD_REL) CI microiteration no. 2 -- Total energy = -15.09785782 -- Lowering of energy = 0.04259999 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.39990D-01 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 1.39990D-01 -+ Wall time for microiteration 0.41679055s - -- CPU (Wall) time for microiteration 0.95826800s( 0.96383090s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 3 -+ Total energy = -15.10221442 -+ Lowering of energy = 0.00435660 - -- (MICDV4_ENLMD_REL) CI microiteration no. 3 -- Total energy = -15.10221442 -- Lowering of energy = 0.00435660 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 6.68601D-02 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 6.68601D-02 -+ Wall time for microiteration 0.41734640s - -- CPU (Wall) time for microiteration 1.23481700s( 1.24102225s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 4 -+ Total energy = -15.10336430 -+ Lowering of energy = 0.00114988 - -- (MICDV4_ENLMD_REL) CI microiteration no. 4 -- Total energy = -15.10336430 -- Lowering of energy = 0.00114988 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.84414D-02 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 1.84414D-02 -+ Wall time for microiteration 0.41587336s - -- CPU (Wall) time for microiteration 0.96459800s( 0.96983010s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 5 -+ Total energy = -15.10355258 -+ Lowering of energy = 0.00018829 - -- (MICDV4_ENLMD_REL) CI microiteration no. 5 -- Total energy = -15.10355258 -- Lowering of energy = 0.00018829 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.86545D-02 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 1.86545D-02 -+ Wall time for microiteration 0.41766227s - -- CPU (Wall) time for microiteration 1.23176500s( 1.23788811s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 6 -+ Total energy = -15.10365534 -+ Lowering of energy = 0.00010276 - -- (MICDV4_ENLMD_REL) CI microiteration no. 6 -- Total energy = -15.10365534 -- Lowering of energy = 0.00010276 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.02051D-02 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 1.02051D-02 -+ Wall time for microiteration 0.41570181s - -- CPU (Wall) time for microiteration 0.96846600s( 0.97378551s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 7 -+ Total energy = -15.10368496 -+ Lowering of energy = 0.00002962 - -- (MICDV4_ENLMD_REL) CI microiteration no. 7 -- Total energy = -15.10368496 -- Lowering of energy = 0.00002962 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 6.64018D-03 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 6.64018D-03 -+ Wall time for microiteration 0.41870350s - -- CPU (Wall) time for microiteration 1.24741500s( 1.25294369s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 8 -+ Total energy = -15.10369583 -+ Lowering of energy = 0.00001087 - -- (MICDV4_ENLMD_REL) CI microiteration no. 8 -- Total energy = -15.10369583 -- Lowering of energy = 0.00001087 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 3.19312D-03 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 3.19312D-03 -+ Wall time for microiteration 0.41609852s - -- CPU (Wall) time for microiteration 0.96903700s( 0.97438777s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 9 -+ Total energy = -15.10370048 -+ Lowering of energy = 0.00000465 - -- (MICDV4_ENLMD_REL) CI microiteration no. 9 -- Total energy = -15.10370048 -- Lowering of energy = 0.00000465 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 3.23467D-03 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 3.23467D-03 -+ Wall time for microiteration 0.41777307s - -- CPU (Wall) time for microiteration 1.22110400s( 1.22825285s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 10 -+ Total energy = -15.10370322 -+ Lowering of energy = 0.00000274 - -- (MICDV4_ENLMD_REL) CI microiteration no. 10 -- Total energy = -15.10370322 -- Lowering of energy = 0.00000274 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.97047D-03 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 1.97047D-03 -+ Wall time for microiteration 0.41673967s - -- CPU (Wall) time for microiteration 0.92580700s( 0.93142437s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 11 -+ Total energy = -15.10370430 -+ Lowering of energy = 0.00000108 - -- (MICDV4_ENLMD_REL) CI microiteration no. 11 -- Total energy = -15.10370430 -- Lowering of energy = 0.00000108 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.39286D-03 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 1.39286D-03 -+ Wall time for microiteration 0.41791135s - -- CPU (Wall) time for microiteration 1.21935300s( 1.22573134s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 12 -+ Total energy = -15.10370471 -+ Lowering of energy = 0.00000041 - -- (MICDV4_ENLMD_REL) CI microiteration no. 12 -- Total energy = -15.10370471 -- Lowering of energy = 0.00000041 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 6.78879D-04 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 6.78879D-04 -+ Wall time for microiteration 0.41635790s - -- CPU (Wall) time for microiteration 0.96845200s( 0.97368623s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 13 -+ Total energy = -15.10370491 -+ Lowering of energy = 0.00000019 - -- (MICDV4_ENLMD_REL) CI microiteration no. 13 -- Total energy = -15.10370491 -- Lowering of energy = 0.00000019 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 7.08771D-04 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 7.08771D-04 -+ Wall time for microiteration 0.42354180s - -- CPU (Wall) time for microiteration 1.24966800s( 1.25543883s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 14 -+ Total energy = -15.10370502 -+ Lowering of energy = 0.00000012 - -- (MICDV4_ENLMD_REL) CI microiteration no. 14 -- Total energy = -15.10370502 -- Lowering of energy = 0.00000012 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 4.23480D-04 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 4.23480D-04 -+ Wall time for microiteration 0.41584093s - -- CPU (Wall) time for microiteration 0.95248500s( 0.95758762s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 15 -+ Total energy = -15.10370507 -+ Lowering of energy = 0.00000005 - -- (MICDV4_ENLMD_REL) CI microiteration no. 15 -- Total energy = -15.10370507 -- Lowering of energy = 0.00000005 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 3.04533D-04 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 3.04533D-04 -+ Wall time for microiteration 0.41808349s - -- CPU (Wall) time for microiteration 1.24777200s( 1.25355540s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 16 -+ Total energy = -15.10370509 -+ Lowering of energy = 0.00000002 - -- (MICDV4_ENLMD_REL) CI microiteration no. 16 -- Total energy = -15.10370509 -- Lowering of energy = 0.00000002 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.50921D-04 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 1.50921D-04 -+ Wall time for microiteration 0.41666777s - -- CPU (Wall) time for microiteration 1.01747300s( 1.05122897s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 17 -+ Total energy = -15.10370510 -+ Lowering of energy = 0.00000001 - -- (MICDV4_ENLMD_REL) CI microiteration no. 17 -- Total energy = -15.10370510 -- Lowering of energy = 0.00000001 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.53262D-04 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 1.53262D-04 -+ Wall time for microiteration 0.41730021s - -- CPU (Wall) time for microiteration 1.24111700s( 1.24705948s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 18 -+ Total energy = -15.10370510 -+ Lowering of energy = 0.00000001 - -- (MICDV4_ENLMD_REL) CI microiteration no. 18 -- Total energy = -15.10370510 -- Lowering of energy = 0.00000001 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 9.48004D-05 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 9.48004D-05 -+ Wall time for microiteration 0.41675383s - -- CPU (Wall) time for microiteration 0.96130400s( 0.96728180s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 19 -+ Total energy = -15.10370510 -+ Lowering of energy = 0.00000000 - -- (MICDV4_ENLMD_REL) CI microiteration no. 19 -- Total energy = -15.10370510 -- Lowering of energy = 0.00000000 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 6.58500D-05 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 6.58500D-05 -+ Wall time for microiteration 0.41868551s - -- CPU (Wall) time for microiteration 1.24445300s( 1.25093647s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 20 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 - -- (MICDV4_ENLMD_REL) CI microiteration no. 20 -- Total energy = -15.10370511 -- Lowering of energy = 0.00000000 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 3.40204D-05 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 3.40204D-05 -+ Wall time for microiteration 0.41628122s - -- CPU (Wall) time for microiteration 0.96835700s( 0.97404379s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 21 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 - -- (MICDV4_ENLMD_REL) CI microiteration no. 21 -- Total energy = -15.10370511 -- Lowering of energy = 0.00000000 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 3.33886D-05 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 3.33886D-05 -+ Wall time for microiteration 0.41618816s - -- CPU (Wall) time for microiteration 1.18932100s( 1.19510286s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 22 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 - -- (MICDV4_ENLMD_REL) CI microiteration no. 22 -- Total energy = -15.10370511 -- Lowering of energy = 0.00000000 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 2.14673D-05 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 2.14673D-05 -+ Wall time for microiteration 0.41732191s - -- CPU (Wall) time for microiteration 0.96339800s( 0.97118922s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 23 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 - -- (MICDV4_ENLMD_REL) CI microiteration no. 23 -- Total energy = -15.10370511 -- Lowering of energy = 0.00000000 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.44211D-05 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 1.44211D-05 -+ Wall time for microiteration 0.41780390s - -- CPU (Wall) time for microiteration 1.23398800s( 1.23978875s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 24 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 - -- (MICDV4_ENLMD_REL) CI microiteration no. 24 -- Total energy = -15.10370511 -- Lowering of energy = 0.00000000 -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 7.72802D-06 - -- Norm of CI residuals (thr = 1.00D-05) -- 1 7.72802D-06 -+ Wall time for microiteration 0.41720308s - -- CPU (Wall) time for microiteration 0.08609000s( 0.08613085s) - -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 25 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 - -- (MICDV4_ENLMD_REL) Micro iterations converged. -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 7.37801D-06 - -- Core energy = 2.30880227 -- Active energies = -17.41250738 -- Final CI energies = -15.10370511 -+ Wall time for microiteration 0.41947213s - -- root 1 ...... converged! - -- I have completed task KR-CI in 26.37510378s (wall time) -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 26 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 -+ -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 4.89162D-06 -+ -+ Wall time for microiteration 0.41700623s -+ -+ -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 27 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 -+ -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 3.20093D-06 -+ -+ Wall time for microiteration 0.41741276s -+ -+ -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 28 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 -+ -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.76410D-06 -+ -+ Wall time for microiteration 0.41627715s -+ -+ -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 29 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 -+ -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.64937D-06 -+ -+ Wall time for microiteration 0.41783292s -+ -+ -+ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 30 -+ Total energy = -15.10370511 -+ Lowering of energy = 0.00000000 -+ -+ Norm of CI residuals (thr = 1.00D-06) -+ 1 1.11914D-06 -+ -+ Wall time for microiteration 0.00072046s -+ -+ -+ (MICDV4_ENLMD_REL_PAR) Micro iterations converged. -+ -+ Core energy = 2.30880227 -+ Active energies = -17.41250738 -+ Final CI energies = -15.10370511 -+ -+ root 1 ...... converged! -+ -+ I have completed task KR-CI in 12.58797884s (wall time) - - (ROPTST) KR-CI calculation ended properly. - -->>> TOTAL CPU (WALL) TIME IN KR-CI: 27.82514200s(28.00508189s) -+>>> TOTAL CPU (WALL) TIME IN KR-CI: 14.02860500s(14.16464686s) - - - -@@ -1699,7 +1800,7 @@ - - (RSETCI) Number of determinants: 3366 (dimension 3366) - -- CPU (Wall) time for generation of determinants: 0.25193400s( 0.25195498s) -+ CPU (Wall) time for generation of determinants: 0.19848500s( 0.20092607s) - - (RSETWOP) Orbital classes: - Inactive orbitals : -@@ -1745,12 +1846,12 @@ - _________________________________ - Total 1 - -- Diagonal and Off-diagonal blocks are exchanged for Y1-HYP -- Diagonal and Off-diagonal blocks are exchanged for Y2-HYP -- Diagonal and Off-diagonal blocks are exchanged for X1-HYP -- Sign of the lower diagonal block is changed for X1-HYP -- Diagonal and Off-diagonal blocks are exchanged for X2-HYP -- Sign of the lower diagonal block is changed for X2-HYP -+ Diagonal and Off-diagonal blocks are exchanged for Y1-HYP -+ Diagonal and Off-diagonal blocks are exchanged for Y2-HYP -+ Diagonal and Off-diagonal blocks are exchanged for X1-HYP -+ Sign of the lower diagonal block is changed for X1-HYP -+ Diagonal and Off-diagonal blocks are exchanged for X2-HYP -+ Sign of the lower diagonal block is changed for X2-HYP - // LUCIAREL called - // CIRUN = PROP1 - // Computing one-electron properties. -@@ -1770,10 +1871,28 @@ - A1-SPS A2 A2 - A2-SPS A2 A2 - -+ =================================================== -+ parallel distribution setup for symmetry irrep 65 -+ =================================================== -+ -+ total number of processes to distribute on : 2 -+ total number of blocks : 13056 -+ total number of active blocks : 29 -+ size of largest TTSS block : 784 -+ overall weighted active block length : 26784 -+ Maximum weighted block size : 7056 -+ -+ ================================ -+ Summation of even distribution -+ ================================ -+ -+ CPU 0 computes 14 blocks with a total weight of 13391 -+ CPU 1 computes 15 blocks with a total weight of 13393 -+ - ============================================================== - ==> allocation of two CI vectors and one resolution vector <== - -- current available free memory in double words: 1999885056 -+ current available free memory in double words: 63885000 - allocate two CI vectors each of length: 3366 - allocate resolution vector of length: 3366 - ============================================================== -@@ -1803,7 +1922,7 @@ - 0 -15.1037051064 0.000000000000 0.000000000000 0.000000000000 (1 ) - ________________________________________________________________________________________________________ - -- -+ - - ******************************************************** - ********* electron Electric Dipole Moment ************** -@@ -1812,9 +1931,9 @@ - E_eff [a.u.] E_eff [GV/cm] - - __________________ _________________ __________________________________________________________ -- EEDM state 1(1 ) state 1(1 ) -0.000110451662 -0.000567965276 -+ EEDM state 1(1 ) state 1(1 ) -0.000110451220 -0.000567963004 - __________________________________________ __________________________________________________________ -- -+ - - ******************************************************** - ********* Hyperfine Structure Constants ************** -@@ -1823,45 +1942,45 @@ - < state | Y1-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] - - __________________ _________________ __________________________________________________________ -- PREFACNUC = -1.5598078852941472E-006 -- MHYP state 1(1 ) state 1(1 ) -0.005905849748 0.000000009212 -+ PREFACNUC = -1.559807885294147E-006 -+ MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 - __________________________________________ __________________________________________________________ - - < state | Y2-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] - - __________________ _________________ __________________________________________________________ -- PREFACNUC = 1.1099508005612513E-005 -- MHYP state 1(1 ) state 1(1 ) -0.000974096023 -0.000000010812 -+ PREFACNUC = 1.109950800561251E-005 -+ MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 - __________________________________________ __________________________________________________________ - - < state | X1-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] - - __________________ _________________ __________________________________________________________ -- PREFACNUC = -1.5598078852941472E-006 -- MHYP state 1(1 ) state 1(1 ) -0.005905849748 0.000000009212 -+ PREFACNUC = -1.559807885294147E-006 -+ MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 - __________________________________________ __________________________________________________________ - - < state | X2-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] - - __________________ _________________ __________________________________________________________ -- PREFACNUC = 1.1099508005612513E-005 -- MHYP state 1(1 ) state 1(1 ) -0.000974096023 -0.000000010812 -+ PREFACNUC = 1.109950800561251E-005 -+ MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 - __________________________________________ __________________________________________________________ - - < state | Z1-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] - - __________________ _________________ __________________________________________________________ -- PREFACNUC = -1.5598078852941472E-006 -- MHYP state 1(1 ) state 1(1 ) -0.006752396302 0.000000010532 -+ PREFACNUC = -1.559807885294147E-006 -+ MHYP state 1(1 ) state 1(1 ) -0.006752216685 0.000000010532 - __________________________________________ __________________________________________________________ - - < state | Z2-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] - - __________________ _________________ __________________________________________________________ -- PREFACNUC = 1.1099508005612513E-005 -- MHYP state 1(1 ) state 1(1 ) -0.001232804132 -0.000000013684 -+ PREFACNUC = 1.109950800561251E-005 -+ MHYP state 1(1 ) state 1(1 ) -0.001232901004 -0.000000013685 - __________________________________________ __________________________________________________________ -- -+ - - ******************************************************** - ********* e-N S-PS interaction Parameter ************* -@@ -1870,13 +1989,13 @@ - e-N S-PS Parameter [a.u.] Norm [a.u.] - - __________________ _________________ __________________________________________________________ -- ENSPS state 1(1 ) state 1(1 ) 0.001238402290 0.001238402290 -+ ENSPS state 1(1 ) state 1(1 ) 0.001238395771 0.001238395771 - __________________________________________ __________________________________________________________ - - e-N S-PS Parameter [a.u.] Norm [a.u.] - - __________________ _________________ __________________________________________________________ -- ENSPS state 1(1 ) state 1(1 ) -0.000041687482 0.000041687482 -+ ENSPS state 1(1 ) state 1(1 ) -0.000041690709 0.000041690709 - __________________________________________ __________________________________________________________ - - ***************************************************** -@@ -1885,35 +2004,35 @@ - - - -- Date and time (Linux) : Sat Dec 7 14:43:18 2019 -- Host name : malaya.tcs -+ Date and time (Linux) : Fri Oct 9 13:31:40 2020 -+ Host name : node3414.kirlia.os - -->>>> Node 0, utime: 33, stime: 0, minflt: 10512, majflt: 0, nvcsw: 712, nivcsw: 1212, maxrss: 192920 -->>>> Total WALL time used in DIRAC: 36s -+>>>> Node 0, utime: 17, stime: 0, minflt: 102299, majflt: 0, nvcsw: 729, nivcsw: 1895, maxrss: 647320 -+>>>> Total WALL time used in DIRAC: 19s - - Dynamical Memory Usage Summary for Master - -- Mean allocation size (Mb) : 234.90 -+ Mean allocation size (Mb) : 8.01 - -- Largest 10 allocations -+ Largest 10 allocations - -- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for WORK in KRCI_CALC -- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for WORK in PSISCF -- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for WORK in PAMSET - 2 -- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for WORK in GMOTRA -- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for WORK in PAMSET - 1 -- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for test allocation of work array in DIRAC mai -- 3.81 Mb at subroutine __allocator_track_if_MOD_allocator_registe for unnamed variable -- 3.81 Mb at subroutine __allocator_track_if_MOD_allocator_registe for unnamed variable -- 3.81 Mb at subroutine __allocator_track_if_MOD_allocator_registe for unnamed variable -- 3.81 Mb at subroutine __allocator_track_if_MOD_allocator_registe for unnamed variable -+ 488.28 Mb at subroutine krci_calc_+0xc4 for WORK in KRCI_CALC -+ 488.28 Mb at subroutine psiscf_+0xa9 for WORK in PSISCF -+ 488.28 Mb at subroutine pamset_+0x16ac for WORK in PAMSET - 2 -+ 488.28 Mb at subroutine gmotra_+0x47d0 for WORK in GMOTRA -+ 488.28 Mb at subroutine pamset_+0x97 for WORK in PAMSET - 1 -+ 488.28 Mb at subroutine MAIN__+0x9af for test allocation of work array in DIRAC mai -+ 3.81 Mb at subroutine set_hop_dbg_+0x788 for unnamed variable -+ 3.81 Mb at subroutine set_hop_dbg_+0x773 for unnamed variable -+ 3.81 Mb at subroutine set_hop_dbg_+0x75e for unnamed variable -+ 3.81 Mb at subroutine set_hop_dbg_+0x749 for unnamed variable - -- Peak memory usage: 15274.30 MB -- Peak memory usage: 14.916 GB -- reached at subroutine : __allocator_track_if_MOD_allocator_registe -+ Peak memory usage: 503.80 MB -+ Peak memory usage: 0.492 GB -+ reached at subroutine : set_hop_dbg_+0x788 - for variable : unnamed variable - - MEMGET high-water mark: 0.00 MB - - ***************************************************** --DIRAC pam run in /home/mknayak/dirac-repo-05-12-18/work/eedm_mhyp_ensps_krci -+DIRAC pam run in /dev/shm/build/DIRAC/19.0/intel-2020a-Python-2.7.18-mpi-int64/easybuild_obj/test/eedm_mhyp_ensps_krci diff --git a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_fix_test_path.patch b/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_fix_test_path.patch deleted file mode 100644 index 61eb0bb3734..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_fix_test_path.patch +++ /dev/null @@ -1,26 +0,0 @@ -# Fix hard coded DIRAC/utils path in fde_response_mag and fde_response_shield tests -# OCT 7th 2020 by B. Hajgato (UGent) -diff -ru DIRAC-19.0-Source.orig/test/fde_response_mag/test DIRAC-19.0-Source/test/fde_response_mag/test ---- DIRAC-19.0-Source.orig/test/fde_response_mag/test 2019-12-12 17:26:15.000000000 +0100 -+++ DIRAC-19.0-Source/test/fde_response_mag/test 2020-10-07 22:41:25.277776298 +0200 -@@ -16,7 +16,7 @@ - - - test.run(['dc_pbe'], ['h2o-1.xyz'], args='--get="numerical_grid"') --os.system('../../../utils/fde-mag/dft_to_fde_grid_convert.py') -+os.system('../../../DIRAC*/utils/fde-mag/dft_to_fde_grid_convert.py') - - shutil.copy('numerical_grid', 'FILEEX') - shutil.copy('numerical_grid', 'GRIDOUT') -diff -ru DIRAC-19.0-Source.orig/test/fde_response_shield/test DIRAC-19.0-Source/test/fde_response_shield/test ---- DIRAC-19.0-Source.orig/test/fde_response_shield/test 2019-12-12 17:26:15.000000000 +0100 -+++ DIRAC-19.0-Source/test/fde_response_shield/test 2020-10-07 22:41:45.348275614 +0200 -@@ -17,7 +17,7 @@ - - - test.run(['dc_pbe'], ['h2o-1.xyz'], args='--get="numerical_grid"') --os.system('../../../utils/fde-mag/dft_to_fde_grid_convert.py') -+os.system('../../../DIRAC*/utils/fde-mag/dft_to_fde_grid_convert.py') - - shutil.copy('numerical_grid', 'FILEEX') - shutil.copy('numerical_grid', 'GRIDOUT') diff --git a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch b/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch deleted file mode 100644 index 5ccef03e4cc..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch +++ /dev/null @@ -1,24 +0,0 @@ -"operators_mo_mtx_elements" doesn't run when mpi is enabled (even if test doesn't use mpi) -see: https://ccportal.ims.ac.jp/en/node/2411 - -Author: Pavel Grochal (INUITS) -Comments from B. Hajgato (UGent) at OCT 5th 2020: -In the test python program both ignore_sign and ignore_order is set to True, -but ignore_order does not seem to work perfectly. -Using ifort 2020.1 and MKL2020.1 on cascadelake a manual comparison passed, meanwhile the automatic -comparison failed. Therefore, test will be disabled. -diff -ru DIRAC-19.0-Source.orig/cmake/custom/test.cmake DIRAC-19.0-Source/cmake/custom/test.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/test.cmake 2019-12-12 17:26:15.000000000 +0100 -+++ DIRAC-19.0-Source/cmake/custom/test.cmake 2020-09-24 12:54:02.524830820 +0200 -@@ -158,9 +158,8 @@ - dirac_test(lucita_q_corrections "short;qcorr;ci" "") - dirac_test(x2c-SCF_to_4c-SCF "short;x2c;4c;scf" "") - dirac_test(import_mos "short;import;scf;mcscf" "") --dirac_test(operators_mo_mtx_elements "short;operators" "") -+# dirac_test(operators_mo_mtx_elements "short;operators" "") - dirac_test(spinorbit-from-spinfree "short;scf;resolve" "") - dirac_test(spinrot "short;response" "") - # disabing eomcc expectation value test until the code is verified - #dirac_test(eomcc_expval "short;cc" "") -- - diff --git a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_use_easybuild_opts.patch b/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_use_easybuild_opts.patch deleted file mode 100644 index e7e16b65880..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DIRAC/DIRAC-19.0_use_easybuild_opts.patch +++ /dev/null @@ -1,70 +0,0 @@ -# Take EasyBuild compiler flags for C, C++, and Fortran -# OCT 5th, 2020 by B. Hajgato (UGent) -# Updated by Alexander Grund (TU Dresden) -diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.C.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.C.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.C.cmake 2021-08-04 17:42:21.340186361 +0200 -+++ DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.C.cmake 2021-08-04 17:53:53.657008099 +0200 -@@ -3,7 +3,5 @@ - message(STATUS "Added gcc -maix64 flag due to IBM AIX XL Fortran and integer*8") - set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -maix64 ") - endif() -- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g") -- set(CMAKE_C_FLAGS_RELEASE "-O2 -Wno-unused") -- set(CMAKE_C_FLAGS_DEBUG "-O0") -+ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unused") - endif() -diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.CXX.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.CXX.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.CXX.cmake 2021-08-04 17:42:21.340186361 +0200 -+++ DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.CXX.cmake 2021-08-04 17:53:53.657008099 +0200 -@@ -1,5 +1,4 @@ - if(CMAKE_CXX_COMPILER_ID MATCHES GNU) -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -Wno-unknown-pragmas -Wno-sign-compare -Woverloaded-virtual -Wwrite-strings -Wno-unused") -- set(CMAKE_CXX_FLAGS_RELEASE "-Ofast -march=native -DNDEBUG -Wno-unused") -- set(CMAKE_CXX_FLAGS_DEBUG "-O0 -DDEBUG") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-unknown-pragmas -Wno-sign-compare -Woverloaded-virtual -Wwrite-strings -Wno-unused") -+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DDEBUG") - endif() -diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.Fortran.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.Fortran.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.Fortran.cmake 2021-08-04 17:42:21.340186361 +0200 -+++ DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.Fortran.cmake 2021-08-04 17:53:53.657008099 +0200 -@@ -4,7 +4,6 @@ - set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -maix64") - message(STATUS "Added gfortran -maix64 flag due to IBM AIX and integer*8") - endif() -- set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -funroll-all-loops -w") -- set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS} -O0 -fbounds-check -finit-real=nan -finit-integer=-9999 -Wall") -- #set(CMAKE_Fortran_FLAGS_DEBUG "-O0") -+ set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -funroll-all-loops -w") -+ set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS} -fbounds-check -finit-real=nan -finit-integer=-9999 -Wall") - endif() -diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.C.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.C.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.C.cmake 2021-08-04 17:42:21.340186361 +0200 -+++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.C.cmake 2021-08-04 17:53:53.657008099 +0200 -@@ -1,5 +1,3 @@ - if(CMAKE_C_COMPILER_ID MATCHES Intel) -- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -wd981 -wd279 -wd383 -wd1572 -wd177") -- set(CMAKE_C_FLAGS_RELEASE "-O2") -- set(CMAKE_C_FLAGS_DEBUG "-O0") -+ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -wd981 -wd279 -wd383 -wd1572 -wd177") - endif() -diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.CXX.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.CXX.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.CXX.cmake 2021-08-04 17:42:21.340186361 +0200 -+++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.CXX.cmake 2021-08-04 17:53:53.657008099 +0200 -@@ -1,5 +1,4 @@ - if(CMAKE_CXX_COMPILER_ID MATCHES Intel) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unknown-pragmas") -- set(CMAKE_CXX_FLAGS_RELEASE "-debug -O3 -DNDEBUG") -- set(CMAKE_CXX_FLAGS_DEBUG "-O0 -debug -DDEBUG") -+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DDEBUG") - endif() -diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.Fortran.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.Fortran.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.Fortran.cmake 2021-08-04 17:42:21.340186361 +0200 -+++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.Fortran.cmake 2021-08-04 17:53:53.657008099 +0200 -@@ -1,5 +1,4 @@ - if(CMAKE_Fortran_COMPILER_ID MATCHES Intel) -- set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w -assume byterecl -g -traceback -DVAR_IFORT") -- set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -ip") -- set(CMAKE_Fortran_FLAGS_DEBUG "-O0") -+ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w -assume byterecl -DVAR_IFORT") -+ set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -ip") - endif() diff --git a/easybuild/easyconfigs/__archive__/d/DMTCP/DMTCP-2.6.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/d/DMTCP/DMTCP-2.6.0-GCCcore-9.3.0.eb deleted file mode 100644 index b4468676295..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DMTCP/DMTCP-2.6.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'DMTCP' -version = '2.6.0' - -homepage = 'http://dmtcp.sourceforge.net/index.html' -description = """DMTCP is a tool to transparently checkpoint the state of multiple -simultaneous applications, including multi-threaded and distributed applications. -It operates directly on the user binary executable, without any Linux kernel modules -or other kernel modifications.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['3ed62a86dd0cb9c828b93ee8c7c852d6f9c96a0efa48bcfe867521adf7bced68'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', - 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb deleted file mode 100644 index 36b8d531771..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# $Id$ -# -## -easyblock = 'PythonPackage' - -name = 'DendroPy' -version = '4.4.0' - -homepage = 'https://pypi.python.org/pypi/DendroPy/' -description = """A Python library for phylogenetics and phylogenetic computing: -reading, writing, simulation, processing and manipulation of phylogenetic trees -(phylogenies) and characters.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -builddependencies = [('binutils', '2.34')] - -fix_python_shebang_for = ['bin/*.py'] - -sanity_check_paths = { - 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["sumtrees.py --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index a206089c0c5..00000000000 --- a/easybuild/easyconfigs/__archive__/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,98 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Devito' -version = '4.6.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.devitoproject.org' -description = """Devito is a domain-specific Language (DSL) and code generation framework for - performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. - Devito performs automated code generation and Just-In-time (JIT) compilation based on symbolic - equations defined in SymPy to create and execute highly optimised Finite Difference stencil kernels on - multiple computer platforms.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('IPython', '7.15.0', versionsuffix), - ('dask', '2.18.1', versionsuffix), -] - -# order is important! -exts_list = [ - ('anytree', '2.8.0', { - 'checksums': ['3f0f93f355a91bc3e6245319bf4c1d50e3416cc7a35cc1133c1ff38306bbccab'], - }), - ('cached-property', '1.5.2', { - 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], - }), - ('cgen', '2020.1', { - 'checksums': ['4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf'], - }), - ('codecov', '2.1.12', { - 'checksums': ['a0da46bb5025426da895af90938def8ee12d37fcbcbbbc15b6dc64cf7ebc51c1'], - }), - ('setuptools_scm', '6.0.1', { - 'checksums': ['d1925a69cb07e9b29416a275b9fadb009a23c148ace905b2fb220649a6c18e92'], - }), - ('platformdirs', '2.2.0', { - 'checksums': ['632daad3ab546bd8e6af0537d09805cec458dce201bccfe23012df73332e181e'], - }), - ('pytools', '2022.1', { - 'checksums': ['197aacf6e1f5d60c715b92438792acb7702aed59ebbfb147fa84eda780e54fee'], - }), - ('codepy', '2019.1', { - 'checksums': ['384f22c37fe987c0ca71951690c3c2fd14dacdeddbeb0fde4fd01cd84859c94e'], - }), - ('coverage', '6.3.1', { - 'checksums': ['6c3f6158b02ac403868eea390930ae64e9a9a2a5bbfafefbb920d29258d9f2f8'], - }), - ('mccabe', '0.6.1', { - 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], - }), - ('pycodestyle', '2.8.0', { - 'checksums': ['eddd5847ef438ea1c7870ca7eb78a9d47ce0cdb4851a5523949f2601d0cbbe7f'], - }), - ('pyflakes', '2.4.0', { - 'checksums': ['05a85c2872edf37a4ed30b0cce2f6093e1d0581f8c19d7393122da7e25b2b24c'], - }), - ('flake8', '4.0.1', { - 'checksums': ['806e034dda44114815e23c16ef92f95c91e4c71100ff52813adf7132a6ad870d'], - }), - ('multidict', '6.0.2', { - 'checksums': ['5ff3bd75f38e4c43f1f470f2df7a4d430b821c4ce22be384e1459cb57d6bb013'], - }), - ('nbval', '0.9.6', { - 'checksums': ['cfefcd2ef66ee2d337d0b252c6bcec4023384eb32e8b9e5fcc3ac80ab8cd7d40'], - }), - ('py-cpuinfo', '8.0.0', { - 'modulename': 'cpuinfo', - 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], - }), - ('contexttimer', '0.3.3', { - 'checksums': ['35a1efd389af3f1ca509f33ff23e17d98b66c8fde5ba2a4eb8a8b7fa456598a5'], - }), - ('pyrevolve', '2.2', { - 'checksums': ['b49aea5cd6c520ac5fcd1d25fa23fe2c5502741d2965f3eee10be067e7b0efb4'], - }), - ('pytest-cov', '3.0.0', { - 'checksums': ['e7f0f5b1617d2210a2cabc266dfe2f4c75a8d32fb89eafb7ad9d06f6d076d470'], - }), - ('pytest-runner', '5.3.1', { - 'modulename': 'pytest', - 'checksums': ['0fce5b8dc68760f353979d99fdd6b3ad46330b6b1837e2077a89ebcf204aac91'], - }), - # devito requires sympy<=1.9,>=1.7 - ('sympy', '1.9', { - 'checksums': ['c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc'], - }), - ('devito', version, { - 'checksums': ['e8acc4840953547c267706195df32738c95d0e51f7592eb0796a0efcc8cc5dbf'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/d/DoubletFinder/DoubletFinder-2.0.3-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/d/DoubletFinder/DoubletFinder-2.0.3-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 0b457648a35..00000000000 --- a/easybuild/easyconfigs/__archive__/d/DoubletFinder/DoubletFinder-2.0.3-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'RPackage' - -name = 'DoubletFinder' -local_commit = '20654b8' -# see DESCRIPTION to determine version -version = '2.0.3' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://github.com/chris-mcginnis-ucsf/DoubletFinder' -description = "R package for detecting doublets in single-cell RNA sequencing data" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['fe0889618b11eb823f5c2232c6fe6fb989a917673590d0a3532642f31b74f36a'] - -dependencies = [ - ('R', '4.0.0'), - ('R-bundle-Bioconductor', '3.11', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb deleted file mode 100644 index 065a4b2b89a..00000000000 --- a/easybuild/easyconfigs/__archive__/d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Doxygen' -version = '1.8.17' - -homepage = 'https://www.doxygen.org' -description = """ - Doxygen is a documentation system for C++, C, Java, Objective-C, Python, - IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some - extent D. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(namelower)s-%(version)s.src.tar.gz'] -checksums = ['2cba988af2d495541cbbe5541b3bee0ee11144dcb23a81eada19f5501fd8b599'] - -builddependencies = [ - ('binutils', '2.34'), - ('Bison', '3.5.3'), - ('CMake', '3.16.4'), - ('flex', '2.6.4'), - ('pkg-config', '0.29.2'), -] -dependencies = [('libiconv', '1.16')] - -configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" - -sanity_check_paths = { - 'files': ["bin/doxygen"], - 'dirs': [], -} - -sanity_check_commands = ["doxygen --help"] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/d/dask/dask-2.18.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/d/dask/dask-2.18.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 375553e44e4..00000000000 --- a/easybuild/easyconfigs/__archive__/d/dask/dask-2.18.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,76 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'dask' -version = '2.18.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://dask.org/' -description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance - at scale for the tools you love.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('bokeh', '2.0.2', versionsuffix), -] - -exts_list = [ - ('fsspec', '0.7.4', { - 'checksums': ['7075fde6d617cd3a97eac633d230d868121a188a46d16a0dcb484eea0cf2b955'], - }), - ('toolz', '0.10.0', { - 'checksums': ['08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560'], - }), - ('locket', '0.2.0', { - 'checksums': ['1fee63c1153db602b50154684f5725564e63a0f6d09366a1cb13dffcec179fb4'], - }), - ('partd', '1.1.0', { - 'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'], - }), - ('HeapDict', '1.0.1', { - 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], - }), - ('zict', '2.0.0', { - 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], - }), - ('tblib', '1.6.0', { - 'checksums': ['229bee3754cb5d98b4837dd5c4405e80cfab57cb9f93220410ad367f8b352344'], - }), - ('msgpack', '1.0.0', { - 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], - }), - ('cloudpickle', '1.4.1', { - 'checksums': ['0b6258a20a143603d53b037a20983016d4e978f554ec4f36b3d0895b947099ae'], - }), - (name, version, { - 'checksums': ['8ed21e2344419fad7c6f648123f6f56cf2480d0ac4fae92d9063adb321f1c490'], - }), - ('distributed', '2.18.0', { - 'checksums': ['902f098fb7558f035333804a5aeba2fb26a2a715388808205a17cbb2e02e0558'], - }), - ('dask-mpi', '2.0.0', { - 'checksums': ['774cd2d69e5f7154e1fa133c22498062edd31507ffa2ea19f4ab4d8975c27bc3'], - }), - ('immutables', '0.14', { - 'checksums': ['a0a1cc238b678455145bae291d8426f732f5255537ed6a5b7645949704c70a78'], - }), - ('contextvars', '2.4', { - 'checksums': ['f38c908aaa59c14335eeea12abea5f443646216c4e29380d7bf34d2018e2c39e'], - }), - ('docrep', '0.2.7', { - 'checksums': ['c48939ae14d79172839a5bbaf5a570add47f6cc44d2c18f6b1fac8f1c38dec4d'], - }), - ('dask-jobqueue', '0.7.1', { - 'checksums': ['d32ddf3e3c7db29ace102037fa5f61c8db2d945176454dc316a6ffdb8bbfe88b'], - }), -] - -sanity_check_paths = { - 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/d/dask/dask-2.18.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/d/dask/dask-2.18.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 42bd1016a78..00000000000 --- a/easybuild/easyconfigs/__archive__/d/dask/dask-2.18.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,76 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'dask' -version = '2.18.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://dask.org/' -description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance - at scale for the tools you love.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('bokeh', '2.0.2', versionsuffix), -] - -exts_list = [ - ('fsspec', '0.7.4', { - 'checksums': ['7075fde6d617cd3a97eac633d230d868121a188a46d16a0dcb484eea0cf2b955'], - }), - ('toolz', '0.10.0', { - 'checksums': ['08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560'], - }), - ('locket', '0.2.0', { - 'checksums': ['1fee63c1153db602b50154684f5725564e63a0f6d09366a1cb13dffcec179fb4'], - }), - ('partd', '1.1.0', { - 'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'], - }), - ('HeapDict', '1.0.1', { - 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], - }), - ('zict', '2.0.0', { - 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], - }), - ('tblib', '1.6.0', { - 'checksums': ['229bee3754cb5d98b4837dd5c4405e80cfab57cb9f93220410ad367f8b352344'], - }), - ('msgpack', '1.0.0', { - 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], - }), - ('cloudpickle', '1.4.1', { - 'checksums': ['0b6258a20a143603d53b037a20983016d4e978f554ec4f36b3d0895b947099ae'], - }), - (name, version, { - 'checksums': ['8ed21e2344419fad7c6f648123f6f56cf2480d0ac4fae92d9063adb321f1c490'], - }), - ('distributed', '2.18.0', { - 'checksums': ['902f098fb7558f035333804a5aeba2fb26a2a715388808205a17cbb2e02e0558'], - }), - ('dask-mpi', '2.0.0', { - 'checksums': ['774cd2d69e5f7154e1fa133c22498062edd31507ffa2ea19f4ab4d8975c27bc3'], - }), - ('immutables', '0.14', { - 'checksums': ['a0a1cc238b678455145bae291d8426f732f5255537ed6a5b7645949704c70a78'], - }), - ('contextvars', '2.4', { - 'checksums': ['f38c908aaa59c14335eeea12abea5f443646216c4e29380d7bf34d2018e2c39e'], - }), - ('docrep', '0.2.7', { - 'checksums': ['c48939ae14d79172839a5bbaf5a570add47f6cc44d2c18f6b1fac8f1c38dec4d'], - }), - ('dask-jobqueue', '0.7.1', { - 'checksums': ['d32ddf3e3c7db29ace102037fa5f61c8db2d945176454dc316a6ffdb8bbfe88b'], - }), -] - -sanity_check_paths = { - 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/d/dd/cudd-3.0.0_disable-pdf-docs.patch b/easybuild/easyconfigs/__archive__/d/dd/cudd-3.0.0_disable-pdf-docs.patch deleted file mode 100644 index 111522d22c9..00000000000 --- a/easybuild/easyconfigs/__archive__/d/dd/cudd-3.0.0_disable-pdf-docs.patch +++ /dev/null @@ -1,94 +0,0 @@ -Disable building the documentation in PDF format -author: Alex Domingo (Vrije Universiteit Brussel) ---- configure.ac.orig 2021-01-09 00:36:31.371946000 +0100 -+++ configure.ac 2021-01-09 00:37:07.878429000 +0100 -@@ -44,7 +44,7 @@ - AC_C_BIGENDIAN - AM_CONDITIONAL([CROSS_COMPILING],[test x$cross_compiling = xyes]) - --# Building documentation requires doxygen, pdflatex, and makeindex. -+# Building documentation requires doxygen - AC_CHECK_PROGS([DOXYGEN], [doxygen]) - if test -z "$DOXYGEN"; then - AC_MSG_WARN([Doxygen not found - continuing without Doxygen support]) -@@ -52,17 +52,6 @@ - AM_CONDITIONAL([HAVE_DOXYGEN],[test -n "$DOXYGEN"]) - AM_COND_IF([HAVE_DOXYGEN], [AC_CONFIG_FILES([Doxyfile])]) - --AC_CHECK_PROGS([PDFLATEX], [pdflatex]) --if test -z "$PDFLATEX"; then -- AC_MSG_WARN([pdflatex not found - unable to compile manual to PDF]) --fi --AC_CHECK_PROGS([MAKEINDEX], [makeindex]) --if test -z "$MAKEINDEX"; then -- AC_MSG_WARN([makeindex not found - unable to compile manual to PDF]) --fi --AM_CONDITIONAL([HAVE_PDFLATEX],[test -n "$PDFLATEX" && test -n "$MAKEINDEX"]) --AM_COND_IF([HAVE_PDFLATEX], [AC_CONFIG_FILES([doc/cudd.tex])]) -- - # Checks for libraries. - #AC_CHECK_LIB([m],[pow]) - AC_SEARCH_LIBS([pow],[m]) ---- Doxyfile.in.orig 2021-01-09 00:35:50.194585000 +0100 -+++ Doxyfile.in 2021-01-09 00:36:07.316734582 +0100 -@@ -1444,7 +1444,7 @@ - # The default value is: NO. - # This tag requires that the tag GENERATE_HTML is set to YES. - --USE_MATHJAX = NO -+USE_MATHJAX = YES - - # When MathJax is enabled you can set the default output format to be used for - # the MathJax output. See the MathJax site (see: ---- Makefile.am.orig 2021-01-09 00:37:27.457616000 +0100 -+++ Makefile.am 2021-01-09 00:37:41.819415000 +0100 -@@ -30,14 +30,13 @@ - include $(top_srcdir)/dddmp/Included.am - include $(top_srcdir)/cplusplus/Included.am - include $(top_srcdir)/nanotrav/Included.am --include $(top_srcdir)/doc/Included.am - - dist-hook: - rm -rf `find $(distdir) -name .svn` - - .PHONY : - --all: html/index.html doc/cudd.pdf -+all: html/index.html - - if HAVE_DOXYGEN - ---- Makefile.in.orig 2021-01-09 00:39:37.608736000 +0100 -+++ Makefile.in 2021-01-09 00:42:18.376279642 +0100 -@@ -123,8 +123,6 @@ - @DDDMP_FALSE@am__append_5 = dddmp/libdddmp.la - @OBJ_TRUE@am__append_6 = $(cplusplus_sources) - @OBJ_FALSE@am__append_7 = cplusplus/libobj.la --@HAVE_PDFLATEX_TRUE@am__append_8 = doc/cudd.pdf doc/cudd.aux doc/cudd.idx doc/cudd.ilg doc/cudd.ind \ --@HAVE_PDFLATEX_TRUE@ doc/cudd.log doc/cudd.out doc/cudd.toc - - subdir = . - ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 -@@ -3144,21 +3142,12 @@ - $(do_subst) $< > $@ - chmod +x $@ - --@HAVE_PDFLATEX_TRUE@doc/cudd.pdf: doc/cudd.tex $(top_srcdir)/doc/phase.pdf --@HAVE_PDFLATEX_TRUE@ @if $(AM_V_P); then dest='2>&1'; else dest='> /dev/null 2>&1'; fi; \ --@HAVE_PDFLATEX_TRUE@ cd doc && eval "$(PDFLATEX) cudd $${dest}" && \ --@HAVE_PDFLATEX_TRUE@ eval "$(MAKEINDEX) cudd $${dest}" && \ --@HAVE_PDFLATEX_TRUE@ eval "$(PDFLATEX) cudd $${dest}" && \ --@HAVE_PDFLATEX_TRUE@ eval "$(PDFLATEX) cudd $${dest}" -- --@HAVE_PDFLATEX_FALSE@doc/cudd.pdf: -- - dist-hook: - rm -rf `find $(distdir) -name .svn` - - .PHONY : - --all: html/index.html doc/cudd.pdf -+all: html/index.html - - @HAVE_DOXYGEN_TRUE@html/index.html: Doxyfile $(lib_LTLIBRARIES) - @HAVE_DOXYGEN_TRUE@ @if $(AM_V_P); then dest='2>&1'; else dest='> /dev/null 2>&1'; fi; \ diff --git a/easybuild/easyconfigs/__archive__/d/dd/dd-0.5.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/d/dd/dd-0.5.6-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 2cb3ecdbd2a..00000000000 --- a/easybuild/easyconfigs/__archive__/d/dd/dd-0.5.6-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,93 +0,0 @@ -easyblock = 'Bundle' - -name = 'dd' -version = '0.5.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/tulip-control/dd' -description = """ -dd is a package for working with binary decision diagrams that includes both a -pure Python implementation and Cython bindings to C libraries (CUDD, Sylvan, -BuDDy). The Python and Cython modules implement the same API, so the same user -code runs with both. All the standard operations on BDDs are available, -including dynamic variable reordering using sifting, garbage collection, -dump/load from files, plotting, and a parser of quantified Boolean -expressions. -This module includes bindings for: CUDD v3.0.0, Sylvan v1.0.0""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -builddependencies = [ - # needed by CUDD - ('Autotools', '20180311'), - ('Doxygen', '1.8.17'), - # needed by Sylvan - ('CMake', '3.16.4'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('networkx', '2.4', versionsuffix), - ('pydot', '1.4.1'), - # needed by Sylvan - ('GMP', '6.2.0'), - ('hwloc', '2.2.0'), -] - -# include bindings for bundled CUDD and Sylvan -local_dd_bindingopts = ['cudd=%(builddir)s/cudd-3.0.0', 'cudd_zdd=%(builddir)s/cudd-3.0.0', 'sylvan'] - -default_easyblock = 'PythonPackage' -default_component_specs = { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCELOWER_TAR_GZ], - 'start_dir': '%(namelower)s-%(version)s', -} - -components = [ - ('CUDD', '3.0.0', { - # building the dd bindings to CUDD requires the build directory of CUDD - 'easyblock': 'ConfigureMake', - 'source_urls': [('https://sourceforge.net/projects/cudd-mirror/files/', 'download')], - 'patches': ['%(namelower)s-%(version)s_disable-pdf-docs.patch'], - 'checksums': [ - 'b8e966b4562c96a03e7fbea239729587d7b395d53cadcc39a7203b49cf7eeb69', # cudd-3.0.0.tar.gz - 'd18ab7a8c09b8d5635a7aabddc409d6de7447685d1db58a11fb8f7fa4576e689', # cudd-3.0.0_disable-pdf-docs.patch - ], - 'preconfigopts': "autoreconf -f -i &&", - }), - ('Sylvan', '1.0.0', { - # dd requires this old version of Sylvan - 'easyblock': 'CMakeMake', - 'source_urls': ['https://github.com/utwente-fmt/sylvan/archive'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}], - 'checksums': ['94e7e5d5aa9fe0a5cec3a734509e1dcf7e6311438bea661bbb7596fd67e0b824'], - }), - ('ply', '3.10', { - 'checksums': ['96e94af7dd7031d8d6dd6e2a8e0de593b511c211a86e28a9c9621c275ac8bacb'], - }), - ('astutils', '0.0.4', { - 'checksums': ['da28d76b9e0893fb0f2678b91a30840f3db99b703aadc69226f500096f60747f'], - }), - (name, version, { - 'patches': ['%(namelower)s-%(version)s_fix-sylvan-linking.patch'], - 'checksums': [ - '0ac1a58b6c567c45d74c8619f484ec43ece5b1aace49000e9b2b75cf38de6b94', # dd-0.5.6.tar.gz - '9a148f6203c416c002844af2fba1ac05b1dc0e7bb70527c244f9b9865a8f2bcf', # dd-0.5.6_fix-sylvan-linking.patch - ], - 'installopts': " ".join(['--install-option="--%s"' % o for o in local_dd_bindingopts]), - }), -] - -sanity_check_paths = { - 'files': ['lib/%s.a' % x for x in ['libcudd', 'libsylvan']] + - ['include/%s.h' % h for h in ['cudd', 'lace', 'sylvan', 'sylvan_gmp']], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "python -c 'import %s'" % p for p in ['ply', 'astutils', 'dd', 'dd.cudd', 'dd.cudd_zdd', 'dd.sylvan'] -] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/d/dd/dd-0.5.6_fix-sylvan-linking.patch b/easybuild/easyconfigs/__archive__/d/dd/dd-0.5.6_fix-sylvan-linking.patch deleted file mode 100644 index 867fbf588c6..00000000000 --- a/easybuild/easyconfigs/__archive__/d/dd/dd-0.5.6_fix-sylvan-linking.patch +++ /dev/null @@ -1,13 +0,0 @@ -Link the dd.sylvan binding library to hwloc, which is used by Sylvan -author: Alex Domingo (Vrije Universiteit Brussel) ---- download.py.orig 2021-01-09 02:55:05.061718000 +0100 -+++ download.py 2021-01-09 02:55:23.961175000 +0100 -@@ -125,7 +125,7 @@ - sources=['dd/sylvan' + pyx], - include_dirs=_join(SYLVAN_INCLUDE), - library_dirs=_join(SYLVAN_LINK), -- libraries=['sylvan'], -+ libraries=['sylvan', 'hwloc'], - extra_compile_args=sylvan_cflags)) - for ext in EXTENSIONS: - if getattr(args, ext) is None: diff --git a/easybuild/easyconfigs/__archive__/d/deepTools/deepTools-3.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/d/deepTools/deepTools-3.3.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 70bb079de61..00000000000 --- a/easybuild/easyconfigs/__archive__/d/deepTools/deepTools-3.3.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'deepTools' -version = '3.3.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://deeptools.readthedocs.io/' -description = """deepTools is a suite of python tools particularly developed for the efficient analysis of - high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('Pysam', '0.16.0.1'), - ('matplotlib', '3.2.1', versionsuffix), - ('plotly.py', '4.8.1'), -] - -exts_list = [ - ('py2bit', '0.3.0', { - 'checksums': ['450555c40cba66957ac8c9a4b6afb625fb34c4bb41638de78c87661ff8b682ef'], - }), - ('pyBigWig', '0.3.17', { - 'modulename': 'pyBigWig', - 'checksums': ['41f64f802689ed72e15296a21a4b7abd3904780b2e4f8146fd29098fc836fd94'], - }), - ('deeptoolsintervals', '0.1.9', { - 'checksums': ['7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6'], - }), - ('numpydoc', '1.0.0', { - 'checksums': ['e481c0799dfda208b6a2c2cb28757fa6b6cbc4d6e43722173697996cf556df7f'], - }), - (name, version, { - 'checksums': ['514240f97e58bcfbf8c8b69ae9071d26569b491f089e1c1c46ba4866d335e322'], - }), -] - -sanity_check_paths = { - 'files': ['bin/bamCompare', 'bin/bamCoverage', 'bin/bamPEFragmentSize', 'bin/computeGCBias', 'bin/computeMatrix', - 'bin/correctGCBias', 'bin/multiBamSummary', 'bin/plotCorrelation', 'bin/plotCoverage', - 'bin/plotHeatmap', 'bin/plotProfile'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/d/dicom2nifti/dicom2nifti-2.2.12-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/d/dicom2nifti/dicom2nifti-2.2.12-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 4b789eae04c..00000000000 --- a/easybuild/easyconfigs/__archive__/d/dicom2nifti/dicom2nifti-2.2.12-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'dicom2nifti' -version = '2.2.12' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/icometrix/dicom2nifti' -description = "Python library for converting dicom files to nifti" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['6ba845b723326882a1da900fc27848f3c1456ddc6e50b698c92f8c96b3894db8'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('pydicom', '2.1.2', versionsuffix), - ('NiBabel', '3.2.0', versionsuffix), -] - -sanity_check_paths = { - 'files': ['bin/dicom2nifti'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb deleted file mode 100644 index e3b9916c69a..00000000000 --- a/easybuild/easyconfigs/__archive__/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'double-conversion' -version = '3.1.5' - -homepage = 'https://github.com/google/double-conversion' -description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/google/%(name)s/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['a63ecb93182134ba4293fd5f22d6e08ca417caafa244afaa751cbfddf6415b13'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -# Build static lib, static lib with -fPIC and shared lib -configopts = [ - '', - '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', - '-DBUILD_SHARED_LIBS=ON' -] - -sanity_check_paths = { - 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', - 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + - ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/d/dtcmp/dtcmp-1.1.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/d/dtcmp/dtcmp-1.1.0-gompi-2020a.eb deleted file mode 100644 index b7289deaa20..00000000000 --- a/easybuild/easyconfigs/__archive__/d/dtcmp/dtcmp-1.1.0-gompi-2020a.eb +++ /dev/null @@ -1,31 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'dtcmp' -version = '1.1.0' - -homepage = 'https://github.com/llnl/dtcmp' - -description = """ - Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://github.com/llnl/%(name)s/releases/download/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['fd2c4485eee560a029f62c8f227df4acdb1edc9340907f4ae2dbee59f05f057d'] - -dependencies = [ - ('lwgrp', '1.0.2'), -] - -configopts = '--with-lwgrp=$EBROOTLWGRP' - -sanity_check_paths = { - 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README'], - 'dirs': [] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/d/dtcmp/dtcmp-1.1.0-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/d/dtcmp/dtcmp-1.1.0-iimpi-2020a.eb deleted file mode 100644 index af20dd5ea46..00000000000 --- a/easybuild/easyconfigs/__archive__/d/dtcmp/dtcmp-1.1.0-iimpi-2020a.eb +++ /dev/null @@ -1,31 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'dtcmp' -version = '1.1.0' - -homepage = 'https://github.com/llnl/dtcmp' - -description = """ - Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI. -""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} - -source_urls = ['https://github.com/llnl/%(name)s/releases/download/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['fd2c4485eee560a029f62c8f227df4acdb1edc9340907f4ae2dbee59f05f057d'] - -dependencies = [ - ('lwgrp', '1.0.2'), -] - -configopts = '--with-lwgrp=$EBROOTLWGRP' - -sanity_check_paths = { - 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README'], - 'dirs': [] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2019.11.001-foss-2020a.eb b/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2019.11.001-foss-2020a.eb deleted file mode 100644 index 93429867da4..00000000000 --- a/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2019.11.001-foss-2020a.eb +++ /dev/null @@ -1,34 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Authors:: Inge Gutheil , Alan O'Cais -# License:: MIT/GPL -# -## - -name = 'ELPA' -version = '2019.11.001' - -homepage = 'https://elpa.mpcdf.mpg.de' -description = """Eigenvalue SoLvers for Petaflop-Applications .""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['10374a8f042e23c7e1094230f7e2993b6f3580908a213dbdf089792d05aff357'] - -builddependencies = [ - ('Autotools', '20180311'), - # remove_xcompiler script requires 'python' command, - # manual_cpp script requires 'python' command and is not compatible yet with Python 3 - ('Python', '2.7.18'), -] - -# When building in parallel, the file test_setup_mpi.mod is sometimes -# used before it is built, leading to an error. This must be a bug in -# the makefile affecting parallel builds. -maxparallel = 1 - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2019.11.001-intel-2020a.eb b/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2019.11.001-intel-2020a.eb deleted file mode 100644 index 9a20079e79c..00000000000 --- a/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2019.11.001-intel-2020a.eb +++ /dev/null @@ -1,34 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Authors:: Inge Gutheil , Alan O'Cais -# License:: MIT/GPL -# -## - -name = 'ELPA' -version = '2019.11.001' - -homepage = 'https://elpa.mpcdf.mpg.de' -description = """Eigenvalue SoLvers for Petaflop-Applications .""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['10374a8f042e23c7e1094230f7e2993b6f3580908a213dbdf089792d05aff357'] - -builddependencies = [ - ('Autotools', '20180311'), - # remove_xcompiler script requires 'python' command, - # manual_cpp script requires 'python' command and is not compatible yet with Python 3 - ('Python', '2.7.18'), -] - -# When building in parallel, the file test_setup_mpi.mod is sometimes -# used before it is built, leading to an error. This must be a bug in -# the makefile affecting parallel builds. -maxparallel = 1 - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2020.05.001-intel-2020a.eb b/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2020.05.001-intel-2020a.eb deleted file mode 100644 index c1731fb6926..00000000000 --- a/easybuild/easyconfigs/__archive__/e/ELPA/ELPA-2020.05.001-intel-2020a.eb +++ /dev/null @@ -1,29 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Authors:: Inge Gutheil , Alan O'Cais -# License:: MIT/GPL -# -## - -name = 'ELPA' -version = '2020.05.001' - -homepage = 'https://elpa.mpcdf.mpg.de' -description = """Eigenvalue SoLvers for Petaflop-Applications .""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['66ff1cf332ce1c82075dc7b5587ae72511d2bcb3a45322c94af6b01996439ce5'] - -builddependencies = [ - ('Autotools', '20180311'), - # remove_xcompiler script requires 'python' command, - # manual_cpp script requires 'python' command and is not compatible yet with Python 3 - ('Python', '2.7.18'), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-8.0.1-foss-2020a.eb b/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-8.0.1-foss-2020a.eb deleted file mode 100644 index 94cf018d2b8..00000000000 --- a/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-8.0.1-foss-2020a.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'ESMF' -version = '8.0.1' - -homepage = 'https://www.earthsystemcog.org/projects/esmf/' -description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing - high-performance, multi-component Earth science modeling applications.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} - -source_urls = ['https://github.com/esmf-org/esmf/archive/'] -sources = ['%%(name)s_%s.tar.gz' % '_'.join(version.split('.'))] -patches = ['ESMF-6.1.1_libopts.patch'] -checksums = [ - '9172fb73f3fe95c8188d889ee72fdadb4f978b1d969e1d8e401e8d106def1d84', # ESMF_8_0_1.tar.gz - '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch -] - -dependencies = [ - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), - ('netCDF-C++4', '4.3.1'), -] - -buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' -buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' - -# too parallel causes the build to become really slow -maxparallel = 8 - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-8.0.1-intel-2020a.eb b/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-8.0.1-intel-2020a.eb deleted file mode 100644 index e8d0a6a65da..00000000000 --- a/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-8.0.1-intel-2020a.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'ESMF' -version = '8.0.1' - -homepage = 'https://www.earthsystemcog.org/projects/esmf/' -description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing - high-performance, multi-component Earth science modeling applications.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/esmf-org/esmf/archive/'] -sources = ['%%(name)s_%s.tar.gz' % '_'.join(version.split('.'))] -patches = ['ESMF-6.1.1_libopts.patch'] -checksums = [ - '9172fb73f3fe95c8188d889ee72fdadb4f978b1d969e1d8e401e8d106def1d84', # ESMF_8_0_1.tar.gz - '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch -] - -dependencies = [ - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), - ('netCDF-C++4', '4.3.1'), -] - -buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' -buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' - -# too parallel causes the build to become really slow -maxparallel = 8 - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/e/ESMPy/ESMPy-8.0.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/e/ESMPy/ESMPy-8.0.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index ac76848c04b..00000000000 --- a/easybuild/easyconfigs/__archive__/e/ESMPy/ESMPy-8.0.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'ESMPy' -version = '8.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://earthsystemmodeling.org/esmpy' -description = "Earth System Modeling Framework (ESMF) Python Interface" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/esmf-org/esmf/archive/'] -sources = ['ESMF_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['9172fb73f3fe95c8188d889ee72fdadb4f978b1d969e1d8e401e8d106def1d84'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy, mpi4py - ('ESMF', version), -] - -start_dir = 'src/addon/ESMPy' - -# ESMPy's setup.py script doesn't support using "pip install" -use_pip = False - -buildopts = "--ESMFMKFILE=$EBROOTESMF/lib/esmf.mk" - -options = {'modulename': 'ESMF'} - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/e/ETE/ETE-3.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/e/ETE/ETE-3.1.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index afc094600e9..00000000000 --- a/easybuild/easyconfigs/__archive__/e/ETE/ETE-3.1.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'ETE' -version = '3.1.2' -versionsuffix = '-Python-3.8.2' - -homepage = 'http://etetoolkit.org' -description = """A Python framework for the analysis and visualization of trees""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://pypi.python.org/packages/source/e/ete3'] -sources = ['ete3-%(version)s.tar.gz'] -checksums = ['4fc987b8c529889d6608fab1101f1455cb5cbd42722788de6aea9c7d0a8e59e9'] - -dependencies = [ - ('lxml', '4.5.2'), - ('Python', '3.8.2'), - ('PyQt5', '5.15.1', versionsuffix), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -options = {'modulename': 'ete3'} - -sanity_check_paths = { - 'files': ['bin/ete3'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.3.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.3.7-GCCcore-9.3.0.eb deleted file mode 100644 index 66a09d62918..00000000000 --- a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.3.7-GCCcore-9.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -name = 'Eigen' -version = '3.3.7' - -homepage = 'https://eigen.tuxfamily.org' -description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, - and related algorithms.""" - -# only includes header files, but requires CMake so using non-system toolchain -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['685adf14bd8e9c015b78097c1dc22f2f01343756f196acdc76a678e1ae352e11'] - -# using CMake built with GCCcore to avoid relying on the system compiler to build it -builddependencies = [ - ('binutils', '2.34'), # to make CMake compiler health check pass on old systems - ('CMake', '3.16.4'), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/e/Emacs/Emacs-27.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/e/Emacs/Emacs-27.1-GCCcore-9.3.0.eb deleted file mode 100644 index a56b74c9ba8..00000000000 --- a/easybuild/easyconfigs/__archive__/e/Emacs/Emacs-27.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Emacs' -version = '27.1' - -homepage = 'https://www.gnu.org/software/emacs/' -description = """GNU Emacs is an extensible, customizable text editor--and more. - At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming - language with extensions to support text editing.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['ffbfa61dc951b92cf31ebe3efc86c5a9d4411a1222b8a4ae6716cfd0e2a584db'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), - ('ncurses', '6.2'), - ('LibTIFF', '4.1.0'), - ('X11', '20200222'), - ('GTK+', '3.24.17'), -] - -# If you want to use Emacs plugins you must install the gnutls command line tools -# osdependencies = [('gnutls-utils')] - -configopts = '--with-gif=no --with-tiff=yes --with-x-toolkit=yes --with-xpm=yes --with-gnutls=no ' - -sanity_check_paths = { - 'files': ["bin/emacs", "bin/emacs-%(version)s", "bin/emacsclient", "bin/etags"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb deleted file mode 100644 index 5f7bead2411..00000000000 --- a/easybuild/easyconfigs/__archive__/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PerlModule' - -name = 'ExifTool' -version = '12.00' - -homepage = 'https://owl.phy.queensu.ca/~phil/exiftool/' -description = """Perl module (Image::ExifTool) and program (exiftool) -to read EXIF information from images""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://cpan.metacpan.org/authors/id/E/EX/EXIFTOOL'] -sources = ['Image-%(name)s-%(version)s.tar.gz'] -checksums = ['d0792cc94ab58a8b3d81b18ccdb8b43848c8fb901b5b7caecdcb68689c6c855a'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Perl', '5.30.2') -] - -options = {'modulename': 'Image::ExifTool'} - -sanity_check_paths = { - 'files': ['bin/exiftool'], - 'dirs': ['lib/perl5/site_perl'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb deleted file mode 100644 index 86a42b12742..00000000000 --- a/easybuild/easyconfigs/__archive__/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'eSpeak-NG' -version = '1.50' - -homepage = 'https://github.com/espeak-ng/espeak-ng' -description = """ -The eSpeak NG is a compact open source software text-to-speech synthesizer -for Linux, Windows, Android and other operating systems. -It supports more than 100 languages and accents. -It is based on the eSpeak engine created by Jonathan Duddington. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://github.com/espeak-ng/espeak-ng/archive'] -sources = ['%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_sonic_fftw.patch', - '%(name)s-%(version)s_mbrola_location.patch', -] -checksums = [ - '5ce9f24ee662b5822a4acc45bed31425e70d7c50707b96b6c1603a335c7759fa', # 1.50.tar.gz - 'dc34e14ef4b8bc174c94ad220cbf35b80e6183298d24883cf252507154ef4ee4', # eSpeak-NG-1.50_sonic_fftw.patch - '1bf9bb98f1fd35ddbd373b504c3215641db532093fc5dd44099a820b80c76f83', # eSpeak-NG-1.50_mbrola_location.patch -] - -builddependencies = [('Autotools', '20180311')] - -dependencies = [ - ('sonic', '20180202'), - ('MBROLA', '3.3', '-voices-20200330'), -] - -preconfigopts = './autogen.sh &&' - -configopts = '--disable-dependency-tracking' - -maxparallel = 1 -sanity_check_paths = { - 'files': ['bin/%sspeak%s' % (x, y) for x in ['', 'e'] for y in ['', '-ng']] + - ['include/espeak%s/speak_lib.h' % x for x in ['', '-ng']] + - ['include/espeak-ng/%s.h' % x for x in ['encoding', 'espeak_ng']] + - ['lib/libespeak%s' % x for x in ['.la', '-ng.a', '-ng.%s' % SHLIB_EXT]], - 'dirs': ['lib/pkgconfig'] -} - -sanity_check_commands = ['%sspeak%s --version' % (x, y) for x in ['', 'e'] for y in ['', '-ng']] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/e/ecCodes/ecCodes-2.18.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/e/ecCodes/ecCodes-2.18.0-gompi-2020a.eb deleted file mode 100644 index a6bd7755e50..00000000000 --- a/easybuild/easyconfigs/__archive__/e/ecCodes/ecCodes-2.18.0-gompi-2020a.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'ecCodes' -version = '2.18.0' - -homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' -description = """ecCodes is a package developed by ECMWF which provides an application programming interface and - a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, - WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': False, 'openmp': True} - -source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] -sources = ['eccodes-%(version)s-Source.tar.gz'] -checksums = ['d88943df0f246843a1a062796edbf709ef911de7269648eef864be259e9704e3'] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('netCDF', '4.7.4'), - ('JasPer', '2.0.14'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), -] - -# Python bindings are now provided by a separate package 'eccodes-python' -configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " -configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " -configopts += "-DENABLE_ECCODES_OMP_THREADS=ON" - -local_exes = ['%s_%s' % (a, b) - for a in ['bufr', 'grib', 'gts', 'metar'] - for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] -local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_exes] + - ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/e/eccodes-python/eccodes-python-1.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/e/eccodes-python/eccodes-python-1.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index b0989e20fa6..00000000000 --- a/easybuild/easyconfigs/__archive__/e/eccodes-python/eccodes-python-1.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'eccodes-python' -version = '1.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/ecmwf/eccodes-python' -description = "Python 3 interface to decode and encode GRIB and BUFR files via the ECMWF ecCodes library." - -toolchain = {'name': 'foss', 'version': '2020a'} - -github_account = 'ecmwf' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['88fcd00e0d30ef8a3f6c11dad9cffefd276540488420660cf124e2a7fcddc6e8'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('ecCodes', '2.18.0'), -] - -options = {'modulename': 'eccodes'} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/e/edlib/edlib-1.3.8.post1-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/e/edlib/edlib-1.3.8.post1-GCC-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 6c7dc443ee4..00000000000 --- a/easybuild/easyconfigs/__archive__/e/edlib/edlib-1.3.8.post1-GCC-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'edlib' -version = '1.3.8.post1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://martinsos.github.io/edlib' -description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['81bc688e8fc69d657a6b5067e104a0924b0217b7ab54547155278935d09346e0'] - -dependencies = [ - ('Python', '3.8.2'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/e/edlib/edlib-1.3.8.post2-iccifort-2020.1.217-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/e/edlib/edlib-1.3.8.post2-iccifort-2020.1.217-Python-3.8.2.eb deleted file mode 100644 index 816a48cd109..00000000000 --- a/easybuild/easyconfigs/__archive__/e/edlib/edlib-1.3.8.post2-iccifort-2020.1.217-Python-3.8.2.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'edlib' -version = '1.3.8.post2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://martinsos.github.io/edlib' -description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -sources = [SOURCE_TAR_GZ] -checksums = ['58c08103174a39cacc0cc01eee93a433b4382fbe85146a627986570d3b2ab79b'] - -dependencies = [ - ('Python', '3.8.2'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/e/elfutils/elfutils-0.182-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/e/elfutils/elfutils-0.182-GCCcore-9.3.0.eb deleted file mode 100644 index 4a282ada13a..00000000000 --- a/easybuild/easyconfigs/__archive__/e/elfutils/elfutils-0.182-GCCcore-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'elfutils' -version = '0.182' - -homepage = 'https://elfutils.org/' - -description = """ - The elfutils project provides libraries and tools for ELF files - and DWARF data. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://sourceware.org/elfutils/ftp/0.182/'] -sources = [SOURCE_TAR_BZ2] -checksums = ['ecc406914edf335f0b7fc084ebe6c460c4d6d5175bfdd6688c1c78d9146b8858'] - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('binutils', '2.34'), - ('bzip2', '1.0.8'), - ('libarchive', '3.4.2'), - ('XZ', '5.2.5'), - ('zstd', '1.4.4'), -] - -configopts = "--disable-debuginfod --disable-libdebuginfod" - -sanity_check_paths = { - 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.so'], - 'dirs': [] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-FCC-4.5.0.eb deleted file mode 100644 index 38abc661b02..00000000000 --- a/easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-FCC-4.5.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'ConfigureMake' - -name = 'expat' -version = '2.2.9' - -homepage = 'https://libexpat.github.io' - -description = """ - Expat is an XML parser library written in C. It is a stream-oriented parser - in which an application registers handlers for things the parser might find - in the XML document (like start tags) -""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] -sources = [SOURCE_TAR_BZ2] -checksums = ['f1063084dc4302a427dabcca499c8312b3a32a29b7d2506653ecc8f950a9a237'] - -builddependencies = [('binutils', '2.36.1')] - -# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. -# Docbook2X needs XML-Parser and XML-Parser needs expat. -# -> circular dependency. "--without-docbook" breaks this circle. -configopts = ['--without-docbook'] - -sanity_check_paths = { - 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-GCCcore-9.3.0.eb deleted file mode 100644 index 7688191e9ce..00000000000 --- a/easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'expat' -version = '2.2.9' - -homepage = 'https://libexpat.github.io' - -description = """ - Expat is an XML parser library written in C. It is a stream-oriented parser - in which an application registers handlers for things the parser might find - in the XML document (like start tags) -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] -sources = [SOURCE_TAR_BZ2] -checksums = ['f1063084dc4302a427dabcca499c8312b3a32a29b7d2506653ecc8f950a9a237'] - -builddependencies = [('binutils', '2.34')] - -# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. -# Docbook2X needs XML-Parser and XML-Parser needs expat. -# -> circular dependency. "--without-docbook" breaks this circle. -configopts = ['--without-docbook'] - -sanity_check_paths = { - 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/e/expect/expect-5.45.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/e/expect/expect-5.45.4-GCCcore-9.3.0.eb deleted file mode 100644 index 7bd543e857b..00000000000 --- a/easybuild/easyconfigs/__archive__/e/expect/expect-5.45.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'expect' -version = '5.45.4' - -homepage = 'https://core.tcl.tk/expect/index' -description = """Expect is a tool for automating interactive applications - such as telnet, ftp, passwd, fsck, rlogin, tip, etc. - Expect really makes this stuff trivial. - Expect is also useful for testing these same applications.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s%(version)s.tar.gz'] -checksums = ['49a7da83b0bdd9f46d04a04deec19c7767bb9a323e40c4781f89caf760b92c34'] - -# we need to specify --exec-prefix as by default it uses the path of Tcl. -configopts = ['--with-tcl=${EBROOTTCL}/lib --exec-prefix=%(installdir)s'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Tcl', '8.6.10'), -] - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/expect'], - 'dirs': ['.'], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb deleted file mode 100644 index d951449e5ef..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb +++ /dev/null @@ -1,63 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Cedric Laczny , Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = 'Bundle' - -name = 'FASTX-Toolkit' -version = '0.0.14' - -homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' -description = """The FASTX-Toolkit is a collection of command line tools for - Short-Reads FASTA/FASTQ files preprocessing.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -default_easyblock = 'ConfigureMake' - -components = [ - ('libgtextutils', '0.7', { - 'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'], - 'sources': [SOURCE_TAR_GZ], - 'patches': ['libgtextutils-%(version)s_fix-bool.patch'], - 'checksums': [ - '792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a', # libgtextutils-0.7.tar.gz - 'bb16a4fd86c2eb12215d8780b09f0898771a73e53889a015e2351f2d737c9a00', # libgtextutils-0.7_fix-bool.patch - ], - 'start_dir': 'libgtextutils-%(version)s', - }), - (name, version, { - 'source_urls': ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'], - 'sources': ['fastx_toolkit-%(version)s.tar.bz2'], - 'checksums': ['9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806'], - 'start_dir': 'fastx_toolkit-%(version)s', - 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", - 'configopts': 'CXXFLAGS="$CXXFLAGS -Wno-implicit-fallthrough"', - }), -] - -sanity_check_paths = { - 'files': - ['bin/fastx_%s' % x for x in - ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', - 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in - ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in - ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', - 'quality_trimmer', 'masker']] + - ['lib/libgtextutils.%s' % SHLIB_EXT, 'lib/libgtextutils.a'], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/FCC/FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/f/FCC/FCC-4.5.0.eb deleted file mode 100644 index f437ec83356..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FCC/FCC-4.5.0.eb +++ /dev/null @@ -1,17 +0,0 @@ -easyblock = 'Toolchain' - -name = 'FCC' -version = '4.5.0' - -homepage = '(none)' -description = """Fujitsu Compiler based compiler toolchain.""" - -toolchain = SYSTEM - -osdependencies = [('binutils')] - -dependencies = [ - ('lang/tcsds-1.2.31', EXTERNAL_MODULE), # provides Fujitsu Compiler 4.5.0 -] - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/f/FDS/FDS-6.7.4-intel-2020a.eb b/easybuild/easyconfigs/__archive__/f/FDS/FDS-6.7.4-intel-2020a.eb deleted file mode 100644 index c577cf076d5..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FDS/FDS-6.7.4-intel-2020a.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'FDS' -version = '6.7.4' - -homepage = 'https://pages.nist.gov/fds-smv/' -description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, - with an emphasis on smoke and heat transport from fires.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} - -source_urls = ['https://github.com/firemodels/fds/archive/'] -sources = ['FDS%(version)s.tar.gz'] -checksums = ['f23050f55adb17a9a3d5e295256159412ccbd746b87e2b4192386ca6353e4517'] - -unpack_options = '--strip-components=1' - -start_dir = 'Build' - -# just run make in the install dir -skipsteps = ['configure', 'install'] -buildininstalldir = True - -buildopts = 'impi_intel_linux_64 FFLAGS="$FFLAGS -fpp" FCOMPL="$FC" obj=fds' - -modextrapaths = {'PATH': 'Build'} - -sanity_check_paths = { - 'files': ['Build/fds'], - 'dirs': [], -} - -sanity_check_commands = [ - "fds 2>&1 | grep 'MPI Enabled;'", - "fds 2>&1 | grep 'OpenMP Enabled;'", -] - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/f/FDS/FDS-6.7.5-intel-2020a.eb b/easybuild/easyconfigs/__archive__/f/FDS/FDS-6.7.5-intel-2020a.eb deleted file mode 100644 index e394da50b68..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FDS/FDS-6.7.5-intel-2020a.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'FDS' -version = '6.7.5' - -homepage = 'https://pages.nist.gov/fds-smv/' -description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, - with an emphasis on smoke and heat transport from fires.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} - -source_urls = ['https://github.com/firemodels/fds/archive/'] -sources = ['FDS%(version)s.tar.gz'] -checksums = ['e09248f61fde5b328656ac2ba5d483c54604c1db65fda6e70d9022226387863b'] - -unpack_options = '--strip-components=1' - -start_dir = 'Build' - -# just run make in the install dir -skipsteps = ['configure', 'install'] -buildininstalldir = True - -buildopts = 'impi_intel_linux_64 FFLAGS="$FFLAGS -fpp" FCOMPL="$FC" obj=fds' - -modextrapaths = {'PATH': 'Build'} - -sanity_check_paths = { - 'files': ['Build/fds'], - 'dirs': [], -} - -sanity_check_commands = [ - "fds 2>&1 | grep 'MPI Enabled;'", - "fds 2>&1 | grep 'OpenMP Enabled;'", -] - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb deleted file mode 100644 index 26e6624b60f..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'FFTW' -version = '1.0.0' -versionsuffix = '-fujitsu' - -homepage = 'https://github.com/fujitsu/fftw3' -description = """This is a fork of FFTW3 for the Armv8-A 64-bit architecture (AArch64) - with 512-bit Scalable Vector Extension (SVE) support.""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/fujitsu/fftw3/archive/refs/tags/'] -sources = ['sve-v%(version)s.tar.gz'] -checksums = ['b5931e352355d8d1ffeb215922f4b96de11b8585c423fceeaffbf3d5436f6f2f'] - -builddependencies = [('Autotools', '20210128')] - -preconfigopts = "touch ChangeLog && autoreconf --verbose --install --symlink --force && " - -configopts = '--disable-doc' - -with_mpi = False - -runtest = 'check' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-GCC-9.3.0-serial.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-GCC-9.3.0-serial.eb deleted file mode 100644 index 5043b400a3f..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-GCC-9.3.0-serial.eb +++ /dev/null @@ -1,20 +0,0 @@ -name = 'FFTW' -version = '3.3.8' -versionsuffix = '-serial' - -homepage = 'http://www.fftw.org' -description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) - in one or more dimensions, of arbitrary input size, and of both real and complex data.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] - -with_mpi = False - -runtest = 'check' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompi-2020a-amd.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompi-2020a-amd.eb deleted file mode 100644 index c03491e739f..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompi-2020a-amd.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'FFTW' -version = '3.3.8' -local_amd_fftw_ver = '2.2' -versionsuffix = '-amd' - -homepage = 'https://developer.amd.com/amd-aocl/fftw/' -description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) -in one or more dimensions, of arbitrary input size, and of both real and complex data. -AMD FFTW includes selective kernels and routines optimized for the AMD EPYC™ processor family.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/amd/amd-fftw/archive/'] -sources = [{ - 'download_filename': '%s.tar.gz' % local_amd_fftw_ver, - 'filename': 'amd-fftw-%s.tar.gz' % local_amd_fftw_ver, -}] -checksums = ['de9d777236fb290c335860b458131678f75aa0799c641490c644c843f0e246f8'] - -configopts = '--enable-amd-opt' - -runtest = 'check' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompi-2020a.eb deleted file mode 100644 index 1e3dfaa89ad..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompi-2020a.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'FFTW' -version = '3.3.8' - -homepage = 'http://www.fftw.org' -description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) - in one or more dimensions, of arbitrary input size, and of both real and complex data.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] - -runtest = 'check' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompic-2020a.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompic-2020a.eb deleted file mode 100644 index e598bcd6fb4..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-gompic-2020a.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'FFTW' -version = '3.3.8' - -homepage = 'http://www.fftw.org' -description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) - in one or more dimensions, of arbitrary input size, and of both real and complex data.""" - -toolchain = {'name': 'gompic', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] - -runtest = 'check' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-intel-2020a.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-intel-2020a.eb deleted file mode 100644 index b148d98715a..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.8-intel-2020a.eb +++ /dev/null @@ -1,30 +0,0 @@ -name = 'FFTW' -version = '3.3.8' - -homepage = 'http://www.fftw.org' -description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) - in one or more dimensions, of arbitrary input size, and of both real and complex data.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = [SOURCELOWER_TAR_GZ] -patches = ['FFTW-%(version)s_fix-icc-no-gcc.patch'] -checksums = [ - '6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303', # fftw-3.3.8.tar.gz - '1b3319b98a2ca4ead68290b3229385c0573e22749a5a2ffb49486a0bbb37dc1e', # FFTW-3.3.8_fix-icc-no-gcc.patch -] - -# no quad precision, requires GCC v4.6 or higher -# see also -# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html -with_quad_prec = False - -# compilation fails on AMD systems when configuring with --enable-avx-128-fma, -# because Intel compilers do not support FMA4 instructions -use_fma4 = False - -runtest = 'check' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/f/FFmpeg/FFmpeg-4.2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/FFmpeg/FFmpeg-4.2.2-GCCcore-9.3.0.eb deleted file mode 100644 index ebdcd7df2f4..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FFmpeg/FFmpeg-4.2.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'FFmpeg' -version = '4.2.2' - -homepage = 'https://www.ffmpeg.org/' -description = """A complete, cross-platform solution to record, convert and stream audio and video.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://ffmpeg.org/releases/'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['b620d187c26f76ca19e74210a0336c3b8380b97730df5cdf45f3e69e89000e5c'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2') -] - -dependencies = [ - ('NASM', '2.14.02'), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('x264', '20191217'), - ('LAME', '3.100'), - ('x265', '3.3'), - ('X11', '20200222'), - ('freetype', '2.10.1'), - ('fontconfig', '2.13.92'), - ('FriBidi', '1.0.9'), -] - -configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' -configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' -configopts += '--enable-libfribidi' - -sanity_check_paths = { - 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe']] + - ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', - 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], - 'dirs': ['include'] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020a.eb b/easybuild/easyconfigs/__archive__/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020a.eb deleted file mode 100644 index b4d0b82e61a..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FIRESTARTER/FIRESTARTER-2.0-gcccuda-2020a.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'CMakeMakeCp' - -name = 'FIRESTARTER' -version = '2.0' - -homepage = 'https://github.com/tud-zih-energy/FIRESTARTER/' -description = """FIRESTARTER: A Processor Stress Test Utility. -FIRESTARTER maximizes the energy consumption of 64-Bit x86 processors by -generating heavy load on the execution units as well as transferring data -between the cores and multiple levels of the memory hierarchy.""" - -toolchain = {'name': 'gcccuda', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/tud-zih-energy/FIRESTARTER/releases/download/v%(version)s/'] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['a3b09ac4ec29c3d24750bf161c58abe6b9c2f86d56f046d2657be72daf63b673'] - -start_dir = 'sources' - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('hwloc', '2.2.0'), -] - -# All configopts, including default values -configopts = '-DFIRESTARTER_BUILD_TYPE=FIRESTARTER_CUDA' -configopts += ' -DFIRESTARTER_LINK_STATIC=ON' -configopts += ' -DFIRESTARTER_BUILD_HWLOC=OFF' -configopts += ' -DFIRESTARTER_THREAD_AFFINITY=ON' - -files_to_copy = [(['FIRESTARTER'], 'bin')] - -sanity_check_commands = ['bin/FIRESTARTER -t 1'] -sanity_check_paths = { - 'files': ['bin/FIRESTARTER'], - 'dirs': ['bin'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 34f5aaf3db5..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen - -easyblock = 'CMakeMake' - -name = 'FLANN' -version = '1.8.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/mariusmuja/flann/' -description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True} -source_urls = ['https://github.com/mariusmuja/flann/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['FLANN-%(version)s_fix-cmake.patch'] - -checksums = [ - 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz - '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-1.8.4_fix-cmake.patch -] - -builddependencies = [('CMake', '3.16.4')] -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-3.8.2'), -] - -configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" - -modextrapaths = {'PYTHONPATH': ['share/flann/python']} - -sanity_check_paths = { - 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', - 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], - 'dirs': ['include/flann', 'lib/pkgconfig', 'share/doc/flann', 'share/flann/python'], -} -sanity_check_commands = ["python -c 'import pyflann'"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/f/FLANN/FLANN-1.8.4_fix-cmake.patch b/easybuild/easyconfigs/__archive__/f/FLANN/FLANN-1.8.4_fix-cmake.patch deleted file mode 100644 index a1932dfb573..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FLANN/FLANN-1.8.4_fix-cmake.patch +++ /dev/null @@ -1,30 +0,0 @@ -# Flann fails to build with newer versions of CMake, see: -# https://stackoverflow.com/questions/50763621/building-flann-with-cmake-fails -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen -diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt -index 49c53f0..0976e41 100644 ---- a/src/cpp/CMakeLists.txt -+++ b/src/cpp/CMakeLists.txt -@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB) - endif() - - if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) -- add_library(flann_cpp SHARED "") -+ add_library(flann_cpp SHARED empty.cpp) - set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) - target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) - -@@ -83,7 +83,7 @@ if (BUILD_C_BINDINGS) - set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) - - if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) -- add_library(flann SHARED "") -+ add_library(flann SHARED empty.cpp) - set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) - target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) - else() -diff --git a/src/cpp/empty.cpp b/src/cpp/empty.cpp -new file mode 100644 -index 0000000..e69de29 diff --git a/easybuild/easyconfigs/__archive__/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 5321fb0cc98..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen - -easyblock = 'CMakeMake' - -name = 'FLANN' -version = '1.9.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/mariusmuja/flann/' -description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/mariusmuja/flann/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['FLANN-1.8.4_fix-cmake.patch'] -checksums = [ - 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz - '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-1.8.4_fix-cmake.patch -] - -builddependencies = [('CMake', '3.16.4')] -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-3.8.2'), -] - -configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" - -modextrapaths = {'PYTHONPATH': ['share/flann/python']} - -sanity_check_paths = { - 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', - 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], - 'dirs': ['include/flann', 'lib/pkgconfig', 'share/flann/python'], -} -sanity_check_commands = ["python -c 'import pyflann'"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb deleted file mode 100644 index b47d9693055..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -# -# author: Dina Mahmoud Ibrahim ( Cairo University ) -# -easyblock = 'ConfigureMake' - -name = 'FLTK' -version = '1.3.5' - -homepage = 'https://www.fltk.org' -description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, - and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL - and its built-in GLUT emulation.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] -sources = ['%(namelower)s-%(version)s-source.tar.gz'] -patches = ['FLTK-1.3.4_fix-LDFLAGS.patch'] -checksums = [ - '8729b2a055f38c1636ba20f749de0853384c1d3e9d1a6b8d4d1305143e115702', # fltk-1.3.5-source.tar.gz - 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch -] - -configopts = '--enable-shared --enable-threads --enable-xft' - -builddependencies = [ - ('binutils', '2.34') -] - -dependencies = [ - ('Mesa', '20.0.2'), - ('libGLU', '9.0.1'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), - ('xprop', '1.2.4'), - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], - 'dirs': ['lib'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb deleted file mode 100644 index 3559c89032e..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'FOX-Toolkit' -version = '1.6.57' - -homepage = 'https://www.fox-toolkit.org/' -description = """FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and -effectively. It offers a wide, and growing, collection of Controls, and -provides state of the art facilities such as drag and drop, selection, as well -as OpenGL widgets for 3D graphical manipulation. FOX also implements icons, -images, and user-convenience features such as status line help, and tooltips.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://fox-toolkit.org/ftp'] -sources = ['fox-%(version)s.tar.gz'] -checksums = ['65ef15de9e0f3a396dc36d9ea29c158b78fad47f7184780357b929c94d458923'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('libGLU', '9.0.1'), - ('X11', '20200222'), -] - -preconfigopts = """sed -i '/^CXXFLAGS=""$/d;/LDFLAGS="-s ${LDFLAGS}"/d' configure.ac && """ -preconfigopts += "autoreconf -f -i && " - -configopts = '--enable-release' - -sanity_check_paths = { - 'files': ['lib/lib%s-%%(version_major_minor)s.%s' % (n, x) for n in ['CHART', 'FOX'] for x in ['a', SHLIB_EXT]] + - ['bin/fox-config'], - 'dirs': ['include'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb deleted file mode 100644 index 8eaac990bbf..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb +++ /dev/null @@ -1,45 +0,0 @@ -# easybuild easyconfig -# -# John Dey jfdey@fredhutch.org -# -# Updated: Pavel Grochal (INUITS) - -easyblock = 'ConfigureMake' - -name = 'FastANI' -version = '1.31' - -homepage = "https://github.com/ParBLiSS/FastANI" -description = """FastANI is developed for fast alignment-free computation of - whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean - nucleotide identity of orthologous gene pairs shared between two microbial - genomes. FastANI supports pairwise comparison of both complete and draft - genome assemblies.""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] -sources = ['v%(version)s.zip'] -patches = ['FastANI-1.2-memcpy.patch'] -checksums = [ - '05104b153f30259eb465d46621056cd670a637e0bf911ff3bf5aa032dcbc1e8b', # v1.31.zip - 'eebcf0b64c31ee360ca79136f644157064ac69747ed13cff70f5c9932c6bb0d5', # FastANI-1.2-memcpy.patch -] - -builddependencies = [('Autotools', '20180311')] - -dependencies = [ - ('GSL', '2.6'), - ('zlib', '1.2.11'), -] - -preconfigopts = 'autoconf && ' - -sanity_check_paths = { - 'files': ['bin/fastANI'], - 'dirs': [] -} - -sanity_check_commands = ["fastANI --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/FastTree/FastTree-2.1.11-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/FastTree/FastTree-2.1.11-GCCcore-9.3.0.eb deleted file mode 100644 index 351d353bcf5..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FastTree/FastTree-2.1.11-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'CmdCp' - -name = 'FastTree' -version = '2.1.11' - -homepage = 'http://www.microbesonline.org/fasttree/' -description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide - or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of - time and memory. """ - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -# HTTPS cert error: -# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... -source_urls = ['http://www.microbesonline.org/fasttree/'] -sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] -checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] - -builddependencies = [('binutils', '2.34')] - -cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] - -files_to_copy = [(['FastTree'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/FastTree'], - 'dirs': [], -} - -sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/Fiona/Fiona-1.8.16-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/f/Fiona/Fiona-1.8.16-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index cf701124ad7..00000000000 --- a/easybuild/easyconfigs/__archive__/f/Fiona/Fiona-1.8.16-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Fiona' -version = '1.8.16' -versionsuffix = "-Python-%(pyver)s" - -homepage = 'https://github.com/Toblerity/Fiona' -description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data -in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, -mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using -multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS -packages such as pyproj, Rtree, and Shapely.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('GDAL', '3.0.4', versionsuffix), - ('Shapely', '1.7.1', versionsuffix), # optional -] - -exts_list = [ - ('cligj', '0.5.0', { - 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], - }), - ('click-plugins', '1.1.1', { - 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], - }), - ('munch', '2.5.0', { - 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], - }), - (name, version, { - 'checksums': ['fd6dfb65959becc916e9f6928618bfd59c16cdbc413ece0fbac61489cd11255f'], - }), -] - -sanity_check_paths = { - 'files': ['bin/fio'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/f/Flask/Flask-1.1.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/f/Flask/Flask-1.1.2-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index d7086e22fe8..00000000000 --- a/easybuild/easyconfigs/__archive__/f/Flask/Flask-1.1.2-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Flask' -version = '1.1.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.palletsprojects.com/p/flask/' -description = """ -Flask is a lightweight WSGI web application framework. It is designed to make -getting started quick and easy, with the ability to scale up to complex -applications. -This module includes the Flask extensions: Flask-Cors""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -dependencies = [ - ('Python', '3.8.2'), -] - -builddependencies = [('binutils', '2.34')] - -exts_list = [ - ('itsdangerous', '1.1.0', { - 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], - }), - ('Werkzeug', '1.0.1', { - 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], - }), - (name, version, { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), - ('Flask-Cors', '3.0.9', { - 'checksums': ['6bcfc100288c5d1bcb1dbb854babd59beee622ffd321e444b05f24d6d58466b8'], - }), -] - -sanity_check_paths = { - 'files': ['bin/flask'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ['flask --version'] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 926df623a6d..00000000000 --- a/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Flye' -version = '2.8.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/fenderglass/Flye' -description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio - and Oxford Nanopore Technologies.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/fenderglass/Flye/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['436ebe884e5000c023d78c098596d22c235c916f91e6c29a79b88a21e611fcb4'] - -dependencies = [('Python', '3.8.2')] - -sanity_check_paths = { - 'files': ['bin/flye'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ['%(namelower)s --help'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 97ef1895c22..00000000000 --- a/easybuild/easyconfigs/__archive__/f/Flye/Flye-2.8.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Flye' -version = '2.8.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/fenderglass/Flye' -description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio - and Oxford Nanopore Technologies.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/fenderglass/Flye/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['f1284bd2a777356fbf808d89052bc0f9bf5602560dde7cf722d7974d9a94d03b'] - -dependencies = [('Python', '3.8.2')] - -sanity_check_paths = { - 'files': ['bin/flye'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ['%(namelower)s --help'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/FoX/FoX-4.1.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/FoX/FoX-4.1.2-GCC-9.3.0.eb deleted file mode 100644 index 59d64f8646d..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FoX/FoX-4.1.2-GCC-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'FoX' -version = '4.1.2' - -homepage = 'http://homepages.see.leeds.ac.uk/~earawa/FoX/' -description = """FoX is an XML library written in Fortran 95. -It allows software developers to read, write and modify XML documents from Fortran applications without the -complications of dealing with multi-language development.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['http://homepages.see.leeds.ac.uk/~earawa/FoX/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['3b749138229e7808d0009a97e2ac47815ad5278df6879a9cc64351a7921ba06f'] - -sanity_check_paths = { - 'files': ['lib/libFoX_%s.a' % x for x in ['common', 'dom', 'fsys', 'sax', 'utils', 'wcml', 'wkml', 'wxml']], - 'dirs': ['finclude', 'lib', 'bin'] -} - -modextrapaths = { - 'CPATH': ['finclude'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/f/FreeImage/FreeImage-3.18.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/FreeImage/FreeImage-3.18.0-GCCcore-9.3.0.eb deleted file mode 100644 index ff19be5b911..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FreeImage/FreeImage-3.18.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'FreeImage' -version = '3.18.0' - -homepage = 'http://freeimage.sourceforge.net' -description = """FreeImage is an Open Source library project for developers who would like to support popular graphics -image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to -use, fast, multithreading safe.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%%(name)s%s.zip' % ''.join(version.split('.'))] -patches = ['%(name)s-%(version)s-fix-makefile.patch'] -checksums = [ - 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip - '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # FreeImage-3.18.0-fix-makefile.patch -] - -builddependencies = [('binutils', '2.34')] - -skipsteps = ['configure'] - -buildopts = ['', '-f Makefile.fip'] -installopts = [ - 'INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib', - '-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib' -] - -dependencies = [('zlib', '1.2.11')] - -sanity_check_paths = { - 'files': ['include/FreeImage.h', 'include/FreeImagePlus.h', 'lib/libfreeimage.a', 'lib/libfreeimage.%s' % SHLIB_EXT, - 'lib/libfreeimageplus.a', 'lib/libfreeimageplus.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb deleted file mode 100644 index 34132127d4a..00000000000 --- a/easybuild/easyconfigs/__archive__/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'FriBidi' -version = '1.0.9' - -homepage = 'https://github.com/fribidi/fribidi' - -description = """ - The Free Implementation of the Unicode Bidirectional Algorithm. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['c5e47ea9026fb60da1944da9888b4e0a18854a0e2410bbfe7ad90a054d36e0c7'] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', - 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/f/Fujitsu/Fujitsu-21.05.eb b/easybuild/easyconfigs/__archive__/f/Fujitsu/Fujitsu-21.05.eb deleted file mode 100644 index 9a68084d7a8..00000000000 --- a/easybuild/easyconfigs/__archive__/f/Fujitsu/Fujitsu-21.05.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'Toolchain' - -name = 'Fujitsu' -version = '21.05' - -homepage = '(none)' -description = """Toolchain using Fujitsu compilers and libraries.""" - -toolchain = SYSTEM - -local_fccver = '4.5.0' -local_comp_tc = ('FCC', local_fccver) -local_comp_mpi_tc = ('ffmpi', local_fccver) - -dependencies = [ - local_comp_tc, - local_comp_mpi_tc, - # Fujitsu's fork of FFTW doesn't seem to support MPI yet (mpi tests fail) - # ('FFTW', '1.0.0', '-fujitsu', local_comp_mpi_tc), - ('FFTW', '1.0.0', '-fujitsu', local_comp_tc) -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/f/fastahack/fastahack-1.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/fastahack/fastahack-1.0.0-GCCcore-9.3.0.eb deleted file mode 100644 index 10b4c25ef18..00000000000 --- a/easybuild/easyconfigs/__archive__/f/fastahack/fastahack-1.0.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'fastahack' -version = '1.0.0' - -homepage = 'https://github.com/ekg/fastahack' -description = """Utilities for indexing and sequence extraction from FASTA files.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'ekg' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-1.0.0_build-libs.patch'] -checksums = [ - 'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae', # v1.0.0.tar.gz - '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4', # fastahack-1.0.0_build-libs.patch -] - -builddependencies = [('binutils', '2.34')] - -skipsteps = ['configure'] - -installopts = 'PREFIX=%(installdir)s ' - -sanity_check_paths = { - 'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb deleted file mode 100644 index 529db9c4abd..00000000000 --- a/easybuild/easyconfigs/__archive__/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'fastp' -version = '0.20.1' - -homepage = 'https://github.com/OpenGene/fastp' -description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. - This tool is developed in C++ with multithreading supported to afford high performance.""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -# https://github.com/OpenGene/fastp -github_account = 'OpenGene' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['e1b663717850bed7cb560c0c540e9a05dd9448ec76978faaf853a6959fd5b1b3'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -skipsteps = ['configure'] - -buildopts = ' CXX=${CXX}' - -preinstallopts = 'mkdir -p %(installdir)s/bin && ' - -installopts = 'PREFIX=%(installdir)s' - -sanity_check_paths = { - 'files': ['bin/fastp'], - 'dirs': [], -} - -sanity_check_commands = [('fastp', '--help')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/fermi-lite/fermi-lite-20190320-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/fermi-lite/fermi-lite-20190320-GCCcore-9.3.0.eb deleted file mode 100644 index 3da97822972..00000000000 --- a/easybuild/easyconfigs/__archive__/f/fermi-lite/fermi-lite-20190320-GCCcore-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Author: Jasper Grimm (UoY) - -easyblock = 'MakeCp' - -name = 'fermi-lite' -version = '20190320' -local_commit = 'b499514' - -homepage = 'https://github.com/lh3/fermi-lite' -description = """Standalone C library for assembling Illumina short reads in small regions.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'lh3' -source_urls = [GITHUB_SOURCE] -sources = ['%s.tar.gz' % local_commit] -patches = [ - '%(name)s-20190320_avoid-bwa-namespace-conflict.patch', - '%(name)s-20190320_build-shared-lib.patch', -] -checksums = [ - 'ea1230e298b8e7193a996b5aceeff7fea44ef00852b0b87d4fcb504bdca0e712', # b499514.tar.gz - # fermi-lite-20190320_avoid-bwa-namespace-conflict.patch - '27600733f1cea8b1d1503b1a67b9d41526e907c1b6321313ff51194e166c1842', - '43398559fbb3910d6d3d1a41af3fb16bf8f26bd7cc34176dfc9a068a551c3f50', # fermi-lite-20190320_build-shared-lib.patch -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('zlib', '1.2.11')] - -files_to_copy = [ - (['fml-asm'], 'bin'), - (['*.a', '*.%s*' % SHLIB_EXT], 'lib'), - (['*.h'], 'include/fml'), - 'test', -] - -sanity_check_paths = { - 'files': ['bin/fml-asm', 'lib/libfml.a', 'lib/libfml.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/festival/festival-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/festival/festival-2.5.0-GCCcore-9.3.0.eb deleted file mode 100644 index 71f5df63488..00000000000 --- a/easybuild/easyconfigs/__archive__/f/festival/festival-2.5.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,139 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'festival' -version = '2.5.0' - -homepage = ['http://festvox.org/festival/'] - -description = """ -University of Edinburgh's Festival Speech Synthesis Systems is a free software -multi-lingual speech synthesis workbench that runs on multiple-platforms -offering black box text to speech, as well as an open architecture for -research in speech synthesis. -It designed as a component of large speech technology systems. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [ - 'http://festvox.org/packed/festival/%(version_major_minor)s', - 'http://festvox.org/packed/festival/%(version_major_minor)s/voices', -] -sources = [{ - 'filename': '%(name)s-%(version)s-release.tar.gz', - 'extract_cmd': 'tar xzf %s -C %(installdir)s --strip-components=1', -}] -local_sources = [ - 'festlex_CMU.tar.gz', - 'festlex_OALD.tar.gz', - 'festlex_POSLEX.tar.gz', - 'festvox_cmu_indic_ben_rm_cg.tar.gz', - 'festvox_cmu_indic_guj_ad_cg.tar.gz', - 'festvox_cmu_indic_guj_dp_cg.tar.gz', - 'festvox_cmu_indic_guj_kt_cg.tar.gz', - 'festvox_cmu_indic_hin_ab_cg.tar.gz', - 'festvox_cmu_indic_kan_plv_cg.tar.gz', - 'festvox_cmu_indic_mar_aup_cg.tar.gz', - 'festvox_cmu_indic_mar_slp_cg.tar.gz', - 'festvox_cmu_indic_pan_amp_cg.tar.gz', - 'festvox_cmu_indic_tam_sdr_cg.tar.gz', - 'festvox_cmu_indic_tel_kpn_cg.tar.gz', - 'festvox_cmu_indic_tel_sk_cg.tar.gz', - 'festvox_cmu_indic_tel_ss_cg.tar.gz', - 'festvox_cmu_us_aew_cg.tar.gz', - 'festvox_cmu_us_ahw_cg.tar.gz', - 'festvox_cmu_us_aup_cg.tar.gz', - 'festvox_cmu_us_awb_cg.tar.gz', - 'festvox_cmu_us_axb_cg.tar.gz', - 'festvox_cmu_us_bdl_cg.tar.gz', - 'festvox_cmu_us_clb_cg.tar.gz', - 'festvox_cmu_us_eey_cg.tar.gz', - 'festvox_cmu_us_fem_cg.tar.gz', - 'festvox_cmu_us_gka_cg.tar.gz', - 'festvox_cmu_us_jmk_cg.tar.gz', - 'festvox_cmu_us_ksp_cg.tar.gz', - 'festvox_cmu_us_ljm_cg.tar.gz', - 'festvox_cmu_us_lnh_cg.tar.gz', - 'festvox_cmu_us_rms_cg.tar.gz', - 'festvox_cmu_us_rxr_cg.tar.gz', - 'festvox_cmu_us_slp_cg.tar.gz', - 'festvox_cmu_us_slt_cg.tar.gz', - 'festvox_kallpc16k.tar.gz', - 'festvox_rablpc16k.tar.gz', -] -for local_x in local_sources: - local_newfilename = local_x.split('.') - local_newfilename[0] = local_newfilename[0] + '-%(version)s' - sources.append({ - 'download_filename': local_x, - 'filename': '.'.join(local_newfilename), - 'extract_cmd': 'tar xzf %s -C %(installdir)s --strip-components=1', - }) - -patches = ['%(name)s-%(version)s_speech_tools.patch'] -checksums = [ - '4c9007426b125290599d931df410e2def51e68a8aeebd89b4a61c7c96c09a4b4', # festival-2.5.0-release.tar.gz - 'c19430919bca45d5368cd4c82af6153fbcc96a487ebd30b78b5f3c08718b7c07', # festlex_CMU.tar.gz - 'e33a345390d4c76f8b987b06a5332bcdd0b168cf67c95ddc3270f9163cbe61f8', # festlex_OALD.tar.gz - 'e7c6e3642dbd5b0d64942bc015a986fdd6244a79e51ec2e8309e63d569e49ea3', # festlex_POSLEX.tar.gz - '56e2144d5eed6c89a451789ef7f37346dd351efdbb86a0fa650432a19b07367f', # festvox_cmu_indic_ben_rm_cg.tar.gz - '4a0ac2d1b15cd41108be803e23f11911be953b50733848a8e67428c642e02ba9', # festvox_cmu_indic_guj_ad_cg.tar.gz - '1a4e17d67db50a6d81f7860b64acc8d41245f6f763ccff4c9386ab9ae9923910', # festvox_cmu_indic_guj_dp_cg.tar.gz - '666017d8d64737c4fd70b72ab6cf846fd8e13de290a5ba494bd1697249a16e9d', # festvox_cmu_indic_guj_kt_cg.tar.gz - '60318e160d994d5174168cc94467c776de81426f91c4f8003206cff953cb79bd', # festvox_cmu_indic_hin_ab_cg.tar.gz - 'd87f4ea342e7cb37e90ddf49dde37f19c1470b3c5a09d00cef3212108107cb31', # festvox_cmu_indic_kan_plv_cg.tar.gz - '0c7509203483fc97c04b670127b20c2d51723b3a16517124e22d095f379cca7f', # festvox_cmu_indic_mar_aup_cg.tar.gz - 'f3be7241d35db1e18d652e2cfa4cb69bae038c3d21c59ed3ce365487894f0d46', # festvox_cmu_indic_mar_slp_cg.tar.gz - 'f1e9238c6b8646a2a252ab855f5773c8ebdf8b3df909e0bbe4a99d7b830a4f3e', # festvox_cmu_indic_pan_amp_cg.tar.gz - '9a4c088ce3bdbf17867d5df918fc3868597061380ae8daf896ce99d33723e570', # festvox_cmu_indic_tam_sdr_cg.tar.gz - '43ad700a82a270530dda44fd4a89b34429c37723cdde130faece4811723ff72b', # festvox_cmu_indic_tel_kpn_cg.tar.gz - '0ee102e8093a549171f5e4ff826ebf3f9eaf84e7d43259777e38cafe4c4b6eea', # festvox_cmu_indic_tel_sk_cg.tar.gz - 'b2e56ca4722e3d025d831fd1eef679ffbf00fe165b68a44a5596321411ffa1f0', # festvox_cmu_indic_tel_ss_cg.tar.gz - '5d9555580b95324fa734b7771c95dced44e7903510358481d24e4fe5c961111c', # festvox_cmu_us_aew_cg.tar.gz - '906492478bd86b5201f72ffe701279b98b3ba94ae74816a0d7f2ba20bc2b5bf7', # festvox_cmu_us_ahw_cg.tar.gz - '455476e1c5246d90aac090a06afa5a4e90c801aebace6fe357900c8e095be826', # festvox_cmu_us_aup_cg.tar.gz - 'b2adbdfeda0cba289bb4da68dd14114d3eb3e7f72049cc8d2cbdfb2df39f6934', # festvox_cmu_us_awb_cg.tar.gz - '172c826df9c8f49ecb03f997749b207a23de8678dcf13706709104c2c597ebfb', # festvox_cmu_us_axb_cg.tar.gz - '1dc6792af9e2c1660a46fe499aa67af4affa665a0bdc08207cc11719baa62f6d', # festvox_cmu_us_bdl_cg.tar.gz - '11c82d1c18ce3db6fb11ca788cc5d84f69f9346aff77c7495f50005d6b042148', # festvox_cmu_us_clb_cg.tar.gz - 'af8590f7c1ba7d5dba22ff52c30a7bb3f55592eabca9615cd712fa4da8f83e13', # festvox_cmu_us_eey_cg.tar.gz - 'f8788c2af4838bb90e0a859f38da66c95961bdff2572001d5a019a2127c74306', # festvox_cmu_us_fem_cg.tar.gz - '47cf21a96adfcad398bd28b4d2548493a2055f75e53cf71344eef3aebc03ab59', # festvox_cmu_us_gka_cg.tar.gz - '711db388bc500331cfda86a46a72193ca1e2c9dc7d5ef16dfc86827e499946f2', # festvox_cmu_us_jmk_cg.tar.gz - '3b8098ac30995ce245d518c5b8fee825917428cb3ebe0409a0b415c919bdd35f', # festvox_cmu_us_ksp_cg.tar.gz - 'aec062c3d0c30719dd7e3e9ee4c427cbaad5e47550e28af2e9f151a41dcad852', # festvox_cmu_us_ljm_cg.tar.gz - 'ece81f42379feba4c392ad723fb68374aff9cd78f57cf629f624b0bd0c928d08', # festvox_cmu_us_lnh_cg.tar.gz - '3167afa3a6ffb5bbc305c94a1e6b671e40783a87a49372fce04c54942872c421', # festvox_cmu_us_rms_cg.tar.gz - 'bf362b6f270b1a4c76be981c3e8bd862fbb17a64e971e5b4a84d970ed5ecec42', # festvox_cmu_us_rxr_cg.tar.gz - 'f1d8e601c9631dfb7f8bd05c341d9fce8899dc9547ed9a652c8ded6ab854de9a', # festvox_cmu_us_slp_cg.tar.gz - '78cb93e361ab016fd23833c56853ddf21e2f1356310f54eed1c09a9755ce9f43', # festvox_cmu_us_slt_cg.tar.gz - '809c4ab5ed9e4df4a658b58d5c56fe35055723f00d81a238168f5a1ebdaed08c', # festvox_kallpc16k.tar.gz - 'ecd14b77c528e94dfb076e44050102fe8fba57e5fe813acf78a66629317f52a5', # festvox_rablpc16k.tar.gz - '0716ea33c8eccee435ab08464657af2ec2b64cf02409cddb868f8ad869e7e172', # festival-2.5.0_speech_tools.patch -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('speech_tools', '2.5.0'), -] - -# LIBS environmental variable interfers $EBROOTSPEECH_TOOLS/libs/Makefile -# line 61: LIBS_ABS=$(subst $(TOP),$$(EST_HOME),$(LIBS)) -prebuildopts = 'unset LIBS &&' - -buildininstalldir = True - -maxparallel = 1 - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/festival%s' % x for x in ['', '_client']] + - ['lib/%s.scm' % x for x in ['siod', 'web', 'cstr', 'fringe']], - 'dirs': ['lib/voices', 'lib/dicts/cmu', 'lib/dicts/oald'] -} - -sanity_check_commands = ['festival%s --version' % x for x in ['', '_client']] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/f/fetchMG/fetchMG-1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/fetchMG/fetchMG-1.0-GCCcore-9.3.0.eb deleted file mode 100644 index 9527b8a198f..00000000000 --- a/easybuild/easyconfigs/__archive__/f/fetchMG/fetchMG-1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'Tarball' - -name = 'fetchMG' -version = '1.0' - -homepage = 'http://vm-lux.embl.de/~mende/fetchMG/about.html' -description = """The program “fetchMG” was written to extract the 40 MGs from genomes and metagenomes -in an easy and accurate manner.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://vm-lux.embl.de/~kultima/share/mOTU/'] -sources = ['%(name)sv%(version)s.tar.gz'] -checksums = ['e3b835b425525513611b7116f89fc11ed015032ffd0494fa058edec1d6e67b17'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Perl', '5.30.2'), -] - -fix_perl_shebang_for = ['%(name)s.pl'] - -sanity_check_paths = { - 'files': ['%(name)s.pl', 'bin/cdbfasta', 'bin/cdbyank', 'bin/hmmsearch'], - 'dirs': [], -} - -sanity_check_commands = [ - "fetchMG.pl -h", - "fetchMG.pl -m extraction -x '' %(installdir)s/example_datasets/example_data.faa" -] - -modextrapaths = {'PATH': ''} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/ffmpi/ffmpi-4.5.0.eb b/easybuild/easyconfigs/__archive__/f/ffmpi/ffmpi-4.5.0.eb deleted file mode 100644 index ea8d25a51e0..00000000000 --- a/easybuild/easyconfigs/__archive__/f/ffmpi/ffmpi-4.5.0.eb +++ /dev/null @@ -1,13 +0,0 @@ -easyblock = 'Toolchain' - -name = 'ffmpi' -version = '4.5.0' - -homepage = '(none)' -description = """Fujitsu Compiler based compiler toolchain, including Fujitsu MPI for MPI support.""" - -toolchain = SYSTEM - -dependencies = [('FCC', version)] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/f/file/file-5.38-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/file/file-5.38-GCCcore-9.3.0.eb deleted file mode 100644 index 02d3d7c9caf..00000000000 --- a/easybuild/easyconfigs/__archive__/f/file/file-5.38-GCCcore-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -## - -easyblock = 'ConfigureMake' - -name = 'file' -version = '5.38' - -homepage = 'https://www.darwinsys.com/file/' -description = """The file command is 'a file type guesser', that is, a command-line tool - that tells you in words what kind of data a file contains.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['ftp://ftp.astron.com/pub/file/'] -sources = [SOURCE_TAR_GZ] -checksums = ['593c2ffc2ab349c5aea0f55fedfe4d681737b6b62376a9b3ad1e77b2cc19fa34'] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), -] - -preconfigopts = "autoreconf -f -i && " - -sanity_check_paths = { - 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], - 'dirs': ['share'] -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/f/filevercmp/filevercmp-20141119-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/filevercmp/filevercmp-20141119-GCCcore-9.3.0.eb deleted file mode 100644 index 7d1d2014556..00000000000 --- a/easybuild/easyconfigs/__archive__/f/filevercmp/filevercmp-20141119-GCCcore-9.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'filevercmp' -version = '20141119' -local_commit = '1a9b779' - -homepage = 'https://github.com/ekg/filevercmp' -description = """filevercmp function as in sort --version-sort.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'ekg' -source_urls = [GITHUB_SOURCE] -sources = ['%s.tar.gz' % local_commit] -patches = ['%(name)s-20141119_build-libs.patch'] -checksums = [ - 'a010e807755302ff12eff3949d92d6011a4df439a29f500cc357c8e2b896e57a', # 1a9b779.tar.gz - 'a361dadab37a7295764822141340a4fabfc86a4d367b5d3408feca7ca06fb5c7', # filevercmp-20141119_build-libs.patch -] - -builddependencies = [('binutils', '2.34')] - -skipsteps = ['configure'] - -installopts = 'DESTDIR="" PREFIX=%(installdir)s ' - -sanity_check_paths = { - 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/f/filevercmp/filevercmp-20141119_build-libs.patch b/easybuild/easyconfigs/__archive__/f/filevercmp/filevercmp-20141119_build-libs.patch deleted file mode 100644 index 4bbc18bd8b1..00000000000 --- a/easybuild/easyconfigs/__archive__/f/filevercmp/filevercmp-20141119_build-libs.patch +++ /dev/null @@ -1,83 +0,0 @@ -# Patch to build static and dynamic libraries. Based on PR by outpaddling: -# https://github.com/ekg/filevercmp/pull/2 - -diff -Nru filevercmp-1a9b779b93d0b244040274794d402106907b71b7.orig/Makefile filevercmp-1a9b779b93d0b244040274794d402106907b71b7/Makefile ---- filevercmp-1a9b779b93d0b244040274794d402106907b71b7.orig/Makefile 2021-05-06 15:39:20.000000000 +0100 -+++ filevercmp-1a9b779b93d0b244040274794d402106907b71b7/Makefile 2021-05-07 14:44:55.000000000 +0100 -@@ -1,13 +1,67 @@ --all: filevercmp - --clean: -- rm -f filevercmp -- rm -f filevercmp.o -+# Use ?= to allow overriding from the env or command-line, e.g. -+# -+# make CXXFLAGS="-O3 -fPIC" install -+# -+# Package managers will override many of these variables automatically, so -+# this is aimed at making it easy to create packages (Debian packages, -+# FreeBSD ports, MacPorts, pkgsrc, etc.) - --.PHONY: all clean -+CC ?= cc -+CFLAGS ?= -O -g #-m64 #-arch ppc - --filevercmp.o: filevercmp.c main.c filevercmp.h -- gcc -c filevercmp.c -+PREFIX ?= /usr/local -+STRIP ?= strip -+INSTALL ?= install -c -+MKDIR ?= mkdir -p -+AR ?= ar -+ARFLAGS ?= rs - --filevercmp: filevercmp.o -- gcc -o filevercmp main.c filevercmp.o -+BIN = filevercmp -+LIB = libfilevercmp.a -+SOVERSION = 0 -+SLIB = libfilevercmp.so -+OBJS = filevercmp.o -+ -+LIBDIR = $(DESTDIR)$(PREFIX)/lib -+BINDIR = $(DESTDIR)$(PREFIX)/bin -+INCDIR = $(DESTDIR)$(PREFIX)/include/filevercmp -+ -+.SUFFIXES:.c .o .pico .so -+ -+.c.o: -+ $(CC) $(CFLAGS) -I. -c -o $@ $< -+ -+.c.pico: -+ $(CC) $(CFLAGS) -I. -fPIC -c -o $@ $< -+ -+all: $(BIN) $(SLIB) $(LIB) -+ -+$(LIB): $(OBJS) -+ $(AR) $(ARFLAGS) $@ $^ -+ -+$(SLIB): $(OBJS:.o=.pico) -+ $(CC) -shared -Wl,-soname,$(SLIB).$(SOVERSION) $(LDFLAGS) -o $@ $^ $(LIBS) -+ ln -sf $@ $(SLIB).$(SOVERSION) -+ -+$(BIN): $(OBJS) main.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) -+ -+install: all -+ $(MKDIR) $(BINDIR) -+ $(MKDIR) $(LIBDIR) -+ $(MKDIR) $(INCDIR) -+ $(INSTALL) $(BIN) $(BINDIR) -+ $(INSTALL) *.h $(INCDIR) -+ $(INSTALL) $(LIB) $(SLIB) $(SLIB).$(SOVERSION) $(LIBDIR) -+ -+install-strip: install -+ $(STRIP) $(BINDIR)/$(BIN) $(LIBDIR)/$(LIB) -+ -+cleanlocal: -+ rm -rf $(BIN) $(LIB) $(SLIB) $(OBJS) $(DESTDIR) -+ rm -fr gmon.out *.o a.out *.dSYM $(BIN) *~ *.a tabix.aux tabix.log \ -+ tabix.pdf *.class libtabix.*.dylib -+ cd htslib && $(MAKE) clean -+ -+clean: cleanlocal-recur diff --git a/easybuild/easyconfigs/__archive__/f/flatbuffers/flatbuffers-1.12.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/flatbuffers/flatbuffers-1.12.0-GCCcore-9.3.0.eb deleted file mode 100644 index c9b52e42459..00000000000 --- a/easybuild/easyconfigs/__archive__/f/flatbuffers/flatbuffers-1.12.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'CMakeNinja' - -name = 'flatbuffers' -version = '1.12.0' - -homepage = 'https://github.com/google/flatbuffers/' -description = """FlatBuffers: Memory Efficient Serialization Library""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['62f2223fb9181d1d6338451375628975775f7522185266cd5296571ac152bc45'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('Ninja', '1.10.0'), -] - -configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' - -sanity_check_paths = { - 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], - 'dirs': ['lib/cmake'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-FCC-4.5.0.eb deleted file mode 100644 index 3baec387181..00000000000 --- a/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-FCC-4.5.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'flex' -version = '2.6.4' - -homepage = 'http://flex.sourceforge.net/' - -description = """ - Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns - in text. -""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] - -builddependencies = [ - ('Bison', '3.7.6'), - ('help2man', '1.48.3'), -] - -dependencies = [ - ('M4', '1.4.18'), -] - -# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct -# header, see https://github.com/westes/flex/issues/241 -preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-GCCcore-9.3.0.eb deleted file mode 100644 index f61ebc628c7..00000000000 --- a/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'flex' -version = '2.6.4' - -homepage = 'http://flex.sourceforge.net/' - -description = """ - Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns - in text. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] - -builddependencies = [ - ('Bison', '3.5.3'), - ('help2man', '1.47.12'), - # use same binutils version that was used when building GCC toolchain - ('binutils', '2.34', '', SYSTEM), -] - -dependencies = [ - ('M4', '1.4.18'), -] - -# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct -# header, see https://github.com/westes/flex/issues/241 -preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb deleted file mode 100644 index 945ac3c6ac7..00000000000 --- a/easybuild/easyconfigs/__archive__/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'fmt' -version = '6.2.1' - -homepage = 'http://fmtlib.net/' -description = "fmt (formerly cppformat) is an open-source formatting library." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] -sources = ['fmt-%(version)s.zip'] -checksums = ['94fea742ddcccab6607b517f6e608b1e5d63d712ddbc5982e44bafec5279881a'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34') -] - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['lib/libfmt.a'], - 'dirs': ['include/fmt', 'lib/cmake'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb deleted file mode 100644 index aefd2a77072..00000000000 --- a/easybuild/easyconfigs/__archive__/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'fmt' -version = '7.0.3' - -homepage = 'http://fmtlib.net/' -description = "fmt (formerly cppformat) is an open-source formatting library." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] -sources = ['fmt-%(version)s.zip'] -checksums = ['decfdf9ad274070fa85f26407b816f5a4d82205ae86bac1990be658d0795ea4d'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34') -] - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['lib/libfmt.a'], - 'dirs': ['include/fmt', 'lib/cmake'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/f/fontconfig/fontconfig-2.13.92-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/fontconfig/fontconfig-2.13.92-GCCcore-9.3.0.eb deleted file mode 100644 index e98c515a9ac..00000000000 --- a/easybuild/easyconfigs/__archive__/f/fontconfig/fontconfig-2.13.92-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'fontconfig' -version = '2.13.92' - -homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' - -description = """ - Fontconfig is a library designed to provide system-wide font configuration, - customization and application access. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] -sources = [SOURCE_TAR_GZ] -checksums = ['3406a05b83a42231e3df68d02bc0a0cf47b3f2e8f11c8ede62267daf5f130016'] - -builddependencies = [ - ('binutils', '2.34'), - ('gperf', '3.1'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('expat', '2.2.9'), - ('freetype', '2.10.1'), - ('util-linux', '2.35'), -] - -configopts = '--disable-docs ' - -sanity_check_paths = { - 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/f/foss/foss-2020a.eb b/easybuild/easyconfigs/__archive__/f/foss/foss-2020a.eb deleted file mode 100644 index 2b0739b47c8..00000000000 --- a/easybuild/easyconfigs/__archive__/f/foss/foss-2020a.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'Toolchain' - -name = 'foss' -version = '2020a' - -homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' -description = """GNU Compiler Collection (GCC) based compiler toolchain, including - OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" - -toolchain = SYSTEM - -local_gccver = '9.3.0' - -# toolchain used to build foss dependencies -local_comp_mpi_tc = ('gompi', version) - -# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain -# because of toolchain preparation functions -dependencies = [ - ('GCC', local_gccver), - ('OpenMPI', '4.0.3', '', ('GCC', local_gccver)), - ('OpenBLAS', '0.3.9', '', ('GCC', local_gccver)), - ('FFTW', '3.3.8', '', local_comp_mpi_tc), - ('ScaLAPACK', '2.1.0', '', local_comp_mpi_tc), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/f/fosscuda/fosscuda-2020a.eb b/easybuild/easyconfigs/__archive__/f/fosscuda/fosscuda-2020a.eb deleted file mode 100644 index 921ff09c9df..00000000000 --- a/easybuild/easyconfigs/__archive__/f/fosscuda/fosscuda-2020a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'Toolchain' - -name = 'fosscuda' -version = '2020a' - -homepage = '(none)' -description = """GCC based compiler toolchain __with CUDA support__, and including - OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" - -toolchain = SYSTEM - -local_gccver = '9.3.0' - -# toolchain used to build fosscuda dependencies -local_comp_mpi_tc = ('gompic', version) - -# compiler toolchain dependencies -# We need GCC, CUDA and OpenMPI as explicit dependencies instead of -# gompic toolchain because of toolchain preperation functions. -dependencies = [ - ('GCC', local_gccver), # part of gompic - ('CUDA', '11.0.2', '', ('GCC', local_gccver)), # part of gompic - ('OpenMPI', '4.0.3', '', ('gcccuda', version)), # part of gompic - ('OpenBLAS', '0.3.9', '', ('GCC', local_gccver)), - ('FFTW', '3.3.8', '', local_comp_mpi_tc), - ('ScaLAPACK', '2.1.0', '', local_comp_mpi_tc), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/f/fpocket/fpocket-3.1.4.2-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/f/fpocket/fpocket-3.1.4.2-gompi-2020a.eb deleted file mode 100644 index 9936652476f..00000000000 --- a/easybuild/easyconfigs/__archive__/f/fpocket/fpocket-3.1.4.2-gompi-2020a.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'MakeCp' - -name = 'fpocket' -version = '3.1.4.2' - -homepage = 'https://github.com/Discngine/fpocket' -description = """The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on -Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and -extract pocket descriptors on a large scale level.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': False, 'cstd': 'c99'} - -source_urls = ['https://github.com/Discngine/fpocket/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['6a801c7a4af0f76a58369b558ca5f6674571e1825024d459bba20bc07ae4f8b7'] - -dependencies = [('netCDF', '4.7.4')] - -maxparallel = 1 - -# Don't overwrite $LD_LIBRARY_PATH, but append fpocket paths to it. -prebuildopts = r'sed -i "s/LD_LIBRARY_PATH=/LD_LIBRARY_PATH=\$(LD_LIBRARY_PATH):/g" makefile && ' -# Use CFLAGS from EB -prebuildopts += 'sed -i "s/-O2.*c99/$CFLAGS/g" makefile && ' - -files_to_copy = [ - (['bin/fpocket', 'bin/tpocket', 'bin/dpocket', 'bin/mdpocket'], 'bin'), - (['man/*'], 'man/man8'), -] - -sanity_check_paths = { - 'files': ['bin/fpocket'], - 'dirs': ['bin', 'man'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 32a031a8418..00000000000 --- a/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,59 +0,0 @@ -# Author: Jasper Grimm (UoY) - -easyblock = 'MesonNinja' - -name = 'freebayes' -version = '1.3.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/ekg/freebayes' -description = """FreeBayes is a Bayesian genetic variant detector designed to find small - polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and - deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and - substitution events) smaller than the length of a short-read sequencing alignment. -""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -github_account = name -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = [ - '%(name)s-1.3.5_find-external-libs.patch', - '%(name)s-1.3.5_fix-includes.patch', - '%(name)s-1.3.5_install-libs-headers.patch', -] -checksums = [ - 'af195a8c54b742d01af5a7e1fd1781a89290d726b310216c83e78c650d7aee49', # v1.3.5.tar.gz - '68b62f532fb658cbee20aa0a9d19a4f5ab942f64510753bc01eb44006bad15dc', # freebayes-1.3.5_find-external-libs.patch - '4c6c74b30bf3b2f04b8a50bbdef26e74f6e2412f3efbd81512226e557c2a53d1', # freebayes-1.3.5_fix-includes.patch - '9a30129ea9457cfd49234b5b4cca0b3f9ac64765f122632f8eb9a1295ee6cb13', # freebayes-1.3.5_install-libs-headers.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Meson', '0.55.1', versionsuffix), - ('Ninja', '1.10.0'), - ('pkgconfig', '1.5.1', versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SAMtools', '1.11'), - ('parallel', '20200522'), - ('intervaltree', '0.1'), - ('libffi', '3.3'), - ('SeqLib', '1.2.0'), - ('vcflib', '1.0.2', versionsuffix), - ('VCFtools', '0.1.16'), -] - -sanity_check_paths = { - 'files': ['bin/%(name)s', 'bin/bamleftalign', 'scripts/%(name)s-parallel'], - 'dirs': ['bin', 'scripts'], -} -sanity_check_commands = ["%(name)s -h"] - -modextrapaths = {'PATH': ['scripts']} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5_find-external-libs.patch b/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5_find-external-libs.patch deleted file mode 100644 index 41e9c926767..00000000000 --- a/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5_find-external-libs.patch +++ /dev/null @@ -1,52 +0,0 @@ -Created by Jasper Grimm (UoY) -Switch to cc.find_library to search for libraries in LD_LIBRARY_PATH -Add dependencies on fastahack, smithwaterman -diff -Nru freebayes-1.3.5.orig/meson.build freebayes-1.3.5/meson.build ---- freebayes-1.3.5.orig/meson.build 2021-05-13 15:56:53.000000000 +0100 -+++ freebayes-1.3.5/meson.build 2021-05-13 16:00:25.000000000 +0100 -@@ -16,10 +16,12 @@ - lzma_dep = dependency('liblzma') - thread_dep = dependency('threads') - --htslib_dep = dependency('htslib', required : false) --tabixpp_dep = cc.find_library('tabixpp', required : false) --vcflib_dep = dependency('libvcflib', required : false) --seqlib_dep = dependency('libseqlib', required : false) -+htslib_dep = dependency('htslib', required : true) -+tabixpp_dep = cc.find_library('tabixpp', required : true) -+vcflib_dep = cc.find_library('libvcflib', required : true) -+seqlib_dep = cc.find_library('libseqlib', required : true) -+fastahack_dep = cc.find_library('libfastahack', required : true) -+sw_dep = cc.find_library('libsw', required : true) - - # for setting a warning_level on the external code in custom_* targets below - warn_quiet = ['warning_level=0'] -@@ -191,7 +193,7 @@ - include_directories : incdir, - cpp_args : extra_cpp_args, - dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep, -- vcflib_dep, seqlib_dep], -+ vcflib_dep, seqlib_dep, fastahack_dep, sw_dep], - install : false, - ) - -@@ -200,7 +202,8 @@ - include_directories : incdir, - cpp_args : extra_cpp_args, - dependencies: [zlib_dep, lzma_dep, thread_dep, -- htslib_dep, tabixpp_dep, vcflib_dep, seqlib_dep], -+ htslib_dep, tabixpp_dep, vcflib_dep, seqlib_dep, -+ fastahack_dep, sw_dep], - link_with : freebayes_lib, - install: true - ) -@@ -210,7 +213,8 @@ - include_directories : incdir, - cpp_args : extra_cpp_args, - dependencies: [zlib_dep, lzma_dep, thread_dep, -- htslib_dep, vcflib_dep, seqlib_dep], -+ htslib_dep, vcflib_dep, seqlib_dep, fastahack_dep, -+ sw_dep], - link_with : freebayes_lib, - install: true - ) diff --git a/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5_install-libs-headers.patch b/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5_install-libs-headers.patch deleted file mode 100644 index c1a34e2432b..00000000000 --- a/easybuild/easyconfigs/__archive__/f/freebayes/freebayes-1.3.5_install-libs-headers.patch +++ /dev/null @@ -1,78 +0,0 @@ -Created by Jasper Grimm (UoY) -Install header files and scripts -Rename static lib to freebayes, and set install to True -Add target to build shared library -diff -Nru freebayes-1.3.5b/meson.build freebayes-1.3.5c/meson.build ---- freebayes-1.3.5b/meson.build 2021-05-13 16:00:36.000000000 +0100 -+++ freebayes-1.3.5c/meson.build 2021-05-13 16:22:17.000000000 +0100 -@@ -173,6 +173,38 @@ - freebayes_src = files('src/freebayes.cpp') - bamleftalign_src = files('src/bamleftalign.cpp') - -+# FreeBayes headers -+freebayes_headers = files( -+ 'src/Allele.h', -+ 'src/AlleleParser.h', -+ 'src/BedReader.h', -+ 'src/Bias.h', -+ 'src/CNV.h', -+ 'src/Contamination.h', -+ 'src/DataLikelihood.h', -+ 'src/Dirichlet.h', -+ 'src/Ewens.h', -+ 'src/FBFasta.h', -+ 'src/Genotype.h', -+ 'src/IndelAllele.h', -+ 'src/LeftAlign.h', -+ 'src/Logging.h', -+ 'src/Marginals.h', -+ 'src/Multinomial.h', -+ 'src/NonCall.h', -+ 'src/Parameters.h', -+ 'src/Product.h', -+ 'src/Result.h', -+ 'src/ResultData.h', -+ 'src/Sample.h', -+ 'src/SegfaultHandler.h', -+ 'src/Sum.h', -+ 'src/TryCatch.h', -+ 'src/Utility.h', -+ 'src/version_git.h', -+ ) -+ -+ - # Include paths - incdir = include_directories( - 'src', -@@ -188,15 +220,29 @@ - ) - - freebayes_lib = static_library( -- 'freebayes_common', -+ 'freebayes', - freebayes_common_src, - include_directories : incdir, - cpp_args : extra_cpp_args, - dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep, - vcflib_dep, seqlib_dep, fastahack_dep, sw_dep], -- install : false, -+ install : true, - ) - -+freebayes_slib = shared_library( -+ 'freebayes', -+ freebayes_common_src, -+ include_directories : incdir, -+ cpp_args : extra_cpp_args, -+ dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep, -+ vcflib_dep, seqlib_dep, fastahack_dep, sw_dep], -+ install : true -+ ) -+ -+install_headers(freebayes_headers, subdir : 'freebayes') -+ -+install_subdir('scripts', install_dir : '') -+ - executable('freebayes', - freebayes_src, - include_directories : incdir, diff --git a/easybuild/easyconfigs/__archive__/f/freeglut/freeglut-3.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/freeglut/freeglut-3.2.1-GCCcore-9.3.0.eb deleted file mode 100644 index 0d85118e8fb..00000000000 --- a/easybuild/easyconfigs/__archive__/f/freeglut/freeglut-3.2.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'freeglut' -version = '3.2.1' - -homepage = 'http://freeglut.sourceforge.net/' -description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['d4000e02102acaf259998c870e25214739d1f16f67f99cb35e4f46841399da68'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -dependencies = [ - ('X11', '20200222'), - ('Mesa', '20.0.2'), - ('libGLU', '9.0.1'), -] - -configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT -configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' -configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT -configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT -configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' -configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT -configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' - -sanity_check_paths = { - 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], - 'dirs': ['include/GL'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/f/freetype/freetype-2.10.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/freetype/freetype-2.10.1-GCCcore-9.3.0.eb deleted file mode 100644 index a360b70e38d..00000000000 --- a/easybuild/easyconfigs/__archive__/f/freetype/freetype-2.10.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -name = 'freetype' -version = '2.10.1' - -homepage = 'https://www.freetype.org' - -description = """ - FreeType 2 is a software font engine that is designed to be small, efficient, - highly customizable, and portable while capable of producing high-quality - output (glyph images). It can be used in graphics libraries, display servers, - font conversion tools, text image generation tools, and many other products - as well. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - GNU_SAVANNAH_SOURCE, - SOURCEFORGE_SOURCE, -] -sources = [SOURCE_TAR_GZ] -checksums = ['3a60d391fd579440561bf0e7f31af2222bc610ad6ce4d9d7bd2165bca8669110'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('bzip2', '1.0.8'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), -] - -configopts = '--enable-freetype-config --with-harfbuzz=no' - -sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', - 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], - 'dirs': ['include/freetype2'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/f/fsom/fsom-20141119-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/f/fsom/fsom-20141119-GCCcore-9.3.0.eb deleted file mode 100644 index 7781af6e261..00000000000 --- a/easybuild/easyconfigs/__archive__/f/fsom/fsom-20141119-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'fsom' -version = '20141119' -local_commit = 'a6ef318' - -homepage = 'https://github.com/ekg/fsom' -description = """A tiny C library for managing SOM (Self-Organizing Maps) neural networks.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'ekg' -source_urls = [GITHUB_SOURCE] -sources = ['%s.tar.gz' % local_commit] -patches = [ - '%(name)s-20141119_build-libs.patch', - '%(name)s-20141119_fix-abs-overload.patch' -] -checksums = [ - '832ec7d0aff53e04fdb8bbaa5be2177de362afac6ed58a59a97abb7eef29cb60', # a6ef318.tar.gz - 'a6349a6462473f011260074eca6ad9826e3c6aeb20674b696c5848d10610cdd7', # fsom-20141119_build-libs.patch - '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639', # fsom-20141119_fix-abs-overload.patch -] - -builddependencies = [('binutils', '2.34')] - -skipsteps = ['configure'] - -installopts = 'PREFIX=%(installdir)s ' - -sanity_check_paths = { - 'files': ['bin/%(name)s', 'lib/libfsom.%s' % SHLIB_EXT], - 'dirs': [], -} -sanity_check_commands = ["%(name)s --help"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/GAMESS-US/GAMESS-US-20230630_add_slurm_support_mpi_target.patch b/easybuild/easyconfigs/__archive__/g/GAMESS-US/GAMESS-US-20230630_add_slurm_support_mpi_target.patch deleted file mode 100644 index 1f5e924f957..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GAMESS-US/GAMESS-US-20230630_add_slurm_support_mpi_target.patch +++ /dev/null @@ -1,26 +0,0 @@ -Add support for Slurm scheduler on MPI targets that do not have any nodefile -given by the user. -author: Alex Domingo (Vrije Universiteit Brussel) ---- rungms.orig 2023-07-01 08:04:29.000000000 +0200 -+++ rungms 2023-12-13 16:29:19.738351362 +0100 -@@ -188,6 +188,7 @@ - set SCHED=none - if ($?PBS_O_LOGNAME) set SCHED=PBS - if ($?SGE_O_LOGNAME) set SCHED=SGE -+if ($?SLURM_JOB_ID) set SCHED=SLURM - if ($SCHED == SGE) then - set SCR=$TMPDIR - echo "SGE has assigned the following compute nodes to this run:" -@@ -805,6 +806,12 @@ - set NNODES=$NNODES[1] - echo "MPI was given $NNODES nodes by PBS..." - breaksw -+ case SLURM: -+ scontrol show hostname "$SLURM_NODELIST" > $HOSTFILE -+ set NNODES=`wc -l $HOSTFILE` -+ set NNODES=$NNODES[1] -+ echo "MPI was given $NNODES nodes by Slurm..." -+ breaksw - default: - # Use use provided list (a new feature to be tested). - if (-e $NCPUS) then diff --git a/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb deleted file mode 100644 index 4296a3c1049..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb +++ /dev/null @@ -1,53 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , -# Kenneth Hoste (UGent) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -# Modified by: Adam Huffman, Jonas Demeulemeester -# The Francis Crick Institute -# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen -## - -easyblock = 'Tarball' - -name = 'GATK' -version = '4.1.5.0' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://www.broadinstitute.org/gatk/' -description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute - to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, - with a primary focus on variant discovery and genotyping as well as strong emphasis on - data quality assurance. Its robust architecture, powerful processing engine and - high-performance computing features make it capable of taking on projects of any size.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] -sources = ['gatk-%(version)s.zip'] -checksums = ['6fc152c2cae0cc54c7c4cfdfd865a64f7054a820f7d02ca2549511af1dd9882b'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [ - ('Java', '1.8', '', SYSTEM), -] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['gatk'], - 'dirs': [], -} -sanity_check_commands = [ - "gatk --help", - "gatk --list", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb deleted file mode 100644 index 007404e1392..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb +++ /dev/null @@ -1,55 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , -# Kenneth Hoste (UGent) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -# Modified by: Adam Huffman, Jonas Demeulemeester -# The Francis Crick Institute -# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen -## - -easyblock = 'Tarball' - -name = 'GATK' -version = '4.1.5.0' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://www.broadinstitute.org/gatk/' -description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute - to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, - with a primary focus on variant discovery and genotyping as well as strong emphasis on - data quality assurance. Its robust architecture, powerful processing engine and - high-performance computing features make it capable of taking on projects of any size.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] -sources = ['gatk-%(version)s.zip'] -checksums = ['6fc152c2cae0cc54c7c4cfdfd865a64f7054a820f7d02ca2549511af1dd9882b'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [ - ('Java', '11', '', SYSTEM), -] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['gatk'], - 'dirs': [], -} -sanity_check_commands = [ - "gatk --help", - "gatk --list", -] - -modloadmsg = "WARNING: GATK v%(version)s support for Java 11 is in beta state. Use at your own risk.\n" - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb deleted file mode 100644 index f93742a9063..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb +++ /dev/null @@ -1,53 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , -# Kenneth Hoste (UGent) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -# Modified by: Adam Huffman, Jonas Demeulemeester -# The Francis Crick Institute -# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen -## - -easyblock = 'Tarball' - -name = 'GATK' -version = '4.1.8.1' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://www.broadinstitute.org/gatk/' -description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute - to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, - with a primary focus on variant discovery and genotyping as well as strong emphasis on - data quality assurance. Its robust architecture, powerful processing engine and - high-performance computing features make it capable of taking on projects of any size.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] -sources = ['gatk-%(version)s.zip'] -checksums = ['42e6de5059232df1ad5785c68c39a53dc1b54afe7bb086d0129f4dc95fb182bc'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [ - ('Java', '1.8', '', SYSTEM), -] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['gatk'], - 'dirs': [], -} -sanity_check_commands = [ - "gatk --help", - "gatk --list", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 5ace496a913..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,55 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'GBprocesS' -local_commit = '82e21929' -version = '2.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://gbprocess.readthedocs.io/' -description = """GBprocesS allows for the extraction of genomic inserts from NGS -data for GBS experiments. Preprocessing is performed in different stages that -are part of a linear pipeline where the steps are performed in order. GBprocesS -provides a flexible way to adjust the functionality to your needs, as the -operations required and the execution order vary depending on the GBS protocol -used.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -# need to use git_config rather than just downloading source tarball, -# because .git subdirectory is required by setuptools-scm to determine version -sources = [{ - 'filename': 'GBprocesS-%%(version)s-%s.tar.gz' % local_commit, - 'git_config': { - 'url': 'https://gitlab.com/dschaumont', - 'repo_name': name, - 'commit': local_commit, - 'keep_git_dir': True, - }, -}] -checksums = [None] - -dependencies = [ - ('Python', '3.8.2'), - ('cutadapt', '2.10', '-Python-%(pyver)s'), - ('Biopython', '1.78', versionsuffix), - ('PEAR', '0.9.11'), -] - -sanity_check_commands = [ - "cd %(builddir)s/GBprocesS && python -m unittest discover -v -s ./test -p test_*.py", - "touch %(builddir)s/17146FL-13-01-01_S97_L002_R1_001.fastq", - "touch %(builddir)s/17146FL-13-01-01_S97_L002_R2_001.fastq", - # Trivial configuration file to use when running gbprocess sanity check - # See https://gitlab.com/dschaumont/GBprocesS/-/blob/master/docs/user_guide.rst - "echo '[General]' > %(builddir)s/config.ini", - "echo 'cores = 1' >> %(builddir)s/config.ini", - "echo 'input_directory = %(builddir)s/' >> %(builddir)s/config.ini", - "echo 'sequencing_type = pe' >> %(builddir)s/config.ini", - "echo 'input_file_name_template = {run:25}_R{orientation:1}_001{extension}' >> %(builddir)s/config.ini", - "echo 'temp_dir = %(builddir)s/' >> %(builddir)s/config.ini", - "gbprocess --debug -c %(builddir)s/config.ini", -] - -options = {'modulename': 'gbprocess'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GCC/GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GCC/GCC-9.3.0.eb deleted file mode 100644 index 0489a3aa7a0..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GCC/GCC-9.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'Bundle' - -name = 'GCC' -version = '9.3.0' - -homepage = 'https://gcc.gnu.org/' -description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, - as well as libraries for these languages (libstdc++, libgcj,...).""" - -toolchain = SYSTEM - -dependencies = [ - ('GCCcore', version), - # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils - ('binutils', '2.34', '', ('GCCcore', version)), -] - -altroot = 'GCCcore' -altversion = 'GCCcore' - -# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/g/GCCcore/GCC-9.x_fix-libsanitizer-cyclades.patch b/easybuild/easyconfigs/__archive__/g/GCCcore/GCC-9.x_fix-libsanitizer-cyclades.patch deleted file mode 100644 index 34119830b4f..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GCCcore/GCC-9.x_fix-libsanitizer-cyclades.patch +++ /dev/null @@ -1,121 +0,0 @@ -From 2b40941d23b1570cdd90083b58fa0f66aa58c86e Mon Sep 17 00:00:00 2001 -From: Tamar Christina -Date: Fri, 21 May 2021 12:16:56 +0100 -Subject: [PATCH] libsanitizer: Remove cyclades from libsanitizer - -The Linux kernel has removed the interface to cyclades from -the latest kernel headers[1] due to them being orphaned for the -past 13 years. - -libsanitizer uses this header when compiling against glibc, but -glibcs itself doesn't seem to have any references to cyclades. - -Further more it seems that the driver is broken in the kernel and -the firmware doesn't seem to be available anymore. - -As such since this is breaking the build of libsanitizer (and so the -GCC bootstrap[2]) I propose to remove this. - -[1] https://lkml.org/lkml/2021/3/2/153 -[2] https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100379 - -libsanitizer/ChangeLog: - - PR sanitizer/100379 - * sanitizer_common/sanitizer_common_interceptors_ioctl.inc: Cherry-pick - llvm-project revision f7c5351552387bd43f6ca3631016d7f0dfe0f135. - * sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise. - * sanitizer_common/sanitizer_platform_limits_posix.h: Likewise. ---- - .../sanitizer_common_interceptors_ioctl.inc | 9 --------- - .../sanitizer_platform_limits_posix.cc | 11 ----------- - .../sanitizer_platform_limits_posix.h | 10 ---------- - 3 files changed, 30 deletions(-) - -diff --git a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc -index 5408ea17c59..7a9cd3f5968 100644 ---- a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc -+++ b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc -@@ -365,15 +365,6 @@ static void ioctl_table_fill() { - - #if SANITIZER_LINUX && !SANITIZER_ANDROID - // _(SIOCDEVPLIP, WRITE, struct_ifreq_sz); // the same as EQL_ENSLAVE -- _(CYGETDEFTHRESH, WRITE, sizeof(int)); -- _(CYGETDEFTIMEOUT, WRITE, sizeof(int)); -- _(CYGETMON, WRITE, struct_cyclades_monitor_sz); -- _(CYGETTHRESH, WRITE, sizeof(int)); -- _(CYGETTIMEOUT, WRITE, sizeof(int)); -- _(CYSETDEFTHRESH, NONE, 0); -- _(CYSETDEFTIMEOUT, NONE, 0); -- _(CYSETTHRESH, NONE, 0); -- _(CYSETTIMEOUT, NONE, 0); - _(EQL_EMANCIPATE, WRITE, struct_ifreq_sz); - _(EQL_ENSLAVE, WRITE, struct_ifreq_sz); - _(EQL_GETMASTRCFG, WRITE, struct_ifreq_sz); -diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc -index d823a12190c..e8fce8a0287 100644 ---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc -+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc -@@ -157,7 +157,6 @@ typedef struct user_fpregs elf_fpregset_t; - # include - #endif - #include --#include - #include - #include - #include -@@ -466,7 +465,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr); - - #if SANITIZER_LINUX && !SANITIZER_ANDROID - unsigned struct_ax25_parms_struct_sz = sizeof(struct ax25_parms_struct); -- unsigned struct_cyclades_monitor_sz = sizeof(struct cyclades_monitor); - #if EV_VERSION > (0x010000) - unsigned struct_input_keymap_entry_sz = sizeof(struct input_keymap_entry); - #else -@@ -833,15 +831,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr); - #endif // SANITIZER_LINUX || SANITIZER_FREEBSD - - #if SANITIZER_LINUX && !SANITIZER_ANDROID -- unsigned IOCTL_CYGETDEFTHRESH = CYGETDEFTHRESH; -- unsigned IOCTL_CYGETDEFTIMEOUT = CYGETDEFTIMEOUT; -- unsigned IOCTL_CYGETMON = CYGETMON; -- unsigned IOCTL_CYGETTHRESH = CYGETTHRESH; -- unsigned IOCTL_CYGETTIMEOUT = CYGETTIMEOUT; -- unsigned IOCTL_CYSETDEFTHRESH = CYSETDEFTHRESH; -- unsigned IOCTL_CYSETDEFTIMEOUT = CYSETDEFTIMEOUT; -- unsigned IOCTL_CYSETTHRESH = CYSETTHRESH; -- unsigned IOCTL_CYSETTIMEOUT = CYSETTIMEOUT; - unsigned IOCTL_EQL_EMANCIPATE = EQL_EMANCIPATE; - unsigned IOCTL_EQL_ENSLAVE = EQL_ENSLAVE; - unsigned IOCTL_EQL_GETMASTRCFG = EQL_GETMASTRCFG; -diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h -index 6a673a7c995..f921bf2b5b5 100644 ---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h -+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h -@@ -1040,7 +1040,6 @@ struct __sanitizer_cookie_io_functions_t { - - #if SANITIZER_LINUX && !SANITIZER_ANDROID - extern unsigned struct_ax25_parms_struct_sz; -- extern unsigned struct_cyclades_monitor_sz; - extern unsigned struct_input_keymap_entry_sz; - extern unsigned struct_ipx_config_data_sz; - extern unsigned struct_kbdiacrs_sz; -@@ -1385,15 +1384,6 @@ struct __sanitizer_cookie_io_functions_t { - #endif // SANITIZER_LINUX || SANITIZER_FREEBSD - - #if SANITIZER_LINUX && !SANITIZER_ANDROID -- extern unsigned IOCTL_CYGETDEFTHRESH; -- extern unsigned IOCTL_CYGETDEFTIMEOUT; -- extern unsigned IOCTL_CYGETMON; -- extern unsigned IOCTL_CYGETTHRESH; -- extern unsigned IOCTL_CYGETTIMEOUT; -- extern unsigned IOCTL_CYSETDEFTHRESH; -- extern unsigned IOCTL_CYSETDEFTIMEOUT; -- extern unsigned IOCTL_CYSETTHRESH; -- extern unsigned IOCTL_CYSETTIMEOUT; - extern unsigned IOCTL_EQL_EMANCIPATE; - extern unsigned IOCTL_EQL_ENSLAVE; - extern unsigned IOCTL_EQL_GETMASTRCFG; --- -2.27.0 - diff --git a/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-8.3.0_fix-xsmin-ppc.patch b/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-8.3.0_fix-xsmin-ppc.patch deleted file mode 100644 index 6ce9ea53525..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-8.3.0_fix-xsmin-ppc.patch +++ /dev/null @@ -1,74 +0,0 @@ -From 37e0df8a9be5a8232f4ccb73cdadb02121ba523f Mon Sep 17 00:00:00 2001 -From: Jiufu Guo -Date: Tue, 10 Mar 2020 13:51:57 +0800 -Subject: [PATCH] rs6000: Check -+0 and NaN for smax/smin generation - -PR93709 mentioned regressions on maxlocval_4.f90 and minlocval_f.f90 which -relates to max of '-inf' and 'nan'. This regression occur on P9 because -P9 new instruction 'xsmaxcdp' is generated. -And for C code `a < b ? b : a` is also generated as `xsmaxcdp` under -O2 -for P9. While this instruction behavior more like C/C++ semantic (a>b?a:b). - -This generates prevents 'xsmaxcdp' to be generated for those cases. -'xsmincdp' also is handled in patch. - -gcc/ -2020-03-10 Jiufu Guo - - PR target/93709 - * gcc/config/rs6000/rs6000.c (rs6000_emit_p9_fp_minmax): Check - NAN and SIGNED_ZEROR for smax/smin. - -gcc/testsuite -2020-03-10 Jiufu Guo - - PR target/93709 - * gcc.target/powerpc/p9-minmax-3.c: New test. ---- - gcc/ChangeLog | 6 ++++++ - gcc/config/rs6000/rs6000.c | 6 +++++- - gcc/testsuite/ChangeLog | 5 +++++ - gcc/testsuite/gcc.target/powerpc/p9-minmax-3.c | 17 +++++++++++++++++ - 4 files changed, 33 insertions(+), 1 deletion(-) - create mode 100644 gcc/testsuite/gcc.target/powerpc/p9-minmax-3.c - -diff --git a/gcc/config/rs6000/rs6000.c b/gcc/config/rs6000/rs6000.c -index 848a4ef451e4..46b7dec2abd4 100644 ---- a/gcc/config/rs6000/rs6000.c -+++ b/gcc/config/rs6000/rs6000.c -@@ -14831,7 +14831,11 @@ rs6000_emit_p9_fp_minmax (rtx dest, rtx op, rtx true_cond, rtx false_cond) - if (rtx_equal_p (op0, true_cond) && rtx_equal_p (op1, false_cond)) - ; - -- else if (rtx_equal_p (op1, true_cond) && rtx_equal_p (op0, false_cond)) -+ /* Only when NaNs and signed-zeros are not in effect, smax could be -+ used for `op0 < op1 ? op1 : op0`, and smin could be used for -+ `op0 > op1 ? op1 : op0`. */ -+ else if (rtx_equal_p (op1, true_cond) && rtx_equal_p (op0, false_cond) -+ && !HONOR_NANS (compare_mode) && !HONOR_SIGNED_ZEROS (compare_mode)) - max_p = !max_p; - - else -diff --git a/gcc/testsuite/gcc.target/powerpc/p9-minmax-3.c b/gcc/testsuite/gcc.target/powerpc/p9-minmax-3.c -new file mode 100644 -index 000000000000..141603e05b43 ---- /dev/null -+++ b/gcc/testsuite/gcc.target/powerpc/p9-minmax-3.c -@@ -0,0 +1,17 @@ -+/* { dg-do compile { target { powerpc*-*-* } } } */ -+/* { dg-require-effective-target powerpc_p9vector_ok } */ -+/* { dg-options "-mdejagnu-cpu=power9 -O2 -mpower9-minmax" } */ -+/* { dg-final { scan-assembler-not "xsmaxcdp" } } */ -+/* { dg-final { scan-assembler-not "xsmincdp" } } */ -+ -+double -+dbl_max1 (double a, double b) -+{ -+ return a < b ? b : a; -+} -+ -+double -+dbl_min1 (double a, double b) -+{ -+ return a > b ? b : a; -+} diff --git a/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-9.3.0.eb deleted file mode 100644 index b47467b1233..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-9.3.0.eb +++ /dev/null @@ -1,69 +0,0 @@ -easyblock = 'EB_GCC' - -name = 'GCCcore' -version = '9.3.0' - -homepage = 'https://gcc.gnu.org/' -description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, - as well as libraries for these languages (libstdc++, libgcj,...).""" - -toolchain = SYSTEM - -source_urls = [ - 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror - 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP - 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR - 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC - 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies - 'https://libisl.sourceforge.io/', # fallback URL for isl - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL - 'https://sourceware.org/pub/newlib/', # for newlib - 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools -] -sources = [ - 'gcc-%(version)s.tar.gz', - 'gmp-6.2.0.tar.bz2', - 'mpfr-4.0.2.tar.bz2', - 'mpc-1.1.0.tar.gz', - 'isl-0.22.1.tar.bz2', - 'newlib-3.3.0.tar.gz', - {'download_filename': '5f6f343.tar.gz', 'filename': 'nvptx-tools-20180301.tar.gz'}, -] -patches = [ - 'GCCcore-6.2.0-fix-find-isl.patch', - 'GCCcore-8.3.0_fix-xsmin-ppc.patch', - 'GCCcore-%(version)s_gmp-c99.patch', - 'GCCcore-%(version)s_vect_broadcasts_masmintel.patch', - 'GCCcore-%(version)s_nvptx_sm_35_default.patch', - 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', - 'GCC-9.x_fix-libsanitizer-cyclades.patch', -] -checksums = [ - '5258a9b6afe9463c2e56b9e8355b1a4bee125ca828b8078f910303bc2ef91fa6', # gcc-9.3.0.tar.gz - 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea', # gmp-6.2.0.tar.bz2 - 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc', # mpfr-4.0.2.tar.bz2 - '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz - '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 - '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66', # newlib-3.3.0.tar.gz - 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # nvptx-tools-20180301.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - 'bea1bce8f50ea6d51b038309eb61dec00a8681fb653d211c539be80f184609a3', # GCCcore-8.3.0_fix-xsmin-ppc.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - 'a32ac9c7d999a8b91bf93dba6a9d81b6ff58b3c89c425ff76090cbc90076685c', # GCCcore-9.3.0_vect_broadcasts_masmintel.patch - '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'b48e48736062e64a6da7cbe7e21a6c1c89422d1f49ef547c73b479a3f3f4935f', # GCC-9.x_fix-libsanitizer-cyclades.patch -] - -builddependencies = [ - ('M4', '1.4.19'), - ('binutils', '2.34'), -] - -languages = ['c', 'c++', 'fortran'] - -withisl = True -withnvptx = True - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-9.3.0_vect_broadcasts_masmintel.patch b/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-9.3.0_vect_broadcasts_masmintel.patch deleted file mode 100644 index 84aee424a2c..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GCCcore/GCCcore-9.3.0_vect_broadcasts_masmintel.patch +++ /dev/null @@ -1,67 +0,0 @@ -From: Jakub Jelinek -Date: Tue, 15 Sep 2020 07:37:48 +0000 (+0200) -Subject: i386: Fix up vector mul and div with broadcasts in -masm=intel mode -X-Git-Url: https://gcc.gnu.org/git/?p=gcc.git;a=commitdiff_plain;h=d0a094ce39fc49681b0d5cfd2ee1d232859c4824 - -i386: Fix up vector mul and div with broadcasts in -masm=intel mode - -These patterns printed bogus <>s around the {1to16} and similar strings. - -2020-09-15 Jakub Jelinek - - PR target/97028 - * config/i386/sse.md (mul3_bcs, - _div3_bcst): Use instead of - <>. - - * gcc.target/i386/avx512f-pr97028.c: Untested fix. - -(cherry picked from commit 0f079e104a8d1994b6b47169a6b45737615eb2d7) ---- - -diff --git a/gcc/config/i386/sse.md b/gcc/config/i386/sse.md -index cbcbe3846ca..3b51fef56f2 100644 ---- a/gcc/config/i386/sse.md -+++ b/gcc/config/i386/sse.md -@@ -1829,7 +1829,7 @@ - (match_operand: 1 "memory_operand" "m")) - (match_operand:VF_AVX512 2 "register_operand" "v")))] - "TARGET_AVX512F && " -- "vmul\t{%1, %2, %0|%0, %2, %1<>}" -+ "vmul\t{%1, %2, %0|%0, %2, %1}" - [(set_attr "prefix" "evex") - (set_attr "type" "ssemul") - (set_attr "mode" "")]) -@@ -1899,7 +1899,7 @@ - (vec_duplicate:VF_AVX512 - (match_operand: 2 "memory_operand" "m"))))] - "TARGET_AVX512F && " -- "vdiv\t{%2, %1, %0|%0, %1, %2<>}" -+ "vdiv\t{%2, %1, %0|%0, %1, %2}" - [(set_attr "prefix" "evex") - (set_attr "type" "ssediv") - (set_attr "mode" "")]) -diff --git a/gcc/testsuite/gcc.target/i386/avx512f-pr97028.c b/gcc/testsuite/gcc.target/i386/avx512f-pr97028.c -new file mode 100644 -index 00000000000..2719108a411 ---- /dev/null -+++ b/gcc/testsuite/gcc.target/i386/avx512f-pr97028.c -@@ -0,0 +1,18 @@ -+/* PR target/97028 */ -+/* { dg-do assemble { target avx512f } } */ -+/* { dg-require-effective-target masm_intel } */ -+/* { dg-options "-O2 -mavx512f -masm=intel" } */ -+ -+#include -+ -+__m512 -+foo (__m512 x, float *y) -+{ -+ return _mm512_mul_ps (x, _mm512_set1_ps (*y)); -+} -+ -+__m512 -+bar (__m512 x, float *y) -+{ -+ return _mm512_div_ps (x, _mm512_set1_ps (*y)); -+} diff --git a/easybuild/easyconfigs/__archive__/g/GD/GD-2.71-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GD/GD-2.71-GCCcore-9.3.0.eb deleted file mode 100644 index dbaba6f514a..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GD/GD-2.71-GCCcore-9.3.0.eb +++ /dev/null @@ -1,55 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Author: Jonas Demeulemeester (The Francis Crick Insitute, London, UK) -# Update to v2.71: Alex Domingo (Vrije Universiteit Brussel) -# - -easyblock = 'Bundle' - -name = 'GD' -version = '2.71' - -homepage = 'https://github.com/lstein/Perl-GD' -description = """GD.pm - Interface to Gd Graphics Library""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Perl', '5.30.2'), - ('libgd', '2.3.0'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), -] - -exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") - -exts_list = [ - ('ExtUtils::PkgConfig', '1.16', { - 'source_tmpl': 'ExtUtils-PkgConfig-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], - 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], - }), - (name, version, { - 'source_tmpl': 'release_%(version_major)s_%(version_minor)s.tar.gz', - 'source_urls': ['https://github.com/lstein/Perl-GD/archive/'], - 'checksums': ['fe67ef1b6ae4a4c79736dc5105c0d08898ceeace022267647528fdef74785add'], - }), -] - -sanity_check_paths = { - 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/%(name)s.pm'], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/%(name)s'], -} - -modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index bf965eccf39..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,60 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDAL' -version = '3.0.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.gdal.org' -description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style - Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model - to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for - data translation and processing.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] -sources = [SOURCELOWER_TAR_XZ] -patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] -checksums = [ - '5569a4daa1abcbba47a9d535172fc335194d9214fdb96cd0f139bb57329ae277', # gdal-3.0.4.tar.xz - '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch -] - -dependencies = [ - ('Python', '3.8.2'), - ('netCDF', '4.7.4'), - ('expat', '2.2.9'), - ('GEOS', '3.8.1', versionsuffix), - ('SQLite', '3.31.1'), - ('libxml2', '2.9.10'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), - ('JasPer', '2.0.14'), - ('LibTIFF', '4.1.0'), - ('zlib', '1.2.11'), - ('cURL', '7.69.1'), - ('PCRE', '8.44'), - ('PROJ', '7.0.0'), - ('libgeotiff', '1.5.1'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('HDF5', '1.10.6'), - ('HDF', '4.2.15'), -] - -preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " -configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' -configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' -configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' -configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' - -sanity_check_paths = { - 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] -} - -sanity_check_commands = ["python -c 'import gdal'"] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 4e5fd81f8ef..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,62 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDAL' -version = '3.0.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.gdal.org' -description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style - Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model - to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for - data translation and processing.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] -sources = [SOURCELOWER_TAR_XZ] -patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] -checksums = [ - '5569a4daa1abcbba47a9d535172fc335194d9214fdb96cd0f139bb57329ae277', # gdal-3.0.4.tar.xz - '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch -] - -dependencies = [ - ('Python', '3.8.2'), - ('netCDF', '4.7.4'), - ('expat', '2.2.9'), - ('GEOS', '3.8.1', versionsuffix), - ('SQLite', '3.31.1'), - ('libxml2', '2.9.10'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), - ('JasPer', '2.0.14'), - ('LibTIFF', '4.1.0'), - ('zlib', '1.2.11'), - ('cURL', '7.69.1'), - ('PCRE', '8.44'), - ('PROJ', '7.0.0'), - ('libgeotiff', '1.5.1'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('HDF5', '1.10.6'), - ('HDF', '4.2.15'), -] - -preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " -configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' -configopts += ' --without-hdf4 --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' -configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' -configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' - -prebuildopts = 'export LDSHARED="$CC -shared" && ' - -sanity_check_paths = { - 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] -} - -sanity_check_commands = ["python -c 'import gdal'"] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 2ee9015802d..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDB' -version = '10.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.gnu.org/software/gdb/gdb.html' -description = "The GNU Project Debugger" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['aaa1223d534c9b700a8bec952d9748ee1977513f178727e1bee520ee000b4f29'] - -builddependencies = [ - ('binutils', '2.34'), - ('makeinfo', '6.7'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('libreadline', '8.0'), - ('ncurses', '6.2'), - ('expat', '2.2.9'), - ('Python', '3.8.2'), - ('ISL', '0.23'), - ('MPC', '1.1.0'), -] - -preconfigopts = "mkdir obj && cd obj && " -configure_cmd_prefix = '../' -prebuildopts = "cd obj && " -preinstallopts = prebuildopts - -configopts = '--with-system-zlib --with-system-readline --with-expat=$EBROOTEXPAT ' -configopts += '--with-python=$EBROOTPYTHON/bin/python --with-isl=$EBROOTISL --with-mpc=$EBROOTMPC ' -configopts += '--enable-tui --enable-plugins --disable-install-libbfd ' - -sanity_check_paths = { - 'files': ['bin/gdb', 'bin/gdbserver'], - 'dirs': [], -} - -sanity_check_commands = [ - 'gdb --help', - 'gdbserver --help', -] - -moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/__archive__/g/GDCM/GDCM-3.0.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GDCM/GDCM-3.0.8-GCCcore-9.3.0.eb deleted file mode 100644 index 044e0a80dc9..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GDCM/GDCM-3.0.8-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'GDCM' -version = '3.0.8' - -homepage = 'https://sourceforge.net/projects/gdcm' -description = "Grassroots DICOM: Cross-platform DICOM implementation" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['33077958ec2fb43361cd4e2889dc901cc4d45c30b7f134950fc57ecd4f0637e1'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -configopts = "-DGDCM_BUILD_DOCBOOK_MANPAGES=0" - -sanity_check_paths = { - 'files': ['lib/libgdcmCommon.a', 'lib/libgdcmDICT.a'], - 'dirs': ['include/gdcm-%(version_major_minor)s', 'lib/gdcm-%(version_major_minor)s'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/__archive__/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb deleted file mode 100644 index 3c02c5d5c02..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb +++ /dev/null @@ -1,58 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDRCopy' -version = '2.1' -local_cudaversion = '11.0.2' -versionsuffix = '-CUDA-%s' % local_cudaversion - -homepage = 'https://github.com/NVIDIA/gdrcopy' -description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'NVIDIA' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['cecc7dcc071107f77396f5553c9109790b6d2298ae29eb2dbbdd52b2a213e4ea'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('CUDAcore', local_cudaversion, '', SYSTEM), - ('Check', '0.15.2'), -] - -build_info_msg = """This easyconfig only installs the library and binaries of GDRCopy. Please -keep in mind that GDRCopy also needs the following kernel modules at runtime: - -1. Kernel module for GDRCopy: improves Host to GPU communication - https://github.com/NVIDIA/gdrcopy - RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' - Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 - -2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication - https://github.com/Mellanox/nv_peer_memory - RPM: 'nvidia_peer_memory' - Requirements: Mellanox HCA with MLNX_OFED 2.1 - -These kernel modules are not listed as system dependencies to lower the system -requirements to build this easyconfig, as they are not needed for the build.""" - -skipsteps = ['configure'] - -local_envopts = "PREFIX=%(installdir)s CUDA=$EBROOTCUDACORE" -prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found -buildopts = "config lib exes %s" % local_envopts -installopts = local_envopts - -sanity_check_paths = { - 'files': ['bin/copybw', 'bin/copylat', 'bin/sanity', 'lib/libgdrapi.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb b/easybuild/easyconfigs/__archive__/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb deleted file mode 100644 index 0209363b19e..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'MakeCp' - -name = 'GEMMA' -version = '0.98.5' - -homepage = 'https://github.com/genetics-statistics/GEMMA' -description = "Genome-wide Efficient Mixed Model Association" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677'] - -builddependencies = [ - ('Eigen', '3.3.7'), - ('Perl', '5.30.2'), - ('Ruby', '2.7.2'), -] - -dependencies = [ - ('GSL', '2.6'), - ('zlib', '1.2.11') -] - -files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] - -runtest = 'check' - -sanity_check_commands = ["gemma -h", "gemma -license"] - -sanity_check_paths = { - 'files': ["bin/gemma"], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GEOS/GEOS-3.8.1-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GEOS/GEOS-3.8.1-GCC-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 5763668f22b..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GEOS/GEOS-3.8.1-GCC-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GEOS' -version = '3.8.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://trac.osgeo.org/geos' -description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://download.osgeo.org/geos/'] -sources = [SOURCELOWER_TAR_BZ2] -patches = ['GEOS-3.7.2_fix-Python3.patch'] -checksums = [ - '4258af4308deb9dbb5047379026b4cd9838513627cb943a44e16c40e42ae17f7', # geos-3.8.1.tar.bz2 - 'e14b54796d9d41261caae64b5a106b4bd8a77f37a51aa9b8ada30d87d208e2e0', # GEOS-3.7.2_fix-Python3.patch -] - -dependencies = [('Python', '3.8.2')] - -builddependencies = [('SWIG', '4.0.1')] - -configopts = '--enable-python' - -sanity_check_paths = { - 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb deleted file mode 100644 index 065c1d4c99c..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GEOS' -version = '3.8.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://trac.osgeo.org/geos' -description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://download.osgeo.org/geos/'] -sources = [SOURCELOWER_TAR_BZ2] -patches = ['GEOS-3.7.2_fix-Python3.patch'] -checksums = [ - '4258af4308deb9dbb5047379026b4cd9838513627cb943a44e16c40e42ae17f7', # geos-3.8.1.tar.bz2 - 'e14b54796d9d41261caae64b5a106b4bd8a77f37a51aa9b8ada30d87d208e2e0', # GEOS-3.7.2_fix-Python3.patch -] - -dependencies = [('Python', '3.8.2')] - -builddependencies = [('SWIG', '4.0.1')] - -configopts = '--enable-python' - -sanity_check_paths = { - 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 68e13c476d9..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,50 +0,0 @@ -# Author J. Sassmannshause (Imperial College London/UK) - -easyblock = 'Waf' - -name = 'GKeyll' -version = '20220803' -local_commit = '4c3e568' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://gkeyll.readthedocs.io' -description = """Gkeyll v2.0 (pronounced as in the book “The Strange Case of Dr. Jekyll -and Mr. Hyde”) is a computational plasma physics code mostly written in C/C++ and LuaJIT. -Gkeyll contains solvers for gyrokinetic equations, Vlasov-Maxwell equations, and -multi-fluid equations. Gkeyll contains ab-initio and novel implementations of a number -of algorithms, and perhaps is unique in using a JIT compiled typeless dynamic language -for as its main implementation language.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -github_account = 'ammarhakim' -source_urls = ['https://github.com/ammarhakim/gkyl/archive'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['075867b602e3a50c13e72f7f0dc680c3591467ce61debd3c9a11f3e5dced0503'] - -dependencies = [ - ('Python', '3.8.2'), - ('ADIOS', '20210804', versionsuffix), - ('Eigen', '3.3.7'), - ('LuaJIT2-OpenResty', '2.1-20220411'), -] - -configopts = '--luajit-inc-dir=$EBROOTLUAJIT2MINOPENRESTY/include/luajit-2.1/ ' -configopts += '--extra-link-libs=" hdf5 mxml bz2 lz4 z zfp gomp" ' - -# Seems to be required as else all cores are being used -buildopts = ' -j %(parallel)s' - -sanity_check_paths = { - 'files': ['bin/gkyl', 'bin/gkyl', 'lib/libcomm.%s' % SHLIB_EXT, - 'lib/libdatastruct.%s' % SHLIB_EXT], - 'dirs': [], -} - -sanity_check_commands = [ - "gkyl -version", - "ctest_Range -?", -] - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/g/GL2PS/GL2PS-1.4.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GL2PS/GL2PS-1.4.2-GCCcore-9.3.0.eb deleted file mode 100644 index 062d067f575..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GL2PS/GL2PS-1.4.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'GL2PS' -version = '1.4.2' - -homepage = 'https://www.geuz.org/gl2ps/' -description = """GL2PS: an OpenGL to PostScript printing library""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://geuz.org/gl2ps/src/'] -sources = [SOURCELOWER_TGZ] -checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34'), -] - -dependencies = [ - ('X11', '20200222'), - ('Mesa', '20.0.2'), - ('libGLU', '9.0.1'), - ('freeglut', '3.2.1'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/GLFW/GLFW-3.3.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GLFW/GLFW-3.3.2-GCCcore-9.3.0.eb deleted file mode 100644 index baea5b4d66f..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GLFW/GLFW-3.3.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'GLFW' -version = '3.3.2' - -homepage = 'https://www.glfw.org' -description = '''GLFW is an Open Source, multi-platform library for OpenGL, - OpenGL ES and Vulkan development on the desktop''' - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['98768e12e615fbe9f3386f5bbfeb91b5a3b45a8c4c77159cef06b1f6ff749537'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('X11', '20200222'), -] - -# build both static and shared libraries -configopts = [ - "-DBUILD_SHARED_LIBS=OFF", - "-DBUILD_SHARED_LIBS=ON", -] - -sanity_check_paths = { - 'files': ['include/GLFW/glfw3.h', 'include/GLFW/glfw3native.h', - 'lib/libglfw3.a', 'lib/libglfw.so', 'lib/pkgconfig/glfw3.pc'], - 'dirs': ['include/GLFW', 'lib/cmake/glfw3', 'lib/pkgconfig'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/GLPK/GLPK-4.65-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GLPK/GLPK-4.65-GCCcore-9.3.0.eb deleted file mode 100644 index 7f625a1131a..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GLPK/GLPK-4.65-GCCcore-9.3.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GLPK' -version = '4.65' - -homepage = 'https://www.gnu.org/software/glpk/' -description = """The GLPK (GNU Linear Programming Kit) package is intended for - solving large-scale linear programming (LP), - mixed integer programming (MIP), and other related problems. - It is a set of routines written in ANSI C - and organized in the form of a callable library.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['4281e29b628864dfe48d393a7bedd781e5b475387c20d8b0158f329994721a10'] - -builddependencies = [('binutils', '2.34')] -dependencies = [('GMP', '6.2.0')] - -configopts = "--with-gmp" - -sanity_check_paths = { - 'files': ['bin/glpsol', 'include/glpk.h'] + - ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/GLib/GLib-2.64.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GLib/GLib-2.64.1-GCCcore-9.3.0.eb deleted file mode 100644 index 809eb95c23c..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GLib/GLib-2.64.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'GLib' -version = '2.64.1' - -homepage = 'https://www.gtk.org/' -description = """GLib is one of the base libraries of the GTK+ project""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['17967603bcb44b6dbaac47988d80c29a3d28519210b28157c2bd10997595bbc7'] - -builddependencies = [ - # Python is required for building against GLib, at least when - # gdbus-codegen or one of the other python scripts are used. - # Since Meson 0.50 and later are Python >=3.5 only we can't build - # Python specific versions of GLib that uses Python 2.x - # thus Python should not be a runtime dependency for GLib. - # Packages that use GLib should either have an explicit - # (build)dependency on Python or it will use the system version - # EasyBuild itself uses. - ('Python', '3.8.2'), - ('Meson', '0.55.1', '-Python-3.8.2'), - ('Ninja', '1.10.0'), - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('libffi', '3.3'), - ('gettext', '0.20.1'), - ('libxml2', '2.9.10'), - ('PCRE', '8.44'), - ('util-linux', '2.35'), -] - -# avoid using hardcoded path to Python binary in build step -preconfigopts = "export PYTHON=python && " - -configopts = "--default-library=both " - -fix_python_shebang_for = ['bin/*'] - -sanity_check_paths = { - 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/GMAP-GSNAP/GMAP-GSNAP-2020-12-17-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GMAP-GSNAP/GMAP-GSNAP-2020-12-17-GCC-9.3.0.eb deleted file mode 100644 index 26e061c343a..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GMAP-GSNAP/GMAP-GSNAP-2020-12-17-GCC-9.3.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# 2016-11-07 modified by: -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'GMAP-GSNAP' -version = '2020-12-17' - -homepage = 'http://research-pub.gene.com/gmap/' -description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences - GSNAP: Genomic Short-read Nucleotide Alignment Program""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['http://research-pub.gene.com/gmap/src/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['436a490a9a6af1e3c1e0ee5389b8507d0428f9f1aaeba76a72352eb32d082562'] - -# with these deps you can use standard compressed files -# details in http://research-pub.gene.com/gmap/src/README -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), -] - -# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length -# details in http://research-pub.gene.com/gmap/src/README -# configopts = 'MAX_STACK_READLENGTH=300' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['bin/gmap', 'bin/gsnap'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.2.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.2.0-GCCcore-9.3.0.eb deleted file mode 100644 index 5619b138b8c..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.2.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GMP' -version = '6.2.0' - -homepage = 'https://gmplib.org/' -description = """ - GMP is a free library for arbitrary precision arithmetic, operating on signed - integers, rational numbers, and floating point numbers. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'precise': True, 'pic': True} - -source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), -] - -# enable C++ interface -configopts = '--enable-cxx' - -# copy libgmp.so* to /lib to make sure that it is picked up by tests -# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) -pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT -testopts = " && rm -r %(installdir)s/lib" - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/lib%s.%s' % (x, e) for x in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + - ['include/gmp.h', 'include/gmpxx.h'], - 'dirs': ['share'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/GObject-Introspection/GObject-Introspection-1.64.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GObject-Introspection/GObject-Introspection-1.64.0-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index e454258f379..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GObject-Introspection/GObject-Introspection-1.64.0-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'GObject-Introspection' -version = '1.64.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://gi.readthedocs.io/en/latest/' -description = """GObject introspection is a middleware layer between C libraries - (using GObject) and language bindings. The C library can be scanned at - compile time and generate a metadata file, in addition to the actual - native C library. Then at runtime, language bindings can read this - metadata and automatically provide bindings to call into the C library.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['eac05a63091c81adfdc8ef34820bcc7e7778c5b9e34734d344fc9e69ddf4fc82'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), - ('Meson', '0.55.1', '-Python-3.8.2'), - ('Ninja', '1.10.0'), - ('flex', '2.6.4'), - ('Bison', '3.5.3'), - ('cairo', '1.16.0'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('GLib', '2.64.1'), - ('libffi', '3.3'), - ('util-linux', '2.35'), -] - -preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " - -sanity_check_paths = { - 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + - ['lib/libgirepository-1.0.' + SHLIB_EXT], - 'dirs': ['include', 'share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch deleted file mode 100644 index 5f28eb043c8..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch +++ /dev/null @@ -1,21 +0,0 @@ -# Don't run gpu based tests on pure cpu builds. -# -# Åke Sandgren -diff -ru gromacs-2018.orig/src/gromacs/gpu_utils/tests/CMakeLists.txt gromacs-2018/src/gromacs/gpu_utils/tests/CMakeLists.txt ---- gromacs-2018.orig/src/gromacs/gpu_utils/tests/CMakeLists.txt 2017-11-27 17:17:46.000000000 +0100 -+++ gromacs-2018/src/gromacs/gpu_utils/tests/CMakeLists.txt 2018-02-05 17:25:59.968121131 +0100 -@@ -82,12 +82,14 @@ - ) - endif() - -+if(GMX_USE_CUDA OR GMX_USE_OPENCL) - gmx_add_unit_test(GpuUtilsUnitTests gpu_utils-test - # Infrastructure - gputest.cpp - # Tests of code - ${SOURCES_FROM_CXX} - ) -+endif() - - if(GMX_USE_CUDA) - target_link_libraries(gpu_utils-test gpu_utilstest_cuda) diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index a7160f51482..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,89 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, -# Ghent University / The Francis Crick Institute -# Authors:: -# * Wiktor Jurkowski -# * Fotis Georgatos -# * George Tsouloupas -# * Kenneth Hoste -# * Adam Huffman -# * Ake Sandgren -# License:: MIT/GPL -# 2019.3 version -# Contribution from the Crick HPC team -# uploaded by J. Sassmannshausen -# - -name = 'GROMACS' -version = '2020.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.gromacs.org' -description = """ -GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the -Newtonian equations of motion for systems with hundreds to millions of -particles. - -This is a CPU only build, containing both MPI and threadMPI builds -for both single and double precision. -It also contains the gmxapi extension for the single precision MPI build. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = [ - 'https://ftp.gromacs.org/pub/gromacs/', - 'ftp://ftp.gromacs.org/pub/gromacs/', -] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', - 'GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch', - 'GROMACS-%(version)s_dont_override_pythonpath_in_tests.patch', - 'GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch', -] -checksums = [ - 'e1666558831a3951c02b81000842223698016922806a8ce152e8f616e29899cf', # gromacs-2020.1.tar.gz - # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch - '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', - # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch - '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06', - # GROMACS-2020.1_dont_override_pythonpath_in_tests.patch - 'dffcafefeb594864c452cbeea3ee13091168c7ab9cd1f63dc8e9d1663dcb928e', - # GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch - '564c4e97e0dd05df1f45415ab5cc755c6b157880b26a816f7d6f7f98b318c900', -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('scikit-build', '0.10.0', versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('networkx', '2.4', versionsuffix), -] - -exts_defaultclass = 'PythonPackage' - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - -exts_list = [ - ('gmxapi', '0.1.0.1', { - 'patches': ['gmxapi-0.1.0.1_drop_cmake_requirement.patch'], - 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", - 'checksums': [ - '3371075975117a32ffe44e8972a4a9330da416f0054e00ee587cdffb217497a0', # gmxapi-0.1.0.1.tar.gz - # gmxapi-0.1.0.1_drop_cmake_requirement.patch - 'c58f1d94e7681bb2931ac90929445dc90f1709a9d8d3be78e55adbda797a2e8c', - ], - }), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.1_dont_override_pythonpath_in_tests.patch b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.1_dont_override_pythonpath_in_tests.patch deleted file mode 100644 index 8b0bdd51a25..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.1_dont_override_pythonpath_in_tests.patch +++ /dev/null @@ -1,15 +0,0 @@ -Don't overwrite PYTHONPATH when executing tests, add to it instead. - -Åke Sandgren, 20200309 -diff -ru gromacs-2020.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt gromacs-2020.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt ---- gromacs-2020.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2020-03-03 17:24:49.000000000 +0100 -+++ gromacs-2020.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2020-03-09 09:18:42.707693465 +0100 -@@ -22,7 +22,7 @@ - get_target_property(GMXAPI_PYTHON_STAGING_DIR _gmxapi staging_dir) - get_target_property(PLUGINPATH gmxapi_extension LIBRARY_OUTPUT_DIRECTORY) - add_custom_target(gmxapi_extension_pytest -- COMMAND ${CMAKE_COMMAND} -E env GMXBIN=${GMXBIN} PYTHONPATH=${GMXAPI_PYTHON_STAGING_DIR} -+ COMMAND ${CMAKE_COMMAND} -E env GMXBIN=${GMXBIN} PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR} - ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} - DEPENDS gmxapi_extension _gmxapi - WORKING_DIRECTORY ${PLUGINPATH}) diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.4-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 7c678d3dc2c..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.4-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,94 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, -# Ghent University / The Francis Crick Institute -# Authors:: -# * Wiktor Jurkowski -# * Fotis Georgatos -# * George Tsouloupas -# * Kenneth Hoste -# * Adam Huffman -# * Ake Sandgren -# License:: MIT/GPL -# 2019.3 version -# Contribution from the Crick HPC team -# uploaded by J. Sassmannshausen -# - -name = 'GROMACS' -version = '2020.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.gromacs.org' -description = """ -GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the -Newtonian equations of motion for systems with hundreds to millions of -particles. - -This is a CPU only build, containing both MPI and threadMPI builds -for both single and double precision. -It also contains the gmxapi extension for the single precision MPI build. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = [ - 'https://ftp.gromacs.org/pub/gromacs/', - 'ftp://ftp.gromacs.org/pub/gromacs/', -] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', - 'GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch', - 'GROMACS-2020.1_dont_override_pythonpath_in_tests.patch', - 'GROMACS-2020_disable_hardware_topology_tests.patch', - 'GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch', - 'GROMACS-2020.4_correct_gcc9_check.patch', -] -checksums = [ - '5519690321b5500c7951aaf53ff624042c3edd1a5f5d6dd1f2d802a3ecdbf4e6', # gromacs-2020.4.tar.gz - # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch - '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', - # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch - '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06', - # GROMACS-2020.1_dont_override_pythonpath_in_tests.patch - 'dffcafefeb594864c452cbeea3ee13091168c7ab9cd1f63dc8e9d1663dcb928e', - # GROMACS-2020_disable_hardware_topology_tests.patch - '47537f0372d9ac693c68b4ecef9c458cbe5a45f856ce7be5aad155213d0d385d', - # GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch - '564c4e97e0dd05df1f45415ab5cc755c6b157880b26a816f7d6f7f98b318c900', - 'fd614b84a48b7702dbb59410f2c6a1604864942caf9594e50c29a73e87023871', # GROMACS-2020.4_correct_gcc9_check.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('scikit-build', '0.10.0', versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('networkx', '2.4', versionsuffix), -] - -exts_defaultclass = 'PythonPackage' - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - -exts_list = [ - ('gmxapi', '0.1.0.1', { - 'patches': ['gmxapi-0.1.0.1_drop_cmake_requirement.patch'], - 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", - 'checksums': [ - '3371075975117a32ffe44e8972a4a9330da416f0054e00ee587cdffb217497a0', # gmxapi-0.1.0.1.tar.gz - # gmxapi-0.1.0.1_drop_cmake_requirement.patch - 'c58f1d94e7681bb2931ac90929445dc90f1709a9d8d3be78e55adbda797a2e8c', - ], - }), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.4_correct_gcc9_check.patch b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.4_correct_gcc9_check.patch deleted file mode 100644 index d6a82ae25f7..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.4_correct_gcc9_check.patch +++ /dev/null @@ -1,14 +0,0 @@ -See https://redmine.gromacs.org/projects/gromacs/repository/revisions/9baf5dcc540878dc0b15d8b945ac760d36fbf75d/diff -IBM VSX should be allowed with GCC 9.x -Patch added to EasyBuild by Simon Branford, University of Birmingham ---- cmake/gmxManageSimd.cmake.orig 2021-02-15 09:23:01.644332000 +0000 -+++ cmake/gmxManageSimd.cmake 2021-02-15 09:23:56.364277044 +0000 -@@ -266,7 +266,7 @@ - - # IBM_VSX and gcc > 9 do not work together, so we need to prevent people from - # choosing a combination that might fail. Issue #3380. -- if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "9") -+ if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10) - message(FATAL_ERROR "IBM_VSX does not work together with gcc > 9. Disable SIMD support (slower), or use an older version of the GNU compiler") - endif() - diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.5-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.5-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 4db73f6b2c5..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020.5-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,94 +0,0 @@ - -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, -# Ghent University / The Francis Crick Institute -# Authors:: -# * Wiktor Jurkowski -# * Fotis Georgatos -# * George Tsouloupas -# * Kenneth Hoste -# * Adam Huffman -# * Ake Sandgren -# * J. Sassmannshausen -# * Dugan Witherick -# License:: MIT/GPL - -name = 'GROMACS' -version = '2020.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.gromacs.org' -description = """ -GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the -Newtonian equations of motion for systems with hundreds to millions of -particles. - -This is a GPU enabled build, containing both MPI and threadMPI builds. - -It also contains the gmxapi extension for the single precision MPI build. -""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = [ - 'https://ftp.gromacs.org/pub/gromacs/', - 'ftp://ftp.gromacs.org/pub/gromacs/', -] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', - 'GROMACS-2019_increase_test_timeout_for_GPU.patch', - 'GROMACS-2020_disable_hardware_topology_tests.patch', - 'GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch', - 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', - 'GROMACS-2020.4_correct_gcc9_check.patch', - 'GROMACS-2020_add-missing-sync.patch', -] -checksums = [ - '7b6aff647f7c8ee1bf12204d02cef7c55f44402a73195bd5f42cf11850616478', # gromacs-2020.5.tar.gz - # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch - '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', - # GROMACS-2019_increase_test_timeout_for_GPU.patch - '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', - # GROMACS-2020_disable_hardware_topology_tests.patch - '47537f0372d9ac693c68b4ecef9c458cbe5a45f856ce7be5aad155213d0d385d', - # GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch - '564c4e97e0dd05df1f45415ab5cc755c6b157880b26a816f7d6f7f98b318c900', - # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch - '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', - 'fd614b84a48b7702dbb59410f2c6a1604864942caf9594e50c29a73e87023871', # GROMACS-2020.4_correct_gcc9_check.patch - '3c9d7017422a722a960d26ad955d7a0f72a1305a6234bcb53851cc62662b96c9', # GROMACS-2020_add-missing-sync.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('scikit-build', '0.10.0', versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('networkx', '2.4', versionsuffix), -] - -exts_defaultclass = 'PythonPackage' - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - -exts_list = [ - ('gmxapi', '0.1.0.1', { - 'patches': ['gmxapi-0.1.0.1_drop_cmake_requirement.patch'], - 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", - 'checksums': [ - '3371075975117a32ffe44e8972a4a9330da416f0054e00ee587cdffb217497a0', # gmxapi-0.1.0.1.tar.gz - # gmxapi-0.1.0.1_drop_cmake_requirement.patch - 'c58f1d94e7681bb2931ac90929445dc90f1709a9d8d3be78e55adbda797a2e8c', - ], - }), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020_add-missing-sync.patch b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020_add-missing-sync.patch deleted file mode 100644 index 706888bd2e4..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020_add-missing-sync.patch +++ /dev/null @@ -1,39 +0,0 @@ -Add missing sync in LINCS and SETTLE CUDA kernels -https://gitlab.com/gromacs/gromacs/-/merge_requests/2499 -Patch added to EasyBuild by Simon Branford (University of Birmingham) -diff --git a/src/gromacs/mdlib/lincs_cuda.cu b/src/gromacs/mdlib/lincs_cuda.cu -index 27ad86f17f..4964a3d040 100644 ---- a/src/gromacs/mdlib/lincs_cuda.cu -+++ b/src/gromacs/mdlib/lincs_cuda.cu -@@ -382,11 +382,15 @@ __launch_bounds__(c_maxThreadsPerBlock) __global__ - sm_threadVirial[d * blockDim.x + (threadIdx.x + dividedAt)]; - } - } -- // Syncronize if not within one warp -+ // Synchronize if not within one warp - if (dividedAt > warpSize / 2) - { - __syncthreads(); - } -+ else -+ { -+ __syncwarp(); -+ } - } - // First 6 threads in the block add the results of 6 tensor components to the global memory address. - if (threadIdx.x < 6) -diff --git a/src/gromacs/mdlib/settle_cuda.cu b/src/gromacs/mdlib/settle_cuda.cu -index c02f0d5884..c6ca1e2452 100644 ---- a/src/gromacs/mdlib/settle_cuda.cu -+++ b/src/gromacs/mdlib/settle_cuda.cu -@@ -352,6 +352,10 @@ __launch_bounds__(c_maxThreadsPerBlock) __global__ - { - __syncthreads(); - } -+ else -+ { -+ __syncwarp(); -+ } - } - // First 6 threads in the block add the 6 components of virial to the global memory address - if (tib < 6) diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020_disable_hardware_topology_tests.patch b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020_disable_hardware_topology_tests.patch deleted file mode 100644 index 7ea7a3fd81a..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020_disable_hardware_topology_tests.patch +++ /dev/null @@ -1,12 +0,0 @@ -Disable hardware topology tests. The failure of these tests is bening. -See https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2020-March/128857.html -author: Alex Domingo (Vrije Universiteit Brussel) ---- src/gromacs/hardware/tests/CMakeLists.txt.orig 2021-01-04 15:03:40.808453000 +0100 -+++ src/gromacs/hardware/tests/CMakeLists.txt 2021-01-04 15:05:46.544205000 +0100 -@@ -33,5 +33,4 @@ - # the research papers on the package. Check out http://www.gromacs.org. - - gmx_add_unit_test(HardwareUnitTests hardware-test -- cpuinfo.cpp -- hardwaretopology.cpp) -+ cpuinfo.cpp) diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch deleted file mode 100644 index ad6ee3c07f5..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch +++ /dev/null @@ -1,39 +0,0 @@ -Fix search for "gmx" binary to allow for double precision builds. - -Åke Sandgren, 20200318 -diff -ru gromacs-2020.1.orig/python_packaging/sample_restraint/tests/conftest.py gromacs-2020.1/python_packaging/sample_restraint/tests/conftest.py ---- gromacs-2020.1.orig/python_packaging/sample_restraint/tests/conftest.py 2020-03-03 17:24:49.000000000 +0100 -+++ gromacs-2020.1/python_packaging/sample_restraint/tests/conftest.py 2020-03-18 07:19:09.611507575 +0100 -@@ -156,7 +156,7 @@ - # TODO: (#2896) Find a more canonical way to identify the GROMACS commandline wrapper binary. - # We should be able to get the GMXRC contents and related hints from a gmxapi - # package resource or from module attributes of a ``gromacs`` stub package. -- allowed_command_names = ['gmx', 'gmx_mpi'] -+ allowed_command_names = ['gmx%s%s' % (m, p) for m in ['', '_mpi'] for p in ['', '_d']] - command = None - for command_name in allowed_command_names: - if command is not None: -diff -ru gromacs-2020.1.orig/python_packaging/src/test/conftest.py gromacs-2020.1/python_packaging/src/test/conftest.py ---- gromacs-2020.1.orig/python_packaging/src/test/conftest.py 2020-03-03 17:24:49.000000000 +0100 -+++ gromacs-2020.1/python_packaging/src/test/conftest.py 2020-03-18 07:19:27.535301581 +0100 -@@ -156,7 +156,7 @@ - # TODO: (#2896) Find a more canonical way to identify the GROMACS commandline wrapper binary. - # We should be able to get the GMXRC contents and related hints from a gmxapi - # package resource or from module attributes of a ``gromacs`` stub package. -- allowed_command_names = ['gmx', 'gmx_mpi'] -+ allowed_command_names = ['gmx%s%s' % (m, p) for m in ['', '_mpi'] for p in ['', '_d']] - command = None - for command_name in allowed_command_names: - if command is not None: -diff -ru gromacs-2020.1.orig/python_packaging/test/conftest.py gromacs-2020.1/python_packaging/test/conftest.py ---- gromacs-2020.1.orig/python_packaging/test/conftest.py 2020-03-03 17:24:49.000000000 +0100 -+++ gromacs-2020.1/python_packaging/test/conftest.py 2020-03-18 07:19:03.967572439 +0100 -@@ -156,7 +156,7 @@ - # TODO: (#2896) Find a more canonical way to identify the GROMACS commandline wrapper binary. - # We should be able to get the GMXRC contents and related hints from a gmxapi - # package resource or from module attributes of a ``gromacs`` stub package. -- allowed_command_names = ['gmx', 'gmx_mpi'] -+ allowed_command_names = ['gmx%s%s' % (m, p) for m in ['', '_mpi'] for p in ['', '_d']] - command = None - for command_name in allowed_command_names: - if command is not None: diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/gmxapi-0.1.0.1_drop_cmake_requirement.patch b/easybuild/easyconfigs/__archive__/g/GROMACS/gmxapi-0.1.0.1_drop_cmake_requirement.patch deleted file mode 100644 index 57e5e610f6c..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/gmxapi-0.1.0.1_drop_cmake_requirement.patch +++ /dev/null @@ -1,16 +0,0 @@ -Drop the cmake requirement from gmxapi, we take that from the dependencies list. - -Åke Sandgren, 20200308 -diff -ru gmxapi-0.1.0.1.orig/setup.py gmxapi-0.1.0.1/setup.py ---- gmxapi-0.1.0.1.orig/setup.py 2019-12-30 12:08:34.000000000 +0100 -+++ gmxapi-0.1.0.1/setup.py 2020-03-08 17:00:54.456270981 +0100 -@@ -152,8 +152,7 @@ - # TODO: (pending infrastructure and further discussion) Replace with CMake variables from GMXAPI version. - version='0.1.0.1', - python_requires='>=3.5, <3.9', -- setup_requires=['cmake>=3.12', -- 'setuptools>=28', -+ setup_requires=['setuptools>=28', - 'scikit-build>=0.7'], - - packages=['gmxapi', 'gmxapi.simulation'], diff --git a/easybuild/easyconfigs/__archive__/g/GSL/GSL-2.6-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GSL/GSL-2.6-GCC-9.3.0.eb deleted file mode 100644 index 0311d9f4790..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GSL/GSL-2.6-GCC-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '2.6' - -homepage = 'https://www.gnu.org/software/gsl/' -description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions - and least-squares fitting.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + - ['include/gsl/gsl_types.h'] + - ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/g/GSL/GSL-2.6-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/g/GSL/GSL-2.6-iccifort-2020.1.217.eb deleted file mode 100644 index af6a5a7298c..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GSL/GSL-2.6-iccifort-2020.1.217.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '2.6' - -homepage = 'https://www.gnu.org/software/gsl/' -description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions - and least-squares fitting.""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + - ['include/gsl/gsl_types.h'] + - ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 6e94e45eec2..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,39 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonPackage' - -name = 'GTDB-Tk' -version = '1.3.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Ecogenomics/GTDBTk' -description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://pypi.python.org/packages/source/g/gtdbtk'] -sources = ['gtdbtk-%(version)s.tar.gz'] -checksums = ['50f83378ae4d1116f9f98fc75088a851f39904772b91f41dab782c2d97dba00f'] - -dependencies = [ - ('Python', '3.8.2'), - ('DendroPy', '4.4.0'), - ('matplotlib', '3.2.1', versionsuffix), - ('prodigal', '2.6.3'), - ('HMMER', '3.3.1'), - ('pplacer', '1.1.alpha19', '', SYSTEM), - ('FastANI', '1.31'), - ('FastTree', '2.1.11'), - ('tqdm', '4.47.0'), -] - -options = {'modulename': 'gtdbtk'} - -sanity_check_paths = { - 'files': ['bin/gtdbtk'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb deleted file mode 100644 index 0358455beba..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb +++ /dev/null @@ -1,76 +0,0 @@ -easyblock = 'Bundle' - -name = 'GTK+' -version = '3.24.17' - -homepage = 'https://developer.gnome.org/gtk3/stable/' -description = """GTK+ is the primary library used to construct user interfaces in GNOME. It - provides all the user interface controls, or widgets, used in a common - graphical application. Its object-oriented API allows you to construct - user interfaces without dealing with the low-level details of drawing and - device interaction. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), - ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), - ('gettext', '0.20.1'), - ('pkg-config', '0.29.2'), - ('cairo', '1.16.0'), - ('Perl', '5.30.2'), -] - -dependencies = [ - ('ATK', '2.36.0'), - ('at-spi2-atk', '2.34.2'), - ('Gdk-Pixbuf', '2.40.0'), - ('Pango', '1.44.7'), - ('libepoxy', '1.5.4'), - ('X11', '20200222'), - ('FriBidi', '1.0.9'), -] - -default_easyblock = 'ConfigureMake' - -default_component_specs = { - 'sources': [SOURCELOWER_TAR_XZ], - 'start_dir': '%(namelower)s-%(version)s', -} - -components = [ - (name, version, { - 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['f210255b221cb0f0db3e7b21399983b715c9dda6eb1e5c2f7fdf38f4f1b6bac0'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes", - }), - ('hicolor-icon-theme', '0.17', { - 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], - 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], - }), - ('adwaita-icon-theme', '3.36.0', { - 'preconfigopts': 'autoreconf -f -i && ', - 'source_urls': [FTPGNOME_SOURCE], - 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], - 'checksums': [ - '1a172112b6da482d3be3de6a0c1c1762886e61e12b4315ae1aae9b69da1ed518', - # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch - 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', - ], - }), -] - -postinstallcmds = ['gtk-update-icon-cache'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', - 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', - 'gtk-update-icon-cache']] + - ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], - 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + - ['share/icons/hicolor', 'share/icons/Adwaita'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/GTS/GTS-0.7.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GTS/GTS-0.7.6-GCCcore-9.3.0.eb deleted file mode 100644 index 278a3261863..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GTS/GTS-0.7.6-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GTS' -version = '0.7.6' - -homepage = 'http://gts.sourceforge.net/' -description = """GTS stands for the GNU Triangulated Surface Library. - It is an Open Source Free Software Library intended to provide a set of useful - functions to deal with 3D surfaces meshed with interconnected triangles.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] - -builddependencies = [ - ('pkg-config', '0.29.2'), - ('binutils', '2.34'), -] - -dependencies = [ - ('GLib', '2.64.1'), -] - -sanity_check_paths = { - 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], - 'dirs': [] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/GTS/GTS-0.7.6-foss-2020a.eb b/easybuild/easyconfigs/__archive__/g/GTS/GTS-0.7.6-foss-2020a.eb deleted file mode 100644 index 8573c81e4e4..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GTS/GTS-0.7.6-foss-2020a.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GTS' -version = '0.7.6' - -homepage = 'http://gts.sourceforge.net/' -description = """GTS stands for the GNU Triangulated Surface Library. - It is an Open Source Free Software Library intended to provide a set of useful - functions to deal with 3D surfaces meshed with interconnected triangles.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('GLib', '2.64.1'), -] - -sanity_check_paths = { - 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], - 'dirs': [] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb deleted file mode 100644 index 919446d1ca5..00000000000 --- a/easybuild/easyconfigs/__archive__/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'Gdk-Pixbuf' -version = '2.40.0' - -homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' -description = """ - The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. - It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it - was distributed as part of GTK+ 2 but it was split off into a separate package - in preparation for the change to GTK+ 3. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = [ - '1582595099537ca8ff3b99c6804350b4c058bb8ad67411bbaae024ee7cead4e6', # gdk-pixbuf-2.40.0.tar.xz -] - -builddependencies = [ - ('Meson', '0.55.1', '-Python-3.8.2'), - ('Ninja', '1.10.0'), - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), - ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), -] - -dependencies = [ - ('GLib', '2.64.1'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('X11', '20200222'), -] - -configopts = "--default-library=both " -configopts += "-Dgio_sniffing=false -Dgir=true -Dman=false " - -sanity_check_paths = { - 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-10.6.2-foss-2020a.eb b/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-10.6.2-foss-2020a.eb deleted file mode 100644 index 3fe28999feb..00000000000 --- a/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-10.6.2-foss-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'Geant4' -version = '10.6.2' - -homepage = 'https://geant4.cern.ch/' -description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. - Its areas of application include high energy, nuclear and accelerator physics, - as well as studies in medical and space science.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -github_account = 'Geant4' -source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -checksums = ['f16c03bb2d346b398d500a3977fa7035d63e6c1f087db239c26f1ca113302daf'] - -builddependencies = [('CMake', '3.16.4')] -dependencies = [ - ('expat', '2.2.9'), - # recommended CLHEP version, see https://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.6.html - ('CLHEP', '2.4.1.3'), -] - -configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += " -DGEANT4_INSTALL_DATA=OFF" - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/g/GenomeTools/GenomeTools-1.6.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GenomeTools/GenomeTools-1.6.1-GCC-9.3.0.eb deleted file mode 100644 index 61723dec866..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GenomeTools/GenomeTools-1.6.1-GCC-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GenomeTools' -version = '1.6.1' - -homepage = 'http://genometools.org' -description = "A comprehensive software library for efficient processing of structured genome annotations." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -github_account = 'genometools' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['528ca143a7f1d42af8614d60ea1e5518012913a23526d82e434f0dad2e2d863f'] - -# GenomeTools-1.6.1 has the following libraries bundled with it: -# bzip2-1.0.6, cgilua-5.1.3, expat-2.0.1, lpeg-0.10.2, lua-5.1.5, luafilesystem-1.5.0, md5-1.2, -# samtools-0.1.18, sqlite-3.8.7.1, tre-0.8.0, zlib-1.2.8 -# -# Bundled libraries can be globally disabled with the option useshared=yes -# However, it is preferable to use the bundled libraries due to the very old versions of some of them - -builddependencies = [('pkg-config', '0.29.2')] -dependencies = [('Pango', '1.44.7')] - -skipsteps = ['configure'] - -buildopts = 'useshared=no errorcheck=no cairo=yes' -installopts = 'prefix=%(installdir)s' - -sanity_check_paths = { - 'files': ['bin/gt', 'bin/genometools-config', 'lib/libgenometools.a', 'lib/libgenometools.%s' % SHLIB_EXT], - 'dirs': ['include', 'share'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 5042f6199a7..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'GetOrganelle' -version = '1.7.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Kinggerm/GetOrganelle' -description = """This toolkit assemblies organelle genome from genomic skimming data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/%(version)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['54923ca971d68620aaf036a324b554084b00f7c209b0b3a234f815c82ee6d079'] - -dependencies = [ - ('Python', '3.8.2'), - ('Bandage', '0.8.1', '_Centos', SYSTEM), - ('SciPy-bundle', '2020.03', versionsuffix), - ('sympy', '1.6.2', versionsuffix), - ('SPAdes', '3.14.1', versionsuffix), - ('Bowtie2', '2.4.1'), - ('BLAST+', '2.10.1'), - ('Perl', '5.30.2'), - ('matplotlib', '3.2.1', versionsuffix) -] - -options = {'modulename': False} - -fix_python_shebang_for = ['bin/*.py'] - -sanity_check_commands = ["get_organelle_from_reads.py -h"] - -sanity_check_paths = { - 'files': ['bin/check_annotations.py', 'bin/get_organelle_from_reads.py', 'bin/slim_graph.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/GffCompare/GffCompare-0.11.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/GffCompare/GffCompare-0.11.6-GCCcore-9.3.0.eb deleted file mode 100644 index 579f86118c8..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GffCompare/GffCompare-0.11.6-GCCcore-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'MakeCp' - -name = 'GffCompare' -version = '0.11.6' - -# Some docs also at GitHub site - this is referred to as canonical -homepage = 'https://ccb.jhu.edu/software/stringtie/gffcompare.shtml' -description = """GffCompare provides classification and reference annotation mapping and - matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -# Switched to GitHub sources owing to SSL error at original download site -source_urls = ['https://github.com/gpertea/gffcompare/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = [ - ( - # GitHub source - '21d37a43b6db1deb30fc5bc5198121a0b65e33edd5be2f55ae6100a34ee5df16', - # Original source - '6095d97301a9c8dbd5e99e8c42860ce5953546277a09a0b46c835019815f6174', - ) - -] - -builddependencies = [('binutils', '2.34')] - -buildopts = " release" - -files_to_copy = ['%(namelower)s', 'LICENSE', 'README.md'] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['%(namelower)s'], - 'dirs': [] -} - -sanity_check_commands = ['%(namelower)s -v'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb deleted file mode 100644 index afd425e4546..00000000000 --- a/easybuild/easyconfigs/__archive__/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Ghostscript' -version = '9.52' - -homepage = 'https://ghostscript.com' -description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to - different targets. It used to be part of the cups printing stack, but is no longer used for that.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c2501d8e8e0814c4a5aa7e443e230e73d7af7f70287546f7b697e5ef49e32176'] - -dependencies = [ - ('zlib', '1.2.11'), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('libjpeg-turbo', '2.0.4'), - ('expat', '2.2.9'), - ('GLib', '2.64.1'), - ('cairo', '1.16.0'), - ('LibTIFF', '4.1.0'), -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -# Do not use local copies of zlib, jpeg, freetype, and png -preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " -preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' - -configopts = "--with-system-libtiff --enable-dynamic" - -postinstallcmds = [ - # build and install shared libs - "make so && make soinstall", - # install header files - "mkdir -p %(installdir)s/include/ghostscript", - "install -v -m644 base/*.h %(installdir)s/include/ghostscript", - "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", -] - -sanity_check_paths = { - 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], - 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/GitPython/GitPython-3.1.9-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/GitPython/GitPython-3.1.9-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 8be02270350..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GitPython/GitPython-3.1.9-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'GitPython' -version = '3.1.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/gitpython-developers/GitPython' -description = """ GitPython is a python library used to interact with Git repositories """ - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Python', '3.8.2'), - ('git', '2.23.0', '-nodocs'), -] - -exts_list = [ - ('smmap', '3.0.4', { - 'checksums': ['9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24'], - }), - ('gitdb', '4.0.5', { - 'checksums': ['c9e1f2d0db7ddb9a704c2a0217be31214e91a4fe1dea1efad19ae42ba0c285c9'], - }), - (name, version, { - 'modulename': 'git', - 'checksums': ['a03f728b49ce9597a6655793207c6ab0da55519368ff5961e4a74ae475b9fa8e'], - }), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/GlobalArrays/GlobalArrays-5.8-intel-2020a.eb b/easybuild/easyconfigs/__archive__/g/GlobalArrays/GlobalArrays-5.8-intel-2020a.eb deleted file mode 100644 index 26b107604c9..00000000000 --- a/easybuild/easyconfigs/__archive__/g/GlobalArrays/GlobalArrays-5.8-intel-2020a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GlobalArrays' -version = '5.8' - -homepage = 'https://hpc.pnl.gov/globalarrays' -description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] -sources = ['v%(version)s/ga-%(version)s.tar.gz'] -checksums = ['64df7d1ea4053d24d84ca361e67a6f51c7b17ed7d626cb18a9fbc759f4a078ac'] - -configopts = ' --with-mpi --enable-i8' -configopts += ' --with-blas8="-L$EBROOTIMKL/mkl/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' -configopts += ' --with-scalapack8="-L$EBROOTIMKL/mkl/lib/intel64 -lmkl_sequential -lmkl_scalapack_ilp64"' - -# select armci network as (Comex) MPI-1 two-sided -configopts += ' --with-mpi-ts' - -sanity_check_paths = { - 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', - 'lib/libcomex.a', 'lib/libga.a'], - 'dirs': ['include'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/Glucose/Glucose-4.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/Glucose/Glucose-4.1-GCC-9.3.0.eb deleted file mode 100644 index 99e834938f8..00000000000 --- a/easybuild/easyconfigs/__archive__/g/Glucose/Glucose-4.1-GCC-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'Bundle' - -name = 'Glucose' -version = '4.1' - -homepage = 'https://www.labri.fr/perso/lsimon/glucose/' -description = """ -Glucose is based on a new scoring scheme (well, not so new now, it was -introduced in 2009) for the clause learning mechanism of so called Modern SAT -solvers (it is based on our IJCAI'09 paper). It is designed to be parallel, since v4.0.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -dependencies = [ - ('zlib', '1.2.11'), -] - -# All components are installed from the same tarball -local_sources = '%s-syrup-%s' % (name.lower(), version) - -default_easyblock = 'MakeCp' -default_component_specs = { - 'source_urls': ['https://www.labri.fr/perso/lsimon/downloads/softwares'], - 'sources': ['%s.tgz' % local_sources], - 'checksums': ['51aa1cf1bed2b14f1543b099e85a56dd1a92be37e6e3eb0c4a1fd883d5cc5029'], -} -components = [ - ('Glucose', version, { - 'start_dir': '%s/simp' % local_sources, - 'files_to_copy': [(['%(namelower)s'], 'bin')], - }), - ('Glucose-Syrup', version, { - 'start_dir': '%s/parallel' % local_sources, - 'files_to_copy': [(['%(namelower)s'], 'bin')], - }), -] - -sanity_check_paths = { - 'files': ['bin/glucose', 'bin/glucose-syrup'], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb deleted file mode 100644 index f19b861f72c..00000000000 --- a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb +++ /dev/null @@ -1,91 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Graphviz' -version = '2.44.1' -versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' -local_pyver_major = '3' - -homepage = 'https://www.graphviz.org/' -description = """Graphviz is open source graph visualization software. Graph visualization - is a way of representing structural information as diagrams of - abstract graphs and networks. It has important applications in networking, - bioinformatics, software engineering, database and web design, machine learning, - and in visual interfaces for other technical domains.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'cstd': 'c++11'} - -source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['Graphviz-2.42.2_skip-install-data-hook.patch'] -checksums = [ - '3aac783a15341c2808141cc38ead408bf3d6ad203e0ed3946c9df595b760edda', # graphviz-2.44.1.tar.gz - '3d06544c435a6255f6a8f3b36df3102060667b50ffd72e4942bbe546b9363859', # Graphviz-2.42.2_skip-install-data-hook.patch -] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), - ('Bison', '3.5.3'), - ('flex', '2.6.4'), - ('SWIG', '4.0.1'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Java', '11', '', SYSTEM), - ('Python', '3.8.2'), - ('FriBidi', '1.0.9'), - ('Gdk-Pixbuf', '2.40.0'), - ('Ghostscript', '9.52'), - ('GTS', '0.7.6'), - ('libgd', '2.3.0'), - ('Pango', '1.44.7'), - ('Perl', '5.30.2'), - ('Qt5', '5.14.1'), - ('Tcl', '8.6.10'), - ('zlib', '1.2.11'), -] - -preconfigopts = './autogen.sh NOCONFIG && ' - -configopts = '--enable-python%s=yes ' % local_pyver_major -configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' -configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' -# Use ltdl from libtool in EB -configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' -configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' -# Override the hardcoded paths to Java libraries -configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' -configopts += '--with-javalibdir=$JAVA_HOME/lib' - -prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' - -postinstallcmds = ['%(installdir)s/bin/dot -c'] # Writes plugin configuration - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['acyclic', 'bcomps', 'ccomps', 'cluster', 'diffimg', 'dijkstra', 'dot', - 'dot_builtins', 'dotty', 'edgepaint', 'gc', 'gml2gv', 'graphml2gv', 'gv2gml', - 'gvcolor', 'gvedit', 'gvgen', 'gvmap', 'gvmap.sh', 'gvpack', 'gvpr', 'gxl2gv', - 'lefty', 'lneato', 'mm2gv', 'nop', 'prune', 'sccmap', 'tred', 'unflatten', - 'vimdot']] + - ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libcdt', 'libcgraph', 'libgvc', 'libgvpr', 'liblab_gamut', - 'libpathplan', 'libxdot']], - 'dirs': ['include', 'lib/graphviz', 'lib/graphviz/java', 'lib/graphviz/python%s' % local_pyver_major, - 'lib/pkgconfig', 'share'] -} - -sanity_check_commands = [ - ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), - ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), - ('python', '-c "import gv"'), -] - -modextrapaths = { - 'CLASSPATH': 'lib/graphviz/java', - 'LD_LIBRARY_PATH': 'lib/graphviz/java', - 'PYTHONPATH': 'lib/graphviz/python%s' % local_pyver_major, - 'TCLLIBPATH': 'lib/graphviz/tcl', -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb deleted file mode 100644 index e532aad271a..00000000000 --- a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb +++ /dev/null @@ -1,86 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Graphviz' -version = '2.44.1' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://www.graphviz.org/' -description = """Graphviz is open source graph visualization software. Graph visualization - is a way of representing structural information as diagrams of - abstract graphs and networks. It has important applications in networking, - bioinformatics, software engineering, database and web design, machine learning, - and in visual interfaces for other technical domains.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'cstd': 'c++11'} - -source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['Graphviz-2.42.2_skip-install-data-hook.patch'] -checksums = [ - '3aac783a15341c2808141cc38ead408bf3d6ad203e0ed3946c9df595b760edda', # graphviz-2.44.1.tar.gz - '3d06544c435a6255f6a8f3b36df3102060667b50ffd72e4942bbe546b9363859', # Graphviz-2.42.2_skip-install-data-hook.patch -] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), - ('Bison', '3.5.3'), - ('flex', '2.6.4'), - ('SWIG', '4.0.1'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Java', '11', '', SYSTEM), - ('FriBidi', '1.0.9'), - ('Gdk-Pixbuf', '2.40.0'), - ('Ghostscript', '9.52'), - ('GTS', '0.7.6'), - ('libgd', '2.3.0'), - ('Pango', '1.44.7'), - ('Perl', '5.30.2'), - ('Qt5', '5.14.1'), - ('Tcl', '8.6.10'), - ('zlib', '1.2.11'), -] - -preconfigopts = './autogen.sh NOCONFIG && ' - -configopts = '--enable-python=no ' -configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' -configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' -# Use ltdl from libtool in EB -configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' -configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' -# Override the hardcoded paths to Java libraries -configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' -configopts += '--with-javalibdir=$JAVA_HOME/lib' - -prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' - -postinstallcmds = ['%(installdir)s/bin/dot -c'] # Writes plugin configuration - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['acyclic', 'bcomps', 'ccomps', 'cluster', 'diffimg', 'dijkstra', 'dot', - 'dot_builtins', 'dotty', 'edgepaint', 'gc', 'gml2gv', 'graphml2gv', 'gv2gml', - 'gvcolor', 'gvedit', 'gvgen', 'gvmap', 'gvmap.sh', 'gvpack', 'gvpr', 'gxl2gv', - 'lefty', 'lneato', 'mm2gv', 'nop', 'prune', 'sccmap', 'tred', 'unflatten', - 'vimdot']] + - ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libcdt', 'libcgraph', 'libgvc', 'libgvpr', 'liblab_gamut', - 'libpathplan', 'libxdot']], - 'dirs': ['include', 'lib/graphviz', 'lib/graphviz/java', 'lib/pkgconfig', 'share'] -} - -sanity_check_commands = [ - ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), - ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), -] - -modextrapaths = { - 'CLASSPATH': 'lib/graphviz/java', - 'LD_LIBRARY_PATH': 'lib/graphviz/java', - 'TCLLIBPATH': 'lib/graphviz/tcl', -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/Guile/Guile-1.8.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/Guile/Guile-1.8.8-GCCcore-9.3.0.eb deleted file mode 100644 index 473db350c1f..00000000000 --- a/easybuild/easyconfigs/__archive__/g/Guile/Guile-1.8.8-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Guile' -version = '1.8.8' - -homepage = 'https://www.gnu.org/software/guile/' -description = """Guile is a programming language, designed to help programmers create flexible applications that - can be extended by users or other programmers with plug-ins, modules, or scripts.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c3471fed2e72e5b04ad133bbaaf16369e8360283679bcf19800bc1b381024050'] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), -] -dependencies = [ - ('libunistring', '0.9.10'), - ('libffi', '3.3'), - ('gc', '7.6.12'), - ('GMP', '6.2.0'), -] - -configopts = " --enable-error-on-warning=no" - -sanity_check_paths = { - 'files': ['bin/guile', 'bin/guile-config', 'bin/guile-snarf', 'bin/guile-tools', - 'include/libguile.h', 'lib/libguile.a', 'lib/libguile.%s' % SHLIB_EXT, - 'lib/pkgconfig/guile-%(version_major_minor)s.pc'], - 'dirs': ['include/guile'], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/g/Guile/Guile-2.2.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/Guile/Guile-2.2.4-GCCcore-9.3.0.eb deleted file mode 100644 index 0e81c676a16..00000000000 --- a/easybuild/easyconfigs/__archive__/g/Guile/Guile-2.2.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Guile' -version = '2.2.4' - -homepage = 'https://www.gnu.org/software/guile/' - -description = """ - Guile is a programming language, designed to help programmers create flexible - applications that can be extended by users or other programmers with plug-ins, - modules, or scripts. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['33b904c0bf4e48e156f3fb1d0e6b0392033bd610c6c9d9a0410c6e0ea96a3e5c'] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), -] - -dependencies = [ - ('gc', '7.6.12'), - ('GMP', '6.2.0'), - ('libffi', '3.3'), - ('libunistring', '0.9.10'), -] - -sanity_check_paths = { - 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', - 'bin/guile-snarf', 'bin/guile-tools', - 'include/guile/%(version_major_minor)s/libguile.h', - 'lib/libguile-%(version_major_minor)s.a', - 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], - 'dirs': ['include/guile/%(version_major_minor)s/libguile', - 'lib/guile/%(version_major_minor)s/ccache'], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 302ab9d01a0..00000000000 --- a/easybuild/easyconfigs/__archive__/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'Gurobi' -version = '9.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.gurobi.com' -description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. -The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern -architectures and multi-core processors, using the most advanced implementations of the -latest algorithms.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] -sources = ['%(namelower)s%(version)s_linux64.tar.gz'] -patches = ['%(name)s-%(version)s_use-eb-python-gurobi-shell.patch'] -checksums = [ - '17e2facda111180eee61eeded0b8716230bbe09faa7c61356dc79f002ff86cb7', # gurobi9.0.1_linux64.tar.gz - 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01', # Gurobi-9.0.1_use-eb-python-gurobi-shell.patch -] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Python', '3.8.2'), -] - -# remove bundled Python interpreter in favour of the dependency in EB -postinstallcmds = ['rm %(installdir)s/bin/python*'] - -license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' - -modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` -Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' -""" - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.6.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.6.0-GCCcore-9.3.0.eb deleted file mode 100644 index 327de01ba2e..00000000000 --- a/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.6.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'g2clib' -version = '1.6.0' - -homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder ('C' version).""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = ['%(name)s-%(version)s.tar'] -patches = ['g2clib-%(version)s-with-JasPer-2.x.patch'] -checksums = [ - 'afec1ea29979b84369d0f46f305ed12f73f1450ec2db737664ec7f75c1163add', # g2clib-1.6.0.tar - '2e62502d7823be5407ea023029dd206930a1034421d141dd346b468e177a7fce', # g2clib-1.6.0-with-JasPer-2.x.patch -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('JasPer', '2.0.14'), - ('libpng', '1.6.37'), -] - -# parallel build tends to fail -maxparallel = 1 - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.6.0-with-JasPer-2.x.patch b/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.6.0-with-JasPer-2.x.patch deleted file mode 100644 index f7c97c5d3d4..00000000000 --- a/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.6.0-with-JasPer-2.x.patch +++ /dev/null @@ -1,15 +0,0 @@ -fix compilation on top of JasPer 2.x -see also http://forum.wrfforum.com/viewtopic.php?f=5&t=10248 -author: Simon Pinches -diff -Nru g2clib-1.6.0-orig/enc_jpeg2000.c g2clib-1.6.0/enc_jpeg2000.c ---- g2clib-1.6.0-orig/enc_jpeg2000.c 2015-05-06 13:54:24.000000000 +0200 -+++ g2clib-1.6.0/enc_jpeg2000.c 2018-07-05 21:55:51.000000000 +0200 -@@ -121,7 +121,7 @@ - image.clrspc_=JAS_CLRSPC_SGRAY; /* grayscale Image */ - image.cmprof_=0; - #endif -- image.inmem_=1; -+ // image.inmem_=1; - - cmpt.tlx_=0; - cmpt.tly_=0; diff --git a/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.4.0-with-JasPer-2.x.patch b/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.4.0-with-JasPer-2.x.patch deleted file mode 100644 index 685b90b46fd..00000000000 --- a/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.4.0-with-JasPer-2.x.patch +++ /dev/null @@ -1,15 +0,0 @@ -fix compilation on top of JasPer 2.x -see also http://forum.wrfforum.com/viewtopic.php?f=5&t=10248 -author: Simon Pinches -diff -Nru g2lib-1.4.0-orig/enc_jpeg2000.c g2lib-1.4.0/enc_jpeg2000.c ---- g2lib-1.4.0-orig/enc_jpeg2000.c 2014-07-08 20:36:50.000000000 +0200 -+++ g2lib-1.4.0/enc_jpeg2000.c 2018-07-06 09:08:10.000000000 +0200 -@@ -139,7 +139,7 @@ - image.clrspc_=JAS_CLRSPC_SGRAY; /* grayscale Image */ - image.cmprof_=0; - #endif -- image.inmem_=1; -+ // image.inmem_=1; - - cmpt.tlx_=0; - cmpt.tly_=0; diff --git a/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-3.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-3.1.0-GCCcore-9.3.0.eb deleted file mode 100644 index e326528759b..00000000000 --- a/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-3.1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -name = 'g2lib' -version = '3.1.0' - -homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [homepage] -sources = ['%(name)s-%(version)s.tar'] -patches = [ - '%(name)s-%(version)s_makefile.patch', - '%(name)s-%(version)s-kind.patch', - '%(name)s-1.4.0-with-JasPer-2.x.patch', -] -checksums = [ - '8a2de259de82094c5867f8d7945359f211592a4a503f9ed65dc60469337414e7', # g2lib-3.1.0.tar - '702f76c77638fb36b662caf96890a69f19c507778c92aa1e163898b150cc8282', # g2lib-3.1.0_makefile.patch - '6412022d37a470e38e4f2c4b7b6bd7cbb9581027b5ff187f4379b7dc0d72cbb5', # g2lib-3.1.0-kind.patch - 'cd4c668dab76ef3b61fa902c2eed24747517d4cbc3ec0aaffab37e6b80946170', # g2lib-1.4.0-with-JasPer-2.x.patch -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('JasPer', '2.0.14'), - ('libpng', '1.6.37'), -] - -buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FFLAGS="$FFLAGS -fno-range-check -I." FC=$FC CC=$CC' - -# parallel build tends to fail -maxparallel = 1 - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-3.1.0-kind.patch b/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-3.1.0-kind.patch deleted file mode 100644 index c808bc39de9..00000000000 --- a/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-3.1.0-kind.patch +++ /dev/null @@ -1,41 +0,0 @@ -# Fix kind of arguments used in iand -# S.D. Pinches, 30.08.2020 -diff -Nru g2lib-3.1.0-orig/intmath.f g2lib-3.1.0/intmath.f ---- g2lib-3.1.0-orig/intmath.f 2017-06-12 21:38:08.000000000 +0200 -+++ g2lib-3.1.0/intmath.f 2020-08-30 18:24:35.724869000 +0200 -@@ -84,7 +84,7 @@ - ilog2_8=0 - i=i_in - if(i<=0) return -- if(iand(i,i-1)/=0) then -+ if(iand(i,i-1_8)/=0) then - !write(0,*) 'iand i-1' - ilog2_8=1 - endif -@@ -129,7 +129,7 @@ - ilog2_4=0 - i=i_in - if(i<=0) return -- if(iand(i,i-1)/=0) then -+ if(iand(i,i-1_4)/=0) then - !write(0,*) 'iand i-1' - ilog2_4=1 - endif -@@ -169,7 +169,7 @@ - ilog2_2=0 - i=i_in - if(i<=0) return -- if(iand(i,i-1)/=0) then -+ if(iand(i,i-1_2)/=0) then - !write(0,*) 'iand i-1' - ilog2_2=1 - endif -@@ -204,7 +204,7 @@ - ilog2_1=0 - i=i_in - if(i<=0) return -- if(iand(i,i-1)/=0) then -+ if(iand(i,i-1_1)/=0) then - !write(0,*) 'iand i-1' - ilog2_1=1 - endif diff --git a/easybuild/easyconfigs/__archive__/g/gc/gc-7.6.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/gc/gc-7.6.12-GCCcore-9.3.0.eb deleted file mode 100644 index f03036ca4e2..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gc/gc-7.6.12-GCCcore-9.3.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gc' -version = '7.6.12' -local_libatomic_version = '7.6.10' - -homepage = 'https://hboehm.info/gc/' - -description = """ - The Boehm-Demers-Weiser conservative garbage collector can be used as a - garbage collecting replacement for C malloc or C++ new. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [ - 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz - 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz - 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, -] -sources = [ - SOURCE_TAR_GZ, - 'libatomic_ops-%s.tar.gz' % local_libatomic_version, -] -checksums = [ - '6cafac0d9365c2f8604f930aabd471145ac46ab6f771e835e57995964e845082', # gc-7.6.12.tar.gz - '587edf60817f56daf1e1ab38a4b3c729b8e846ff67b4f62a6157183708f099af', # libatomic_ops-7.6.10.tar.gz -] - -builddependencies = [ - ('binutils', '2.34'), -] - -preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' - -sanity_check_paths = { - 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, - 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], - 'dirs': ['include/gc', 'share'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/gcccuda/gcccuda-2020a.eb b/easybuild/easyconfigs/__archive__/g/gcccuda/gcccuda-2020a.eb deleted file mode 100644 index c8488c1a27a..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gcccuda/gcccuda-2020a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = "Toolchain" - -name = 'gcccuda' -version = '2020a' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" - -toolchain = SYSTEM - -local_gcc_version = '9.3.0' - -# compiler toolchain dependencies -dependencies = [ - ('GCC', local_gcc_version), - ('CUDA', '11.0.2', '', ('GCC', local_gcc_version)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/g/gdbm/gdbm-1.18.1-foss-2020a.eb b/easybuild/easyconfigs/__archive__/g/gdbm/gdbm-1.18.1-foss-2020a.eb deleted file mode 100644 index ed1e50db570..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gdbm/gdbm-1.18.1-foss-2020a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gdbm' -version = '1.18.1' - -homepage = 'https://www.gnu.org.ua/software/gdbm/' -description = """GNU dbm (or GDBM, for short) is a library of -database functions that use extensible hashing and work similar to the standard UNIX dbm. -These routines are provided to a programmer needing to create and manipulate a hashed database.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://ftp.gnu.org/gnu/gdbm'] -sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['86e613527e5dba544e73208f42b78b7c022d4fa5a6d5498bf18c8d6f745b91dc'] - -dependencies = [] - -sanity_check_paths = { - 'files': [ - 'bin/gdbm_load', 'bin/gdbmtool', - 'lib/libgdbm.a', 'lib/libgdbm.%s' % SHLIB_EXT, - ], - 'dirs': [] -} - -sanity_check_commands = ['gdbmtool --help'] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/gengetopt/gengetopt-2.23-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/gengetopt/gengetopt-2.23-GCCcore-9.3.0.eb deleted file mode 100644 index 6d7bd73ae1b..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gengetopt/gengetopt-2.23-GCCcore-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gengetopt' -version = '2.23' - -homepage = 'https://www.gnu.org/software/gengetopt/gengetopt.html' -description = "Gengetopt is a tool to write command line option parsing code for C programs." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_XZ] -checksums = ['b941aec9011864978dd7fdeb052b1943535824169d2aa2b0e7eae9ab807584ac'] - -builddependencies = [ - ('binutils', '2.34'), - ('texinfo', '6.7'), # provides makeinfo -] - -sanity_check_paths = { - 'files': ['bin/gengetopt'], - 'dirs': ['share'], -} - -sanity_check_commands = ["gengetopt --help"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/geocube/geocube-0.0.14-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/geocube/geocube-0.0.14-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 59dde6b6a15..00000000000 --- a/easybuild/easyconfigs/__archive__/g/geocube/geocube-0.0.14-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'geocube' -version = '0.0.14' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://corteva.github.io/geocube/latest/' -description = "Tool to convert geopandas vector data into rasterized xarray data." - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6e3819fdf5f6bec45296c3eb3e852b89e42569a6119de9feb01e3e9816e59c1a'] - -dependencies = [ - ('Python', '3.8.2'), - ('Open-Data-Cube-Core', '1.8.3', versionsuffix), - ('geopandas', '0.8.1', versionsuffix), - ('rioxarray', '0.1.1', versionsuffix), -] - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/geopandas/geopandas-0.8.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/geopandas/geopandas-0.8.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 997f9454160..00000000000 --- a/easybuild/easyconfigs/__archive__/g/geopandas/geopandas-0.8.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'geopandas' -version = '0.8.1' -versionsuffix = "-Python-%(pyver)s" - -homepage = 'https://github.com/geopandas/geopandas' -description = """GeoPandas is a project to add support for geographic data to pandas objects. -It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series -and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and -perform geometric operations.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Shapely', '1.7.1', versionsuffix), - ('Fiona', '1.8.16', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('networkx', '2.4', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('pyproj', '2.6.1.post1', versionsuffix), -] - -exts_list = [ - ('descartes', '1.1.0', { - 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('Deprecated', '1.2.10', { - 'checksums': ['525ba66fb5f90b07169fdd48b6373c18f1ee12728ca277ca44567a367d9d7f74'], - }), - ('mapclassify', '2.3.0', { - 'checksums': ['bfe1ec96afe7f866560d25f9f00e5c4dae97d5b69dfe758dbe02c4993261365b'], - }), - (name, version, { - 'checksums': ['e28a729e44ac53c1891b54b1aca60e3bc0bb9e88ad0f2be8e301a03b9510f6e2'], - }), -] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb deleted file mode 100644 index 1ecd5f36852..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gettext' -version = '0.20.1' - -homepage = 'https://www.gnu.org/software/gettext/' -description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may -build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools -and documentation""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['66415634c6e8c3fa8b71362879ec7575e27da43da562c798a8a2f223e6e47f5c'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('libxml2', '2.9.10'), - ('ncurses', '6.2'), -] - -configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' - -sanity_check_paths = { - 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, - 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -sanity_check_commands = [ - "gettext --help", - "msginit --help", -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/gffread/gffread-0.11.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/gffread/gffread-0.11.6-GCCcore-9.3.0.eb deleted file mode 100644 index 3343d6f2de1..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gffread/gffread-0.11.6-GCCcore-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -easyblock = 'MakeCp' - -name = 'gffread' -version = '0.11.6' - -homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' -description = """GFF/GTF parsing utility providing format conversions, -region filtering, FASTA sequence extraction and more.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://ccb.jhu.edu/software/stringtie/dl/'] -sources = [SOURCE_TAR_GZ] -checksums = ['05841bfa0ad6eade333ee5fe153197ab74cf300e80d43c255e480f6b1d5da1ab'] - -builddependencies = [('binutils', '2.34')] - -buildopts = " release" - -files_to_copy = ['%(name)s', 'LICENSE'] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['%(name)s'], - 'dirs': [] -} - -sanity_check_commands = ['%(name)s '] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb deleted file mode 100644 index d3d4062b124..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'gflags' -version = '2.2.2' - -homepage = 'https://github.com/gflags/gflags' -description = """ -The gflags package contains a C++ library that implements commandline flags -processing. It includes built-in support for standard types such as string -and the ability to define flags in the source file in which they are used. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/gflags/gflags/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' - -sanity_check_paths = { - 'files': ['bin/gflags_completions.sh'] + - ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, - 'libgflags.a', 'libgflags_nothreads.a']] + - ['include/gflags/gflags_completions.h'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/g/giflib/giflib-5.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/giflib/giflib-5.2.1-GCCcore-9.3.0.eb deleted file mode 100644 index 68cf86e8ce3..00000000000 --- a/easybuild/easyconfigs/__archive__/g/giflib/giflib-5.2.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'giflib' -version = '5.2.1' - -homepage = 'http://giflib.sourceforge.net/' -description = """giflib is a library for reading and writing gif images. -It is API and ABI compatible with libungif which was in wide use while -the LZW compression algorithm was patented.""" - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [('binutils', '2.34')] - -skipsteps = ['configure'] - -installopts = 'PREFIX=%(installdir)s' - -sanity_check_paths = { - 'files': ['bin/giftool'], - 'dirs': [] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/g/git/git-2.23.0-GCCcore-9.3.0-nodocs.eb b/easybuild/easyconfigs/__archive__/g/git/git-2.23.0-GCCcore-9.3.0-nodocs.eb deleted file mode 100644 index 1c64da82489..00000000000 --- a/easybuild/easyconfigs/__archive__/g/git/git-2.23.0-GCCcore-9.3.0-nodocs.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'git' -version = '2.23.0' -versionsuffix = '-nodocs' - -homepage = 'https://git-scm.com/' -description = """Git is a free and open source distributed version control system designed -to handle everything from small to very large projects with speed and efficiency.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/git/git/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['7d84f5d6f48e95b467a04a8aa1d474e0d21abc7877998af945568d2634fea46a'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), -] - -dependencies = [ - ('cURL', '7.69.1'), - ('expat', '2.2.9'), - ('gettext', '0.20.1'), - ('Perl', '5.30.2'), -] - -preconfigopts = 'make configure && ' - -# Work around git build system bug. If LIBS contains -lpthread, then configure -# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" - -sanity_check_paths = { - 'files': ['bin/git'], - 'dirs': ['libexec/git-core', 'share'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/glew/glew-2.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/glew/glew-2.1.0-GCCcore-9.3.0.eb deleted file mode 100644 index a0965a5fb11..00000000000 --- a/easybuild/easyconfigs/__archive__/g/glew/glew-2.1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# Contribution from the Crick HPC team -# uploaded by J. Sassmannshausen - -easyblock = 'ConfigureMake' - -name = 'glew' -version = '2.1.0' - -homepage = 'http://glew.sourceforge.net/' -description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source -C/C++ extension loading library. GLEW provides efficient run-time mechanisms -for determining which OpenGL extensions are supported on the target platform.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s-%(version)s.tgz'] -checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('Mesa', '20.0.2')] - -skipsteps = ['configure'] - -preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' -install_cmd = 'make install.all' - -sanity_check_paths = { - 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + - ['bin/glewinfo', 'bin/visualinfo'] + - ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], - 'dirs': ['', ] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/g/glog/glog-0.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/glog/glog-0.4.0-GCCcore-9.3.0.eb deleted file mode 100644 index cab2d201006..00000000000 --- a/easybuild/easyconfigs/__archive__/g/glog/glog-0.4.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'glog' -version = '0.4.0' - -homepage = 'https://github.com/google/glog' -description = "A C++ implementation of the Google logging module." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/google/glog/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['f28359aeba12f30d73d9e4711ef356dc842886968112162bc73002645139c39c'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -dependencies = [ - ('gflags', '2.2.2'), - ('libunwind', '1.3.1'), -] - -configopts = '-DBUILD_SHARED_LIBS=ON ' - -sanity_check_paths = { - 'files': ['include/glog/logging.h', 'include/glog/raw_logging.h', 'lib/libglog.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/g/gmpy2/gmpy2-2.1.0b5-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/gmpy2/gmpy2-2.1.0b5-GCC-9.3.0.eb deleted file mode 100644 index 827dfedd402..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gmpy2/gmpy2-2.1.0b5-GCC-9.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'gmpy2' -version = '2.1.0b5' - -homepage = 'https://github.com/aleaxit/gmpy' -description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['8951bcfc61c0f40102b92a4777daf9eb85445b537c4d09086deb0e097190bef0'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [ - ('GMP', '6.2.0'), - ('MPFR', '4.0.2'), - ('MPC', '1.1.0'), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/gmsh/gmsh-4.7.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/gmsh/gmsh-4.7.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 1cd483b4e7d..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gmsh/gmsh-4.7.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'gmsh' -version = '4.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://gmsh.info/' -description = """Gmsh is a 3D finite element grid generator with a built-in CAD engine and post-processor.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {"usempi": True} - -source_urls = ['https://gmsh.info/src/'] -sources = ['%(name)s-%(version)s-source.tgz'] -checksums = ['c984c295116c757ed165d77149bd5fdd1068cbd7835e9bcd077358b503891c6a'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('SWIG', '4.0.1'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('PETSc', '3.12.4', versionsuffix), - ('SLEPc', '3.12.2', versionsuffix), -] - -separate_build_dir = True - -configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1 ' -configopts += '-DENABLE_BUILD_LIB=ON -DENABLE_BUILD_SHARED=ON -DENABLE_BUILD_DYNAMIC=ON' - -modextrapaths = {'PYTHONPATH': ['lib64']} - -sanity_check_paths = { - 'files': ['bin/gmsh', 'lib64/gmsh.py', 'lib64/libgmsh.a', 'lib64/libgmsh.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/gmsh/gmsh-4.7.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/g/gmsh/gmsh-4.7.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 59cec494ae4..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gmsh/gmsh-4.7.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'gmsh' -version = '4.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://gmsh.info/' -description = """Gmsh is a 3D finite element grid generator with a built-in CAD engine and post-processor.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {"usempi": True} - -source_urls = ['https://gmsh.info/src/'] -sources = ['%(name)s-%(version)s-source.tgz'] -checksums = ['c984c295116c757ed165d77149bd5fdd1068cbd7835e9bcd077358b503891c6a'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('SWIG', '4.0.1'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('PETSc', '3.12.4', versionsuffix), - ('SLEPc', '3.12.2', versionsuffix), -] - -separate_build_dir = True - -configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1 ' -configopts += '-DENABLE_BUILD_LIB=ON -DENABLE_BUILD_SHARED=ON -DENABLE_BUILD_DYNAMIC=ON' - -modextrapaths = {'PYTHONPATH': ['lib64']} - -sanity_check_paths = { - 'files': ['bin/gmsh', 'lib64/gmsh.py', 'lib64/libgmsh.a', 'lib64/libgmsh.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-5.2.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-5.2.8-GCCcore-9.3.0.eb deleted file mode 100644 index a9826b3c2b0..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-5.2.8-GCCcore-9.3.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html -## -easyblock = 'ConfigureMake' - -name = 'gnuplot' -version = '5.2.8' - -homepage = 'http://gnuplot.sourceforge.net/' -description = """Portable interactive, function plotting utility""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] -sources = [SOURCE_TAR_GZ] -checksums = ['60a6764ccf404a1668c140f11cc1f699290ab70daa1151bb58fed6139a28ac37'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), - ('Autotools', '20180311'), -] - -dependencies = [ - ('ncurses', '6.2'), - ('cairo', '1.16.0'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('libgd', '2.3.0'), - ('Pango', '1.44.7'), - ('libcerf', '1.13'), - ('X11', '20200222'), - ('Qt5', '5.14.1'), - ('Lua', '5.3.5'), -] - -preconfigopts = 'autoreconf && ' - -configopts = '--with-qt=qt5 --without-latex ' - -sanity_check_paths = { - 'files': ['bin/gnuplot'], - 'dirs': [] -} -# make sure that pdf terminal type is available -sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/g/golf/golf-2020a.eb b/easybuild/easyconfigs/__archive__/g/golf/golf-2020a.eb deleted file mode 100644 index ae255e41a5d..00000000000 --- a/easybuild/easyconfigs/__archive__/g/golf/golf-2020a.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'Toolchain' - -name = 'golf' -version = '2020a' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, including - OpenBLAS (BLAS and LAPACK support) and FFTW.""" - -toolchain = SYSTEM - -local_gccver = '9.3.0' - -dependencies = [ - ('GCC', local_gccver), - ('OpenBLAS', '0.3.9', '', ('GCC', local_gccver)), - ('FFTW', '3.3.8', '-serial', ('GCC', local_gccver)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/g/gomkl/gomkl-2020a.eb b/easybuild/easyconfigs/__archive__/g/gomkl/gomkl-2020a.eb deleted file mode 100644 index 8ebab529cfb..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gomkl/gomkl-2020a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = "Toolchain" - -name = 'gomkl' -version = '2020a' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" - -toolchain = SYSTEM - -local_comp = ('GCC', '9.3.0') - -dependencies = [ - local_comp, - ('OpenMPI', '4.0.3', '', local_comp), - ('imkl', '2020.1.217', '', ('gompi', version)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/g/gompi/gompi-2020a.eb b/easybuild/easyconfigs/__archive__/g/gompi/gompi-2020a.eb deleted file mode 100644 index 15ee0f5a7cc..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gompi/gompi-2020a.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = "Toolchain" - -name = 'gompi' -version = '2020a' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, - including OpenMPI for MPI support.""" - -toolchain = SYSTEM - -local_gccver = '9.3.0' - -# compiler toolchain dependencies -dependencies = [ - ('GCC', local_gccver), # includes both GCC and binutils - ('OpenMPI', '4.0.3', '', ('GCC', local_gccver)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/g/gompic/gompic-2020a.eb b/easybuild/easyconfigs/__archive__/g/gompic/gompic-2020a.eb deleted file mode 100644 index a44a4fa4cb2..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gompic/gompic-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = "Toolchain" - -name = 'gompic' -version = '2020a' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, - including OpenMPI for MPI support with CUDA features enabled.""" - -toolchain = SYSTEM - -local_gccver = '9.3.0' - -# compiler toolchain dependencies -dependencies = [ - ('GCC', local_gccver), # part of gcccuda - ('CUDA', '11.0.2', '', ('GCC', local_gccver)), # part of gcccuda - ('OpenMPI', '4.0.3', '', ('gcccuda', version)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/g/googletest/googletest-1.10.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/googletest/googletest-1.10.0-GCCcore-9.3.0.eb deleted file mode 100644 index 18cacbd5270..00000000000 --- a/easybuild/easyconfigs/__archive__/g/googletest/googletest-1.10.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'googletest' -version = '1.10.0' - -homepage = 'https://github.com/google/googletest' -description = "Google's framework for writing C++ tests on a variety of platforms" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/google/googletest/archive/'] -sources = ['release-%(version)s.tar.gz'] -checksums = ['9dc9157a9a1551ec7a7e43daea9a694a0bb5fb8bec81235d8a1e6ef64c716dcb'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] -# build twice, once for static, once for shared libraries -configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] -separate_build_dir = True - -sanity_check_paths = { - 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] - for local_ext in ['a', SHLIB_EXT]], - 'dirs': ['include/gmock', 'include/gtest'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/gperf/gperf-3.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/gperf/gperf-3.1-GCCcore-9.3.0.eb deleted file mode 100644 index 8f058bba931..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gperf/gperf-3.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gperf' -version = '3.1' - -homepage = 'https://www.gnu.org/software/gperf/' - -description = """ - GNU gperf is a perfect hash function generator. For a given list of strings, - it produces a hash function and hash table, in form of C or C++ code, for - looking up a value depending on the input string. The hash function is - perfect, which means that the hash table has no collisions, and the hash - table lookup needs a single string comparison only. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/gperf'], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/g/gperftools/gperftools-2.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/gperftools/gperftools-2.8-GCCcore-9.3.0.eb deleted file mode 100644 index aea9da26672..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gperftools/gperftools-2.8-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gperftools' -version = '2.8' - -homepage = 'https://github.com/gperftools/gperftools' -description = """ -gperftools is a collection of a high-performance multi-threaded malloc() -implementation, plus some pretty nifty performance analysis tools. -Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'gperftools' -source_urls = [GITHUB_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['b09193adedcc679df2387042324d0d54b93d35d062ea9bff0340f342a709e860'] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), -] - -dependencies = [ - ('libunwind', '1.3.1'), -] - -preconfigopts = "autoreconf -f -i && " -configopts = '--enable-libunwind' - -sanity_check_paths = { - 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, - 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-FCC-4.5.0.eb deleted file mode 100644 index 454055a271d..00000000000 --- a/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-FCC-4.5.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'ConfigureMake' - -name = 'groff' -version = '1.22.4' - -homepage = 'https://www.gnu.org/software/groff' -description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands - and produces formatted output.""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -source_urls = ['https://ftp.gnu.org/gnu/groff'] -sources = [SOURCE_TAR_GZ] -checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] - -builddependencies = [ - ('binutils', '2.36.1'), - ('makeinfo', '6.7'), -] - -sanity_check_paths = { - 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], - 'dirs': ['lib/groff', 'share'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-GCCcore-9.3.0.eb deleted file mode 100644 index dbcd9eff63f..00000000000 --- a/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'groff' -version = '1.22.4' - -homepage = 'https://www.gnu.org/software/groff' -description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands - and produces formatted output.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://ftp.gnu.org/gnu/groff'] -sources = [SOURCE_TAR_GZ] -checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] - -builddependencies = [ - ('binutils', '2.34'), - ('makeinfo', '6.7', '-minimal'), -] - -sanity_check_paths = { - 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], - 'dirs': ['lib/groff', 'share'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.10-GCCcore-9.3.0.eb deleted file mode 100644 index 162b41ce551..00000000000 --- a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.10-GCCcore-9.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gzip' -version = '1.10' - -homepage = 'https://www.gnu.org/software/gzip/' -description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['c91f74430bf7bc20402e1f657d0b252cb80aa66ba333a25704512af346633c68'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], - 'dirs': [], -} - -sanity_check_commands = [True, ('gzip', '--version')] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb deleted file mode 100644 index 7e6b5eefbe8..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb +++ /dev/null @@ -1,61 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'HDF' -version = '4.2.15' - -homepage = 'https://support.hdfgroup.org/products/hdf4/' - -description = """ - HDF (also known as HDF4) is a library and multi-object file format for - storing and managing data between machines. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['HDF-4.2.15_fix-aarch64.patch'] -checksums = [ - 'dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459', # hdf-4.2.15.tar.gz - '1b4341e309cccefc6ea4310c8f8b08cc3dfe1fa9609b7fa7aee80e4dac598473', # HDF-4.2.15_fix-aarch64.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('Bison', '3.5.3'), - ('flex', '2.6.4'), -] - -dependencies = [ - ('libjpeg-turbo', '2.0.4'), - ('Szip', '2.1.1'), - ('zlib', '1.2.11'), - ('libtirpc', '1.2.6'), -] - -preconfigopts = "LIBS='-ltirpc' " -local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' -local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' -configopts = [ - local_common_configopts, - # Cannot build shared libraries and Fortran... - # https://trac.osgeo.org/gdal/wiki/HDF#IncompatibilitywithNetCDFLibraries - # netcdf must be disabled to allow HDF to be used by GDAL - local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", -] - -modextrapaths = {'CPATH': 'include/hdf'} - -sanity_check_paths = { - 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', - 'lib/libmfhdf.%s' % SHLIB_EXT], - 'dirs': ['include/hdf'], -} - -sanity_check_commands = [ - "h4cc --help", - "ncdump -V", -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-gompi-2020a.eb deleted file mode 100644 index 270b74dd8d1..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-gompi-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HDF5' -version = '1.10.6' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa'] - -dependencies = [ - ('zlib', '1.2.11'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-gompic-2020a.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-gompic-2020a.eb deleted file mode 100644 index f4d0af166f7..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-gompic-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HDF5' -version = '1.10.6' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'gompic', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa'] - -dependencies = [ - ('zlib', '1.2.11'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-iimpi-2020a.eb deleted file mode 100644 index 0555d93603c..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-iimpi-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HDF5' -version = '1.10.6' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa'] - -dependencies = [ - ('zlib', '1.2.11'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-iimpic-2020a.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-iimpic-2020a.eb deleted file mode 100644 index 07d6cc4ac79..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-iimpic-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HDF5' -version = '1.10.6' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'iimpic', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa'] - -dependencies = [ - ('zlib', '1.2.11'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-iompi-2020a.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-iompi-2020a.eb deleted file mode 100644 index ddde88aa068..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.10.6-iompi-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HDF5' -version = '1.10.6' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'iompi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa'] - -dependencies = [ - ('zlib', '1.2.11'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.12.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.12.0-gompi-2020a.eb deleted file mode 100644 index d03032ba3d1..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.12.0-gompi-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HDF5' -version = '1.12.0' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['a62dcb276658cb78e6795dd29bf926ed7a9bc4edf6e77025cd2c689a8f97c17a'] - -dependencies = [ - ('zlib', '1.2.11'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.12.0-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.12.0-iimpi-2020a.eb deleted file mode 100644 index e7c9aa79e88..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.12.0-iimpi-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HDF5' -version = '1.12.0' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['a62dcb276658cb78e6795dd29bf926ed7a9bc4edf6e77025cd2c689a8f97c17a'] - -dependencies = [ - ('zlib', '1.2.11'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-3.3.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-3.3.0-foss-2020a.eb deleted file mode 100644 index ae6973dd4ee..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-3.3.0-foss-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -## -# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = 'CMakeMake' - -name = "HH-suite" -version = "3.3.0" - -homepage = 'https://github.com/soedinglab/hh-suite' -description = """HH-suite is an open-source software package for sensitive protein sequence searching. - It contains programs that can search for similar protein sequences in protein sequence databases.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True} - -source_urls = ["https://github.com/soedinglab/hh-suite/archive"] -sources = ["v%(version)s.tar.gz"] -checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('libpng', '1.6.37'), -] - -sanity_check_paths = { - 'files': ["bin/hhalign", "bin/hhblits", "bin/hhconsensus", "bin/hhfilter", "bin/hhmake", "bin/hhsearch"], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HISAT2/HISAT2-2.2.1-foss-2020a.eb b/easybuild/easyconfigs/__archive__/h/HISAT2/HISAT2-2.2.1-foss-2020a.eb deleted file mode 100644 index 6061ecdaa0b..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HISAT2/HISAT2-2.2.1-foss-2020a.eb +++ /dev/null @@ -1,50 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: GPLv3.0 -# -# Notes:: -# 2.2.1 - changes from Adam Huffman -## - -easyblock = 'MakeCp' - -name = 'HISAT2' -version = '2.2.1' - -homepage = 'https://ccb.jhu.edu/software/%(namelower)s/index.shtml' -description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads - (both DNA and RNA) against the general human population (as well as against a single reference genome).""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [{ - 'source_urls': ['https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi'], - 'download_filename': 'download', - 'filename': '%(namelower)s-%(version)s-source.zip', -}] -checksums = ['48e933330d4d8470d2b3dfe7ec3918f2e98a75f7381891e23b7df1fb4f135eb1'] - -dependencies = [ - ('NGS', '2.10.5'), - ('ncbi-vdb', '2.10.7'), -] - -buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' -buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" - -local_executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', - 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l', 'hisat2-repeat', 'extract_exons.py', - 'extract_splice_sites.py', 'hisat2_extract_exons.py', 'hisat2_extract_snps_haplotypes_UCSC.py', - 'hisat2_extract_snps_haplotypes_VCF.py', 'hisat2_extract_splice_sites.py', - 'hisat2_read_statistics.py', 'hisat2_simulate_reads.py'] -files_to_copy = [(local_executables, 'bin'), 'scripts', 'example'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_executables], - 'dirs': ['scripts', 'example'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.1-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.1-gompi-2020a.eb deleted file mode 100644 index 874c88e4871..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.1-gompi-2020a.eb +++ /dev/null @@ -1,68 +0,0 @@ -## -# EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Nils Christian , -# Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a -# component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = 'ConfigureMake' - -name = 'HMMER' -version = '3.3.1' - -homepage = 'http://hmmer.org/' -description = """HMMER is used for searching sequence databases for homologs - of protein sequences, and for making protein sequence alignments. It - implements methods using probabilistic models called profile hidden Markov - models (profile HMMs). Compared to BLAST, FASTA, and other sequence - alignment and database search tools based on older scoring methodology, - HMMER aims to be significantly more accurate and more able to detect remote - homologs because of the strength of its underlying mathematical models. In the - past, this strength came at significant computational expense, but in the new - HMMER3 project, HMMER is now essentially as fast as BLAST.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = [ - 'http://eddylab.org/software/hmmer/', - 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', -] -sources = ['hmmer-%(version)s.tar.gz'] -checksums = ['8ce66a6930869534ad84bc7c9a5a566fd57188d6726c74c12fcd39c3c9c99bd5'] - -builddependencies = [('Python', '3.8.2')] - -configopts = '--enable-mpi' - -runtest = 'check' - -installopts = ' && cd easel && make install' - -local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', - 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', - 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', - 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', - 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', - 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', - 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', - 'nhmmer', 'nhmmscan', 'phmmer'] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in local_bin_files], - 'dirs': ['bin', 'share'], -} - -sanity_check_commands = [ - "esl-construct -h", - "hmmsearch -h", - "nhmmer -h", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb deleted file mode 100644 index c1940bbb311..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb +++ /dev/null @@ -1,68 +0,0 @@ -## -# EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Nils Christian , -# Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a -# component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = 'ConfigureMake' - -name = 'HMMER' -version = '3.3.1' - -homepage = 'http://hmmer.org/' -description = """HMMER is used for searching sequence databases for homologs - of protein sequences, and for making protein sequence alignments. It - implements methods using probabilistic models called profile hidden Markov - models (profile HMMs). Compared to BLAST, FASTA, and other sequence - alignment and database search tools based on older scoring methodology, - HMMER aims to be significantly more accurate and more able to detect remote - homologs because of the strength of its underlying mathematical models. In the - past, this strength came at significant computational expense, but in the new - HMMER3 project, HMMER is now essentially as fast as BLAST.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} - -source_urls = [ - 'http://eddylab.org/software/hmmer/', - 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', -] -sources = ['hmmer-%(version)s.tar.gz'] -checksums = ['8ce66a6930869534ad84bc7c9a5a566fd57188d6726c74c12fcd39c3c9c99bd5'] - -builddependencies = [('Python', '3.8.2')] - -configopts = '--enable-mpi' - -runtest = 'check' - -installopts = ' && cd easel && make install' - -local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', - 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', - 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', - 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', - 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', - 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', - 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', - 'nhmmer', 'nhmmscan', 'phmmer'] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in local_bin_files], - 'dirs': ['bin', 'share'], -} - -sanity_check_commands = [ - "esl-construct -h", - "hmmsearch -h", - "nhmmer -h", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-gompi-2020a.eb deleted file mode 100644 index 587aa80b012..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.3.2-gompi-2020a.eb +++ /dev/null @@ -1,78 +0,0 @@ -## -# EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Nils Christian , -# Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a -# component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = 'ConfigureMake' - -name = 'HMMER' -version = '3.3.2' - -homepage = 'http://hmmer.org/' -description = """HMMER is used for searching sequence databases for homologs - of protein sequences, and for making protein sequence alignments. It - implements methods using probabilistic models called profile hidden Markov - models (profile HMMs). Compared to BLAST, FASTA, and other sequence - alignment and database search tools based on older scoring methodology, - HMMER aims to be significantly more accurate and more able to detect remote - homologs because of the strength of its underlying mathematical models. In the - past, this strength came at significant computational expense, but in the new - HMMER3 project, HMMER is now essentially as fast as BLAST.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = [ - 'http://eddylab.org/software/hmmer/', - 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', -] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_fix_perl.patch'] -checksums = [ - '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz - '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch -] - -builddependencies = [ - ('Python', '3.8.2'), - ('Perl', '5.30.2', '-minimal'), -] - -configopts = '--enable-mpi' - -buildopts = ' V=1 ' - -testopts = buildopts -runtest = 'check' - -installopts = ' && cd easel && make install' - -local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', - 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', - 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', - 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', - 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', - 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', - 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', - 'nhmmer', 'nhmmscan', 'phmmer'] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in local_bin_files], - 'dirs': ['bin', 'share'], -} - -sanity_check_commands = [ - "esl-construct -h", - "hmmsearch -h", - "nhmmer -h", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-Fujitsu-21.05.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-Fujitsu-21.05.eb deleted file mode 100644 index e6a43addd5f..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-Fujitsu-21.05.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HPL' -version = '2.3' - -homepage = 'https://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) - arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available - implementation of the High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'Fujitsu', 'version': '21.05'} -toolchainopts = {'usempi': True, 'openmp': True} - -source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] -sources = [SOURCELOWER_TAR_GZ] -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] -checksums = [ - '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz - '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-foss-2020a.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-foss-2020a.eb deleted file mode 100644 index 975ddeef5a8..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-foss-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HPL' -version = '2.3' - -homepage = 'https://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) - arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available - implementation of the High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] -sources = [SOURCELOWER_TAR_GZ] -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] -checksums = [ - '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz - '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-fosscuda-2020a.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-fosscuda-2020a.eb deleted file mode 100644 index 4ac95fa12be..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-fosscuda-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HPL' -version = '2.3' - -homepage = 'https://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) - arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available - implementation of the High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] -sources = [SOURCELOWER_TAR_GZ] -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] -checksums = [ - '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz - '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intel-2020.06-impi-18.5.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intel-2020.06-impi-18.5.eb deleted file mode 100644 index 1ace61bd4e5..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intel-2020.06-impi-18.5.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HPL' -version = '2.3' - -homepage = 'https://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) - arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available - implementation of the High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'intel', 'version': '2020.06-impi-18.5'} -toolchainopts = {'usempi': True} - -source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] -sources = [SOURCELOWER_TAR_GZ] -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] -checksums = [ - '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz - '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intel-2020a.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intel-2020a.eb deleted file mode 100644 index e671c6be5e7..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intel-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HPL' -version = '2.3' - -homepage = 'https://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) - arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available - implementation of the High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] -sources = [SOURCELOWER_TAR_GZ] -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] -checksums = [ - '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz - '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intelcuda-2020a.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intelcuda-2020a.eb deleted file mode 100644 index cd4ae0ee2bc..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-intelcuda-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HPL' -version = '2.3' - -homepage = 'https://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) - arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available - implementation of the High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'intelcuda', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] -sources = [SOURCELOWER_TAR_GZ] -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] -checksums = [ - '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz - '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.10.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.10.2-GCC-9.3.0.eb deleted file mode 100644 index a8975a53237..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.10.2-GCC-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# 1.4 modified by: -# Adam Huffman, Jonas Demeulemeester -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'HTSlib' -version = '1.10.2' - -homepage = "https://www.htslib.org/" -description = """A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['e3b543de2f71723830a1e0472cf5489ec27d0fbeb46b1103e14a11b7177d1939'] - -# cURL added for S3 support -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('cURL', '7.69.1'), -] - -sanity_check_paths = { - 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.12-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.12-GCC-9.3.0.eb deleted file mode 100644 index c066440f568..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HTSlib/HTSlib-1.12-GCC-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# 1.4 modified by: -# Adam Huffman, Jonas Demeulemeester -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'HTSlib' -version = '1.12' - -homepage = "https://www.htslib.org/" -description = """A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['2280141b46e953ba4ae01b98335a84f8e6ccbdb6d5cdbab7f70ee4f7e3b6f4ca'] - -# cURL added for S3 support -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('cURL', '7.69.1'), -] - -sanity_check_paths = { - 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/HarfBuzz/HarfBuzz-2.6.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/h/HarfBuzz/HarfBuzz-2.6.4-GCCcore-9.3.0.eb deleted file mode 100644 index a44c15f6bd1..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HarfBuzz/HarfBuzz-2.6.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'HarfBuzz' -version = '2.6.4' - -homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' -description = """HarfBuzz is an OpenType text shaping engine.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['9413b8d96132d699687ef914ebb8c50440efc87b3f775d25856d7ec347c03c12'] - -builddependencies = [ - ('binutils', '2.34'), - ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('GLib', '2.64.1'), - ('ICU', '66.1'), - ('cairo', '1.16.0'), - ('freetype', '2.10.1'), -] - -configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " - -sanity_check_paths = { - 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], - 'dirs': [] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/h/Harminv/Harminv-1.4.1-intel-2020a.eb b/easybuild/easyconfigs/__archive__/h/Harminv/Harminv-1.4.1-intel-2020a.eb deleted file mode 100644 index f65da482983..00000000000 --- a/easybuild/easyconfigs/__archive__/h/Harminv/Harminv-1.4.1-intel-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Harminv' -version = '1.4.1' - -homepage = 'https://github.com/stevengj/harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially - decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those - sinusoids.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} - -source_urls = ['https://github.com/stevengj/harminv/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e1b923c508a565f230aac04e3feea23b888b47d8e19b08816a97ee4444233670'] - -configopts = "--with-pic --with-blas=mkl_em64t --with-lapack=mkl_em64t --enable-shared" - -sanity_check_paths = { - 'files': ['bin/harminv', 'lib/libharminv.a', 'lib/libharminv.%s' % SHLIB_EXT], - 'dirs': ['include'] -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/h/HeFFTe/HeFFTe-1.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/h/HeFFTe/HeFFTe-1.0-foss-2020a.eb deleted file mode 100644 index a843130f7b5..00000000000 --- a/easybuild/easyconfigs/__archive__/h/HeFFTe/HeFFTe-1.0-foss-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'HeFFTe' -version = '1.0' - -homepage = 'https://icl.utk.edu/fft' -description = "Highly Efficient FFT for Exascale (HeFFTe) library" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://bitbucket.org/icl/heffte/get/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['0902479fb5b1bad01438ca0a72efd577a3529c3d8bad0028f3c18d3a4935ca74'] - -builddependencies = [('CMake', '3.16.4')] - -build_shared_libs = True - -configopts = "-DHeffte_ENABLE_FFTW=ON -DFFTW_ROOT=$EBROOTFFTW -DHeffte_ENABLE_CUDA=OFF -DHeffte_ENABLE_MKL=OFF" - -sanity_check_paths = { - 'files': ['lib/libheffte.%s' % SHLIB_EXT], - 'dirs': ['include', 'lib/cmake/Heffte', 'share/heffte/examples'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.3-foss-2020a-TensorFlow-2.3.1-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.3-foss-2020a-TensorFlow-2.3.1-Python-3.8.2.eb deleted file mode 100644 index d713fb9b6e0..00000000000 --- a/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.3-foss-2020a-TensorFlow-2.3.1-Python-3.8.2.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Horovod' -version = '0.21.3' -local_tf_version = '2.3.1' -versionsuffix = '-TensorFlow-{}-Python-%(pyver)s'.format(local_tf_version) - -homepage = 'https://github.com/uber/horovod' -description = "Horovod is a distributed training framework for TensorFlow." - -toolchain = {'name': 'foss', 'version': '2020a'} - -builddependencies = [ - ('CMake', '3.16.4'), - ('flatbuffers', '1.12.0'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), -] - -preinstallopts = 'HOROVOD_WITH_MPI=1 ' -preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' - -exts_list = [ - ('cloudpickle', '1.6.0', { - 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], - }), - ('horovod', version, { - 'checksums': ['dee8b2387b1ec9f54fe1737a95b992a52ce20cb3f1a4388017215fae14978f95'], - }), -] - -sanity_check_paths = { - 'files': ['bin/horovodrun'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.3-fosscuda-2020a-TensorFlow-2.3.1-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.3-fosscuda-2020a-TensorFlow-2.3.1-Python-3.8.2.eb deleted file mode 100644 index 3e0922f4ada..00000000000 --- a/easybuild/easyconfigs/__archive__/h/Horovod/Horovod-0.21.3-fosscuda-2020a-TensorFlow-2.3.1-Python-3.8.2.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Horovod' -version = '0.21.3' -local_tf_version = '2.3.1' -versionsuffix = '-TensorFlow-{}-Python-%(pyver)s'.format(local_tf_version) - -homepage = 'https://github.com/uber/horovod' -description = "Horovod is a distributed training framework for TensorFlow." - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -builddependencies = [ - ('CMake', '3.16.4'), - ('flatbuffers', '1.12.0'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), - ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), -] - -preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_OPERATIONS=NCCL ' -preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' - -maxparallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend - -exts_list = [ - ('cloudpickle', '1.6.0', { - 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], - }), - ('horovod', version, { - 'checksums': ['dee8b2387b1ec9f54fe1737a95b992a52ce20cb3f1a4388017215fae14978f95'], - }), -] - -sanity_check_paths = { - 'files': ['bin/horovodrun'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.18.2-foss-2020a.eb b/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.18.2-foss-2020a.eb deleted file mode 100644 index 6075f4d2c08..00000000000 --- a/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.18.2-foss-2020a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'Hypre' -version = '2.18.2' - -homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' -description = """Hypre is a library for solving large, sparse linear systems of equations on massively - parallel computers. The problems of interest arise in the simulation codes being developed at LLNL - and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/hypre-space/hypre/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['28007b5b584eaf9397f933032d8367788707a2d356d78e47b99e551ab10cc76a'] - -start_dir = 'src' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.18.2-intel-2020a.eb b/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.18.2-intel-2020a.eb deleted file mode 100644 index 3a608227254..00000000000 --- a/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.18.2-intel-2020a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'Hypre' -version = '2.18.2' - -homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' -description = """Hypre is a library for solving large, sparse linear systems of equations on massively - parallel computers. The problems of interest arise in the simulation codes being developed at LLNL - and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/hypre-space/hypre/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['28007b5b584eaf9397f933032d8367788707a2d356d78e47b99e551ab10cc76a'] - -start_dir = 'src' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.21.0_use-c++14-for-nvcc.patch b/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.21.0_use-c++14-for-nvcc.patch deleted file mode 100644 index 7c25fd7f5ca..00000000000 --- a/easybuild/easyconfigs/__archive__/h/Hypre/Hypre-2.21.0_use-c++14-for-nvcc.patch +++ /dev/null @@ -1,13 +0,0 @@ -Change only the CUDA compliation to use c++14 -Patch by Simon Branford (University of Birmingham) ---- src/configure.orig 2021-06-19 12:44:05.690180000 +0100 -+++ src/configure 2021-06-19 12:44:19.303311554 +0100 -@@ -8886,7 +8886,7 @@ - - if test "$hypre_user_chose_cuflags" = "no" - then -- CUFLAGS="-lineinfo -expt-extended-lambda -dc -std=c++11 --x cu" -+ CUFLAGS="-lineinfo -expt-extended-lambda -dc -std=c++14 --x cu" - if test "$hypre_using_debug" = "yes" - then - CUFLAGS="-g -O0 ${CUFLAGS}" diff --git a/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index e5b6606d7a1..00000000000 --- a/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.10.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -sources = [SOURCE_TAR_GZ] -patches = ['h5py-%(version)s_avoid-mpi-init.patch'] -checksums = [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch -] - -builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('HDF5', '1.10.6'), -] - -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 882b4eadad5..00000000000 --- a/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.10.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'usempi': True} - -sources = [SOURCE_TAR_GZ] -patches = ['h5py-%(version)s_avoid-mpi-init.patch'] -checksums = [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch -] - -builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('HDF5', '1.10.6'), -] - -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb deleted file mode 100644 index 09fbf6019b4..00000000000 --- a/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.10.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -sources = [SOURCE_TAR_GZ] -patches = ['h5py-%(version)s_avoid-mpi-init.patch'] -checksums = [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch -] - -dependencies = [ - ('Python', '2.7.18'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('HDF5', '1.10.6'), -] - -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 608b362bad6..00000000000 --- a/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.10.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -sources = [SOURCE_TAR_GZ] -patches = ['h5py-%(version)s_avoid-mpi-init.patch'] -checksums = [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch -] - -builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('HDF5', '1.10.6'), -] - -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-intelcuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-intelcuda-2020a-Python-3.8.2.eb deleted file mode 100644 index df0ef2dd6aa..00000000000 --- a/easybuild/easyconfigs/__archive__/h/h5py/h5py-2.10.0-intelcuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.10.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'intelcuda', 'version': '2020a'} -toolchainopts = {'usempi': True} - -sources = [SOURCE_TAR_GZ] -patches = ['h5py-%(version)s_avoid-mpi-init.patch'] -checksums = [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch -] - -builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('HDF5', '1.10.6'), -] - -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/harmony/harmony-1.0.0-20200224-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/h/harmony/harmony-1.0.0-20200224-foss-2020a-R-4.0.0.eb deleted file mode 100644 index f9a8af0de99..00000000000 --- a/easybuild/easyconfigs/__archive__/h/harmony/harmony-1.0.0-20200224-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'RPackage' - -name = 'harmony' -local_commit = '88b1e2a' -# see DESCRIPTION to determine version, -# but also take date of last commit into account (since version isn't always bumped) -version = '1.0.0-20200224' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://portals.broadinstitute.org/harmony' -description = "Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets." - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/immunogenomics/harmony/archive/'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['8e017d1525b0124ecda1f54fcbf74930d72f20b11b75f5e24443f4e200ee1eab'] - -dependencies = [ - ('R', '4.0.0'), - ('R-bundle-Bioconductor', '3.11', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb deleted file mode 100644 index 77bffeabf8a..00000000000 --- a/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'help2man' -version = '1.47.12' - -homepage = 'https://www.gnu.org/software/help2man/' -description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_XZ] -checksums = ['7d0ba64cf9d16ec97cc11aafb659b55aa7bdec99072ff2aec5fcecf0fbeab160'] - -builddependencies = [ - # use same binutils version that was used when building GCC toolchain - ('binutils', '2.34', '', SYSTEM), -] - -sanity_check_paths = { - 'files': ['bin/help2man'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.48.3-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.48.3-FCC-4.5.0.eb deleted file mode 100644 index 0bfc535fb8e..00000000000 --- a/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.48.3-FCC-4.5.0.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'help2man' -version = '1.48.3' - -homepage = 'https://www.gnu.org/software/help2man/' -description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_XZ] -checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] - -sanity_check_paths = { - 'files': ['bin/help2man'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/hierfstat/hierfstat-0.5-7-foss-2020a-R-4.0.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/h/hierfstat/hierfstat-0.5-7-foss-2020a-R-4.0.0-Python-3.8.2.eb deleted file mode 100644 index 4a17082748d..00000000000 --- a/easybuild/easyconfigs/__archive__/h/hierfstat/hierfstat-0.5-7-foss-2020a-R-4.0.0-Python-3.8.2.eb +++ /dev/null @@ -1,55 +0,0 @@ -easyblock = 'Bundle' - -name = 'hierfstat' -version = '0.5-7' -versionsuffix = '-R-%(rver)s-Python-3.8.2' - -homepage = 'https://cran.r-project.org/package=hierfstat' -description = """Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in -the hierarchy.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('R', '4.0.0'), - ('sf', '0.9-5', versionsuffix), -] - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -exts_list = [ - ('spdep', '1.1-5', { - 'checksums': ['47cb46cf5cf1f4386eb1b5e4d8541d577d7f2939e74addbdb884ecf2323f6d5d'], - }), - ('adegenet', '2.1.3', { - 'checksums': ['0790114ecb22642683b5be1f4b3a6a49856e06dc2f9e21b9cba4390c2257f6c6'], - }), - ('RcppParallel', '5.0.2', { - 'checksums': ['8ca200908c6365aafb2063be1789f0894969adc03c0f523c6cc45434b8236f81'], - }), - ('gaston', '1.5.6', { - 'checksums': ['2f9b8f8d16c20cfa3426b57aabf1d63a9e9ab6e4689f0fec1e8ea6251d8ea6af'], - }), - (name, version, { - 'checksums': ['a38eb5758e3fc3683ec83f94138525eed3d8b7e330f894bab2f821557e98e836'], - }), -] - -modextrapaths = {'R_LIBS_SITE': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/h/hifiasm/hifiasm-0.15.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/h/hifiasm/hifiasm-0.15.2-GCCcore-9.3.0.eb deleted file mode 100644 index 0fff990852e..00000000000 --- a/easybuild/easyconfigs/__archive__/h/hifiasm/hifiasm-0.15.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# Author: Jasper Grimm (UoY) - -easyblock = 'MakeCp' - -name = 'hifiasm' -version = '0.15.2' - -homepage = 'https://github.com/chhylp123/hifiasm' -description = """Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'chhylp123' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['e49e38341d6c943902cebc8b0e517e20a6e919659f3dab2bcc24c062524a72da'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('zlib', '1.2.11')] - -buildopts = 'CC="$CC" CXX="$CXX" CPPFLAGS="$CPPFLAGS"' - -files_to_copy = [ - ([name], 'bin'), - (['*.h'], 'include/hifiasm'), - 'LICENSE', 'README.md', -] - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': [], -} -sanity_check_commands = ["%(name)s -h"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb deleted file mode 100644 index 4e14be74eac..00000000000 --- a/easybuild/easyconfigs/__archive__/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,88 +0,0 @@ -easyblock = 'Bundle' - -name = 'horton' -version = '2.1.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://theochem.github.io/horton' -description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written - primarily in the Python programming language. (HORTON is named after the helpful - pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON - is to provide a platform for testing new ideas on the quantum many-body problem - at a reasonable computational cost. Although HORTON is primarily designed to be - a quantum-chemistry program, it can perform computations involving model - Hamiltonians, and could be extended for computations in nuclear physics.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '2.7.18'), - ('h5py', '2.10.0', versionsuffix), - ('matplotlib', '2.2.5', versionsuffix), -] - -local_horton_prebuildopts = ' '.join([ - 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', - 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', - 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', - 'LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH', -]) - -# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc -local_horton_runtest = ' '.join([ - 'export MPLBACKEND=agg;', - '%s python setup.py build_ext -i; ' % local_horton_prebuildopts, - 'nosetests -v', -]) - -default_component_specs = { - 'sources': [SOURCE_TAR_GZ], - 'start_dir': '%(name)s-%(version)s', -} - -# Horton 2.1.1 requires very specific versions of libxc (2.2.2) and Libint (2.0.3), -# so we install these as components along with Horton itself -components = [ - ('Libint', '2.0.3', { - 'toolchainopts': {'pic': True}, - 'source_urls': ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'], - 'sources': ['libint-%(version)s-stable.tgz'], - 'checksums': ['5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02'], - 'start_dir': 'libint-%(version)s-stable', - 'easyblock': 'EB_Libint', - }), - ('libxc', '2.2.2', { - 'easyblock': 'ConfigureMake', - # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. - # Tests also fail with Intel Compilers on Haswell when optarch is enabled. - 'toolchainopts': {'lowopt': True, 'optarch': False}, - 'source_urls': ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'], - 'checksums': ['6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642'], - 'configopts': 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran', - 'parallel': 1, - 'runtest': 'check', - }), - (name, version, { - 'source_urls': ['https://github.com/theochem/horton/releases/download/%(version)s'], - 'checksums': ['4b3f87920d881030ba80f097326a744de2cfee5316aa4499cc9a6501f64b5060'], - 'easyblock': 'PythonPackage', - 'use_pip': False, - 'prebuildopts': local_horton_prebuildopts, - 'runtest': local_horton_runtest, - }), -] - -fix_python_shebang_for = ['bin/*.py'] - -sanity_check_paths = { - 'files': ['include/xc.h', 'lib/libint2.a', 'lib/libint2.%s' % SHLIB_EXT] + - ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['bin', 'include/horton', 'include/libint2', 'lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "python -c 'import horton'", - "horton-esp-fit.py --version", -] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb deleted file mode 100644 index a4faff0a428..00000000000 --- a/easybuild/easyconfigs/__archive__/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '2.2.0' - -homepage = 'https://www.open-mpi.org/projects/hwloc/' - -description = """ - The Portable Hardware Locality (hwloc) software package provides a portable - abstraction (across OS, versions, architectures, ...) of the hierarchical - topology of modern architectures, including NUMA memory nodes, sockets, shared - caches, cores and simultaneous multithreading. It also gathers various system - attributes such as cache and memory information as well as the locality of I/O - devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily - aims at helping applications with gathering information about modern computing - hardware so as to exploit it accordingly and efficiently. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake -# cfr. https://github.com/open-mpi/hwloc/issues/315 -toolchainopts = {'vectorize': False} - -source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] -checksums = ['2defba03ddd91761b858cbbdc2e3a6e27b44e94696dbfa21380191328485a433'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('numactl', '2.0.13'), - ('libxml2', '2.9.10'), - ('libpciaccess', '0.16'), -] - -configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " - -sanity_check_paths = { - 'files': ['bin/lstopo', 'include/hwloc/linux.h', - 'lib/libhwloc.%s' % SHLIB_EXT], - 'dirs': ['share/man/man3'], -} -sanity_check_commands = ['lstopo'] - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-5.6.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-5.6.0-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index db87c407a3d..00000000000 --- a/easybuild/easyconfigs/__archive__/h/hypothesis/hypothesis-5.6.0-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -easyblock = 'PythonPackage' - -name = 'hypothesis' -version = '5.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://github.com/HypothesisWorks/hypothesis" -description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized - by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets - you find more bugs in your code with less work.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['22fb60bd0c6eb7849121a7df263a91da23b4e8506d3ba9e92ac696d2720ac0f5'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('Python', '3.8.2')] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/ICU/ICU-66.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/i/ICU/ICU-66.1-GCCcore-9.3.0.eb deleted file mode 100644 index 17b26cee098..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ICU/ICU-66.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ICU' -version = '66.1' - -homepage = 'https://icu-project.org/' -description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization - support for software applications.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] -sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] -checksums = ['52a3f2209ab95559c1cf0a14f24338001f389615bf00e2585ef3dbc43ecf0a2e'] - -builddependencies = [ - ('binutils', '2.34'), - ('Python', '3.8.2'), -] - -start_dir = 'source' - -sanity_check_paths = { - 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], - 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/i/IDBA-UD/IDBA-UD-1.1.3-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/i/IDBA-UD/IDBA-UD-1.1.3-GCC-9.3.0.eb deleted file mode 100644 index 4ef50bfe528..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IDBA-UD/IDBA-UD-1.1.3-GCC-9.3.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# Updated: Pavel Grochal (INUITS) -# License: GPLv2 - -# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock -# to be sure everything is copied and we run ./configure in prebuildopts - -# modified by Tom Strempel -easyblock = 'MakeCp' - -name = 'IDBA-UD' -version = '1.1.3' - -homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' -description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads - Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. - IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth - contigs are removed iteratively with cutoff threshold from low to high to reduce the errors - in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled - locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD - can iterate k value of de Bruijn graph to a very large value with less gaps and less branches - to form long contigs in both low-depth and high-depth regions.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] -sources = ['idba-%(version)s.tar.gz'] -checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] - -prebuildopts = './configure && ' - -# we delete every .o and Makefile file which is left in bin folder -buildopts = ' && rm -fr bin/*.o bin/Makefile*' - -files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] - -pretestopts = "cd test && " -runtest = "check" - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", - "idba_ud", "parallel_blat", "idba_tran_test"]], - 'dirs': [""], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/i/ILAMB/ILAMB-2.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/i/ILAMB/ILAMB-2.5-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 996cfc03d61..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ILAMB/ILAMB-2.5-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'ILAMB' -version = '2.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.ilamb.org/' -description = """ -The International Land Model Benchmarking (ILAMB) project is a model-data intercomparison and integration project -designed to improve the performance of land models and, in parallel, improve the design of new measurement campaigns -to reduce uncertainties associated with key land surface processes. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('SciPy-bundle', '2020.03', versionsuffix), - ('sympy', '1.6.2', versionsuffix), - ('netcdf4-python', '1.5.3', versionsuffix), - ('Cartopy', '0.18.0', versionsuffix), - ('UDUNITS', '2.2.26'), # needed for cf-units -] - -exts_list = [ - ('antlr4-python3-runtime', '4.7.2', { - 'modulename': 'antlr4', - 'checksums': ['168cdcec8fb9152e84a87ca6fd261b3d54c8f6358f42ab3b813b14a7193bb50b'], - }), - ('cf-units', '2.1.4', { - 'checksums': ['25f81ad994af30713ee8f5ef18ffddd83c6ec1ac308e1bd89d45de9d2e0f1c31'], - }), - (name, version, { - 'modulename': 'ILAMB', - 'checksums': ['d156ab01a2e895fb6ca0da870d385e8872b434e928061f2b440582fa8eb247a5'], - }), -] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/i/IPM/IPM-2.0.6-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/i/IPM/IPM-2.0.6-gompi-2020a.eb deleted file mode 100644 index 62da3ad2b08..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IPM/IPM-2.0.6-gompi-2020a.eb +++ /dev/null @@ -1,45 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'IPM' -version = '2.0.6' - -homepage = 'https://github.com/nerscadmin/IPM' - -description = """ - IPM is a portable profiling infrastructure for parallel codes. It provides - a low-overhead profile of application performance and resource utilization - in a parallel program. Communication, computation, and IO are the primary - focus. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = [' https://github.com/nerscadmin/%(name)s/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['aee102e2b95627869083ed4df5612264b09335da1a0b9fe034f15241f63778bf'] - -builddependencies = [ - ('Autotools', '20180311'), -] - -dependencies = [ - ('libunwind', '1.3.1'), - ('PAPI', '6.0.0'), -] - -preconfigopts = "./bootstrap.sh && " - -# don't use the provided libtool, but the one provided via Autotools build dep -preconfigopts += "sed -e 's,$(top_builddir)/libtool,$(EBROOTLIBTOOL)/bin/libtool,' -i.eb configure && " - -configopts = '--enable-posixio -with-gnu-ld --with-papi=$EBROOTPAPI --with-libunwind=$EBROOTLIBUNWIND' - -sanity_check_paths = { - 'files': ['bin/ipm_parse', 'etc/ipm_key_mpi', - 'lib/libipm.%s' % SHLIB_EXT, 'lib/libipmf.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/i/IPM/IPM-2.0.6-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/i/IPM/IPM-2.0.6-iimpi-2020a.eb deleted file mode 100644 index 2681c6f1bb5..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IPM/IPM-2.0.6-iimpi-2020a.eb +++ /dev/null @@ -1,45 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'IPM' -version = '2.0.6' - -homepage = 'https://github.com/nerscadmin/IPM' - -description = """ - IPM is a portable profiling infrastructure for parallel codes. It provides - a low-overhead profile of application performance and resource utilization - in a parallel program. Communication, computation, and IO are the primary - focus. -""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} - -source_urls = [' https://github.com/nerscadmin/%(name)s/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['aee102e2b95627869083ed4df5612264b09335da1a0b9fe034f15241f63778bf'] - -builddependencies = [ - ('Autotools', '20180311'), -] - -dependencies = [ - ('libunwind', '1.3.1'), - ('PAPI', '6.0.0'), -] - -preconfigopts = "./bootstrap.sh && " - -# don't use the provided libtool, but the one provided via Autotools build dep -preconfigopts += "sed -e 's,$(top_builddir)/libtool,$(EBROOTLIBTOOL)/bin/libtool,' -i.eb configure && " - -configopts = '--enable-posixio -with-gnu-ld --with-papi=$EBROOTPAPI --with-libunwind=$EBROOTLIBUNWIND' - -sanity_check_paths = { - 'files': ['bin/ipm_parse', 'etc/ipm_key_mpi', - 'lib/libipm.%s' % SHLIB_EXT, 'lib/libipmf.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/i/IPM/IPM-2.0.6-iompi-2020a.eb b/easybuild/easyconfigs/__archive__/i/IPM/IPM-2.0.6-iompi-2020a.eb deleted file mode 100644 index c5015075f1c..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IPM/IPM-2.0.6-iompi-2020a.eb +++ /dev/null @@ -1,45 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'IPM' -version = '2.0.6' - -homepage = 'https://github.com/nerscadmin/IPM' - -description = """ - IPM is a portable profiling infrastructure for parallel codes. It provides - a low-overhead profile of application performance and resource utilization - in a parallel program. Communication, computation, and IO are the primary - focus. -""" - -toolchain = {'name': 'iompi', 'version': '2020a'} - -source_urls = [' https://github.com/nerscadmin/%(name)s/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['aee102e2b95627869083ed4df5612264b09335da1a0b9fe034f15241f63778bf'] - -builddependencies = [ - ('Autotools', '20180311'), -] - -dependencies = [ - ('libunwind', '1.3.1'), - ('PAPI', '6.0.0'), -] - -preconfigopts = "./bootstrap.sh && " - -# don't use the provided libtool, but the one provided via Autotools build dep -preconfigopts += "sed -e 's,$(top_builddir)/libtool,$(EBROOTLIBTOOL)/bin/libtool,' -i.eb configure && " - -configopts = '--enable-posixio -with-gnu-ld --with-papi=$EBROOTPAPI --with-libunwind=$EBROOTLIBUNWIND' - -sanity_check_paths = { - 'files': ['bin/ipm_parse', 'etc/ipm_key_mpi', - 'lib/libipm.%s' % SHLIB_EXT, 'lib/libipmf.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.13.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.13.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index a4d44125d7c..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.13.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,164 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'IPython' -version = '7.13.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://ipython.org/index.html' -description = """IPython provides a rich architecture for interactive computing with: - Powerful interactive shells (terminal and Qt-based). - A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. - Support for interactive data visualization and use of GUI toolkits. - Flexible, embeddable interpreters to load into your own projects. - Easy to use, high performance tools for parallel computing.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('ZeroMQ', '4.3.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('PyYAML', '5.3'), # required for jupyter_nbextensions_configurator -] - -exts_list = [ - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('ipython', version, { - 'modulename': 'IPython', - 'checksums': ['ca478e52ae1f88da0102360e57e528b92f3ae4316aabac80a2cd7f7ab2efb48a'], - }), - ('pexpect', '4.8.0', { - 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], - }), - ('pickleshare', '0.7.5', { - 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], - }), - ('prompt_toolkit', '3.0.4', { - 'checksums': ['ebe6b1b08c888b84c50d7f93dee21a09af39860144ff6130aadbd61ae8d29783'], - }), - ('ptyprocess', '0.6.0', { - 'use_pip': False, - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], - }), - ('simplegeneric', '0.8.1', { - 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], - }), - ('traitlets', '4.3.3', { - 'checksums': ['d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7'], - }), - ('parso', '0.6.2', { - 'checksums': ['0c5659e0c6eba20636f99a04f469798dca8da279645ce5c387315b2c23912157'], - }), - ('jedi', '0.16.0', { - 'checksums': ['d5c871cb9360b414f981e7072c52c33258d598305280fef91c6cae34739d65d5'], - }), - ('testpath', '0.4.4', { - 'use_pip': False, - 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], - }), - ('Send2Trash', '1.5.0', { - 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], - }), - ('webencodings', '0.5.1', { - 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], - }), - ('html5lib', '1.0.1', { - 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], - }), - ('bleach', '3.1.3', { - 'checksums': ['f8dfd8a7e26443e986c4e44df31870da8e906ea61096af06ba5d5cc2d519842a'], - }), - ('vcversioner', '2.16.0.0', { - 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], - }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('pandocfilters', '1.4.2', { - 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], - }), - ('pyzmq', '19.0.0', { - 'modulename': 'zmq', - 'checksums': ['5e1f65e576ab07aed83f444e201d86deb01cd27dcf3f37c727bc8729246a60a8'], - }), - ('entrypoints', '0.3', { - 'use_pip': False, - 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], - }), - ('jupyter_core', '4.6.3', { - 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], - }), - ('nbformat', '5.0.4', { - 'checksums': ['562de41fc7f4f481b79ab5d683279bf3a168858268d4387b489b7b02be0b324a'], - }), - ('mistune', '0.8.4', { - 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], - }), - ('defusedxml', '0.6.0', { - 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], - }), - ('nbconvert', '5.6.1', { - 'checksums': ['21fb48e700b43e82ba0e3142421a659d7739b65568cc832a13976a77be16b523'], - }), - ('terminado', '0.8.3', { - 'use_pip': False, - 'checksums': ['4804a774f802306a7d9af7322193c5390f1da0abb429e082a10ef1d46e6fb2c2'], - }), - ('tornado', '6.0.4', { - 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], - }), - ('jupyter_client', '6.1.0', { - 'checksums': ['61429e7d2c4b385135d31054944dd3f23a1c6affb0ca3d4328d42fc9ba82b7f5'], - }), - ('backcall', '0.1.0', { - 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], - }), - ('ipykernel', '5.2.0', { - 'checksums': ['37c65d2e2da3326e5cf114405df6d47d997b8a3eba99e2cc4b75833bf71a5e18'], - }), - ('prometheus_client', '0.7.1', { - 'checksums': ['71cd24a2b3eb335cb800c7159f423df1bd4dcd5171b234be15e3f31ec9f622da'], - }), - ('pyrsistent', '0.15.7', { - 'checksums': ['cdc7b5e3ed77bed61270a47d35434a30617b9becdf2478af76ad2c6ade307280'], - }), - ('ipywidgets', '7.5.1', { - 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], - }), - ('jupyter_contrib_core', '0.3.3', { - 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], - }), - ('jupyter_nbextensions_configurator', '0.4.1', { - 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], - }), - ('notebook', '6.0.3', { - 'checksums': ['47a9092975c9e7965ada00b9a20f0cf637d001db60d241d479f53c0be117ad48'], - }), - ('widgetsnbextension', '3.5.1', { - 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], - }), - ('ipympl', '0.5.6', { - 'checksums': ['076240e606f4dc1f23b7ecc3303c759f5718dc16f9a119382776c6cb382a53e9'], - }), -] - -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} - -sanity_check_paths = { - 'files': ['bin/ipython'], - 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/IPython', - 'share/jupyter' - ], -} - -sanity_check_commands = [ - "ipython -h", - "jupyter notebook --help", - "iptest", -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.13.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.13.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 12e60f7bcee..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.13.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,166 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'IPython' -version = '7.13.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://ipython.org/index.html' -description = """IPython provides a rich architecture for interactive computing with: - Powerful interactive shells (terminal and Qt-based). - A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. - Support for interactive data visualization and use of GUI toolkits. - Flexible, embeddable interpreters to load into your own projects. - Easy to use, high performance tools for parallel computing.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('ZeroMQ', '4.3.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('PyYAML', '5.3'), # required for jupyter_nbextensions_configurator -] - -check_ldshared = True - -exts_list = [ - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('ipython', version, { - 'modulename': 'IPython', - 'checksums': ['ca478e52ae1f88da0102360e57e528b92f3ae4316aabac80a2cd7f7ab2efb48a'], - }), - ('pexpect', '4.8.0', { - 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], - }), - ('pickleshare', '0.7.5', { - 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], - }), - ('prompt_toolkit', '3.0.4', { - 'checksums': ['ebe6b1b08c888b84c50d7f93dee21a09af39860144ff6130aadbd61ae8d29783'], - }), - ('ptyprocess', '0.6.0', { - 'use_pip': False, - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], - }), - ('simplegeneric', '0.8.1', { - 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], - }), - ('traitlets', '4.3.3', { - 'checksums': ['d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7'], - }), - ('parso', '0.6.2', { - 'checksums': ['0c5659e0c6eba20636f99a04f469798dca8da279645ce5c387315b2c23912157'], - }), - ('jedi', '0.16.0', { - 'checksums': ['d5c871cb9360b414f981e7072c52c33258d598305280fef91c6cae34739d65d5'], - }), - ('testpath', '0.4.4', { - 'use_pip': False, - 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], - }), - ('Send2Trash', '1.5.0', { - 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], - }), - ('webencodings', '0.5.1', { - 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], - }), - ('html5lib', '1.0.1', { - 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], - }), - ('bleach', '3.1.3', { - 'checksums': ['f8dfd8a7e26443e986c4e44df31870da8e906ea61096af06ba5d5cc2d519842a'], - }), - ('vcversioner', '2.16.0.0', { - 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], - }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('pandocfilters', '1.4.2', { - 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], - }), - ('pyzmq', '19.0.0', { - 'modulename': 'zmq', - 'checksums': ['5e1f65e576ab07aed83f444e201d86deb01cd27dcf3f37c727bc8729246a60a8'], - }), - ('entrypoints', '0.3', { - 'use_pip': False, - 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], - }), - ('jupyter_core', '4.6.3', { - 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], - }), - ('nbformat', '5.0.4', { - 'checksums': ['562de41fc7f4f481b79ab5d683279bf3a168858268d4387b489b7b02be0b324a'], - }), - ('mistune', '0.8.4', { - 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], - }), - ('defusedxml', '0.6.0', { - 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], - }), - ('nbconvert', '5.6.1', { - 'checksums': ['21fb48e700b43e82ba0e3142421a659d7739b65568cc832a13976a77be16b523'], - }), - ('terminado', '0.8.3', { - 'use_pip': False, - 'checksums': ['4804a774f802306a7d9af7322193c5390f1da0abb429e082a10ef1d46e6fb2c2'], - }), - ('tornado', '6.0.4', { - 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], - }), - ('jupyter_client', '6.1.0', { - 'checksums': ['61429e7d2c4b385135d31054944dd3f23a1c6affb0ca3d4328d42fc9ba82b7f5'], - }), - ('backcall', '0.1.0', { - 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], - }), - ('ipykernel', '5.2.0', { - 'checksums': ['37c65d2e2da3326e5cf114405df6d47d997b8a3eba99e2cc4b75833bf71a5e18'], - }), - ('prometheus_client', '0.7.1', { - 'checksums': ['71cd24a2b3eb335cb800c7159f423df1bd4dcd5171b234be15e3f31ec9f622da'], - }), - ('pyrsistent', '0.15.7', { - 'checksums': ['cdc7b5e3ed77bed61270a47d35434a30617b9becdf2478af76ad2c6ade307280'], - }), - ('ipywidgets', '7.5.1', { - 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], - }), - ('jupyter_contrib_core', '0.3.3', { - 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], - }), - ('jupyter_nbextensions_configurator', '0.4.1', { - 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], - }), - ('notebook', '6.0.3', { - 'checksums': ['47a9092975c9e7965ada00b9a20f0cf637d001db60d241d479f53c0be117ad48'], - }), - ('widgetsnbextension', '3.5.1', { - 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], - }), - ('ipympl', '0.5.6', { - 'checksums': ['076240e606f4dc1f23b7ecc3303c759f5718dc16f9a119382776c6cb382a53e9'], - }), -] - -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} - -sanity_check_paths = { - 'files': ['bin/ipython'], - 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/IPython', - 'share/jupyter' - ], -} - -sanity_check_commands = [ - "ipython -h", - "jupyter notebook --help", - "iptest", -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.15.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.15.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 875d06a3f5e..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.15.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,164 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'IPython' -version = '7.15.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://ipython.org/index.html' -description = """IPython provides a rich architecture for interactive computing with: - Powerful interactive shells (terminal and Qt-based). - A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. - Support for interactive data visualization and use of GUI toolkits. - Flexible, embeddable interpreters to load into your own projects. - Easy to use, high performance tools for parallel computing.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('ZeroMQ', '4.3.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('PyYAML', '5.3'), # required for jupyter_nbextensions_configurator -] - -exts_list = [ - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('ipython', version, { - 'modulename': 'IPython', - 'checksums': ['0ef1433879816a960cd3ae1ae1dc82c64732ca75cec8dab5a4e29783fb571d0e'], - }), - ('pexpect', '4.8.0', { - 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], - }), - ('pickleshare', '0.7.5', { - 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], - }), - ('wcwidth', '0.1.9', { - 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], - }), - ('prompt_toolkit', '3.0.5', { - 'checksums': ['563d1a4140b63ff9dd587bda9557cffb2fe73650205ab6f4383092fb882e7dc8'], - }), - ('ptyprocess', '0.6.0', { - 'use_pip': False, - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], - }), - ('simplegeneric', '0.8.1', { - 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], - }), - ('traitlets', '4.3.3', { - 'checksums': ['d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7'], - }), - ('parso', '0.7.0', { - 'checksums': ['908e9fae2144a076d72ae4e25539143d40b8e3eafbaeae03c1bfe226f4cdf12c'], - }), - ('jedi', '0.17.0', { - 'checksums': ['df40c97641cb943661d2db4c33c2e1ff75d491189423249e989bcea4464f3030'], - }), - ('testpath', '0.4.4', { - 'use_pip': False, - 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], - }), - ('Send2Trash', '1.5.0', { - 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], - }), - ('webencodings', '0.5.1', { - 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], - }), - ('html5lib', '1.0.1', { - 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], - }), - ('bleach', '3.1.5', { - 'checksums': ['3c4c520fdb9db59ef139915a5db79f8b51bc2a7257ea0389f30c846883430a4b'], - }), - ('vcversioner', '2.16.0.0', { - 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], - }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('pandocfilters', '1.4.2', { - 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], - }), - ('pyzmq', '19.0.1', { - 'modulename': 'zmq', - 'checksums': ['13a5638ab24d628a6ade8f794195e1a1acd573496c3b85af2f1183603b7bf5e0'], - }), - ('entrypoints', '0.3', { - 'use_pip': False, - 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], - }), - ('jupyter_core', '4.6.3', { - 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], - }), - ('nbformat', '5.0.6', { - 'checksums': ['049af048ed76b95c3c44043620c17e56bc001329e07f83fec4f177f0e3d7b757'], - }), - ('mistune', '0.8.4', { - 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], - }), - ('defusedxml', '0.6.0', { - 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], - }), - ('nbconvert', '5.6.1', { - 'checksums': ['21fb48e700b43e82ba0e3142421a659d7739b65568cc832a13976a77be16b523'], - }), - ('terminado', '0.8.3', { - 'use_pip': False, - 'checksums': ['4804a774f802306a7d9af7322193c5390f1da0abb429e082a10ef1d46e6fb2c2'], - }), - ('tornado', '6.0.4', { - 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], - }), - ('jupyter_client', '6.1.3', { - 'checksums': ['3a32fa4d0b16d1c626b30c3002a62dfd86d6863ed39eaba3f537fade197bb756'], - }), - ('backcall', '0.1.0', { - 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], - }), - ('ipykernel', '5.3.0', { - 'checksums': ['731adb3f2c4ebcaff52e10a855ddc87670359a89c9c784d711e62d66fccdafae'], - }), - ('prometheus_client', '0.8.0', { - 'checksums': ['c6e6b706833a6bd1fd51711299edee907857be10ece535126a158f911ee80915'], - }), - ('pyrsistent', '0.16.0', { - 'checksums': ['28669905fe725965daa16184933676547c5bb40a5153055a8dee2a4bd7933ad3'], - }), - ('ipywidgets', '7.5.1', { - 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], - }), - ('jupyter_contrib_core', '0.3.3', { - 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], - }), - ('jupyter_nbextensions_configurator', '0.4.1', { - 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], - }), - ('notebook', '6.0.3', { - 'checksums': ['47a9092975c9e7965ada00b9a20f0cf637d001db60d241d479f53c0be117ad48'], - }), - ('widgetsnbextension', '3.5.1', { - 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], - }), -] - -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} - -sanity_check_paths = { - 'files': ['bin/ipython'], - 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/IPython', - 'share/jupyter' - ], -} - -sanity_check_commands = [ - "ipython -h", - "jupyter notebook --help", - "iptest", -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.15.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.15.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index b3fbac11ac5..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IPython/IPython-7.15.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,164 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'IPython' -version = '7.15.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://ipython.org/index.html' -description = """IPython provides a rich architecture for interactive computing with: - Powerful interactive shells (terminal and Qt-based). - A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. - Support for interactive data visualization and use of GUI toolkits. - Flexible, embeddable interpreters to load into your own projects. - Easy to use, high performance tools for parallel computing.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('ZeroMQ', '4.3.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('PyYAML', '5.3'), # required for jupyter_nbextensions_configurator -] - -exts_list = [ - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('ipython', version, { - 'modulename': 'IPython', - 'checksums': ['0ef1433879816a960cd3ae1ae1dc82c64732ca75cec8dab5a4e29783fb571d0e'], - }), - ('pexpect', '4.8.0', { - 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], - }), - ('pickleshare', '0.7.5', { - 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], - }), - ('wcwidth', '0.1.9', { - 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], - }), - ('prompt_toolkit', '3.0.5', { - 'checksums': ['563d1a4140b63ff9dd587bda9557cffb2fe73650205ab6f4383092fb882e7dc8'], - }), - ('ptyprocess', '0.6.0', { - 'use_pip': False, - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], - }), - ('simplegeneric', '0.8.1', { - 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], - }), - ('traitlets', '4.3.3', { - 'checksums': ['d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7'], - }), - ('parso', '0.7.0', { - 'checksums': ['908e9fae2144a076d72ae4e25539143d40b8e3eafbaeae03c1bfe226f4cdf12c'], - }), - ('jedi', '0.17.0', { - 'checksums': ['df40c97641cb943661d2db4c33c2e1ff75d491189423249e989bcea4464f3030'], - }), - ('testpath', '0.4.4', { - 'use_pip': False, - 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], - }), - ('Send2Trash', '1.5.0', { - 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], - }), - ('webencodings', '0.5.1', { - 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], - }), - ('html5lib', '1.0.1', { - 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], - }), - ('bleach', '3.1.5', { - 'checksums': ['3c4c520fdb9db59ef139915a5db79f8b51bc2a7257ea0389f30c846883430a4b'], - }), - ('vcversioner', '2.16.0.0', { - 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], - }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('pandocfilters', '1.4.2', { - 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], - }), - ('pyzmq', '19.0.1', { - 'modulename': 'zmq', - 'checksums': ['13a5638ab24d628a6ade8f794195e1a1acd573496c3b85af2f1183603b7bf5e0'], - }), - ('entrypoints', '0.3', { - 'use_pip': False, - 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], - }), - ('jupyter_core', '4.6.3', { - 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], - }), - ('nbformat', '5.0.6', { - 'checksums': ['049af048ed76b95c3c44043620c17e56bc001329e07f83fec4f177f0e3d7b757'], - }), - ('mistune', '0.8.4', { - 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], - }), - ('defusedxml', '0.6.0', { - 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], - }), - ('nbconvert', '5.6.1', { - 'checksums': ['21fb48e700b43e82ba0e3142421a659d7739b65568cc832a13976a77be16b523'], - }), - ('terminado', '0.8.3', { - 'use_pip': False, - 'checksums': ['4804a774f802306a7d9af7322193c5390f1da0abb429e082a10ef1d46e6fb2c2'], - }), - ('tornado', '6.0.4', { - 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], - }), - ('jupyter_client', '6.1.3', { - 'checksums': ['3a32fa4d0b16d1c626b30c3002a62dfd86d6863ed39eaba3f537fade197bb756'], - }), - ('backcall', '0.1.0', { - 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], - }), - ('ipykernel', '5.3.0', { - 'checksums': ['731adb3f2c4ebcaff52e10a855ddc87670359a89c9c784d711e62d66fccdafae'], - }), - ('prometheus_client', '0.8.0', { - 'checksums': ['c6e6b706833a6bd1fd51711299edee907857be10ece535126a158f911ee80915'], - }), - ('pyrsistent', '0.16.0', { - 'checksums': ['28669905fe725965daa16184933676547c5bb40a5153055a8dee2a4bd7933ad3'], - }), - ('ipywidgets', '7.5.1', { - 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], - }), - ('jupyter_contrib_core', '0.3.3', { - 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], - }), - ('jupyter_nbextensions_configurator', '0.4.1', { - 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], - }), - ('notebook', '6.0.3', { - 'checksums': ['47a9092975c9e7965ada00b9a20f0cf637d001db60d241d479f53c0be117ad48'], - }), - ('widgetsnbextension', '3.5.1', { - 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], - }), -] - -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} - -sanity_check_paths = { - 'files': ['bin/ipython'], - 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/IPython', - 'share/jupyter' - ], -} - -sanity_check_commands = [ - "ipython -h", - "jupyter notebook --help", - "iptest", -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/IQ-TREE/IQ-TREE-1.6.12-foss-2020a.eb b/easybuild/easyconfigs/__archive__/i/IQ-TREE/IQ-TREE-1.6.12-foss-2020a.eb deleted file mode 100644 index ae724d9537b..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IQ-TREE/IQ-TREE-1.6.12-foss-2020a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'IQ-TREE' -version = '1.6.12' - -homepage = 'http://www.iqtree.org/' -description = """Efficient phylogenomic software by maximum likelihood""" - -toolchain = {'name': 'foss', 'version': '2020a'} -# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary - -github_account = 'Cibiv' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['9614092de7a157de82c9cc402b19cc8bfa0cb0ffc93b91817875c2b4bb46a284'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Eigen', '3.3.7'), -] -dependencies = [('zlib', '1.2.11')] - -configopts = [ - '-DIQTREE_FLAGS=omp', - '-DIQTREE_FLAGS=mpi', -] - -sanity_check_paths = { - 'files': ['bin/iqtree', 'bin/iqtree-mpi'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/i/IQ-TREE/IQ-TREE-2.1.2-foss-2020a.eb b/easybuild/easyconfigs/__archive__/i/IQ-TREE/IQ-TREE-2.1.2-foss-2020a.eb deleted file mode 100644 index bc8aac08b95..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IQ-TREE/IQ-TREE-2.1.2-foss-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'IQ-TREE' -version = '2.1.2' - -# HTTPS is not working -homepage = 'http://www.iqtree.org/' -description = """Efficient phylogenomic software by maximum likelihood""" - -toolchain = {'name': 'foss', 'version': '2020a'} -# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary - -source_urls = ['https://github.com/iqtree/iqtree2/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_use_EB_LSD2.patch'] -checksums = [ - '3aaf5ac7f60d852ac8b733fb82832c049ca48b7203a6a865e99c5af359fcca5a', # v2.1.2.tar.gz - 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816', # IQ-TREE-2.1.2_use_EB_LSD2.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Eigen', '3.3.7'), -] -dependencies = [ - ('zlib', '1.2.11'), - ('Boost', '1.72.0'), - ('LSD2', '1.9.7'), -] - -local_conf_opts = ' -DUSE_LSD2=ON ' -configopts = [ - '-DIQTREE_FLAGS=omp' + local_conf_opts, - '-DIQTREE_FLAGS=mpi' + local_conf_opts, -] - -sanity_check_paths = { - 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb deleted file mode 100644 index 36cd6cc503e..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb +++ /dev/null @@ -1,69 +0,0 @@ -easyblock = 'Bundle' - -name = 'IRkernel' -version = '1.1' -versionsuffix = '-R-%(rver)s-Python-%(pyver)s' - -homepage = 'https://irkernel.github.io' -description = """The R kernel for the 'Jupyter' environment executes R code - which the front-end (Jupyter Notebook or other front-ends) submits to the - kernel via the network.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('R', '3.6.3'), - ('Python', '3.8.2'), - ('IPython', '7.15.0', '-Python-%(pyver)s'), - ('ZeroMQ', '4.3.2'), -] - -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/', - 'https://cran.rstudio.com/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -exts_list = [ - ('repr', '1.1.0', { - 'checksums': ['743fe018f9e3e54067a970bc38b6b8c0c0498b43f88d179ac4a959c2013a5f96'], - }), - ('IRdisplay', '0.7.0', { - 'checksums': ['91eac9acdb92ed0fdc58e5da284aa4bb957ada5eef504fd89bec136747999089'], - }), - ('pbdZMQ', '0.3-3', { - 'checksums': ['ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca'], - }), - (name, version, { - 'checksums': ['2469431c468a3f586ffe8adc260fa368fd8d6b4e65bde318f941fb1692ee38ee'], - }), -] - -modextrapaths = { - 'R_LIBS_SITE': '', - 'JUPYTER_PATH': '%(name)s' -} - -# IPython notebook looks for the json kernel file in kernels/IRkernel -# We start the kernel with default bitmapType 'cairo'. This is a more sensible default -# for headless nodes. See https://github.com/IRkernel/IRkernel/issues/388 -local_kerneldir = '%(installdir)s/IRkernel' -postinstallcmds = [ - 'mkdir -p %s/kernels/ir' % local_kerneldir, - 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir), - ('sed -i \'s/"IRkernel::main()"/"options(bitmapType=\\x27cairo\\x27); IRkernel::main()"/g\'' - ' %s/kernels/ir/kernel.json') % local_kerneldir -] - -sanity_check_paths = { - 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], - 'dirs': [name], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb deleted file mode 100644 index a671c1eff88..00000000000 --- a/easybuild/easyconfigs/__archive__/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb +++ /dev/null @@ -1,69 +0,0 @@ -easyblock = 'Bundle' - -name = 'IRkernel' -version = '1.2' -versionsuffix = '-R-%(rver)s-Python-%(pyver)s' - -homepage = 'https://irkernel.github.io' -description = """The R kernel for the 'Jupyter' environment executes R code - which the front-end (Jupyter Notebook or other front-ends) submits to the - kernel via the network.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('R', '4.0.0'), - ('Python', '3.8.2'), - ('IPython', '7.15.0', '-Python-%(pyver)s'), - ('ZeroMQ', '4.3.2'), -] - -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/', - 'https://cran.rstudio.com/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -exts_list = [ - ('repr', '1.1.3', { - 'checksums': ['531b43d413b51cbc96e3b9162493c975d9395bb9532e500ad51cd99b36a53562'], - }), - ('IRdisplay', '1.0', { - 'checksums': ['8967ec58656ede561d20ab07dd9ef27de088c0ea099e325242b3860a63964b96'], - }), - ('pbdZMQ', '0.3-5', { - 'checksums': ['4d8088b3365d612a661f0078bcba50357cb3a7ec04a699348b4312fd6fd811ed'], - }), - (name, version, { - 'checksums': ['5fb4dbdb741d05043120a8be0eb73f054b607d9854f314bd79cfec08d219ff91'], - }), -] - -modextrapaths = { - 'R_LIBS_SITE': '', - 'JUPYTER_PATH': '%(name)s' -} - -# IPython notebook looks for the json kernel file in kernels/IRkernel -# We start the kernel with default bitmapType 'cairo'. This is a more sensible default -# for headless nodes. See https://github.com/IRkernel/IRkernel/issues/388 -local_kerneldir = '%(installdir)s/IRkernel' -postinstallcmds = [ - 'mkdir -p %s/kernels/ir' % local_kerneldir, - 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir), - ('sed -i \'s/"IRkernel::main()"/"options(bitmapType=\\x27cairo\\x27); IRkernel::main()"/g\'' - ' %s/kernels/ir/kernel.json') % local_kerneldir -] - -sanity_check_paths = { - 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], - 'dirs': [name], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/i/ISL/ISL-0.23-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/i/ISL/ISL-0.23-GCCcore-9.3.0.eb deleted file mode 100644 index e2973d809d4..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ISL/ISL-0.23-GCCcore-9.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ISL' -version = '0.23' - -homepage = 'http://isl.gforge.inria.fr/' -description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://isl.gforge.inria.fr/'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d'] - -builddependencies = [('binutils', '2.34')] -dependencies = [('GMP', '6.2.0')] - -sanity_check_paths = { - 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], - 'dirs': ['include/isl'] -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 1f129fdda19..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,67 +0,0 @@ -# Contributors: -# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University -# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) -# -easyblock = 'CMakePythonPackage' - -name = 'ITK' -version = '5.1.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://itk.org' -description = """Insight Segmentation and Registration Toolkit (ITK) provides - an extensive suite of software tools for registering and segmenting - multidimensional imaging data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://github.com/InsightSoftwareConsortium/ITK/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix_wrap_vtkglue.patch'] -checksums = [ - '651284ce6f68e8bd31db176a6b53f5679209a8ed5b6b5480c3591d66c6e10b60', # v5.1.2.tar.gz - '9dee2fbb5239d3a441e11f7f993af3b5879b83f9385d611f509eaf6b686ef8fe', # ITK-5.1.2_fix_wrap_vtkglue.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Bison', '3.5.3'), - ('Eigen', '3.3.7'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('double-conversion', '3.1.5'), - ('expat', '2.2.9'), - ('HDF5', '1.10.6'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('SWIG', '4.0.1'), - ('VTK', '8.2.0', versionsuffix), - ('zlib', '1.2.11'), -] - -local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'SWIG', 'ZLIB'] -local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] - -configopts = '-DBUILD_TESTING=OFF ' -configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' -configopts += '-DITK_WRAP_PYTHON=ON ' -configopts += ' '.join(local_sys_cmake) - -build_shared_libs = True - -# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 -prebuildopts = "LC_ALL=C " - -local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', 'ITKReview', 'ITKVTK', 'ITKVtkGlue'] - -sanity_check_paths = { - 'files': ['bin/itkTestDriver'] + - ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (i, SHLIB_EXT) for i in local_lib_names], - 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-foss-2020a.eb b/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-foss-2020a.eb deleted file mode 100644 index 93e38ad421c..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-foss-2020a.eb +++ /dev/null @@ -1,65 +0,0 @@ -# Contributors: -# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University -# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) -# -easyblock = 'CMakeMake' - -name = 'ITK' -version = '5.1.2' - -homepage = 'https://itk.org' -description = """Insight Segmentation and Registration Toolkit (ITK) provides - an extensive suite of software tools for registering and segmenting - multidimensional imaging data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -github_account = 'InsightSoftwareConsortium' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = [ - '651284ce6f68e8bd31db176a6b53f5679209a8ed5b6b5480c3591d66c6e10b60', # v5.1.2.tar.gz -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Bison', '3.5.3'), - ('Eigen', '3.3.7'), -] - -dependencies = [ - ('double-conversion', '3.1.5'), - ('expat', '2.2.9'), - ('HDF5', '1.10.6'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('VTK', '8.2.0', '-Python-3.8.2'), - ('zlib', '1.2.11'), -] - -local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] -local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] - -configopts = '-DBUILD_TESTING=OFF ' -configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' -configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' -configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK -configopts += ' '.join(local_sys_cmake) - -build_shared_libs = True - -# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 -prebuildopts = "LC_ALL=C " - -local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', - 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] - -sanity_check_paths = { - 'files': ['bin/itkTestDriver'] + - ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (i, SHLIB_EXT) for i in local_lib_names], - 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index ce90113f564..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,68 +0,0 @@ -# Contributors: -# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University -# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) -# -easyblock = 'CMakePythonPackage' - -name = 'ITK' -version = '5.1.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://itk.org' -description = """Insight Segmentation and Registration Toolkit (ITK) provides - an extensive suite of software tools for registering and segmenting - multidimensional imaging data.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://github.com/InsightSoftwareConsortium/ITK/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix_wrap_vtkglue.patch'] -checksums = [ - '651284ce6f68e8bd31db176a6b53f5679209a8ed5b6b5480c3591d66c6e10b60', # v5.1.2.tar.gz - '9dee2fbb5239d3a441e11f7f993af3b5879b83f9385d611f509eaf6b686ef8fe', # ITK-5.1.2_fix_wrap_vtkglue.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Bison', '3.5.3'), - ('Eigen', '3.3.7'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('double-conversion', '3.1.5'), - ('expat', '2.2.9'), - ('HDF5', '1.10.6'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('SWIG', '4.0.1'), - ('VTK', '8.2.0', versionsuffix), - ('zlib', '1.2.11'), -] - -local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'SWIG', 'ZLIB'] -local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] - -configopts = '-DBUILD_TESTING=OFF ' -configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' -configopts += '-DITK_WRAP_PYTHON=ON ' -configopts += '-DITK_USE_CUFFTW=ON ' -configopts += ' '.join(local_sys_cmake) - -build_shared_libs = True - -# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 -prebuildopts = "LC_ALL=C " - -local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', 'ITKReview', 'ITKVTK', 'ITKVtkGlue'] - -sanity_check_paths = { - 'files': ['bin/itkTestDriver'] + - ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (i, SHLIB_EXT) for i in local_lib_names], - 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-fosscuda-2020a.eb b/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-fosscuda-2020a.eb deleted file mode 100644 index e4cfb4c1e83..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2-fosscuda-2020a.eb +++ /dev/null @@ -1,66 +0,0 @@ -# Contributors: -# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University -# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) -# -easyblock = 'CMakeMake' - -name = 'ITK' -version = '5.1.2' - -homepage = 'https://itk.org' -description = """Insight Segmentation and Registration Toolkit (ITK) provides - an extensive suite of software tools for registering and segmenting - multidimensional imaging data.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -github_account = 'InsightSoftwareConsortium' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = [ - '651284ce6f68e8bd31db176a6b53f5679209a8ed5b6b5480c3591d66c6e10b60', # v5.1.2.tar.gz -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Bison', '3.5.3'), - ('Eigen', '3.3.7'), -] - -dependencies = [ - ('double-conversion', '3.1.5'), - ('expat', '2.2.9'), - ('HDF5', '1.10.6'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('VTK', '8.2.0', '-Python-3.8.2'), - ('zlib', '1.2.11'), -] - -local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] -local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] - -configopts = '-DBUILD_TESTING=OFF ' -configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' -configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' -configopts += '-DITK_USE_CUFFTW:BOOL=ON ' -configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK -configopts += ' '.join(local_sys_cmake) - -build_shared_libs = True - -# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 -prebuildopts = "LC_ALL=C " - -local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', - 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] - -sanity_check_paths = { - 'files': ['bin/itkTestDriver'] + - ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (i, SHLIB_EXT) for i in local_lib_names], - 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2_fix_wrap_vtkglue.patch b/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2_fix_wrap_vtkglue.patch deleted file mode 100644 index 8662a49e11a..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ITK/ITK-5.1.2_fix_wrap_vtkglue.patch +++ /dev/null @@ -1,14 +0,0 @@ -Fix python module definition in VtkGlue -issue: https://github.com/InsightSoftwareConsortium/ITK/issues/2026 -author: Alex Domingo (Vrije Universiteit Brussel) ---- Modules/Bridge/VtkGlue/wrapping/VtkGlue.i.orig 2021-01-06 14:55:31.848234000 +0100 -+++ Modules/Bridge/VtkGlue/wrapping/VtkGlue.i 2021-01-06 14:55:42.113503000 +0100 -@@ -48,7 +48,7 @@ - #endif - - #ifdef SWIGPYTHON --%module(package=\"itk\",threads=\"1\") VtkGluePython -+%module(package="itk",threads="1") VtkGluePython - - %{ - #include "vtkPythonUtil.h" diff --git a/easybuild/easyconfigs/__archive__/i/ITSx/ITSx-1.1.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/i/ITSx/ITSx-1.1.2-GCCcore-9.3.0.eb deleted file mode 100644 index cefae3f6932..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ITSx/ITSx-1.1.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'Tarball' - -name = 'ITSx' -version = '1.1.2' - -homepage = 'https://microbiology.se/software/itsx/' -description = '''ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of -fungi and other eukaryotes for use in environmental sequencing.''' - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://microbiology.se/sw/'] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['45a9e99583189488e6cdfc37172732a330901ed713d92c8d5e7631a39fc4e72e'] - -dependencies = [('Perl', '5.30.2')] - -fix_perl_shebang_for = ['ITSx'] - -sanity_check_paths = { - 'files': ['ITSx'], - 'dirs': ['ITSx_db'], -} - -sanity_check_commands = ['ITSx --help'] - -modextrapaths = {'PATH': ''} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb deleted file mode 100644 index b08495a6ea2..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Ravi Tripathi -# Email: ravi89@uab.edu - -easyblock = 'ConfigureMake' - -name = 'ImageMagick' -version = '7.0.10-1' - -homepage = 'https://www.imagemagick.org/' -description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/ImageMagick/ImageMagick/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['61fcd748d3c3962c614c2df2645cf09ba7ae95b495cb27148dd5d2a8fc995713'] - -dependencies = [ - ('bzip2', '1.0.8'), - ('X11', '20200222'), - ('Ghostscript', '9.52'), - ('JasPer', '2.0.14'), - ('libjpeg-turbo', '2.0.4'), - ('LibTIFF', '4.1.0'), - ('LittleCMS', '2.9'), - ('Pango', '1.44.7'), -] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -configopts = "--with-gslib --with-x" - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', - 'include/%(name)s-%(version_major)s', 'lib', 'share'], -} - -modextravars = {'MAGICK_HOME': '%(installdir)s'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/i/iVar/iVar-1.3.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/i/iVar/iVar-1.3.1-GCC-9.3.0.eb deleted file mode 100644 index 2203cdecab7..00000000000 --- a/easybuild/easyconfigs/__archive__/i/iVar/iVar-1.3.1-GCC-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Authors:: Dugan Witherick (University of Warwick) -# License:: MIT/GPL -# $Id$ -# -## - -easyblock = 'ConfigureMake' - -name = 'iVar' -version = '1.3.1' - -homepage = 'https://github.com/andersen-lab/ivar' -description = """ -iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. -""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -github_account = 'andersen-lab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['a5fb33e8e8fffedbb0836cb7c2f8b19d50f7f90112a9dca1f6a8e9f322056e6f'] - -builddependencies = [('Autotools', '20180311')] -dependencies = [ - ('HTSlib', '1.10.2'), -] - -preconfigopts = './autogen.sh &&' - -sanity_check_paths = { - 'files': ['bin/ivar'], - 'dirs': [], -} - -sanity_check_commands = ['ivar version'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/i/iccifort/iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/i/iccifort/iccifort-2020.1.217.eb deleted file mode 100644 index 98e64dff918..00000000000 --- a/easybuild/easyconfigs/__archive__/i/iccifort/iccifort-2020.1.217.eb +++ /dev/null @@ -1,40 +0,0 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild - -name = 'iccifort' -version = '2020.1.217' - -homepage = 'https://software.intel.com/en-us/intel-compilers/' -description = "Intel C, C++ & Fortran compilers" - -toolchain = SYSTEM - -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16530/'] -sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] -patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] -checksums = [ - # parallel_studio_xe_2020_update1_composer_edition.tgz - '26c7e7da87b8a83adfd408b2a354d872be97736abed837364c1bf10f4469b01e', - # iccifort-2020.1.217_no_mpi_rt_dependency.patch - '61b558089d3d9253fad2139a16dc0899b9f839f34303e094efd70b281fc41a96', -] - -local_gccver = '9.3.0' - -dependencies = [ - ('GCCcore', local_gccver), - ('binutils', '2.34', '', ('GCCcore', local_gccver)), -] - -# list of regex for components to install -# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources -# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide -components = [ - 'intel-comp', 'intel-ccomp', 'intel-fcomp', 'intel-icc', 'intel-ifort', - 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)' -] - -dontcreateinstalldir = True - -license_file = HOME + '/licenses/intel/license.lic' - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/i/iccifort/iccifort-2020.1.217_no_mpi_rt_dependency.patch b/easybuild/easyconfigs/__archive__/i/iccifort/iccifort-2020.1.217_no_mpi_rt_dependency.patch deleted file mode 100644 index 65900e15cbd..00000000000 --- a/easybuild/easyconfigs/__archive__/i/iccifort/iccifort-2020.1.217_no_mpi_rt_dependency.patch +++ /dev/null @@ -1,13 +0,0 @@ -don't install Intel MPI runtime components (mpi-rt), cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/3793 -author: Bart Oldeman (Compute Canada), updated for 2020.1.217 by Kenneth Hoste (HPC-UGent) ---- parallel_studio_xe_2020_update1_composer_edition/pset/mediaconfig.xml.orig 2020-03-31 17:31:11.362126388 +0200 -+++ parallel_studio_xe_2020_update1_composer_edition/pset/mediaconfig.xml 2020-03-31 17:31:30.691960582 +0200 -@@ -870,7 +870,7 @@ - - ${COMPLIB_ROOT} - 1585047222050 -- -+ - Intel Fortran Compiler for Intel(R) 64 - Intel Fortran Compiler 19.1 Update 1 - インテル(R) Fortran コンパイラー (インテル(R) 64) diff --git a/easybuild/easyconfigs/__archive__/i/iccifortcuda/iccifortcuda-2020a.eb b/easybuild/easyconfigs/__archive__/i/iccifortcuda/iccifortcuda-2020a.eb deleted file mode 100644 index 1239af68d39..00000000000 --- a/easybuild/easyconfigs/__archive__/i/iccifortcuda/iccifortcuda-2020a.eb +++ /dev/null @@ -1,18 +0,0 @@ -easyblock = 'Toolchain' - -name = 'iccifortcuda' -version = '2020a' - -homepage = '(none)' -description = "Intel C, C++ & Fortran compilers with CUDA toolkit" - -toolchain = SYSTEM - -local_compver = '2020.1.217' - -dependencies = [ - ('iccifort', local_compver), - ('CUDA', '11.0.2', '', ('iccifort', local_compver)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/i/ichorCNA/ichorCNA-0.3.2-20191219-foss-2020a.eb b/easybuild/easyconfigs/__archive__/i/ichorCNA/ichorCNA-0.3.2-20191219-foss-2020a.eb deleted file mode 100644 index c91d2422031..00000000000 --- a/easybuild/easyconfigs/__archive__/i/ichorCNA/ichorCNA-0.3.2-20191219-foss-2020a.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'RPackage' - -name = 'ichorCNA' -local_commit = '5bfc03e' -version = '0.3.2-20191219' -github_account = 'broadinstitute' - -homepage = 'https://github.com/broadinstitute/ichorCNA/wiki' -description = """ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole -genome sequencing""" - -source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['38dbee4f4127fc27c4bd51fe3d99cb9eebea6fa9a15463127384923c217f1d74'] - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('R', '4.0.0'), - ('R-bundle-Bioconductor', '3.11', '-R-%(rver)s'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['ichorCNA'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/i/igraph/igraph-0.8.2-foss-2020a.eb b/easybuild/easyconfigs/__archive__/i/igraph/igraph-0.8.2-foss-2020a.eb deleted file mode 100644 index 4e17a8b60e2..00000000000 --- a/easybuild/easyconfigs/__archive__/i/igraph/igraph-0.8.2-foss-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'igraph' -version = '0.8.2' - -homepage = 'https://igraph.org' -description = """igraph is a collection of network analysis tools with the emphasis on -efficiency, portability and ease of use. igraph is open source and free. igraph can be -programmed in R, Python and C/C++.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] -sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['718a471e7b8cbf02e3e8006153b7be6a22f85bb804283763a0016280e8a60e95'] - -builddependencies = [ - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('GLPK', '4.65'), - ('libxml2', '2.9.10'), - ('zlib', '1.2.11'), -] - -preconfigopts = "autoreconf -i && " -# Remove hardcoded links to BLAS/LAPACK -preconfigopts += "sed -i 's/-lblas/$LIBBLAS/' configure && " -preconfigopts += "sed -i 's/-llapack/$LIBLAPACK/' configure && " - -configopts = "--with-external-blas --with-external-lapack --with-external-glpk" - -sanity_check_paths = { - 'files': ['lib/libigraph.%s' % x for x in [SHLIB_EXT, 'la', 'a']] + ['lib/pkgconfig/igraph.pc'] + - ['include/igraph/igraph%s.h' % x for x in ['', '_blas', '_constants', '_lapack', '_types', '_version']], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/i/iimpi/iimpi-2020.06-impi-18.5.eb b/easybuild/easyconfigs/__archive__/i/iimpi/iimpi-2020.06-impi-18.5.eb deleted file mode 100644 index c1db1db4503..00000000000 --- a/easybuild/easyconfigs/__archive__/i/iimpi/iimpi-2020.06-impi-18.5.eb +++ /dev/null @@ -1,18 +0,0 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild -easyblock = 'Toolchain' - -name = 'iimpi' -version = '2020.06-impi-18.5' - -homepage = 'https://software.intel.com/parallel-studio-xe' -description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" - -toolchain = SYSTEM - -local_compver = '2020.1.217' -dependencies = [ - ('iccifort', local_compver), - ('impi', '2018.5.288', '', ('iccifort', local_compver)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/i/iimpi/iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/i/iimpi/iimpi-2020a.eb deleted file mode 100644 index 4c30378af97..00000000000 --- a/easybuild/easyconfigs/__archive__/i/iimpi/iimpi-2020a.eb +++ /dev/null @@ -1,18 +0,0 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild -easyblock = 'Toolchain' - -name = 'iimpi' -version = '2020a' - -homepage = 'https://software.intel.com/parallel-studio-xe' -description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" - -toolchain = SYSTEM - -local_compver = '2020.1.217' -dependencies = [ - ('iccifort', local_compver), - ('impi', '2019.7.217', '', ('iccifort', local_compver)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/i/iimpic/iimpic-2020a.eb b/easybuild/easyconfigs/__archive__/i/iimpic/iimpic-2020a.eb deleted file mode 100644 index 2e42b2593f3..00000000000 --- a/easybuild/easyconfigs/__archive__/i/iimpic/iimpic-2020a.eb +++ /dev/null @@ -1,20 +0,0 @@ -# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ -easyblock = "Toolchain" - -name = 'iimpic' -version = '2020a' - -homepage = '(none)' -description = """Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA.""" - -toolchain = SYSTEM - -local_compver = '2020.1.217' - -dependencies = [ - ('iccifort', local_compver), - ('CUDA', '11.0.2', '', ('iccifort', local_compver)), - ('impi', '2019.7.217', '', ('iccifortcuda', version)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-gompi-2020a.eb deleted file mode 100644 index d662fdae171..00000000000 --- a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-gompi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ - -name = 'imkl' -version = '2020.1.217' - -homepage = 'https://software.intel.com/mkl' -description = """Intel Math Kernel Library is a library of highly optimized, - extensively threaded math routines for science, engineering, and financial - applications that require maximum performance. Core math functions include - BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] -sources = ['l_mkl_%(version)s.tgz'] -checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] - -dontcreateinstalldir = True - -components = ['intel-mkl'] - -license_file = HOME + '/licenses/intel/license.lic' - -interfaces = True - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb deleted file mode 100644 index a683875dd81..00000000000 --- a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb +++ /dev/null @@ -1,26 +0,0 @@ -# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ - -name = 'imkl' -version = '2020.1.217' - -homepage = 'https://software.intel.com/mkl' -description = """Intel Math Kernel Library is a library of highly optimized, - extensively threaded math routines for science, engineering, and financial - applications that require maximum performance. Core math functions include - BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" - -toolchain = {'name': 'iimpi', 'version': '2020.06-impi-18.5'} - -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] -sources = ['l_mkl_%(version)s.tgz'] -checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] - -dontcreateinstalldir = True - -components = ['intel-mkl'] - -license_file = HOME + '/licenses/intel/license.lic' - -interfaces = True - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iimpi-2020a.eb deleted file mode 100644 index aef431b9b6d..00000000000 --- a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iimpi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ - -name = 'imkl' -version = '2020.1.217' - -homepage = 'https://software.intel.com/mkl' -description = """Intel Math Kernel Library is a library of highly optimized, - extensively threaded math routines for science, engineering, and financial - applications that require maximum performance. Core math functions include - BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} - -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] -sources = ['l_mkl_%(version)s.tgz'] -checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] - -dontcreateinstalldir = True - -components = ['intel-mkl'] - -license_file = HOME + '/licenses/intel/license.lic' - -interfaces = True - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iimpic-2020a.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iimpic-2020a.eb deleted file mode 100644 index dbfbc356455..00000000000 --- a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iimpic-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ - -name = 'imkl' -version = '2020.1.217' - -homepage = 'https://software.intel.com/mkl' -description = """Intel Math Kernel Library is a library of highly optimized, - extensively threaded math routines for science, engineering, and financial - applications that require maximum performance. Core math functions include - BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" - -toolchain = {'name': 'iimpic', 'version': '2020a'} - -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] -sources = ['l_mkl_%(version)s.tgz'] -checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] - -dontcreateinstalldir = True - -components = ['intel-mkl'] - -license_file = HOME + '/licenses/intel/license.lic' - -interfaces = True - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iompi-2020a.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iompi-2020a.eb deleted file mode 100644 index 1f80ac1e253..00000000000 --- a/easybuild/easyconfigs/__archive__/i/imkl/imkl-2020.1.217-iompi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ - -name = 'imkl' -version = '2020.1.217' - -homepage = 'https://software.intel.com/mkl' -description = """Intel Math Kernel Library is a library of highly optimized, - extensively threaded math routines for science, engineering, and financial - applications that require maximum performance. Core math functions include - BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" - -toolchain = {'name': 'iompi', 'version': '2020a'} - -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] -sources = ['l_mkl_%(version)s.tgz'] -checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] - -dontcreateinstalldir = True - -components = ['intel-mkl'] - -license_file = HOME + '/licenses/intel/license.lic' - -interfaces = True - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/i/immunedeconv/immunedeconv-2.0.2-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/i/immunedeconv/immunedeconv-2.0.2-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 34b9bf200a6..00000000000 --- a/easybuild/easyconfigs/__archive__/i/immunedeconv/immunedeconv-2.0.2-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,62 +0,0 @@ -easyblock = 'Bundle' - -name = 'immunedeconv' -version = '2.0.2' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://github.com/icbi-lab/immunedeconv' -description = """ -immunedeconv is an R package for unified access to computational methods for -estimating immune cell fractions from bulk RNA sequencing data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('R', '4.0.0'), - ('R-bundle-Bioconductor', '3.11', versionsuffix), -] - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz' -} - -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -exts_list = [ - ('MCPcounter', '1.1.0', { - 'source_tmpl': '8c37884.tar.gz', - 'source_urls': ['https://github.com/ebecht/MCPcounter/archive'], - 'start_dir': 'Source', - 'checksums': ['bfe73a0334c874a0d6b0afc8f868da95583124602aedc06b84b67e392869e5f6'], - }), - ('xCell', '1.2', { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/dviraran/xCell/archive'], - 'checksums': ['52dcd5cfb5c8a4870cb485ee57f34d7830b23bdc61fd3012d859fdcc22ad941c'], - }), - ('EPIC', '1.1', { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/GfellerLab/EPIC/archive'], - 'checksums': ['95bea4a5bd1fb57a94055198475a2237b2181b2a499a97ec5055637c987d159f'], - }), - (name, version, { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/icbi-lab/immunedeconv/archive'], - 'checksums': ['be8df125fa5e66888d58b7afd4705b62f2f6d66cf0f1766d5117ec06840b2cf9'], - }), -] - -modextrapaths = {'R_LIBS_SITE': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb deleted file mode 100644 index e27d2ec5b55..00000000000 --- a/easybuild/easyconfigs/__archive__/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb +++ /dev/null @@ -1,22 +0,0 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild - -name = 'impi' -version = '2018.5.288' - -homepage = 'https://software.intel.com/en-us/intel-mpi-library/' -description = "Intel MPI Library, compatible with MPICH ABI" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] -sources = ['l_mpi_%(version)s.tgz'] -checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] - -dontcreateinstalldir = True - -components = ['intel-mpi', 'intel-psxe', 'intel-imb'] - -# set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = True - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb deleted file mode 100644 index 07f8323810c..00000000000 --- a/easybuild/easyconfigs/__archive__/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb +++ /dev/null @@ -1,40 +0,0 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild - -name = 'impi' -version = '2019.7.217' - -homepage = 'https://software.intel.com/en-us/intel-mpi-library/' -description = "Intel MPI Library, compatible with MPICH ABI" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/'] -sources = ['l_mpi_%(version)s.tgz'] -checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] - -dependencies = [ - # needed by libfabric provider MLX introduced in Intel MPI v2019.6, - # https://software.intel.com/en-us/articles/improve-performance-and-stability-with-intel-mpi-library-on-infiniband - ('UCX', '1.8.0'), -] - -dontcreateinstalldir = True - -components = ['intel-mpi', 'intel-psxe', 'intel-imb'] - -# set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = True - -modextravars = { - # to enable SLURM integration with srun (site-specific) - # 'I_MPI_PMI_LIBRARY': 'libpmi2.so', - - # set this if mpirun gives you a floating point exception (SIGFPE), see - # https://software.intel.com/en-us/forums/intel-clusters-and-hpc-technology/topic/852307 - # 'I_MPI_HYDRA_TOPOLIB': 'ipl', -} - -# may be needed if you enable I_MPI_PMI_LIBRARY above -# osdependencies = [('slurm-libpmi')] - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb b/easybuild/easyconfigs/__archive__/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb deleted file mode 100644 index 8a5646c25c1..00000000000 --- a/easybuild/easyconfigs/__archive__/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb +++ /dev/null @@ -1,40 +0,0 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild - -name = 'impi' -version = '2019.7.217' - -homepage = 'https://software.intel.com/en-us/intel-mpi-library/' -description = "Intel MPI Library, compatible with MPICH ABI" - -toolchain = {'name': 'iccifortcuda', 'version': '2020a'} - -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/'] -sources = ['l_mpi_%(version)s.tgz'] -checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] - -dependencies = [ - # needed by libfabric provider MLX introduced in Intel MPI v2019.6, - # https://software.intel.com/en-us/articles/improve-performance-and-stability-with-intel-mpi-library-on-infiniband - ('UCX', '1.8.0'), -] - -dontcreateinstalldir = True - -components = ['intel-mpi', 'intel-psxe', 'intel-imb'] - -# set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = True - -modextravars = { - # to enable SLURM integration with srun (site-specific) - # 'I_MPI_PMI_LIBRARY': 'libpmi2.so', - - # set this if mpirun gives you a floating point exception (SIGFPE), see - # https://software.intel.com/en-us/forums/intel-clusters-and-hpc-technology/topic/852307 - # 'I_MPI_HYDRA_TOPOLIB': 'ipl', -} - -# may be needed if you enable I_MPI_PMI_LIBRARY above -# osdependencies = [('slurm-libpmi')] - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/i/inferCNV/inferCNV-1.3.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/i/inferCNV/inferCNV-1.3.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 294022f5b18..00000000000 --- a/easybuild/easyconfigs/__archive__/i/inferCNV/inferCNV-1.3.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'RPackage' - -name = 'inferCNV' -version = '1.3.3' -versionsuffix = '-Python-%(pyver)s' -local_biocver = '3.11' - -homepage = 'https://github.com/broadinstitute/inferCNV/wiki' -description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence - for somatic large-scale chromosomal copy number alterations, such as gains or - deletions of entire chromosomes or large segments of chromosomes.""" - -source_urls = [GITHUB_SOURCE] -sources = ['%(namelower)s-v%(version)s.tar.gz'] -checksums = ['693f7399a232a6cdd7f84bb4038420bdc5ca681545f9b124edb256c390fba541'] - -github_account = 'broadinstitute' -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('R', '4.0.0'), - ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), - ('rjags', '4-10', '-R-%(rver)s'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['infercnv'], -} - -options = {'modulename': 'infercnv'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/i/intel/intel-2020.06-impi-18.5.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2020.06-impi-18.5.eb deleted file mode 100644 index cfabfdcb03f..00000000000 --- a/easybuild/easyconfigs/__archive__/i/intel/intel-2020.06-impi-18.5.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'Toolchain' - -name = 'intel' -version = '2020.06-impi-18.5' - -homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' -description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." - -toolchain = SYSTEM - -local_compver = '2020.1.217' -local_gccver = '9.3.0' -dependencies = [ - ('GCCcore', local_gccver), - ('binutils', '2.34', '', ('GCCcore', local_gccver)), - ('iccifort', local_compver), - ('impi', '2018.5.288', '', ('iccifort', local_compver)), - ('imkl', local_compver, '', ('iimpi', version)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/i/intel/intel-2020a.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2020a.eb deleted file mode 100644 index 99726a2e2be..00000000000 --- a/easybuild/easyconfigs/__archive__/i/intel/intel-2020a.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'Toolchain' - -name = 'intel' -version = '2020a' - -homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' -description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." - -toolchain = SYSTEM - -local_compver = '2020.1.217' -local_gccver = '9.3.0' -dependencies = [ - ('GCCcore', local_gccver), - ('binutils', '2.34', '', ('GCCcore', local_gccver)), - ('iccifort', local_compver), - ('impi', '2019.7.217', '', ('iccifort', local_compver)), - ('imkl', local_compver, '', ('iimpi', version)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/i/intelcuda/intelcuda-2020a.eb b/easybuild/easyconfigs/__archive__/i/intelcuda/intelcuda-2020a.eb deleted file mode 100644 index 49ffa18e384..00000000000 --- a/easybuild/easyconfigs/__archive__/i/intelcuda/intelcuda-2020a.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'Toolchain' - -name = 'intelcuda' -version = '2020a' - -homepage = '(none)' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, - Intel MPI & Intel MKL, with CUDA toolkit""" - -toolchain = SYSTEM - -local_compver = '2020.1.217' -dependencies = [ - ('iccifort', local_compver), - ('CUDA', '11.0.2', '', ('iccifort', local_compver)), - ('impi', '2019.7.217', '', ('iccifortcuda', version)), - ('imkl', local_compver, '', ('iimpic', version)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/i/intervaltree/intervaltree-0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/i/intervaltree/intervaltree-0.1-GCCcore-9.3.0.eb deleted file mode 100644 index b72834694a6..00000000000 --- a/easybuild/easyconfigs/__archive__/i/intervaltree/intervaltree-0.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'intervaltree' -version = '0.1' - -homepage = 'https://github.com/ekg/intervaltree' -description = """An interval tree can be used to efficiently find a set of numeric intervals - overlapping or containing another interval. This library provides a basic implementation of an - interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'ekg' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307'] - -builddependencies = [('binutils', '2.34')] - -skipsteps = ['configure'] - -preinstallopts = 'DESTDIR="" PREFIX=%(installdir)s' - -sanity_check_paths = { - 'files': ['bin/interval_tree_test', 'include/intervaltree/IntervalTree.h'], - 'dirs': [], -} -sanity_check_commands = ["interval_tree_test"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/i/intltool/intltool-0.51.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/i/intltool/intltool-0.51.0-GCCcore-9.3.0.eb deleted file mode 100644 index 284ffe7421e..00000000000 --- a/easybuild/easyconfigs/__archive__/i/intltool/intltool-0.51.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'intltool' -version = '0.51.0' - -homepage = 'https://freedesktop.org/wiki/Software/intltool/' -description = """intltool is a set of tools to centralize translation of - many different file formats using GNU gettext-compatible PO files.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] -sources = [SOURCE_TAR_GZ] -patches = ['intltool-%(version)s_fix-Perl-compat.patch'] -checksums = [ - '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz - 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch -] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Perl', '5.30.2'), -] - -sanity_check_paths = { - 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/i/iomkl/iomkl-2020a.eb b/easybuild/easyconfigs/__archive__/i/iomkl/iomkl-2020a.eb deleted file mode 100644 index abc327a638f..00000000000 --- a/easybuild/easyconfigs/__archive__/i/iomkl/iomkl-2020a.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = "Toolchain" - -name = 'iomkl' -version = '2020a' - -homepage = 'https://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & - OpenMPI.""" - -toolchain = SYSTEM - -local_compver = '2020.1.217' - -dependencies = [ - ('iccifort', local_compver), - ('OpenMPI', '4.0.3', '', ('iccifort', local_compver)), - ('imkl', local_compver, '', ('iompi', version)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/i/iompi/iompi-2020a.eb b/easybuild/easyconfigs/__archive__/i/iompi/iompi-2020a.eb deleted file mode 100644 index 496a912655d..00000000000 --- a/easybuild/easyconfigs/__archive__/i/iompi/iompi-2020a.eb +++ /dev/null @@ -1,19 +0,0 @@ -# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ -easyblock = "Toolchain" - -name = 'iompi' -version = '2020a' - -homepage = 'https://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" - -toolchain = SYSTEM - -local_compver = '2020.1.217' - -dependencies = [ - ('iccifort', local_compver), - ('OpenMPI', '4.0.3', '', ('iccifort', local_compver)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/__archive__/j/JAGS/JAGS-4.3.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/j/JAGS/JAGS-4.3.0-foss-2020a.eb deleted file mode 100644 index 03264fda9c0..00000000000 --- a/easybuild/easyconfigs/__archive__/j/JAGS/JAGS-4.3.0-foss-2020a.eb +++ /dev/null @@ -1,36 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel - -easyblock = 'ConfigureMake' - -name = 'JAGS' -version = '4.3.0' - -homepage = 'http://mcmc-jags.sourceforge.net/' -description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis - of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download') -] -sources = [SOURCE_TAR_GZ] -checksums = ['8ac5dd57982bfd7d5f0ee384499d62f3e0bb35b5f1660feb368545f1186371fc'] - -configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' - - -sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], - 'dirs': [], -} - -modextrapaths = { - 'JAGS_INCLUDE': 'include/%(name)s', - 'JAGS_LIB': 'lib', -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-2.0.14-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-2.0.14-GCCcore-9.3.0.eb deleted file mode 100644 index c35a612e4a1..00000000000 --- a/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-2.0.14-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'JasPer' -version = '2.0.14' - -homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' - -description = """ - The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in - the JPEG-2000 Part-1 standard. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.ece.uvic.ca/~frodo/jasper/software/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['2a1f61e55afe8b4ce8115e1508c5d7cb314d56dfcc2dd323f90c072f88ccf57b'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -separate_build_dir = True - -configopts = '-DJAS_ENABLE_DOC=OFF ' - -sanity_check_paths = { - 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], - 'dirs': ['include'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-2.0.16-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-2.0.16-GCCcore-9.3.0.eb deleted file mode 100644 index b32ff8e50fa..00000000000 --- a/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-2.0.16-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'JasPer' -version = '2.0.16' - -homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' - -description = """ - The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in - the JPEG-2000 Part-1 standard. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GITHUB_LOWER_SOURCE] -github_account = 'mdadams' -sources = ['version-%(version)s.tar.gz'] -checksums = ['f1d8b90f231184d99968f361884e2054a1714fdbbd9944ba1ae4ebdcc9bbfdb1'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -separate_build_dir = True - -configopts = '-DJAS_ENABLE_DOC=OFF ' - -sanity_check_paths = { - 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], - 'dirs': ['include'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/j/JsonCpp/JsonCpp-1.9.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/j/JsonCpp/JsonCpp-1.9.4-GCCcore-9.3.0.eb deleted file mode 100644 index 287d84a1143..00000000000 --- a/easybuild/easyconfigs/__archive__/j/JsonCpp/JsonCpp-1.9.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = "CMakeNinja" - -name = 'JsonCpp' -version = '1.9.4' - -homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' -description = """ JsonCpp is a C++ library that allows manipulating JSON values, - including serialization and deserialization to and from strings. It can also preserve existing comment in - unserialization/serialization steps, making it a convenient format to store user input files. """ - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['e34a628a8142643b976c7233ef381457efad79468c67cb1ae0b83a33d7493999'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Ninja', '1.10.0'), - ('pkg-config', '0.29.2'), - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ['include/json/json.h', 'lib/libjsoncpp.so'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/j/jax/TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d_mlir-build-env.patch b/easybuild/easyconfigs/__archive__/j/jax/TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d_mlir-build-env.patch deleted file mode 100644 index ad451807936..00000000000 --- a/easybuild/easyconfigs/__archive__/j/jax/TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d_mlir-build-env.patch +++ /dev/null @@ -1,12 +0,0 @@ -make TensorFlow pick up on build environment defined by EasyBuild -author: Denis Kristak, Pavel Grochal (INUITS) ---- tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d/third_party/mlir/tblgen.bzl.orig 2021-08-13 16:18:12.735593126 +0200 -+++ tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d/third_party/mlir/tblgen.bzl 2021-08-13 16:18:48.615675683 +0200 -@@ -173,6 +173,7 @@ - inputs = trans_srcs, - executable = ctx.executable.tblgen, - arguments = [args], -+ use_default_shell_env = True, - mnemonic = "TdGenerate", - ) - diff --git a/easybuild/easyconfigs/__archive__/j/jbigkit/jbigkit-2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/j/jbigkit/jbigkit-2.1-GCCcore-9.3.0.eb deleted file mode 100644 index 17e3d06b740..00000000000 --- a/easybuild/easyconfigs/__archive__/j/jbigkit/jbigkit-2.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -# EasyBuild easyconfig -easyblock = 'MakeCp' - -name = 'jbigkit' -version = '2.1' - -homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' - -description = """JBIG-KIT is a software implementation of the JBIG1 data - compression standard (ITU-T T.82), which was designed for bi-level image - data, such as scanned documents.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] -sources = [SOURCE_TAR_GZ] -patches = [ - '%(name)s-%(version)s_libpath.patch', - '%(name)s-%(version)s_shlib.patch', -] -checksums = [ - 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932', # jbigkit-2.1.tar.gz - '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce', # jbigkit-2.1_libpath.patch - '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696', # jbigkit-2.1_shlib.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -files_to_copy = [ - (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), - (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), - (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), -] - -sanity_check_paths = { - 'files': ['lib/libjbig85.a', 'lib/libjbig.a', - 'bin/pbmtojbg', 'bin/jbgtopbm', - 'include/jbig.h', 'include/jbig_ar.h', - ], - 'dirs': ['bin', 'include', 'lib'] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/j/jemalloc/jemalloc-5.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/j/jemalloc/jemalloc-5.2.1-GCCcore-9.3.0.eb deleted file mode 100644 index ead39ccbcee..00000000000 --- a/easybuild/easyconfigs/__archive__/j/jemalloc/jemalloc-5.2.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'jemalloc' -version = '5.2.1' - -homepage = 'http://jemalloc.net' -description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and - scalable concurrency support.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/jemalloc/jemalloc/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['ed51b0b37098af4ca6ed31c22324635263f8ad6471889e0592a9c0dba9136aea'] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), -] - -# From version 5.2.1 (or maybe earlier) it does no longer build, -# nor try to install, documentation if xsltproc is missing. -# So we can use normal installation. -preconfigopts = "./autogen.sh && " -configopts = "--with-version=%(version)s-0-g0000 " # build with version info - -sanity_check_paths = { - 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, - 'include/jemalloc/jemalloc.h'], - 'dirs': [], -} - -# jemalloc can be used via $LD_PRELOAD, but we don't enable this by -# default, you need to opt-in to it -# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.3.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 593d5f1cec3..00000000000 --- a/easybuild/easyconfigs/__archive__/k/Keras/Keras-2.3.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Keras' -version = '2.3.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://keras.io/' -description = """ -Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('h5py', '2.10.0', versionsuffix), - ('TensorFlow', '2.3.1', versionsuffix), -] - -exts_list = [ - ('Keras_Applications', '1.0.8', { - 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], - }), - ('Keras_Preprocessing', '1.1.2', { - 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], - }), - (name, version, { - 'checksums': ['321d43772006a25a1d58eea17401ef2a34d388b588c9f7646c34796151ebc8cc'], - }), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/k/Kraken/Kraken-1.1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/k/Kraken/Kraken-1.1.1-GCCcore-9.3.0.eb deleted file mode 100644 index 671e915621b..00000000000 --- a/easybuild/easyconfigs/__archive__/k/Kraken/Kraken-1.1.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PackedBinary' - -name = 'Kraken' -version = '1.1.1' - -homepage = 'https://ccb.jhu.edu/software/%(namelower)s/' -description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, - usually obtained through metagenomic studies. Previous attempts by other - bioinformatics software to accomplish this task have often used sequence - alignment or machine learning techniques that were quite slow, leading to - the development of less sensitive but much faster abundance estimation - programs. Kraken aims to achieve high sensitivity and high speed by - utilizing exact alignments of k-mers and a novel classification algorithm.""" - -# Part is compiled with CXX, the rest is in Perl -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -github_account = 'DerrickWood' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-1.1_CXX-CXXFLAGS.patch'] -checksums = [ - '73e48f40418f92b8cf036ca1da727ca3941da9b78d4c285b81ba3267326ac4ee', # v1.1.1.tar.gz - '84c017d6a80ccaac1e23561c83cac90bcc3d62baa8d31657a7dafbc2c3f29726', # Kraken-1.1.1_CXX-CXXFLAGS.patch -] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Perl', '5.30.2'), - # Jellyfish 1.x might not be required anymore in version 1.1.1, - # see https://github.com/DerrickWood/kraken/issues/69 - ('wget', '1.20.3'), -] - -install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' -install_cmd += './install_%(namelower)s.sh %(installdir)s' - -sanity_check_paths = { - 'files': ['add_to_library.sh', 'build_kraken_db.sh', 'check_for_jellyfish.sh', 'classify', 'clean_db.sh', - 'cp_into_tempfile.pl', 'db_shrink', 'db_sort', 'download_genomic_library.sh', - 'download_taxonomy.sh', 'kraken', 'kraken-build', 'kraken-filter', 'krakenlib.pm', - 'kraken-mpa-report', 'kraken-report', 'kraken-translate', 'make_seqid_to_taxid_map', - 'read_merger.pl', 'report_gi_numbers.pl', 'set_lcas', 'shrink_db.sh', - 'standard_installation.sh', 'upgrade_db.sh', 'verify_gi_numbers.pl'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/k/Kraken2/Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch b/easybuild/easyconfigs/__archive__/k/Kraken2/Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch deleted file mode 100644 index 0acdcfb8bfe..00000000000 --- a/easybuild/easyconfigs/__archive__/k/Kraken2/Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch +++ /dev/null @@ -1,12 +0,0 @@ -tweak Makefile such that $CXX and $CXXFLAGS are picked up from the environment -B. Hajgato (Free University Brussels, VUB), Kenneth Hoste (HPC-UGent) ---- kraken2-2.0.6-beta/src/Makefile.orig 2018-06-26 21:19:26.000000000 +0200 -+++ kraken2-2.0.6-beta/src/Makefile 2018-07-09 14:00:54.566891002 +0200 -@@ -1,5 +1,5 @@ --CXX = g++ --CXXFLAGS = -fopenmp -Wall -std=c++11 -O3 -+CXX ?= g++ -+CXXFLAGS ?= -fopenmp -Wall -std=c++11 -O3 - CXXFLAGS += -DLINEAR_PROBING - - .PHONY: all clean install diff --git a/easybuild/easyconfigs/__archive__/k/Kraken2/Kraken2-2.0.9-beta-gompi-2020a-Perl-5.30.2.eb b/easybuild/easyconfigs/__archive__/k/Kraken2/Kraken2-2.0.9-beta-gompi-2020a-Perl-5.30.2.eb deleted file mode 100644 index 4254c46096b..00000000000 --- a/easybuild/easyconfigs/__archive__/k/Kraken2/Kraken2-2.0.9-beta-gompi-2020a-Perl-5.30.2.eb +++ /dev/null @@ -1,55 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'Kraken2' -version = '2.0.9-beta' -versionsuffix = '-Perl-%(perlver)s' - -homepage = 'http://www.ccb.jhu.edu/software/%(namelower)s/' -description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, - usually obtained through metagenomic studies. Previous attempts by other - bioinformatics software to accomplish this task have often used sequence - alignment or machine learning techniques that were quite slow, leading to - the development of less sensitive but much faster abundance estimation - programs. Kraken aims to achieve high sensitivity and high speed by - utilizing exact alignments of k-mers and a novel classification algorithm.""" - -# part is compiled with $CXX, the rest is in Perl -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'openmp': True, 'cstd': 'c++11'} - -github_account = 'DerrickWood' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = [ - '%(name)s-2.0.7-beta_CXX-CXXFLAGS.patch', - 'Kraken2-2.1.2_fix_ncbi_https_server.patch', -] -checksums = [ - '0287cf4df4b5d5511a9132d9ab37a8d76864bae445579efb9cb76db7e9c09eba', # v2.0.9-beta.tar.gz - '191291e51a846d193a12486ab84496d5dd221a05c84648688b1351bb84d7adb2', # Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch - '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116', # Kraken2-2.1.2_fix_ncbi_https_server.patch -] - -dependencies = [ - ('Perl', '5.30.2'), - ('BLAST+', '2.10.1'), - ('wget', '1.20.3'), -] - -install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' -install_cmd += './install_kraken2.sh %(installdir)s' - -sanity_check_paths = { - 'files': [ - '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh', - 'build_db', 'build_gg_taxonomy.pl', 'build_kraken2_db.sh', 'build_rdp_taxonomy.pl', 'build_silva_taxonomy.pl', - 'classify', 'clean_db.sh', 'cp_into_tempfile.pl', 'download_genomic_library.sh', 'download_taxonomy.sh', - 'dump_table', 'estimate_capacity', 'kraken2', 'kraken2-build', 'kraken2-inspect', 'kraken2lib.pm', - 'lookup_accession_numbers.pl', 'make_seqid2taxid_map.pl', 'mask_low_complexity.sh', 'rsync_from_ncbi.pl', - 'scan_fasta_file.pl'], - 'dirs': [], -} - -modextrapaths = {'PATH': ''} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/k/kallisto/kallisto-0.46.1-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/k/kallisto/kallisto-0.46.1-iimpi-2020a.eb deleted file mode 100644 index 8cd48cc2de6..00000000000 --- a/easybuild/easyconfigs/__archive__/k/kallisto/kallisto-0.46.1-iimpi-2020a.eb +++ /dev/null @@ -1,38 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'CMakeMake' - -name = 'kallisto' -version = '0.46.1' - -homepage = 'https://pachterlab.github.io/kallisto/' -description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally - of target sequences using high-throughput sequencing reads.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -github_account = 'pachterlab' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231'] - -builddependencies = [ - ('Autotools', '20180311'), - ('CMake', '3.16.4'), -] - -dependencies = [('HDF5', '1.10.6')] - -preconfigopts = "cd ../%(name)s-%(version)s/ext/htslib/ && autoreconf && cd - &&" - -maxparallel = 1 - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['bin/kallisto'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 04ae795d6f7..00000000000 --- a/easybuild/easyconfigs/__archive__/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,67 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'kedro' -version = '0.16.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/quantumblacklabs/kedro' -description = """ -Kedro is an open-source Python framework that applies software engineering -best-practice to data and machine-learning pipelines. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('IPython', '7.15.0', versionsuffix), -] - -exts_list = [ - ('anyconfig', '0.9.7', { - 'checksums': ['4d6016ae6eecc5e502bc7e99ae0639c5710c5c67bde5f21b06b9eaafd9ce0e7e'], - }), - ('cachetools', '4.1.1', { - 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], - }), - ('binaryornot', '0.4.4', { - 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], - }), - ('arrow', '0.16.0', { - 'checksums': ['92aac856ea5175c804f7ccb96aca4d714d936f1c867ba59d747a8096ec30e90a'], - }), - ('jinja2-time', '0.2.0', { - 'checksums': ['d14eaa4d315e7688daa4969f616f226614350c48730bfa1692d2caebd8c90d40'], - }), - ('poyo', '0.5.0', { - 'checksums': ['e26956aa780c45f011ca9886f044590e2d8fd8b61db7b1c1cf4e0869f48ed4dd'], - }), - ('whichcraft', '0.6.1', { - 'checksums': ['acdbb91b63d6a15efbd6430d1d7b2d36e44a71697e93e19b7ded477afd9fce87'], - }), - ('cookiecutter', '1.6.0', { - 'checksums': ['1316a52e1c1f08db0c9efbf7d876dbc01463a74b155a0d83e722be88beda9a3e'], - }), - ('fsspec', '0.6.3', { - 'checksums': ['7a6d48af15b2416c5007706039e6d46d083c89229e7cdf6474b5ef5e7e687b00'], - }), - ('jmespath', '0.10.0', { - 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], - }), - ('pip-tools', '5.0.0', { - 'modulename': 'piptools', - 'checksums': ['2045d0414e9db71c036443efa229ff1b76dfe47a3cb022d6154a1c9e207f0867'], - }), - ('python-json-logger', '0.1.9', { - 'modulename': 'pythonjsonlogger', - 'checksums': ['e3636824d35ba6a15fc39f573588cba63cf46322a5dc86fb2f280229077e9fbe'], - }), - ('toposort', '1.5', { - 'checksums': ['dba5ae845296e3bf37b042c640870ffebcdeb8cd4df45adaa01d8c5476c557dd'], - }), - (name, version, { - 'checksums': ['84f992aaa6451e3b1c9fef2671fdebcc6715b027db7e22471adf8572214da6d1'], - }), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/k/kim-api/kim-api-2.1.3-foss-2020a.eb b/easybuild/easyconfigs/__archive__/k/kim-api/kim-api-2.1.3-foss-2020a.eb deleted file mode 100644 index 68e8c08230c..00000000000 --- a/easybuild/easyconfigs/__archive__/k/kim-api/kim-api-2.1.3-foss-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'kim-api' -version = '2.1.3' - -homepage = 'https://openkim.org/' -description = """Open Knowledgebase of Interatomic Models. - -KIM is an API and OpenKIM is a collection of interatomic models (potentials) for -atomistic simulations. This is a library that can be used by simulation programs -to get access to the models in the OpenKIM database. - -This EasyBuild only installs the API, the models can be installed with the -package openkim-models, or the user can install them manually by running - kim-api-collections-management install user MODELNAME -or - kim-api-collections-management install user OpenKIM -to install them all. - """ - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://s3.openkim.org/kim-api/'] -sources = ['%(name)s-%(version)s.txz'] -checksums = ['88a5416006c65a2940d82fad49de0885aead05bfa8b59f87d287db5516b9c467'] - -dependencies = [ - ('CMake', '3.16.4'), # Also needed to install models, thus not just a builddependency. -] - -maxparallel = 1 - -modextravars = { - 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' -} - -sanity_check_paths = { - 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/k/kim-api/kim-api-2.1.3-intel-2020a.eb b/easybuild/easyconfigs/__archive__/k/kim-api/kim-api-2.1.3-intel-2020a.eb deleted file mode 100644 index 5b698d28523..00000000000 --- a/easybuild/easyconfigs/__archive__/k/kim-api/kim-api-2.1.3-intel-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'kim-api' -version = '2.1.3' - -homepage = 'https://openkim.org/' -description = """Open Knowledgebase of Interatomic Models. - -KIM is an API and OpenKIM is a collection of interatomic models (potentials) for -atomistic simulations. This is a library that can be used by simulation programs -to get access to the models in the OpenKIM database. - -This EasyBuild only installs the API, the models can be installed with the -package openkim-models, or the user can install them manually by running - kim-api-collections-management install user MODELNAME -or - kim-api-collections-management install user OpenKIM -to install them all. - """ - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://s3.openkim.org/kim-api/'] -sources = ['%(name)s-%(version)s.txz'] -checksums = ['88a5416006c65a2940d82fad49de0885aead05bfa8b59f87d287db5516b9c467'] - -dependencies = [ - ('CMake', '3.16.4'), # Also needed to install models, thus not just a builddependency. -] - -maxparallel = 1 - -modextravars = { - 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' -} - -sanity_check_paths = { - 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/LAME/LAME-3.100-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/LAME/LAME-3.100-GCCcore-9.3.0.eb deleted file mode 100644 index ec35bdb7ddc..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LAME/LAME-3.100-GCCcore-9.3.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Author: Stephane Thiell -### - -easyblock = 'ConfigureMake' - -name = 'LAME' -version = '3.100' - -homepage = 'http://lame.sourceforge.net/' -description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['LAME-3.99.5_check-tgetent.patch'] -checksums = [ - 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz - '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), -] - -dependencies = [('ncurses', '6.2')] - -preconfigopts = "autoconf && " - -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - -sanity_check_paths = { - 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/__archive__/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb deleted file mode 100644 index 64fb76ca4d1..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb +++ /dev/null @@ -1,109 +0,0 @@ -name = 'LAMMPS' -version = '3Mar2020' -local_python_versionsuffix = '-Python-%(pyver)s' -versionsuffix = local_python_versionsuffix -versionsuffix += '-kokkos' - -homepage = 'https://lammps.sandia.gov/' -description = """LAMMPS is a classical molecular dynamics code, and an acronym -for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has -potentials for solid-state materials (metals, semiconductors) and soft matter -(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be -used to model atoms or, more generically, as a parallel particle simulator at -the atomic, meso, or continuum scale. LAMMPS runs on single processors or in -parallel using message-passing techniques and a spatial-decomposition of the -simulation domain. The code is designed to be easy to modify or extend with new -functionality. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++11'} - -# 'https://github.com/lammps/lammps/archive/' -source_urls = [GITHUB_LOWER_SOURCE] -sources = [ - 'stable_%(version)s.tar.gz', - {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, -] -# see https://github.com/lammps/lammps/pull/1483 for why this is needed -patches = [ - 'LAMMPS-3Mar2020_fix-docs-build.patch', - 'lammps-stable_3Mar2020_hack_openmp_gcc9.patch', -] -checksums = [ - 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz - 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py - '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch - '41a0bcb828be22d38bb489bbd4b1fd7803d7771a2308371f01e961c52b8c869f', # lammps-stable_3Mar2020_hack_openmp_gcc9.patch -] - -local_source_dir_name = '%(namelower)s-%(version)s' - -builddependencies = [ - ('CMake', '3.16.4'), - ('pkg-config', '0.29.2'), - ('archspec', '0.1.0', local_python_versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), - ('netCDF', '4.7.4'), - ('GSL', '2.6'), - ('zlib', '1.2.11'), - ('gzip', '1.10'), - ('cURL', '7.69.1'), - ('HDF5', '1.10.6'), - ('tbb', '2020.1'), - ('PCRE', '8.44'), - ('libxml2', '2.9.10'), - ('FFmpeg', '4.2.2'), - ('Voro++', '0.4.6'), - ('kim-api', '2.1.3'), - ('Eigen', '3.3.7'), - ('yaff', '1.6.0', local_python_versionsuffix), - ('PLUMED', '2.6.0', local_python_versionsuffix), - ('ScaFaCoS', '1.0.1'), - ('VTK', '8.2.0', local_python_versionsuffix), -] - -# To use additional custom configuration options, use the 'configopts' easyconfig parameter -# See docs and lammps easyblock for more information. -# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options - -# Disable building the docs -configopts = "-DBUILD_DOC=off " - -# auto-enabled by easyblock -# 'GPU' - if cuda package is present and kokkos is disabled -# 'KOKKOS' - if kokkos is enabled (by default) -# -# not enabled (yet), needs more work/additional dependencies: -# 'LATTE', - https://lammps.sandia.gov/doc/Build_extras.html#latte-package -# 'MSCG', - https://lammps.sandia.gov/doc/Build_extras.html#mscg-package -general_packages = [ - 'ASPHERE', 'BODY', 'CLASS2', 'COLLOID', 'COMPRESS', 'CORESHELL', 'DIPOLE', - 'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC', - 'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID', - 'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI', -] - -# not enabled (yet), needs more work/additional dependencies: -# ADIOS - https://lammps.sandia.gov/doc/Build_extras.html#user-adios-package -# AWPMD - https://lammps.sandia.gov/doc/Build_extras.html#user-awpmd-package -# QUIP - https://lammps.sandia.gov/doc/Build_extras.html#user-quip-package -user_packages = [ - 'ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE', - 'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC', - 'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC', - 'SCAFACOS', 'SDPD', 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', 'VTK' -] - -enhance_sanity_check = True - -# run short test case to make sure installation doesn't produce blatently incorrect results; -# this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b -sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/__archive__/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb deleted file mode 100644 index b7c188891e1..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb +++ /dev/null @@ -1,118 +0,0 @@ -name = 'LAMMPS' -version = '3Mar2020' -local_python_versionsuffix = '-Python-%(pyver)s' -versionsuffix = local_python_versionsuffix -versionsuffix += '-kokkos' - -homepage = 'https://lammps.sandia.gov/' -description = """LAMMPS is a classical molecular dynamics code, and an acronym -for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has -potentials for solid-state materials (metals, semiconductors) and soft matter -(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be -used to model atoms or, more generically, as a parallel particle simulator at -the atomic, meso, or continuum scale. LAMMPS runs on single processors or in -parallel using message-passing techniques and a spatial-decomposition of the -simulation domain. The code is designed to be easy to modify or extend with new -functionality. -""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++11'} - -# 'https://github.com/lammps/lammps/archive/' -source_urls = [GITHUB_LOWER_SOURCE] -sources = [ - 'stable_%(version)s.tar.gz', - {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, -] -patches = [ - 'LAMMPS-3Mar2020_fix-docs-build.patch', - 'lammps-stable_3Mar2020_intel_ebflag.patch', -] -checksums = [ - 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz - 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py - '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch - '3b04681bf8d5c60818a197905f68c83e477ef41824278ebc05d437ecac6d5c0a', # lammps-stable_3Mar2020_intel_ebflag.patch -] - -local_source_dir_name = '%(namelower)s-%(version)s' - -builddependencies = [ - ('CMake', '3.16.4'), - ('pkg-config', '0.29.2'), - ('archspec', '0.1.0', local_python_versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), - ('netCDF', '4.7.4'), - ('GSL', '2.6'), - ('zlib', '1.2.11'), - ('gzip', '1.10'), - ('cURL', '7.69.1'), - ('HDF5', '1.10.6'), - ('tbb', '2020.1'), - ('PCRE', '8.44'), - ('libxml2', '2.9.10'), - ('FFmpeg', '4.2.2'), - ('Voro++', '0.4.6'), - ('kim-api', '2.1.3'), - ('Eigen', '3.3.7'), - ('yaff', '1.6.0', local_python_versionsuffix), - ('PLUMED', '2.6.0', local_python_versionsuffix), - ('ScaFaCoS', '1.0.1'), - # See below for why this is not included - # ('VTK', '8.2.0', local_python_versionsuffix), -] - -# Build the documentation with an initialized MPI, otherwise sphinx-build will crash. -# This is known issue with intel/2020a. See easybuilders/easybuild-easyconfigs issue #10213 -local_doccmake = '%(builddir)s/%(namelower)s-stable_%(version)s/cmake/Modules/Documentation.cmake' -preconfigopts = "sed -i 's/sphinx-build/%%(mpi_cmd_prefix)s sphinx-build/g' %s &&" % local_doccmake - -# To use additional custom configuration options, use the 'configopts' easyconfig parameter -# See docs and lammps easyblock for more information. -# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options - -# Disable building the docs -configopts = "-DBUILD_DOC=off " - -# auto-enabled by easyblock -# 'GPU' - if cuda package is present and kokkos is disabled -# 'KOKKOS' - if kokkos is enabled (by default) -# -# not enabled (yet), needs more work/additional dependencies: -# 'LATTE', - https://lammps.sandia.gov/doc/Build_extras.html#latte-package -# 'MSCG', - https://lammps.sandia.gov/doc/Build_extras.html#mscg-package -general_packages = [ - 'ASPHERE', 'BODY', 'CLASS2', 'COLLOID', 'COMPRESS', 'CORESHELL', 'DIPOLE', - 'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC', - 'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID', - 'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI', -] - -# not enabled (yet), needs more work/additional dependencies: -# ADIOS - https://lammps.sandia.gov/doc/Build_extras.html#user-adios-package -# AWPMD - https://lammps.sandia.gov/doc/Build_extras.html#user-awpmd-package -# QUIP - https://lammps.sandia.gov/doc/Build_extras.html#user-quip-package -# VTK - support is available in the foss version but currently fails to build for intel -# due to https://software.intel.com/en-us/forums/intel-fortran-compiler/topic/746611 -# see https://github.com/lammps/lammps/issues/1964 for details -user_packages = [ - 'ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE', - 'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC', - 'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC', - 'SCAFACOS', 'SDPD', 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF' -] - -enhance_sanity_check = True - -# run short test case to make sure installation doesn't produce blatently incorrect results; -# this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b -# (requires an MPI context for intel/2020a) -sanity_check_commands = ["cd %(builddir)s && %(mpi_cmd_prefix)s python lammps_vs_yaff_test_single_point_energy.py"] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/LAMMPS/LAMMPS-3Mar2020_fix-docs-build.patch b/easybuild/easyconfigs/__archive__/l/LAMMPS/LAMMPS-3Mar2020_fix-docs-build.patch deleted file mode 100644 index 65d5defb1ec..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LAMMPS/LAMMPS-3Mar2020_fix-docs-build.patch +++ /dev/null @@ -1,31 +0,0 @@ -fix hanging during building of documentation (hanging sphinx-build processes), -and prevent auto-downloading of Sphinx and dependencies to build documentation (already provided via EasyBuild) -author: Kenneth Hoste (HPC-UGent) ---- lammps-stable_3Mar2020/cmake/Modules/Documentation.cmake.orig 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/cmake/Modules/Documentation.cmake 2020-05-03 11:26:14.441071541 +0200 -@@ -3,8 +3,6 @@ - ############################################################################### - option(BUILD_DOC "Build LAMMPS documentation" OFF) - if(BUILD_DOC) -- include(ProcessorCount) -- ProcessorCount(NPROCS) - find_package(PythonInterp 3 REQUIRED) - - set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv) -@@ -22,14 +20,14 @@ - OUTPUT requirements.txt - DEPENDS docenv - COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt -- COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade -+ #COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade - COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters - ) - - add_custom_command( - OUTPUT html - DEPENDS ${DOC_SOURCES} docenv requirements.txt -- COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html -+ COMMAND sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html - ) - - add_custom_target( diff --git a/easybuild/easyconfigs/__archive__/l/LAMMPS/lammps-stable_3Mar2020_hack_openmp_gcc9.patch b/easybuild/easyconfigs/__archive__/l/LAMMPS/lammps-stable_3Mar2020_hack_openmp_gcc9.patch deleted file mode 100644 index f36d414562c..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LAMMPS/lammps-stable_3Mar2020_hack_openmp_gcc9.patch +++ /dev/null @@ -1,3969 +0,0 @@ -Patch generated by recursively applying -lammps-stable_3Mar2020.orig/src/USER-OMP/hack_openmp_for_pgi_gcc9.sh -to the 'src' directory, which allows this version of LAMMPS to build -for GCC 9. - -Alan O'Cais 20200324 -diff -Nru lammps-stable_3Mar2020.orig/src/MPIIO/dump_atom_mpiio.cpp lammps-stable_3Mar2020/src/MPIIO/dump_atom_mpiio.cpp ---- lammps-stable_3Mar2020.orig/src/MPIIO/dump_atom_mpiio.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/MPIIO/dump_atom_mpiio.cpp 2020-03-20 16:49:44.619401713 +0100 -@@ -587,7 +587,7 @@ - mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char)); - mpifh_buffer_line_per_thread[i][0] = '\0'; - --#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) -+#pragma omp parallel default(shared) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) - { - int tid = omp_get_thread_num(); - int m=0; -@@ -677,7 +677,7 @@ - mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char)); - mpifh_buffer_line_per_thread[i][0] = '\0'; - --#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) -+#pragma omp parallel default(shared) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) - { - int tid = omp_get_thread_num(); - int m=0; -diff -Nru lammps-stable_3Mar2020.orig/src/MPIIO/dump_cfg_mpiio.cpp lammps-stable_3Mar2020/src/MPIIO/dump_cfg_mpiio.cpp ---- lammps-stable_3Mar2020.orig/src/MPIIO/dump_cfg_mpiio.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/MPIIO/dump_cfg_mpiio.cpp 2020-03-20 16:49:44.623401733 +0100 -@@ -365,7 +365,7 @@ - mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char)); - mpifh_buffer_line_per_thread[i][0] = '\0'; - --#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) -+#pragma omp parallel default(shared) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) - { - int tid = omp_get_thread_num(); - int m=0; -diff -Nru lammps-stable_3Mar2020.orig/src/MPIIO/dump_custom_mpiio.cpp lammps-stable_3Mar2020/src/MPIIO/dump_custom_mpiio.cpp ---- lammps-stable_3Mar2020.orig/src/MPIIO/dump_custom_mpiio.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/MPIIO/dump_custom_mpiio.cpp 2020-03-20 16:49:44.627401752 +0100 -@@ -612,7 +612,7 @@ - mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char)); - mpifh_buffer_line_per_thread[i][0] = '\0'; - --#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) -+#pragma omp parallel default(shared) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) - { - int tid = omp_get_thread_num(); - int m=0; -diff -Nru lammps-stable_3Mar2020.orig/src/MPIIO/dump_xyz_mpiio.cpp lammps-stable_3Mar2020/src/MPIIO/dump_xyz_mpiio.cpp ---- lammps-stable_3Mar2020.orig/src/MPIIO/dump_xyz_mpiio.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/MPIIO/dump_xyz_mpiio.cpp 2020-03-20 16:49:44.631401773 +0100 -@@ -350,7 +350,7 @@ - mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char)); - mpifh_buffer_line_per_thread[i][0] = '\0'; - --#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) -+#pragma omp parallel default(shared) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) - { - int tid = omp_get_thread_num(); - int m=0; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-DIFFRACTION/compute_saed.cpp lammps-stable_3Mar2020/src/USER-DIFFRACTION/compute_saed.cpp ---- lammps-stable_3Mar2020.orig/src/USER-DIFFRACTION/compute_saed.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-DIFFRACTION/compute_saed.cpp 2020-03-20 16:49:45.761407407 +0100 -@@ -418,7 +418,7 @@ - double frac = 0.1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(offset,ASFSAED,typelocal,xlocal,Fvec,m,frac) -+#pragma omp parallel default(shared) shared(offset,ASFSAED,typelocal,xlocal,Fvec,m,frac) - #endif - { - double *f = new double[ntypes]; // atomic structure factor by type -diff -Nru lammps-stable_3Mar2020.orig/src/USER-DIFFRACTION/compute_xrd.cpp lammps-stable_3Mar2020/src/USER-DIFFRACTION/compute_xrd.cpp ---- lammps-stable_3Mar2020.orig/src/USER-DIFFRACTION/compute_xrd.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-DIFFRACTION/compute_xrd.cpp 2020-03-20 16:49:45.765407427 +0100 -@@ -353,7 +353,7 @@ - double frac = 0.1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(typelocal,xlocal,Fvec,m,frac,ASFXRD) -+#pragma omp parallel default(shared) shared(typelocal,xlocal,Fvec,m,frac,ASFXRD) - #endif - { - double *f = new double[ntypes]; // atomic structure factor by type -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/angle_charmm_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/angle_charmm_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/angle_charmm_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/angle_charmm_intel.cpp 2020-03-20 16:49:46.332410255 +0100 -@@ -134,7 +134,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oeangle,ov0,ov1,ov2,ov3,ov4,ov5) - #endif -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/angle_harmonic_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/angle_harmonic_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/angle_harmonic_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/angle_harmonic_intel.cpp 2020-03-20 16:49:46.336410275 +0100 -@@ -134,7 +134,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oeangle,ov0,ov1,ov2,ov3,ov4,ov5) - #endif -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/bond_fene_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/bond_fene_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/bond_fene_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/bond_fene_intel.cpp 2020-03-20 16:49:46.339410290 +0100 -@@ -127,7 +127,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oebond,ov0,ov1,ov2,ov3,ov4,ov5) - #endif -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/bond_harmonic_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/bond_harmonic_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/bond_harmonic_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/bond_harmonic_intel.cpp 2020-03-20 16:49:46.342410305 +0100 -@@ -127,7 +127,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oebond,ov0,ov1,ov2,ov3,ov4,ov5) - #endif -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_charmm_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/dihedral_charmm_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_charmm_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/dihedral_charmm_intel.cpp 2020-03-20 16:49:46.347410330 +0100 -@@ -148,7 +148,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oevdwl,oecoul,oedihedral,ov0,ov1,ov2,ov3,ov4,ov5, \ - opv0,opv1,opv2,opv3,opv4,opv5) -@@ -522,7 +522,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oevdwl,oecoul,oedihedral,ov0,ov1,ov2,ov3,ov4,ov5, \ - opv0,opv1,opv2,opv3,opv4,opv5) -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_fourier_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/dihedral_fourier_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_fourier_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/dihedral_fourier_intel.cpp 2020-03-20 16:49:46.351410350 +0100 -@@ -127,7 +127,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oedihedral,ov0,ov1,ov2,ov3,ov4,ov5) - #endif -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_harmonic_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/dihedral_harmonic_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_harmonic_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/dihedral_harmonic_intel.cpp 2020-03-20 16:49:46.354410364 +0100 -@@ -127,7 +127,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oedihedral,ov0,ov1,ov2,ov3,ov4,ov5) - #endif -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_opls_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/dihedral_opls_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_opls_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/dihedral_opls_intel.cpp 2020-03-20 16:49:46.358410384 +0100 -@@ -131,7 +131,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oedihedral,ov0,ov1,ov2,ov3,ov4,ov5) - #endif -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/fix_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/fix_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/fix_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/fix_intel.cpp 2020-03-20 16:49:46.364410414 +0100 -@@ -220,7 +220,7 @@ - comm->nthreads = nomp; - } else { - int nthreads; -- #pragma omp parallel default(none) shared(nthreads) -+ #pragma omp parallel default(shared) - nthreads = omp_get_num_threads(); - comm->nthreads = nthreads; - } -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/improper_cvff_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/improper_cvff_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/improper_cvff_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/improper_cvff_intel.cpp 2020-03-20 16:49:46.385410519 +0100 -@@ -138,7 +138,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oeimproper,ov0,ov1,ov2,ov3,ov4,ov5) - #endif -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/improper_harmonic_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/improper_harmonic_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/improper_harmonic_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/improper_harmonic_intel.cpp 2020-03-20 16:49:46.389410539 +0100 -@@ -139,7 +139,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(f_start,f_stride,fc) \ - reduction(+:oeimproper,ov0,ov1,ov2,ov3,ov4,ov5) - #endif -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/npair_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/npair_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/npair_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/npair_intel.cpp 2020-03-20 16:49:46.414410664 +0100 -@@ -263,7 +263,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(overflow, nstencilp, binstart, binend) - #endif - { -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/pppm_disp_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/pppm_disp_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/pppm_disp_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/pppm_disp_intel.cpp 2020-03-20 16:49:46.509411137 +0100 -@@ -728,7 +728,7 @@ - int flag = 0; - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr, delx, dely, delz, sft, p2g, nup, nlow, nxlo,\ - nylo, nzlo, nxhi, nyhi, nzhi) reduction(+:flag) if(!_use_lrt) - #endif -@@ -802,7 +802,7 @@ - int nthr = comm->nthreads; - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nthr, nlocal, global_density) if(!_use_lrt) - #endif - { -@@ -908,7 +908,7 @@ - - // reduce all the perthread_densities into global_density - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nthr, global_density) if(!_use_lrt) - #endif - { -@@ -950,7 +950,7 @@ - int nthr = comm->nthreads; - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nthr, nlocal, global_density) if(!_use_lrt) - #endif - { -@@ -1058,7 +1058,7 @@ - - // reduce all the perthread_densities into global_density - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nthr, global_density) if(!_use_lrt) - #endif - { -@@ -1233,7 +1233,7 @@ - int nthr = comm->nthreads; - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nthr, nlocal, global_density) if(!_use_lrt) - #endif - { -@@ -1342,7 +1342,7 @@ - - // reduce all the perthread_densities into global_density - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nthr, global_density) if(!_use_lrt) - #endif - { -@@ -1385,7 +1385,7 @@ - - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) if(!_use_lrt) - #endif - { -@@ -1535,7 +1535,7 @@ - FFT_SCALAR * _noalias const particle_ekz = this->particle_ekz; - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) if(!_use_lrt) - #endif - { -@@ -1733,7 +1733,7 @@ - - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) if(!_use_lrt) - #endif - { -@@ -1880,7 +1880,7 @@ - FFT_SCALAR * _noalias const particle_ekz = this->particle_ekz; - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) if(!_use_lrt) - #endif - { -@@ -2077,7 +2077,7 @@ - - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) if(!_use_lrt) - #endif - { -@@ -2311,7 +2311,7 @@ - FFT_SCALAR * _noalias const particle_ekz6 = this->particle_ekz6; - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) if(!_use_lrt) - #endif - { -@@ -2602,7 +2602,7 @@ - - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) if(!_use_lrt) - #endif - { -@@ -2761,7 +2761,7 @@ - int nthr = comm->nthreads; - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) if(!_use_lrt) - #endif - { -diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/pppm_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/pppm_intel.cpp ---- lammps-stable_3Mar2020.orig/src/USER-INTEL/pppm_intel.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-INTEL/pppm_intel.cpp 2020-03-20 16:49:46.515411167 +0100 -@@ -360,7 +360,7 @@ - error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) reduction(+:flag) if(!_use_lrt) - #endif - { -@@ -434,7 +434,7 @@ - nthr = comm->nthreads; - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nthr, nlocal, global_density) if(!_use_lrt) - #endif - { -@@ -537,7 +537,7 @@ - // reduce all the perthread_densities into global_density - if (nthr > 1) { - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nthr, global_density) if(!_use_lrt) - #endif - { -@@ -586,7 +586,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) if(!_use_lrt) - #endif - { -@@ -737,7 +737,7 @@ - } - - #if defined(_OPENMP) -- #pragma omp parallel default(none) \ -+ #pragma omp parallel default(shared) \ - shared(nlocal, nthr) if(!_use_lrt) - #endif - { -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_charmm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_charmm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_charmm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_charmm_omp.cpp 2020-03-20 16:49:48.136419251 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_class2_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_class2_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_class2_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_class2_omp.cpp 2020-03-20 16:49:48.139419266 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_delta_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_delta_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_delta_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_delta_omp.cpp 2020-03-20 16:49:48.141419276 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_omp.cpp 2020-03-20 16:49:48.144419291 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_periodic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_periodic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_periodic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_periodic_omp.cpp 2020-03-20 16:49:48.147419306 +0100 -@@ -49,7 +49,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_shift_exp_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_shift_exp_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_shift_exp_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_shift_exp_omp.cpp 2020-03-20 16:49:48.149419316 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_shift_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_shift_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_shift_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_shift_omp.cpp 2020-03-20 16:49:48.152419330 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_squared_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_squared_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_squared_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_squared_omp.cpp 2020-03-20 16:49:48.154419341 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_dipole_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_dipole_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_dipole_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_dipole_omp.cpp 2020-03-20 16:49:48.157419355 +0100 -@@ -51,7 +51,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_fourier_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_fourier_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_fourier_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_fourier_omp.cpp 2020-03-20 16:49:48.160419370 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_fourier_simple_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_fourier_simple_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_fourier_simple_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_fourier_simple_omp.cpp 2020-03-20 16:49:48.164419390 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_harmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_harmonic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_harmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_harmonic_omp.cpp 2020-03-20 16:49:48.166419400 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_quartic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_quartic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_quartic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_quartic_omp.cpp 2020-03-20 16:49:48.169419415 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_sdk_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_sdk_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_sdk_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_sdk_omp.cpp 2020-03-20 16:49:48.171419425 +0100 -@@ -49,7 +49,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_table_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/angle_table_omp.cpp 2020-03-20 16:49:48.174419440 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nanglelist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_class2_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_class2_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_class2_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_class2_omp.cpp 2020-03-20 16:49:48.177419455 +0100 -@@ -47,7 +47,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_fene_expand_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_fene_expand_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_fene_expand_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_fene_expand_omp.cpp 2020-03-20 16:49:48.179419465 +0100 -@@ -48,7 +48,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_fene_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_fene_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_fene_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_fene_omp.cpp 2020-03-20 16:49:48.182419480 +0100 -@@ -48,7 +48,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_gromos_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_gromos_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_gromos_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_gromos_omp.cpp 2020-03-20 16:49:48.184419490 +0100 -@@ -44,7 +44,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_omp.cpp 2020-03-20 16:49:48.187419505 +0100 -@@ -46,7 +46,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp 2020-03-20 16:49:48.189419515 +0100 -@@ -46,7 +46,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_shift_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_shift_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_shift_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_shift_omp.cpp 2020-03-20 16:49:48.191419525 +0100 -@@ -46,7 +46,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_morse_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_morse_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_morse_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_morse_omp.cpp 2020-03-20 16:49:48.194419540 +0100 -@@ -46,7 +46,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_nonlinear_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_nonlinear_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_nonlinear_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_nonlinear_omp.cpp 2020-03-20 16:49:48.196419550 +0100 -@@ -46,7 +46,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_quartic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_quartic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_quartic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_quartic_omp.cpp 2020-03-20 16:49:48.199419565 +0100 -@@ -52,7 +52,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_table_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/bond_table_omp.cpp 2020-03-20 16:49:48.202419580 +0100 -@@ -46,7 +46,7 @@ - const int inum = neighbor->nbondlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_charmm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_charmm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_charmm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_charmm_omp.cpp 2020-03-20 16:49:48.205419595 +0100 -@@ -56,7 +56,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_class2_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_class2_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_class2_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_class2_omp.cpp 2020-03-20 16:49:48.209419615 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp 2020-03-20 16:49:48.212419630 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_fourier_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_fourier_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_fourier_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_fourier_omp.cpp 2020-03-20 16:49:48.215419645 +0100 -@@ -49,7 +49,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_harmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_harmonic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_harmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_harmonic_omp.cpp 2020-03-20 16:49:48.218419660 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_helix_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_helix_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_helix_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_helix_omp.cpp 2020-03-20 16:49:48.222419680 +0100 -@@ -53,7 +53,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_multi_harmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_multi_harmonic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_multi_harmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_multi_harmonic_omp.cpp 2020-03-20 16:49:48.227419705 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_nharmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_nharmonic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_nharmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_nharmonic_omp.cpp 2020-03-20 16:49:48.230419719 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_opls_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_opls_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_opls_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_opls_omp.cpp 2020-03-20 16:49:48.235419744 +0100 -@@ -51,7 +51,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_quadratic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_quadratic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_quadratic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_quadratic_omp.cpp 2020-03-20 16:49:48.238419759 +0100 -@@ -51,7 +51,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_table_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_table_omp.cpp 2020-03-20 16:49:48.241419774 +0100 -@@ -113,7 +113,7 @@ - const int inum = neighbor->ndihedrallist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/domain_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/domain_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/domain_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/domain_omp.cpp 2020-03-20 16:49:48.244419789 +0100 -@@ -45,7 +45,7 @@ - const int nlocal = atom->nlocal; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - imageint idim,otherdims; -@@ -143,7 +143,7 @@ - const int num = n; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < num; i++) { - x[i].x = h[0]*x[i].x + h[5]*x[i].y + h[4]*x[i].z + boxlo[0]; -@@ -163,7 +163,7 @@ - const int num = n; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < num; i++) { - double delta0 = x[i].x - boxlo[0]; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/ewald_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/ewald_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/ewald_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/ewald_omp.cpp 2020-03-20 16:49:48.247419804 +0100 -@@ -104,7 +104,7 @@ - v0=v1=v2=v3=v4=v5=0.0; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) reduction(+:eng_tmp,v0,v1,v2,v3,v4,v5) -+#pragma omp parallel default(shared) reduction(+:eng_tmp,v0,v1,v2,v3,v4,v5) - #endif - { - -@@ -234,7 +234,7 @@ - const int nthreads = comm->nthreads; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - int i,ifrom,ito,k,l,m,n,ic,tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_gravity_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_gravity_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_gravity_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_gravity_omp.cpp 2020-03-20 16:49:48.250419819 +0100 -@@ -69,7 +69,7 @@ - - if (rmass) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(-:grav) -+#pragma omp parallel for default(shared) reduction(-:grav) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { -@@ -81,7 +81,7 @@ - } - } else { - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(-:grav) -+#pragma omp parallel for default(shared) reduction(-:grav) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_neigh_history_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_neigh_history_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_neigh_history_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_neigh_history_omp.cpp 2020-03-20 16:49:48.254419839 +0100 -@@ -73,7 +73,7 @@ - maxpartner = 0; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - -@@ -199,7 +199,7 @@ - for (int i = 0; i < nall_neigh; i++) npartner[i] = 0; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - -@@ -373,7 +373,7 @@ - maxpartner = 0; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - -@@ -525,7 +525,7 @@ - - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_asphere_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nh_asphere_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_asphere_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_nh_asphere_omp.cpp 2020-03-20 16:49:48.256419849 +0100 -@@ -82,7 +82,7 @@ - // merged with FixNHOMP instead of calling it for the COM update. - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { -@@ -122,7 +122,7 @@ - // principal moments of inertia - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { -@@ -163,7 +163,7 @@ - - if (which == NOBIAS) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { -@@ -177,7 +177,7 @@ - } - } else if (which == BIAS) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - double buf[3]; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nh_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_nh_omp.cpp 2020-03-20 16:49:48.259419864 +0100 -@@ -57,7 +57,7 @@ - if (allremap) domain->x2lamda(nlocal); - else { - #if defined (_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & dilate_group_bit) -@@ -207,7 +207,7 @@ - if (allremap) domain->lamda2x(nlocal); - else { - #if defined (_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & dilate_group_bit) -@@ -235,7 +235,7 @@ - - if (which == NOBIAS) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { -@@ -253,7 +253,7 @@ - } - } else if (which == BIAS) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - double buf[3]; -@@ -289,7 +289,7 @@ - if (atom->rmass) { - const double * _noalias const rmass = atom->rmass; - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { -@@ -303,7 +303,7 @@ - const double *_noalias const mass = atom->mass; - const int * _noalias const type = atom->type; - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { -@@ -330,7 +330,7 @@ - // x update by full step only for atoms in group - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { -@@ -352,7 +352,7 @@ - - if (which == NOBIAS) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { -@@ -363,7 +363,7 @@ - } - } else if (which == BIAS) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - double buf[3]; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_sphere_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nh_sphere_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_sphere_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_nh_sphere_omp.cpp 2020-03-20 16:49:48.262419879 +0100 -@@ -85,7 +85,7 @@ - // 4 cases depending on radius vs shape and rmass vs mass - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { -@@ -115,7 +115,7 @@ - - if (which == NOBIAS) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { -@@ -129,7 +129,7 @@ - } - } else if (which == BIAS) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - double buf[3]; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nve_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nve_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nve_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_nve_omp.cpp 2020-03-20 16:49:48.279419964 +0100 -@@ -41,7 +41,7 @@ - if (atom->rmass) { - const double * const rmass = atom->rmass; - #if defined (_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { -@@ -58,7 +58,7 @@ - const double * const mass = atom->mass; - const int * const type = atom->type; - #if defined (_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { -@@ -87,7 +87,7 @@ - if (atom->rmass) { - const double * const rmass = atom->rmass; - #if defined (_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { -@@ -101,7 +101,7 @@ - const double * const mass = atom->mass; - const int * const type = atom->type; - #if defined (_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nve_sphere_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nve_sphere_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nve_sphere_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_nve_sphere_omp.cpp 2020-03-20 16:49:48.281419974 +0100 -@@ -49,7 +49,7 @@ - // update v,x,omega for all particles - // d_omega/dt = torque / inertia - #if defined(_OPENMP) --#pragma omp parallel for default(none) -+#pragma omp parallel for default(shared) - #endif - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { -@@ -76,7 +76,7 @@ - double * const * const mu = atom->mu; - if (dlm == NODLM) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) -+#pragma omp parallel for default(shared) - #endif - for (int i = 0; i < nlocal; i++) { - double g0,g1,g2,msq,scale; -@@ -95,7 +95,7 @@ - } - } else { - #if defined(_OPENMP) --#pragma omp parallel for default(none) -+#pragma omp parallel for default(shared) - #endif - // Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme - for (int i = 0; i < nlocal; i++) { -@@ -223,7 +223,7 @@ - // d_omega/dt = torque / inertia - - #if defined(_OPENMP) --#pragma omp parallel for default(none) -+#pragma omp parallel for default(shared) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nvt_sllod_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nvt_sllod_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nvt_sllod_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_nvt_sllod_omp.cpp 2020-03-20 16:49:48.290420019 +0100 -@@ -114,7 +114,7 @@ - MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two); - - #if defined(_OPENMP) --#pragma omp parallel for default(none) shared(h_two) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - double vdelu0,vdelu1,vdelu2,buf[3]; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_omp.cpp 2020-03-20 16:49:48.296420049 +0100 -@@ -70,7 +70,7 @@ - if (narg > 3) { - #if defined(_OPENMP) - if (strcmp(arg[3],"0") == 0) --#pragma omp parallel default(none) shared(nthreads) -+#pragma omp parallel default(shared) - nthreads = omp_get_num_threads(); - else - nthreads = force->inumeric(FLERR,arg[3]); -@@ -134,7 +134,7 @@ - thr = new ThrData *[nthreads]; - _nthr = nthreads; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(lmp) -+#pragma omp parallel default(shared) - #endif - { - const int tid = get_tid(); -@@ -186,7 +186,7 @@ - thr = new ThrData *[nthreads]; - _nthr = nthreads; - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - const int tid = get_tid(); -@@ -350,7 +350,7 @@ - double *drho = atom->drho; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(f,torque,erforce,de,drho) -+#pragma omp parallel default(shared) - #endif - { - const int tid = get_tid(); -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_nh_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_nh_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_nh_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_nh_omp.cpp 2020-03-20 16:49:48.313420133 +0100 -@@ -89,7 +89,7 @@ - double akt=0.0, akr=0.0; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) shared(scale_r,scale_t,scale_v) schedule(static) reduction(+:akt,akr) -+#pragma omp parallel for default(shared) schedule(static) reduction(+:akt,akr) - #endif - for (int ibody = 0; ibody < nbody; ibody++) { - double mbody[3],tbody[3],fquat[4]; -@@ -250,7 +250,7 @@ - int i; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) private(i) reduction(+:s0,s1,s2,s3,s4,s5) -+#pragma omp parallel for default(shared) private(i) reduction(+:s0,s1,s2,s3,s4,s5) - #endif - for (i = 0; i < nlocal; i++) { - const int ibody = body[i]; -@@ -289,7 +289,7 @@ - int i; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) private(i) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5) -+#pragma omp parallel for default(shared) private(i) reduction(+:s0,s1,s2,s3,s4,s5) - #endif - for (i = 0; i < nlocal; i++) { - const int ibody = body[i]; -@@ -330,7 +330,7 @@ - memset(&sum[0][0],0,6*nbody*sizeof(double)); - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -373,7 +373,7 @@ - MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world); - - #if defined(_OPENMP) --#pragma omp parallel for default(none) private(ibody) schedule(static) -+#pragma omp parallel for default(shared) private(ibody) schedule(static) - #endif - for (ibody = 0; ibody < nbody; ibody++) { - fcm[ibody][0] = all[ibody][0] + langextra[ibody][0]; -@@ -388,7 +388,7 @@ - - if (id_gravity) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) private(ibody) schedule(static) -+#pragma omp parallel for default(shared) private(ibody) schedule(static) - #endif - for (ibody = 0; ibody < nbody; ibody++) { - fcm[ibody][0] += gvec[0]*masstotal[ibody]; -@@ -433,7 +433,7 @@ - const double dtf2 = dtf * 2.0; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) shared(scale_t,scale_r) schedule(static) reduction(+:akt,akr) -+#pragma omp parallel for default(shared) schedule(static) reduction(+:akt,akr) - #endif - for (int ibody = 0; ibody < nbody; ibody++) { - double mbody[3],tbody[3],fquat[4]; -@@ -554,7 +554,7 @@ - if (allremap) domain->x2lamda(nlocal); - else { - #if defined (_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & dilate_group_bit) -@@ -586,7 +586,7 @@ - if (allremap) domain->lamda2x(nlocal); - else { - #if defined (_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) - if (mask[i] & dilate_group_bit) -@@ -631,7 +631,7 @@ - int i; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5) -+#pragma omp parallel for default(shared) private(i) reduction(+:v0,v1,v2,v3,v4,v5) - #endif - for (i = 0; i < nlocal; i++) { - const int ibody = body[i]; -@@ -832,7 +832,7 @@ - int i; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5) -+#pragma omp parallel for default(shared) private(i) reduction(+:v0,v1,v2,v3,v4,v5) - #endif - for (i = 0; i < nlocal; i++) { - const int ibody = body[i]; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_omp.cpp 2020-03-20 16:49:48.327420203 +0100 -@@ -47,7 +47,7 @@ - void FixRigidOMP::initial_integrate(int vflag) - { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int ibody = 0; ibody < nbody; ibody++) { - -@@ -120,7 +120,7 @@ - double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(+:s0,s1,s2,s3,s4,s5) -+#pragma omp parallel for default(shared) reduction(+:s0,s1,s2,s3,s4,s5) - #endif - for (int i = 0; i < nlocal; i++) { - const int ibody = body[i]; -@@ -158,7 +158,7 @@ - double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5) -+#pragma omp parallel for default(shared) reduction(+:s0,s1,s2,s3,s4,s5) - #endif - for (int i = 0; i < nlocal; i++) { - const int ibody = body[i]; -@@ -199,7 +199,7 @@ - memset(&sum[0][0],0,6*nbody*sizeof(double)); - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -246,7 +246,7 @@ - // fflag,tflag = 0 for some dimensions in 2d - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int ibody = 0; ibody < nbody; ibody++) { - fcm[ibody][0] = all[ibody][0] + langextra[ibody][0]; -@@ -261,7 +261,7 @@ - - if (id_gravity) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int ibody = 0; ibody < nbody; ibody++) { - fcm[ibody][0] += gvec[0]*masstotal[ibody]; -@@ -280,7 +280,7 @@ - // update vcm and angmom - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int ibody = 0; ibody < nbody; ibody++) { - -@@ -346,7 +346,7 @@ - const int nlocal = atom->nlocal; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) -+#pragma omp parallel for default(shared) reduction(+:v0,v1,v2,v3,v4,v5) - #endif - for (int i = 0; i < nlocal; i++) { - const int ibody = body[i]; -@@ -546,7 +546,7 @@ - const int nlocal = atom->nlocal; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) -+#pragma omp parallel for default(shared) reduction(+:v0,v1,v2,v3,v4,v5) - #endif - for (int i = 0; i < nlocal; i++) { - const int ibody = body[i]; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_small_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_small_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_small_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_small_omp.cpp 2020-03-20 16:49:48.331420223 +0100 -@@ -46,7 +46,7 @@ - { - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int ibody = 0; ibody < nlocal_body; ibody++) { - -@@ -117,7 +117,7 @@ - const int nthreads=comm->nthreads; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int ibody = 0; ibody < nlocal_body+nghost_body; ibody++) { - double * _noalias const fcm = body[ibody].fcm; -@@ -132,7 +132,7 @@ - // and then each thread only processes some bodies. - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -183,7 +183,7 @@ - - if (langflag) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int ibody = 0; ibody < nlocal_body; ibody++) { - double * _noalias const fcm = body[ibody].fcm; -@@ -201,7 +201,7 @@ - - if (id_gravity) { - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int ibody = 0; ibody < nbody; ibody++) { - double * _noalias const fcm = body[ibody].fcm; -@@ -222,7 +222,7 @@ - // update vcm and angmom, recompute omega - - #if defined(_OPENMP) --#pragma omp parallel for default(none) schedule(static) -+#pragma omp parallel for default(shared) schedule(static) - #endif - for (int ibody = 0; ibody < nlocal_body; ibody++) { - Body &b = body[ibody]; -@@ -294,7 +294,7 @@ - const int nlocal = atom->nlocal; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) -+#pragma omp parallel for default(shared) reduction(+:v0,v1,v2,v3,v4,v5) - #endif - for (int i = 0; i < nlocal; i++) { - const int ibody = atom2body[i]; -@@ -489,7 +489,7 @@ - const int nlocal = atom->nlocal; - - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) -+#pragma omp parallel for default(shared) reduction(+:v0,v1,v2,v3,v4,v5) - #endif - for (int i = 0; i < nlocal; i++) { - const int ibody = atom2body[i]; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_class2_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_class2_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_class2_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/improper_class2_omp.cpp 2020-03-20 16:49:48.336420248 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->nimproperlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_cossq_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_cossq_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_cossq_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/improper_cossq_omp.cpp 2020-03-20 16:49:48.339420263 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->nimproperlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_cvff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_cvff_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_cvff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/improper_cvff_omp.cpp 2020-03-20 16:49:48.342420278 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->nimproperlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_fourier_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_fourier_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_fourier_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/improper_fourier_omp.cpp 2020-03-20 16:49:48.346420298 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->nimproperlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_harmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_harmonic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_harmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/improper_harmonic_omp.cpp 2020-03-20 16:49:48.348420308 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->nimproperlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_ring_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_ring_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_ring_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/improper_ring_omp.cpp 2020-03-20 16:49:48.351420323 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->nimproperlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_umbrella_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_umbrella_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_umbrella_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/improper_umbrella_omp.cpp 2020-03-20 16:49:48.354420338 +0100 -@@ -50,7 +50,7 @@ - const int inum = neighbor->nimproperlist; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/msm_cg_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/msm_cg_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/msm_cg_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/msm_cg_omp.cpp 2020-03-20 16:49:48.358420358 +0100 -@@ -310,7 +310,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/msm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/msm_omp.cpp 2020-03-20 16:49:48.362420378 +0100 -@@ -52,7 +52,7 @@ - MSM::compute(eflag,vflag); - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -158,7 +158,7 @@ - const int n=nn; - - #if defined(_OPENMP) --#pragma omp parallel default(none) reduction(+:v0,v1,v2,v3,v4,v5,emsm) -+#pragma omp parallel default(shared) reduction(+:v0,v1,v2,v3,v4,v5,emsm) - #endif - { - double esum,v0sum,v1sum,v2sum,v3sum,v4sum,v5sum; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_atomonly_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_atomonly_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_atomonly_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_atomonly_omp.cpp 2020-03-20 16:49:48.364420388 +0100 -@@ -36,7 +36,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_ghost_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_ghost_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_ghost_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_ghost_omp.cpp 2020-03-20 16:49:48.367420403 +0100 -@@ -42,7 +42,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nall); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_omp.cpp 2020-03-20 16:49:48.369420413 +0100 -@@ -40,7 +40,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_multi_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_multi_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_multi_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_multi_omp.cpp 2020-03-20 16:49:48.372420428 +0100 -@@ -41,7 +41,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_nsq_ghost_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_nsq_ghost_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_nsq_ghost_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_nsq_ghost_omp.cpp 2020-03-20 16:49:48.375420443 +0100 -@@ -42,7 +42,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nall); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_nsq_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_nsq_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_nsq_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_nsq_omp.cpp 2020-03-20 16:49:48.378420458 +0100 -@@ -42,7 +42,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp 2020-03-20 16:49:48.381420473 +0100 -@@ -37,7 +37,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp 2020-03-20 16:49:48.384420487 +0100 -@@ -46,7 +46,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nall); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newtoff_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newtoff_omp.cpp 2020-03-20 16:49:48.387420503 +0100 -@@ -42,7 +42,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newton_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newton_omp.cpp 2020-03-20 16:49:48.390420517 +0100 -@@ -41,7 +41,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp 2020-03-20 16:49:48.392420527 +0100 -@@ -41,7 +41,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_halffull_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_halffull_newtoff_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_halffull_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_halffull_newtoff_omp.cpp 2020-03-20 16:49:48.395420542 +0100 -@@ -38,7 +38,7 @@ - NPAIR_OMP_INIT; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(inum_full); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_halffull_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_halffull_newton_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_halffull_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_halffull_newton_omp.cpp 2020-03-20 16:49:48.398420557 +0100 -@@ -38,7 +38,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(inum_full); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newtoff_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newtoff_omp.cpp 2020-03-20 16:49:48.401420572 +0100 -@@ -43,7 +43,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newton_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newton_omp.cpp 2020-03-20 16:49:48.404420587 +0100 -@@ -42,7 +42,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp 2020-03-20 16:49:48.407420602 +0100 -@@ -43,7 +43,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp 2020-03-20 16:49:48.409420612 +0100 -@@ -47,7 +47,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nall); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp 2020-03-20 16:49:48.412420627 +0100 -@@ -44,7 +44,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newton_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newton_omp.cpp 2020-03-20 16:49:48.415420642 +0100 -@@ -43,7 +43,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp 2020-03-20 16:49:48.417420652 +0100 -@@ -47,7 +47,7 @@ - const int respamiddle = list->respamiddle; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp 2020-03-20 16:49:48.421420672 +0100 -@@ -46,7 +46,7 @@ - const int respamiddle = list->respamiddle; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp 2020-03-20 16:49:48.423420682 +0100 -@@ -46,7 +46,7 @@ - const int respamiddle = list->respamiddle; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp 2020-03-20 16:49:48.426420697 +0100 -@@ -48,7 +48,7 @@ - const int respamiddle = list->respamiddle; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp 2020-03-20 16:49:48.429420712 +0100 -@@ -49,7 +49,7 @@ - const int respamiddle = list->respamiddle; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp 2020-03-20 16:49:48.432420727 +0100 -@@ -43,7 +43,7 @@ - NPAIR_OMP_INIT; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newton_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newton_omp.cpp 2020-03-20 16:49:48.435420742 +0100 -@@ -42,7 +42,7 @@ - NPAIR_OMP_INIT; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp 2020-03-20 16:49:48.437420752 +0100 -@@ -41,7 +41,7 @@ - - NPAIR_OMP_INIT; - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp 2020-03-20 16:49:48.440420767 +0100 -@@ -45,7 +45,7 @@ - NPAIR_OMP_INIT; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp 2020-03-20 16:49:48.442420777 +0100 -@@ -46,7 +46,7 @@ - NPAIR_OMP_INIT; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(list) -+#pragma omp parallel default(shared) - #endif - NPAIR_OMP_SETUP(nlocal); - -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_adp_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_adp_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_adp_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_adp_omp.cpp 2020-03-20 16:49:48.446420797 +0100 -@@ -62,7 +62,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_agni_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_agni_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_agni_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_agni_omp.cpp 2020-03-20 16:49:48.449420812 +0100 -@@ -49,7 +49,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_airebo_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_airebo_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_airebo_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_airebo_omp.cpp 2020-03-20 16:49:48.461420871 +0100 -@@ -58,7 +58,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) reduction(+:pv0,pv1,pv2) -+#pragma omp parallel default(shared) reduction(+:pv0,pv1,pv2) - #endif - { - int ifrom, ito, tid; -@@ -104,7 +104,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - int i,j,ii,jj,n,jnum,itype,jtype; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_beck_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_beck_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_beck_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_beck_omp.cpp 2020-03-20 16:49:48.464420887 +0100 -@@ -45,7 +45,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_long_omp.cpp 2020-03-20 16:49:48.467420901 +0100 -@@ -51,7 +51,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_msm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_msm_omp.cpp 2020-03-20 16:49:48.470420916 +0100 -@@ -48,7 +48,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_wolf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_wolf_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_wolf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_wolf_omp.cpp 2020-03-20 16:49:48.474420936 +0100 -@@ -45,7 +45,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_born_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_born_omp.cpp 2020-03-20 16:49:48.477420951 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_brownian_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_brownian_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_brownian_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_brownian_omp.cpp 2020-03-20 16:49:48.480420966 +0100 -@@ -135,7 +135,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_brownian_poly_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_brownian_poly_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_brownian_poly_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_brownian_poly_omp.cpp 2020-03-20 16:49:48.484420986 +0100 -@@ -135,7 +135,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_cut_omp.cpp 2020-03-20 16:49:48.486420996 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_long_omp.cpp 2020-03-20 16:49:48.489421011 +0100 -@@ -51,7 +51,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_msm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_msm_omp.cpp 2020-03-20 16:49:48.492421026 +0100 -@@ -48,7 +48,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_long_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_buck_long_coul_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_long_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_buck_long_coul_long_omp.cpp 2020-03-20 16:49:48.497421051 +0100 -@@ -56,7 +56,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -@@ -320,7 +320,7 @@ - const int nthreads = comm->nthreads; - const int inum = list->inum_inner; - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -@@ -345,7 +345,7 @@ - const int inum = list->inum_middle; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -@@ -375,7 +375,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_buck_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_buck_omp.cpp 2020-03-20 16:49:48.500421066 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_colloid_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_colloid_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_colloid_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_colloid_omp.cpp 2020-03-20 16:49:48.503421081 +0100 -@@ -46,7 +46,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_comb_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_comb_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_comb_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_comb_omp.cpp 2020-03-20 16:49:48.507421101 +0100 -@@ -52,7 +52,7 @@ - Short_neigh_thr(); - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -@@ -411,7 +411,7 @@ - - // loop over full neighbor list of my atoms - #if defined(_OPENMP) --#pragma omp parallel for private(ii) default(none) shared(potal,fac11e) -+#pragma omp parallel for private(ii) default(shared) - #endif - for (ii = 0; ii < inum; ii ++) { - double fqi,fqj,fqij,fqji,fqjj,delr1[3]; -@@ -564,7 +564,7 @@ - const int nthreads = comm->nthreads; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - int nj,*neighptrj; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_cut_omp.cpp 2020-03-20 16:49:48.510421116 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_cut_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_cut_soft_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_cut_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_cut_soft_omp.cpp 2020-03-20 16:49:48.512421126 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_debye_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_debye_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_debye_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_debye_omp.cpp 2020-03-20 16:49:48.515421141 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_diel_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_diel_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_diel_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_diel_omp.cpp 2020-03-20 16:49:48.517421151 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_dsf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_dsf_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_dsf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_dsf_omp.cpp 2020-03-20 16:49:48.520421166 +0100 -@@ -52,7 +52,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_long_omp.cpp 2020-03-20 16:49:48.523421181 +0100 -@@ -52,7 +52,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_long_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_long_soft_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_long_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_long_soft_omp.cpp 2020-03-20 16:49:48.526421196 +0100 -@@ -51,7 +51,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_msm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_msm_omp.cpp 2020-03-20 16:49:48.529421211 +0100 -@@ -49,7 +49,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_wolf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_wolf_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_wolf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_wolf_omp.cpp 2020-03-20 16:49:48.531421220 +0100 -@@ -45,7 +45,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_dpd_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_dpd_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_dpd_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_dpd_omp.cpp 2020-03-20 16:49:48.535421241 +0100 -@@ -80,7 +80,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_dpd_tstat_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_dpd_tstat_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_dpd_tstat_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_dpd_tstat_omp.cpp 2020-03-20 16:49:48.538421255 +0100 -@@ -79,7 +79,7 @@ - random_thr[0] = random; - } - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eam_cd_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_eam_cd_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eam_cd_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_eam_cd_omp.cpp 2020-03-20 16:49:48.545421290 +0100 -@@ -77,7 +77,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eam_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_eam_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eam_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_eam_omp.cpp 2020-03-20 16:49:48.551421320 +0100 -@@ -59,7 +59,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_edip_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_edip_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_edip_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_edip_omp.cpp 2020-03-20 16:49:48.555421340 +0100 -@@ -50,7 +50,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eim_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_eim_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eim_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_eim_omp.cpp 2020-03-20 16:49:48.558421355 +0100 -@@ -57,7 +57,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gauss_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gauss_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gauss_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_gauss_cut_omp.cpp 2020-03-20 16:49:48.561421370 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gauss_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gauss_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gauss_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_gauss_omp.cpp 2020-03-20 16:49:48.563421380 +0100 -@@ -45,7 +45,7 @@ - double occ = 0.0; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) reduction(+:occ) -+#pragma omp parallel default(shared) reduction(+:occ) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gayberne_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gayberne_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gayberne_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_gayberne_omp.cpp 2020-03-20 16:49:48.566421395 +0100 -@@ -45,7 +45,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hertz_history_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hertz_history_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hertz_history_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hertz_history_omp.cpp 2020-03-20 16:49:48.569421410 +0100 -@@ -69,7 +69,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hooke_history_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hooke_history_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hooke_history_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hooke_history_omp.cpp 2020-03-20 16:49:48.572421425 +0100 -@@ -70,7 +70,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hooke_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hooke_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hooke_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hooke_omp.cpp 2020-03-20 16:49:48.575421440 +0100 -@@ -65,7 +65,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp 2020-03-20 16:49:48.578421455 +0100 -@@ -74,7 +74,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp 2020-03-20 16:49:48.581421470 +0100 -@@ -74,7 +74,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj96_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj96_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj96_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj96_cut_omp.cpp 2020-03-20 16:49:48.584421485 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp 2020-03-20 16:49:48.586421495 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp 2020-03-20 16:49:48.589421510 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp 2020-03-20 16:49:48.592421525 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp 2020-03-20 16:49:48.595421540 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp 2020-03-20 16:49:48.597421550 +0100 -@@ -49,7 +49,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp 2020-03-20 16:49:48.601421569 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp 2020-03-20 16:49:48.605421590 +0100 -@@ -51,7 +51,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_omp.cpp 2020-03-20 16:49:48.608421604 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cubic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cubic_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cubic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cubic_omp.cpp 2020-03-20 16:49:48.611421620 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp 2020-03-20 16:49:48.614421634 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp 2020-03-20 16:49:48.617421649 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp 2020-03-20 16:49:48.619421659 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp 2020-03-20 16:49:48.622421674 +0100 -@@ -53,7 +53,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp 2020-03-20 16:49:48.625421689 +0100 -@@ -52,7 +52,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp 2020-03-20 16:49:48.628421704 +0100 -@@ -52,7 +52,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp 2020-03-20 16:49:48.632421724 +0100 -@@ -49,7 +49,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp 2020-03-20 16:49:48.635421739 +0100 -@@ -45,7 +45,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp 2020-03-20 16:49:48.639421759 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_omp.cpp 2020-03-20 16:49:48.642421774 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_soft_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_soft_omp.cpp 2020-03-20 16:49:48.645421789 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp 2020-03-20 16:49:48.648421804 +0100 -@@ -70,7 +70,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp 2020-03-20 16:49:48.652421824 +0100 -@@ -93,7 +93,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp 2020-03-20 16:49:48.657421849 +0100 -@@ -93,7 +93,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp 2020-03-20 16:49:48.661421869 +0100 -@@ -93,7 +93,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_expand_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_expand_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_expand_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_expand_omp.cpp 2020-03-20 16:49:48.665421889 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp 2020-03-20 16:49:48.669421909 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_gromacs_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_gromacs_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_gromacs_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_gromacs_omp.cpp 2020-03-20 16:49:48.673421929 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_long_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_long_coul_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_long_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_long_coul_long_omp.cpp 2020-03-20 16:49:48.681421968 +0100 -@@ -56,7 +56,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -@@ -318,7 +318,7 @@ - const int nthreads = comm->nthreads; - const int inum = list->inum_inner; - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -@@ -343,7 +343,7 @@ - const int inum = list->inum_middle; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -@@ -373,7 +373,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp 2020-03-20 16:49:48.692422023 +0100 -@@ -96,7 +96,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -@@ -379,7 +379,7 @@ - const int nthreads = comm->nthreads; - const int inum = list->inum_inner; - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -@@ -404,7 +404,7 @@ - const int inum = list->inum_middle; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -@@ -458,7 +458,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp 2020-03-20 16:49:48.695422038 +0100 -@@ -45,7 +45,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp 2020-03-20 16:49:48.698422053 +0100 -@@ -51,7 +51,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_omp.cpp 2020-03-20 16:49:48.701422068 +0100 -@@ -47,7 +47,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp 2020-03-20 16:49:48.704422083 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_smooth_linear_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_smooth_linear_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_smooth_linear_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_smooth_linear_omp.cpp 2020-03-20 16:49:48.707422098 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_smooth_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_smooth_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_smooth_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_smooth_omp.cpp 2020-03-20 16:49:48.709422108 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lubricate_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lubricate_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lubricate_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lubricate_omp.cpp 2020-03-20 16:49:48.713422128 +0100 -@@ -109,7 +109,7 @@ - - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lubricate_poly_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lubricate_poly_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lubricate_poly_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_lubricate_poly_omp.cpp 2020-03-20 16:49:48.717422148 +0100 -@@ -106,7 +106,7 @@ - - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_meam_spline_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_meam_spline_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_meam_spline_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_meam_spline_omp.cpp 2020-03-20 16:49:48.721422168 +0100 -@@ -57,7 +57,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_morse_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_morse_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_morse_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_morse_omp.cpp 2020-03-20 16:49:48.724422183 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_morse_smooth_linear_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_morse_smooth_linear_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_morse_smooth_linear_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_morse_smooth_linear_omp.cpp 2020-03-20 16:49:48.727422198 +0100 -@@ -47,7 +47,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp 2020-03-20 16:49:48.731422218 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp 2020-03-20 16:49:48.735422238 +0100 -@@ -51,7 +51,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_omp.cpp 2020-03-20 16:49:48.737422248 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_peri_lps_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_peri_lps_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_peri_lps_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_peri_lps_omp.cpp 2020-03-20 16:49:48.741422268 +0100 -@@ -62,7 +62,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_peri_pmb_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_peri_pmb_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_peri_pmb_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_peri_pmb_omp.cpp 2020-03-20 16:49:48.744422283 +0100 -@@ -58,7 +58,7 @@ - } - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_resquared_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_resquared_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_resquared_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_resquared_omp.cpp 2020-03-20 16:49:48.754422332 +0100 -@@ -45,7 +45,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_soft_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_soft_omp.cpp 2020-03-20 16:49:48.756422342 +0100 -@@ -47,7 +47,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_sw_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_sw_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_sw_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_sw_omp.cpp 2020-03-20 16:49:48.759422358 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_table_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_table_omp.cpp 2020-03-20 16:49:48.762422372 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_mod_c_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_mod_c_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_mod_c_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_mod_c_omp.cpp 2020-03-20 16:49:48.765422388 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_mod_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_mod_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_mod_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_mod_omp.cpp 2020-03-20 16:49:48.768422402 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_omp.cpp 2020-03-20 16:49:48.772422422 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_table_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_table_omp.cpp 2020-03-20 16:49:48.776422442 +0100 -@@ -68,7 +68,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_cut_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_cut_omp.cpp 2020-03-20 16:49:48.784422482 +0100 -@@ -92,7 +92,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_long_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_long_omp.cpp 2020-03-20 16:49:48.789422507 +0100 -@@ -93,7 +93,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_long_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_long_soft_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_long_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_long_soft_omp.cpp 2020-03-20 16:49:48.794422532 +0100 -@@ -93,7 +93,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_ufm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_ufm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_ufm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_ufm_omp.cpp 2020-03-20 16:49:48.798422552 +0100 -@@ -45,7 +45,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_vashishta_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_vashishta_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_vashishta_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_vashishta_omp.cpp 2020-03-20 16:49:48.802422572 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_vashishta_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_vashishta_table_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_vashishta_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_vashishta_table_omp.cpp 2020-03-20 16:49:48.806422592 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_yukawa_colloid_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_yukawa_colloid_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_yukawa_colloid_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_yukawa_colloid_omp.cpp 2020-03-20 16:49:48.809422607 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_yukawa_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_yukawa_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_yukawa_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_yukawa_omp.cpp 2020-03-20 16:49:48.813422627 +0100 -@@ -43,7 +43,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_zbl_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_zbl_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_zbl_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pair_zbl_omp.cpp 2020-03-20 16:49:48.817422647 +0100 -@@ -44,7 +44,7 @@ - const int inum = list->inum; - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - int ifrom, ito, tid; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_cg_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pppm_cg_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_cg_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pppm_cg_omp.cpp 2020-03-20 16:49:48.823422677 +0100 -@@ -59,7 +59,7 @@ - PPPMCGOMP::~PPPMCGOMP() - { - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -81,7 +81,7 @@ - PPPMCG::allocate(); - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -122,7 +122,7 @@ - const int twoorder = 2*order; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - double snx,sny,snz; -@@ -216,7 +216,7 @@ - double sf0=0.0,sf1=0.0,sf2=0.0,sf3=0.0,sf4=0.0,sf5=0.0; - - #if defined(_OPENMP) --#pragma omp parallel default(none) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) -+#pragma omp parallel default(shared) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) - #endif - { - double snx,sny,snz,sqk; -@@ -314,7 +314,7 @@ - PPPMCG::compute(eflag,vflag); - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -351,7 +351,7 @@ - const int iy = nyhi_out - nylo_out + 1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - const double * _noalias const q = atom->q; -@@ -443,7 +443,7 @@ - const int nthreads = comm->nthreads; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - FFT_SCALAR dx,dy,dz,x0,y0,z0,ekx,eky,ekz; -@@ -524,7 +524,7 @@ - const int nthreads = comm->nthreads; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - int i,ifrom,ito,tid,l,m,n,nx,ny,nz,mx,my,mz; -@@ -617,7 +617,7 @@ - const int nthreads = comm->nthreads; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - FFT_SCALAR dx,dy,dz,x0,y0,z0; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_disp_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pppm_disp_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_disp_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pppm_disp_omp.cpp 2020-03-20 16:49:48.831422716 +0100 -@@ -59,7 +59,7 @@ - PPPMDispOMP::~PPPMDispOMP() - { - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -87,7 +87,7 @@ - PPPMDisp::allocate(); - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -114,7 +114,7 @@ - void PPPMDispOMP::compute_gf() - { - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - -@@ -204,7 +204,7 @@ - void PPPMDispOMP::compute_gf_6() - { - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - double *prd; -@@ -311,7 +311,7 @@ - - PPPMDisp::compute(eflag,vflag); - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -366,7 +366,7 @@ - - int flag = 0; - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(+:flag) schedule(static) -+#pragma omp parallel for default(shared) reduction(+:flag) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - -@@ -419,7 +419,7 @@ - const int iy = nyhi_out - nylo_out + 1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - const double * _noalias const q = atom->q; -@@ -509,7 +509,7 @@ - const int iy = nyhi_out_6 - nylo_out_6 + 1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; -@@ -613,7 +613,7 @@ - const int iy = nyhi_out_6 - nylo_out_6 + 1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; -@@ -723,7 +723,7 @@ - - #if defined(_OPENMP) - const int nthreads = comm->nthreads; --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -828,7 +828,7 @@ - - #if defined(_OPENMP) - const int nthreads = comm->nthreads; --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -935,7 +935,7 @@ - - #if defined(_OPENMP) - const int nthreads = comm->nthreads; --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1034,7 +1034,7 @@ - - #if defined(_OPENMP) - const int nthreads = comm->nthreads; --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1138,7 +1138,7 @@ - - #if defined(_OPENMP) - const int nthreads = comm->nthreads; --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1248,7 +1248,7 @@ - - #if defined(_OPENMP) - const int nthreads = comm->nthreads; --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1350,7 +1350,7 @@ - - #if defined(_OPENMP) - const int nthreads = comm->nthreads; --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1486,7 +1486,7 @@ - - #if defined(_OPENMP) - const int nthreads = comm->nthreads; --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1663,7 +1663,7 @@ - - #if defined(_OPENMP) - const int nthreads = comm->nthreads; --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_disp_tip4p_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pppm_disp_tip4p_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_disp_tip4p_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pppm_disp_tip4p_omp.cpp 2020-03-20 16:49:48.839422756 +0100 -@@ -56,7 +56,7 @@ - { - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -84,7 +84,7 @@ - PPPMDispTIP4P::allocate(); - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -111,7 +111,7 @@ - void PPPMDispTIP4POMP::compute_gf() - { - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - -@@ -198,7 +198,7 @@ - void PPPMDispTIP4POMP::compute_gf_6() - { - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - double *prd; -@@ -302,7 +302,7 @@ - PPPMDispTIP4P::compute(eflag,vflag); - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -358,7 +358,7 @@ - - int flag = 0; - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(+:flag) schedule(static) -+#pragma omp parallel for default(shared) reduction(+:flag) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - dbl3_t xM; -@@ -434,7 +434,7 @@ - - int flag = 0; - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(+:flag) schedule(static) -+#pragma omp parallel for default(shared) reduction(+:flag) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - -@@ -487,7 +487,7 @@ - const int iy = nyhi_out - nylo_out + 1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - const double * _noalias const q = atom->q; -@@ -582,7 +582,7 @@ - const int iy = nyhi_out_6 - nylo_out_6 + 1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; -@@ -684,7 +684,7 @@ - const int iy = nyhi_out_6 - nylo_out_6 + 1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; -@@ -795,7 +795,7 @@ - const double boxloz = boxlo[2]; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - dbl3_t xM; -@@ -903,7 +903,7 @@ - const double boxloz = boxlo[2]; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - double s1,s2,s3,sf; -@@ -1018,7 +1018,7 @@ - const double * const * const x = atom->x; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1119,7 +1119,7 @@ - const double hz_inv = nz_pppm_6/zprd_slab; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1226,7 +1226,7 @@ - const double * const * const x = atom->x; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1325,7 +1325,7 @@ - const double * const * const x = atom->x; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1458,7 +1458,7 @@ - const double hz_inv = nz_pppm_6/zprd_slab; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -1632,7 +1632,7 @@ - const double * const * const x = atom->x; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pppm_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pppm_omp.cpp 2020-03-20 16:49:48.845422786 +0100 -@@ -61,7 +61,7 @@ - PPPM::allocate(); - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -81,7 +81,7 @@ - PPPMOMP::~PPPMOMP() - { - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -122,7 +122,7 @@ - const int twoorder = 2*order; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - double snx,sny,snz; -@@ -216,7 +216,7 @@ - double sf0=0.0,sf1=0.0,sf2=0.0,sf3=0.0,sf4=0.0,sf5=0.0; - - #if defined(_OPENMP) --#pragma omp parallel default(none) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) -+#pragma omp parallel default(shared) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) - #endif - { - double snx,sny,snz,sqk; -@@ -314,7 +314,7 @@ - PPPM::compute(eflag,vflag); - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -352,7 +352,7 @@ - const int iy = nyhi_out - nylo_out + 1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - const double * _noalias const q = atom->q; -@@ -449,7 +449,7 @@ - const double boxloz = boxlo[2]; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - FFT_SCALAR x0,y0,z0,ekx,eky,ekz; -@@ -534,7 +534,7 @@ - const double boxloz = boxlo[2]; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - double s1,s2,s3,sf; -@@ -627,7 +627,7 @@ - const double * _noalias const q = atom->q; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - FFT_SCALAR dx,dy,dz,x0,y0,z0; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_tip4p_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pppm_tip4p_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_tip4p_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/pppm_tip4p_omp.cpp 2020-03-20 16:49:48.851422816 +0100 -@@ -61,7 +61,7 @@ - PPPMTIP4POMP::~PPPMTIP4POMP() - { - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -83,7 +83,7 @@ - PPPMTIP4P::allocate(); - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -124,7 +124,7 @@ - const int twoorder = 2*order; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - double snx,sny,snz; -@@ -218,7 +218,7 @@ - double sf0=0.0,sf1=0.0,sf2=0.0,sf3=0.0,sf4=0.0,sf5=0.0; - - #if defined(_OPENMP) --#pragma omp parallel default(none) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) -+#pragma omp parallel default(shared) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) - #endif - { - double snx,sny,snz,sqk; -@@ -316,7 +316,7 @@ - PPPMTIP4P::compute(eflag,vflag); - - #if defined(_OPENMP) --#pragma omp parallel default(none) shared(eflag,vflag) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -355,7 +355,7 @@ - - int flag = 0; - #if defined(_OPENMP) --#pragma omp parallel for default(none) reduction(+:flag) schedule(static) -+#pragma omp parallel for default(shared) reduction(+:flag) schedule(static) - #endif - for (int i = 0; i < nlocal; i++) { - dbl3_t xM; -@@ -416,7 +416,7 @@ - const int iy = nyhi_out - nylo_out + 1; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - const double * _noalias const q = atom->q; -@@ -521,7 +521,7 @@ - const double boxloz = boxlo[2]; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - dbl3_t xM; -@@ -632,7 +632,7 @@ - const double boxloz = boxlo[2]; - - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - double s1,s2,s3,sf; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/reaxc_forces_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/reaxc_forces_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/reaxc_forces_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/reaxc_forces_omp.cpp 2020-03-20 16:49:48.863422876 +0100 -@@ -146,7 +146,7 @@ - reax_list *bonds = (*lists) + BONDS; - - #if defined(_OPENMP) --#pragma omp parallel default(shared) //default(none) -+#pragma omp parallel default(shared) //default(shared) - #endif - { - int i, j, k, pj, pk, start_j, end_j; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp 2020-03-20 16:49:48.867422896 +0100 -@@ -57,7 +57,7 @@ - const int nthreads = control->nthreads; - - #if defined(_OPENMP) --#pragma omp parallel default(shared) //default(none) -+#pragma omp parallel default(shared) //default(shared) - #endif - { - int i, j, k, pi, pk; -diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/respa_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/respa_omp.cpp ---- lammps-stable_3Mar2020.orig/src/USER-OMP/respa_omp.cpp 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/USER-OMP/respa_omp.cpp 2020-03-20 16:49:48.887422996 +0100 -@@ -146,7 +146,7 @@ - const int nall = atom->nlocal + atom->nghost; - const int nthreads = comm->nthreads; - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -241,7 +241,7 @@ - const int nall = atom->nlocal + atom->nghost; - const int nthreads = comm->nthreads; - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) -@@ -394,7 +394,7 @@ - const int nall = atom->nlocal + atom->nghost; - const int nthreads = comm->nthreads; - #if defined(_OPENMP) --#pragma omp parallel default(none) -+#pragma omp parallel default(shared) - #endif - { - #if defined(_OPENMP) diff --git a/easybuild/easyconfigs/__archive__/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch b/easybuild/easyconfigs/__archive__/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch deleted file mode 100644 index 51cc9e246a6..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch +++ /dev/null @@ -1,26 +0,0 @@ -# remove hard coded -xHost flag for intel compilers (useful on AMD systems, as -xHost may lead to mmx/sse code) -# OCT 26th 2020 by B. Hajgato (UGent) -diff -ru lammps-stable_3Mar2020.orig/cmake/Modules/Packages/USER-INTEL.cmake lammps-stable_3Mar2020/cmake/Modules/Packages/USER-INTEL.cmake ---- lammps-stable_3Mar2020.orig/cmake/Modules/Packages/USER-INTEL.cmake 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/cmake/Modules/Packages/USER-INTEL.cmake 2020-10-27 08:54:15.816960998 +0100 -@@ -77,7 +77,7 @@ - if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512") - else() -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ") - endif() - include(CheckCXXCompilerFlag) - foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict) -diff -ru lammps-stable_3Mar2020.orig/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi lammps-stable_3Mar2020/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi ---- lammps-stable_3Mar2020.orig/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi 2020-03-03 16:27:12.000000000 +0100 -+++ lammps-stable_3Mar2020/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi 2020-10-26 16:41:59.900088648 +0100 -@@ -7,7 +7,7 @@ - # specify flags and libraries needed for your compiler - - CC = mpiicpc -std=c++11 --OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \ -+OPTFLAGS = ${EBVAROPTFLAGS} -fp-model fast=2 -no-prec-div -qoverride-limits \ - -qopt-zmm-usage=high - CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \ - -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \ diff --git a/easybuild/easyconfigs/__archive__/l/LIBSVM/LIBSVM-3.24-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/LIBSVM/LIBSVM-3.24-GCCcore-9.3.0.eb deleted file mode 100644 index 3ea274e0802..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LIBSVM/LIBSVM-3.24-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'MakeCp' - -name = 'LIBSVM' -version = '3.24' - -homepage = 'https://www.csie.ntu.edu.tw/~cjlin/libsvm/' -description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression - (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'cjlin1' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%s.tar.gz' % version.replace('.', '')] -patches = ['LIBSVM-3.23_shared_lib.patch'] -checksums = [ - '3ba1ac74ee08c4dd57d3a9e4a861ffb57dab88c6a33fd53eac472fc84fbb2a8f', # v324.tar.gz - 'c0ede89365949644f5d7f11382a3f176fd76317c7f5ae5769226ff7c3a801fe6', # LIBSVM-3.23_shared_lib.patch -] - -dependencies = [('binutils', '2.34')] - -local_bins = ['svm-%s' % x for x in ['predict', 'scale', 'train']] - -files_to_copy = [ - (local_bins, 'bin'), - (['svm.o'], 'lib'), - (['libsvm*'], 'lib'), - (['svm.h'], 'include/libsvm'), - 'tools' -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_bins] + ['lib/libsvm.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/LLDB/LLDB-11.0.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/l/LLDB/LLDB-11.0.0-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 0eb1b746d19..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LLDB/LLDB-11.0.0-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'CMakeNinja' - -name = 'LLDB' -version = '11.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://lldb.llvm.org/' -description = """The debugger component of the LLVM project""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] -sources = [ - 'lldb-%(version)s.src.tar.xz', -] -checksums = [ - '8570c09f57399e21e0eea0dcd66ae0231d47eafc7a04d6fe5c4951b13c4d2c72', # lldb-11.0.0.src.tar.xz -] - -builddependencies = [ - ('binutils', '2.34'), - ('Clang', version), - ('CMake', '3.16.4'), - ('Ninja', '1.10.0'), - ('SWIG', '4.0.1'), -] - -dependencies = [ - ('ncurses', '6.2'), - ('libedit', '20191231'), - ('libxml2', '2.9.10'), - ('XZ', '5.2.5'), - ('Python', '3.8.2'), -] - -sanity_check_paths = { - 'files': ['bin/lldb', 'bin/lldb-server'], - 'dirs': [], -} - -moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/__archive__/l/LLVM/LLVM-9.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/LLVM/LLVM-9.0.1-GCCcore-9.3.0.eb deleted file mode 100644 index 80df8394089..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LLVM/LLVM-9.0.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'LLVM' -version = '9.0.1' - -homepage = "https://llvm.org/" -description = """The LLVM Core libraries provide a modern source- and target-independent - optimizer, along with code generation support for many popular CPUs - (as well as some less common ones!) These libraries are built around a well - specified code representation known as the LLVM intermediate representation - ("LLVM IR"). The LLVM Core libraries are well documented, and it is - particularly easy to invent your own language (or port an existing compiler) - to use LLVM as an optimizer and code generator.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'cstd': 'gnu++11'} - -source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s'] -sources = ['llvm-%(version)s.src.tar.xz'] -checksums = ['00a1ee1f389f81e9979f3a640a01c431b3021de0d42278f6508391a2f0b81c9a'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('Python', '3.8.2'), -] - -dependencies = [ - ('ncurses', '6.2'), - ('zlib', '1.2.11'), -] - -build_shared_libs = True - -sanity_check_paths = { - 'files': ['bin/llvm-ar', 'bin/FileCheck'], - 'dirs': ['include/llvm', 'include/llvm-c'], -} - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/l/LMDB/LMDB-0.9.24-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/LMDB/LMDB-0.9.24-GCCcore-9.3.0.eb deleted file mode 100644 index 9a9385b33d5..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LMDB/LMDB-0.9.24-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'MakeCp' - -name = 'LMDB' -version = '0.9.24' - -homepage = 'https://symas.com/lmdb' -description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance - of a pure in-memory database while retaining the persistence of standard disk-based databases.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/LMDB/lmdb/archive/'] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['44602436c52c29d4f301f55f6fd8115f945469b868348e3cddaf91ab2473ea26'] - -builddependencies = [('binutils', '2.34')] - -buildopts = 'CC="$CC" OPT="$CFLAGS"' - -runtest = 'test' - -files_to_copy = [ - (['lmdb.h', 'midl.h'], 'include'), - (['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'], 'bin'), - (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), -] - -sanity_check_paths = { - 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', - 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/LMfit/LMfit-1.0.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/l/LMfit/LMfit-1.0.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 52b2741dc15..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LMfit/LMfit-1.0.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'LMfit' -version = '1.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://lmfit.github.io/lmfit-py' -description = """Lmfit provides a high-level interface to non-linear optimization -and curve fitting problems for Python""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('asteval', '0.9.21', { - 'checksums': ['ee14ba2211cda1c76114e3e7b552cdd57e940309203d5f4106e6d6f2c2346a2e'], - }), - ('uncertainties', '3.1.5', { - 'checksums': ['9122c1e7e074196883b4a7a946e8482807b2f89675cb5e3798b87e0608ede903'], - }), - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['d249eb756899360f4d2a544c9458f47fc8f765ac22c09e099530585fd64e286e'], - }), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/l/LSD2/LSD2-1.9.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/LSD2/LSD2-1.9.7-GCCcore-9.3.0.eb deleted file mode 100644 index dcfde9c1f4f..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LSD2/LSD2-1.9.7-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'LSD2' -version = '1.9.7' - -homepage = 'https://github.com/tothuhien/lsd2' -description = "Least-squares methods to estimate rates and dates from phylogenies" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'tothuhien' - -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix_cmake_to_build_lib_and_binary.patch'] -checksums = [ - 'aee27370c77375adb1786da7d189652fd61b34129ea92641175d753846d4b270', # v1.9.7.tar.gz - # LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch - '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6', -] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -build_shared_libs = True - -sanity_check_paths = { - 'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.10-GCCcore-9.3.0.eb deleted file mode 100644 index 54e56fb1519..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.10-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -## - -easyblock = 'ConfigureMake' - -name = 'LZO' -version = '2.10' - -homepage = 'https://www.oberhumer.com/opensource/lzo/' -description = "Portable lossless data compression library" - -source_urls = [homepage + 'download/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -builddependencies = [('binutils', '2.34')] - -configopts = '--enable-shared' - -runtest = 'test' - -sanity_check_paths = { - 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], - 'dirs': ['include'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/l/LevelDB/LevelDB-1.22-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/LevelDB/LevelDB-1.22-GCCcore-9.3.0.eb deleted file mode 100644 index b5841675faa..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LevelDB/LevelDB-1.22-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'LevelDB' -version = '1.22' - -homepage = 'https://github.com/google/leveldb' -description = """LevelDB is a fast key-value storage library written at Google that provides an - ordered mapping from string keys to string values.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/google/leveldb/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['55423cac9e3306f4a9502c738a001e4a339d1a38ffbee7572d4a07d5d63949b2'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -configopts = '-DBUILD_SHARED_LIBS=ON -DLEVELDB_BUILD_BENCHMARKS=OFF ' - -sanity_check_paths = { - 'files': ['include/leveldb/cache.h', 'include/leveldb/table.h', - 'lib/libleveldb.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb deleted file mode 100644 index cf4eb2b08e9..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos , Alan O'Cais (JSC) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# https://hpcbios.readthedocs.org/en/latest/ -## -easyblock = 'ConfigureMake' - -name = 'LibTIFF' -version = '4.1.0' - -homepage = 'https://libtiff.maptools.org/' -description = "tiff: Library and tools for reading and writing TIFF data files" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'https://download.osgeo.org/libtiff/', -] -sources = ['tiff-%(version)s.tar.gz'] -checksums = ['5d29f32517dadb6dbcd1255ea5bbc93a2b54b94fbf83653b4d65c7d6775b8634'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.4'), - ('XZ', '5.2.5'), - ('jbigkit', '2.1'), - ('zstd', '1.4.4'), -] - -configopts = "--enable-ld-version-script " -configopts += "--disable-webp " - -sanity_check_paths = { - 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, - 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.6-foss-2020a.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.6-foss-2020a.eb deleted file mode 100644 index 97a00710a0c..00000000000 --- a/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.6-foss-2020a.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'Libint' -version = '1.1.6' - -homepage = 'https://sourceforge.net/p/libint/' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/evaleev/libint/archive/'] -sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] -checksums = ['f201b0c621df678cfe8bdf3990796b8976ff194aba357ae398f2f29b0e2985a6'] - -builddependencies = [('Autotools', '20180311')] - -preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && " - -# these are important for CP2K -# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT -configopts = "--with-libint-max-am=5 --with-libderiv-max-am1=4 " - -configopts += " --enable-deriv --enable-r12" - -sanity_check_paths = { - 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + - ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], - 'dirs': [], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.6-intel-2020a.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.6-intel-2020a.eb deleted file mode 100644 index 2508446e85a..00000000000 --- a/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.6-intel-2020a.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'Libint' -version = '1.1.6' - -homepage = 'https://sourceforge.net/p/libint/' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/evaleev/libint/archive/'] -sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] -checksums = ['f201b0c621df678cfe8bdf3990796b8976ff194aba357ae398f2f29b0e2985a6'] - -builddependencies = [('Autotools', '20180311')] - -preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && " - -# these are important for CP2K -# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT -configopts = "--with-libint-max-am=5 --with-libderiv-max-am1=4 " - -configopts += " --enable-deriv --enable-r12" - -sanity_check_paths = { - 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + - ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], - 'dirs': [], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb deleted file mode 100644 index 103d1e997b8..00000000000 --- a/easybuild/easyconfigs/__archive__/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb +++ /dev/null @@ -1,49 +0,0 @@ -name = 'Libint' -version = '2.6.0' -local_lmax = 6 -# custom configuration, to be used as dependency for CP2K -versionsuffix = '-lmax-%s-cp2k' % local_lmax - -homepage = 'https://github.com/evaleev/libint' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://github.com/evaleev/libint/archive'] -sources = ['v%(version)s.tar.gz'] -patches = [ - 'Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch', - 'Libint-2.6.0_remove-test-eri.patch', -] -checksums = [ - '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz - # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch - 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', - # Libint-2.6.0_remove-test-eri.patch - 'e47868901250078adeb35b80ab866ba8063ad9756881d1b557cb925334df653b', -] - -builddependencies = [ - ('Autotools', '20180311'), - ('GMP', '6.2.0'), - ('Boost', '1.72.0'), - ('Eigen', '3.3.7'), - ('Python', '2.7.18'), -] - -# configure options as required by CP2K, -# see Jenkinsfile in https://github.com/cp2k/libint-cp2k -local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) -local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) - -libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax -libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am -libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am -libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am -libint_compiler_configopts += '--enable-generic-code --disable-unrolling' - -with_fortran = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/Libint/Libint-2.6.0-iimpi-2020a-lmax-6-cp2k.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-2.6.0-iimpi-2020a-lmax-6-cp2k.eb deleted file mode 100644 index 1052541bd3d..00000000000 --- a/easybuild/easyconfigs/__archive__/l/Libint/Libint-2.6.0-iimpi-2020a-lmax-6-cp2k.eb +++ /dev/null @@ -1,44 +0,0 @@ -name = 'Libint' -version = '2.6.0' -local_lmax = 6 -# custom configuration, to be used as dependency for CP2K -versionsuffix = '-lmax-%s-cp2k' % local_lmax - -homepage = 'https://github.com/evaleev/libint' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://github.com/evaleev/libint/archive'] -sources = ['v%(version)s.tar.gz'] -patches = ['Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch'] -checksums = [ - '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz - # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch - 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', -] - -builddependencies = [ - ('Autotools', '20180311'), - ('GMP', '6.2.0'), - ('Boost', '1.72.0'), - ('Eigen', '3.3.7'), - ('Python', '2.7.18'), -] - -# configure options as required by CP2K, -# see Jenkinsfile in https://github.com/cp2k/libint-cp2k -local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) -local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) - -libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax -libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am -libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am -libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am -libint_compiler_configopts += '--enable-generic-code --disable-unrolling' - -with_fortran = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/Lingeling/Lingeling-bcp-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/Lingeling/Lingeling-bcp-GCC-9.3.0.eb deleted file mode 100644 index 9b8a1315b64..00000000000 --- a/easybuild/easyconfigs/__archive__/l/Lingeling/Lingeling-bcp-GCC-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'MakeCp' - -name = 'Lingeling' -version = 'bcp' -local_commit = '7d5db72420b95ab356c98ca7f7a4681ed2c59c70' - -homepage = 'http://fmv.jku.at/lingeling/' -description = """ -One of the design principles of the state-of-the-art SAT solver Lingeling is to -use as compact data structures as possible. These reduce memory usage, increase -cache efficiency and thus improve runtime, particularly, when using multiple -solver instances on multi-core machines, as in our parallel portfolio solver -Plingeling and our cube and conquer solver Treengeling.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'arminbiere' -source_urls = [GITHUB_LOWER_SOURCE] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['cf04c8f5706c14f00dd66e4db529c48513a450cc0f195242d8d0762b415f4427'] - -# Custom execution of configure at build time because Lingeling has a custom script incompatible with configure step -prebuildopts = "./configure.sh && " -prebuildopts += "sed -i 's/CFLAGS=-W -Wall -O3/CFLAGS+=-W -Wall/' makefile && " -buildopts = 'CC="$CC"' - -local_bins = ['lingeling', 'ilingeling', 'plingeling', 'treengeling'] -files_to_copy = [(local_bins, 'bin')] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_bins], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/l/LittleCMS/LittleCMS-2.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/LittleCMS/LittleCMS-2.9-GCCcore-9.3.0.eb deleted file mode 100644 index f02cf0fcf1b..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LittleCMS/LittleCMS-2.9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'LittleCMS' -version = '2.9' - -homepage = 'http://www.littlecms.com/' -description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, - with special focus on accuracy and performance. """ - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] -sources = ['lcms2-%(version)s.tar.gz'] -checksums = ['48c6fdf98396fa245ed86e622028caf49b96fa22f3e5734f853f806fbc8e7d20'] - -builddependencies = [ - # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.34'), -] - -dependencies = [('libjpeg-turbo', '2.0.4')] - -sanity_check_paths = { - 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', - 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], - 'dirs': ['share/man'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/l/Lua/Lua-5.3.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/Lua/Lua-5.3.5-GCCcore-9.3.0.eb deleted file mode 100644 index 1608391454a..00000000000 --- a/easybuild/easyconfigs/__archive__/l/Lua/Lua-5.3.5-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'Lua' -version = '5.3.5' - -homepage = 'https://www.lua.org/' -description = """Lua is a powerful, fast, lightweight, embeddable scripting language. - Lua combines simple procedural syntax with powerful data description constructs based - on associative arrays and extensible semantics. Lua is dynamically typed, - runs by interpreting bytecode for a register-based virtual machine, - and has automatic memory management with incremental garbage collection, - making it ideal for configuration, scripting, and rapid prototyping.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.%(namelower)s.org/ftp/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['0c2eed3f960446e1a3e4b9a1ca2f3ff893b6ce41942cf54d5dd59ab4b3b058ac'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('ncurses', '6.2'), - ('libreadline', '8.0'), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/l/LuaJIT2-OpenResty/LuaJIT2-OpenResty-2.1-20220411-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/LuaJIT2-OpenResty/LuaJIT2-OpenResty-2.1-20220411-GCC-9.3.0.eb deleted file mode 100644 index e1507faabad..00000000000 --- a/easybuild/easyconfigs/__archive__/l/LuaJIT2-OpenResty/LuaJIT2-OpenResty-2.1-20220411-GCC-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This is the LuaJIT fork from openresty, not to be mixed up -# with the original LuaJIT version! -# Autor: J. Sassmannshausen (Imperial College London/UK) - -easyblock = 'ConfigureMake' - -name = "LuaJIT2-OpenResty" -version = "2.1-20220411" - -homepage = "https://github.com/openresty/luajit2" -description = """openresty/luajit2 - OpenResty's maintained branch of LuaJIT. -LuaJIT is a Just-In-Time Compiler (JIT) for the Lua -programming language. Lua is a powerful, dynamic and light-weight programming -language. It may be embedded or used as a general-purpose, stand-alone -language. """ - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/openresty/luajit2/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['d3f2c870f8f88477b01726b32accab30f6e5d57ae59c5ec87374ff73d0794316'] - -skipsteps = ['configure'] - -installopts = 'PREFIX=%(installdir)s' - -sanity_check_commands = ['luajit -v'] - -sanity_check_paths = { - 'files': ["bin/luajit"], - 'dirs': [] -} - -moduleclass = "lang" diff --git a/easybuild/easyconfigs/__archive__/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 3d0a546bfe3..00000000000 --- a/easybuild/easyconfigs/__archive__/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'leidenalg' -version = '0.8.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/vtraag/leidenalg' -description = """Implementation of the Leiden algorithm for various quality -functions to be used with igraph in Python.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -builddependencies = [ - ('pkg-config', '0.29.2'), - ('PyYAML', '5.3'), - ('Bison', '3.5.3'), - ('libtool', '2.4.6'), - ('flex', '2.6.4'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('igraph', '0.8.2'), - ('python-igraph', '0.8.0'), -] - -use_pip = False - -exts_list = [ - # Test-only dependency - ('ddt', '1.4.1', { - 'checksums': ['0595e70d074e5777771a45709e99e9d215552fb1076443a25fad6b23d8bf38da'], - }), - (name, version, { - 'buildopts': '--use-pkg-config', - 'installopts': '--use-pkg-config', - 'testopts': '--use-pkg-config', - 'runtest': 'python setup.py test', - 'checksums': ['02cc8e87d2000ea1da60e9efc9287764fe81e445ab9850ec728b006c37620289'], - }), -] - -sanity_check_commands = ["python -c 'import leidenalg; import igraph as ig; " - "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), " - "leidenalg.ModularityVertexPartition)'"] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libFLAME/libFLAME-2.2-GCCcore-9.3.0-amd.eb b/easybuild/easyconfigs/__archive__/l/libFLAME/libFLAME-2.2-GCCcore-9.3.0-amd.eb deleted file mode 100644 index c12623e8c9e..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libFLAME/libFLAME-2.2-GCCcore-9.3.0-amd.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libFLAME' -version = '2.2' -versionsuffix = '-amd' - -homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame' -description = """AMD fork of libFLAME. libFLAME is a portable library for dense matrix computations, -providing much of the functionality present in LAPACK.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/amd/libflame/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['12b9c1f92d2c2fa637305aaa15cf706652406f210eaa5cbc17aaea9fcfa576dc'] - -# '--enable-max-arg-list-hack --enable-dynamic-build' requires 'file' function from GNU Make 4.x -builddependencies = [ - ('binutils', '2.34'), - ('Python', '3.8.2'), - ('make', '4.3'), # needed on Cent OS 7 where make 3 is installed -] - -dependencies = [('BLIS', '2.2', versionsuffix)] - -# Use unset FLIBS to let configure pick up LDFLAGS -preconfigopts = 'unset FLIBS && ' -preconfigopts += 'LIBS="-lblis-mt $LIBS" ' -preconfigopts += 'LDFLAGS="$LDFLAGS -L$EBROOTBLIS/lib -fopenmp -lm -lpthread" ' -preconfigopts += 'CFLAGS="$CFLAGS -I$EBROOTBLIS/include/blis" ' - -configopts = '--enable-max-arg-list-hack ' -configopts += '--enable-lapack2flame ' -configopts += '--enable-external-lapack-interfaces ' -configopts += '--enable-cblas-interfaces ' -configopts += '--enable-dynamic-build ' -configopts += '--enable-multithreading=openmp ' - -# libFLAME C++ Template API tests -# runtest = 'checkcpp LIBBLAS=$EBROOTBLIS/lib/libblis.a' - -# sanity_check_commands = [ -# 'cd %(builddir)s/%(namelower)s-%(version)s/test ' -# '&& make LIBBLAS=$EBROOTBLIS/lib/libblis-mt.so LDFLAGS="-fopenmp -lm -lpthread" ' -# '&& ./test_libfame.x' -# ] - -sanity_check_paths = { - 'files': ['include/FLAME.h', 'lib/libflame.a', 'lib/libflame.%s' % SHLIB_EXT], - 'dirs': ['lib'], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/l/libFLAME/libFLAME-5.2.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libFLAME/libFLAME-5.2.0-GCCcore-9.3.0.eb deleted file mode 100644 index 3a8514561af..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libFLAME/libFLAME-5.2.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,53 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libFLAME' -version = '5.2.0' - -homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame' -description = """libFLAME is a portable library for dense matrix computations, -providing much of the functionality present in LAPACK.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/flame/libflame/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['997c860f351a5c7aaed8deec00f502167599288fd0559c92d5bfd77d0b4d475c'] - -# '--enable-max-arg-list-hack --enable-dynamic-build' requires 'file' function from GNU Make 4.x -builddependencies = [ - ('binutils', '2.34'), - ('Python', '3.8.2'), - ('make', '4.3'), # needed on Cent OS 7 where make 3 is installed -] - -dependencies = [('BLIS', '0.8.0')] - -# Use unset FLIBS to let configure pick up LDFLAGS -preconfigopts = 'unset FLIBS && ' -preconfigopts += 'LIBS="-lblis $LIBS" ' -preconfigopts += 'LDFLAGS="$LDFLAGS -L$EBROOTBLIS/lib -fopenmp -lm -lpthread" ' -preconfigopts += 'CFLAGS="$CFLAGS -I$EBROOTBLIS/include/blis" ' - -configopts = '--enable-max-arg-list-hack ' -configopts += '--enable-lapack2flame ' -configopts += '--enable-external-lapack-interfaces ' -configopts += '--enable-cblas-interfaces ' -configopts += '--enable-dynamic-build ' -configopts += '--enable-multithreading=openmp ' - -# libFLAME C++ Template API tests -# runtest = 'checkcpp LIBBLAS=$EBROOTBLIS/lib/libblis.a' - -# sanity_check_commands = [ -# 'cd %(builddir)s/%(namelower)s-%(version)s/test ' -# '&& make LIBBLAS=$EBROOTBLIS/lib/libblis-mt.so LDFLAGS="-fopenmp -lm -lpthread" ' -# '&& ./test_libfame.x' -# ] - -sanity_check_paths = { - 'files': ['include/FLAME.h', 'lib/libflame.a', 'lib/libflame.%s' % SHLIB_EXT], - 'dirs': ['lib'], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/l/libGLU/libGLU-9.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libGLU/libGLU-9.0.1-GCCcore-9.3.0.eb deleted file mode 100644 index 8ef28f6771b..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libGLU/libGLU-9.0.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libGLU' -version = '9.0.1' - -homepage = 'https://mesa.freedesktop.org/archive/glu/' -description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://mesa.freedesktop.org/archive/glu/'] -sources = ['glu-%(version)s.tar.gz'] -checksums = ['f6f484cfcd51e489afe88031afdea1e173aa652697e4c19ddbcb8260579a10f7'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Mesa', '20.0.2'), -] - -sanity_check_paths = { - 'files': ['lib/libGLU.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/l/libMemcached/libMemcached-1.0.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libMemcached/libMemcached-1.0.18-GCCcore-9.3.0.eb deleted file mode 100644 index 273fe7eaa5a..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libMemcached/libMemcached-1.0.18-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libMemcached' -version = '1.0.18' - -homepage = 'https://memcached.org' -description = """libMemcached is an open source C/C++ client library and tools for - the memcached server (http://danga.com/memcached). It has been designed to be light - on memory usage, thread safe, and provide full access to server side methods.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://launchpad.net/libmemcached/%(version_major_minor)s/%(version)s/+download/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['libMemcached-1.0.18-bugfix-comparison.patch'] -checksums = [ - 'e22c0bb032fde08f53de9ffbc5a128233041d9f33b5de022c0978a2149885f82', # libmemcached-1.0.18.tar.gz - '92a105c91bf0c6a7b3d7aa35a041a071db07f777f5b812ed2499ffc892c3fe5a', # libMemcached-1.0.18-bugfix-comparison.patch -] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['lib/libmemcached.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/l/libRmath/libRmath-4.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libRmath/libRmath-4.0.0-GCCcore-9.3.0.eb deleted file mode 100644 index b8e77941f80..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libRmath/libRmath-4.0.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'ConfigureMake' - -name = 'libRmath' -version = '4.0.0' - -homepage = 'https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library' -description = """The routines supporting the distribution and special functions in R and a few others are declared - in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] -sources = ['R-%(version)s.tar.gz'] -checksums = ['06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('cURL', '7.69.1'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('zlib', '1.2.11'), - ('PCRE2', '10.34'), -] - -maxparallel = 1 - -start_dir = 'src/nmath/standalone' - -preconfigopts = 'cd %(builddir)s/R-%(version)s && ' -configopts = '--with-readline=no --with-recommended-packages=no --with-x=no' - -postinstallcmds = ["cp -r %(builddir)s/R-%(version)s/src/include/R_ext %(installdir)s/include/"] - -runtest = 'check' - -sanity_check_paths = { - 'files': ["lib/libRmath.%s" % SHLIB_EXT, "lib/libRmath.a", - "lib/pkgconfig/libRmath.pc", - "include/Rmath.h"], - 'dirs': [] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb deleted file mode 100644 index c60d93c060f..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'libarchive' -version = '3.4.2' - -homepage = 'https://www.libarchive.org/' - -description = """ - Multi-format archive and compression library -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.libarchive.org/downloads/'] -sources = [SOURCE_TAR_GZ] -checksums = ['b60d58d12632ecf1e8fad7316dc82c6b9738a35625746b47ecdcaf4aed176176'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('XZ', '5.2.5'), -] - -sanity_check_paths = { - 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], - 'dirs': ['bin', 'share/man/man3'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/l/libcdms/libcdms-3.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/l/libcdms/libcdms-3.1.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 8879958666e..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libcdms/libcdms-3.1.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libcdms' -version = '3.1.2' -versionsuffix = "-Python-%(pyver)s" - -homepage = 'https://github.com/CDAT/libcdms/' -description = """Climate Data Management System Library.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/CDAT/libcdms/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['2010ef24f8f8c14a6f997206ec342e6fed9703b81f8641d70bebc992a3855e8c'] - -dependencies = [ - ('netCDF', '4.7.4'), - ('JasPer', '2.0.14'), - ('g2clib', '1.6.0'), - ('libjpeg-turbo', '2.0.4'), - ('Python', '3.8.2'), - ('libdrs', '3.1.2'), -] - -configopts = "--prefix=%(installdir)s --enable-drs=yes" -configopts += '--enable-hdf=no --enable-pp=yes --enable-ql=no --enable-grib2 ' -configopts += '--cache-file=/dev/null ' -configopts += '--with-nclib=$EBROOTNETCDF/include --with-ncinc=$EBROOTNETCDF/include ' -configopts += '--with-ncincf=$EBROOTNETCDF/include ' -configopts += '--with-drslib=$EBROOTLIBDRS/include --with-drsinc=$EBROOTLIBDRS/include ' -configopts += '--with-drsincf=$EBROOTLIBDRS/include ' -configopts += '--with-jasperlib=$EBROOTJASPER/lib64 ' -configopts += '--with-grib2lib=$EBROOTG2CLIB/lib --with-grib2inc=$EBROOTG2CLIB/include ' - -# `make install` doesn't create the directories? -preinstallopts = 'mkdir -p %(installdir)s/{bin,lib,include,man/man3} && ' - -# Must be sequential, the three build steps each add to the libcdms.a archive -maxparallel = 1 - -sanity_check_paths = { - 'files': [ - 'bin/cddump', 'bin/cdfile', 'bin/cdimport', 'bin/cudump', 'bin/cuget', - 'include/cdunif.h', 'lib/libcdms.a', 'lib/libcdms.%s' % SHLIB_EXT, - ], - 'dirs': [], -} - -sanity_check_commands = ['cuget -h 2>&1 | grep "Usage: cuget"'] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/l/libcerf/libcerf-1.13-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libcerf/libcerf-1.13-GCCcore-9.3.0.eb deleted file mode 100644 index 24ee94e903b..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libcerf/libcerf-1.13-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'libcerf' -version = '1.13' - -homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' - -description = """ - libcerf is a self-contained numeric library that provides an efficient and - accurate implementation of complex error functions, along with Dawson, - Faddeeva, and Voigt functions. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] -sources = ['libcerf-v%(version)s.tar.gz'] -checksums = ['e4699f81af838aef5b3e77209fec8e9820a4f492d598fb5a070800854976a305'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('Perl', '5.30.2'), # required for pod2html -] - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['lib/libcerf.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/l/libcircle/libcircle-0.3-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/l/libcircle/libcircle-0.3-gompi-2020a.eb deleted file mode 100644 index 169c6665c3e..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libcircle/libcircle-0.3-gompi-2020a.eb +++ /dev/null @@ -1,41 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for libcircle: -# ---------------------------------------------------------------------------- -# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Petar Forai -# ---------------------------------------------------------------------------- - -easyblock = 'ConfigureMake' - -name = 'libcircle' -version = '0.3' - -homepage = 'https://github.com/hpc/libcircle/' - -description = """ - An API to provide an efficient distributed queue on a cluster. libcircle is an - API for distributing embarrassingly parallel workloads using self-stabilization. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = ['https://github.com/hpc/%(name)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] - -builddependencies = [ - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -preconfigopts = './autogen.sh && ' - -sanity_check_paths = { - 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libcircle/libcircle-0.3-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/l/libcircle/libcircle-0.3-iimpi-2020a.eb deleted file mode 100644 index e76089d4004..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libcircle/libcircle-0.3-iimpi-2020a.eb +++ /dev/null @@ -1,41 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for libcircle: -# ---------------------------------------------------------------------------- -# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Petar Forai -# ---------------------------------------------------------------------------- - -easyblock = 'ConfigureMake' - -name = 'libcircle' -version = '0.3' - -homepage = 'https://github.com/hpc/libcircle/' - -description = """ - An API to provide an efficient distributed queue on a cluster. libcircle is an - API for distributing embarrassingly parallel workloads using self-stabilization. -""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = ['https://github.com/hpc/%(name)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] - -builddependencies = [ - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -preconfigopts = './autogen.sh && ' - -sanity_check_paths = { - 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libctl/libctl-4.0.0-intel-2020a.eb b/easybuild/easyconfigs/__archive__/l/libctl/libctl-4.0.0-intel-2020a.eb deleted file mode 100644 index e20c9f0d5dd..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libctl/libctl-4.0.0-intel-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libctl' -version = '4.0.0' - -homepage = 'https://github.com/stevengj/libctl' -description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/stevengj/libctl/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['b0f46ed29acd13be542a4988d7f0604b10869d6b4c41916c539dc99711fb5458'] - -dependencies = [('Guile', '2.2.4')] - -# fix for guile-config being broken because shebang line contains full path to bin/guile -configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' - -sanity_check_paths = { - 'files': ['bin/gen-ctl-io', 'lib/libctl.a', 'lib/libctlgeom.a'], - 'dirs': ['include', 'share/libctl'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libdap/libdap-3.20.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libdap/libdap-3.20.7-GCCcore-9.3.0.eb deleted file mode 100644 index bb48cf95058..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libdap/libdap-3.20.7-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libdap' -version = '3.20.7' - -homepage = 'https://www.opendap.org/software/libdap' -description = """A C++ SDK which contains an implementation of DAP 2.0 and - DAP4.0. This includes both Client- and Server-side support classes.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['6856813d0b29e70a36e8a53e9cf20ad680d21d615952263e9c6586704539e78c'] - -builddependencies = [ - ('binutils', '2.34'), - ('Bison', '3.5.3'), - ('flex', '2.6.4'), -] - -dependencies = [ - ('cURL', '7.69.1'), - ('libxml2', '2.9.10'), - ('libtirpc', '1.2.6'), - ('PCRE', '8.44'), - ('util-linux', '2.35'), -] - -configopts = 'TIRPC_LIBS="-ltirpc"' - -sanity_check_paths = { - 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libdeflate/libdeflate-1.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libdeflate/libdeflate-1.7-GCCcore-9.3.0.eb deleted file mode 100644 index ed28e6f2838..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libdeflate/libdeflate-1.7-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'ConfigureMake' - -name = 'libdeflate' -version = '1.7' - -homepage = 'https://github.com/ebiggers/libdeflate' -description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'ebiggers' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['a5e6a0a9ab69f40f0f59332106532ca76918977a974e7004977a9498e3f11350'] - -builddependencies = [('binutils', '2.34')] - -skipsteps = ['configure'] - -installopts = 'PREFIX=%(installdir)s' - -sanity_check_paths = { - 'files': [ - 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', - 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, - 'include/%(name)s.h', - ], - 'dirs': [], -} -sanity_check_commands = [ - '%(name)s-gzip -h', - '%(name)s-gunzip -h', -] - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.100-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.100-GCCcore-9.3.0.eb deleted file mode 100644 index 46f83b9a4b5..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.100-GCCcore-9.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'libdrm' -version = '2.4.100' - -homepage = 'https://dri.freedesktop.org' -description = """Direct Rendering Manager runtime library.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://dri.freedesktop.org/libdrm/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6a5337c054c0c47bc16607a21efa2b622e08030be4101ef4a241c5eb05b6619b'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] -dependencies = [('X11', '20200222')] - -# installing manpages requires an extra build dependency (docbook xsl) -configopts = '--disable-manpages' - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libdrs/libdrs-3.1.2-foss-2020a.eb b/easybuild/easyconfigs/__archive__/l/libdrs/libdrs-3.1.2-foss-2020a.eb deleted file mode 100644 index 22e376b6020..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libdrs/libdrs-3.1.2-foss-2020a.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libdrs' -version = '3.1.2' - -homepage = 'https://github.com/CDAT/libdrs/' -description = """PCMDI's old DRS format implementation""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/CDAT/libdrs/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['90e10191116a78228739276078a0ddcf0d6458516f192e9e79fecb2beeceb3fa'] - -dependencies = [ - ('netCDF', '4.7.4'), - ('g2clib', '1.6.0'), -] - -start_dir = 'lib' - -skipsteps = ['configure'] - -prebuildopts = 'export MAKEFILE=libdrs_Makefile.Linux.gfortran && ' -prebuildopts += 'sed "s#@cdat_EXTERNALS@#%(installdir)s#g;" $MAKEFILE.in > $MAKEFILE && ' -prebuildopts += 'sed "s#libdrs#libdrsfortran#g;" $MAKEFILE.in > $MAKEFILE.fortran && ' -prebuildopts += 'sed -i "s#@cdat_EXTERNALS@#%(installdir)s#g;" $MAKEFILE.fortran && ' - -build_cmd = 'make -f libdrs_Makefile.Linux.gfortran && ' -build_cmd += 'make -f libdrs_Makefile.Linux.gfortran.fortran' - -install_cmd = 'make -f libdrs_Makefile.Linux.gfortran install && ' -install_cmd += 'make -f libdrs_Makefile.Linux.gfortran.fortran install' - -sanity_check_paths = { - 'files': [ - 'include/drscdf.h', 'include/drsdef.h', - 'lib/libdrs.a', 'lib/libdrs.%s' % SHLIB_EXT, - 'lib/libdrsfortran.a', 'lib/libdrsfortran.%s' % SHLIB_EXT, - ], - 'dirs': [], -} - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/l/libedit/libedit-20191231-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libedit/libedit-20191231-GCCcore-9.3.0.eb deleted file mode 100644 index 4f31fdf03e4..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libedit/libedit-20191231-GCCcore-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libedit' -version = '20191231' - -homepage = 'https://thrysoee.dk/editline/' -description = """ -This BSD-style licensed command line editor library provides generic line editing, -history, and tokenization functions, similar to those found in GNU Readline. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://thrysoee.dk/editline/'] -sources = ['%(namelower)s-%(version)s-3.1.tar.gz'] -checksums = ['dbb82cb7e116a5f8025d35ef5b4f7d4a3cdd0a3909a146a39112095a2d229071'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('ncurses', '6.2')] - -sanity_check_paths = { - 'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'], - 'dirs': [] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libelf/libelf-0.8.13-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libelf/libelf-0.8.13-GCCcore-9.3.0.eb deleted file mode 100644 index 74d2ca7bfe9..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libelf/libelf-0.8.13-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libelf' -version = '0.8.13' - -homepage = 'https://directory.fsf.org/wiki/Libelf' -description = """libelf is a free ELF object file access library""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [ - 'http://www.mr511.de/software/', - 'https://fossies.org/linux/misc/old/', -] -sources = [SOURCE_TAR_GZ] -checksums = ['591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d'] - -builddependencies = [ - ('binutils', '2.34'), -] - -modextrapaths = {'CPATH': 'include/libelf'} - -sanity_check_paths = { - 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], - 'dirs': ['lib/pkgconfig'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb deleted file mode 100644 index 988a8d4fc3f..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'libepoxy' -version = '1.5.4' - -homepage = 'https://github.com/anholt/libepoxy' -description = "Epoxy is a library for handling OpenGL function pointer management for you" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'anholt' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['c926fcc606901f3e03e371027056fd478da43e01ce2da7ffc48b5a0de0ca107c'] - -builddependencies = [ - ('binutils', '2.34'), - ('Meson', '0.55.1', '-Python-3.8.2'), - ('Ninja', '1.10.0'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('X11', '20200222'), - ('Mesa', '20.0.2'), -] - -configopts = '-Degl=yes --libdir %(installdir)s/lib ' - -sanity_check_paths = { - 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', - 'gl', 'glx_generated', 'glx']] + - ['lib/libepoxy.%s' % SHLIB_EXT], - 'dirs': ['lib'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libevent/libevent-2.1.11-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libevent/libevent-2.1.11-GCCcore-9.3.0.eb deleted file mode 100644 index 46b3823d2dc..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libevent/libevent-2.1.11-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libevent' -version = '2.1.11' - -homepage = 'https://libevent.org/' - -description = """ - The libevent API provides a mechanism to execute a callback function when - a specific event occurs on a file descriptor or after a timeout has been - reached. Furthermore, libevent also support callbacks due to signals or - regular timeouts. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] -sources = ['%(name)s-%(version)s-stable.tar.gz'] -checksums = ['a65bac6202ea8c5609fd5c7e480e6d25de467ea1917c08290c521752f147283d'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', - 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.10.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.10.1-GCCcore-9.3.0.eb deleted file mode 100644 index fdce77b96f7..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.10.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libfabric' -version = '1.10.1' - -homepage = 'https://ofiwg.github.io/libfabric/' -description = """ -Libfabric is a core component of OFI. It is the library that defines and exports -the user-space API of OFI, and is typically the only software that applications -deal with directly. It works in conjunction with provider libraries, which are -often integrated directly into libfabric. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'ofiwg' -source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] -sources = [SOURCE_TAR_BZ2] -checksums = ['889fa8c99eed1ff2a5fd6faf6d5222f2cf38476b24f3b764f2cbb5900fee8284'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -osdependencies = [OS_PKG_IBVERBS_DEV] - -# Disable deprecated "sockets" provider -configopts = "--disable-sockets " - -# Disable usNIC provider by default as this requires specific osdependencies -# If you want to enable this provider you need to uncomment the following line: -# osdependencies.append(('libnl3-devel', 'libnl3-dev')) -configopts += "--disable-usnic " - -sanity_check_paths = { - 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + - ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], - 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] -} - -sanity_check_commands = ['fi_info'] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.11.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.11.0-GCCcore-9.3.0.eb deleted file mode 100644 index 82b1664b4ab..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.11.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libfabric' -version = '1.11.0' - -homepage = 'https://ofiwg.github.io/libfabric/' -description = """ -Libfabric is a core component of OFI. It is the library that defines and exports -the user-space API of OFI, and is typically the only software that applications -deal with directly. It works in conjunction with provider libraries, which are -often integrated directly into libfabric. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'ofiwg' -source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] -sources = [SOURCE_TAR_BZ2] -checksums = ['9938abf628e7ea8dcf60a94a4b62d499fbc0dbc6733478b6db2e6a373c80d58f'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -osdependencies = [OS_PKG_IBVERBS_DEV] - -# Disable deprecated "sockets" provider -configopts = "--disable-sockets " - -# Disable usNIC provider by default as this requires specific osdependencies -# If you want to enable this provider you need to uncomment the following line: -# osdependencies.append(('libnl3-devel', 'libnl3-dev')) -configopts += "--disable-usnic " - -sanity_check_paths = { - 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + - ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], - 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] -} - -sanity_check_commands = ['fi_info'] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb deleted file mode 100644 index abfdf31e832..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libfabric' -version = '1.9.1' - -homepage = 'https://ofiwg.github.io/libfabric/' -description = """ -Libfabric is a core component of OFI. It is the library that defines and exports -the user-space API of OFI, and is typically the only software that applications -deal with directly. It works in conjunction with provider libraries, which are -often integrated directly into libfabric. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'ofiwg' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['765fdf71d99d179d89480c82271f62da5f186f61fe3907b1a450a63713312c6a'] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -osdependencies = [OS_PKG_IBVERBS_DEV] - -preconfigopts = "./autogen.sh && " - -# Disable deprecated "sockets" provider -configopts = "--disable-sockets " - -# Disable usNIC provider by default as this requires specific osdependencies -# If you want to enable this provider you need to uncomment the following line: -# osdependencies.append(('libnl3-devel', 'libnl3-dev')) -configopts += "--disable-usnic " - -sanity_check_paths = { - 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + - ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], - 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] -} - -sanity_check_commands = ['fi_info'] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libffcall/libffcall-2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libffcall/libffcall-2.2-GCCcore-9.3.0.eb deleted file mode 100644 index 560d6e76e25..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libffcall/libffcall-2.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'libffcall' -version = '2.2' - -homepage = 'https://www.gnu.org/software/libffcall/' - -description = """ - GNU Libffcall is a collection of four libraries which can be used to build - foreign function call interfaces in embedded interpreters -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['ebfa37f97b6c94fac24ecf3193f9fc829517cf81aee9ac2d191af993d73cb747'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['include/avcall.h', 'include/callback.h', 'include/trampoline.h', - 'include/vacall.h', 'lib/libavcall.a', 'lib/libcallback.a', - 'lib/libtrampoline.a', 'lib/libvacall.a'], - 'dirs': [], -} - -maxparallel = 1 - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.3-GCCcore-9.3.0.eb deleted file mode 100644 index 246ea276b29..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libffi' -version = '3.3' - -homepage = 'https://sourceware.org/libffi/' -description = """The libffi library provides a portable, high level programming interface to - various calling conventions. This allows a programmer to call any function - specified by a call interface description at run-time.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'ftp://sourceware.org/pub/%(name)s/', - 'https://www.mirrorservice.org/sites/sourceware.org/pub/%(name)s/', -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['72fba7922703ddfa7a028d513ac15a85c8d54c8d67f55fa5a4802885dc652056'] - -builddependencies = [ - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], - 'dirs': ['include', 'share'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libgd/libgd-2.3.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libgd/libgd-2.3.0-GCCcore-9.3.0.eb deleted file mode 100644 index 140f6156f7a..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libgd/libgd-2.3.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libgd' -version = '2.3.0' - -homepage = 'https://libgd.github.io/' -description = "GD is an open source code library for the dynamic creation of images by programmers." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['32590e361a1ea6c93915d2448ab0041792c11bae7b18ee812514fe08b2c6a342'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('fontconfig', '2.13.92'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), -] - -configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " -configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" - -sanity_check_paths = { - 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], - 'dirs': ["bin", "include"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libgeotiff/libgeotiff-1.5.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libgeotiff/libgeotiff-1.5.1-GCCcore-9.3.0.eb deleted file mode 100644 index 11fd20dd163..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libgeotiff/libgeotiff-1.5.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libgeotiff' -version = '1.5.1' - -homepage = 'https://directory.fsf.org/wiki/Libgeotiff' -description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] -sources = [SOURCE_TAR_GZ] -checksums = ['f9e99733c170d11052f562bcd2c7cb4de53ed405f7acdde4f16195cd3ead612c'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('PROJ', '7.0.0'), - ('libjpeg-turbo', '2.0.4'), - ('zlib', '1.2.11'), - ('SQLite', '3.31.1'), - ('LibTIFF', '4.1.0'), - ('cURL', '7.69.1'), -] - -configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' -configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' - -sanity_check_paths = { - 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], - 'dirs': ['include', 'share'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libgit2/libgit2-1.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libgit2/libgit2-1.1.0-GCCcore-9.3.0.eb deleted file mode 100644 index 49d4c98708c..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libgit2/libgit2-1.1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'libgit2' -version = '1.1.0' - -homepage = 'https://libgit2.org/' -description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant -linkable library with a solid API, allowing you to write native speed custom Git applications in any language -which supports C bindings.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'libgit2' -source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['41a6d5d740fd608674c7db8685685f45535323e73e784062cf000a633d420d1e'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('PCRE', '8.44'), - # OS dependency should be preferred if the os version is more recent than this version - # ('OpenSSL', '1.1.1b'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -sanity_check_paths = { - 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/l/libglvnd/libglvnd-1.2.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libglvnd/libglvnd-1.2.0-GCCcore-9.3.0.eb deleted file mode 100644 index c5d7432d6aa..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libglvnd/libglvnd-1.2.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libglvnd' -version = '1.2.0' - -homepage = 'https://github.com/NVIDIA/libglvnd' -description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/NVIDIA/libglvnd/releases/download/v%(version)s/'] -sources = ['libglvnd-%(version)s.tar.gz'] -checksums = ['2dacbcfa47b7ffb722cbddc0a4f1bc3ecd71d2d7bb461bceb8e396dc6b81dc6d'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [('X11', '20200222')] - -# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. -allow_prepend_abs_path = True -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} - -sanity_check_paths = { - 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], - 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libiconv/libiconv-1.16-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libiconv/libiconv-1.16-GCCcore-9.3.0.eb deleted file mode 100644 index 55abc5c157c..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libiconv/libiconv-1.16-GCCcore-9.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libiconv' -version = '1.16' - -homepage = 'https://www.gnu.org/software/libiconv' -description = "Libiconv converts from one character encoding to another through Unicode conversion" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['e6a1b1b589654277ee790cce3734f07876ac4ccfaecbee8afa0b649cf529cc04'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', - 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], - 'dirs': ['share'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libidn/libidn-1.35-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libidn/libidn-1.35-GCCcore-9.3.0.eb deleted file mode 100644 index 73cdb3980e0..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libidn/libidn-1.35-GCCcore-9.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libidn' -version = '1.35' - -homepage = 'http://www.gnu.org/software/%(name)s' -description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. -Libidn's purpose is to encode and decode internationalized domain names.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['f11af1005b46b7b15d057d7f107315a1ad46935c7fcdf243c16e46ec14f0fe1e'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], - 'dirs': ['include'], -} -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libidn2/libidn2-2.3.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libidn2/libidn2-2.3.0-GCCcore-9.3.0.eb deleted file mode 100644 index 9ed652bbf0c..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libidn2/libidn2-2.3.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'ConfigureMake' - -name = 'libidn2' -version = '2.3.0' - -homepage = 'https://www.gnu.org/software/libidn' -description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. -Libidn's purpose is to encode and decode internationalized domain names.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://ftpmirror.gnu.org/gnu/libidn'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e1cb1db3d2e249a6a3eb6f0946777c2e892d5c5dc7bd91c74394fc3a01cab8b5'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/idn2', 'lib/libidn2.%s' % SHLIB_EXT], - 'dirs': ['include'], -} -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libjpeg-turbo/libjpeg-turbo-2.0.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libjpeg-turbo/libjpeg-turbo-2.0.4-GCCcore-9.3.0.eb deleted file mode 100644 index e98cd35c5d2..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libjpeg-turbo/libjpeg-turbo-2.0.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'libjpeg-turbo' -version = '2.0.4' - -homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' - -description = """ - libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to - accelerate baseline JPEG compression and decompression. libjpeg is a library - that implements JPEG image encoding, decoding and transcoding. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['33dd8547efd5543639e890efbf2ef52d5a21df81faf41bb940657af916a23406'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34'), -] - -dependencies = [ - ('NASM', '2.14.02'), -] - -configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' - -runtest = "test" - -sanity_check_paths = { - 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', - 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', - 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', - 'lib/libturbojpeg.%s' % SHLIB_EXT], - 'dirs': ['include', 'share'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libmatheval/libmatheval-1.1.11-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libmatheval/libmatheval-1.1.11-GCCcore-9.3.0.eb deleted file mode 100644 index 3b9931220cc..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libmatheval/libmatheval-1.1.11-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libmatheval' -version = '1.1.11' - -homepage = 'https://www.gnu.org/software/libmatheval/' -description = """GNU libmatheval is a library (callable from C and Fortran) to parse - and evaluate symbolic expressions input as text.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -patches = ['libmatheval-%(version)s_fix-matheval-test.patch'] -checksums = [ - '474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab', # libmatheval-1.1.11.tar.gz - '2888ee1ba32bb864b655e53e13b06eafc23b598faed80b90585d41c98e2ae073', # libmatheval-1.1.11_fix-matheval-test.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('flex', '2.6.4'), - ('Bison', '3.5.3'), - ('Guile', '1.8.8'), -] - -configopts = '--with-pic ' - -# fix for guile-config being broken because shebang line contains full path to bin/guile -configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' - -sanity_check_paths = { - 'files': ['lib/libmatheval.a', 'include/matheval.h'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libmicrohttpd/libmicrohttpd-0.9.71-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libmicrohttpd/libmicrohttpd-0.9.71-GCCcore-9.3.0.eb deleted file mode 100644 index d54a6e55183..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libmicrohttpd/libmicrohttpd-0.9.71-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'libmicrohttpd' -version = '0.9.71' - -homepage = 'https://www.gnu.org/software/libmicrohttpd/' - -description = """ - GNU libmicrohttpd is a small C library that is supposed to make it easy to run - an HTTP server as part of another application. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://ftp.gnu.org/gnu/libmicrohttpd/'] -sources = [SOURCE_TAR_GZ] -checksums = ['e8f445e85faf727b89e9f9590daea4473ae00ead38b237cf1eda55172b89b182'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('cURL', '7.69.1')] - -sanity_check_paths = { - 'files': ['include/microhttpd.h', 'lib/%%(name)s.%s' % SHLIB_EXT, - 'share/man/man3/%(name)s.3'], - 'dirs': [] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libobjcryst/libobjcryst-2017.2.3-intel-2020a.eb b/easybuild/easyconfigs/__archive__/l/libobjcryst/libobjcryst-2017.2.3-intel-2020a.eb deleted file mode 100644 index 38a784b00dc..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libobjcryst/libobjcryst-2017.2.3-intel-2020a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'SCons' - -name = 'libobjcryst' -version = '2017.2.3' - -homepage = 'https://github.com/diffpy/libobjcryst' -description = "ObjCryst++ is Object-Oriented Crystallographic Library for C++" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/diffpy/libobjcryst/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['libobjcryst-2017.2.3_sconscript_local.patch'] -checksums = [ - 'd48de43a15c3227ac39422831c31285c695f8ec560b31420f0f31356de1a3bb0', # v2017.2.3.tar.gz - 'e86c7c1d9b9b89535757e21216307acf0d102fc72543f155a02bf75e6fba7b25', # libobjcryst-2017.2.3_sconscript_local.patch -] - -builddependencies = [ - ('SCons', '3.1.2'), -] -dependencies = [ - ('Boost', '1.72.0'), -] - -prefix_arg = 'prefix=' - -sanity_check_paths = { - 'files': ['lib/libObjCryst.%s' % SHLIB_EXT], - 'dirs': ['include/ObjCryst'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libobjcryst/libobjcryst-2017.2.3_sconscript_local.patch b/easybuild/easyconfigs/__archive__/l/libobjcryst/libobjcryst-2017.2.3_sconscript_local.patch deleted file mode 100644 index 51bcfc5b25c..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libobjcryst/libobjcryst-2017.2.3_sconscript_local.patch +++ /dev/null @@ -1,23 +0,0 @@ -Add SConscript.local to pass through EB environment to the compiler - -author: Jakub Zárybnický (Inuits) ---- libobjcryst-2017.2.3/sconscript.local 1970-01-01 01:00:00.000000000 +0100 -+++ libobjcryst-2017.2.3/sconscript.local 2020-09-22 15:33:59.098143895 +0200 -@@ -0,0 +1,10 @@ -+Import('env') -+ -+import os -+ -+env.Replace(CC=os.environ['CC']) -+env.Replace(CXX=os.environ['CXX']) -+env.Replace(CFLAGS=os.environ['CFLAGS']) -+env.Replace(CPPFLAGS=os.environ['CPPFLAGS']) -+env.Replace(CXXFLAGS=os.environ['CXXFLAGS']) -+env.Replace(LDFLAGS=os.environ['LDFLAGS']) - ---- libobjcryst-2017.2.3/SConstruct 1970-01-01 01:00:00.000000000 +0100 -+++ libobjcryst-2017.2.3/SConstruct 2020-09-22 15:33:59.098143895 +0200 -@@ -1,1 +1,1 @@ -- MACOSX_DEPLOYMENT_TARGET -+ MACOSX_DEPLOYMENT_TARGET INTEL_LICENSE_FILE - diff --git a/easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.16-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.16-GCCcore-9.3.0.eb deleted file mode 100644 index a5f69896b65..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.16-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpciaccess' -version = '0.16' - -homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' -description = """Generic PCI access library.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.x.org/releases/individual/lib/'] -sources = [SOURCE_TAR_GZ] -checksums = ['84413553994aef0070cf420050aa5c0a51b1956b404920e21b81e96db6a61a27'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), - ('xorg-macros', '1.19.2'), -] - -sanity_check_paths = { - 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb deleted file mode 100644 index 00726da9fca..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO - -easyblock = 'CMakeMake' - -name = 'libplinkio' -version = '0.9.8' - -homepage = "https://github.com/mfranberg/libplinkio" -description = """A small C and Python library for reading PLINK genotype files.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'cstd': 'gnu17', 'extra_cflags': '-w'} - -github_account = "mfranberg" -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['de54dd4789b2da9b937a1f445dc6976153211dc35b4376a4cf561ad2ee861075'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ['lib/libplinkio.%s' % SHLIB_EXT], - 'dirs': ['include/plinkio'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.37-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.37-GCCcore-9.3.0.eb deleted file mode 100644 index c0e8bbb3edd..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.37-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpng' -version = '1.6.37' - -homepage = 'http://www.libpng.org/pub/png/libpng.html' - -description = "libpng is the official PNG reference library" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['daeb2620d829575513e35fecc83f0d3791a620b9b93d800b763542ece9390fb4'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('zlib', '1.2.11')] - -local_majminver = ''.join(version.split('.')[:2]) - -sanity_check_paths = { - 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', - 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, - 'lib/libpng%s.a' % local_majminver, - 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], - 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb deleted file mode 100644 index 8971e851e81..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '8.0' - -homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' -description = """ - The GNU Readline library provides a set of functions for use by applications - that allow users to edit command lines as they are typed in. Both Emacs and - vi editing modes are available. The Readline library includes additional - functions to maintain a list of previously-entered command lines, to recall - and perhaps reedit those lines, and perform csh-like history expansion on - previous commands. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://ftp.gnu.org/gnu/readline'] -sources = ['readline-%(version)s.tar.gz'] -checksums = ['e339f51971478d369f8a053a330a190781acb9864cf4c541060f12078948e461'] - -builddependencies = [ - ('binutils', '2.34'), -] -dependencies = [ - ('ncurses', '6.2'), -] - -# for the termcap symbols, use EB ncurses -buildopts = "SHLIB_LIBS='-lncurses'" - -sanity_check_paths = { - 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x - for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', - 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.1-FCC-4.5.0.eb deleted file mode 100644 index ca514afa042..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.1-FCC-4.5.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '8.1' - -homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' -description = """ - The GNU Readline library provides a set of functions for use by applications - that allow users to edit command lines as they are typed in. Both Emacs and - vi editing modes are available. The Readline library includes additional - functions to maintain a list of previously-entered command lines, to recall - and perhaps reedit those lines, and perform csh-like history expansion on - previous commands. -""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://ftp.gnu.org/gnu/readline'] -sources = ['readline-%(version)s.tar.gz'] -checksums = ['f8ceb4ee131e3232226a17f51b164afc46cd0b9e6cef344be87c65962cb82b02'] - -builddependencies = [ - ('binutils', '2.36.1'), -] -dependencies = [ - ('ncurses', '6.2'), -] - -# for the termcap symbols, use EB ncurses -buildopts = "SHLIB_LIBS='-lncurses'" - -sanity_check_paths = { - 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x - for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', - 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libsigsegv/libsigsegv-2.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libsigsegv/libsigsegv-2.12-GCCcore-9.3.0.eb deleted file mode 100644 index d0a133dcfbc..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libsigsegv/libsigsegv-2.12-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'libsigsegv' -version = '2.12' - -homepage = 'https://www.gnu.org/software/libsigsegv/' - -description = "GNU libsigsegv is a library for handling page faults in user mode." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['3ae1af359eebaa4ffc5896a1aee3568c052c99879316a1ab57f8fe1789c390b6'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['include/sigsegv.h', 'lib/libsigsegv.a', 'lib/libsigsegv.la'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libsndfile/libsndfile-1.0.28-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libsndfile/libsndfile-1.0.28-GCCcore-9.3.0.eb deleted file mode 100644 index edd49876514..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libsndfile/libsndfile-1.0.28-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libsndfile' -version = '1.0.28' - -homepage = 'http://www.mega-nerd.com/libsndfile' -description = """Libsndfile is a C library for reading and writing files containing sampled sound - (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://www.mega-nerd.com/libsndfile/files/'] -sources = [SOURCE_TAR_GZ] -checksums = ['1ff33929f042fa333aed1e8923aa628c3ee9e1eb85512686c55092d1e5a9dfa9'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -configopts = '--enable-octave=no' - -sanity_check_paths = { - 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], - 'dirs': ['bin'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libsodium/libsodium-1.0.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libsodium/libsodium-1.0.18-GCCcore-9.3.0.eb deleted file mode 100644 index 63fea2c389d..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libsodium/libsodium-1.0.18-GCCcore-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libsodium' -version = '1.0.18' - -homepage = 'https://doc.libsodium.org/' - -description = """ - Sodium is a modern, easy-to-use software library for encryption, decryption, - signatures, password hashing and more. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'https://download.libsodium.org/libsodium/releases/', - 'https://download.libsodium.org/libsodium/releases/old/', - 'https://download.libsodium.org/libsodium/releases/old/unsupported/', -] -sources = [SOURCE_TAR_GZ] -checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] - -builddependencies = [ - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], - 'dirs': ['include/sodium', 'lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libtirpc/libtirpc-1.2.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libtirpc/libtirpc-1.2.6-GCCcore-9.3.0.eb deleted file mode 100644 index 2ac13a65f04..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libtirpc/libtirpc-1.2.6-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libtirpc' -version = '1.2.6' - -homepage = 'https://sourceforge.net/projects/libtirpc/' -description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_BZ2] -checksums = ['4278e9a5181d5af9cd7885322fdecebc444f9a3da87c526e7d47f7a12a37d1cc'] - -configopts = '--enable-static --enable-shared --disable-gssapi' - -builddependencies = [ - ('binutils', '2.34') -] - -sanity_check_paths = { - 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], - 'dirs': ['include/tirpc', 'lib'], -} - -modextrapaths = {'CPATH': 'include/tirpc'} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-FCC-4.5.0.eb deleted file mode 100644 index 157c8b2ee55..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-FCC-4.5.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'ConfigureMake' - -name = 'libtool' -version = '2.4.6' - -homepage = 'https://www.gnu.org/software/libtool' - -description = """ - GNU libtool is a generic library support script. Libtool hides the complexity - of using shared libraries behind a consistent, portable interface. -""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] - -builddependencies = [ - ('binutils', '2.36.1'), -] - -dependencies = [ - ('M4', '1.4.18'), -] - -sanity_check_paths = { - 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], - 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-GCCcore-9.3.0.eb deleted file mode 100644 index da5ae743abb..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-GCCcore-9.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libtool' -version = '2.4.6' - -homepage = 'https://www.gnu.org/software/libtool' - -description = """ - GNU libtool is a generic library support script. Libtool hides the complexity - of using shared libraries behind a consistent, portable interface. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('M4', '1.4.18'), -] - -sanity_check_paths = { - 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], - 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libunistring/libunistring-0.9.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libunistring/libunistring-0.9.10-GCCcore-9.3.0.eb deleted file mode 100644 index 1c6d15ed0d0..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libunistring/libunistring-0.9.10-GCCcore-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libunistring' -version = '0.9.10' - -homepage = 'https://www.gnu.org/software/libunistring/' - -description = """ - This library provides functions for manipulating Unicode strings and for - manipulating C strings according to the Unicode standard. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['eb8fb2c3e4b6e2d336608377050892b54c3c983b646c561836550863003c05d7'] - -builddependencies = [ - ('binutils', '2.34'), -] - -maxparallel = 1 - -sanity_check_paths = { - 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs': ['include/unistring'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb deleted file mode 100644 index 7160f197bb6..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libunwind' -version = '1.3.1' - -homepage = 'https://www.nongnu.org/libunwind/' -description = """The primary goal of libunwind is to define a portable and efficient C programming interface - (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the - preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain - (non-local goto). The API supports both local (same-process) and remote (across-process) operation. - As such, the API is useful in a number of applications""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SAVANNAH_SOURCE] -sources = [SOURCE_TAR_GZ] -patches = ['libunwind-1.3.1_fix_ppc64_fpreg_t.patch'] -checksums = [ - '43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8', - '61a507eec7ece286b06be698c742f0016d8c605eaeedf34f451cf1d0e510ec86', # libunwind-1.3.1_fix_ppc64_fpreg_t.patch -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('XZ', '5.2.5'), -] - -preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' - -sanity_check_paths = { - 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb deleted file mode 100644 index c6769e53157..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libvdwxc' -version = '0.4.0' - -homepage = 'https://libvdwxc.org' -description = """libvdwxc is a general library for evaluating energy and potential for -exchange-correlation (XC) functionals from the vdW-DF family that can be used with various -of density functional theory (DFT) codes.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] -sources = [SOURCE_TAR_GZ] -checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] - -preconfigopts = 'unset CC && unset FC && ' - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', - 'libvdwxc_q0test', 'libvdwxc_q0test2']] + - ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] - for y in ['a', SHLIB_EXT]], - 'dirs': ['include'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libwebp/libwebp-1.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libwebp/libwebp-1.1.0-GCCcore-9.3.0.eb deleted file mode 100644 index 3b35abfaf1a..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libwebp/libwebp-1.1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libwebp' -version = '1.1.0' - -homepage = 'https://developers.google.com/speed/webp/' -description = """WebP is a modern image format that provides superior -lossless and lossy compression for images on the web. Using WebP, -webmasters and web developers can create smaller, richer images that -make the web faster.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98a052268cc4d5ece27f76572a7f50293f439c17a98e67c4ea0c7ed6f50ef043'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('giflib', '5.2.1'), -] - -configopts = "--enable-libwebpmux" - -sanity_check_paths = { - 'files': ['include/webp/%s' % f for f in ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h']] + - ['lib/lib%s.a' % x for x in ['webp', 'webpdemux', 'webpmux']] + - ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['webp', 'webpdemux', 'webpmux']], - 'dirs': ['lib/'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libxc/libxc-3.0.1-foss-2020a.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-3.0.1-foss-2020a.eb deleted file mode 100644 index ea6a5438b34..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libxc/libxc-3.0.1-foss-2020a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '3.0.1' - -homepage = 'https://www.tddft.org/programs/libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. -toolchainopts = {'lowopt': True} - -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] -sources = [SOURCE_TAR_GZ] -patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] -checksums = [ - '836692f2ab60ec3aca0cca105ed5d0baa7d182be07cc9d0daa7b80ee1362caf7', # libxc-3.0.1.tar.gz - '27338d9f63ce33386a6241e7bd8edde66ac8684d103acf0e6cbb5bde011730b9', # libxc-3.0_no-longdouble.patch -] - -configopts = '--enable-static --enable-shared --enable-fortran' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include'], -} - -maxparallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libxc/libxc-3.0.1-intel-2020a.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-3.0.1-intel-2020a.eb deleted file mode 100644 index 88cc4ffb5eb..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libxc/libxc-3.0.1-intel-2020a.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '3.0.1' - -homepage = 'https://www.tddft.org/programs/libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. -# Tests also fail with Intel Compilers on Haswell when optarch is enabled. -toolchainopts = {'lowopt': True, 'optarch': False} - -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] -sources = [SOURCE_TAR_GZ] -patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] -checksums = [ - '836692f2ab60ec3aca0cca105ed5d0baa7d182be07cc9d0daa7b80ee1362caf7', # libxc-3.0.1.tar.gz - '27338d9f63ce33386a6241e7bd8edde66ac8684d103acf0e6cbb5bde011730b9', # libxc-3.0_no-longdouble.patch -] - -configopts = '--enable-static --enable-shared --enable-fortran' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include'], -} - -maxparallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-GCC-9.3.0.eb deleted file mode 100644 index eef83bd8402..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-GCC-9.3.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'libxc' -version = '4.3.4' - -homepage = 'https://libxc.gitlab.io' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] -sources = [SOURCE_TAR_GZ] -patches = [ - 'libxc-%(version)s_lm-fix.patch', - 'libxc-%(version)s_fix-CMakeLists.patch', - 'libxc-%(version)s_fix-timeout.patch', -] -checksums = [ - ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', - '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz - 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch - '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch - 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Perl', '5.30.2'), -] - -separate_build_dir = True - -local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" - -# perform iterative build to get both static and shared libraries -configopts = [ - local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', - local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', -] - -maxparallel = 1 - -# make sure that built libraries (libxc*.so*) in build directory are picked when running tests -# this is required when RPATH linking is used -pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/xc-info', 'bin/xc-threshold'] + - ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb deleted file mode 100644 index a70cfe95e73..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb +++ /dev/null @@ -1,62 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'libxc' -version = '4.3.4' - -homepage = 'https://libxc.gitlab.io' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] -sources = [SOURCE_TAR_GZ] -patches = [ - 'libxc-%(version)s_rename-F03.patch', - 'libxc-%(version)s_lm-fix.patch', - 'libxc-%(version)s_fix-CMakeLists.patch', - 'libxc-%(version)s_fix-timeout.patch', -] -checksums = [ - ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', - '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz - 'e494be3ca2026998f2dd7c6b03a4e662f204fd3d963271e588f9f0d5739e76b5', # libxc-4.3.4_rename-F03.patch - 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch - '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch - 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Perl', '5.30.2'), -] - -separate_build_dir = True - -# rename *.F03 source file since Intel Fortran compiler doesn't like that extension -# also requires patch file to rename file in CMakeLists.txt and src/Makefile.in -preconfigopts = "mv ../libxc-%(version)s/src/libxc_master.F03 ../libxc-%(version)s/src/libxc_master_F03.F90 && " - -local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" - -# perform iterative build to get both static and shared libraries -configopts = [ - local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', - local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', -] - -maxparallel = 1 - -# make sure that built libraries (libxc*.so*) in build directory are picked when running tests -# this is required when RPATH linking is used -pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/xc-info', 'bin/xc-threshold'] + - ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb deleted file mode 100644 index 3669c4c6bca..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'libxml2' -version = '2.9.10' - -homepage = 'http://xmlsoft.org/' - -description = """ - Libxml2 is the XML C parser and toolchain developed for the Gnome project - (but usable outside of the Gnome platform). -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] -sources = [SOURCE_TAR_XZ] -checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('XZ', '5.2.5'), - ('zlib', '1.2.11'), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb deleted file mode 100644 index 85eb068bdbc..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxslt' -version = '1.1.34' - -homepage = 'http://xmlsoft.org/' -description = """Libxslt is the XSLT C library developed for the GNOME project - (but usable outside of the Gnome platform).""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] -sources = [SOURCE_TAR_XZ] -checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('libxml2', '2.9.10'), -] - -# Make sure it doesn't pick up OS installed libgcrypt or Python -configopts = '--with-crypto=no --with-python=no ' - -sanity_check_paths = { - 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb deleted file mode 100644 index 72a6d90dabd..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxsmm' -version = '1.16.1' - -homepage = 'https://github.com/hfp/libxsmm' -description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications -targeting Intel Architecture (x86).""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/hfp/libxsmm/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['93dc7a3ec40401988729ddb2c6ea2294911261f7e6cd979cf061b5c3691d729d'] - -# install both static and dynamic version -installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] - -skipsteps = ['configure'] -maxparallel = 1 - -sanity_check_paths = { - 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], - 'dirs': ['share'] -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/l/libxsmm/libxsmm-1.16.1-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/l/libxsmm/libxsmm-1.16.1-iccifort-2020.1.217.eb deleted file mode 100644 index 7640a431e03..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libxsmm/libxsmm-1.16.1-iccifort-2020.1.217.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxsmm' -version = '1.16.1' - -homepage = 'https://github.com/hfp/libxsmm' -description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications -targeting Intel Architecture (x86).""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://github.com/hfp/libxsmm/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['93dc7a3ec40401988729ddb2c6ea2294911261f7e6cd979cf061b5c3691d729d'] - -# install both static and dynamic version -installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] - -skipsteps = ['configure'] -maxparallel = 1 - -sanity_check_paths = { - 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], - 'dirs': ['share'] -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/l/libyaml/libyaml-0.2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/libyaml/libyaml-0.2.2-GCCcore-9.3.0.eb deleted file mode 100644 index e869dacf3f1..00000000000 --- a/easybuild/easyconfigs/__archive__/l/libyaml/libyaml-0.2.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Nils Christian -# License:: MIT/GPL -# $Id$ -## - -easyblock = 'ConfigureMake' - -name = 'libyaml' -version = '0.2.2' - -homepage = 'https://pyyaml.org/wiki/LibYAML' - -description = """LibYAML is a YAML parser and emitter written in C.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://pyyaml.org/download/libyaml/'] -sources = ['yaml-%(version)s.tar.gz'] -checksums = ['4a9100ab61047fd9bd395bcef3ce5403365cafd55c1e0d0299cde14958e47be9'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.%s" % SHLIB_EXT], - 'dirs': ["lib/pkgconfig"] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/likwid/likwid-5.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/likwid/likwid-5.1.0-GCCcore-9.3.0.eb deleted file mode 100644 index 82fb22f2165..00000000000 --- a/easybuild/easyconfigs/__archive__/l/likwid/likwid-5.1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'likwid' -version = '5.1.0' - -homepage = 'https://github.com/RRZE-HPC/likwid' - -description = """ - Likwid stands for Like I knew what I am doing. This project contributes easy - to use command line tools for Linux to support programmers in developing high - performance multi threaded programs. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['5a180702a1656c6315b861a85031ab4cb090424aec42cbbb326b849e29f55571'] - -builddependencies = [('binutils', '2.34')] - -skipsteps = ['configure'] - -buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' - -maxparallel = 1 - -installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ=""' - -sanity_check_paths = { - 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', - 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', - 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, - 'lib/liblikwid.%s' % SHLIB_EXT], - 'dirs': ['man/man1'] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/l/line_profiler/line_profiler-3.1.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/l/line_profiler/line_profiler-3.1.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 4a173fd5ecf..00000000000 --- a/easybuild/easyconfigs/__archive__/l/line_profiler/line_profiler-3.1.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'line_profiler' -version = '3.1.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pyutils/line_profiler' -description = """line_profiler is a module for doing line-by-line profiling -of functions. kernprof is a convenient script for running either -line_profiler or the Python standard library's cProfile or profile modules, -depending on what is available.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['e73ff429236d59d48ce7028484becfa01449b3d52abdcf7337e0ff2acdc5093c'] - -builddependencies = [ - ('scikit-build', '0.10.0', versionsuffix), - ('CMake', '3.16.4'), - ('Ninja', '1.10.0'), -] -dependencies = [ - ('Python', '3.8.2'), - ('IPython', '7.15.0', versionsuffix), -] - -sanity_check_paths = { - 'files': ['bin/kernprof'], - 'dirs': [], -} - -sanity_check_commands = ['kernprof --help'] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/l/lpsolve/lpsolve-5.5.2.11-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/lpsolve/lpsolve-5.5.2.11-GCC-9.3.0.eb deleted file mode 100644 index 02e23eead60..00000000000 --- a/easybuild/easyconfigs/__archive__/l/lpsolve/lpsolve-5.5.2.11-GCC-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'CmdCp' - -name = 'lpsolve' -version = '5.5.2.11' - -homepage = 'https://sourceforge.net/projects/lpsolve/' -description = "Mixed Integer Linear Programming (MILP) solver" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['lp_solve_%(version)s_source.tar.gz'] -checksums = [ - '6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f', # lp_solve_5.5.2.11_source.tar.gz -] - -local_lpsolve_ver = '%(version_major)s%(version_minor)s' -start_dir = 'lpsolve%s' % local_lpsolve_ver - -local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' -local_comp_cmd += "sh ccc" -cmds_map = [('.*', local_comp_cmd)] - -local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver -files_to_copy = [ - (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), - (['../lp*.h'], 'include'), -] - -sanity_check_paths = { - 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], - 'dirs': ['include'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/l/lwgrp/lwgrp-1.0.2-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/l/lwgrp/lwgrp-1.0.2-gompi-2020a.eb deleted file mode 100644 index 4578bfff72e..00000000000 --- a/easybuild/easyconfigs/__archive__/l/lwgrp/lwgrp-1.0.2-gompi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'lwgrp' -version = '1.0.2' - -homepage = 'https://github.com/llnl/lwgrp' - -description = """ - The Light-weight Group Library provides methods for MPI codes to quickly create - and destroy process groups -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://github.com/llnl/%(name)s/releases/download/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['c9d4233946e40f01efd0b4644fd9224becec51b9b5f8cbf45f5bac3129b5b536'] - -sanity_check_paths = { - 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], - 'dirs': ['share/%(name)s'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/lwgrp/lwgrp-1.0.2-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/l/lwgrp/lwgrp-1.0.2-iimpi-2020a.eb deleted file mode 100644 index 7c202048b16..00000000000 --- a/easybuild/easyconfigs/__archive__/l/lwgrp/lwgrp-1.0.2-iimpi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'lwgrp' -version = '1.0.2' - -homepage = 'https://github.com/llnl/lwgrp' - -description = """ - The Light-weight Group Library provides methods for MPI codes to quickly create - and destroy process groups -""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} - -source_urls = ['https://github.com/llnl/%(name)s/releases/download/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['c9d4233946e40f01efd0b4644fd9224becec51b9b5f8cbf45f5bac3129b5b536'] - -sanity_check_paths = { - 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], - 'dirs': ['share/%(name)s'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/lxml/lxml-4.5.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/lxml/lxml-4.5.2-GCCcore-9.3.0.eb deleted file mode 100644 index 09d53e4ff21..00000000000 --- a/easybuild/easyconfigs/__archive__/l/lxml/lxml-4.5.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'lxml' -version = '4.5.2' - -homepage = 'https://lxml.de/' -description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://lxml.de/files/'] -sources = [SOURCE_TGZ] -checksums = ['cdc13a1682b2a6241080745b1953719e7fe0850b40a5c71ca574f090a1391df6'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('libxml2', '2.9.10'), - ('libxslt', '1.1.34'), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/l/lz4/lz4-1.9.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/l/lz4/lz4-1.9.2-GCCcore-9.3.0.eb deleted file mode 100644 index 5d203094ab0..00000000000 --- a/easybuild/easyconfigs/__archive__/l/lz4/lz4-1.9.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'lz4' -version = '1.9.2' - -homepage = 'https://lz4.github.io/lz4/' -description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. - It features an extremely fast decoder, with speed in multiple GB/s per core.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = '%(name)s' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['658ba6191fa44c92280d4aa2c271b0f4fbc0e34d249578dd05e50e76d0e5efcc'] - -builddependencies = [('binutils', '2.34')] - -skipsteps = ['configure'] - -installopts = "PREFIX=%(installdir)s" - -runtest = 'check' - -sanity_check_paths = { - 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], - 'dirs': ["lib/pkgconfig"] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-FCC-4.5.0.eb deleted file mode 100644 index bc86a842bf0..00000000000 --- a/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-FCC-4.5.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'M4' -version = '1.4.18' - -homepage = 'https://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', -] - -checksums = [ - 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz - 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch - '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch -] - -# use binutils from the OS, since M4 is itself a dependency of the easybuilt binutils (via flex and Bison) -osdependencies = [('binutils')] - -# workaround for https://bugs.llvm.org/show_bug.cgi?id=16404 -preconfigopts = 'export LDFLAGS="--rtlib=compiler-rt $LDFLAGS" && ' - -# '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 -configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" - -sanity_check_paths = { - 'files': ['bin/m4'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-GCCcore-9.3.0.eb deleted file mode 100644 index e0dffd89a28..00000000000 --- a/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'M4' -version = '1.4.18' - -homepage = 'https://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', -] - -checksums = [ - 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz - 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch - '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch -] - -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.34', '', SYSTEM)] - -# '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 -configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" - -sanity_check_paths = { - 'files': ['bin/m4'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.453-GCC-9.3.0-with-extensions.eb b/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.453-GCC-9.3.0-with-extensions.eb deleted file mode 100644 index 93c6ef58ba6..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.453-GCC-9.3.0-with-extensions.eb +++ /dev/null @@ -1,48 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) -# 7.305 modified by: -# Adam Huffman (The Francis Crick Institute) -# 7.453 switch to Bundle by: -# Alex Domingo (Vrije Universiteit Brussel) - -easyblock = 'Bundle' - -name = 'MAFFT' -version = '7.453' -versionsuffix = '-with-extensions' - -homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' -description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. -It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment -of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -default_easyblock = 'ConfigureMake' -default_component_specs = { - 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], - 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], - 'checksums': ['8b2f0d6249c575f80cd51278ab45dd149b8ac9b159adac20fd1ddc7a6722af11'], - 'skipsteps': ['configure'], - 'installopts': 'PREFIX=%(installdir)s', -} - -components = [ - (name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', - }), - ('%s Extensions' % name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', - }), -] - -sanity_check_paths = { - 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions - 'dirs': ['libexec/mafft'], -} - -sanity_check_commands = ['mafft --version'] - -modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.453-gompi-2020a-with-extensions.eb b/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.453-gompi-2020a-with-extensions.eb deleted file mode 100644 index 9691e5ede81..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.453-gompi-2020a-with-extensions.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'Bundle' - -name = 'MAFFT' -version = '7.453' -versionsuffix = '-with-extensions' - -homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' -description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. -It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment -of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True} - -default_easyblock = 'ConfigureMake' -default_component_specs = { - 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], - 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], - 'checksums': ['8b2f0d6249c575f80cd51278ab45dd149b8ac9b159adac20fd1ddc7a6722af11'], - 'skipsteps': ['configure'], - 'installopts': 'PREFIX=%(installdir)s', -} - -components = [ - (name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', - }), - ('%s Extensions' % name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', - }), - ('%s MPI' % name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/MPI', - }), -] - -sanity_check_paths = { - 'files': ['bin/mafft'] + ['libexec/mafft/%s' % x for x in [ - 'mxscarnamod', # installed by MAFFT Extensions - 'mpiscript', 'nodepair_mpi', # installed by MAFFT MPI - ]], - 'dirs': ['libexec/mafft'], -} - -sanity_check_commands = ['mafft --version'] - -modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} - -modextravars = {'MAFFT_N_THREADS_PER_PROCESS': '1'} -# MAFFT MPI requires other environment variables that depend on job resources -# More information at at https://mafft.cbrc.jp/alignment/software/mpi.html - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.453-iimpi-2020a-with-extensions.eb b/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.453-iimpi-2020a-with-extensions.eb deleted file mode 100644 index d2fee363feb..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.453-iimpi-2020a-with-extensions.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'Bundle' - -name = 'MAFFT' -version = '7.453' -versionsuffix = '-with-extensions' - -homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' -description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. -It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment -of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'usempi': True} - -default_easyblock = 'ConfigureMake' -default_component_specs = { - 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], - 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], - 'checksums': ['8b2f0d6249c575f80cd51278ab45dd149b8ac9b159adac20fd1ddc7a6722af11'], - 'skipsteps': ['configure'], - 'installopts': 'PREFIX=%(installdir)s', -} - -components = [ - (name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', - }), - ('%s Extensions' % name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', - }), - ('%s MPI' % name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/MPI', - }), -] - -sanity_check_paths = { - 'files': ['bin/mafft'] + ['libexec/mafft/%s' % x for x in [ - 'mxscarnamod', # installed by MAFFT Extensions - 'mpiscript', 'nodepair_mpi', # installed by MAFFT MPI - ]], - 'dirs': ['libexec/mafft'], -} - -sanity_check_commands = ['mafft --version'] - -modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} - -modextravars = {'MAFFT_N_THREADS_PER_PROCESS': '1'} -# MAFFT MPI requires other environment variables that depend on job resources -# More information at at https://mafft.cbrc.jp/alignment/software/mpi.html - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.470-GCC-9.3.0-with-extensions.eb b/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.470-GCC-9.3.0-with-extensions.eb deleted file mode 100644 index 6586c5b9bff..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.470-GCC-9.3.0-with-extensions.eb +++ /dev/null @@ -1,48 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) -# 7.305 modified by: -# Adam Huffman (The Francis Crick Institute) -# 7.453 switch to Bundle by: -# Alex Domingo (Vrije Universiteit Brussel) - -easyblock = 'Bundle' - -name = 'MAFFT' -version = '7.470' -versionsuffix = '-with-extensions' - -homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' -description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. -It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment -of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -default_easyblock = 'ConfigureMake' -default_component_specs = { - 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], - 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], - 'checksums': ['7d7e6c58a1060e061feec507a3dcba567be94e7d335ab87499134abc3731b00f'], - 'skipsteps': ['configure'], - 'installopts': 'PREFIX=%(installdir)s', -} - -components = [ - (name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', - }), - ('%s Extensions' % name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', - }), -] - -sanity_check_paths = { - 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions - 'dirs': ['libexec/mafft'], -} - -sanity_check_commands = ['mafft --version'] - -modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.470-gompi-2020a-with-extensions.eb b/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.470-gompi-2020a-with-extensions.eb deleted file mode 100644 index 7aba188bc66..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.470-gompi-2020a-with-extensions.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'Bundle' - -name = 'MAFFT' -version = '7.470' -versionsuffix = '-with-extensions' - -homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' -description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. -It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment -of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True} - -default_easyblock = 'ConfigureMake' -default_component_specs = { - 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], - 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], - 'checksums': ['7d7e6c58a1060e061feec507a3dcba567be94e7d335ab87499134abc3731b00f'], - 'skipsteps': ['configure'], - 'installopts': 'PREFIX=%(installdir)s', -} - -components = [ - (name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', - }), - ('%s Extensions' % name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', - }), - ('%s MPI' % name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/MPI', - }), -] - -sanity_check_paths = { - 'files': ['bin/mafft'] + ['libexec/mafft/%s' % x for x in [ - 'mxscarnamod', # installed by MAFFT Extensions - 'mpiscript', 'nodepair_mpi', # installed by MAFFT MPI - ]], - 'dirs': ['libexec/mafft'], -} - -sanity_check_commands = ['mafft --version'] - -modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} - -modextravars = {'MAFFT_N_THREADS_PER_PROCESS': '1'} -# MAFFT MPI requires other environment variables that depend on job resources -# More information at at https://mafft.cbrc.jp/alignment/software/mpi.html - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.471-iimpi-2020a-with-extensions.eb b/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.471-iimpi-2020a-with-extensions.eb deleted file mode 100644 index 144e21d2653..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MAFFT/MAFFT-7.471-iimpi-2020a-with-extensions.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'Bundle' - -name = 'MAFFT' -version = '7.471' -versionsuffix = '-with-extensions' - -homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' -description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. -It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment -of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'usempi': True} - -default_easyblock = 'ConfigureMake' -default_component_specs = { - 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], - 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], - 'checksums': ['2c4993e9ebdaf4dcc6ea2b0daf30f58cbbe98fdba3e2cfcb46145bb2c62e94ef'], - 'skipsteps': ['configure'], - 'installopts': 'PREFIX=%(installdir)s', -} - -components = [ - (name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', - }), - ('%s Extensions' % name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', - }), - ('%s MPI' % name, version, { - 'start_dir': 'mafft-%(version)s%(versionsuffix)s/MPI', - }), -] - -sanity_check_paths = { - 'files': ['bin/mafft'] + ['libexec/mafft/%s' % x for x in [ - 'mxscarnamod', # installed by MAFFT Extensions - 'mpiscript', 'nodepair_mpi', # installed by MAFFT MPI - ]], - 'dirs': ['libexec/mafft'], -} - -sanity_check_commands = ['mafft --version'] - -modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} - -modextravars = {'MAFFT_N_THREADS_PER_PROCESS': '1'} -# MAFFT MPI requires other environment variables that depend on job resources -# More information at at https://mafft.cbrc.jp/alignment/software/mpi.html - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MAJIQ/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/__archive__/m/MAJIQ/numpy-1.12.0-mkl.patch deleted file mode 100644 index 3d09924f966..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MAJIQ/numpy-1.12.0-mkl.patch +++ /dev/null @@ -1,55 +0,0 @@ -fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries -by Kenneth Hoste (HPC-UGent) -diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py ---- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 -@@ -628,7 +628,10 @@ - return options - - def library_option(self, lib): -- return "-l" + lib -+ if lib[0]=='-': -+ return lib -+ else: -+ return "-l" + lib - def library_dir_option(self, dir): - return "-L" + dir - -diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py ---- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 -@@ -675,7 +675,7 @@ - if is_string(default): - return [default] - return default -- return [b for b in [a.strip() for a in libs.split(',')] if b] -+ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] - - def get_libraries(self, key='libraries'): - if hasattr(self, '_lib_names'): -@@ -756,6 +756,9 @@ - # make sure we preserve the order of libs, as it can be important - found_dirs, found_libs = [], [] - for lib in libs: -+ if lib[0] == '-': -+ found_libs.append(lib) -+ continue - for lib_dir in lib_dirs: - found_lib = self._find_lib(lib_dir, lib, exts) - if found_lib: -diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py ---- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 -@@ -123,3 +123,12 @@ - - replace_method(UnixCCompiler, 'create_static_lib', - UnixCCompiler_create_static_lib) -+ -+def UnixCCompiler_library_option(self, lib): -+ if lib[0]=='-': -+ return lib -+ else: -+ return "-l" + lib -+ -+replace_method(UnixCCompiler, 'library_option', -+ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/__archive__/m/MATIO/MATIO-1.5.19-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MATIO/MATIO-1.5.19-GCCcore-9.3.0.eb deleted file mode 100644 index ff9dfee5a25..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MATIO/MATIO-1.5.19-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2014-2015 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## -easyblock = 'ConfigureMake' - -name = 'MATIO' -version = '1.5.19' - -homepage = 'https://sourceforge.net/projects/matio/' -description = """matio is an C library for reading and writing Matlab MAT files.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_ZIP] -checksums = ['7774c03c77e46b999249bc376b054148cb922d8074db155b05e8fbd6d457d64e'] - -preconfigopts = 'chmod +x configure && ' - -builddependencies = [('binutils', '2.34')] - -dependencies = [('zlib', '1.2.11')] - -sanity_check_paths = { - 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/m/MATLAB/MATLAB-2020a.eb b/easybuild/easyconfigs/__archive__/m/MATLAB/MATLAB-2020a.eb deleted file mode 100644 index ca7cf4f428c..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MATLAB/MATLAB-2020a.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'MATLAB' -version = '2020a' - -homepage = 'https://www.mathworks.com/products/matlab' -description = """MATLAB is a high-level language and interactive environment - that enables you to perform computationally intensive tasks faster than with - traditional programming languages such as C, C++, and Fortran.""" - -toolchain = SYSTEM - -sources = ['R%(version)s_Linux.iso'] -checksums = ['6a6ef2a854591132fe7674df8c86665913480a8d945a40aa2ad2bd632a51abf4'] -download_instructions = f'Download {sources[0]} from mathworks.com' - -java_options = '-Xmx2048m' - -osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files - -# Use EB_MATLAB_KEY environment variable or uncomment and modify license key -# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' - -# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or -# uncomment and modify the following variables for installation with floating license server -# license_file = 'my-license-file' -# license_server = 'my-license-server' -# license_server_port = '1234' - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb b/easybuild/easyconfigs/__archive__/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb deleted file mode 100644 index e21748be660..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'MakeCp' - -name = 'MBROLA' -version = '3.3' -local_commit_voices = 'fe05a0c' -local_version_voices = '20200330' -versionsuffix = '-voices-%s' % local_version_voices - -homepage = ['https://github.com/numediart/MBROLA%s' % x for x in ['', '-voices']] - -description = """ -MBROLA is a speech synthesizer based on the concatenation of diphones. -It takes a list of phonemes as input, together with prosodic information -(duration of phonemes and a piecewise linear description of pitch), -and produces speech samples on 16 bits (linear), -at the sampling frequency of the diphone database. - -MBROLA voices project provides list of MBROLA speech synthesizer voices. -It is intended to provide easier collaboration and -automatic updates for individual users and packagers. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/numediart/MBROLA%s/archive' % x for x in ['', '-voices']] -sources = [{ - 'download_filename': '%s.tar.gz' % version, - 'filename': SOURCE_TAR_GZ -}, { - 'download_filename': '%s.tar.gz' % local_commit_voices, - 'filename': '%%(name)s-voices-%s.tar.gz' % local_version_voices, -}] -patches = ['%(name)s-%(version)s_makefile.patch'] -checksums = [ - 'c01ded2c0a05667e6df2439c1c02b011a5df2bfdf49e24a524630686aea2b558', # MBROLA-3.3.tar.gz - '0dee14739f82fa247204791248b2d98a87e3f86f8cbb3a5844950103a41d33ba', # MBROLA-voices-20200330.tar.gz - '3f06bffdf900c51b531f473a760c50842ccf92a9d0598bd17fd556d049593a9e', # MBROLA-3.3_makefile.patch -] - -builddependencies = [('binutils', '2.34')] - -files_to_copy = [ - (['Bin/mbrola'], 'bin'), - (['../MBROLA-voices*/data/*'], 'share/mbrola'), -] - -sanity_check_paths = { - 'files': ['bin/mbrola'], - 'dirs': ['share/mbrola'] -} - -sanity_check_commands = ['mbrola -h'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/MCL/MCL-14.137-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MCL/MCL-14.137-GCCcore-9.3.0.eb deleted file mode 100644 index 8e9c58e58aa..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MCL/MCL-14.137-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MCL' -version = '14.137' - -homepage = 'https://micans.org/mcl/' -description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast -and scalable unsupervised cluster algorithm for graphs (also known as networks) based -on simulation of (stochastic) flow in graphs. """ - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://micans.org/%(namelower)s/src/'] -sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] -patches = ['%(name)s-%(version)s_fixperl.patch'] -checksums = [ - 'b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497', # mcl-14-137.tar.gz - '46988a287b2ee400a54fa485176d043b2a2d6589b6257cc6cf9c21689ea3842d', # MCL-14.137_fixperl.patch -] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Perl', '5.30.2'), -] - -configopts = '--enable-blast ' - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['clm', 'clmformat', 'clxdo', 'mcl', 'mclblastline', 'mclcm', 'mclpipeline', 'mcx', - 'mcxarray', 'mcxassemble', 'mcxdeblast', 'mcxdump', 'mcxi', 'mcxload', 'mcxmap', - 'mcxrand', 'mcxsubs']], - 'dirs': ['share'] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MDBM/MDBM-4.13.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MDBM/MDBM-4.13.0-GCCcore-9.3.0.eb deleted file mode 100644 index 4c8bacb63d8..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MDBM/MDBM-4.13.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MDBM' -version = '4.13.0' - -homepage = 'https://github.com/yahoo/mdbm' - -description = """MDBM is a super-fast memory-mapped key/value store""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/yahoo/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['99cec32e02639048f96abf4475eb3f97fc669541560cd030992bab155f0cb7f8'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('CppUnit', '1.15.1'), - ('libreadline', '8.0'), -] - -skipsteps = ['configure'] - -prebuildopts = 'sed -i -e "s/error/no-error/ ; s@/tmp/install@%(installdir)s@" Makefile.base && ' -prebuildopts += 'LDADD=-ldl' - -sanity_check_paths = { - 'files': ['bin/mdbm_config', 'include/mdbm.h', 'lib64/libmdbm.so'], - 'dirs': ['bin', 'include', 'lib64'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb b/easybuild/easyconfigs/__archive__/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb deleted file mode 100644 index 5f479fba0be..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MDSplus-Java' -version = '7.96.12' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://mdsplus.org' -description = """MDSplus is a set of software tools for data acquisition and storage and a methodology - for management of complex scientific data.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/MDSplus/mdsplus/archive'] -sources = ['stable_release-%s.zip' % version.replace('.', '-')] -patches = ['MDSplus-Java-%(version)s_classpath.patch'] -checksums = [ - '72f97f5ecf4eac40629c0e0c869cc48f7b8caa52ea9dc52d77c37d436190a318', # stable_release-7-96-12.zip - 'f2919aa5992b6364a9234bbb35230eecb84d123779c0580461f939bbc7039013', # MDSplus-Java-7.96.12_classpath.patch -] - -builddependencies = [ - ('binutils', '2.34') -] - -dependencies = [ - ('Java', '13', '', SYSTEM), - ('MDSplus', version), -] - -preconfigopts = 'find . -type f -regex .*Makefile.* -maxdepth 12 ' -preconfigopts += '-exec sed -i "s/JAVASOURCE = 6/JAVASOURCE = 8/g" {} \\; && ' -preconfigopts += 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' - -configopts = '--with-jdk=$JAVA_HOME --enable-java_only --disable-doxygen-doc --disable-valgrind' - -maxparallel = 1 - -sanity_check_paths = { - 'files': ['bin/jTraverser', 'bin/jScope', 'bin/jServer'], - 'dirs': ['bin', 'include', 'java/classes'], -} - -modextrapaths = {'CLASSPATH': 'java/classes/*'} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch b/easybuild/easyconfigs/__archive__/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch deleted file mode 100644 index 17ef23ee344..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch +++ /dev/null @@ -1,142 +0,0 @@ -use $EBROOTMDSPLUSMINJAVA environment variable to refer to installation directory - -author: Simon Pinches - -diff -Nru mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jDispatcherIp.template mdsplus-stable_release-7-84-6/java/jdispatcher/jDispatcherIp.template ---- mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jDispatcherIp.template 2019-09-02 18:02:07.000000000 +0200 -+++ mdsplus-stable_release-7-84-6/java/jdispatcher/jDispatcherIp.template 2019-09-26 16:26:07.000000000 +0200 -@@ -2,7 +2,7 @@ - #! - # - exec env \ --LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MDSPLUS_DIR/lib \ --SHLIB_PATH=$MDSPLUS_DIR/lib \ --CLASSPATH=$HOME:$MDSPLUS_DIR/java/classes/jScope.jar:$MDSPLUS_DIR/java/classes/jTraverser.jar:$MDSPLUS_DIR/java/classes/jDispatcher.jar:$MDSPLUS_DIR/java/classes: \ -+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/lib \ -+SHLIB_PATH=$EBROOTMDSPLUSMINJAVA/lib \ -+CLASSPATH=$HOME:$EBROOTMDSPLUSMINJAVA/java/classes/jScope.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jTraverser.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jDispatcher.jar:$EBROOTMDSPLUSMINJAVA/java/classes: \ - java jDispatcherIp $1 $2 $3 $4 $5 -diff -Nru mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jDispatchMonitor.template mdsplus-stable_release-7-84-6/java/jdispatcher/jDispatchMonitor.template ---- mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jDispatchMonitor.template 2019-09-02 18:02:07.000000000 +0200 -+++ mdsplus-stable_release-7-84-6/java/jdispatcher/jDispatchMonitor.template 2019-09-26 16:26:08.000000000 +0200 -@@ -2,7 +2,7 @@ - #! - # - exec env \ --LD_LIBRARY_PATH=$MDSPLUS_DIR/lib \ --SHLIB_PATH=$MDSPLUS_DIR/lib \ --CLASSPATH=$HOME:$MDSPLUS_DIR/java/classes/jScope.jar:$MDSPLUS_DIR/java/classes/jTraverser.jar:$MDSPLUS_DIR/java/classes/jDispatcher.jar:$MDSPLUS_DIR/java/classes: \ -+LD_LIBRARY_PATH=$EBROOTMDSPLUSMINJAVA/lib \ -+SHLIB_PATH=$EBROOTMDSPLUSMINJAVA/lib \ -+CLASSPATH=$HOME:$EBROOTMDSPLUSMINJAVA/java/classes/jScope.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jTraverser.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jDispatcher.jar:$EBROOTMDSPLUSMINJAVA/java/classes: \ - java jDispatchMonitor $1 $2 $3 $4 $5 -diff -Nru mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jServer.template mdsplus-stable_release-7-84-6/java/jdispatcher/jServer.template ---- mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jServer.template 2019-09-02 18:02:07.000000000 +0200 -+++ mdsplus-stable_release-7-84-6/java/jdispatcher/jServer.template 2019-09-26 16:26:08.000000000 +0200 -@@ -2,7 +2,7 @@ - #! - # - exec env \ --LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MDSPLUS_DIR/lib \ --SHLIB_PATH=$MDSPLUS_DIR/lib \ --CLASSPATH=$HOME:$MDSPLUS_DIR/java/classes/jScope.jar:$MDSPLUS_DIR/java/classes/jTraverser.jar:$MDSPLUS_DIR/java/classes/jDispatcher.jar:$MDSPLUS_DIR/java/classes: \ -+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/lib \ -+SHLIB_PATH=$EBROOTMDSPLUSMINJAVA/lib \ -+CLASSPATH=$HOME:$EBROOTMDSPLUSMINJAVA/java/classes/jScope.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jTraverser.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jDispatcher.jar:$EBROOTMDSPLUSMINJAVA/java/classes: \ - java -Xss10M jServer $1 -diff -Nru mdsplus-stable_release-7-84-6.orig/java/jscope/jScope.template mdsplus-stable_release-7-84-6/java/jscope/jScope.template ---- mdsplus-stable_release-7-84-6.orig/java/jscope/jScope.template 2019-09-02 18:02:07.000000000 +0200 -+++ mdsplus-stable_release-7-84-6/java/jscope/jScope.template 2019-09-26 16:26:08.000000000 +0200 -@@ -4,17 +4,17 @@ - # - lib=lib - if java -d64 -version > /dev/null 2>&1; then -- if [ -r $MDSPLUS_DIR/lib64 ] ; then -+ if [ -r $EBROOTMDSPLUSMINJAVA/lib64 ] ; then - lib=/lib64 - fi - else -- if [ -r $MDSPLUS_DIR/lib32 ]; then -+ if [ -r $EBROOTMDSPLUSMINJAVA/lib32 ]; then - lib=lib32 - fi - fi - exec env \ --LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ --SHLIB_PATH=$SHLIB_PATH:$MDSPLUS_DIR/${lib} \ --DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ --CLASSPATH=$HOME:$MDSPLUS_DIR/java/classes/jScope.jar:$MDSPLUS_DIR/java/classes:$HOME:$MDSPLUS_DIR/java/classes/mdsobjects.jar \ --java -Xmx512M -Djava.library.path=$MDSPLUS_DIR/${lib} jScope $1 $2 $3 $4 $5 $6 $7 -+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ -+SHLIB_PATH=$SHLIB_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ -+DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ -+CLASSPATH=$HOME:$EBROOTMDSPLUSMINJAVA/java/classes/jScope.jar:$EBROOTMDSPLUSMINJAVA/java/classes:$HOME:$EBROOTMDSPLUSMINJAVA/java/classes/mdsobjects.jar \ -+java -Xmx512M -Djava.library.path=$EBROOTMDSPLUSMINJAVA/${lib} jScope $1 $2 $3 $4 $5 $6 $7 -diff -Nru mdsplus-stable_release-7-84-6.orig/java/jtraverser/jTraverser.template mdsplus-stable_release-7-84-6/java/jtraverser/jTraverser.template ---- mdsplus-stable_release-7-84-6.orig/java/jtraverser/jTraverser.template 2019-09-02 18:02:07.000000000 +0200 -+++ mdsplus-stable_release-7-84-6/java/jtraverser/jTraverser.template 2019-09-26 16:26:08.000000000 +0200 -@@ -4,17 +4,17 @@ - # - lib=lib - if java -d64 -version > /dev/null 2>&1; then -- if [ -r $MDSPLUS_DIR/lib64 ] ; then -+ if [ -r $EBROOTMDSPLUSMINJAVA/lib64 ] ; then - lib=/lib64 - fi - else -- if [ -r $MDSPLUS_DIR/lib32 ]; then -+ if [ -r $EBROOTMDSPLUSMINJAVA/lib32 ]; then - lib=lib32 - fi - fi - exec env \ --LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ --SHLIB_PATH=$SHLIB_PATH:$MDSPLUS_DIR/${lib} \ --DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ --CLASSPATH=$MDSPLUS_DIR/java/classes/jTraverser.jar:$MDSPLUS_DIR/java/classes/jScope.jar:$MDSPLUS_DIR/java/classes/jDevices.jar \ --java -Xss5M -Djava.library.path=$MDSPLUS_DIR/${lib} jTraverser $1 $2 $3 $4 $5 $6 $7 -+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ -+SHLIB_PATH=$SHLIB_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ -+DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ -+CLASSPATH=$EBROOTMDSPLUSMINJAVA/java/classes/jTraverser.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jScope.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jDevices.jar \ -+java -Xss5M -Djava.library.path=$EBROOTMDSPLUSMINJAVA/${lib} jTraverser $1 $2 $3 $4 $5 $6 $7 -diff -Nru mdsplus-stable_release-7-84-6.orig/java/jtraverser2/jTraverser2.template mdsplus-stable_release-7-84-6/java/jtraverser2/jTraverser2.template ---- mdsplus-stable_release-7-84-6.orig/java/jtraverser2/jTraverser2.template 2019-09-02 18:02:07.000000000 +0200 -+++ mdsplus-stable_release-7-84-6/java/jtraverser2/jTraverser2.template 2019-09-26 16:26:08.000000000 +0200 -@@ -1,16 +1,16 @@ - #!/bin/sh - lib=lib - if java -d64 -version > /dev/null 2>&1; then -- if [ -r $MDSPLUS_DIR/lib64 ] ; then -+ if [ -r $EBROOTMDSPLUSMINJAVA/lib64 ] ; then - lib=/lib64 - fi - else -- if [ -r $MDSPLUS_DIR/lib32 ]; then -+ if [ -r $EBROOTMDSPLUSMINJAVA/lib32 ]; then - lib=lib32 - fi - fi - exec env \ --LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ --SHLIB_PATH=$SHLIB_PATH:$MDSPLUS_DIR/${lib} \ --DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ --java -jar $MDSPLUS_DIR/java/classes/jTraverser2.jar "$@" -+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ -+SHLIB_PATH=$SHLIB_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ -+DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ -+java -jar $EBROOTMDSPLUSMINJAVA/java/classes/jTraverser2.jar "$@" -diff -Nru mdsplus-stable_release-7-84-6.orig/Makefile.in mdsplus-stable_release-7-84-6/Makefile.in ---- mdsplus-stable_release-7-84-6.orig/Makefile.in 2019-09-02 18:02:07.000000000 +0200 -+++ mdsplus-stable_release-7-84-6/Makefile.in 2019-09-26 16:28:01.000000000 +0200 -@@ -40,8 +40,8 @@ - D3D_PACKAGE = d3dshr - - ifeq "@JAVA_ONLY@" "yes" --NON_JAR = --PARTS = $(JAVA_JAR) -+NON_JAR = @JAVA_APS@ -+PARTS = $(NON_JAR) $(JAVA_JAR) - else - NON_JAR = \ - mdsshr \ diff --git a/easybuild/easyconfigs/__archive__/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 5e5baeb1f93..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,49 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MDSplus-Python' -version = '7.96.12' -local_pyver = '3.8.2' - -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://mdsplus.org' -description = """MDSplus is a set of software tools for data acquisition and storage and a methodology - for management of complex scientific data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/MDSplus/mdsplus/archive'] -sources = ['stable_release-%s.zip' % version.replace('.', '-')] -checksums = ['72f97f5ecf4eac40629c0e0c869cc48f7b8caa52ea9dc52d77c37d436190a318'] - -dependencies = [ - ('Python', local_pyver), - ('SciPy-bundle', '2020.03', versionsuffix), - ('MDSplus', version), -] - -local_moddir = 'lib/python%(pyshortver)s/site-packages/MDSplus' - -skipsteps = ['build', 'test'] - -configopts = '--disable-doxygen-doc --disable-java' -# hardcode version via configure script (git is unavailable) -configopts += ' RELEASE_VERSION=%(version)s BRANCH=stable' - -# install by simply copying into a subdir because -# running setup.py will try to make an egg link instead of installing. -install_cmd = 'mkdir -p %(installdir)s/' + local_moddir -install_cmd += ' && pwd && cp -a python/MDSplus/* %(installdir)s/' + local_moddir + '/' - -sanity_check_paths = { - 'files': [], - 'dirs': [local_moddir], -} - -# MDSplus.__version__ shows an ugly non-fatal warning, -# the logic in the mdsplus package seems broken and may need patching. -sanity_check_commands = [ - ('python', "-c 'import MDSplus ; print(MDSplus.__version__)'"), -] -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb deleted file mode 100644 index ca72487726f..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MDSplus' -version = '7.96.12' - -homepage = 'https://mdsplus.org' -description = """MDSplus is a set of software tools for data acquisition and storage and a methodology - for management of complex scientific data.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] -sources = ['stable_release-%s.zip' % version.replace('.', '-')] -checksums = ['72f97f5ecf4eac40629c0e0c869cc48f7b8caa52ea9dc52d77c37d436190a318'] - -builddependencies = [ - ('binutils', '2.34') -] - -dependencies = [ - ('libxml2', '2.9.10'), - ('zlib', '1.2.11'), - ('ncurses', '6.2'), - ('libreadline', '8.0') -] - -configopts = '--disable-doxygen-doc --disable-java' -# hardcode version via configure script (git is unavailable) -configopts += ' RELEASE_VERSION=%(version)s BRANCH=stable' - -preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' - -maxparallel = 1 - -modextravars = { - 'MDSPLUS_DIR': '%(installdir)s', - 'MDS_PATH': '%(installdir)s/tdi', -} - -modextrapaths = { - 'IDL_PATH': 'idl', -} - -sanity_check_paths = { - 'files': ['lib/libMdsLib.%s' % SHLIB_EXT, 'lib/libTreeShr.%s' % SHLIB_EXT, - 'include/mdslib.h', 'include/mdsobjects.h'], - 'dirs': ['bin', 'tdi'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.96.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.96.8-GCCcore-9.3.0.eb deleted file mode 100644 index 97b4b1cd4d3..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.96.8-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MDSplus' -version = '7.96.8' - -homepage = 'https://mdsplus.org/' -description = """MDSplus is a set of software tools for data acquisition and storage and a methodology - for management of complex scientific data.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] -sources = ['stable_release-%s.zip' % version.replace('.', '-')] -checksums = ['d63ae3b6ea5ca9228a1f680780000fb220ea97a55d71a8a93258741a352f247d'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('libxml2', '2.9.10'), - ('zlib', '1.2.11'), - ('ncurses', '6.2'), - ('libreadline', '8.0') -] - -configopts = [' --disable-doxygen-doc --disable-java --disable-valgrind' - ' --without-idl --without-labview --without-srb --without-gsi' - ' --without-x --without-docker-image'] - -preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' - -maxparallel = 1 - -modextravars = { - 'MDSPLUS_DIR': '%(installdir)s', - 'MDS_PATH': '%(installdir)s/tdi', -} - -sanity_check_paths = { - 'files': ['lib/libMdsLib.so', 'lib/libTreeShr.so', 'include/mdslib.h', - 'include/mdsobjects.h'], - 'dirs': ['bin', 'include', 'lib', 'tdi'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.4-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 3864e8187a8..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.4-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -# Updated: Pavel Grochal (INUITS) - -easyblock = 'PythonBundle' - -name = 'MDTraj' -version = '1.9.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://mdtraj.org' -description = "Read, write and analyze MD trajectories with only a few lines of Python code." - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('zlib', '1.2.11'), -] - -exts_list = [ - ('astor', '0.8.1', { - 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], - }), - ('pymbar', '3.0.5', { - 'checksums': ['b079a7d0b9fbc8a92850277b664bb582991ef5ac399b3607e695569148f6c784'], - }), - ('mdtraj', version, { - 'checksums': ['d5d28be24dd5f38e8b272c3a445a6cdbffc374b30e891c5535f65bb20f7e8b24'], - }), -] - -# The unit tests of MDTraj are a pain to get to work: they require -# a massive number of extra dependencies. See -# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.4-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.4-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 3207f3f4b1e..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MDTraj/MDTraj-1.9.4-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,41 +0,0 @@ -# Updated: Pavel Grochal (INUITS) - -easyblock = 'PythonBundle' - -name = 'MDTraj' -version = '1.9.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://mdtraj.org' -description = "Read, write and analyze MD trajectories with only a few lines of Python code." - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'openmp': True} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('zlib', '1.2.11'), -] - -exts_list = [ - ('astor', '0.8.1', { - 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], - }), - ('pymbar', '3.0.5', { - 'checksums': ['b079a7d0b9fbc8a92850277b664bb582991ef5ac399b3607e695569148f6c784'], - }), - ('mdtraj', version, { - 'checksums': ['d5d28be24dd5f38e8b272c3a445a6cdbffc374b30e891c5535f65bb20f7e8b24'], - }), -] - -# The unit tests of MDTraj are a pain to get to work: they require -# a massive number of extra dependencies. See -# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb deleted file mode 100644 index 71ad1983c8b..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Bumped from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'CMakeMake' - -name = 'MEGAHIT' -version = '1.2.9' - -homepage = 'https://github.com/voutcn/megahit' -description = """An ultra-fast single-node solution for large and complex - metagenomics assembly via succinct de Bruijn graph""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('zlib', '1.2.11'), -] - -dependencies = [ - ('bzip2', '1.0.8'), - ('gzip', '1.10'), -] - -sanity_check_paths = { - 'files': [ - 'bin/%(namelower)s', - 'bin/%(namelower)s_core', - 'bin/%(namelower)s_core_no_hw_accel', - 'bin/%(namelower)s_core_popcnt', - 'bin/%(namelower)s_toolkit', - ], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MEM/MEM-20191023-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/m/MEM/MEM-20191023-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 78a75cf2a28..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MEM/MEM-20191023-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'RPackage' - -name = 'MEM' -local_commit = '6b92476' -version = '20191023' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://github.com/cytolab/mem' -description = "Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores." - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/cytolab/mem/archive/'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['735cc340fb644ddc4bd760d6897d3911561ea4735db10e799ff34e36ba138a86'] - -dependencies = [ - ('R', '4.0.0'), - ('R-bundle-Bioconductor', '3.11', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.1.0-GCCcore-9.3.0.eb deleted file mode 100644 index cab62698e8b..00000000000 --- a/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'METIS' -version = '5.1.0' - -homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' - -description = """ - METIS is a set of serial programs for partitioning graphs, partitioning - finite element meshes, and producing fill reducing orderings for sparse - matrices. The algorithms implemented in METIS are based on the multilevel - recursive-bisection, multilevel k-way, and multi-constraint partitioning - schemes. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', -] -sources = [SOURCELOWER_TAR_GZ] - -# We use 32bit for indices and 64bit for content -patches = ['%(name)s-%(version)s-use-doubles.patch'] - -checksums = [ - '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2', # source - '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67', # patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -configopts = ['', 'shared=1'] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/MLxtend/MLxtend-0.17.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/MLxtend/MLxtend-0.17.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 4b534edd8c1..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MLxtend/MLxtend-0.17.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,24 +0,0 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -easyblock = 'PythonPackage' - -name = 'MLxtend' -version = '0.17.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://rasbt.github.io/mlxtend/" -description = """Mlxtend (machine learning extensions) is a Python library of useful tools for the day-to-day data - science tasks.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['66d10059630a84c394cd8d82bca62c3da77b9fe6566f03656f2b52e353b8fe06'] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/m/MPC/MPC-1.1.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MPC/MPC-1.1.0-GCC-9.3.0.eb deleted file mode 100644 index 0c9808f6708..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MPC/MPC-1.1.0-GCC-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MPC' -version = '1.1.0' - -homepage = 'http://www.multiprecision.org/' -description = """Gnu Mpc is a C library for the arithmetic of - complex numbers with arbitrarily high precision and correct - rounding of the result. It extends the principles of the IEEE-754 - standard for fixed precision real floating point numbers to - complex numbers, providing well-defined semantics for every - operation. At the same time, speed of operation at high precision - is a major design goal.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'] - -dependencies = [ - ('GMP', '6.2.0'), - ('MPFR', '4.0.2'), -] - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], - 'dirs': [] -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/MPC/MPC-1.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MPC/MPC-1.1.0-GCCcore-9.3.0.eb deleted file mode 100644 index 1ef1d746c85..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MPC/MPC-1.1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MPC' -version = '1.1.0' - -homepage = 'http://www.multiprecision.org/' -description = """Gnu Mpc is a C library for the arithmetic of - complex numbers with arbitrarily high precision and correct - rounding of the result. It extends the principles of the IEEE-754 - standard for fixed precision real floating point numbers to - complex numbers, providing well-defined semantics for every - operation. At the same time, speed of operation at high precision - is a major design goal.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'] - -builddependencies = [('binutils', '2.34')] -dependencies = [ - ('GMP', '6.2.0'), - ('MPFR', '4.0.2'), -] - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], - 'dirs': [] -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/MPFR/MPFR-4.0.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MPFR/MPFR-4.0.2-GCCcore-9.3.0.eb deleted file mode 100644 index ec4a2a9ac07..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MPFR/MPFR-4.0.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MPFR' -version = '4.0.2' - -homepage = 'https://www.mpfr.org' - -description = """ - The MPFR library is a C library for multiple-precision floating-point - computations with correct rounding. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] -sources = [SOURCELOWER_TAR_BZ2] -patches = ['%(name)s-%(version)s_include_float.patch'] -checksums = [ - 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc', # mpfr-4.0.2.tar.bz2 - '9e462dd578ad2a8a111983dd7fad60d08f6e481b6dd43abb12f53e5721a51364', # MPFR-4.0.2_include_float.patch -] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('GMP', '6.2.0'), -] - -runtest = 'check' - -# copy libmpfr.so* to /lib to make sure that it is picked up by tests -# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) -pretestopts = "mkdir -p %%(installdir)s/lib && cp -a src/.libs/libmpfr.%s* %%(installdir)s/lib && " % SHLIB_EXT -testopts = " && rm -r %(installdir)s/lib" - -sanity_check_paths = { - 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], - 'dirs': [], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/MPFR/MPFR-4.0.2_include_float.patch b/easybuild/easyconfigs/__archive__/m/MPFR/MPFR-4.0.2_include_float.patch deleted file mode 100644 index 477839388df..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MPFR/MPFR-4.0.2_include_float.patch +++ /dev/null @@ -1,10 +0,0 @@ -Upstream patch from https://www.mpfr.org/mpfr-current/#fixed -Prepated for EasyBuild by Simon Branford (Uni. of Birmingham) -diff -Naurd mpfr-4.0.2-a/src/mpfr-impl.h mpfr-4.0.2-b/src/mpfr-impl.h ---- mpfr-4.0.2-a/src/mpfr-impl.h 2019-01-27 18:30:16.000000000 +0000 -+++ mpfr-4.0.2-b/src/mpfr-impl.h 2019-06-02 17:05:36.145226719 +0000 -@@ -57,6 +57,7 @@ - - #include - #include -+#include /* for FLT_RADIX, etc., tested below */ diff --git a/easybuild/easyconfigs/__archive__/m/MPICH/MPICH-3.3.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MPICH/MPICH-3.3.2-GCC-9.3.0.eb deleted file mode 100644 index f0d956cda41..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MPICH/MPICH-3.3.2-GCC-9.3.0.eb +++ /dev/null @@ -1,14 +0,0 @@ -name = 'MPICH' -version = '3.3.2' - -homepage = 'https://www.mpich.org/' -description = """MPICH is a high-performance and widely portable implementation -of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://www.mpich.org/static/tarballs/%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['4bfaf8837a54771d3e4922c84071ef80ffebddbb6971a006038d91ee7ef959b9'] - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/m/MRCPP/MRCPP-1.3.6-foss-2020a.eb b/easybuild/easyconfigs/__archive__/m/MRCPP/MRCPP-1.3.6-foss-2020a.eb deleted file mode 100644 index 4702a4e30f0..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MRCPP/MRCPP-1.3.6-foss-2020a.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'MRCPP' -version = '1.3.6' - -homepage = 'https://mrcpp.readthedocs.io' -description = """MultiResolution Computation Program Package""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = ['https://github.com/MRChemSoft/mrcpp/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['2502e71f086a8bb5ea635d0c6b86e7ff60220a45583e96a08b3cfe7c9db4cecf'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Eigen', '3.3.7') -] - -configopts = "-DENABLE_MPI=True -DENABLE_OPENMP=True" -runtest = 'test' - -sanity_check_paths = { - 'files': ['lib/libmrcpp.%s' % SHLIB_EXT], - 'dirs': ['include/MRCPP'] -} - -modextravars = {'MRCPP_DIR': '%(installdir)s/share/cmake/MRCPP/'} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/MRChem/MRChem-1.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/MRChem/MRChem-1.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 2f9dfbcb7f8..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MRChem/MRChem-1.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'MRChem' -version = '1.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://mrchem.readthedocs.io' -description = """MRChem is a numerical real-space code for molecular electronic -structure calculations within the self-consistent field (SCF) approximations of -quantum chemistry: Hartree-Fock and Density Functional Theory.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = ['https://github.com/MRChemSoft/mrchem/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['9cdda4d30b2baabb26400742f78ef8f3fc50a54f5218c8b6071b0cbfbed746c3'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Eigen', '3.3.7') -] - -dependencies = [ - ('MRCPP', '1.3.6'), - ('Python', '3.8.2'), - ('XCFun', '2.1.0') -] - -configopts = "-DENABLE_MPI=True -DENABLE_OPENMP=True" -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/mrchem', 'bin/mrchem.x'], - 'dirs': ['lib'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/m/MRtrix/MRtrix-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/MRtrix/MRtrix-3.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 6639a2df29b..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MRtrix/MRtrix-3.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,29 +0,0 @@ -name = 'MRtrix' -version = '3.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.brain.org.au/software/index.html#mrtrix' -description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner - robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'cstd': 'c++11'} - -source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['3afceb3cb3f7e9977d881c174ff6ab62d3fd2c64533104566d38286e9fdfa458'] - -builddependencies = [ - ('Eigen', '3.3.7'), - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('zlib', '1.2.11'), - ('Python', '3.8.2'), - ('Mesa', '20.0.2'), - ('Qt5', '5.14.1'), - ('LibTIFF', '4.1.0'), - ('FFTW', '3.3.8'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb deleted file mode 100644 index a6f0d4b23e9..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'MUMPS' -version = '5.2.1' -versionsuffix = '-metis' - -homepage = 'https://graal.ens-lyon.fr/MUMPS/' -description = "A parallel sparse direct solver" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] -sources = ['%(name)s_%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD - '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS -] -checksums = [ - 'd988fc34dfc8f5eee0533e361052a972aa69cc39ab193e7f987178d24981744a', # MUMPS_5.2.1.tar.gz - 'e31019bedcce13acaa1867352edd99e1f67a97bb3fb7b96c7f10459c0fe301fd', # MUMPS-5.2.1_shared-pord.patch - '8973d64f44d509f1f85c6abb8b8ac9c330775f30c712f9a9e974c5541836d841', # MUMPS-5.2.1_shared-mumps.patch -] - -dependencies = [ - ('SCOTCH', '6.0.9'), - ('METIS', '5.1.0'), -] - -maxparallel = 1 -buildopts = 'all SONAME_VERSION="%(version)s"' - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb deleted file mode 100644 index bf3702d4047..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'MUMPS' -version = '5.2.1' -versionsuffix = '-metis' - -homepage = 'https://graal.ens-lyon.fr/MUMPS/' -description = "A parallel sparse direct solver" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] -sources = ['%(name)s_%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD - '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS -] -checksums = [ - 'd988fc34dfc8f5eee0533e361052a972aa69cc39ab193e7f987178d24981744a', # MUMPS_5.2.1.tar.gz - 'e31019bedcce13acaa1867352edd99e1f67a97bb3fb7b96c7f10459c0fe301fd', # MUMPS-5.2.1_shared-pord.patch - '8973d64f44d509f1f85c6abb8b8ac9c330775f30c712f9a9e974c5541836d841', # MUMPS-5.2.1_shared-mumps.patch -] - -dependencies = [ - ('SCOTCH', '6.0.9'), - ('METIS', '5.1.0'), -] - -maxparallel = 1 -buildopts = 'all SONAME_VERSION="%(version)s"' - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1_shared-mumps.patch b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1_shared-mumps.patch deleted file mode 100644 index 7e6b26372a2..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1_shared-mumps.patch +++ /dev/null @@ -1,66 +0,0 @@ -source: https://src.fedoraproject.org/rpms/MUMPS/blob/master/f/MUMPS-shared.patch -author: Antonio Trande (sagitter@fedoraproject.org) -Create a shared version of the MUMPS library. - -Index: mumps/src/Makefile -=================================================================== ---- mumps.orig/src/Makefile -+++ mumps/src/Makefile -@@ -23,8 +23,10 @@ - - include $(topdir)/Makefile.inc - --mumps_lib: $(libdir)/libmumps_common$(PLAT)$(LIBEXT) \ -- $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) -+mumps_lib: $(libdir)/libmumps_common$(PLAT).a \ -+ $(libdir)/libmumps_common$(PLAT).so \ -+ $(libdir)/lib$(ARITH)mumps$(PLAT).a \ -+ $(libdir)/lib$(ARITH)mumps$(PLAT).so - - OBJS_COMMON_MOD = \ - lr_common.o \ -@@ -167,14 +169,23 @@ - $(ARITH)tools.o\ - $(ARITH)type3_root.o - --$(libdir)/libmumps_common$(PLAT)$(LIBEXT): $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) -- $(AR)$@ $? -+$(libdir)/libmumps_common$(PLAT).a: $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) -+ $(AR) $@ $? - $(RANLIB) $@ - --$(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT): $(OBJS_MOD) $(OBJS_OTHER) -- $(AR)$@ $? -+$(libdir)/libmumps_common$(PLAT).so: $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) -+ $(FC) -shared $^ -Wl,-soname,libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) $(LORDERINGS) -lpthread $(MUMPS_LIBF77) $(MPIFLIB) $(MPICLIB) $(METISLIB) -o $(libdir)/libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs -+ ln -fs libmumps_common$(PLAT)-$(SONAME_VERSION).so $@ -+ -+$(libdir)/lib$(ARITH)mumps$(PLAT).a: $(OBJS_MOD) $(OBJS_OTHER) -+ $(AR) $@ $? - $(RANLIB) $@ - -+$(libdir)/lib$(ARITH)mumps$(PLAT).so: $(OBJS_MOD) $(OBJS_OTHER) -+ $(FC) -shared $^ -Wl,-soname,lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) -lmumps_common$(PLAT) $(MUMPS_LIBF77) $(LORDERINGS) -lpthread $(MPIFLIB) $(METISLIB) $(SCALAP) -o $(libdir)/lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs -+ ln -fs lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $@ -+ -+ - # Dependencies between modules: - $(ARITH)mumps_load.o: $(ARITH)mumps_comm_buffer.o \ - $(ARITH)mumps_struc_def.o \ -@@ -290,13 +301,13 @@ - - .SUFFIXES: .c .F .o - .F.o: -- $(FC) $(OPTF) $(INCS) $(IORDERINGSF) $(ORDERINGSF) -I. -I../include -c $*.F $(OUTF)$*.o -+ $(FC) $(OPTF) $(INCS) $(IORDERINGSF) $(ORDERINGSF) -I. -I../include -fPIC -c $*.F $(OUTF)$*.o - .c.o: -- $(CC) $(OPTC) $(INCS) -I../include $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -c $*.c $(OUTC)$*.o -+ $(CC) $(OPTC) $(INCS) -I../include $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -fPIC -c $*.c $(OUTC)$*.o - - $(ARITH)mumps_c.o: mumps_c.c - $(CC) $(OPTC) $(INCS) $(CDEFS) -DMUMPS_ARITH=MUMPS_ARITH_$(ARITH) \ -- $(IORDERINGSC) $(ORDERINGSC) -I../include -c mumps_c.c $(OUTC)$@ -+ $(IORDERINGSC) $(ORDERINGSC) -I../include -fPIC -c mumps_c.c $(OUTC)$@ - - - clean: diff --git a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1_shared-pord.patch b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1_shared-pord.patch deleted file mode 100644 index 10edc5b7eb8..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.2.1_shared-pord.patch +++ /dev/null @@ -1,80 +0,0 @@ -source: https://src.fedoraproject.org/rpms/MUMPS/blob/master/f/MUMPS-shared-pord.patch -author: Antonio Trande (sagitter@fedoraproject.org) -Create static and shared versions of the PORD library. - -Index: mumps/PORD/lib/Makefile -=================================================================== ---- mumps.orig/PORD/lib/Makefile -+++ mumps/PORD/lib/Makefile -@@ -9,7 +9,7 @@ - - INCLUDES = -I../include - --COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) -+COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) -fPIC - - OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \ - multisector.o gelim.o bucket.o tree.o \ -@@ -24,12 +24,16 @@ - .c.o: - $(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o - --libpord$(LIBEXT):$(OBJS) -- $(AR)$@ $(OBJS) -+libpord$(PLAT).a:$(OBJS) -+ $(AR) $@ $(OBJS) - $(RANLIB) $@ - -+libpord$(PLAT).so: $(OBJS) -+ $(CC) -shared $(OBJS) -Wl,-soname,libpord$(PLAT)-$(SONAME_VERSION).so -o libpord$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs -+ ln -fs libpord$(PLAT)-$(SONAME_VERSION).so $@ -+ - clean: - rm -f *.o - - realclean: -- rm -f *.o libpord.a -+ rm -f *.o libpord*.a *.so -Index: mumps/Makefile -=================================================================== ---- mumps.orig/Makefile -+++ mumps/Makefile -@@ -54,7 +54,7 @@ - multi_example: s d c z - (cd examples ; $(MAKE) multi) - --requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) -+requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT).a $(libdir)/libpord$(PLAT).so - - # dummy MPI library (sequential version) - -@@ -62,19 +62,26 @@ - (cd libseq; $(MAKE)) - - # Build the libpord.a library and copy it into $(topdir)/lib --$(libdir)/libpord$(PLAT)$(LIBEXT): -+$(libdir)/libpord$(PLAT).a: - if [ "$(LPORDDIR)" != "" ] ; then \ - cd $(LPORDDIR); \ - $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \ - fi; - if [ "$(LPORDDIR)" != "" ] ; then \ -- cp $(LPORDDIR)/libpord$(LIBEXT) $@; \ -+ cp $(LPORDDIR)/libpord$(PLAT).a $@; \ - fi; - -+$(libdir)/libpord$(PLAT).so: -+ if [ "$(LPORDDIR)" != "" ] ; then \ -+ cd $(LPORDDIR); make CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" ARFUNCT= RANLIB="$(RANLIB)" libpord$(PLAT).so; fi; -+ if [ "$(LPORDDIR)" != "" ] ; then \ -+ cp -a $(LPORDDIR)/libpord*.so lib/; fi; -+ -+ - clean: - (cd src; $(MAKE) clean) - (cd examples; $(MAKE) clean) -- (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT)) -+ (cd $(libdir); $(RM) *$(PLAT).a *$(PLAT).so) - (cd libseq; $(MAKE) clean) - if [ "$(LPORDDIR)" != "" ] ; then \ - cd $(LPORDDIR); $(MAKE) realclean; \ diff --git a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.6.2_shared-pord.patch b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.6.2_shared-pord.patch deleted file mode 100644 index 98dc0371d60..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-5.6.2_shared-pord.patch +++ /dev/null @@ -1,46 +0,0 @@ -Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch -Author: micketeer@gmail.com -Updatd to version 5.5.0: J. Sassmannshausen/ICL (UK) -Updatd to version 5.5.1: maxim-masterov (SURF) -Updatd to version 5.6.1: Petr Král (INUITS) -Updatd to version 5.6.2: Petr Král (INUITS) -diff -u MUMPS_5.6.2/Makefile.orig MUMPS_5.6.2/Makefile ---- MUMPS_5.6.2/Makefile.orig 2023-10-11 11:36:26.000000000 +0200 -+++ MUMPS_5.6.2/Makefile 2024-04-09 13:02:40.710623825 +0200 -@@ -65,7 +65,7 @@ - - include Makefile.inc - --prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) -+prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT).so - - prerequisitesshared: Makefile.inc $(LIBSEQNEEDED)sharedlibseq $(libdir)/libpord$(PLAT)$(LIBEXT_SHARED) - -@@ -103,8 +103,11 @@ - cp $(LPORDDIR)/libpord$(PLAT)$(LIBEXT_SHARED) $@; \ - fi; - -- -- -+$(libdir)/libpord$(PLAT).so: -+ if [ "$(LPORDDIR)" != "" ] ; then \ -+ cd $(LPORDDIR); make CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" ARFUNCT= RANLIB="$(RANLIB)" libpord$(PLAT).so; fi; -+ if [ "$(LPORDDIR)" != "" ] ; then \ -+ cp -a $(LPORDDIR)/libpord*.so lib/; fi; - - clean: - (cd src; $(MAKE) clean) -diff -u MUMPS_5.6.1/PORD/lib/Makefile.orig MUMPS_5.6.1/PORD/lib/Makefile ---- MUMPS_5.6.1/PORD/lib/Makefile.orig 2023-07-11 09:51:28.000000000 +0200 -+++ MUMPS_5.6.1/PORD/lib/Makefile 2023-07-26 10:47:36.312139519 +0200 -@@ -31,6 +31,10 @@ - libpord$(PLAT)$(LIBEXT_SHARED):$(OBJS) - $(CC) -shared $(OBJS) -o libpord.so - -+libpord$(PLAT).so: $(OBJS) -+ $(CC) -shared $(OBJS) -Wl,-soname,libpord$(PLAT)-$(SONAME_VERSION).so -o libpord$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs -+ ln -fs libpord$(PLAT)-$(SONAME_VERSION).so $@ -+ - clean: - rm -f *.o - diff --git a/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb deleted file mode 100644 index 5ee222e2706..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Cedric Laczny , Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## -## -# updated by: -# Adam Huffman -# The Francis Crick Institute - -name = 'MUMmer' -version = '3.23' - -homepage = 'http://mummer.sourceforge.net/' - -description = """ - MUMmer is a system for rapidly aligning entire genomes, - whether in complete or draft form. AMOS makes use of it. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] -sources = ['%(name)s%(version)s.tar.gz'] -checksums = ['1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f'] - -builddependencies = [('binutils', '2.34')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-9.3.0.eb deleted file mode 100644 index c63acb20d3d..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'ConfigureMake' - -name = 'MUMmer' -version = '4.0.0beta2' - -homepage = 'http://mummer.sourceforge.net/' - -description = """ - MUMmer is a system for rapidly aligning entire genomes, - whether in complete or draft form. AMOS makes use of it. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = ['cece76e418bf9c294f348972e5b23a0230beeba7fd7d042d5584ce075ccd1b93'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', - 'bin/repeat-match', 'bin/show-aligns', 'bin/show-coords', - 'bin/show-tiling', 'bin/show-snps', 'bin/show-diff', 'bin/exact-tandems', - 'bin/mummerplot', 'bin/promer', 'bin/dnadiff', - ], - 'dirs': ['include', 'lib', 'libexec'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb deleted file mode 100644 index a747217d2f7..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'MakeCp' - -name = 'MUSCLE' -version = '3.8.31' - -homepage = 'https://drive5.com/muscle/' -description = """MUSCLE is one of the best-performing multiple alignment programs - according to published benchmark tests, with accuracy and speed that are consistently - better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users - learn everything they need to know about MUSCLE in a few minutes-only a handful of - command-line options are needed to perform common alignment tasks.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] -sources = ['%(namelower)s%(version)s_src.tar.gz'] -patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] -checksums = [ - '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz - '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch -] - -builddependencies = [ - ('binutils', '2.34'), -] - -files_to_copy = [ - (["muscle"], 'bin')] - -sanity_check_paths = { - 'files': ["bin/muscle"], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MaSuRCA/MaSuRCA-4.0.1-foss-2020a-Perl-5.30.2.eb b/easybuild/easyconfigs/__archive__/m/MaSuRCA/MaSuRCA-4.0.1-foss-2020a-Perl-5.30.2.eb deleted file mode 100644 index 284ef9ba056..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MaSuRCA/MaSuRCA-4.0.1-foss-2020a-Perl-5.30.2.eb +++ /dev/null @@ -1,66 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2017 University of Geneva -# Authors:: Yann Sagon -# License:: MIT/GPL -# $Id$ -# -## - -easyblock = 'ConfigureMake' - -name = 'MaSuRCA' -version = '4.0.1' -versionsuffix = '-Perl-%(perlver)s' - -homepage = 'http://www.genome.umd.edu/masurca.html' - -description = '''MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph - and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing - only short reads from Illumina sequencing or a mixture of short reads and long reads - (Sanger, 454, Pacbio and Nanopore).''' - -toolchain = {'name': 'foss', 'version': '2020a'} - -# need a temporary url to download it. Do it manually here: -# http://www.genome.umd.edu/masurca_form.html - -source_urls = ['https://github.com/alekseyzimin/masurca/releases/download/v%(version)s'] -sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['68628acaf3681d09288b48a35fec7909b347b84494fb26c84051942256299870'] - -dependencies = [ - ('libreadline', '8.0'), - ('Tcl', '8.6.10'), - ('Boost', '1.72.0'), - ('zlib', '1.2.11'), - ('Perl', '5.30.2'), - ('bzip2', '1.0.8'), -] - -buildopts = "install-special" -start_dir = "global-1" - -postinstallcmds = [ - # fix location of 'bin' in install prefix in runCA and runCA-dedupe scripts - # escaping single quotes within single quotes is tricky, so we use $'...' to use ANSI C-like escaping - "sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA", - "sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA-dedupe", - # fix hardcoded path in masurca script, just point back to 'bin' subdirectory instead - "sed -i 's@../CA8/Linux-amd64/bin@../bin@g' %(installdir)s/bin/masurca", - # commands to install built-in version of Flye - "cd ../Flye && make && cp -a ../Flye %(installdir)s", -] - -sanity_check_paths = { - 'files': ['bin/masurca', 'Flye/bin/flye'], - 'dirs': ['include', 'lib'], -} - -sanity_check_commands = [ - "masurca --help", - "runCA --help", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/Mako/Mako-1.1.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/Mako/Mako-1.1.2-GCCcore-9.3.0.eb deleted file mode 100644 index a3c8fa01f79..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Mako/Mako-1.1.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Mako' -version = '1.1.2' - -homepage = 'https://www.makotemplates.org' -description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['3139c5d64aa5d175dbafb95027057128b5fbd05a40c53999f3905ceb53366d9d'] - -builddependencies = [('binutils', '2.34')] -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -sanity_check_paths = { - 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/MariaDB-connector-c/MariaDB-connector-c-3.1.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MariaDB-connector-c/MariaDB-connector-c-3.1.7-GCCcore-9.3.0.eb deleted file mode 100644 index 65b1182cd02..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MariaDB-connector-c/MariaDB-connector-c-3.1.7-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'MariaDB-connector-c' -version = '3.1.7' - -homepage = 'https://downloads.mariadb.org/connector-c/' -description = "MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/MariaDB/mariadb-connector-c/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['c6bda309fd71aa01e5d32c48768cb4fb5abcb760b1272e270901f4e47cd759d6'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -# don't use gold linker, leads to error: "invalid use of VERSION in input file" -configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd'" - -sanity_check_paths = { - 'files': ['lib/mariadb/libmariadbclient.a', 'lib/mariadb/libmariadb.%s' % SHLIB_EXT], - 'dirs': ['include/mariadb'], -} - -modextrapaths = { - 'CPATH': ['include/mariadb'], - 'LD_LIBRARY_PATH': ['lib/mariadb'], - 'LIBRARY_PATH': ['lib/mariadb'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/m/Mash/Mash-2.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/Mash/Mash-2.2-GCC-9.3.0.eb deleted file mode 100644 index d5b65358598..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Mash/Mash-2.2-GCC-9.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# Updated to v2.2 -# R.QIAO - -easyblock = 'ConfigureMake' - -name = 'Mash' -version = '2.2' - -homepage = 'http://mash.readthedocs.org' -description = "Fast genome and metagenome distance estimation using MinHash" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'cstd': 'c++17'} - -source_urls = ['https://github.com/marbl/Mash/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = [ - 'Mash-%(version)s_fix-hardcoding.patch', - 'Mash-2.1_disable-memcpy-wrap.patch', -] -checksums = [ - '7ad006dbf0d6ffc3e164713ba955aab4cd24eaf85c864ac905f48cd8ba332691', # v2.2.tar.gz - '0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5', # Mash-2.2_fix-hardcoding.patch - '40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch -] - -builddependencies = [('Autotools', '20180311')] -dependencies = [ - ('CapnProto', '0.8.0'), - ('GSL', '2.6'), - ('zlib', '1.2.11'), -] - -preconfigopts = "./bootstrap.sh && " -configopts = "--with-capnp=$EBROOTCAPNPROTO --with-gsl=$EBROOTGSL" - -sanity_check_paths = { - 'files': ['bin/mash', 'lib/libmash.a'], - 'dirs': ['include/mash'], -} - -sanity_check_commands = ['mash --version'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.3_version-string-without-spaces.patch b/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.3_version-string-without-spaces.patch deleted file mode 100644 index 90cebc98599..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.3_version-string-without-spaces.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- meep-1.3/libctl/Makefile.in.orig 2015-03-31 17:47:53.000000000 +0200 -+++ meep-1.3/libctl/Makefile.in 2015-04-08 13:23:54.206192661 +0200 -@@ -369,7 +369,7 @@ - ############################################################################## - - # what is printed out when invoking your program with --version: --VERSION_STRING = "Meep @VERSION@, Copyright (C) 2005-2015 Massachusetts Insitute of Technology." -+VERSION_STRING = "Meep_@VERSION@,_Copyright_(C)_2005-2015_Massachusetts_Insitute_of_Technology." - MY_DEFS = -DHAVE_CTL_HOOKS=1 -DHAVE_CTL_EXPORT_HOOK=1 - PROGRAM_NAME = meep - SPECIFICATION_FILE = $(PROGRAM_NAME).scm diff --git a/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.4.3-intel-2020a.eb b/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.4.3-intel-2020a.eb deleted file mode 100644 index db639ea5fe1..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.4.3-intel-2020a.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Meep' -version = '1.4.3' - -homepage = 'https://github.com/stevengj/meep' -description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package - developed at MIT to model electromagnetic systems.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True, 'opt': True, 'unroll': True, 'pic': True} - -source_urls = ['https://github.com/stevengj/meep/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['Meep-1.3_version-string-without-spaces.patch'] -checksums = [ - '1105b369c3f7f4aae0de62e933e49f4e3c94b8031a7eb39e2ee315d4cea46b02', # meep-1.4.3.tar.gz - '9d1ade5d656ab20feb18661a06a73aa9a36e1e583b98a630b7810ca7ffc91af6', # Meep-1.3_version-string-without-spaces.patch -] - -dependencies = [ - ('Harminv', '1.4.1'), - ('HDF5', '1.10.6'), - ('libctl', '4.0.0'), - ('GSL', '2.6'), - ('FFTW', '3.3.8'), - ('Guile', '2.2.4'), -] - -configopts = "--with-pic --with-mpi --with-blas=mkl_em64t --with-lapack=mkl_em64t --without-gcc-arch " -configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " - -# fix for guile-config being broken because shebang line contains full path to bin/guile -configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' - -sanity_check_paths = { - 'files': ['bin/meep', 'include/meep.hpp', 'lib/libmeep.a', 'lib/libmeep.%s' % SHLIB_EXT, 'lib/pkgconfig/meep.pc'], - 'dirs': ['include/meep', 'share/meep'], -} - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-5.7.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-5.7.1-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index dc3f54d18a4..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-5.7.1-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,28 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = "PythonPackage" - -name = 'Mercurial' -version = '5.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.mercurial-scm.org' -description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects -of any size and offers an easy and intuitive interface. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.mercurial-scm.org/release/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['cb5139144ccb2ef648f36963c8606d47dea1cb0e22aa2c055d6f860ce3fde7b0'] - -dependencies = [ - ('binutils', '2.34'), - ('Python', '3.8.2') -] - -sanity_check_commands = ["hg --help"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb deleted file mode 100644 index 7fab5b51576..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,70 +0,0 @@ -# This is a Mesa using software rendering via Gallium-DRI and libglvnd -# - libglvnd can dynamically choose between system-installed NVidia -# libGLX/libEGL or the software renderers provided by this Mesa -# - EGL is available -# -# Software renderers are enabled based on system architecture: -# - llvmpipe: the high-performance Gallium LLVM driver -# - swr: Intel's OpenSWR -# Default renderer is llvmpipe. SWR can be enabled by setting the environment -# variable GALLIUM_DRIVER=swr - -name = 'Mesa' -version = '20.0.2' - -homepage = 'https://www.mesa3d.org/' -description = """Mesa is an open-source implementation of the OpenGL specification - - a system for rendering interactive 3D graphics.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [ - 'https://mesa.freedesktop.org/archive/', - 'https://mesa.freedesktop.org/archive/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', -] -sources = [SOURCELOWER_TAR_XZ] -patches = ['Mesa-%(version)s-match-swrast-loosely.patch'] -checksums = [ - 'aa54f1cb669550606aab8ceb475105d15aeb814fca5a778ce70d0fd10e98e86f', # mesa-20.0.2.tar.xz - 'e86abc2b9a9ad3e2fc604ad5d9bfe15a62e842e9900365fe7061849ea7438d90', # Mesa-20.0.2-match-swrast-loosely.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('Meson', '0.55.1', '-Python-3.8.2'), - ('Ninja', '1.10.0'), - ('flex', '2.6.4'), - ('Bison', '3.5.3'), - ('pkg-config', '0.29.2'), - ('Mako', '1.1.2'), - ('libxml2', '2.9.10'), - ('expat', '2.2.9'), - ('gettext', '0.20.1'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('zstd', '1.4.4'), - ('libdrm', '2.4.100'), - ('libglvnd', '1.2.0'), - ('libunwind', '1.3.1'), - ('LLVM', '9.0.1'), - ('X11', '20200222'), -] - -configopts = "-Dplatforms=x11 -Dosmesa=gallium -Ddri-drivers='' -Dvulkan-drivers='' " -configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" - -# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host -# If you need a different configuration, it possible to override those values by setting your own configopts -# configopts += " -Dgallium-drivers=swrast,swr -Dswr-arches=avx,avx2,skx,knl" - -# symlink indirect to mesa GLX, similar to Debian, see -# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 -# This helps in certain X forwarding situations (e.g. XQuartz) -postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/Meson/Meson-0.53.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/Meson/Meson-0.53.2-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 6ef0e836a9f..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Meson/Meson-0.53.2-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Meson' -version = '0.53.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://mesonbuild.com' -description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['3e8f830f33184397c2eb0b651ec502adb63decb28978bdc84b3558d71284c21f'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('Ninja', '1.10.0'), -] - -options = {'modulename': 'mesonbuild'} - -sanity_check_paths = { - 'files': ['bin/meson'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/Meson/Meson-0.55.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/Meson/Meson-0.55.1-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 82f015e3d8d..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Meson/Meson-0.55.1-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Meson' -version = '0.55.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://mesonbuild.com' -description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['3b5741f884e04928bdfa1947467ff06afa6c98e623c25cef75adf71ca39ce080'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('Ninja', '1.10.0'), -] - -options = {'modulename': 'mesonbuild'} - -sanity_check_paths = { - 'files': ['bin/meson'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 5e48d817d92..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,39 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'MetaPhlAn' -version = '3.0.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/biobakery/MetaPhlAn' -description = """MetaPhlAn is a computational tool for profiling the composition - of microbial communities from metagenomic shotgun sequencing data """ - -source_urls = ['https://github.com/biobakery/MetaPhlAn/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['de965469e4f93e3dd5c9e2dac8914f7debd242c196f343cd7cefd8c7faddd33c'] - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Biopython', '1.78', versionsuffix), - ('Pysam', '0.16.0.1'), - ('DendroPy', '4.4.0'), - ('CMSeq', '1.0.3', versionsuffix), - ('biom-format', '2.1.10', versionsuffix), - ('h5py', '2.10.0', versionsuffix), - ('PhyloPhlAn', '3.0', versionsuffix), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} -sanity_check_commands = [('%(namelower)s', '-h')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MetaPhlAn2/MetaPhlAn2-2.7.8-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/MetaPhlAn2/MetaPhlAn2-2.7.8-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 56ae20a89fe..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MetaPhlAn2/MetaPhlAn2-2.7.8-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,56 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'Tarball' - -name = 'MetaPhlAn2' -version = '2.7.8' -versionsuffix = '-Python-%(pyver)s' - -bitbucket_account = 'biobakery' -homepage = 'https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/' -description = """MetaPhlAn is a computational tool for profiling the composition of microbial - communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing - data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now - possible to perform accurate strain-level microbial profiling.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/biobakery/MetaPhlAn/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['MetaPhlAn2-2.7.8_fix-download-db.patch'] -checksums = [ - ( - # checksum for 2.7.8.tar.gz downloaded from GitHub - 'f28fa38c4a23265bae8e3e07d53ad8cc1f4f504c115932d90d3e852120bb6180', - # alternative checksum for original 2.7.8.tar.gz downloaded from Bitbucket (same source files) - '24cd29c8b1d475adbe6b354391ce455fcfe9ef2266b6fb6635dee2bdb6a3edd3', - ), - '55b49148a48a5685b2456f420ddc6caa0b1f480f845f95869a656bba4194b9ca', # MetaPhlAn2-2.7.8_fix-download-db.patch -] - -dependencies = [ - ('Bowtie2', '2.4.1'), - ('Perl', '5.30.2'), - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -# needed to create database during installation -# the database is used if --input_type is fastq, fasta, multifasta, or multifastq -# otherwise database creation will be tried on first use with one of the above options -# and likely fail because a normal user can't write in the software directory -postinstallcmds = ['%(installdir)s/%(namelower)s.py --install'] - -modextrapaths = { - 'PATH': '', - 'mpa_dir': '', -} - -sanity_check_paths = { - 'files': ['%(namelower)s.py', 'strainphlan.py'], - 'dirs': ['utils', 'strainphlan_src', 'strainphlan_tutorial'], -} - -sanity_check_commands = ['%(namelower)s.py -v'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MetaPhlAn2/MetaPhlAn2-2.7.8_fix-download-db.patch b/easybuild/easyconfigs/__archive__/m/MetaPhlAn2/MetaPhlAn2-2.7.8_fix-download-db.patch deleted file mode 100644 index cdce3f36e01..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MetaPhlAn2/MetaPhlAn2-2.7.8_fix-download-db.patch +++ /dev/null @@ -1,59 +0,0 @@ -download database from Dropbox rather than Bitbucket (see repo is removed there) - -see https://github.com/biobakery/MetaPhlAn/commit/ca6684acda58c5b0cdc8820c00fd93c237744a0f -diff --git a/metaphlan2.py b/metaphlan2.py -index d1d68f1..2ea6a60 100755 ---- a/metaphlan2.py -+++ b/metaphlan2.py -@@ -58,7 +58,8 @@ - - - # set the location of the database download url --DATABASE_DOWNLOAD = "https://bitbucket.org/biobakery/metaphlan2/downloads/" -+DATABASE_DOWNLOAD = "https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AADHWzATSQcI0CNFD0sk7MAga" -+FILE_LIST= "https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAA4XDP85WHon_eHvztxkamTa/file_list.txt?dl=1" - # get the directory that contains this script - metaphlan2_script_install_folder = os.path.dirname(os.path.abspath(__file__)) - # get the default database folder -@@ -715,7 +716,7 @@ def download(url, download_file): - sys.stderr.write("\nFile {} already present!\n".format(download_file)) - - --def download_unpack_tar(url, download_file_name, folder, bowtie2_build, nproc): -+def download_unpack_tar(FILE_LIST, download_file_name, folder, bowtie2_build, nproc): - """ - Download the url to the file and decompress into the folder - """ -@@ -732,13 +733,21 @@ def download_unpack_tar(url, download_file_name, folder, bowtie2_build, nproc): - sys.exit("ERROR: The directory is not writeable: " + folder + ". " - "Please modify the permissions.") - -+ #Download the list of all the files in the Dropbox folder -+ list_file_path = os.path.join(folder, "file_list.txt") -+ download(FILE_LIST, list_file_path) -+ -+ if os.path.isfile(list_file_path): -+ with open(list_file_path) as f: -+ ls_f = dict( [row.strip().split() for row in f]) -+ - tar_file = os.path.join(folder, "mpa_" + download_file_name + ".tar") -- url_tar_file = os.path.join(url, "mpa_" + download_file_name + ".tar") -+ url_tar_file = ls_f["mpa_" + download_file_name + ".tar"] - download(url_tar_file, tar_file) - - # download MD5 checksum - md5_file = os.path.join(folder, "mpa_" + download_file_name + ".md5") -- url_md5_file = os.path.join(url, "mpa_" + download_file_name + ".md5") -+ url_md5_file = ls_f["mpa_" + download_file_name + ".md5"] - download(url_md5_file, md5_file) - - md5_md5 = None -@@ -824,7 +833,7 @@ def check_and_install_database(index, bowtie2_db, bowtie2_build, nproc): - # download the tar archive and decompress - sys.stderr.write("\nDownloading MetaPhlAn2 database\nPlease note due to " - "the size this might take a few minutes\n") -- download_unpack_tar(DATABASE_DOWNLOAD, index, bowtie2_db, bowtie2_build, nproc) -+ download_unpack_tar(FILE_LIST, index, bowtie2_db, bowtie2_build, nproc) - sys.stderr.write("\nDownload complete\n") - - diff --git a/easybuild/easyconfigs/__archive__/m/Metagenome-Atlas/Metagenome-Atlas-2.4.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/Metagenome-Atlas/Metagenome-Atlas-2.4.3-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 734af30d1f0..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Metagenome-Atlas/Metagenome-Atlas-2.4.3-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,90 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonBundle' - -name = 'Metagenome-Atlas' -version = '2.4.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/metagenome-atlas/atlas' -description = """Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. -It handles all steps from QC, Assembly, Binning, to Annotation.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('snakemake', '5.26.1', versionsuffix), - ('Biopython', '1.78', versionsuffix), - ('BBMap', '38.87'), - # dependencies below were discovered from running test suite - ('CheckM', '1.1.3', versionsuffix), - ('IPython', '7.15.0', versionsuffix), -] - -exts_list = [ - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('ruamel.yaml.clib', '0.2.2', { - 'modulename': False, - 'checksums': ['2d24bd98af676f4990c4d715bcdc2a60b19c56a3fb3a763164d2d8ca0e806ba7'], - }), - ('ruamel.yaml', '0.16.12', { - 'checksums': ['076cc0bc34f1966d920a49f18b52b6ad559fbe656a0748e3535cf7b3f29ebf9e'], - }), - ('colorlover', '0.3.0', { - 'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'], - }), - ('retrying', '1.3.3', { - 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], - }), - ('plotly', '4.11.0', { - 'checksums': ['b6ad5c3d2cbf056a782e3c6833a334c45a5453a12dc8a48df971602509e8d3d6'], - }), - ('cufflinks', '0.17.3', { - 'checksums': ['48c1b3406dc030004121966489eebc5518cea70fd4e3f16379b491328501a644'], - }), - ('arrow', '0.17.0', { - 'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'], - }), - ('jinja2-time', '0.2.0', { - 'checksums': ['d14eaa4d315e7688daa4969f616f226614350c48730bfa1692d2caebd8c90d40'], - }), - ('text-unidecode', '1.3', { - 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], - }), - ('python-slugify', '4.0.1', { - 'modulename': 'slugify', - 'checksums': ['69a517766e00c1268e5bbfc0d010a0a8508de0b18d30ad5a1ff357f8ae724270'], - }), - ('binaryornot', '0.4.4', { - 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], - }), - ('poyo', '0.5.0', { - 'checksums': ['e26956aa780c45f011ca9886f044590e2d8fd8b61db7b1c1cf4e0869f48ed4dd'], - }), - ('cookiecutter', '1.7.2', { - 'checksums': ['efb6b2d4780feda8908a873e38f0e61778c23f6a2ea58215723bcceb5b515dac'], - }), - (name, version, { - 'modulename': 'atlas', - 'patches': ['Metagenome-Atlas-2.4.3_remove-hardcoded-conda.patch'], - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/metagenome-atlas/atlas/archive/'], - 'checksums': [ - '00bc2af287efe239520f952b4057f640dd58feea16be797ff07e89f935d687ae', # 2.4.3.tar.gz - # Metagenome-Atlas-2.4.3_remove-hardcoded-conda.patch - '6cc6e9aa08091ae78f287f30628aa56568aa0e0af348d85fbdc27a4da1a77022', - ], - }), -] - -# https://metagenome-atlas.readthedocs.io/en/latest/usage/getting_started.html#set-up-of-cluster-execution -modloadmsg = "%(name)s requires snakemake configuration to run jobs.\n" -modloadmsg += "The configuration can be found in $EBROOTMETAGENOMEMINATLAS/snakemake-config \n" -modloadmsg += "or obtained from: https://github.com/metagenome-atlas/clusterprofile.git \n " - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/Metagenome-Atlas/Metagenome-Atlas-2.4.3_remove-hardcoded-conda.patch b/easybuild/easyconfigs/__archive__/m/Metagenome-Atlas/Metagenome-Atlas-2.4.3_remove-hardcoded-conda.patch deleted file mode 100644 index 0841ef18153..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Metagenome-Atlas/Metagenome-Atlas-2.4.3_remove-hardcoded-conda.patch +++ /dev/null @@ -1,42 +0,0 @@ -remove conda-related hardcoded arguments for snakemake - -author: Pavel Grochal (INUITS) - -diff -rub --new-file atlas-2.4.3.orig/atlas/atlas.py atlas-2.4.3/atlas/atlas.py ---- atlas-2.4.3.orig/atlas/atlas.py 2020-09-15 09:05:26.000000000 +0200 -+++ atlas-2.4.3/atlas/atlas.py 2020-10-21 13:58:19.738035955 +0200 -@@ -129,7 +129,7 @@ - "snakemake --snakefile {snakefile} --directory {working_dir} " - "{jobs} --rerun-incomplete " - "--configfile '{config_file}' --nolock " -- " {profile} --use-conda {conda_prefix} {dryrun} " -+ " {profile} {dryrun} " - " {target_rule} " - " {args} " - ).format( -@@ -140,8 +140,7 @@ - profile="" if (profile is None) else "--profile {}".format(profile), - dryrun="--dryrun" if dryrun else "", - args=" ".join(snakemake_args), -- target_rule=workflow if workflow!="None" else "", -- conda_prefix= "--conda-prefix "+os.path.join(db_dir,'conda_envs') -+ target_rule=workflow if workflow!="None" else "" - ) - logging.info("Executing: %s" % cmd) - try: -@@ -183,14 +182,13 @@ - cmd = ( - "snakemake --snakefile {snakefile} " - "--jobs {jobs} --rerun-incomplete " -- "--nolock --use-conda --conda-prefix {conda_prefix} " -+ "--nolock " - "--config database_dir='{db_dir}' {add_args} " - "{args}" - ).format( - snakefile=get_snakefile("rules/download.snakefile"), - jobs=jobs, - db_dir=db_dir, -- conda_prefix=os.path.join(db_dir,'conda_envs'), - add_args="" if snakemake_args and snakemake_args[0].startswith("-") else "--", - args=" ".join(snakemake_args), - ) diff --git a/easybuild/easyconfigs/__archive__/m/Mini-XML/Mini-XML-2.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/Mini-XML/Mini-XML-2.12-GCCcore-9.3.0.eb deleted file mode 100644 index 9035db82f73..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Mini-XML/Mini-XML-2.12-GCCcore-9.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Mini-XML' -version = '2.12' - -homepage = 'https://www.msweet.org/mxml' -description = """Mini-XML is a small XML parsing library that you can use to read XML data files or strings in your - application without requiring large non-standard libraries""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/michaelrsweet/mxml/releases/download/v%(version)s/'] -sources = ['mxml-%(version)s.tar.gz'] -checksums = ['6bfb53baa1176e916855bd3b6d592fd5b962c3c259aacdb5670d90c57ce4034f'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['include/mxml.h', 'lib/libmxml.a', 'lib/libmxml.%s' % SHLIB_EXT], - 'dirs': ['share/man'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/m/MiniCARD/MiniCARD-1.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MiniCARD/MiniCARD-1.2-GCC-9.3.0.eb deleted file mode 100644 index bfca2ad6fc6..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MiniCARD/MiniCARD-1.2-GCC-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'Bundle' - -name = 'MiniCARD' -version = '1.2' - -homepage = 'https://github.com/liffiton/minicard' -description = """ -MiniCARD is a *cardinality solver* based on MiniSAT [www.minisat.se]. MiniCARD -handles cardinality constraints natively, using the same efficient data -structures and techniques MiniSAT uses for clauses, giving it much better -performance on cardinality constraints than CNF encodings of those constraints -passed to a typical SAT solver. It can read the standard DIMACS CNF format, -the OPB pseudo-boolean format (with linear cardinality constraints only), and -CNF+, a format that extends CNF to include cardinality constraints.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++03'} - -github_account = 'liffiton' -source_urls = [GITHUB_LOWER_SOURCE] - -dependencies = [ - ('zlib', '1.2.11'), -] - -default_easyblock = 'MakeCp' -default_component_specs = { - 'sources': [{'filename': 'v%(version)s.tar.gz', 'extract_cmd': "tar --strip-components 1 -xzf %s"}], - 'checksums': ['d5bb2f154efa08f85db4fbe2ea6dc2ed0514f6b9b1b93e2d79b2d2bae76c20cf'], - 'start_dir': '%(namelower)s', - 'prebuildopts': 'MROOT=%(builddir)s CFLAGS="$CXXFLAGS -Wno-parentheses -fpermissive"', - 'files_to_copy': [(['%(namelower)s'], 'bin')], -} -components = [ - (name, version), - ('MiniCARD_Encodings', version), - ('MiniCARD_Simp_Encodings', version), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['minicard', 'minicard_encodings', 'minicard_simp_encodings']], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/m/MiniSat/MiniSat-2.2.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MiniSat/MiniSat-2.2.0-GCC-9.3.0.eb deleted file mode 100644 index ab6e0499917..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MiniSat/MiniSat-2.2.0-GCC-9.3.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'Bundle' - -name = 'MiniSat' -version = '2.2.0' - -homepage = 'http://minisat.se/' -description = """ -MiniSat is a minimalistic, open-source SAT solver, developed to help -researchers and developers alike to get started on SAT.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++03'} - -source_urls = ['https://github.com/niklasso/minisat/archive/releases'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -default_easyblock = 'MakeCp' -default_component_specs = { - 'sources': [{'filename': '%(version)s.tar.gz', 'extract_cmd': "tar --strip-components 1 -xzf %s"}], - 'checksums': ['3ed44da999744c0a1be269df23c3ed8731cdb83c44a4f3aa29b3d6859bb2a4da'], - 'prebuildopts': 'MROOT=%(builddir)s CFLAGS="$CXXFLAGS -Wno-parentheses -fpermissive"', - 'buildopts': "EXEC=%(namelower)s", - 'files_to_copy': [(['%(namelower)s'], 'bin')], -} -components = [ - ('MiniSat-core', version, { - 'start_dir': 'core', - }), - ('MiniSat-simp', version, { - 'start_dir': 'simp', - }), -] - -sanity_check_paths = { - 'files': ['bin/minisat-core', 'bin/minisat-simp'], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/m/MiniSat/MiniSat-20130925-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/MiniSat/MiniSat-20130925-GCC-9.3.0.eb deleted file mode 100644 index a4def008b6c..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MiniSat/MiniSat-20130925-GCC-9.3.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MiniSat' -version = '20130925' -local_commit = '37dc6c67e2af26379d88ce349eb9c4c6160e8543' - -homepage = 'http://minisat.se/' -description = """ -MiniSat is a minimalistic, open-source SAT solver, developed to help -researchers and developers alike to get started on SAT.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++03'} - -github_account = 'niklasso' -source_urls = [GITHUB_LOWER_SOURCE] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['3db05b02f91c4b097b7962e523225aa5e6fa9a6c0d42704a170b01b069cdfcfe'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -configure_cmd = "make config" -prefix_opt = 'prefix=' - -# disable indiscriminate static linking to avoid needing static libs of glibc -preconfigopts = "sed -i 's/LDFLAGS += --static/LDFLAGS += /g' Makefile &&" - -# lower strictness of compilation and add CXXFLAGS from EB -local_comp_flags = "-Wno-c++11-compat -fpermissive $CXXFLAGS" - -prebuildopts = 'MINISAT_REL="-D NDEBUG" CXXFLAGS="%s"' % local_comp_flags -buildopts = 'all' - -preinstallopts = 'CXXFLAGS="%s"' % local_comp_flags - -sanity_check_paths = { - 'files': ['bin/minisat', 'lib/libminisat.a', 'lib/libminisat.%s' % SHLIB_EXT], - 'dirs': ['include/minisat'], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8-GCCcore-9.3.0.eb deleted file mode 100644 index 1673b54829c..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8-GCCcore-9.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -easyblock = 'MakeCp' - -name = 'Molden' -version = '6.8' - -homepage = 'https://www3.cmbi.umcn.nl/molden' -description = """Molden is a package for displaying Molecular Density from the - Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical - packages Mopac/Ampac""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden'] -sources = ['%(namelower)s%(version)s.tar.gz'] -patches = [ - 'Molden-6.8_fix_makefile_for_easybuild.patch', - 'Molden-6.8_fix_arg_handling.patch', -] -checksums = [ - '4dfbf6524b60112afb5720cba3c200a07a0f57b5d190e05ec14cceae1edf5782', # molden6.8.tar.gz - '0f516ba436595dad9b3cdfa60fe4d9c85652b2210203bebe9d7962f3a1702e68', # Molden-6.8_fix_makefile_for_easybuild.patch - '1fc29a8a62044d04cdd0495ea6c9ff79af6e77628b941b4822c2a46f8c8c705e', # Molden-6.8_fix_arg_handling.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('makedepend', '1.0.6'), -] - -dependencies = [ - ('X11', '20200222'), - ('libglvnd', '1.2.0'), - ('libGLU', '9.0.1'), -] - -buildopts = 'CC="$CC" FC="$F90" all' - -maxparallel = 1 - -files_to_copy = [(['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']], 'bin'), - 'CopyRight', 'README', 'REGISTER'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']] + ['README', 'REGISTER'], - 'dirs': [], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8_fix_arg_handling.patch b/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8_fix_arg_handling.patch deleted file mode 100644 index 6b49322e750..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8_fix_arg_handling.patch +++ /dev/null @@ -1,25 +0,0 @@ -Use F2003 functions for argument handling. - -Åke Sandgren, 2021-04-29 -diff -ru molden6.8.orig/src/molden.f molden6.8/src/molden.f ---- molden6.8.orig/src/molden.f 2021-01-20 17:54:58.000000000 +0100 -+++ molden6.8/src/molden.f 2021-04-29 08:49:09.667816492 +0200 -@@ -3812,15 +3812,15 @@ - endif - - iredir = 0 -- nargs = iargc() -- call getarg(0,liris) -+ nargs = COMMAND_ARGUMENT_COUNT() -+ call GET_COMMAND_ARGUMENT(0,liris) - call parsfn(liris,linlen(liris),20) - - ntargs = 0 - n = 0 - if (nargs.gt.0) then - 2013 n = n + 1 -- call getarg(n,liris) -+ call GET_COMMAND_ARGUMENT(n,liris) - if (liris(1:1).eq.'-') then - if (liris(1:2).eq.'-5') ido5d = 1 - if (liris(1:2).eq.'-7') ido7f = 1 diff --git a/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8_fix_makefile_for_easybuild.patch b/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8_fix_makefile_for_easybuild.patch deleted file mode 100644 index 12facfb0934..00000000000 --- a/easybuild/easyconfigs/__archive__/m/Molden/Molden-6.8_fix_makefile_for_easybuild.patch +++ /dev/null @@ -1,81 +0,0 @@ -Make makefile EasyBuild friendly. - -Åke Sandgren, 2021-04-29 -diff -ru molden6.8.orig/makefile molden6.8/makefile ---- molden6.8.orig/makefile 2021-04-07 20:48:56.000000000 +0200 -+++ molden6.8/makefile 2021-04-29 08:52:17.139037202 +0200 -@@ -13,10 +13,10 @@ - # Disregard compiler warnings on rdmolf.f - # - # --CC = cc -+#CC = cc - LIBS = -lX11 -lm - LDR = ${FC} --LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm -+LIBSG = -lGLU -lGL -lXmu -lX11 -lm - ARCH := $(shell getconf LONG_BIT) - AFLAG= -m$(ARCH) - EXTEN= -@@ -29,20 +29,6 @@ - uname := $(shell uname -s) - os := - --ifeq ($(uname), Linux) -- os := $(shell head -n 1 /etc/issue | cut -d" " -f1) -- ifeq ($(os), Ubuntu) -- EXTEN = exten -- EXTENZ = exten2 -- LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lX11 -lm -- endif -- ifeq ($(os), Debian) -- LIBSG = -L/usr/lib/X11 -lGLU -lGL -lX11 -lm -- endif -- -- choosefc := 'yes' --endif -- - ifneq (,$(findstring CYGWIN,$(uname))) - uname := Linux - choosefc := 'yes' -@@ -53,16 +39,6 @@ - endif - - --ifneq ($(choosefc), $(empty)) -- comg77 := $(shell which g77 | grep -i g77) -- comgfort := $(shell which gfortran | grep -i gfortran) -- ifneq ($(comg77), $(empty)) -- FC = g77 -- endif -- ifneq ($(comgfort), $(empty)) -- FC = gfortran -- endif --endif - - print-% : ; @echo $* = $($*) - # -@@ -108,17 +84,17 @@ - EXT = ${EXTRAZ} - endif - FFLAGS = -g ${AFLAG} --LIBS = -L/usr/X11R6/lib -lX11 -lm -+LIBS = -lX11 -lm - ifeq ($(AFLAG),"-m64") --LIBS = -L/usr/X11R6/lib64 -lX11 -lm -+LIBS = -lX11 -lm - endif - LDR = ${FC} -g ${AFLAG} --CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -+CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 - ifeq ($(os), Debian) -- CFLAGS = ${AFLAG} ${EXTRAZ} -c -I/usr/include/X11 -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -- LIBS = -L/usr/lib/X11 -lX11 -lm -+ CFLAGS = ${AFLAG} ${EXTRAZ} -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -+ LIBS = -lX11 -lm - ifeq ($(AFLAG),"-m64") -- LIBS = -L/usr/X11R6/lib64 -lX11 -lm -+ LIBS = -lX11 -lm - endif - endif - ifeq ($(os), FreeBSD) diff --git a/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.7a-foss-2020a.eb b/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.7a-foss-2020a.eb deleted file mode 100644 index 8affddc7c40..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.7a-foss-2020a.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MrBayes' -version = '3.2.7a' - -homepage = 'http://mrbayes.csit.fsu.edu' -description = "MrBayes is a program for the Bayesian estimation of phylogeny." - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -github_account = 'NBISweden' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['3eed2e3b1d9e46f265b6067a502a89732b6f430585d258b886e008e846ecc5c6'] - -builddependencies = [ - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('beagle-lib', '3.1.2'), - ('libreadline', '8.0'), -] - -configopts = "--with-mpi=yes" - -sanity_check_paths = { - 'files': ['bin/mb'], - 'dirs': ['share/doc', 'share/examples'], -} - - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MultiQC/MultiQC-1.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/MultiQC/MultiQC-1.9-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 4e53c31a7bd..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MultiQC/MultiQC-1.9-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,67 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Adam Huffman -# The Francis Crick Institute -# Elements derived from work by Pablo Escobar -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. -# See: https://click.palletsprojects.com/en/7.x/python3/ - -easyblock = 'PythonBundle' - -name = 'MultiQC' -version = '1.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://multiqc.info' -description = """Aggregate results from bioinformatics analyses across many samples into a single - report. - - MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general - use tool, perfect for summarising the output from numerous bioinformatics tools.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('PyYAML', '5.3'), - ('networkx', '2.4', versionsuffix), -] - -exts_list = [ - ('simplejson', '3.17.0', { - 'checksums': ['2b4b2b738b3b99819a17feaf118265d0753d5536049ea570b3c43b51c4701e81'], - }), - ('colormath', '3.0.0', { - 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], - }), - ('spectra', '0.0.11', { - 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], - }), - ('Markdown', '3.2.1', { - 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], - }), - ('lzstring', '1.0.4', { - 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], - }), - ('humanfriendly', '8.2', { - 'checksums': ['bf52ec91244819c780341a3438d5d7b09f431d3f113a475147ac9b7b167a3d12'], - }), - ('coloredlogs', '14.0', { - 'checksums': ['a1fab193d2053aa6c0a97608c4342d031f1f93a3d1218432c59322441d31a505'], - }), - ('multiqc', version, { - 'checksums': ['b11e217db5f2f6595b845539ad8e090327b98ac8f354c4470f59d5b2ed8f39ab'], - }), -] - -sanity_check_paths = { - 'files': ['bin/multiqc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["multiqc --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/MultiQC/MultiQC-1.9-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/MultiQC/MultiQC-1.9-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 8c992d977e6..00000000000 --- a/easybuild/easyconfigs/__archive__/m/MultiQC/MultiQC-1.9-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,67 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Adam Huffman -# The Francis Crick Institute -# Elements derived from work by Pablo Escobar -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. -# See: https://click.palletsprojects.com/en/7.x/python3/ - -easyblock = 'PythonBundle' - -name = 'MultiQC' -version = '1.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://multiqc.info' -description = """Aggregate results from bioinformatics analyses across many samples into a single - report. - - MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general - use tool, perfect for summarising the output from numerous bioinformatics tools.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('PyYAML', '5.3'), - ('networkx', '2.4', versionsuffix), -] - -exts_list = [ - ('simplejson', '3.17.0', { - 'checksums': ['2b4b2b738b3b99819a17feaf118265d0753d5536049ea570b3c43b51c4701e81'], - }), - ('colormath', '3.0.0', { - 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], - }), - ('spectra', '0.0.11', { - 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], - }), - ('Markdown', '3.2.1', { - 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], - }), - ('lzstring', '1.0.4', { - 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], - }), - ('humanfriendly', '8.2', { - 'checksums': ['bf52ec91244819c780341a3438d5d7b09f431d3f113a475147ac9b7b167a3d12'], - }), - ('coloredlogs', '14.0', { - 'checksums': ['a1fab193d2053aa6c0a97608c4342d031f1f93a3d1218432c59322441d31a505'], - }), - ('multiqc', version, { - 'checksums': ['b11e217db5f2f6595b845539ad8e090327b98ac8f354c4470f59d5b2ed8f39ab'], - }), -] - -sanity_check_paths = { - 'files': ['bin/multiqc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["multiqc --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/maeparser/maeparser-1.3.0-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/m/maeparser/maeparser-1.3.0-iimpi-2020a.eb deleted file mode 100644 index c00793c0c3c..00000000000 --- a/easybuild/easyconfigs/__archive__/m/maeparser/maeparser-1.3.0-iimpi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'maeparser' -version = '1.3.0' - -homepage = 'https://github.com/schrodinger/maeparser' -description = "maeparser is a parser for Schrodinger Maestro files." - -toolchain = {'name': 'iimpi', 'version': '2020a'} - -source_urls = ['https://github.com/schrodinger/maeparser/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['fa8f9336de1e5d1cabec29a6da04547b1fb040bb32ba511ff30b4a14097c751c'] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [('Boost', '1.72.0')] - -sanity_check_paths = { - 'files': ['lib/libmaeparser.%s' % SHLIB_EXT], - 'dirs': ['include/maeparser', 'lib/cmake'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/magma/magma-2.5.4-fosscuda-2020a.eb b/easybuild/easyconfigs/__archive__/m/magma/magma-2.5.4-fosscuda-2020a.eb deleted file mode 100644 index 4e43eb2d087..00000000000 --- a/easybuild/easyconfigs/__archive__/m/magma/magma-2.5.4-fosscuda-2020a.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = "CMakeMake" - -name = 'magma' -version = '2.5.4' - -homepage = 'https://icl.cs.utk.edu/magma/' -description = """The MAGMA project aims to develop a dense linear algebra library similar to - LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'pic': True, 'openmp': True} - -source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/'] -sources = [SOURCE_TAR_GZ] -patches = ['magma-2.5.4_allow-all-sms.patch'] -checksums = [ - '7734fb417ae0c367b418dea15096aef2e278a423e527c615aab47f0683683b67', # magma-2.5.4.tar.gz - '4e47ecc080ff761866f179c9b383b8930e4daa2fcee1c2a48db585fc50531561', # magma-2.5.4_allow-all-sms.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) -cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0'] -# make sure both static and shared libs are built -configopts = [ - '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') -] - -sanity_check_paths = { - 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], - 'dirs': ['include'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/make/make-4.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/make/make-4.3-GCCcore-9.3.0.eb deleted file mode 100644 index 9df4a391891..00000000000 --- a/easybuild/easyconfigs/__archive__/m/make/make-4.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -## -# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## -easyblock = 'ConfigureMake' - -name = 'make' -version = '4.3' - -homepage = 'https://www.gnu.org/software/make/make.html' -description = "GNU version of make utility" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['e05fdde47c5f7ca45cb697e973894ff4f5d79e13b750ed57d7b66d8defc78e19'] - -builddependencies = [('binutils', '2.34')] - -postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] - -sanity_check_paths = { - 'files': ['bin/gmake', 'bin/make'], - 'dirs': [] -} - -sanity_check_commands = [ - "gmake --help", - "make --help", -] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.6-GCCcore-9.3.0.eb deleted file mode 100644 index ec3dfa9388d..00000000000 --- a/easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.6-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'makedepend' -version = '1.0.6' - -homepage = 'https://linux.die.net/man/1/makedepend' -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [XORG_UTIL_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['845f6708fc850bf53f5b1d0fb4352c4feab3949f140b26f71b22faba354c3365'] - -builddependencies = [ - ('binutils', '2.34'), - ('xproto', '7.0.31'), - ('xorg-macros', '1.19.2'), -] - -sanity_check_paths = { - 'files': ['bin/makedepend'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb deleted file mode 100644 index a2aec147f59..00000000000 --- a/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'makeinfo' -version = '6.7' - -homepage = 'https://www.gnu.org/software/texinfo/' -description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} - -source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] -sources = ['texinfo-%(version)s.tar.xz'] -checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] - -builddependencies = [('binutils', '2.36.1')] - -sanity_check_paths = { - 'files': ['bin/makeinfo'], - 'dirs': ['share'], -} - -sanity_check_commands = ["makeinfo --help"] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0-minimal.eb b/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0-minimal.eb deleted file mode 100644 index d8bc53de55d..00000000000 --- a/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0-minimal.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'makeinfo' -version = '6.7' -versionsuffix = '-minimal' - -homepage = 'https://www.gnu.org/software/texinfo/' -description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project. - -This is a minimal build with very basic functionality. Should only be used for build dependencies. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] -sources = ['texinfo-%(version)s.tar.xz'] -checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] - -builddependencies = [ - ('binutils', '2.34'), -] -dependencies = [ - ('Perl', '5.30.2', '-minimal'), -] - -configopts = '--disable-perl-xs --disable-perl-api-texi-build --disable-pod-simple-texinfo-tests ' - -sanity_check_paths = { - 'files': ['bin/makeinfo'], - 'dirs': ['share'], -} - -sanity_check_commands = ["makeinfo --help"] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb deleted file mode 100644 index 400f61cb376..00000000000 --- a/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'makeinfo' -version = '6.7' - -homepage = 'https://www.gnu.org/software/texinfo/' -description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] -sources = ['texinfo-%(version)s.tar.xz'] -checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] - -builddependencies = [('binutils', '2.34')] -dependencies = [('Perl', '5.30.2')] - -sanity_check_paths = { - 'files': ['bin/makeinfo'], - 'dirs': ['share'], -} - -sanity_check_commands = ["makeinfo --help"] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb deleted file mode 100644 index 7633e9131e0..00000000000 --- a/easybuild/easyconfigs/__archive__/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'manta' -version = '1.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Illumina/manta' -description = """ -Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. -It is optimized for analysis of germline variation in small sets of individuals and -somatic variation in tumor/normal sample pairs. Manta discovers, assembles and -scores large-scale SVs, medium-sized indels and large insertions within a -single efficient workflow. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -github_account = 'Illumina' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['76ce7c4a95a3b92cb16381f9a3b091afa234948ae6f028982abbd49e21206421'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Doxygen', '1.8.17'), -] - -dependencies = [ - ('Python', '2.7.18'), - ('Boost', '1.72.0'), - ('zlib', '1.2.11'), -] - -local_binaries = ['CheckSVLoci', 'DumpSVLoci', 'EstimateSVLoci', 'GenerateSVCandidates', 'GetAlignmentStats', - 'GetChromDepth', 'MergeAlignmentStats', 'MergeSVLoci', 'SummarizeAlignmentStats', 'SummarizeSVLoci', - 'TestAssembler'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['configManta.py', 'runMantaWorkflowDemo.py']] + - ['libexec/%s' % x for x in local_binaries], - 'dirs': ['lib/python', 'share'], -} - -sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] - -modextrapaths = { - 'PATH': 'libexec', - 'PYTHONPATH': 'lib/python', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-foss-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-foss-2020a-Python-2.7.18.eb deleted file mode 100644 index 2cb199a7d20..00000000000 --- a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-foss-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,61 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'matplotlib' -version = '2.2.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '2.7.18'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('Tkinter', '%(pyver)s'), -] - -exts_list = [ - ('Cycler', '0.10.0', { - 'modulename': 'cycler', - 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), - ('subprocess32', '3.5.4', { - 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], - }), - ('backports.functools_lru_cache', '1.6.1', { - 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], - }), - ('kiwisolver', '1.1.0', { - 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], - }), - (name, version, { - 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'checksums': ['a3037a840cd9dfdc2df9fee8af8f76ca82bfab173c0f9468193ca7a89a2b60ea'], - }), -] - -postinstallcmds = [ - 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', -] - -sanity_check_commands = [ - """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, - "python -c 'from mpl_toolkits.mplot3d import Axes3D'", -] - -# use non-interactive plotting backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'Agg'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-fosscuda-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-fosscuda-2020a-Python-2.7.18.eb deleted file mode 100644 index 3c38fb85ba3..00000000000 --- a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-fosscuda-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,61 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'matplotlib' -version = '2.2.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '2.7.18'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('Tkinter', '%(pyver)s'), -] - -exts_list = [ - ('Cycler', '0.10.0', { - 'modulename': 'cycler', - 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), - ('subprocess32', '3.5.4', { - 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], - }), - ('backports.functools_lru_cache', '1.6.1', { - 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], - }), - ('kiwisolver', '1.1.0', { - 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], - }), - (name, version, { - 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'checksums': ['a3037a840cd9dfdc2df9fee8af8f76ca82bfab173c0f9468193ca7a89a2b60ea'], - }), -] - -postinstallcmds = [ - 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', -] - -sanity_check_commands = [ - """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, - "python -c 'from mpl_toolkits.mplot3d import Axes3D'", -] - -# use non-interactive plotting backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'Agg'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-intel-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-intel-2020a-Python-2.7.18.eb deleted file mode 100644 index 1508e3659e3..00000000000 --- a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-2.2.5-intel-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,61 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'matplotlib' -version = '2.2.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '2.7.18'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('Tkinter', '%(pyver)s'), -] - -exts_list = [ - ('Cycler', '0.10.0', { - 'modulename': 'cycler', - 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), - ('subprocess32', '3.5.4', { - 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], - }), - ('backports.functools_lru_cache', '1.6.1', { - 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], - }), - ('kiwisolver', '1.1.0', { - 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], - }), - (name, version, { - 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'checksums': ['a3037a840cd9dfdc2df9fee8af8f76ca82bfab173c0f9468193ca7a89a2b60ea'], - }), -] - -postinstallcmds = [ - 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', -] - -sanity_check_commands = [ - """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, - "python -c 'from mpl_toolkits.mplot3d import Axes3D'", -] - -# use non-interactive plotting backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'Agg'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 5a005f7d497..00000000000 --- a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'matplotlib' -version = '3.2.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('Tkinter', '%(pyver)s'), -] - -exts_list = [ - ('Cycler', '0.10.0', { - 'modulename': 'cycler', - 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), - ('kiwisolver', '1.1.0', { - 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], - }), - (name, version, { - 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'checksums': ['ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee'], - }), -] - -sanity_check_commands = [ - """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, - "python -c 'from mpl_toolkits.mplot3d import Axes3D'", -] - -# use non-interactive plotting backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'Agg'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index b9eefa998a5..00000000000 --- a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'matplotlib' -version = '3.2.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('Tkinter', '%(pyver)s'), -] - -exts_list = [ - ('Cycler', '0.10.0', { - 'modulename': 'cycler', - 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), - ('kiwisolver', '1.1.0', { - 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], - }), - (name, version, { - 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'checksums': ['ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee'], - }), -] - -sanity_check_commands = [ - """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, - "python -c 'from mpl_toolkits.mplot3d import Axes3D'", -] - -# use non-interactive plotting backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'Agg'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 7427fb4c6e3..00000000000 --- a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,53 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'matplotlib' -version = '3.2.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('Tkinter', '%(pyver)s'), -] - -check_ldshared = True - -exts_list = [ - ('Cycler', '0.10.0', { - 'modulename': 'cycler', - 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), - ('kiwisolver', '1.1.0', { - 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], - }), - (name, version, { - 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'checksums': ['ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee'], - }), -] - -sanity_check_commands = [ - """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, - "python -c 'from mpl_toolkits.mplot3d import Axes3D'", -] - -# use non-interactive plotting backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'Agg'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-intelcuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-intelcuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 28d9733036f..00000000000 --- a/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-3.2.1-intelcuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,53 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'matplotlib' -version = '3.2.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'intelcuda', 'version': '2020a'} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('Tkinter', '%(pyver)s'), -] - -check_ldshared = True - -exts_list = [ - ('Cycler', '0.10.0', { - 'modulename': 'cycler', - 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), - ('kiwisolver', '1.1.0', { - 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], - }), - (name, version, { - 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'checksums': ['ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee'], - }), -] - -sanity_check_commands = [ - """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, - "python -c 'from mpl_toolkits.mplot3d import Axes3D'", -] - -# use non-interactive plotting backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'Agg'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/mauveAligner/libGenome-4736_gcc-6.1.patch b/easybuild/easyconfigs/__archive__/m/mauveAligner/libGenome-4736_gcc-6.1.patch deleted file mode 100644 index 4bf1efb6e0c..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mauveAligner/libGenome-4736_gcc-6.1.patch +++ /dev/null @@ -1,17 +0,0 @@ -http://deb.debian.org/debian/pool/main/libg/libgenome/libgenome_1.3.11+svn20110227.4616-3.debian.tar.xz -Author: Andreas Tille -Last-Update: Fri, 12 Aug 2016 10:35:40 +0200 -Bug-Debian: https://bugs.debian.org/831188 -Description: THis declaration makes gcc-6.1 fail so simply drop it - ---- a/libGenome/gnDefs.cpp -+++ b/libGenome/gnDefs.cpp -@@ -4,8 +4,4 @@ - - #include "libGenome/gnDefs.h" - --// some compilers don't have abs() for 64 bit ints --int64 abs( int64 a ){ -- return a < 0 ? -a : a; --} - diff --git a/easybuild/easyconfigs/__archive__/m/mauveAligner/libMems-4736_debian.patch b/easybuild/easyconfigs/__archive__/m/mauveAligner/libMems-4736_debian.patch deleted file mode 100644 index 345ef999ffb..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mauveAligner/libMems-4736_debian.patch +++ /dev/null @@ -1,407 +0,0 @@ -# Selected patches from -# http://deb.debian.org/debian/pool/main/libm/libmems/libmems_1.6.0+4725-8.debian.tar.xz -# SEP 18th 2020 by B. Hajgato (UGent) -Author: Andrei Zavada -Last-Update: Sat, 18 Apr 2015 23:27:38 +0300 -Description: fix ctors of {MatchLeftEnd,LabeledMem}Comparator to enable sort/3 with g++-4.9 - ---- a/libMems/Aligner.cpp -+++ b/libMems/Aligner.cpp -@@ -939,7 +939,7 @@ public: - MatchLeftEndComparator( unsigned seq = 0 ){ - m_seq = seq; - } -- MatchLeftEndComparator( MatchLeftEndComparator& msc ){ -+ MatchLeftEndComparator( const MatchLeftEndComparator& msc ){ - m_seq = msc.m_seq; - } - // TODO?? make this do a wraparound comparison if all is equal? ---- a/libMems/Aligner.h -+++ b/libMems/Aligner.h -@@ -49,7 +49,7 @@ public: - LabeledMemComparator( uint seq ){ - m_seq = seq; - } -- LabeledMemComparator( LabeledMemComparator& lmc ){ -+ LabeledMemComparator( const LabeledMemComparator& lmc ){ - m_seq = lmc.m_seq; - } - boolean operator()(const LabeledMem& a, const LabeledMem& b) const{ -Author: Andrei Zavada -Last-Update: Sat, 18 Apr 2015 23:27:39 +0300 -Description: fix a -Wformat (boy, that's a bloody serious error) - ---- - libMems/dmSML/dmsort.c | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - ---- a/libMems/dmSML/dmsort.c -+++ b/libMems/dmSML/dmsort.c -@@ -825,7 +825,7 @@ int InitdmSML( long working_mb, long buf - if ( fgets(buf, sizeof(buf), fp) ) - { - sscanf(buf, "MemTotal: %ld kB", &memTotal); -- fprintf( stderr, buf ); -+ fprintf( stderr, "%s", buf ); - } - fclose(fp); - // allocate about 6/10 of physical memory -Description: Updates the boost.m4 file to correct problems with gcc-5 - This patch updates the m4/boost.m4 file to the git version d9ff75 - of boost.m4 upstream - . -Author: Gert Wollny - -Origin: other, https://github.com/tsuna/boost.m4 -Bug-Debian: https://bugs.debian.org/795344 -Forwarded: no -Last-Update: 2015-08-17 - ---- libmems-1.6.0+4725.orig/m4/boost.m4 -+++ libmems-1.6.0+4725/m4/boost.m4 -@@ -22,7 +22,7 @@ - # along with this program. If not, see . - - m4_define([_BOOST_SERIAL], [m4_translit([ --# serial 23 -+# serial 24 - ], [# - ], [])]) - -@@ -72,8 +72,25 @@ dnl strip `\n' with backquotes, not the - dnl boost_cv_lib_version='1_37\r' for instance, which breaks - dnl everything else. - dnl Cannot use 'dnl' after [$4] because a trailing dnl may break AC_CACHE_CHECK -+dnl -+dnl Beware that GCC 5, when expanding macros, may embed # line directives -+dnl a within single line: -+dnl -+dnl # 1 "conftest.cc" -+dnl # 1 "" -+dnl # 1 "" -+dnl # 1 "conftest.cc" -+dnl # 1 "/opt/local/include/boost/version.hpp" 1 3 -+dnl # 2 "conftest.cc" 2 -+dnl boost-lib-version = -+dnl # 2 "conftest.cc" 3 -+dnl "1_56" -+dnl -+dnl So get rid of the # lines, and glue the remaining ones together. - (eval "$ac_cpp conftest.$ac_ext") 2>&AS_MESSAGE_LOG_FD | -+ grep -v '#' | - tr -d '\r' | -+ tr -s '\n' ' ' | - $SED -n -e "$1" >conftest.i 2>&1], - [$3], - [$4]) -@@ -208,7 +225,7 @@ AC_LANG_POP([C++])dnl - AC_CACHE_CHECK([for Boost's header version], - [boost_cv_lib_version], - [m4_pattern_allow([^BOOST_LIB_VERSION$])dnl -- _BOOST_SED_CPP([/^boost-lib-version = /{s///;s/\"//g;p;q;}], -+ _BOOST_SED_CPP([[/^boost-lib-version = /{s///;s/[\" ]//g;p;q;}]], - [#include - boost-lib-version = BOOST_LIB_VERSION], - [boost_cv_lib_version=`cat conftest.i`])]) -@@ -216,7 +233,7 @@ boost-lib-version = BOOST_LIB_VERSION], - boost_major_version=`echo "$boost_cv_lib_version" | sed 's/_//;s/_.*//'` - case $boost_major_version in #( - '' | *[[!0-9]]*) -- AC_MSG_ERROR([invalid value: boost_major_version=$boost_major_version]) -+ AC_MSG_ERROR([invalid value: boost_major_version='$boost_major_version']) - ;; - esac - fi -@@ -557,13 +574,40 @@ BOOST_FIND_LIB([chrono], [$1], - [boost/chrono.hpp], - [boost::chrono::thread_clock d;]) - if test $enable_static_boost = yes && test $boost_major_version -ge 135; then -- BOOST_FILESYSTEM_LIBS="$BOOST_FILESYSTEM_LIBS $BOOST_SYSTEM_LIBS" -+ BOOST_CHRONO_LIBS="$BOOST_CHRONO_LIBS $BOOST_SYSTEM_LIBS" - fi - LIBS=$boost_filesystem_save_LIBS - LDFLAGS=$boost_filesystem_save_LDFLAGS - ])# BOOST_CHRONO - - -+# BOOST_CONTEXT([PREFERRED-RT-OPT]) -+# ----------------------------------- -+# Look for Boost.Context. For the documentation of PREFERRED-RT-OPT, see the -+# documentation of BOOST_FIND_LIB above. This library was introduced in Boost -+# 1.51.0 -+BOOST_DEFUN([Context], -+[BOOST_FIND_LIB([context], [$1], -+ [boost/context/all.hpp],[[ -+// creates a stack -+void * stack_pointer = new void*[4096]; -+std::size_t const size = sizeof(void*[4096]); -+ -+// context fc uses f() as context function -+// fcontext_t is placed on top of context stack -+// a pointer to fcontext_t is returned -+fc = ctx::make_fcontext(stack_pointer, size, f); -+return ctx::jump_fcontext(&fcm, fc, 3) == 6;]],[dnl -+namespace ctx = boost::context; -+// context -+static ctx::fcontext_t fcm, *fc; -+// context-function -+static void f(intptr_t i) { -+ ctx::jump_fcontext(fc, &fcm, i * 2); -+}]) -+])# BOOST_CONTEXT -+ -+ - # BOOST_CONVERSION() - # ------------------ - # Look for Boost.Conversion (cast / lexical_cast) -@@ -573,6 +617,44 @@ BOOST_FIND_HEADER([boost/lexical_cast.hp - ])# BOOST_CONVERSION - - -+# BOOST_COROUTINE([PREFERRED-RT-OPT]) -+# ----------------------------------- -+# Look for Boost.Coroutine. For the documentation of PREFERRED-RT-OPT, see the -+# documentation of BOOST_FIND_LIB above. This library was introduced in Boost -+# 1.53.0 -+BOOST_DEFUN([Coroutine], -+[ -+boost_coroutine_save_LIBS=$LIBS -+boost_coroutine_save_LDFLAGS=$LDFLAGS -+# Link-time dependency from coroutine to context -+BOOST_CONTEXT([$1]) -+# Starting from Boost 1.55 a dependency on Boost.System is added -+if test $boost_major_version -ge 155; then -+ BOOST_SYSTEM([$1]) -+fi -+m4_pattern_allow([^BOOST_(CONTEXT|SYSTEM)_(LIBS|LDFLAGS)]) -+LIBS="$LIBS $BOOST_CONTEXT_LIBS $BOOST_SYSTEM_LIBS" -+LDFLAGS="$LDFLAGS $BOOST_CONTEXT_LDFLAGS" -+ -+BOOST_FIND_LIB([coroutine], [$1], -+ [boost/coroutine/coroutine.hpp], -+ [boost::coroutines::coroutine< int(int) > coro; coro.empty();]) -+ -+# Link-time dependency from coroutine to context, existed only in 1.53, in 1.54 -+# coroutine doesn't use context from its headers but from its library. -+if test $boost_major_version -eq 153 || test $enable_static_boost = yes && test $boost_major_version -ge 154; then -+ BOOST_COROUTINE_LIBS="$BOOST_COROUTINE_LIBS $BOOST_CONTEXT_LIBS" -+ BOOST_COROUTINE_LDFLAGS="$BOOST_COROUTINE_LDFLAGS $BOOST_CONTEXT_LDFLAGS" -+fi -+if test $enable_static_boost = yes && test $boost_major_version -ge 155; then -+ BOOST_COROUTINE_LIBS="$BOOST_COROUTINE_LIBS $BOOST_SYSTEM_LIBS" -+ BOOST_COROUTINE_LDFLAGS="$BOOST_COROUTINE_LDFLAGS $BOOST_SYSTEM_LDFLAGS" -+fi -+LIBS=$boost_coroutine_save_LIBS -+LDFLAGS=$boost_coroutine_save_LDFLAGS -+])# BOOST_COROUTINE -+ -+ - # BOOST_CRC() - # ----------- - # Look for Boost.CRC -@@ -699,6 +781,15 @@ BOOST_DEFUN([Lambda], - [BOOST_FIND_HEADER([boost/lambda/lambda.hpp])]) - - -+# BOOST_LOCALE() -+# -------------- -+# Look for Boost.Locale -+BOOST_DEFUN([Locale], -+[BOOST_FIND_LIB([locale], [$1], -+ [boost/locale.hpp], -+ [[boost::locale::generator gen; std::locale::global(gen(""));]]) -+])# BOOST_LOCALE -+ - # BOOST_LOG([PREFERRED-RT-OPT]) - # ----------------------------- - # Look for Boost.Log. For the documentation of PREFERRED-RT-OPT, see the -@@ -794,6 +885,12 @@ BOOST_DEFUN([Preprocessor], - [BOOST_FIND_HEADER([boost/preprocessor/repeat.hpp])]) - - -+# BOOST_RANGE() -+# -------------------- -+# Look for Boost.Range -+BOOST_DEFUN([Range], -+[BOOST_FIND_HEADER([boost/range/adaptors.hpp])]) -+ - # BOOST_UNORDERED() - # ----------------- - # Look for Boost.Unordered -@@ -1199,6 +1296,8 @@ if test x$boost_cv_inc_path != xno; then - # I'm not sure about my test for `il' (be careful: Intel's ICC pre-defines - # the same defines as GCC's). - for i in \ -+ _BOOST_mingw_test(5, 0) \ -+ _BOOST_gcc_test(5, 0) \ - _BOOST_mingw_test(4, 10) \ - _BOOST_gcc_test(4, 10) \ - _BOOST_mingw_test(4, 9) \ -Description: Add some dependencies to the linker command -Author: Andreas Tille -Bug-Debian: https://bugs.debian.org/ -Forwarded: no -Last-Update: 2015-08-17 - ---- libmems-1.6.0+4725.orig/libMems/Makefile.am -+++ libmems-1.6.0+4725/libMems/Makefile.am -@@ -61,7 +61,7 @@ libmems_include_HEADERS = $(LIBMEMS_H) - # build libraries with gcc (no suffix) - lib_LTLIBRARIES = libMems-1.6.la - libMems_1_6_la_SOURCES = $(LIBMEMS_SRC) $(HOMOLOGYHMM_SRC) $(DMSML_SRC) -- -+libMems_1_6_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@ @BOOST_SYSTEM_LIBS@ - libMems_1_6_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION) - - homologyhmm_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)/HomologyHMM -Description: Correct compilation with g++-6 -Author: Gert Wollny -Bug-Debian: https://bugs.debian.org/811870 -Forwarded: yes -Bug: https://sourceforge.net/p/mauve/bugs/46/ -Last-Update: 2016-06-30 - ---- a/libMems/ProgressiveAligner.cpp -+++ b/libMems/ProgressiveAligner.cpp -@@ -1599,7 +1599,7 @@ - c.SetLeftEnd(child_1, ancestral_matches[mI]->LeftEnd(1)); - c.SetOrientation(child_1, ancestral_matches[mI]->Orientation(1)); - c.SetLength(ancestral_matches[mI]->Length(1), child_1); -- cga_list.push_back(make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI])); -+ cga_list.push_back(boost::tuples::make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI])); - } - - stack node_stack; -Author: Andreas Tille -Last-Updated: Tue, 08 Nov 2016 14:16:07 +0100 -Description: This patch *really* enables droping the version - from package names but it is not activated here since this might - be considered a "transition" and we are in transition freeze. - ---- a/libMems/Makefile.am -+++ b/libMems/Makefile.am -@@ -55,19 +55,19 @@ dmSML/util.c dmSML/sorting.c dmSML/dmsor - dmSML/timing.c dmSML/sml.c - - --libmems_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME) -+libmems_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME) - libmems_include_HEADERS = $(LIBMEMS_H) - - # build libraries with gcc (no suffix) --lib_LTLIBRARIES = libMems-1.6.la --libMems_1_6_la_SOURCES = $(LIBMEMS_SRC) $(HOMOLOGYHMM_SRC) $(DMSML_SRC) --libMems_1_6_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@ @BOOST_SYSTEM_LIBS@ --libMems_1_6_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION) -+lib_LTLIBRARIES = libMems.la -+libMems_la_SOURCES = $(LIBMEMS_SRC) $(HOMOLOGYHMM_SRC) $(DMSML_SRC) -+libMems_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@ @BOOST_SYSTEM_LIBS@ -+libMems_la_LDFLAGS= -version-info @GENERIC_LIBRARY_VERSION@ - --homologyhmm_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)/HomologyHMM -+homologyhmm_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)/HomologyHMM - homologyhmm_include_HEADERS = $(HOMOLOGYHMM_H) - --dmsml_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)/dmSML -+dmsml_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)/dmSML - dmsml_include_HEADERS = $(DMSML_H) - - EXTRA_DIST = \ -Description: Fix FTBFS with Boost 1.62 - Add missing include so that BOOST_WORKAROUND is defined. -Author: Graham Inggs -Last-Update: 2016-11-08 -Bug-Debian: https://bugs.debian.org/843628 - ---- a/libMems/AbstractMatch.h -+++ b/libMems/AbstractMatch.h -@@ -16,6 +16,7 @@ - #include "libGenome/gnClone.h" - #include - #include -+#include - #include - #include - #include ---- a/libMems/dmSML/Makefile.am -+++ b/libMems/dmSML/Makefile.am -@@ -12,7 +12,7 @@ alibc.c awin32aio.c buffer.c \ - util.c sorting.c dmsort.c \ - timing.c sml.c - --library_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)/dmSML -+library_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)/dmSML - - library_include_HEADERS = $(DMSML_H) - -Author: Andreas Tille -Last-Updated: Sun, 19 Apr 2015 20:20:17 +0200 -Description: Fix lintian error - E: libmems-1.6-dev: pkg-config-bad-directive usr/lib/x86_64-linux-gnu/pkgconfig/libMems-1.6.pc -Wno-deprecated - by not appending "-Wno-deprecated" - ---- a/configure.ac -+++ b/configure.ac -@@ -73,7 +73,7 @@ dnl Check what compiler we're using - AM_CONDITIONAL(ICC, test x$CXX = xicc ) - EXTRA_CXX_FLAGS="" - if( test x$CC == "xgcc" ) then -- EXTRA_CXX_FLAGS="-Wno-deprecated" -+ EXTRA_CXX_FLAGS="" - fi - AC_SUBST(EXTRA_CXX_FLAGS) - -Author: Andreas Tille -Last-Update: Wed, 18 Jul 2018 15:15:58 +0200 -Description: Drop version number from library file name - ---- a/Makefile.am -+++ b/Makefile.am -@@ -8,7 +8,7 @@ projects/libMems.sln \ - projects/libMems.vcproj - - pkgconfigdir = $(libdir)/pkgconfig --pkgconfig_DATA = libMems-@GENERIC_API_VERSION@.pc -+pkgconfig_DATA = libMems.pc - - SUBDIRS = libMems - ---- /dev/null -+++ b/libMems.pc.in -@@ -0,0 +1,12 @@ -+prefix=@prefix@ -+exec_prefix=@exec_prefix@ -+libdir=@libdir@ -+includedir=@includedir@ -+ -+Name: libMems -+Description: c++ library supporting DNA sequence and genome alignment -+Version: @VERSION@ -+Requires: libGenome-1.3 libMUSCLE-3.7 -+Libs: -L${libdir} @OPENMP_CXXFLAGS@ -lMems @BOOST_SYSTEM_LDFLAGS@ @BOOST_SYSTEM_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_PROGRAM_OPTIONS_LIBS@ @BOOST_IOSTREAMS_LIBS@ @LIBS@ -+Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@ @BOOST_CPPFLAGS@ @OPENMP_CXXFLAGS@ @EXTRA_CXX_FLAGS@ -+ ---- a/libMems-1.6.pc.in -+++ /dev/null -@@ -1,12 +0,0 @@ --prefix=@prefix@ --exec_prefix=@exec_prefix@ --libdir=@libdir@ --includedir=@includedir@ -- --Name: libMems --Description: c++ library supporting DNA sequence and genome alignment --Version: @VERSION@ --Requires: libGenome-1.3 libMUSCLE-3.7 --Libs: -L${libdir} @OPENMP_CXXFLAGS@ -lMems-@GENERIC_API_VERSION@ @BOOST_SYSTEM_LDFLAGS@ @BOOST_SYSTEM_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_PROGRAM_OPTIONS_LIBS@ @BOOST_IOSTREAMS_LIBS@ @LIBS@ --Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@-@GENERIC_API_VERSION@ @BOOST_CPPFLAGS@ @OPENMP_CXXFLAGS@ @EXTRA_CXX_FLAGS@ -- ---- a/configure.ac -+++ b/configure.ac -@@ -133,5 +133,5 @@ AC_PROG_GCC_TRADITIONAL - dnl SAVE_LIBRARY_VERSION - AC_SUBST(LIBTOOL_VERSION_INFO) - --AC_OUTPUT(Makefile libMems/Makefile libMems-1.6.pc ) -+AC_OUTPUT(Makefile libMems/Makefile libMems.pc ) - #doc/html/Makefile doc/man/Makefile doc/man/man3/Makefile) diff --git a/easybuild/easyconfigs/__archive__/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb deleted file mode 100644 index a429edbf8d4..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb +++ /dev/null @@ -1,122 +0,0 @@ -easyblock = 'Bundle' - -name = 'mauveAligner' -version = '4736' - -homepage = 'https://darlinglab.org/mauve/mauve.html' -description = """ -Mauve is a system for constructing multiple genome alignments in the presence -of large-scale evolutionary events such as rearrangement and inversion. -Multiple genome alignments provide a basis for research into comparative -genomics and the study of genome-wide evolutionary dynamics. -This version was built without Graphical User Interface. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -# you can download the sources in the following way: -# --- START SCRIPT --- -# ver=4736 -# for i in libGenome libMems mauveAligner muscle sgEvolver -# do -# svn co -r $ver https://svn.code.sf.net/p/mauve/code/$i/trunk $i -# tar jcf ${i}-${ver}.tar.bz2 $i -# done -# --- END SCRIPT --- -# We cannot provide checksums, because there is no way to use the original svn directory timestamp - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), - ('Perl', '5.30.2'), - ('Boost', '1.72.0'), -] - -default_easyblock = 'ConfigureMake' - -default_component_specs = { - 'sources': [SOURCE_TAR_BZ2], - 'start_dir': '%(name)s', -} - -components = [ - ('libGenome', version, { - 'patches': ['libGenome-4736_gcc-6.1.patch'], - 'checksums': [ - None, # libGenome-4736.tar.bz2 - 'e628dcd7264b15805194f1df5d0c47f571477c0ea09183750e07984f4ce35cf8', # libGenome-4736_gcc-6.1.patch - ], - }), - ('muscle', version, { - 'patches': ['muscle-4736_makefile_deps.patch'], - 'checksums': [ - None, # muscle-4736.tar.bz2 - '5937e43d5f1d7ce5ed4f4904673a62f072db8211897ca2d58cdef6f9261c6146', # muscle-4736_makefile_deps.patch - ], - }), - ('libMems', version, { - 'patches': ['libMems-4736_debian.patch'], - 'checksums': [ - None, # libMems-4736.tar.bz2 - '92865fb29560985226a51cc4f61a30083580ca456d35b74d2e67d595c6242ad1', # libMems-4736_debian.patch - ], - }), - ('mauveAligner', version, { - 'patches': [ - 'mauveAligner-4736_debian.patch', - 'mauveAligner-4736_fix-getopt.patch', - ], - 'checksums': [ - None, # mauveAligner-4736.tar.bz2 - '2786bd29bedb224f232e7909972b549fe95f520ddac2cbb076e2082647dc68ae', # mauveAligner-4736_debian.patch - 'e40edc401303b337070470e52ec13968d0aafca43e4adb332e33b8a6aef34f19', # mauveAligner-4736_fix-getopt.patch - ], - }), - ('sgEvolver', version, { - 'patches': [ - 'sgEvolver-4736_dropversion.patch', - 'sgEvolver-4736_fix-getopt.patch', - ], - 'checksums': [ - None, # sgEvolver-4736.tar.bz2 - 'efc3397039dd525669f6c525b20d75ad64c51cd25912192e695067de4cfbeadc', # sgEvolver-4736_dropversion.patch - '58afcf31f707b265fda81d45cd243c8cd279eed5a843a42f8030ef930f3bdd6c', # sgEvolver-4736_fix-getopt.patch - ], - }), -] - -preconfigopts = './autogen.sh && env PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig ' - -postinstallcmds = [ - 'mkdir -p %(installdir)s/lib/perl5/site_perl', - 'cp %(builddir)s/sgEvolver/src/simujobparams.pm %(installdir)s/lib/perl5/site_perl/.', -] - -local_bin = ['addUnalignedIntervals', 'alignmentProjector', 'backbone_global_to_local', 'bbAnalyze', 'bbFilter', - 'coordinateTranslate', 'createBackboneMFA', 'extractBCITrees', 'getAlignmentWindows', 'getOrthologList', - 'maf2xmfa', 'makeBadgerMatrix', 'mauveAligner', 'mauveStatic', 'mauveToXMFA', 'mfa2xmfa', - 'mfaToMultiFiles', 'muscle', 'progressiveMauve', 'progressiveMauveStatic', 'projectAndStrip', - 'randomGeneSample', 'repeatoire', 'scoreAlignment', 'scoreAlignment2', 'scoregen.pl', 'sgEvolver', - 'simujobgen.pl', 'simujobrun.pl', 'stripGapColumns', 'stripSubsetLCBs', 'toGrimmFormat', 'toMultiFastA', - 'toRawSequence', 'uniqueMerCount', 'uniquifyTrees', 'xmfa2maf'] - -local_lib = ['Genome-1.3', 'Mems', 'MUSCLE-3.7'] - -sanity_check_paths = { - 'files': ['lib/lib%s.%s' % (x, y) for x in local_lib for y in ['a', 'la', SHLIB_EXT]] + - ['bin/%s' % x for x in local_bin] + - ['lib/perl5/site_perl/simujobparams.pm'], - 'dirs': ['include/lib%s' % x for x in local_lib] + - ['share', 'lib/pkgconfig'], -} - -sanity_check_commands = ["mauveAligner --help 2>&1 | grep '^mauveAligner'"] - -modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/mauveAligner/mauveAligner-4736_debian.patch b/easybuild/easyconfigs/__archive__/m/mauveAligner/mauveAligner-4736_debian.patch deleted file mode 100644 index 09b6fac7ae9..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mauveAligner/mauveAligner-4736_debian.patch +++ /dev/null @@ -1,35 +0,0 @@ -http://deb.debian.org/debian/pool/main/p/progressivemauve/progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz -Author: Giovanni Mascellani -Bug-Debian: https://bugs.debian.org/914049 -Subject: Fix FTBFS with boost1.67 - -Make an explicit call to the constructor for NeighborhoodGroup (which is -an alias for a specialization of boost::tuple), which is not marked -as "explicit". - ---- a/src/repeatoire.cpp -+++ b/src/repeatoire.cpp -@@ -1591,7 +1591,7 @@ void processNovelSubsetMatches( GappedMa - getSubsets(M_j,-direction*ni_parity*nj_parity).push_back(nj_link); - //getExtraSubsets(M_j,-direction*ni_parity*nj_parity).push_back(nj_link); - // push M_n onto the heap -- novel_subset_list.push_back(M_n); -+ novel_subset_list.push_back(NeighborhoodGroup{M_n}); - //procrastination_queue.push(M_n); - novel_subset_count++; - } -Description: Enable building against unversioned libs -Author: Andreas Tille -Last-Updates: Fri, 27 Jul 2018 06:32:17 +0200 - ---- a/configure.ac -+++ b/configure.ac -@@ -43,7 +43,7 @@ AC_DEFINE(GETOPT_UNDEFINED,[],"Define th - ()") - ) - --PKG_CHECK_MODULES(DEPS, libMems-1.6 >= 1.0.0) -+PKG_CHECK_MODULES(DEPS, libMems >= 1.0.0) - AC_SUBST(DEPS_CFLAGS) - AC_SUBST(DEPS_LIBS) - diff --git a/easybuild/easyconfigs/__archive__/m/mauveAligner/mauveAligner-4736_fix-getopt.patch b/easybuild/easyconfigs/__archive__/m/mauveAligner/mauveAligner-4736_fix-getopt.patch deleted file mode 100644 index 9290d1c1dd8..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mauveAligner/mauveAligner-4736_fix-getopt.patch +++ /dev/null @@ -1,15 +0,0 @@ -fix build of mauveAligner on RHEL8 (without breaking build on CentOS 7) -/usr/include/bits/getopt_core.h:91:12: error: declaration of int getopt(int, char* const*, const char*) throw () has a different exception specifier -author: Kenneth Hoste (HPC-UGent) ---- mauveAligner/src/getopt.h.orig 2022-02-25 10:23:21.301489496 +0100 -+++ mauveAligner/src/getopt.h 2022-02-25 10:26:13.940751386 +0100 -@@ -146,7 +146,8 @@ - /* Many other libraries have conflicting prototypes for getopt, with - differences in the consts, in stdlib.h. To avoid compilation - errors, only prototype getopt for the GNU C library. */ --extern int getopt (int ___argc, char *const *___argv, const char *__shortopts); -+extern int getopt (int ___argc, char *const *___argv, const char *__shortopts) -+ __THROW __nonnull ((2, 3)); - # elif GETOPT_UNDEFINED /* not __GNU_LIBRARY__ */ - extern int getopt (); - # endif /* __GNU_LIBRARY__ */ diff --git a/easybuild/easyconfigs/__archive__/m/mauveAligner/muscle-4736_makefile_deps.patch b/easybuild/easyconfigs/__archive__/m/mauveAligner/muscle-4736_makefile_deps.patch deleted file mode 100755 index 4d1d54b14c6..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mauveAligner/muscle-4736_makefile_deps.patch +++ /dev/null @@ -1,16 +0,0 @@ -# based on: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=905384 -# based on: Description: Correct the libMUSCLE.la dependency -# based on: This allows automake to generate proper dependencies. -# based on: Author: Adrian Bunk -# SEP 17th 2020 by B. Hajgato (UGent) - ---- libmuscle-3.7+4565.orig/libMUSCLE/Makefile.am -+++ libmuscle-3.7+4565/libMUSCLE/Makefile.am -@@ -36,6 +36,6 @@ bin_PROGRAMS = muscle - - - muscle_SOURCES = main.cpp --muscle_LDADD = $(top_builddir)/libMUSCLE/libMUSCLE-3.7.la -+muscle_LDADD = libMUSCLE-3.7.la - - diff --git a/easybuild/easyconfigs/__archive__/m/mauveAligner/sgEvolver-4736_dropversion.patch b/easybuild/easyconfigs/__archive__/m/mauveAligner/sgEvolver-4736_dropversion.patch deleted file mode 100644 index 07bb4d8bc7b..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mauveAligner/sgEvolver-4736_dropversion.patch +++ /dev/null @@ -1,13 +0,0 @@ -# drop version of libMems -# SEP 18th 2020 by B. Hajgato(UGent) ---- configure.ac.orig 2020-09-18 14:53:03.370907242 +0200 -+++ configure.ac 2020-09-18 14:53:16.571362128 +0200 -@@ -39,7 +39,7 @@ - ()") - ) - --PKG_CHECK_MODULES(DEPS, libMems-1.6 >= 1.0.0) -+PKG_CHECK_MODULES(DEPS, libMems >= 1.0.0) - AC_SUBST(DEPS_CFLAGS) - AC_SUBST(DEPS_LIBS) - diff --git a/easybuild/easyconfigs/__archive__/m/mauveAligner/sgEvolver-4736_fix-getopt.patch b/easybuild/easyconfigs/__archive__/m/mauveAligner/sgEvolver-4736_fix-getopt.patch deleted file mode 100644 index 50aee5f8f92..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mauveAligner/sgEvolver-4736_fix-getopt.patch +++ /dev/null @@ -1,15 +0,0 @@ -fix build of sgEvolver on RHEL8 (without breaking build on CentOS 7) -/usr/include/bits/getopt_core.h:91:12: error: declaration of int getopt(int, char* const*, const char*) throw () has a different exception specifier -author: Kenneth Hoste (HPC-UGent) ---- sgEvolver/src/getopt.h.orig 2022-02-25 10:33:10.015721000 +0100 -+++ sgEvolver/src/getopt.h 2022-02-25 10:33:33.950344000 +0100 -@@ -146,7 +146,8 @@ - /* Many other libraries have conflicting prototypes for getopt, with - differences in the consts, in stdlib.h. To avoid compilation - errors, only prototype getopt for the GNU C library. */ --extern int getopt (int ___argc, char *const *___argv, const char *__shortopts); -+extern int getopt (int ___argc, char *const *___argv, const char *__shortopts) -+ __THROW __nonnull ((2, 3)); - # elif GETOPT_UNDEFINED /* not __GNU_LIBRARY__ */ - extern int getopt (); - # endif /* __GNU_LIBRARY__ */ diff --git a/easybuild/easyconfigs/__archive__/m/mbuffer/mbuffer-20191016-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/mbuffer/mbuffer-20191016-GCCcore-9.3.0.eb deleted file mode 100644 index cc0435d165f..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mbuffer/mbuffer-20191016-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'mbuffer' -version = "20191016" - -homepage = 'https://www.maier-komor.de/mbuffer.html' - -description = """ - mbuffer is a tool for buffering data streams with a large set of unique features. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.maier-komor.de/software/mbuffer'] -sources = ['%(name)s-%(version)s.tgz'] -checksums = ['8dc210454765c18901074bc16e126c655135a486e73d69855caf74a157ddbe17'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/mbuffer'], - 'dirs': [], -} - -sanity_check_commands = [('mbuffer', '--version')] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/meshalyzer/meshalyzer-2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/meshalyzer/meshalyzer-2.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index c3d187109ff..00000000000 --- a/easybuild/easyconfigs/__archive__/m/meshalyzer/meshalyzer-2.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'MakeCp' - -name = 'meshalyzer' -version = '2.0' -versionsuffix = '-Python-3.8.2' - -homepage = 'https://git.opencarp.org/openCARP/meshalyzer' -description = "Graphical program for display time dependent data on 3D finite elment meshes" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://git.opencarp.org/openCARP/%(name)s/-/archive/v%(version)s'] -sources = ['%(name)s-v%(version)s.tar.gz'] -patches = ['meshalyzer-2.0_fix-VTK-linking.patch'] -checksums = [ - '9c79ecb1f051da29ff2e2f35ff14ff36a92ca931ca64147d1cd6286edde2309f', # meshalyzer-v2.0.tar.gz - '23f55c2290ea9b62440bdf8e0c1006116438beb7c4b7065b8cf136387a537e0f', # meshalyzer-2.0_fix-VTK-linking.patch -] - -local_vtk_majmin_ver = '8.2' -dependencies = [ - ('libpng', '1.6.37'), - ('FLTK', '1.3.5'), - ('glew', '2.1.0'), - ('freeglut', '3.2.1'), - ('HDF5', '1.10.6'), - ('VTK', '%s.0' % local_vtk_majmin_ver, versionsuffix), -] - -buildopts = 'HDF5_ROOT=$EBROOTHDF5 LIB_EXT=".so" ' -buildopts += 'VTK_INCDIR=$EBROOTVTK/include/vtk-%s/ VTK_LIBDIR=$EBROOTVTK/lib' % local_vtk_majmin_ver - -files_to_copy = [(['meshalyzer'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/meshalyzer'], - 'dirs': [], -} - -sanity_check_commands = ["meshalyzer --help"] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index bb93c14359e..00000000000 --- a/easybuild/easyconfigs/__archive__/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'MakeCp' - -name = 'meshalyzer' -local_commit = 'b1ab66863a293768cd23b444f16efe00d0acef4e' -version = '20200308' # datestamp of commit -versionsuffix = '-Python-3.8.2' - -homepage = 'https://git.opencarp.org/openCARP/meshalyzer' -description = "Graphical program for display time dependent data on 3D finite element meshes" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://git.opencarp.org/openCARP/meshalyzer/-/archive/%s' % local_commit] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = ['meshalyzer-2.0_fix-VTK-linking.patch'] -checksums = [ - 'b1df0be12d377a4e12e0d1f2cd17820b9d5cc3a5a813a17d187ee72adf5a8500', # meshalyzer-20200308.tar.gz - '23f55c2290ea9b62440bdf8e0c1006116438beb7c4b7065b8cf136387a537e0f', # meshalyzer-2.0_fix-VTK-linking.patch -] - -local_vtk_majmin_ver = '8.2' -dependencies = [ - ('libpng', '1.6.37'), - ('FLTK', '1.3.5'), - ('glew', '2.1.0'), - ('freeglut', '3.2.1'), - ('HDF5', '1.10.6'), - ('VTK', '%s.0' % local_vtk_majmin_ver, versionsuffix), -] - -buildopts = 'HDF5_ROOT=$EBROOTHDF5 LIB_EXT=".%s" ' % SHLIB_EXT -buildopts += 'VTK_INCDIR=$EBROOTVTK/include/vtk-%s/ VTK_LIBDIR=$EBROOTVTK/lib' % local_vtk_majmin_ver - -files_to_copy = [(['meshalyzer'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/meshalyzer'], - 'dirs': [], -} - -sanity_check_commands = ["meshalyzer --help"] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/meshtool/meshtool-16-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/meshtool/meshtool-16-GCC-9.3.0.eb deleted file mode 100644 index 902b818d665..00000000000 --- a/easybuild/easyconfigs/__archive__/m/meshtool/meshtool-16-GCC-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'MakeCp' - -name = 'meshtool' -version = '16' - -homepage = 'https://bitbucket.org/aneic/meshtool' -description = """Meshtool is a command-line tool written in C++. It is designed to apply various manipulations to -volumetric meshes.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://bitbucket.org/aneic/meshtool/get/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['822e715b363603dfe320b4b530ad4a77cc5ecd0ccb692d77e01b6ecfe7da9d38'] - -prebuildopts = 'sed -i "s/-march=native/$CXXFLAGS/g" switches.def && ' - -files_to_copy = [(['meshtool'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/meshtool'], - 'dirs': [], -} - -sanity_check_commands = ["meshtool help"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/minibar/minibar-20200326-iccifort-2020.1.217-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/minibar/minibar-20200326-iccifort-2020.1.217-Python-3.8.2.eb deleted file mode 100644 index 38056c2aa75..00000000000 --- a/easybuild/easyconfigs/__archive__/m/minibar/minibar-20200326-iccifort-2020.1.217-Python-3.8.2.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'Tarball' - -name = 'minibar' -local_commit_id = '938ae51' -version = '20200326' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/calacademy-research/minibar' -description = " Dual barcode and primer demultiplexing for MinION sequenced reads" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://github.com/calacademy-research/%(name)s/archive'] -sources = [{'download_filename': '%s.tar.gz' % local_commit_id, 'filename': SOURCE_TAR_GZ}] -checksums = ['f6bc7b310f05fc67990e5b1944473ca46a5c303f2944f7e678eac6525472e649'] - -dependencies = [ - ('Python', '3.8.2'), - ('edlib', '1.3.8.post2', versionsuffix), -] - -postinstallcmds = ["chmod a+x %(installdir)s/minibar.py"] - -sanity_check_paths = { - 'files': ['minibar.py'], - 'dirs': [], -} - -sanity_check_commands = ["minibar.py -h"] - -modextrapaths = {'PATH': ''} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb deleted file mode 100644 index acf1c417a9b..00000000000 --- a/easybuild/easyconfigs/__archive__/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Adam Huffman -# Big Data Institute, University of Oxford - -easyblock = 'MakeCp' - -name = 'minimap2' -version = '2.17' - -homepage = 'https://github.com/lh3/minimap2' -description = """Minimap2 is a fast sequence mapping and alignment -program that can find overlaps between long noisy reads, or map long -reads or their assemblies to a reference genome optionally with detailed -alignment (i.e. CIGAR). At present, it works efficiently with query -sequences from a few kilobases to ~100 megabases in length at an error -rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited -test data sets, minimap2 is over 20 times faster than most other -long-read aligners. It will replace BWA-MEM for long reads and contig -alignment.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] -sources = ['%(name)s-%(version)s.tar.bz2'] -checksums = ['b68ac8882d33cc63e9e3246775062aeb159b6990ff7f38099172c3fe6f8a2742'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('zlib', '1.2.11')] - -buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' - -files_to_copy = [ - (['%(name)s'], 'bin'), - (['lib%(name)s.a'], 'lib'), - (['*.h'], 'include'), - 'LICENSE.txt', 'NEWS.md', 'README.md', - (['%(name)s.1'], 'share/man/man1') -] - -sanity_check_paths = { - 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], - 'dirs': ['include'] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/misha/misha-4.0.10-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/m/misha/misha-4.0.10-foss-2020a-R-4.0.0.eb deleted file mode 100644 index d5e5b5693ec..00000000000 --- a/easybuild/easyconfigs/__archive__/m/misha/misha-4.0.10-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'RPackage' - -name = 'misha' -version = '4.0.10' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://github.com/tanaylab/misha' -description = """The misha package is intended to help users to efficiently analyze genomic data achieved - from various experiments.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/tanaylab/misha/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['a8780b8c1e0153a9a01e7793157c0abc7c31ec53ac074d61b688e2ada0da3ba2'] - -dependencies = [('R', '4.0.0')] - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 9785a631b44..00000000000 --- a/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'molmod' -version = '1.4.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://molmod.github.io/molmod/' -description = "MolMod is a Python library with many components that are useful to write molecular modeling programs." - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -patches = ['molmod-1.4.5_deprecated_time_method.patch'] -checksums = [ - '69c625fe081ea498371642d6237a8958cfc89608908fa8daa475f5d9dc5dc47c', # molmod-1.4.5.tar.gz - '7de0dae2accd908ff7b40f5f848ffabdb9267dadbfb8cc4d2d98444995282e2d', # molmod-1.4.5_deprecated_time_method.patch -] - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), -] - -runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" -runtest += "python setup.py build_ext -i; nosetests -v" - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index bf5849e0892..00000000000 --- a/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'molmod' -version = '1.4.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://molmod.github.io/molmod/' -description = "MolMod is a Python library with many components that are useful to write molecular modeling programs." - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -patches = ['molmod-1.4.5_deprecated_time_method.patch'] -checksums = [ - '69c625fe081ea498371642d6237a8958cfc89608908fa8daa475f5d9dc5dc47c', # molmod-1.4.5.tar.gz - '7de0dae2accd908ff7b40f5f848ffabdb9267dadbfb8cc4d2d98444995282e2d', # molmod-1.4.5_deprecated_time_method.patch -] - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), -] - -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - -runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" -runtest += "python setup.py build_ext -i; nosetests -v" - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.5_deprecated_time_method.patch b/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.5_deprecated_time_method.patch deleted file mode 100644 index 33594754c11..00000000000 --- a/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.4.5_deprecated_time_method.patch +++ /dev/null @@ -1,42 +0,0 @@ -Molmod is not compatible with Python 3.8 due to its deprecated -use of time.clock() (which is no longer supported as of 3.8) - -Alan O'Cais, 20200324 -diff -Nru molmod-1.4.5.orig/molmod/log.py molmod-1.4.5/molmod/log.py ---- molmod-1.4.5.orig/molmod/log.py 2019-09-11 20:34:14.000000000 +0200 -+++ molmod-1.4.5/molmod/log.py 2020-03-20 10:05:41.874916780 +0100 -@@ -388,11 +388,11 @@ - - def start(self): - assert self._start is None -- self._start = time.clock() -+ self._start = time.process_time() - - def stop(self): - assert self._start is not None -- self.cpu += time.clock() - self._start -+ self.cpu += time.process_time() - self._start - self._start = None - - -diff -Nru molmod-1.4.5.orig/molmod/minimizer.py molmod-1.4.5/molmod/minimizer.py ---- molmod-1.4.5.orig/molmod/minimizer.py 2019-09-11 20:34:14.000000000 +0200 -+++ molmod-1.4.5/molmod/minimizer.py 2020-03-20 10:06:39.712207523 +0100 -@@ -1414,7 +1414,7 @@ - except ConstraintError: - self._screen("CONSTRAINT PROJECT FAILED", newline=True) - return False -- self.last_end = time.clock() -+ self.last_end = time.process_time() - - def propagate(self): - # compute the new direction -@@ -1474,7 +1474,7 @@ - else: - converged = False - # timing -- end = time.clock() -+ end = time.process_time() - self._screen("%5.2f" % (end - self.last_end), newline=True) - self.last_end = end - # check convergence, part 2 diff --git a/easybuild/easyconfigs/__archive__/m/mongolite/mongolite-2.3.0-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/m/mongolite/mongolite-2.3.0-foss-2020a-R-4.0.0.eb deleted file mode 100644 index c4bc5ce6c21..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mongolite/mongolite-2.3.0-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'RPackage' - -name = 'mongolite' -version = '2.3.0' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/web/packages/%(name)s' -description = """High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. - Includes support for aggregation, indexing, map-reduce, streaming, encryption, - enterprise authentication, and GridFS. The online user manual provides an overview - of the available methods in the package: .""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/jeroen/mongolite/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['ea691b3f74571152212f3ab96e1f0413240534d1ca4659f12b653bffac97bf66'] - -dependencies = [('R', '4.0.0')] - -osdependencies = [ - OS_PKG_OPENSSL_DEV, - ('cyrus-sasl-devel', 'libsasl2-dev'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['mongolite'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/moonjit/moonjit-2.2.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/moonjit/moonjit-2.2.0-GCCcore-9.3.0.eb deleted file mode 100644 index 131ffa74942..00000000000 --- a/easybuild/easyconfigs/__archive__/m/moonjit/moonjit-2.2.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = "moonjit" -version = "2.2.0" - -homepage = "https://github.com/moonjit/moonjit" -description = """Moonjit is a Just-In-Time Compiler (JIT) for the Lua -programming language. Lua is a powerful, dynamic and light-weight programming -language. It may be embedded or used as a general-purpose, stand-alone -language.""" - - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['83deb2c880488dfe7dd8ebf09e3b1e7613ef4b8420de53de6f712f01aabca2b6'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('ncurses', '6.2'), - ('libreadline', '8.0'), -] - -skipsteps = ['configure'] -installopts = 'PREFIX=%(installdir)s' - -sanity_check_paths = { - 'files': ['bin/luajit', 'lib/libluajit-5.1.a', 'lib/libluajit-5.1.%s.%s' % (SHLIB_EXT, version)], - 'dirs': ['include'], -} - -moduleclass = "lang" diff --git a/easybuild/easyconfigs/__archive__/m/motif/motif-2.3.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/motif/motif-2.3.8-GCCcore-9.3.0.eb deleted file mode 100644 index 3a575b0a0c8..00000000000 --- a/easybuild/easyconfigs/__archive__/m/motif/motif-2.3.8-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'motif' -version = '2.3.8' - -homepage = 'https://motif.ics.com/' -description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building - applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. - It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] - -builddependencies = [ - ('Autotools', '20180311'), - ('flex', '2.6.4'), - ('Bison', '3.5.3'), - ('binutils', '2.34'), - ('util-linux', '2.35'), -] - -dependencies = [ - ('X11', '20200222'), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('libjpeg-turbo', '2.0.4'), - ('bzip2', '1.0.8'), -] - -# makefile is not parallel safe -maxparallel = 1 - -sanity_check_paths = { - 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], - 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10-gompi-2020a.eb deleted file mode 100644 index b6f12100979..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10-gompi-2020a.eb +++ /dev/null @@ -1,38 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'CMakeMake' - -name = 'mpifileutils' -version = '0.10' - -homepage = 'https://hpc.github.io/mpifileutils/' - -description = """ - MPI-Based File Utilities For Distributed Systems -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://github.com/hpc/%(name)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['5a71a9acd9841c3c258fc0eaea942f18abcb40098714cc90462b57696c07e3c5'] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('attr', '2.4.48'), - ('bzip2', '1.0.8'), - ('dtcmp', '1.1.0'), - ('libarchive', '3.4.2'), - ('libcircle', '0.3'), - ('lwgrp', '1.0.2'), -] - -sanity_check_paths = { - 'files': ['bin/dsync', 'include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10-iimpi-2020a.eb deleted file mode 100644 index d67c00c80fa..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10-iimpi-2020a.eb +++ /dev/null @@ -1,38 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'CMakeMake' - -name = 'mpifileutils' -version = '0.10' - -homepage = 'https://hpc.github.io/mpifileutils/' - -description = """ - MPI-Based File Utilities For Distributed Systems -""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} - -source_urls = ['https://github.com/hpc/%(name)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['5a71a9acd9841c3c258fc0eaea942f18abcb40098714cc90462b57696c07e3c5'] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('attr', '2.4.48'), - ('bzip2', '1.0.8'), - ('dtcmp', '1.1.0'), - ('libarchive', '3.4.2'), - ('libcircle', '0.3'), - ('lwgrp', '1.0.2'), -] - -sanity_check_paths = { - 'files': ['bin/dsync', 'include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb deleted file mode 100644 index 9f133d3bb42..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'mpifileutils' -version = "0.10.1" - -homepage = 'https://hpc.github.io/mpifileutils/' - -description = """ - MPI-Based File Utilities For Distributed Systems -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://github.com/hpc/%(name)s/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['mpifileutils-%(version)s_fix_acl_xattr_problem.patch'] -checksums = [ - '4c8409ef4140f6f557d0e93f0c1267baf5d893c203b29fb7a33d9bc3c5a5d25c', # v0.10.1.tar.gz - # mpifileutils-0.10.1_fix_acl_xattr_problem.patch - 'e540ceaeb99758f4776252069d56b703411824ba83f48b474fc18785868151a2', -] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('attr', '2.4.48'), - ('bzip2', '1.0.8'), - ('dtcmp', '1.1.0'), - ('libarchive', '3.4.2'), - ('libcircle', '0.3'), - ('lwgrp', '1.0.2'), -] - -sanity_check_paths = { - 'files': ['bin/dsync', 'include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10.1_fix_acl_xattr_problem.patch b/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10.1_fix_acl_xattr_problem.patch deleted file mode 100644 index 72ad6e42556..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mpifileutils/mpifileutils-0.10.1_fix_acl_xattr_problem.patch +++ /dev/null @@ -1,40 +0,0 @@ -Copy of mpifileutils PR #401 - -commit 19b5e6b5d417a5b42c24f8a914fb72e297baecfb -Author: Ake Sandgren -Date: Sat Oct 3 09:17:47 2020 +0200 - - Fix problems with copying xattrs that contain ACLs causing write-protected dirs - Fixes issue https://github.com/hpc/mpifileutils/issues/400 - - Signed-off-by: Åke Sandgren - -diff --git a/src/common/mfu_flist_copy.c b/src/common/mfu_flist_copy.c -index 3d9109c..187be5d 100644 ---- a/src/common/mfu_flist_copy.c -+++ b/src/common/mfu_flist_copy.c -@@ -324,14 +324,16 @@ static int mfu_copy_xattrs( - - /* set attribute on destination object */ - if(got_val) { -- errno = 0; -- int setrc = lsetxattr(dest_path, name, val, (size_t) val_size, 0); -- if(setrc != 0) { -- /* failed to set attribute */ -- MFU_LOG(MFU_LOG_ERR, "Failed to set value for name=%s on `%s' llistxattr() (errno=%d %s)", -- name, dest_path, errno, strerror(errno) -- ); -- rc = -1; -+ if (strncmp(name, "system.posix_acl", 16)) { -+ errno = 0; -+ int setrc = lsetxattr(dest_path, name, val, (size_t) val_size, 0); -+ if(setrc != 0) { -+ /* failed to set attribute */ -+ MFU_LOG(MFU_LOG_ERR, "Failed to set value for name=%s on `%s' llistxattr() (errno=%d %s)", -+ name, dest_path, errno, strerror(errno) -+ ); -+ rc = -1; -+ } - } - } - diff --git a/easybuild/easyconfigs/__archive__/m/mpmath/mpmath-1.1.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/m/mpmath/mpmath-1.1.0-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index df62a37d287..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mpmath/mpmath-1.1.0-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,40 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Author: Adam Huffman -# adam.huffman@crick.ac.uk -# The Francis Crick Institute - -easyblock = 'PythonPackage' - -name = 'mpmath' -version = '1.1.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://mpmath.org/' -description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex - types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation - can be performed just as well at 10-digit or 1000-digit precision, with either real or complex - numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely - high precision work.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'] - -builddependencies = [ - ('binutils', '2.34') -] - -dependencies = [ - ('Python', '3.8.2'), -] - -runtest = 'python -c "import mpmath; mpmath.runtests();"' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/muParser/muParser-2.3.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/muParser/muParser-2.3.2-GCCcore-9.3.0.eb deleted file mode 100644 index 43052676a10..00000000000 --- a/easybuild/easyconfigs/__archive__/m/muParser/muParser-2.3.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'muParser' -version = '2.3.2' - -homepage = 'https://beltoforion.de/article.php?a=muparser' - -description = """ - muParser is an extensible high performance math expression parser library - written in C++. It works by transforming a mathematical expression into - bytecode and precalculating constant parts of the expression. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/beltoforion/muparser/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['b35fc84e3667d432e3414c8667d5764dfa450ed24a99eeef7ee3f6647d44f301'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -sanity_check_paths = { - 'files': ['include/muParser.h', 'lib/libmuparser.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/m/multichoose/multichoose-1.0.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/multichoose/multichoose-1.0.3-GCCcore-9.3.0.eb deleted file mode 100644 index f50a0f7a19c..00000000000 --- a/easybuild/easyconfigs/__archive__/m/multichoose/multichoose-1.0.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'MakeCp' - -name = 'multichoose' -version = '1.0.3' - -homepage = 'https://github.com/ekg/multichoose' -description = """generate multiset combinations (n multichoose k).""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'ekg' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877'] - -builddependencies = [('binutils', '2.34')] - -local_bins = [name, 'multipermute'] -files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/multichoose')] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_bins], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/m/mxmlplus/libmxmlplus-0.9.2_stdcpp_compliance.patch b/easybuild/easyconfigs/__archive__/m/mxmlplus/libmxmlplus-0.9.2_stdcpp_compliance.patch deleted file mode 100644 index 531b664d522..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mxmlplus/libmxmlplus-0.9.2_stdcpp_compliance.patch +++ /dev/null @@ -1,285 +0,0 @@ -Update code to build with newer compliant compilers - -More recent C++ standards removed features like exception specifiers. - -This patch removes the exception specifiers, removes some extra qualifiers on -member functions and ensures that access to members of dependent bases is -qualified via this->. - -Author: Lars Viklund -diff --git a/libmxmlplus-0.9.2.orig/include/mxml_document.h b/libmxmlplus-0.9.2/include/mxml_document.h -index 26add9d..6ae8d86 100644 ---- a/libmxmlplus-0.9.2.orig/include/mxml_document.h -+++ b/libmxmlplus-0.9.2/include/mxml_document.h -@@ -71,7 +71,7 @@ public: - \param style the mode in which the document is read/written - \see stylemacros - */ -- Document( std::istream &in, const int style = 0 ) throw( MalformedError ); -+ Document( std::istream &in, const int style = 0 ); - - /** Destroys the document. - If you provided a stream at document creation, the stream is NOT colsed. -@@ -141,7 +141,7 @@ public: - \param stream the input stream used for reading the data. - \see Node::read() - */ -- virtual void read( std::istream &stream ) throw(MalformedError); -+ virtual void read( std::istream &stream ); - - }; - -diff --git a/libmxmlplus-0.9.2.orig/include/mxml_iterator.h b/libmxmlplus-0.9.2/include/mxml_iterator.h -index eda07fe..636b86f 100644 ---- a/libmxmlplus-0.9.2.orig/include/mxml_iterator.h -+++ b/libmxmlplus-0.9.2/include/mxml_iterator.h -@@ -75,21 +75,21 @@ __iterator<__Node> __iterator<__Node>::operator-( int count ) - template< class __Node > - __iterator<__Node> &__deep_iterator<__Node>::__next() - { -- assert( m_node != 0 ); -+ assert( this->m_node != 0 ); - -- if ( m_node->child() != 0 ) { -- m_node = m_node->child(); -+ if ( this->m_node->child() != 0 ) { -+ this->m_node = this->m_node->child(); - } -- else if ( m_node->next() != 0 ) { -- m_node = m_node->next(); -+ else if ( this->m_node->next() != 0 ) { -+ this->m_node = this->m_node->next(); - } - else { -- while ( m_node->parent() != 0 ) { -- m_node = m_node->parent(); -- if ( m_node->next() != 0 ) -+ while ( this->m_node->parent() != 0 ) { -+ this->m_node = this->m_node->parent(); -+ if ( this->m_node->next() != 0 ) - break; - } -- m_node = m_node->next(); // can be NULL -+ this->m_node = this->m_node->next(); // can be NULL - } - - return *this; -@@ -142,16 +142,16 @@ __iterator<__Node> &__find_iterator<__Node>::__find() - int matches; - while ( this->m_node != 0 ) { - matches = 0; -- if ( m_name != "" && m_name == m_node->name() ) -+ if ( m_name != "" && m_name == this->m_node->name() ) - matches++; - -- if ( m_attr != "" && m_node->hasAttribute( m_attr ) ) { -+ if ( m_attr != "" && this->m_node->hasAttribute( m_attr ) ) { - matches++; -- if ( m_valattr != "" && m_node->getAttribute( m_attr ) == m_valattr ) -+ if ( m_valattr != "" && this->m_node->getAttribute( m_attr ) == m_valattr ) - matches++; - } - -- if ( m_data != "" && m_node->data().find( m_data ) != std::string::npos ) -+ if ( m_data != "" && this->m_node->data().find( m_data ) != std::string::npos ) - matches++; - - if ( matches < m_maxmatch ) -@@ -184,7 +184,7 @@ __path_iterator<__Node>::__path_iterator( __Node *nd, std::string path ): - template< class __Node > - __iterator<__Node> &__path_iterator<__Node>::__next() - { -- __Node *ptr = m_node; -+ __Node *ptr = this->m_node; - std::string name; - std::string::size_type pos = m_path.rfind('/'); - -@@ -197,11 +197,11 @@ __iterator<__Node> &__path_iterator<__Node>::__next() - name = m_path.substr( pos ); - } - -- m_node = m_node->next(); -+ this->m_node = this->m_node->next(); - // todo: this sucks, must re-do it better -- while ( m_node ) { -- if ( name == "*" || m_node->name() == name ) break; -- m_node = m_node->next(); -+ while ( this->m_node ) { -+ if ( name == "*" || this->m_node->name() == name ) break; -+ this->m_node = this->m_node->next(); - } - - return *this; -@@ -210,14 +210,14 @@ __iterator<__Node> &__path_iterator<__Node>::__next() - template< class __Node > - __iterator<__Node> &__path_iterator<__Node>::__prev() - { -- assert( m_node != 0 ); -+ assert( this->m_node != 0 ); - -- __Node *ptr = m_node; -- m_node = m_node->prev(); -+ __Node *ptr = this->m_node; -+ this->m_node = this->m_node->prev(); - // todo: this sucks, must re-do it better -- while ( m_node != 0 ) { -- if ( m_node->name() == ptr->name() ) break; -- m_node = m_node->prev(); -+ while ( this->m_node != 0 ) { -+ if ( this->m_node->name() == ptr->name() ) break; -+ this->m_node = this->m_node->prev(); - } - - return *this; -@@ -250,9 +250,9 @@ __Node *__path_iterator<__Node>::subfind( __Node *parent, - template< class __Node > - __iterator<__Node> &__path_iterator<__Node>::__find() - { -- if ( m_node == 0 ) return *this; -+ if ( this->m_node == 0 ) return *this; - -- __Node *rootNode = m_node; -+ __Node *rootNode = this->m_node; - std::string firstName; - std::string::size_type pos; - if ( rootNode->nodeType() == Node::typeDocument ) -@@ -262,7 +262,7 @@ __iterator<__Node> &__path_iterator<__Node>::__find() - rootNode = rootNode->next(); - if ( ! rootNode ) - { -- m_node = 0; -+ this->m_node = 0; - return *this; - } - } -@@ -295,10 +295,10 @@ __iterator<__Node> &__path_iterator<__Node>::__find() - { - if ( pos == std::string::npos ) - { -- m_node = rootNode; -+ this->m_node = rootNode; - } - else { -- m_node = subfind( rootNode, pos+1 ); -+ this->m_node = subfind( rootNode, pos+1 ); - } - break; - } -diff --git a/libmxmlplus-0.9.2.orig/include/mxml_node.h b/libmxmlplus-0.9.2/include/mxml_node.h -index ca6035d..f6e229e 100644 ---- a/libmxmlplus-0.9.2.orig/include/mxml_node.h -+++ b/libmxmlplus-0.9.2/include/mxml_node.h -@@ -214,8 +214,7 @@ public: - @throws MXML::MalformedError if the node is invalid - @throws MXML::IOError in case of hard errors on the stream - */ -- Node( std::istream &in, const int style = 0, const int line=1, const int pos=0 ) -- throw( MalformedError ); -+ Node( std::istream &in, const int style = 0, const int line=1, const int pos=0 ); - - /* Creates a new node - Depending on the types the node could have a name, a data or both. -@@ -309,8 +308,7 @@ public: - @return the attribute value, if it exists - @throws MXML::NotFoundError if the attribute name can't be found. - */ -- const std::string getAttribute( const std::string name ) const -- throw( NotFoundError ); -+ const std::string getAttribute( const std::string name ) const; - - /** Sets the value of a given attribute. - This is a shortcut instead of searching for an attribute in -@@ -319,8 +317,7 @@ public: - @return the attribute value, if it exists - @throws MXML::NotFoundError if the attribute name can't be found. - */ -- void setAttribute( const std::string name, const std::string value ) -- throw( NotFoundError ); -+ void setAttribute( const std::string name, const std::string value ); - - /** Returns true if the node has a given attribute. - The found attribute is cached, so if you make this method follow -@@ -372,7 +369,7 @@ public: - @param child the node to be removed - @throw NotFoundError if the node is not in the child list - */ -- void Node::removeChild( Node *child ) throw( NotFoundError ); -+ void removeChild( Node *child ); - - - Node *parent() const { return m_parent; } -@@ -391,7 +388,7 @@ public: - ...Or how many levels are above this node. - Can be called also for nodes that have not a valid symbolic path. - */ -- int Node::depth() const; -+ int depth() const; - - /** Returns a symbolic path leading to the node. - A Node path is the the list of all the ancestor node names, plus the -@@ -412,7 +409,7 @@ public: - @return the path leading to the node, or an empty string if the node - has not a valid path. - */ -- std::string Node::path() const; -+ std::string path() const; - - - /* Clones the node and all its children. -diff --git a/libmxmlplus-0.9.2.orig/src/mxml_document.cpp b/libmxmlplus-0.9.2/src/mxml_document.cpp -index c09f6f9..60961bf 100644 ---- a/libmxmlplus-0.9.2.orig/src/mxml_document.cpp -+++ b/libmxmlplus-0.9.2/src/mxml_document.cpp -@@ -27,7 +27,6 @@ Document::Document( Document &doc ) - } - - Document::Document( std::istream &in, const int style ) -- throw( MalformedError ) - { - m_style = style; - m_root = new Node( Node::typeDocument ); -@@ -55,7 +54,6 @@ void Document::write( std::ostream &stream, const int style ) const - - - void Document::read( std::istream &stream ) -- throw( MalformedError ) - { - if ( m_root->child() != 0 ) { - delete m_root; -diff --git a/libmxmlplus-0.9.2.orig/src/mxml_node.cpp b/libmxmlplus-0.9.2/src/mxml_node.cpp -index f5e1631..e69b512 100644 ---- a/libmxmlplus-0.9.2.orig/src/mxml_node.cpp -+++ b/libmxmlplus-0.9.2/src/mxml_node.cpp -@@ -38,7 +38,7 @@ namespace MXML - - - Node::Node( std::istream &in, const int style, const int l, const int pos ) -- throw( MalformedError ): Element( l, pos ) -+ : Element( l, pos ) - { - // variables to optimize data node promotion in tag nodes - bool promote_data = true; -@@ -382,7 +382,6 @@ Node::~Node() - /* Search routines */ - - const std::string Node::getAttribute( const std::string name ) const -- throw( NotFoundError ) - { - AttribList::const_iterator iter = m_attrib.begin(); - -@@ -395,7 +394,6 @@ const std::string Node::getAttribute( const std::string name ) const - } - - void Node::setAttribute( const std::string name, const std::string value ) -- throw( NotFoundError ) - { - AttribList::iterator iter = m_attrib.begin(); - -@@ -423,7 +421,6 @@ bool Node::hasAttribute( const std::string name ) const - - /* unlink routines */ - void Node::removeChild( Node *child ) -- throw( NotFoundError ) - { - if (child->parent() != this ) - throw NotFoundError( Error::errHyerarcy, this ); diff --git a/easybuild/easyconfigs/__archive__/m/mxmlplus/mxmlplus-0.9.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/m/mxmlplus/mxmlplus-0.9.2-GCC-9.3.0.eb deleted file mode 100644 index db55c92fdb8..00000000000 --- a/easybuild/easyconfigs/__archive__/m/mxmlplus/mxmlplus-0.9.2-GCC-9.3.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'mxmlplus' -version = '0.9.2' - -homepage = 'http://mxml.sourceforge.net' -description = """Mxml is a pure C library (yet having an object oriented layout) that is meant to help developers - implementing XML file interpretation in their projects.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -local_dash_version = '-'.join(version.split('.')) -source_urls = [('https://sourceforge.net/projects/mxml/files/mxmlplus/%s/' % local_dash_version, 'download')] -sources = ['libmxmlplus-%(version)s.tar.gz'] -patches = ['libmxmlplus-%(version)s_stdcpp_compliance.patch'] -checksums = [ - 'f97b7be94c05b7da626b256a899f40f3182b40d9efcde1f128dc1bf0ad1b622a', # libmxmlplus-0.9.2.tar.gz - '2814309c4fea52ee8f83836276746156c9be5f6bbc99e69d93d506ff160cdf17', # libmxmlplus-0.9.2_stdcpp_compliance.patch -] - -configopts = '--enable-shared' - -buildopts = 'CXXFLAGS="$CXXFLAGS -fpermissive"' - -sanity_check_paths = { - 'files': ['include/mxml.h', 'lib/libmxmlplus.a', 'lib/libmxmlplus.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.14-foss-2020a-mpi.eb b/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.14-foss-2020a-mpi.eb deleted file mode 100644 index 1c7c0e6e88f..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.14-foss-2020a-mpi.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'NAMD' -version = '2.14' -versionsuffix = '-mpi' - -homepage = 'https://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of - large biomolecular systems.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True, 'openmp': False, 'pic': True} - -source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] -sources = ['NAMD_%(version)s_Source.tar.gz'] -checksums = ['34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235'] - -dependencies = [ - ('Tcl', '8.6.10'), -] - -# /bin/csh is required by 'config' script -osdependencies = ['tcsh'] - -# Hard to make charm build the mpi version with gcc on POWER, so we don't currently try -charm_arch = 'mpi-linux-x86_64' -charm_extra_cxxflags = '-fpermissive' - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.14-intel-2020a-mpi.eb b/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.14-intel-2020a-mpi.eb deleted file mode 100644 index 576c8836ad9..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.14-intel-2020a-mpi.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'NAMD' -version = '2.14' -versionsuffix = '-mpi' - -homepage = 'https://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of - large biomolecular systems.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True, 'openmp': False, 'pic': True} - -source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] -sources = ['NAMD_%(version)s_Source.tar.gz'] -patches = ['NAMD-2.14-use_system_mremap_decl.patch'] -checksums = [ - '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz - 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch -] - -dependencies = [ - ('Tcl', '8.6.10'), - ('FFTW', '3.3.8'), -] - -# /bin/csh is required by 'config' script -osdependencies = ['tcsh'] - -# Hard to make charm build the mpi version with gcc on POWER, so we don't currently try -charm_arch = 'mpi-linux-x86_64' -charm_extra_cxxflags = '-fpermissive' - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.14.02-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.14.02-GCCcore-9.3.0.eb deleted file mode 100644 index 4ab7a9fc7ab..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.14.02-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html -## - -easyblock = 'ConfigureMake' - -name = 'NASM' -version = '2.14.02' - -homepage = 'https://www.nasm.us/' - -description = """NASM: General-purpose x86 assembler""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['34fd26c70a277a9fdd54cb5ecf389badedaf48047b269d1008fbc819b24e80bc'] - -builddependencies = [ - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ['bin/nasm'], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/n/NBO/NBO-7.0.10-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/NBO/NBO-7.0.10-GCC-9.3.0.eb deleted file mode 100644 index 2414fc80f57..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NBO/NBO-7.0.10-GCC-9.3.0.eb +++ /dev/null @@ -1,55 +0,0 @@ -# this recipe is configured for use with Gaussian G16, revision A03 or later - -easyblock = 'MakeCp' - -name = 'NBO' -version = '7.0.10' - -homepage = 'http://nbo.chem.wisc.edu/' -description = """ The Natural Bond Orbital (NBO) program is a discovery tool -for chemical insights from complex wavefunctions. """ - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers - -download_instructions = """ -NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx -The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz -""" -sources = ['nbo%(version)s-src.tar.gz'] -patches = [ - 'NBO-%(version)s_make.patch', -] -checksums = [ - {'nbo7.0.10-src.tar.gz': 'a60d1f4d4592ec386b5378841d9fba75918c48b50de08d8de0a50db42bc96da1'}, - {'NBO-7.0.10_make.patch': 'c37f5a9980c56198f9610611b0fbda8ad65c961ec19b163d602dc3330fced145'}, -] - -dependencies = [ - ('OpenBLAS', '0.3.9'), -] - -local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers - -buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' -buildopts += 'INT=%s ' % local_intlength - -maxparallel = 1 - -files_to_copy = ['bin', 'dox', 'man', 'tests'] - -postinstallcmds = [ - 'sed -i -e "s|setenv GAUNBO.*|setenv GAUNBO g16nbo|" %(installdir)s/bin/gaunbo{6,7}', - 'sed -i -e "s|setenv BINDIR.*|setenv BINDIR %(installdir)s/bin|" %(installdir)s/bin/gaunbo{6,7}', - 'sed -i -e "s|setenv INT.*|setenv INT %s|" %%(installdir)s/bin/gaunbo{6,7}' % local_intlength, - 'cp %(builddir)s/nbo7/gennbo %(builddir)s/nbo7/gennbo.sh %(installdir)s/bin', - 'sed -i -e "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo', - 'sed -i "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo.sh', -] - -sanity_check_paths = { - 'files': ['bin/%s.%s.exe' % (x, local_intlength) for x in ('gennbo', 'g09nbo', 'g16nbo', 'nbo7')], - 'dirs': [], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/__archive__/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb deleted file mode 100644 index 700f896be0e..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb +++ /dev/null @@ -1,29 +0,0 @@ -name = 'NCCL' -version = '2.8.3' -local_gcc_ver = '9.3.0' -local_cuda_version = '11.0.2' -versionsuffix = '-CUDA-%s' % local_cuda_version - -homepage = 'https://developer.nvidia.com/nccl' -description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective -communication primitives that are performance optimized for NVIDIA GPUs.""" - -toolchain = {'name': 'GCCcore', 'version': local_gcc_ver} - -builddependencies = [('GCC', local_gcc_ver, '', SYSTEM)] -dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] - -github_account = 'NVIDIA' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s-1.tar.gz'] -patches = [ - 'NCCL-2.8.3_fix-isend-irecv.patch', - 'NCCL-2.16.2_fix-cpuid.patch', -] -checksums = [ - {'v2.8.3-1.tar.gz': '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6'}, - {'NCCL-2.8.3_fix-isend-irecv.patch': '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92'}, - {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/n/NCL/NCL-6.6.2-foss-2020a.eb b/easybuild/easyconfigs/__archive__/n/NCL/NCL-6.6.2-foss-2020a.eb deleted file mode 100644 index edae6cd5b31..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NCL/NCL-6.6.2-foss-2020a.eb +++ /dev/null @@ -1,49 +0,0 @@ -name = 'NCL' -version = '6.6.2' - -homepage = 'https://www.ncl.ucar.edu' -description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True} - -source_urls = ['https://github.com/NCAR/ncl/archive/'] -sources = ['%(version)s.tar.gz'] -patches = [ - 'NCL-6.4.0_fix-types.patch', -] -checksums = [ - 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e', # 6.6.2.tar.gz - 'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f', # NCL-6.4.0_fix-types.patch -] - -builddependencies = [ - ('makedepend', '1.0.6'), - ('Bison', '3.5.3'), - ('flex', '2.6.4'), -] - -dependencies = [ - ('cURL', '7.69.1'), - ('JasPer', '2.0.14'), - ('g2lib', '3.1.0'), - ('g2clib', '1.6.0'), - ('HDF', '4.2.15'), - ('HDF5', '1.10.6'), - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), - ('Szip', '2.1.1'), - ('freetype', '2.10.1'), - ('zlib', '1.2.11'), - ('GDAL', '3.0.4', '-Python-3.8.2'), - ('UDUNITS', '2.2.26'), - ('ESMF', '8.0.1'), - ('bzip2', '1.0.8'), - ('cairo', '1.16.0'), - ('libiconv', '1.16'), - ('GSL', '2.6'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/NCL/NCL-6.6.2-intel-2020a.eb b/easybuild/easyconfigs/__archive__/n/NCL/NCL-6.6.2-intel-2020a.eb deleted file mode 100644 index 3d271b1a8fc..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NCL/NCL-6.6.2-intel-2020a.eb +++ /dev/null @@ -1,46 +0,0 @@ -name = 'NCL' -version = '6.6.2' - -homepage = 'https://www.ncl.ucar.edu' -description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True} - -source_urls = ['https://github.com/NCAR/ncl/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['NCL-6.4.0_fix-types.patch'] -checksums = [ - 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e', # 6.6.2.tar.gz - 'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f', # NCL-6.4.0_fix-types.patch -] - -builddependencies = [ - ('makedepend', '1.0.6'), - ('Bison', '3.5.3'), - ('flex', '2.6.4'), -] -dependencies = [ - ('cURL', '7.69.1'), - ('JasPer', '2.0.14'), - ('g2lib', '3.1.0'), - ('g2clib', '1.6.0'), - ('HDF', '4.2.15'), - ('HDF5', '1.10.6'), - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), - ('Szip', '2.1.1'), - ('freetype', '2.10.1'), - ('zlib', '1.2.11'), - ('GDAL', '3.0.4', '-Python-3.8.2'), - ('UDUNITS', '2.2.26'), - ('ESMF', '8.0.1'), - ('bzip2', '1.0.8'), - ('cairo', '1.16.0'), - ('libiconv', '1.16'), - ('GSL', '2.6'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.4'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/NCO/NCO-4.9.7-foss-2020a.eb b/easybuild/easyconfigs/__archive__/n/NCO/NCO-4.9.7-foss-2020a.eb deleted file mode 100644 index 576e69a29bd..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NCO/NCO-4.9.7-foss-2020a.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'NCO' -version = '4.9.7' - -homepage = "https://nco.sourceforge.net" -description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/nco/nco/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['934e247d9592f3e6087ea8985507077873559b52679b9c9a1ecae40668a352dc'] - -builddependencies = [ - ('Bison', '3.5.3'), - ('flex', '2.6.4'), -] - -dependencies = [ - ('UDUNITS', '2.2.26'), - ('expat', '2.2.9'), - ('ANTLR', '2.7.7', '-Java-11'), - ('libdap', '3.20.7'), - ('GSL', '2.6'), - ('netCDF', '4.7.4'), - ('ESMF', '8.0.1'), # ncremap needs ESMF_RegridWeightGen -] - -sanity_check_paths = { - 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', - 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + - ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/NFFT/NFFT-3.5.2-foss-2020a.eb b/easybuild/easyconfigs/__archive__/n/NFFT/NFFT-3.5.2-foss-2020a.eb deleted file mode 100644 index dc2182b4582..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NFFT/NFFT-3.5.2-foss-2020a.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'NFFT' -version = '3.5.2' - -homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' -description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine - library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more - dimensions, of arbitrary input size, and of complex data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/NFFT/nfft/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['c68b22de2b914328d5d9fd33778defc66b226c72ef4c103956bbf36bbcd18e45'] - -dependencies = [('FFTW', '3.3.8')] - -builddependencies = [('Autotools', '20180311')] - -configure_cmd_prefix = './bootstrap.sh ; ' - -sanity_check_paths = { - 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb deleted file mode 100644 index c6f2f988ec1..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'Bundle' - -name = 'NGS' -version = '2.10.5' - -homepage = 'https://github.com/ncbi/ngs' -description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups -produced from Next Generation Sequencing.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [ - ('binutils', '2.34'), - ('Perl', '5.30.2'), -] - -dependencies = [('Java', '11', '', SYSTEM)] - -default_easyblock = 'ConfigureMake' -default_component_specs = { - 'source_urls': ['https://github.com/ncbi/ngs/archive'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'checksums': ['c39ee65a625e3646e0212c5d8be846e45d368c644a053d3b54cf63f53853f02f'], -} - -components = [ - ('NGS-SDK', version, { - 'start_dir': 'ngs-%(version)s/%(namelower)s', - 'configopts': '--build-prefix=%(builddir)s', # change default build directory - }), - ('NGS-Java', version, { - 'start_dir': 'ngs-%(version)s/%(namelower)s', - 'configopts': '--build-prefix=%(builddir)s', # change default build directory - }), -] - -sanity_check_paths = { - 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), - ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], - 'dirs': ['include/ngs', 'share'], -} - -modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/n/NLTK/NLTK-3.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/NLTK/NLTK-3.5-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index c84a8e1cdd0..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NLTK/NLTK-3.5-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'NLTK' -version = '3.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.nltk.org/' -description = "NLTK is a leading platform for building Python programs to work with human language data." - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('tqdm', '4.47.0'), -] - -exts_list = [ - ('regex', '2020.7.14', { - 'checksums': ['3a3af27a8d23143c49a3420efe5b3f8cf1a48c6fc8bc6856b03f638abc1833bb'], - }), - (name, version, { - 'source_tmpl': SOURCELOWER_ZIP, - 'checksums': ['845365449cd8c5f9731f7cb9f8bd6fd0767553b9d53af9eb1b3abf7700936b35'], - }), -] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/n/NLTK/NLTK-3.5-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/NLTK/NLTK-3.5-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 89a294b1345..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NLTK/NLTK-3.5-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'NLTK' -version = '3.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.nltk.org/' -description = "NLTK is a leading platform for building Python programs to work with human language data." - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('tqdm', '4.47.0'), -] - -exts_list = [ - ('regex', '2020.7.14', { - 'checksums': ['3a3af27a8d23143c49a3420efe5b3f8cf1a48c6fc8bc6856b03f638abc1833bb'], - }), - (name, version, { - 'source_tmpl': SOURCELOWER_ZIP, - 'checksums': ['845365449cd8c5f9731f7cb9f8bd6fd0767553b9d53af9eb1b3abf7700936b35'], - }), -] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/n/NLopt/NLopt-2.6.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/NLopt/NLopt-2.6.1-GCCcore-9.3.0.eb deleted file mode 100644 index 578a181a5fe..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NLopt/NLopt-2.6.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# 2019-06-05 John Dey jfdey@fredhutch.org fizwit@github.com - updated for CMake -easyblock = 'CMakeMake' - -name = 'NLopt' -version = '2.6.1' - -homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' -description = """ NLopt is a free/open-source library for nonlinear optimization, - providing a common interface for a number of different free optimization routines - available online as well as original implementations of various other algorithms. """ - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/stevengj/nlopt/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['66d63a505187fb6f98642703bd0ef006fedcae2f9a6d1efa4f362ea919a02650'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34'), -] - -configopts = [ - '-DBUILD_SHARED_LIBS=ON', - '-DBUILD_SHARED_LIBS=OFF' -] - -sanity_check_paths = { - 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/n/NSPR/NSPR-4.25-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/NSPR/NSPR-4.25-GCCcore-9.3.0.eb deleted file mode 100644 index 8cfc285f74d..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NSPR/NSPR-4.25-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'NSPR' -version = '4.25' - -homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' -description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level - and libc-like functions.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://archive.mozilla.org/pub/nspr/releases/v%(version)s/src/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['0bc309be21f91da4474c56df90415101c7f0c7c7cab2943cd943cd7896985256'] - -builddependencies = [('binutils', '2.34')] - -configopts = "--disable-debug --enable-optimize --enable-64bit" - -sanity_check_paths = { - 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, - 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, - 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, - 'lib/pkgconfig/nspr.pc'], - 'dirs': ['include/nspr'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/n/NSS/NSS-3.51-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/NSS/NSS-3.51-GCCcore-9.3.0.eb deleted file mode 100644 index 4d53515db28..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NSS/NSS-3.51-GCCcore-9.3.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -easyblock = 'MakeCp' - -name = 'NSS' -version = '3.51' - -homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' -description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development - of security-enabled client and server applications.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'NSS-3.39_pkgconfig.patch', - '%(name)s-%(version)s_fix_kremlin_ppc64le.patch', - 'NSS-3.42.1_CVE-2021-43527.patch', -] -checksums = [ - '75348b3b3229362486c57a880db917da1f96ef4eb639dc9cc2ff17d72268459c', # nss-3.51.tar.gz - '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch - '2fc7bd556737d34a62c06f86899863b7071b71943ffb4facfb413a087b8bee2e', # NSS-3.51_fix_kremlin_ppc64le.patch - 'cc17945edcc8f6d951e8710a4e99604439a1758e38539d1b7b8c0cd95ac59355', # NSS-3.42.1_CVE-2021-43527.patch -] - -builddependencies = [('binutils', '2.34')] -dependencies = [ - ('NSPR', '4.25'), - ('zlib', '1.2.11'), -] - -# building in parallel fails -maxparallel = 1 - -# fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" NSS_ENABLE_WERROR=0 ' -# fix c standard causing missing functions -buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' -# also install pkgconfig file (see patch) -buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" - -files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] - -sanity_check_paths = { - 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], - 'dirs': ['include/dbm', 'include/nss'], -} - -sanity_check_commands = [ - "multinit --help", - "nss-config --version", -] - -modextrapaths = {'CPATH': 'include/nss'} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/n/NSS/NSS-3.51_fix_kremlin_ppc64le.patch b/easybuild/easyconfigs/__archive__/n/NSS/NSS-3.51_fix_kremlin_ppc64le.patch deleted file mode 100644 index 56e2edda9b1..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NSS/NSS-3.51_fix_kremlin_ppc64le.patch +++ /dev/null @@ -1,28 +0,0 @@ -Patch based on https://github.com/FStarLang/kremlin/pull/167 -Prepared for EasyBuild by Simon Branford of the BEAR Software team at the University of Birmingham -diff -aur nss-3.51.orig/nss/lib/freebl/verified/kremlin/include/kremlin/internal/types.h nss-3.51/nss/lib/freebl/verified/kremlin/include/kremlin/internal/types.h ---- nss-3.51.orig/nss/lib/freebl/verified/kremlin/include/kremlin/internal/types.h 2020-03-23 20:23:06.943356000 +0000 -+++ nss-3.51/nss/lib/freebl/verified/kremlin/include/kremlin/internal/types.h 2020-03-23 20:24:27.270377000 +0000 -@@ -56,7 +56,8 @@ - #include - typedef __m128i FStar_UInt128_uint128; - #elif !defined(KRML_VERIFIED_UINT128) && !defined(_MSC_VER) && \ -- (defined(__x86_64__) || defined(__x86_64) || defined(__aarch64__)) -+ (defined(__x86_64__) || defined(__x86_64) || defined(__aarch64__) || \ -+ (defined(__powerpc64__) && defined(__LITTLE_ENDIAN__))) - typedef unsigned __int128 FStar_UInt128_uint128; - #else - typedef struct FStar_UInt128_uint128_s { -diff -aur nss-3.51.orig/nss/lib/freebl/verified/kremlin/kremlib/dist/minimal/fstar_uint128_gcc64.h nss-3.51/nss/lib/freebl/verified/kremlin/kremlib/dist/minimal/fstar_uint128_gcc64.h ---- nss-3.51.orig/nss/lib/freebl/verified/kremlin/kremlib/dist/minimal/fstar_uint128_gcc64.h 2020-03-23 20:23:06.947505000 +0000 -+++ nss-3.51/nss/lib/freebl/verified/kremlin/kremlib/dist/minimal/fstar_uint128_gcc64.h 2020-03-23 20:25:20.007003000 +0000 -@@ -25,7 +25,8 @@ - #include "LowStar_Endianness.h" - - #if !defined(KRML_VERIFIED_UINT128) && !defined(_MSC_VER) && \ -- (defined(__x86_64__) || defined(__x86_64) || defined(__aarch64__)) -+ (defined(__x86_64__) || defined(__x86_64) || defined(__aarch64__) || \ -+ (defined(__powerpc64__) && defined(__LITTLE_ENDIAN__))) - - /* GCC + using native unsigned __int128 support */ - diff --git a/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-20.11.eb b/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-20.11.eb deleted file mode 100644 index d284520538b..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-20.11.eb +++ /dev/null @@ -1,69 +0,0 @@ -name = 'NVHPC' -version = '20.11' - -homepage = 'https://developer.nvidia.com/hpc-sdk/' -description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" - -toolchain = SYSTEM - -# By downloading, you accept the HPC SDK Software License Agreement -# https://docs.nvidia.com/hpc-sdk/eula/index.html -source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] -local_tarball_tmpl = 'nvhpc_2020_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' -sources = [local_tarball_tmpl % '%(arch)s'] -checksums = [ - { - local_tarball_tmpl % 'x86_64': - 'c80fc26e5ba586696f7030f03054c1aaca0752a891c7923faf47eb23b66857ec', - local_tarball_tmpl % 'ppc64le': - '99e5a5437e82f3914e0fe81feb761a5b599a3fe8b31f3c2cac8ae47e8cdc7b0f' - } -] - -local_gccver = '9.3.0' -dependencies = [ - ('GCCcore', local_gccver), - ('binutils', '2.34', '', ('GCCcore', local_gccver)), - # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails - ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) -] - -# specify default CUDA version that should be used by NVHPC -# should match one of the CUDA versions that are included with this NVHPC version -# (see install_components/Linux_x86_64/20.7/cuda/) -# for NVHPC 20.7, those are: 11.0, 10.2, 10.1; -# this version can be tweaked from the EasyBuild command line with -# --try-amend=default_cuda_version="10.2" (for example) -default_cuda_version = '11.0' - -# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. -# The following list gives examples for the easyconfig -# -# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA -# 1) Bundled CUDA -# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with -# default_cuda_version = "11.0" -# in this easyconfig file; alternatively, it can be specified through the command line during installation with -# --try-amend=default_cuda_version="10.2" -# 2) CUDA provided via EasyBuild -# Use CUDAcore as a dependency, for example -# dependencies = [('CUDAcore', '11.0.2')] -# The parameter default_cuda_version still can be set as above. -# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) -# -# Define a NVHPC-default Compute Capability -# cuda_compute_capabilities = "8.0" -# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 -# Only single values supported, not lists of values! -# -# Options to add/remove things to/from environment module (defaults shown) -# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) -# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI -# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) -# module_add_profilers = False # Add NVHPC's NVIDIA Profilers -# module_add_nccl = False # Add NVHPC's NCCL library -# module_add_nvshmem = False # Add NVHPC's NVSHMEM library -# module_add_cuda = False # Add NVHPC's bundled CUDA - -# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-20.7.eb b/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-20.7.eb deleted file mode 100644 index 48e81e6c353..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-20.7.eb +++ /dev/null @@ -1,60 +0,0 @@ -name = 'NVHPC' -version = '20.7' - -homepage = 'https://developer.nvidia.com/hpc-sdk/' -description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" - -toolchain = SYSTEM - -# By downloading, you accept the HPC SDK Software License Agreement -# https://docs.nvidia.com/hpc-sdk/eula/index.html -source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] -sources = ['nvhpc_2020_%(version_major)s%(version_minor)s_Linux_x86_64_cuda_multi.tar.gz'] -checksums = ['a5c5c8726d2210f2310a852c6d6e03c9ef8c75e3643e9c94e24909f5e9c2ea7a'] - -local_gccver = '9.3.0' -dependencies = [ - ('GCCcore', local_gccver), - ('binutils', '2.34', '', ('GCCcore', local_gccver)), - # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails - ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) -] - -# specify default CUDA version that should be used by NVHPC -# should match one of the CUDA versions that are included with this NVHPC version -# (see install_components/Linux_x86_64/20.7/cuda/) -# for NVHPC 20.7, those are: 11.0, 10.2, 10.1; -# this version can be tweaked from the EasyBuild command line with --try-amend=default_cuda_version="10.2" (for example) -default_cuda_version = '11.0' - -# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. -# The following list gives examples for the easyconfig -# -# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA -# 1) Bundled CUDA -# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with -# default_cuda_version = "11.0" -# in this easyconfig file; alternatively, it can be specified through the command line during installation with -# --try-amend=default_cuda_version="10.2" -# 2) CUDA provided via EasyBuild -# Use CUDAcore as a dependency, for example -# dependencies = [('CUDAcore', '11.0.2')] -# The parameter default_cuda_version still can be set as above. -# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) -# -# Define a NVHPC-default Compute Capability -# cuda_compute_capabilities = "8.0" -# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 -# Only single values supported, not lists of values! -# -# Options to add/remove things to/from environment module (defaults shown) -# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) -# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI -# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) -# module_add_profilers = False # Add NVHPC's NVIDIA Profilers -# module_add_nccl = False # Add NVHPC's NCCL library -# module_add_nvshmem = False # Add NVHPC's NVSHMEM library -# module_add_cuda = False # Add NVHPC's bundled CUDA - -# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-20.9.eb b/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-20.9.eb deleted file mode 100644 index ff21a9bc94f..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NVHPC/NVHPC-20.9.eb +++ /dev/null @@ -1,69 +0,0 @@ -name = 'NVHPC' -version = '20.9' - -homepage = 'https://developer.nvidia.com/hpc-sdk/' -description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" - -toolchain = SYSTEM - -# By downloading, you accept the HPC SDK Software License Agreement -# https://docs.nvidia.com/hpc-sdk/eula/index.html -source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] -local_tarball_tmpl = 'nvhpc_2020_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' -sources = [local_tarball_tmpl % '%(arch)s'] -checksums = [ - { - local_tarball_tmpl % 'x86_64': - 'fe665ab611b03846a90bd70ca4e08c1e59ab527364b971ed0304e0ae73c778d8', - local_tarball_tmpl % 'ppc64le': - 'b2966d4047e1dfd981ce63b333ab9c0acbdc2a6a505fa217456ac9fa3b8e7474' - } -] - -local_gccver = '9.3.0' -dependencies = [ - ('GCCcore', local_gccver), - ('binutils', '2.34', '', ('GCCcore', local_gccver)), - # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails - ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) -] - -# specify default CUDA version that should be used by NVHPC -# should match one of the CUDA versions that are included with this NVHPC version -# (see install_components/Linux_x86_64/20.7/cuda/) -# for NVHPC 20.7, those are: 11.0, 10.2, 10.1; -# this version can be tweaked from the EasyBuild command line with -# --try-amend=default_cuda_version="10.2" (for example) -default_cuda_version = '11.0' - -# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. -# The following list gives examples for the easyconfig -# -# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA -# 1) Bundled CUDA -# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with -# default_cuda_version = "11.0" -# in this easyconfig file; alternatively, it can be specified through the command line during installation with -# --try-amend=default_cuda_version="10.2" -# 2) CUDA provided via EasyBuild -# Use CUDAcore as a dependency, for example -# dependencies = [('CUDAcore', '11.0.2')] -# The parameter default_cuda_version still can be set as above. -# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) -# -# Define a NVHPC-default Compute Capability -# cuda_compute_capabilities = "8.0" -# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 -# Only single values supported, not lists of values! -# -# Options to add/remove things to/from environment module (defaults shown) -# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) -# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI -# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) -# module_add_profilers = False # Add NVHPC's NVIDIA Profilers -# module_add_nccl = False # Add NVHPC's NCCL library -# module_add_nvshmem = False # Add NVHPC's NVSHMEM library -# module_add_cuda = False # Add NVHPC's bundled CUDA - -# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/__archive__/n/NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index a1bf3cec920..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'NanoFilt' -version = '2.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/wdecoster/nanofilt' -description = """Filtering and trimming of long read sequencing data.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/wdecoster/nanofilt/archive/v%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['83e3a581b7bf8a4b2e63b1a9b659baea6908448cbca9a0d42893f1cd4021d113'] - -dependencies = [ - ('Python', '3.8.2'), - ('Biopython', '1.78', versionsuffix), -] - -sanity_check_paths = { - 'files': ['bin/NanoFilt'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["NanoFilt --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/n/NanopolishComp/NanopolishComp-0.6.11-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/NanopolishComp/NanopolishComp-0.6.11-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index d9ca6006f61..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NanopolishComp/NanopolishComp-0.6.11-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'NanopolishComp' -version = '0.6.11' -versionsuffix = "-Python-%(pyver)s" - -homepage = 'https://adrienleger.com/NanopolishComp/' -description = "NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['753eed9ed93d12b15b693c43382c73379064d86eeef651611fa27abe7f8a44b3'] - -dependencies = [ - ('Python', '3.8.2'), - ('tqdm', '4.47.0'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -options = {'modulename': '%(name)s'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/n/NiBabel/NiBabel-3.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/NiBabel/NiBabel-3.2.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index f0f79f5f682..00000000000 --- a/easybuild/easyconfigs/__archive__/n/NiBabel/NiBabel-3.2.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'NiBabel' -version = '3.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://nipy.github.io/nibabel' -description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, - including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT - as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and - annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Pillow', '7.0.0', versionsuffix), - ('pydicom', '2.1.2', versionsuffix), -] - -exts_list = [ - ('bz2file', '0.98', { - 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], - }), - ('nibabel', version, { - 'checksums': ['5827b644d1b0833603710dac198f5f8cbb9002769f97001a191e863b32f5956c'], - }), -] - -fix_python_shebang_for = ['bin/*'] - -sanity_check_paths = { - 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "nib-diff --help", - "parrec2nii --help", -] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/n/Nilearn/Nilearn-0.7.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/Nilearn/Nilearn-0.7.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 4137e09b86a..00000000000 --- a/easybuild/easyconfigs/__archive__/n/Nilearn/Nilearn-0.7.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Nilearn' -version = '0.7.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://nilearn.github.io/' -description = """Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e7c9df82a31319366f02919794e0ec4eacbae1fb24c41c826070c2a3acf117e6'] - -dependencies = [ - ('Python', '3.8.2'), - ('NiBabel', '3.2.0', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb deleted file mode 100644 index fe62223f1a7..00000000000 --- a/easybuild/easyconfigs/__archive__/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'CmdCp' - -name = 'Ninja' -version = '1.10.0' - -homepage = 'https://ninja-build.org/' -description = "Ninja is a small build system with a focus on speed." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/ninja-build/ninja/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['3810318b08489435f8efc19c05525e80a993af5a55baa0dfeae0465a9d45f99f'] - -builddependencies = [ - ('binutils', '2.34'), - ('Python', '3.8.2'), -] - -cmds_map = [('.*', "./configure.py --bootstrap")] - -files_to_copy = [(['ninja'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/ninja'], - 'dirs': [], -} - -sanity_check_commands = ["ninja --version"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/nanocompore/nanocompore-1.0.0rc3-2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/nanocompore/nanocompore-1.0.0rc3-2-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index def8bb1467c..00000000000 --- a/easybuild/easyconfigs/__archive__/n/nanocompore/nanocompore-1.0.0rc3-2-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,65 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'nanocompore' -version = '1.0.0rc3-2' -versionsuffix = "-Python-%(pyver)s" - -homepage = 'https://nanocompore.rna.rocks/' -description = "Nanocompore identifies differences in ONT nanopore " -description += "sequencing raw signal corresponding to RNA modifications by comparing 2 samples" - -toolchain = {'name': 'intel', 'version': '2020a'} - -builddependencies = [ - ('poetry', '1.0.9', versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('tqdm', '4.47.0'), - ('matplotlib', '3.2.1', versionsuffix), - ('Seaborn', '0.10.1', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('statsmodels', '0.11.1', versionsuffix), - ('PyYAML', '5.3'), -] - -# poetry has unnecessarily restrictive dependencies -local_nanocompore_preinstallopts = r"""sed -i'' 's/\^/>=/g' pyproject.toml && """ -local_nanocompore_preinstallopts += """sed -i'' 's/~/>=/g' pyproject.toml && """ - -# removing argparse from dependencies - it is part of python standard library since 3.6+ -local_bedparse_preinstallopts = """sed -i'' 's/argparse//' setup.py && """ - -exts_list = [ - ('pyfaidx', '0.5.9.1', { - 'checksums': ['eda8af04ba4da4fd63fdc35a62e0e41dfc06aa1a511728dfbdd7707e3b382855'], - }), - ('bedparse', '0.2.3', { - 'preinstallopts': local_bedparse_preinstallopts, - 'checksums': ['d1597b3de525a8d2e4ffe9ca73b2d6b59c1f54f0fe3ad248b42c2f36e50ce8f3'], - }), - (name, version, { - 'preinstallopts': local_nanocompore_preinstallopts, - 'source_tmpl': 'v1.0.0rc3-2.tar.gz', - 'source_urls': ['https://github.com/tleonardi/nanocompore/archive'], - 'checksums': ['a978bc955e5a672fddfc9561523909c69d5bd23d42ca9a3c50ddf77b19d187da'], - }), -] - -sanity_check_paths = { - 'files': ['bin/nanocompore'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - 'nanocompore -h', - # cannot use runtest in extension because import of the package is needed - # assertion of the tool's computation results fail, possibly because this - # has not been thought of in nanocompore source code (possible lack of support for python 3.5+) - # already created an issue https://github.com/tleonardi/nanocompore/issues/156 - # 'cd %%(builddir)s/%s/%s-%s/tests && pytest -vv' % (name, name, version) -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index d99fe25a560..00000000000 --- a/easybuild/easyconfigs/__archive__/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'MakeCp' - -name = 'nanopolish' -version = '0.13.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/jts/nanopolish' -description = "Software package for signal-level analysis of Oxford Nanopore sequencing data." - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://github.com/jts/nanopolish/archive/', - 'https://github.com/mateidavid/fast5/archive/', -] -sources = [ - {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, - {'download_filename': 'v0.6.5.tar.gz', 'filename': 'fast5-v0.6.5.tar.gz'}, -] -checksums = [ - # nanopolish-0.13.2.tar.gz - 'be9ab70ff0753519323e4cd0e6be50b164c4239bd9c20ffa5207c2d6fc20d120', - 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz -] - -builddependencies = [('Eigen', '3.3.7')] - -dependencies = [ - ('zlib', '1.2.11'), - ('Python', '3.8.2'), - ('Biopython', '1.78', versionsuffix), - ('Pysam', '0.16.0.1'), - ('HDF5', '1.10.6'), - ('HTSlib', '1.10.2'), - ('minimap2', '2.17'), -] - -prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " -buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall" - -runtest = 'test ' + buildopts - -files_to_copy = [(['nanopolish'], 'bin'), 'scripts'] - -postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"] - -sanity_check_paths = { - 'files': ['bin/nanopolish'], - 'dirs': ['scripts'], -} - -modextrapaths = {'PATH': 'scripts'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/n/ncbi-vdb/ncbi-vdb-2.10.7-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/n/ncbi-vdb/ncbi-vdb-2.10.7-gompi-2020a.eb deleted file mode 100644 index 6c2afb4fb51..00000000000 --- a/easybuild/easyconfigs/__archive__/n/ncbi-vdb/ncbi-vdb-2.10.7-gompi-2020a.eb +++ /dev/null @@ -1,49 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncbi-vdb' -version = '2.10.7' - -homepage = 'https://github.com/ncbi/ncbi-vdb' -description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for - using data in the INSDC Sequence Read Archives.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -github_account = 'ncbi' -source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -patches = ['ncbi-vdb-%(version)s_fix-LD_LIBRARY_PATH.patch'] -checksums = [ - 'ca8c87b7a852dca4cb44256bd05bc9353eac862a6158b2cfed75e81c7dbe3f22', # ncbi-vdb-2.10.7.tar.gz - 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch -] - -builddependencies = [('Perl', '5.30.2')] - -dependencies = [ - ('NGS', '2.10.5'), - ('file', '5.38'), # provides libmagic - ('HDF5', '1.10.6'), - ('libxml2', '2.9.10'), - ('bzip2', '1.0.8'), -] - -# add addtional libraries needed to statically link HDF5 from EB -preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl &&" - -configopts = "--build-prefix=%(builddir)s " # change default build directory -configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS/jar/ngs-java.jar " -configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" - -# replace hardcoded optimization flags with EB settings -prebuildopts = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " -preinstallopts = 'EBFLAGS="$CFLAGS" ' - -sanity_check_paths = { - 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + - [('lib/libncbi-%s.%s' % (x, e), 'lib64/libncbi-%s.%s' % (x, e)) - for x in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/n/ncdf4/ncdf4-1.17-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/n/ncdf4/ncdf4-1.17-foss-2020a-R-4.0.0.eb deleted file mode 100644 index d10dda330a5..00000000000 --- a/easybuild/easyconfigs/__archive__/n/ncdf4/ncdf4-1.17-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'RPackage' - -name = 'ncdf4' -version = '1.17' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/web/packages/%(name)s' -description = "ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6'] - -dependencies = [ - ('R', '4.0.0'), - ('netCDF', '4.7.4'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['ncdf4'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/n/ncdu/ncdu-1.15.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/ncdu/ncdu-1.15.1-GCCcore-9.3.0.eb deleted file mode 100644 index 2eb66659dcb..00000000000 --- a/easybuild/easyconfigs/__archive__/n/ncdu/ncdu-1.15.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'ConfigureMake' - -name = 'ncdu' -version = '1.15.1' - -homepage = 'https://dev.yorhel.nl/%(name)s' -description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a - remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular - desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like - environment with ncurses installed.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://dev.yorhel.nl/download/'] -sources = [SOURCE_TAR_GZ] -checksums = ['b02ddc4dbf1db139cc6fbbe2f54a282770380f0ca5c17089855eab52a9ea3fb0'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('ncurses', '6.2')] - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-FCC-4.5.0.eb deleted file mode 100644 index 04fddafce58..00000000000 --- a/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-FCC-4.5.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '6.2' - -homepage = 'https://www.gnu.org/software/ncurses/' -description = """ - The Ncurses (new curses) library is a free software emulation of curses in - System V Release 4.0, and more. It uses Terminfo format, supports pads and - color and multiple highlights and forms characters and function-key mapping, - and has all the other SYSV-curses enhancements over BSD Curses. -""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] - -builddependencies = [('binutils', '2.36.1')] - -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " -configopts = [ - # default build - local_common_configopts, - # the UTF-8 enabled version (ncursesw) - local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", -] - -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] - -local_libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb deleted file mode 100644 index e0ba575910a..00000000000 --- a/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '6.2' - -homepage = 'https://www.gnu.org/software/ncurses/' -description = """ - The Ncurses (new curses) library is a free software emulation of curses in - System V Release 4.0, and more. It uses Terminfo format, supports pads and - color and multiple highlights and forms characters and function-key mapping, - and has all the other SYSV-curses enhancements over BSD Curses. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] - -builddependencies = [('binutils', '2.34')] - -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " -configopts = [ - # build ncurses: serial build in default paths with shared libraries - local_common_configopts, - # build ncursesw: serial with UTF-8 - local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", -] - -# Symlink libtinfo to libncurses -# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for x in libncurses{.,_,w}*; do ln -s "${x}" "${x/ncurses/tinfo}"; done'] - -_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw -_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] -_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + - ['lib/libncurses++%s.a' % x for x in _target_suffix], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/n/ncview/ncview-2.1.8-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/n/ncview/ncview-2.1.8-gompi-2020a.eb deleted file mode 100644 index 0be266f955c..00000000000 --- a/easybuild/easyconfigs/__archive__/n/ncview/ncview-2.1.8-gompi-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -## -easyblock = 'ConfigureMake' - -name = 'ncview' -version = '2.1.8' - -homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' -description = """Ncview is a visual browser for netCDF format files. -Typically you would use ncview to get a quick and easy, push-button -look at your netCDF files. You can view simple movies of the data, -view along various dimensions, take a look at the actual data values, -change color maps, invert the data, etc.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] -sources = [SOURCE_TAR_GZ] -checksums = ['e8badc507b9b774801288d1c2d59eb79ab31b004df4858d0674ed0d87dfc91be'] - -# specified compiler is hard checked against (full path to) compiler used for netCDF... -preconfigopts = "CC=$(which $CC) " -configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " -configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" - -dependencies = [ - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), - ('UDUNITS', '2.2.26'), - ('X11', '20200222'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ['bin/ncview'], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/n/neptune-client/neptune-client-0.4.129-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/neptune-client/neptune-client-0.4.129-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 8a205ac11af..00000000000 --- a/easybuild/easyconfigs/__archive__/n/neptune-client/neptune-client-0.4.129-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,82 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'neptune-client' -version = '0.4.129' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://docs.neptune.ai' -description = """ -Neptune is an experiment tracking hub that brings organization and collaboration to your data science team. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('GitPython', '3.1.9', versionsuffix), - ('Pillow-SIMD', '7.1.2', versionsuffix), - ('PyYAML', '5.3'), -] - -exts_list = [ - ('jsonref', '0.2', { - 'checksums': ['f3c45b121cf6257eafabdc3a8008763aed1cd7da06dbabc59a9e4d2a5e4e6697'], - }), - ('pyrsistent', '0.14.11', { - 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], - }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('swagger-spec-validator', '2.7.3', { - 'checksums': ['f4f23ee4dbd52bfcde90b1144dde22304add6260e9f29252e9fd7814c9b8fd16'], - }), - ('bravado-core', '5.16.1', { - 'checksums': ['e2681d179d3b6baca3f34f43cd3c5af34f9b776328b6ed437b10ae8e3e2f8ced'], - }), - ('msgpack', '1.0.0', { - 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], - }), - ('simplejson', '3.17.0', { - 'checksums': ['2b4b2b738b3b99819a17feaf118265d0753d5536049ea570b3c43b51c4701e81'], - }), - ('monotonic', '1.5', { - 'checksums': ['23953d55076df038541e648a53676fb24980f7a1be290cdda21300b3bc21dfb0'], - }), - ('typing-extensions', '3.7.4.2', { - 'modulename': 'typing_extensions', - 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', - 'checksums': ['79ee589a3caca649a9bfd2a8de4709837400dfa00b6cc81962a1e6a1815969ae'], - }), - ('bravado', '11.0.2', { - 'checksums': ['4dd64288a5230f2a1333d65dee6a6774821338f8329eb56293f9f24c73e33ed8'], - }), - ('xmltodict', '0.12.0', { - 'checksums': ['50d8c638ed7ecb88d90561beedbf720c9b4e851a9fa6c47ebd64e99d166d8a21'], - }), - ('py3nvml', '0.2.6', { - 'checksums': ['98416c8b57136b81aba2007165f63717a10701f131347bfde7541524aba6d7cb'], - }), - ('PyJWT', '1.7.1', { - 'modulename': 'jwt', - 'checksums': ['8d59a976fb773f3e6a39c85636357c4f0e242707394cadadd9814f5cbaa20e96'], - }), - ('websocket_client', '0.57.0', { - 'modulename': 'websocket', - 'checksums': ['d735b91d6d1692a6a181f2a8c9e0238e5f6373356f561bb9dc4c7af36f452010'], - }), - ('oauthlib', '3.1.0', { - 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], - }), - ('requests-oauthlib', '1.3.0', { - 'modulename': 'requests_oauthlib', - 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], - }), - (name, version, { - 'modulename': 'neptune', - 'checksums': ['ddaf851a5c4ca22397b2dcafbcfd213f3264a76828b50acdc3f45034597c70f4'], - }), -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020a.eb deleted file mode 100644 index 751ca26705f..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020a.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'netCDF-C++4' -version = '4.3.1' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] - -dependencies = [('netCDF', '4.7.4')] - -sanity_check_paths = { - 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020a.eb deleted file mode 100644 index 9ea1a78c17f..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020a.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'netCDF-C++4' -version = '4.3.1' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] - -dependencies = [('netCDF', '4.7.4')] - -sanity_check_paths = { - 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.2-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.2-gompi-2020a.eb deleted file mode 100644 index 0dbf0787958..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.2-gompi-2020a.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'netCDF-Fortran' -version = '4.5.2' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['0b05c629c70d6d224a3be28699c066bfdfeae477aea211fbf034d973a8309b49'] - -builddependencies = [ - ('M4', '1.4.18'), -] - -dependencies = [('netCDF', '4.7.4')] - -# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) -maxparallel = 1 - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.2-gompic-2020a.eb b/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.2-gompic-2020a.eb deleted file mode 100644 index 14d517c7ead..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.2-gompic-2020a.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'netCDF-Fortran' -version = '4.5.2' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompic', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['0b05c629c70d6d224a3be28699c066bfdfeae477aea211fbf034d973a8309b49'] - -builddependencies = [ - ('M4', '1.4.18'), -] - -dependencies = [('netCDF', '4.7.4')] - -# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) -maxparallel = 1 - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2020a.eb deleted file mode 100644 index a4cb50c334e..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2020a.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'netCDF-Fortran' -version = '4.5.2' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['0b05c629c70d6d224a3be28699c066bfdfeae477aea211fbf034d973a8309b49'] - -builddependencies = [ - ('M4', '1.4.18'), -] - -dependencies = [('netCDF', '4.7.4')] - -# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) -maxparallel = 1 - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-gompi-2020a.eb deleted file mode 100644 index 3a526a4536d..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-gompi-2020a.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'netCDF' -version = '4.7.4' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['netCDF-%(version)s-fix-mpi-info-f2c.patch'] -checksums = [ - '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b', # v4.7.4.tar.gz - '7ff8a922ca3be35fca261a94f725abde32807f17c196c475053a570f03eb7396', # netCDF-4.7.4-fix-mpi-info-f2c.patch -] - -builddependencies = [ - ('Autotools', '20180311'), - ('CMake', '3.16.4'), - ('Doxygen', '1.8.17'), -] - -dependencies = [ - ('HDF5', '1.10.6'), - ('cURL', '7.69.1'), - ('Szip', '2.1.1'), -] - -# make sure both static and shared libs are built -configopts = [ - "-DBUILD_SHARED_LIBS=OFF ", - "-DBUILD_SHARED_LIBS=ON ", -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-gompic-2020a.eb b/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-gompic-2020a.eb deleted file mode 100644 index ec6fae398bc..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-gompic-2020a.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'netCDF' -version = '4.7.4' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompic', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['netCDF-%(version)s-fix-mpi-info-f2c.patch'] -checksums = [ - '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b', # v4.7.4.tar.gz - '7ff8a922ca3be35fca261a94f725abde32807f17c196c475053a570f03eb7396', # netCDF-4.7.4-fix-mpi-info-f2c.patch -] - -builddependencies = [ - ('Autotools', '20180311'), - ('CMake', '3.16.4'), - ('Doxygen', '1.8.17'), -] - -dependencies = [ - ('HDF5', '1.10.6'), - ('cURL', '7.69.1'), - ('Szip', '2.1.1'), -] - -# make sure both static and shared libs are built -configopts = [ - "-DBUILD_SHARED_LIBS=OFF ", - "-DBUILD_SHARED_LIBS=ON ", -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-iimpi-2020a.eb deleted file mode 100644 index aa9a82dfc22..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-iimpi-2020a.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'netCDF' -version = '4.7.4' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b'] - -builddependencies = [ - ('Autotools', '20180311'), - ('CMake', '3.16.4'), - ('Doxygen', '1.8.17'), -] - -dependencies = [ - ('HDF5', '1.10.6'), - ('cURL', '7.69.1'), - ('Szip', '2.1.1'), -] - -# make sure both static and shared libs are built -configopts = [ - "-DBUILD_SHARED_LIBS=OFF ", - "-DBUILD_SHARED_LIBS=ON ", -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-iompi-2020a.eb b/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-iompi-2020a.eb deleted file mode 100644 index 6ac63c3f2f3..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netCDF/netCDF-4.7.4-iompi-2020a.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'netCDF' -version = '4.7.4' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'iompi', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b'] - -builddependencies = [ - ('Autotools', '20180311'), - ('CMake', '3.16.4'), - ('Doxygen', '1.8.17'), -] - -dependencies = [ - ('HDF5', '1.10.6'), - ('cURL', '7.69.1'), - ('Szip', '2.1.1'), -] - -# make sure both static and shared libs are built -configopts = [ - "-DBUILD_SHARED_LIBS=OFF ", - "-DBUILD_SHARED_LIBS=ON ", -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index f870ad6f02b..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'netcdf4-python' -version = '1.5.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://unidata.github.io/netcdf4-python/' -description = """Python/numpy interface to netCDF.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy - ('netCDF', '4.7.4'), - ('cURL', '7.69.1'), -] - -exts_list = [ - ('cftime', '1.2.0', { - 'checksums': ['ff0a175edda260357ff7d24a32bbe0a8c72eafd5f6a404ce487127f9d01836db'], - }), - (name, version, { - 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], - 'source_tmpl': 'netCDF4-%(version)s.tar.gz', - 'checksums': [ - '2a3ca855848f4bbf07fac366da77a681fcead18c0a8813d91d46302f562dc3be', # netCDF4-1.5.3.tar.gz - # netcdf4-python-1.1.8-avoid-diskless-test.patch - 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', - ], - }), -] - -fix_python_shebang_for = ['bin/*'] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.3-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 49d63780d0c..00000000000 --- a/easybuild/easyconfigs/__archive__/n/netcdf4-python/netcdf4-python-1.5.3-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'netcdf4-python' -version = '1.5.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://unidata.github.io/netcdf4-python/' -description = """Python/numpy interface to netCDF.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy - ('netCDF', '4.7.4'), - ('cURL', '7.69.1'), -] - -exts_list = [ - ('cftime', '1.2.0', { - 'checksums': ['ff0a175edda260357ff7d24a32bbe0a8c72eafd5f6a404ce487127f9d01836db'], - }), - (name, version, { - 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], - 'source_tmpl': 'netCDF4-%(version)s.tar.gz', - 'checksums': [ - '2a3ca855848f4bbf07fac366da77a681fcead18c0a8813d91d46302f562dc3be', # netCDF4-1.5.3.tar.gz - # netcdf4-python-1.1.8-avoid-diskless-test.patch - 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', - ], - }), -] - -fix_python_shebang_for = ['bin/*'] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/n/nettle/nettle-3.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/nettle/nettle-3.6-GCCcore-9.3.0.eb deleted file mode 100644 index 00568388db8..00000000000 --- a/easybuild/easyconfigs/__archive__/n/nettle/nettle-3.6-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'nettle' -version = '3.6' - -homepage = 'https://www.lysator.liu.se/~nisse/nettle/' -description = """Nettle is a cryptographic library that is designed to fit easily - in more or less any context: In crypto toolkits for object-oriented - languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, - or even in kernel space.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['d24c0d0f2abffbc8f4f34dcf114b0f131ec3774895f3555922fe2f40f3d5e3f1'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), -] - -dependencies = [ - ('GMP', '6.2.0'), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - [('lib/libhogweed.a', 'lib64/libhogweed.a'), - ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), - ('lib/libnettle.a', 'lib64/libnettle.a'), - ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], - 'dirs': ['include/nettle'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/n/networkTools/networkTools-2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/networkTools/networkTools-2-GCC-9.3.0.eb deleted file mode 100644 index b30d88584fc..00000000000 --- a/easybuild/easyconfigs/__archive__/n/networkTools/networkTools-2-GCC-9.3.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -# # -# This is a contribution from HPCNow! (http://hpcnow.com) -# Copyright:: HPCNow! -# Authors:: Erica Bianco , Helena Gomez -# License:: GPL-v3.0 -# # - -easyblock = 'MakeCp' - -name = 'networkTools' -version = '2' - -homepage = 'http://faculty.scs.illinois.edu/schulten/software/networkTools/' -description = """Dynamical Network Analysis is a method of characterizing allosteric -signalling through biomolecular complexes.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['http://faculty.scs.illinois.edu/schulten/software/networkTools'] -sources = ['%(name)s.tgz'] -checksums = ['fb98a414b56ab8b5dc57d97c67961a4cf311fc99f296bab44420513ecae70863'] - -files_to_copy = [(['%(builddir)s/%(name)s/gncommunities'], 'bin'), (['%(builddir)s/%(name)s/subopt'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/gncommunities', 'bin/subopt'], - 'dirs': [] -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.4-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 05a8d774d8a..00000000000 --- a/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.4-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'networkx' -version = '2.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/networkx' -description = """NetworkX is a Python package for the creation, manipulation, -and study of the structure, dynamics, and functions of complex networks.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # required for numpy, scipy, ... -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.4-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.4-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index fbf5c235e0a..00000000000 --- a/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.4-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'networkx' -version = '2.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/networkx' -description = """NetworkX is a Python package for the creation, manipulation, -and study of the structure, dynamics, and functions of complex networks.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # required for numpy, scipy, ... -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.4-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.4-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 3cd2b458db8..00000000000 --- a/easybuild/easyconfigs/__archive__/n/networkx/networkx-2.4-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'networkx' -version = '2.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/networkx' -description = """NetworkX is a Python package for the creation, manipulation, -and study of the structure, dynamics, and functions of complex networks.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # required for numpy, scipy, ... -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/nglview/nglview-2.7.7-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/nglview/nglview-2.7.7-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 0ec7656d936..00000000000 --- a/easybuild/easyconfigs/__archive__/n/nglview/nglview-2.7.7-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'nglview' -version = '2.7.7' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/arose/nglview' -description = "IPython widget to interactively view molecular structures and trajectories." - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('IPython', '7.15.0', versionsuffix), -] - -exts_list = [ - ('widgetsnbextension', '3.5.1', { - 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], - }), - (name, version, { - 'checksums': ['fd84e20f0c1e183f2c429509c4a64b226e8591253545358062f48f3ec7dafddb'], - }), -] - -sanity_check_paths = { - 'files': ['bin/nglview'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/n/nodejs/nodejs-12.16.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/nodejs/nodejs-12.16.1-GCCcore-9.3.0.eb deleted file mode 100644 index 7caee6b0409..00000000000 --- a/easybuild/easyconfigs/__archive__/n/nodejs/nodejs-12.16.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'nodejs' -version = '12.16.1' # 12.16.1 was LTS on 2020-05-22 -local_libversion = '72' - -homepage = 'https://nodejs.org' -description = """Node.js is a platform built on Chrome's JavaScript runtime - for easily building fast, scalable network applications. Node.js uses an - event-driven, non-blocking I/O model that makes it lightweight and efficient, - perfect for data-intensive real-time applications that run across distributed devices.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://%(name)s.org/dist/v%(version)s/'] -sources = ['node-v%(version)s.tar.gz'] -checksums = ['4fe8c3454f9bee5bbe72d44aa25cd931859b3037b7a9473081b3b2bd1b465b95'] - -builddependencies = [ - ('binutils', '2.34'), - ('Python', '2.7.18'), -] - -configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run -] - -# Link libv8 libs to libnode -postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), -] - -sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], - 'dirs': ['lib/node_modules', 'include/node'] -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/n/nsync/nsync-1.24.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/nsync/nsync-1.24.0-GCCcore-9.3.0.eb deleted file mode 100644 index 21319bfbbbd..00000000000 --- a/easybuild/easyconfigs/__archive__/n/nsync/nsync-1.24.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'CMakeNinja' - -name = 'nsync' -version = '1.24.0' - -homepage = 'https://github.com/google/nsync' -description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/google/nsync/archive/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['47a6eb2a295be5121a1904a6a775722338a20dc02ee3eec4169ed2c3f203617a'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('Ninja', '1.10.0'), -] - -sanity_check_paths = { - 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/n/numactl/numactl-2.0.13-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/n/numactl/numactl-2.0.13-GCCcore-9.3.0.eb deleted file mode 100644 index 8bbab9492c6..00000000000 --- a/easybuild/easyconfigs/__archive__/n/numactl/numactl-2.0.13-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'numactl' -version = '2.0.13' - -homepage = 'https://github.com/numactl/numactl' - -description = """ - The numactl program allows you to run your application program on specific - cpu's and memory nodes. It does this by supplying a NUMA memory policy to - the operating system before running your program. The libnuma library provides - convenient ways for you to add NUMA memory policies into your own program. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/numactl/numactl/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['97ee012b2f294903530424b4ff7f28bcaad6a356897ce8777383f87e5c2e325d'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), -] - -preconfigopts = "./autogen.sh && " - -sanity_check_paths = { - 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], - 'dirs': ['share/man', 'include'] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/n/numba/llvmlite-0.30.0_fix-ffi-Makefile.patch b/easybuild/easyconfigs/__archive__/n/numba/llvmlite-0.30.0_fix-ffi-Makefile.patch deleted file mode 100644 index ba8332525af..00000000000 --- a/easybuild/easyconfigs/__archive__/n/numba/llvmlite-0.30.0_fix-ffi-Makefile.patch +++ /dev/null @@ -1,13 +0,0 @@ -Make sure easybuild libs are used for llvmlite -Author: Ariel Lozano (ULB) ---- a/ffi/Makefile.linux 2019-10-10 21:15:38.000000000 +0200 -+++ b/ffi/Makefile.linux 2019-11-13 12:22:07.061890000 +0100 -@@ -7,7 +7,7 @@ - - CXXFLAGS := $(CPPFLAGS) $(CXXFLAGS) $(LLVM_CXXFLAGS) $(CXX_FLTO_FLAGS) - LDFLAGS := $(LDFLAGS) $(LLVM_LDFLAGS) $(LD_FLTO_FLAGS) --LIBS = $(LLVM_LIBS) -+LIBS := $(LIBS) $(LLVM_LIBS) - INCLUDE = core.h - SRC = assembly.cpp bitcode.cpp core.cpp initfini.cpp module.cpp value.cpp \ - executionengine.cpp transforms.cpp passmanagers.cpp targets.cpp dylib.cpp \ diff --git a/easybuild/easyconfigs/__archive__/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index a6726acb9f0..00000000000 --- a/easybuild/easyconfigs/__archive__/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,48 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'PythonBundle' - -name = 'numba' -version = '0.50.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://numba.pydata.org/' -description = """Numba is an Open Source NumPy-aware optimizing compiler for -Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM -compiler infrastructure to compile Python syntax to machine code.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('LLVM', '9.0.1'), -] - -exts_list = [ - ('llvmlite', '0.33.0', { - 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], - 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", - 'checksums': [ - # llvmlite-0.31.0.tar.gz - '9c8aae96f7fba10d9ac864b443d1e8c7ee4765c31569a2b201b3d0b67d8fc596', - # llvmlite-0.31.0_fix-ffi-Makefile.patch - '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', - ], - }), - (name, version, { - 'checksums': ['c9e5752821530694294db41ee19a4b00e5826c689821907f6c2ece9a02756b29'], - }), -] - -fix_python_shebang_for = ['bin/*'] - -sanity_check_paths = { - 'files': ['bin/numba', 'bin/pycc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["numba --help"] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/n/numba/numba-0.50.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/numba/numba-0.50.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index e7f41cff219..00000000000 --- a/easybuild/easyconfigs/__archive__/n/numba/numba-0.50.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,51 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'PythonBundle' - -name = 'numba' -version = '0.50.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://numba.pydata.org/' -description = """Numba is an Open Source NumPy-aware optimizing compiler for -Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM -compiler infrastructure to compile Python syntax to machine code.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('LLVM', '9.0.1'), -] - -# required because we're building Python packages using Intel compilers on top of Python built with GCC -check_ldshared = True - -exts_list = [ - ('llvmlite', '0.33.0', { - 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], - 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", - 'checksums': [ - # llvmlite-0.31.0.tar.gz - '9c8aae96f7fba10d9ac864b443d1e8c7ee4765c31569a2b201b3d0b67d8fc596', - # llvmlite-0.31.0_fix-ffi-Makefile.patch - '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', - ], - }), - (name, version, { - 'checksums': ['c9e5752821530694294db41ee19a4b00e5826c689821907f6c2ece9a02756b29'], - }), -] - -fix_python_shebang_for = ['bin/*'] - -sanity_check_paths = { - 'files': ['bin/numba', 'bin/pycc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["numba --help"] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index f666a1a95a7..00000000000 --- a/easybuild/easyconfigs/__archive__/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,47 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'PythonBundle' - -name = 'numba' -version = '0.50.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://numba.pydata.org/' -description = """Numba is an Open Source NumPy-aware optimizing compiler for -Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM -compiler infrastructure to compile Python syntax to machine code.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('LLVM', '9.0.1'), -] - -exts_list = [ - ('llvmlite', '0.33.0', { - 'patches': ['llvmlite-0.30.0_fix-ffi-Makefile.patch'], - 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", - 'checksums': [ - '9c8aae96f7fba10d9ac864b443d1e8c7ee4765c31569a2b201b3d0b67d8fc596', # llvmlite-0.33.0.tar.gz - # llvmlite-0.30.0_fix-ffi-Makefile.patch - '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', - ], - }), - (name, version, { - 'checksums': ['89e81b51b880f9b18c82b7095beaccc6856fcf84ba29c4f0ced42e4e5748a3a7'], - }), -] - -fix_python_shebang_for = ['bin/*'] - -sanity_check_paths = { - 'files': ['bin/numba', 'bin/pycc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["numba --help"] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/n/numba/numba-0.52.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/numba/numba-0.52.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 486d8774ca1..00000000000 --- a/easybuild/easyconfigs/__archive__/n/numba/numba-0.52.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,47 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'PythonBundle' - -name = 'numba' -version = '0.52.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://numba.pydata.org/' -description = """Numba is an Open Source NumPy-aware optimizing compiler for -Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM -compiler infrastructure to compile Python syntax to machine code.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('LLVM', '9.0.1'), -] - -exts_list = [ - ('llvmlite', '0.35.0', { - 'patches': ['llvmlite-0.31.0_fix-ffi-Makefile.patch'], - 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", - 'checksums': [ - '80e51d5aa02ad72da9870e89d21f9b152b0220ca551b4596a6c0614bcde336fc', # llvmlite-0.35.0.tar.gz - # llvmlite-0.31.0_fix-ffi-Makefile.patch - '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', - ], - }), - (name, version, { - 'checksums': ['44661c5bd85e3d3619be0a40eedee34e397e9ccb3d4c458b70e10bf95d1ce933'], - }), -] - -fix_python_shebang_for = ['bin/*'] - -sanity_check_paths = { - 'files': ['bin/numba', 'bin/pycc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["numba --help"] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/n/numexpr/numexpr-2.7.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/numexpr/numexpr-2.7.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index fefaef0ab1b..00000000000 --- a/easybuild/easyconfigs/__archive__/n/numexpr/numexpr-2.7.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'numexpr' -version = '2.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://numexpr.readthedocs.io/en/latest/' -description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. - It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into - code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a - compiler at runtime.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/pydata/numexpr/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['5c6ae3bb5688184b922b43fc47de49d642576d0feec55a1b679caa66efae90a1'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/n/numexpr/numexpr-2.7.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/n/numexpr/numexpr-2.7.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 63851a07ed5..00000000000 --- a/easybuild/easyconfigs/__archive__/n/numexpr/numexpr-2.7.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'numexpr' -version = '2.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://numexpr.readthedocs.io/en/latest/' -description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. - It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into - code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a - compiler at runtime.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/pydata/numexpr/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['5c6ae3bb5688184b922b43fc47de49d642576d0feec55a1b679caa66efae90a1'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/n/numpy/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/__archive__/n/numpy/numpy-1.12.0-mkl.patch deleted file mode 100644 index 3d09924f966..00000000000 --- a/easybuild/easyconfigs/__archive__/n/numpy/numpy-1.12.0-mkl.patch +++ /dev/null @@ -1,55 +0,0 @@ -fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries -by Kenneth Hoste (HPC-UGent) -diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py ---- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 -@@ -628,7 +628,10 @@ - return options - - def library_option(self, lib): -- return "-l" + lib -+ if lib[0]=='-': -+ return lib -+ else: -+ return "-l" + lib - def library_dir_option(self, dir): - return "-L" + dir - -diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py ---- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 -@@ -675,7 +675,7 @@ - if is_string(default): - return [default] - return default -- return [b for b in [a.strip() for a in libs.split(',')] if b] -+ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] - - def get_libraries(self, key='libraries'): - if hasattr(self, '_lib_names'): -@@ -756,6 +756,9 @@ - # make sure we preserve the order of libs, as it can be important - found_dirs, found_libs = [], [] - for lib in libs: -+ if lib[0] == '-': -+ found_libs.append(lib) -+ continue - for lib_dir in lib_dirs: - found_lib = self._find_lib(lib_dir, lib, exts) - if found_lib: -diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py ---- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 -@@ -123,3 +123,12 @@ - - replace_method(UnixCCompiler, 'create_static_lib', - UnixCCompiler_create_static_lib) -+ -+def UnixCCompiler_library_option(self, lib): -+ if lib[0]=='-': -+ return lib -+ else: -+ return "-l" + lib -+ -+replace_method(UnixCCompiler, 'library_option', -+ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-2.0.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-2.0.5-GCCcore-9.3.0.eb deleted file mode 100644 index cec6a1c4ee2..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-2.0.5-GCCcore-9.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany -# Authors:: Bernd Mohr -# Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'ConfigureMake' - -name = 'OPARI2' -version = '2.0.5' - -homepage = 'https://www.score-p.org' -description = """ - OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a - source-to-source instrumentation tool for OpenMP and hybrid codes. - It surrounds OpenMP directives and runtime library calls with calls - to the POMP2 measurement interface. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.vi-hps.org/cms/upload/packages/opari2/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = [ - '9034dd7596ac2176401090fd5ced45d0ab9a9404444ff767f093ccce68114ef5', # opari2-2.0.5.tar.gz -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], - 'dirs': [], -} - -sanity_check_commands = ['opari2-config --help'] - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OPERA-MS/OPERA-MS-0.9.0-20200802-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OPERA-MS/OPERA-MS-0.9.0-20200802-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index a551767bee9..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OPERA-MS/OPERA-MS-0.9.0-20200802-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,63 +0,0 @@ -easyblock = 'MakeCp' - -name = 'OPERA-MS' -local_commit = 'c18b4f3' -version = '0.9.0-20200802' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/CSB5/OPERA-MS' -description = """OPERA-MS is a hybrid metagenomic assembler which combines the - advantages of short and long-read technologies to provide high quality - assemblies, addressing issues of low contiguity for short-read only assemblies, - and low base-pair quality for long-read only assemblies.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/CSB5/OPERA-MS/archive/'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['fa2caa223e1cd54d26cf650b96fef7c92ced016204deedd120c9844a51656a6d'] - -dependencies = [ - ('Perl', '5.30.2'), - ('Statistics-R', '0.34'), - ('Python', '3.8.2'), -] - -buildopts = 'CFLAGS="$CFLAGS"' - -files_to_copy = [ - 'OPERA-MS.pl', - 'bin', - 'src_utils', - 'tools_opera_ms', - (['OPERA-LG/bin'], 'OPERA-LG'), -] - -postinstallcmds = [ - "echo '#!/bin/sh\n exec perl %(installdir)s/OPERA-MS.pl $@' > %(installdir)s/bin/OPERA-MS", - 'chmod +x %(installdir)s/bin/OPERA-MS', - 'ln -s $EBROOTPERL/bin/perl %(installdir)s/tools_opera_ms/perl', - '%(installdir)s/bin/OPERA-MS ' + ' '.join([ - '--contig-file test_files/contigs.fasta', - '--short-read1 test_files/R1.fastq.gz', - '--short-read2 test_files/R2.fastq.gz', - '--long-read test_files/long_read.fastq', - '--no-ref-clustering', - '--out-dir $TMPDIR', - ]), -] - -fix_perl_shebang_for = ['bin/*.pl', 'OPERA-MS.pl', 'OPERA-LG/bin/*.pl'] -fix_python_shebang_for = ['bin/*.py', 'OPERA-LG/bin/*.py'] - -sanity_check_paths = { - 'files': ['bin/OPERA-MS'], - 'dirs': [], -} - -sanity_check_commands = [ - 'OPERA-MS --help', - 'OPERA-MS check-dependency', -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb deleted file mode 100644 index 41bb5469e0f..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OSU-Micro-Benchmarks' -version = '5.6.3' - -homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' -description = """OSU Micro-Benchmarks""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] - -local_benchmark_dirs = [ - 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] -] -modextrapaths = {'PATH': local_benchmark_dirs} - -sanity_check_paths = { - 'files': [], - 'dirs': local_benchmark_dirs, -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb deleted file mode 100644 index 97a07efe746..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OSU-Micro-Benchmarks' -version = '5.6.3' - -homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' -description = """OSU Micro-Benchmarks""" - -toolchain = {'name': 'gompic', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] - -configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA' - -local_benchmark_dirs = [ - 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] -] -modextrapaths = {'PATH': local_benchmark_dirs} - -sanity_check_paths = { - 'files': [], - 'dirs': local_benchmark_dirs, -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb deleted file mode 100644 index 3583eab1477..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OSU-Micro-Benchmarks' -version = '5.6.3' - -homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' -description = """OSU Micro-Benchmarks""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] - -local_benchmark_dirs = [ - 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] -] -modextrapaths = {'PATH': local_benchmark_dirs} - -sanity_check_paths = { - 'files': [], - 'dirs': local_benchmark_dirs, -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb deleted file mode 100644 index ec8aaa2a8b9..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OSU-Micro-Benchmarks' -version = '5.6.3' - -homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' -description = """OSU Micro-Benchmarks""" - -toolchain = {'name': 'iimpic', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] - -configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA' - -local_benchmark_dirs = [ - 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] -] -modextrapaths = {'PATH': local_benchmark_dirs} - -sanity_check_paths = { - 'files': [], - 'dirs': local_benchmark_dirs, -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb deleted file mode 100644 index d5dc6602bbc..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OSU-Micro-Benchmarks' -version = '5.7.1' - -homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' -description = """OSU Micro-Benchmarks""" - -toolchain = {'name': 'ffmpi', 'version': '4.5.0'} -toolchainopts = {'usempi': True} - -source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] -sources = [SOURCELOWER_TGZ] -checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] - -local_benchmark_dirs = [ - 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] -] -modextrapaths = {'PATH': local_benchmark_dirs} - -sanity_check_paths = { - 'files': [], - 'dirs': local_benchmark_dirs, -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-2.2-GCCcore-9.3.0.eb deleted file mode 100644 index 75ec06996ed..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-2.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany -# Authors:: Bernd Mohr -# Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_Score_minus_P' - -name = 'OTF2' -version = '2.2' - -homepage = 'https://www.score-p.org' -description = """ - The Open Trace Format 2 is a highly scalable, memory efficient event trace - data format plus support library. It is the new standard trace format for - Scalasca, Vampir, and TAU and is open for other tools. - -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.vi-hps.org/cms/upload/packages/otf2/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = [ - 'd0519af93839dc778eddca2ce1447b1ee23002c41e60beac41ea7fe43117172d', # otf2-2.2.tar.gz -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.34'), -] - -dependencies = [ - # SIONlib container support (optional): - ('SIONlib', '1.7.6', '-tools'), -] - -# set $PYTHON_FOR_GENERATOR to ':' to disable Python support (since we're not included Python 2.x as dependency) -preconfigopts = "export PYTHON_FOR_GENERATOR=':' && " - -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/otf2-config', 'include/otf2/otf2.h', - 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], - 'dirs': [], -} - -sanity_check_commands = ['otf2-config --help'] - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/o/Open-Data-Cube-Core/Open-Data-Cube-Core-1.8.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/Open-Data-Cube-Core/Open-Data-Cube-Core-1.8.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 3fe37438d6f..00000000000 --- a/easybuild/easyconfigs/__archive__/o/Open-Data-Cube-Core/Open-Data-Cube-Core-1.8.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,59 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Open-Data-Cube-Core' -version = '1.8.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/opendatacube/datacube-core' -description = """ -The Open Data Cube Core provides an integrated gridded data analysis -environment for decades of analysis ready earth observation satellite and -related data from multiple satellite and other acquisition systems.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('dask', '2.18.1', versionsuffix), # provides dask, distributed and toolz - ('netcdf4-python', '1.5.3', versionsuffix), - ('psycopg2', '2.8.6', versionsuffix), - ('pyproj', '2.6.1.post1', versionsuffix), - ('PyYAML', '5.3'), - ('rasterio', '1.1.7', versionsuffix), # provides rasterio and affine - ('Shapely', '1.7.1', versionsuffix), - ('xarray', '0.16.1', versionsuffix), -] - -exts_list = [ - ('cachetools', '4.1.1', { - 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], - }), - ('cloudpickle', '1.4.1', { - 'checksums': ['0b6258a20a143603d53b037a20983016d4e978f554ec4f36b3d0895b947099ae'], - }), - ('pyrsistent', '0.17.3', { - 'checksums': ['2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e'], - }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('lark-parser', '0.9.0', { - 'checksums': ['9e7589365d6b6de1cca40b0eaec31104a3fb96a37a11a9dfd5098e95b50aa6cd'], - 'modulename': 'lark', - }), - ('SQLAlchemy', '1.3.20', { - 'checksums': ['d2f25c7f410338d31666d7ddedfa67570900e248b940d186b48461bd4e5569a1'], - }), - ('datacube', version, { - 'checksums': ['d1e1a49c615fdaebf6e6008da7f925bc09e9d7bf94f259a1c596d266d1c36649'], - }), -] - -sanity_check_paths = { - 'files': ['bin/datacube%s' % x - for x in ['', '-fixer', '-ncml', '-search', '-simple-replica', '-stacker', '-worker']], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch b/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch deleted file mode 100644 index cc556272dd6..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch +++ /dev/null @@ -1,23 +0,0 @@ -This fixes inexact calculations on POWER, see https://github.com/xianyi/OpenBLAS/issues/2923 -From https://github.com/xianyi/OpenBLAS/pull/3062 - -Backported by Alexander Grund (TU Dresden) - ---- - param.h | 6 ++++++ - 1 file changed, 6 insertions(+) - -diff --git a/param.h b/param.h -index 6c5e0f107b..6a790ab615 100644 ---- a/param.h -+++ b/param.h -@@ -2239,6 +2239,9 @@ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - #define GEMM_DEFAULT_OFFSET_B 65536 - #define GEMM_DEFAULT_ALIGN 0x0ffffUL - -+#define SWITCH_RATIO 16 -+#define GEMM_PREFERED_SIZE 16 -+ - #define SGEMM_DEFAULT_UNROLL_M 16 - #define SGEMM_DEFAULT_UNROLL_N 8 - #define DGEMM_DEFAULT_UNROLL_M 16 diff --git a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch b/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch deleted file mode 100644 index 191ed747bb4..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch +++ /dev/null @@ -1,22 +0,0 @@ -From c9d32674eaa2602184c2719dde15ac3fbebf41b7 Mon Sep 17 00:00:00 2001 -From: Martin Kroeker -Date: Sun, 9 Aug 2020 19:17:04 +0200 -Subject: [PATCH] Add memory barrier to the blas_lock implementation for Linux - -as recommended by cparrott73 in #2760 ---- - common_power.h | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/common_power.h b/common_power.h -index aa19794b5..e0685f760 100644 ---- a/common_power.h -+++ b/common_power.h -@@ -105,6 +105,7 @@ static void INLINE blas_lock(volatile unsigned long *address){ - " bne- 1f\n" - " stwcx. %2,0, %1\n" - " bne- 0b\n" -+ " isync\n" - "1: " - : "=&r"(ret) - : "r"(address), "r" (val) diff --git a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch b/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch deleted file mode 100644 index a4075d8535d..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch +++ /dev/null @@ -1,50 +0,0 @@ -From 3094fc6c83c7a623f9a7e7846eb711a8a99ddfff Mon Sep 17 00:00:00 2001 -From: Alexander Grund -Date: Thu, 1 Oct 2020 15:41:42 +0200 -Subject: [PATCH] Lazyly reinit threads after a fork in OMP mode - -This initializes the per-thread memory buffers which get -cleared/released on a fork via pthread_at_fork. Not doing so leads to -each thread calling blas_memory_alloc on almost every execution which -slows down the code significantly as the threads race for the memory -allocation using locks to serialize that. ---- - driver/others/blas_server_omp.c | 18 ++++++++++++++++++ - 1 file changed, 18 insertions(+) - -diff --git a/driver/others/blas_server_omp.c b/driver/others/blas_server_omp.c -index d126955e4..da0a5674a 100644 ---- a/driver/others/blas_server_omp.c -+++ b/driver/others/blas_server_omp.c -@@ -48,6 +48,21 @@ - - #else - -+#ifndef likely -+#ifdef __GNUC__ -+#define likely(x) __builtin_expect(!!(x), 1) -+#else -+#define likely(x) (x) -+#endif -+#endif -+#ifndef unlikely -+#ifdef __GNUC__ -+#define unlikely(x) __builtin_expect(!!(x), 0) -+#else -+#define unlikely(x) (x) -+#endif -+#endif -+ - #ifndef OMP_SCHED - #define OMP_SCHED static - #endif -@@ -350,6 +365,9 @@ static void exec_threads(blas_queue_t *queue, int buf_index){ - - int exec_blas(BLASLONG num, blas_queue_t *queue){ - -+ // Handle lazy re-init of the thread-pool after a POSIX fork -+ if (unlikely(blas_server_avail == 0)) blas_thread_init(); -+ - BLASLONG i, buf_index; - - if ((num <= 0) || (queue == NULL)) return 0; diff --git a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb deleted file mode 100644 index 0e4b7e6439e..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -name = 'OpenBLAS' -version = '0.3.9' - -homepage = 'https://xianyi.github.com/OpenBLAS/' -description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = [ - # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble - 'https://www.netlib.org/lapack/timing/', - 'https://github.com/xianyi/OpenBLAS/archive/', -] -sources = ['v%(version)s.tar.gz'] -patches = [ - ('large.tgz', '.'), - ('timing.tgz', '.'), - '%(name)s-0.3.7_add-missing-params-for-power.patch', - '%(name)s-0.3.7_fix-missing-sync-on-power.patch', - '%(name)s-0.3.7_reinit-threads-after-fork.patch', - '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', - '%(name)s-%(version)s_fix-lapack_h.patch', -] -checksums = [ - '17d4677264dfbc4433e97076220adc79b050e4f8a083ea3f853a53af253bc380', # v0.3.9.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.7_add-missing-params-for-power.patch - '969ac4708092a6862cd9a03541c5c0588b191513d15492b022319daed5a1cd89', - # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch - 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', - # OpenBLAS-0.3.7_reinit-threads-after-fork.patch - 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', - # OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch - '4b3ab7260975ea2cfd7460731c0201b2c1e374cd83ae90d55b8da3e670633ba0', - '9210a94ae418b4ce6d9f7fab4e00dd3155451f5ef3769536a4d954a2149ca733', # OpenBLAS-0.3.9_fix-lapack_h.patch -] - -builddependencies = [ - ('make', '4.3'), -] - -# extensive testing can be enabled by uncommenting the line below -# runtest = 'PATH=.:$PATH lapack-timing' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.9_fix-lapack_h.patch b/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.9_fix-lapack_h.patch deleted file mode 100644 index e4fc0d416d4..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.3.9_fix-lapack_h.patch +++ /dev/null @@ -1,73 +0,0 @@ -From ee2e758278b5d82b7242f505ea694f082ef65879 Mon Sep 17 00:00:00 2001 -From: Martin Kroeker -Date: Fri, 13 Mar 2020 20:34:13 +0100 -Subject: [PATCH] Move declarations of lapack_complex_custom types outside the - extern C - -fixes #2510 ---- - lapack-netlib/LAPACKE/include/lapack.h | 44 ++++++++++++++------------ - 1 file changed, 23 insertions(+), 21 deletions(-) - -diff --git a/lapack-netlib/LAPACKE/include/lapack.h b/lapack-netlib/LAPACKE/include/lapack.h -index 0a6226fe4..36e53ec24 100644 ---- a/lapack-netlib/LAPACKE/include/lapack.h -+++ b/lapack-netlib/LAPACKE/include/lapack.h -@@ -12,27 +12,6 @@ - - #include - --#ifdef __cplusplus --extern "C" { --#endif -- --/*----------------------------------------------------------------------------*/ --#ifndef lapack_int --#define lapack_int int --#endif -- --#ifndef lapack_logical --#define lapack_logical lapack_int --#endif -- --/* f2c, hence clapack and MacOS Accelerate, returns double instead of float -- * for sdot, slange, clange, etc. */ --#if defined(LAPACK_F2C) -- typedef double lapack_float_return; --#else -- typedef float lapack_float_return; --#endif -- - /* Complex types are structures equivalent to the - * Fortran complex types COMPLEX(4) and COMPLEX(8). - * -@@ -88,6 +67,29 @@ extern "C" { - - #endif /* LAPACK_COMPLEX_CUSTOM */ - -+ -+#ifdef __cplusplus -+extern "C" { -+#endif -+ -+/*----------------------------------------------------------------------------*/ -+#ifndef lapack_int -+#define lapack_int int -+#endif -+ -+#ifndef lapack_logical -+#define lapack_logical lapack_int -+#endif -+ -+/* f2c, hence clapack and MacOS Accelerate, returns double instead of float -+ * for sdot, slange, clange, etc. */ -+#if defined(LAPACK_F2C) -+ typedef double lapack_float_return; -+#else -+ typedef float lapack_float_return; -+#endif -+ -+ - /* Callback logical functions of one, two, or three arguments are used - * to select eigenvalues to sort to the top left of the Schur form. - * The value is selected if function returns TRUE (non-zero). */ diff --git a/easybuild/easyconfigs/__archive__/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb deleted file mode 100644 index 27cd59d0004..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,61 +0,0 @@ -name = 'OpenBabel' -version = '3.1.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://openbabel.org' -description = """Open Babel is a chemical toolbox designed to speak the many - languages of chemical data. It's an open, collaborative project allowing anyone - to search, convert, analyze, or store data from molecular modeling, chemistry, - solid-state materials, biochemistry, or related areas.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] -patches = [ - # Fix test failure with Python 3 - # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch - 'OpenBabel-3.1.1_fix-distgeom-test.patch', - 'OpenBabel-3.1.1_fix-testobconv_writers.patch', - 'OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch', -] -checksums = [ - 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz - '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch - '6d0b153caadc53141e1578972d632afb82b2fc4abdec6c5f07552b45a20e980c', # OpenBabel-3.1.1_fix-testobconv_writers.patch - # OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch - 'cc0396b38a78ef70c869cd93887210c64d6f4293c016aec9269b5a0230fdb51c', -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('SWIG', '4.0.1'), -] -dependencies = [ - ('Python', '3.8.2'), - ('zlib', '1.2.11'), - ('libxml2', '2.9.10'), - ('Eigen', '3.3.7'), - ('RapidJSON', '1.1.0'), - ('cairo', '1.16.0'), # optional: for .png output - ('Boost', '1.72.0'), - ('maeparser', '1.3.0'), - ('CoordgenLibs', '3.0.1'), -] - -configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' -# Enable support for OpenMP compilation of forcefield code (optional) -configopts += '-DENABLE_OPENMP=ON ' - -# OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR -# (set in the easyblock) having invalid values. Work around this with some symlinks. -postinstallcmds = [ - 'ln -s %(installdir)s/lib/openbabel/3.1.0 %(installdir)s/lib/openbabel/%(version)s', - 'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s', -] - -pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT -runtest = 'test' - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/o/OpenBabel/OpenBabel-3.1.1_fix-testobconv_writers.patch b/easybuild/easyconfigs/__archive__/o/OpenBabel/OpenBabel-3.1.1_fix-testobconv_writers.patch deleted file mode 100644 index 967ae059019..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenBabel/OpenBabel-3.1.1_fix-testobconv_writers.patch +++ /dev/null @@ -1,23 +0,0 @@ -fix broken test by tweaking floating point value that is slightly off -see also https://github.com/openbabel/openbabel/issues/2246 -author: Kenneth Hoste (HPC-UGent) ---- openbabel-openbabel-3-1-1/test/testobconv_writers.py.orig 2022-01-12 20:12:01.480069896 +0100 -+++ openbabel-openbabel-3-1-1/test/testobconv_writers.py 2022-01-12 20:12:12.180174159 +0100 -@@ -2876,7 +2876,7 @@ - 2.4146659588503769, - 4.189331679349326, - 4.052466878708012, -- -1.4648575597102012 -+ -1.4648575597102014 - ], - "y": [ - 1.5846, -@@ -2891,7 +2891,7 @@ - 2.4146659588503769, - 4.189331679349326, - 4.052466878708012, -- -1.4648575597102012 -+ -1.4648575597102014 - ], - "style": { - "annotation": [ diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb deleted file mode 100644 index 3a3d84de760..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb +++ /dev/null @@ -1,69 +0,0 @@ -name = 'OpenCV' -version = '4.2.0' -versionsuffix = '-Python-%(pyver)s-contrib' - -# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake -local_ippicv_hash = '32e315a5b106a7b89dbed51c28f8120a48b368b4' - -homepage = 'https://opencv.org/' -description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision - and machine learning software library. OpenCV was built to provide - a common infrastructure for computer vision applications and to accelerate - the use of machine perception in the commercial products. - Includes extra modules for OpenCV from the contrib repository.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [ - {'source_urls': ['https://github.com/opencv/opencv/archive/'], - 'download_filename': '%(version)s.zip', 'filename': SOURCELOWER_ZIP}, - {'source_urls': ['https://github.com/opencv/opencv_contrib/archive/'], - 'download_filename': '%(version)s.zip', 'filename': '%(namelower)s_contrib-%(version)s.zip'}, - {'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], - 'filename': 'ippicv_2019_lnx_intel64_general_20180723.tgz', 'extract_cmd': "cp %s %(builddir)s"}, -] -checksums = [ - '55bd939079d141a50fca74bde5b61b339dd0f0ece6320ec76859aaff03c90d9f', # opencv-4.2.0.zip - 'a4c0b1fb169a68085f7deefdeca8429aafadf3e1798abec0c1a1a7fc83e11a69', # opencv_contrib-4.2.0.zip - 'fc167cb60deb8924339a7050f3da168bb02e221b2d6b8c00139d1fa7eace0c7d', # ippicv_2019_lnx_intel64_general_20180723.tgz -] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # for numpy - ('zlib', '1.2.11'), - ('FFmpeg', '4.2.2'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('libwebp', '1.1.0'), - ('OpenEXR', '2.4.1'), - ('JasPer', '2.0.14'), - ('Java', '11', '', SYSTEM), - ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), - ('GLib', '2.64.1'), - ('GTK+', '3.24.17'), - ('HDF5', '1.10.6'), # needed by hdf from contrib -] - -configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules' - -enhance_sanity_check = True - -local_contrib_libs = [ - 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', - 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', - 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', - 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' -] - -sanity_check_paths = { - 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index bb85b7a793f..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,48 +0,0 @@ -name = 'OpenCV' -version = '4.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://opencv.org/' -description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision - and machine learning software library. OpenCV was built to provide - a common infrastructure for computer vision applications and to accelerate - the use of machine perception in the commercial products.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://github.com/opencv/opencv/archive/', - # the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake - 'https://raw.githubusercontent.com/opencv/opencv_3rdparty/32e315a5b106a7b89dbed51c28f8120a48b368b4/ippicv', -] -sources = [ - '%(version)s.zip', - {'filename': 'ippicv_2019_lnx_intel64_general_20180723.tgz', 'extract_cmd': "cp %s %(builddir)s"}, -] -checksums = [ - '55bd939079d141a50fca74bde5b61b339dd0f0ece6320ec76859aaff03c90d9f', # 4.2.0.zip - 'fc167cb60deb8924339a7050f3da168bb02e221b2d6b8c00139d1fa7eace0c7d', # ippicv_2019_lnx_intel64_general_20180723.tgz -] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy - ('zlib', '1.2.11'), - ('FFmpeg', '4.2.2'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('libwebp', '1.1.0'), - ('OpenEXR', '2.4.1'), - ('JasPer', '2.0.14'), - ('Java', '11', '', SYSTEM), - ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), - ('GLib', '2.64.1'), - ('GTK+', '3.24.17'), -] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/o/OpenCoarrays/OpenCoarrays-2.2.0-cafrun-OpenMPI-mpiexec.patch b/easybuild/easyconfigs/__archive__/o/OpenCoarrays/OpenCoarrays-2.2.0-cafrun-OpenMPI-mpiexec.patch deleted file mode 100644 index f7df9974c2d..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenCoarrays/OpenCoarrays-2.2.0-cafrun-OpenMPI-mpiexec.patch +++ /dev/null @@ -1,14 +0,0 @@ -# - Replaces the call to system-wide mpiexec by the mpiexec from EASYBUILD -# -# author: Jiri Furst ---- OpenCoarrays-2.2.0.orig/src/extensions/cafrun.in 2018-08-12 21:57:19.475509128 +0200 -+++ OpenCoarrays-2.2.0/src/extensions/cafrun.in 2018-08-12 22:00:21.411583642 +0200 -@@ -55,7 +55,7 @@ - # - - caf_version='@CAF_VERSION@' --CAFRUN="@MPIEXEC@" -+CAFRUN=$EBROOTOPENMPI/bin/mpiexec - if [[ "${CAFRUN}" == @*@ ]]; then - CAFRUN=mpiexec - fi diff --git a/easybuild/easyconfigs/__archive__/o/OpenCoarrays/OpenCoarrays-2.9.2-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/o/OpenCoarrays/OpenCoarrays-2.9.2-gompi-2020a.eb deleted file mode 100644 index 9f32611938d..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenCoarrays/OpenCoarrays-2.9.2-gompi-2020a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenCoarrays' -version = '2.9.2' - -homepage = 'https://github.com/sourceryinstitute/opencoarrays' -description = """OpenCoarrays is an open-source software project that supports -the coarray Fortran (CAF) parallel programming features of the Fortran 2008 -standard and several features proposed for Fortran 2015 in the draft Technical -Specification TS 18508 Additional Parallel Features in Fortran.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/sourceryinstitute/opencoarrays/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -patches = ['OpenCoarrays-2.2.0-cafrun-OpenMPI-mpiexec.patch'] -checksums = [ - '6c200ca49808c75b0a2dfa984304643613b6bc77cc0044bee093f9afe03698f7', # OpenCoarrays-2.9.2.tar.gz - # OpenCoarrays-2.2.0-cafrun-OpenMPI-mpiexec.patch - '5d410cc78c80dfa54237f874a0627260ad0b4b2f272d8f0f9ce317375bcc796f', -] - -separate_build_dir = True - -builddependencies = [('CMake', '3.16.4')] - -sanity_check_paths = { - 'files': ['bin/caf', 'bin/cafrun', 'include/opencoarrays.mod', ('lib/libcaf_mpi.a', 'lib64/libcaf_mpi.a')], - 'dirs': [], -} - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/o/OpenEXR/OpenEXR-2.4.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/o/OpenEXR/OpenEXR-2.4.1-GCCcore-9.3.0.eb deleted file mode 100644 index 868b39021a3..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenEXR/OpenEXR-2.4.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenEXR' -version = '2.4.1' - -homepage = 'https://www.openexr.com/' -description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic - for use in computer imaging applications""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/openexr/openexr/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['3ebbe9a8e67edb4a25890b98c598e9fe23b10f96d1416d6a3ff0732e99d001c1'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' - -sanity_check_paths = { - 'files': ['lib/lib%s-%%(version_major)s_%%(version_minor)s.%s' % (x, SHLIB_EXT) for x in - ['Half', 'Iex', 'IexMath', 'IlmImf', 'IlmImfUtil', 'IlmThread', 'Imath']] + - ['bin/exr%s' % x for x in - ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']], - 'dirs': ['include/OpenEXR', 'share'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-8-foss-2020a.eb b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-8-foss-2020a.eb deleted file mode 100644 index 96f51b4a579..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-8-foss-2020a.eb +++ /dev/null @@ -1,40 +0,0 @@ -name = 'OpenFOAM' -version = '8' - -homepage = 'https://www.openfoam.org/' -description = """OpenFOAM is a free, open source CFD software package. - OpenFOAM has an extensive range of features to solve anything from complex fluid flows - involving chemical reactions, turbulence and heat transfer, - to solid dynamics and electromagnetics.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'cstd': 'c++11'} - -source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] -sources = ['version-%(version)s.tar.gz'] -patches = [ - 'OpenFOAM-%(version)s-cleanup.patch', -] -checksums = [ - '94ba11cbaaa12fbb5b356e01758df403ac8832d69da309a5d79f76f42eb008fc', # version-8.tar.gz - 'e3fac8049611ee109f07eb5b0ed4b1526782a21b3f12435e03529d56c8483b9f', # OpenFOAM-8-cleanup.patch -] - -dependencies = [ - ('libreadline', '8.0'), - ('ncurses', '6.2'), - # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) - ('METIS', '5.1.0'), - ('SCOTCH', '6.0.9'), - ('CGAL', '4.14.3', '-Python-3.8.2'), - ('ParaView', '5.8.0', '-Python-3.8.2-mpi'), - ('gnuplot', '5.2.8'), -] - -builddependencies = [ - ('Bison', '3.5.3'), - ('CMake', '3.16.4'), - ('flex', '2.6.4'), -] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006-cleanup.patch b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006-cleanup.patch deleted file mode 100644 index 83fc1fc99be..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006-cleanup.patch +++ /dev/null @@ -1,244 +0,0 @@ -# - Replace the OpenFOAM third-party libraries with EASYBUILD variables. -# - Set install dir, compiler, etc using EASYBUILD -# -# authors: Ward Poelmans , Kenneth Hoste (HPC-UGent), Mark Olesen , -# Simon Branford (University of Birmingham) ---- OpenFOAM-v2006/etc/bashrc.orig 2020-06-17 09:50:41.597725494 +0200 -+++ OpenFOAM-v2006/etc/bashrc 2020-06-30 15:56:06.646000167 +0200 -@@ -87,7 +87,7 @@ - # = SYSTEMOPENMPI | OPENMPI | SYSTEMMPI | MPI | MPICH | MPICH-GM | - # HPMPI | CRAY-MPICH | FJMPI | QSMPI | SGIMPI | INTELMPI | USERMPI - # Also possible to use INTELMPI-xyz etc and define your own wmake rule --export WM_MPLIB=SYSTEMOPENMPI -+export WM_MPLIB=EASYBUILDMPI - - - #------------------------------------------------------------------------------ ---- OpenFOAM-v2006/etc/config.sh/CGAL.orig 2020-06-05 16:25:51.180144612 +0200 -+++ OpenFOAM-v2006/etc/config.sh/CGAL 2020-06-30 15:58:42.238053513 +0200 -@@ -43,33 +43,9 @@ - #------------------------------------------------------------------------------ - # USER EDITABLE PART: Changes made here may be lost with the next upgrade - --boost_version=boost_1_66_0 --cgal_version=CGAL-4.12.2 -- --export BOOST_ARCH_PATH="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$boost_version" --export CGAL_ARCH_PATH="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cgal_version" -+##EasyBuild## settings -+export BOOST_ARCH_PATH="$EBROOTBOOST" -+export CGAL_ARCH_PATH="$EBROOTCGAL" - - # END OF (NORMAL) USER EDITABLE PART - #------------------------------------------------------------------------------ --if [ -n "$FOAM_VERBOSE" ] && [ -n "$PS1" ] --then -- echo "Using boost ($boost_version) -> $BOOST_ARCH_PATH" 1>&2 -- echo "Using CGAL ($cgal_version) -> $CGAL_ARCH_PATH" 1>&2 --fi -- --if command -v _foamAddLibAuto >/dev/null # Normal sourcing (not makeCGAL) --then -- _foamAddLibAuto $BOOST_ARCH_PATH lib$WM_COMPILER_LIB_ARCH -- _foamAddLibAuto $CGAL_ARCH_PATH lib$WM_COMPILER_LIB_ARCH -- -- # GMP/MPFR may have already been added with ThirdParty compiler, but cannot -- # be certain so add here. Any duplicates will be removed later. -- -- _foamAddLibAuto $GMP_ARCH_PATH # No fallback libdir -- _foamAddLibAuto $MPFR_ARCH_PATH # No fallback libdir -- -- unset boost_version cgal_version -- --fi -- --#------------------------------------------------------------------------------ ---- OpenFOAM-v2006/etc/config.sh/FFTW.orig 2020-06-16 23:00:24.789061285 +0200 -+++ OpenFOAM-v2006/etc/config.sh/FFTW 2020-06-30 15:59:10.966063364 +0200 -@@ -35,23 +35,8 @@ - #------------------------------------------------------------------------------ - # USER EDITABLE PART: Changes made here may be lost with the next upgrade - --fftw_version=fftw-3.3.7 --export FFTW_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$fftw_version -+##EasyBuild## settings -+export FFTW_ARCH_PATH="$EBROOTFFTW" - - # END OF (NORMAL) USER EDITABLE PART - #------------------------------------------------------------------------------ --if [ -n "$FOAM_VERBOSE" ] && [ -n "$PS1" ] --then -- echo "Using fftw ($fftw_version) -> $FFTW_ARCH_PATH" 1>&2 --fi -- --if command -v _foamAddLibAuto >/dev/null # Normal sourcing (not makeFFTW) --then -- -- _foamAddLibAuto $FFTW_ARCH_PATH lib$WM_COMPILER_LIB_ARCH -- -- unset fftw_version -- --fi -- --#------------------------------------------------------------------------------ ---- OpenFOAM-v2006/etc/config.sh/metis.orig 2020-05-15 09:54:01.540288016 +0200 -+++ OpenFOAM-v2006/etc/config.sh/metis 2020-06-30 16:00:13.954084959 +0200 -@@ -34,8 +34,9 @@ - #------------------------------------------------------------------------------ - # USER EDITABLE PART: Changes made here may be lost with the next upgrade - --METIS_VERSION=metis-5.1.0 --export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION -+##Easybuild## settings -+METIS_VERSION="metis-$EBVERSIONMETIS" -+[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH="$METIS_ROOT" - - # END OF (NORMAL) USER EDITABLE PART - #------------------------------------------------------------------------------ ---- OpenFOAM-v2006/etc/config.sh/mpi.orig 2020-06-05 16:10:11.232814840 +0200 -+++ OpenFOAM-v2006/etc/config.sh/mpi 2020-06-30 16:00:36.982092855 +0200 -@@ -95,6 +95,10 @@ - _foamEtc -config mpi-user # <- Adjustments (optional) - ;; - -+EASYBUILDMPI) -+ export FOAM_MPI=mpi -+ ;; -+ - SYSTEMMPI) - export FOAM_MPI=mpi-system - _foamEtc -config mpi-system # <- Adjustments (optional) ---- OpenFOAM-v2006/etc/config.sh/paraview.orig 2020-05-22 21:53:42.378012246 +0200 -+++ OpenFOAM-v2006/etc/config.sh/paraview 2020-06-30 16:03:36.766154495 +0200 -@@ -57,7 +57,8 @@ - #------------------------------------------------------------------------------ - # USER EDITABLE PART: Changes made here may be lost with the next upgrade - --ParaView_VERSION=5.6.3 -+##Easybuild## settings -+ParaView_VERSION="$EBVERSIONPARAVIEW" - ParaView_QT=qt-system - - # END OF (NORMAL) USER EDITABLE PART -@@ -124,7 +125,8 @@ - ;; - esac - -- export ParaView_DIR="$archDir/ParaView-$ParaView_VERSION" -+ ##Easybuild## settings -+ export ParaView_DIR="$EBROOTPARAVIEW" - pv_plugin_dir="$FOAM_LIBBIN/paraview-$pv_api" - - # Set paths if binaries are present -@@ -132,26 +134,6 @@ - then - export PATH="$ParaView_DIR/bin:$PATH" - -- # QT libraries as required, and Qt5_DIR for the root directory. -- # Another possibility: "qtpaths --qt-version" -- qtDir="$archDir/$ParaView_QT" -- if [ -d "$qtDir" ] -- then -- case "$ParaView_QT" in -- (*-5*) -- export Qt5_DIR="$qtDir" -- ;; -- esac -- for libDir in "lib$WM_COMPILER_LIB_ARCH" "lib" -- do -- if [ -d "$qtDir/$libDir" ] -- then -- export LD_LIBRARY_PATH="$qtDir/$libDir:$LD_LIBRARY_PATH" -- break -- fi -- done -- fi -- - # ParaView libraries - # - 5.4 and earlier: lib/paraview-X.X - # - 5.5 and later: lib/, but could also be lib64/ ---- OpenFOAM-v2006/etc/config.sh/scotch.orig 2020-05-15 09:54:01.568287943 +0200 -+++ OpenFOAM-v2006/etc/config.sh/scotch 2020-06-30 16:01:02.414101574 +0200 -@@ -34,8 +34,10 @@ - #------------------------------------------------------------------------------ - # USER EDITABLE PART: Changes made here may be lost with the next upgrade - --SCOTCH_VERSION=scotch_6.0.9 --export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION -+##Easybuild## settings -+export SCOTCH_VERSION="scotch_$EBVERSIONSCOTCH" -+export SCOTCH_ARCH_PATH="$EBROOTSCOTCH" -+[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH="$SCOTCH_ROOT" - - # END OF (NORMAL) USER EDITABLE PART - #------------------------------------------------------------------------------ ---- OpenFOAM-v2006/etc/config.sh/vtk.orig 2020-04-08 10:31:42.745647922 +0200 -+++ OpenFOAM-v2006/etc/config.sh/vtk 2020-06-30 16:01:31.054111393 +0200 -@@ -34,53 +34,12 @@ - #------------------------------------------------------------------------------ - # USER EDITABLE PART: Changes made here may be lost with the next upgrade - --vtk_version=VTK-8.2.0 --mesa_version=mesa-17.1.1 --mesa_llvm=none -- --export VTK_DIR="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$vtk_version" --export MESA_ARCH_PATH="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$mesa_version" --export LLVM_ARCH_PATH="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH/$mesa_llvm" -+##Easybuild## settings -+export VTK_DIR="$EBROOTVTK" -+export MESA_ARCH_PATH="$EBROOTMESA" - - # Define paraview-mesa directory as required - unset ParaView_MESA_DIR - - # END OF (NORMAL) USER EDITABLE PART - #------------------------------------------------------------------------------ --if [ -n "$FOAM_VERBOSE" ] && [ -n "$PS1" ] --then -- echo "Using vtk" 1>&2 -- echo " vtk ($vtk_version) $VTK_DIR" 1>&2 -- echo " mesa ($mesa_version) $MESA_ARCH_PATH" 1>&2 -- echo " llvm ($mesa_llvm) $LLVM_ARCH_PATH" 1>&2 -- if [ -d "$ParaView_MESA_DIR" ] -- then -- echo " paraview-mesa $ParaView_MESA_DIR" 1>&2 -- fi --fi -- --if command -v _foamAddLib >/dev/null # normal sourcing --then -- -- # Set paths if binaries are present -- if [ -d "$VTK_DIR" ] -- then -- # Uses lib/ and not lib64/ -- _foamAddLib "$VTK_DIR/lib" -- else -- unset VTK_DIR -- fi -- -- if [ -d "$MESA_ARCH_PATH" ] -- then -- _foamAddLibAuto "$LLVM_ARCH_PATH" -- _foamAddLibAuto "$MESA_ARCH_PATH" -- else -- unset LLVM_ARCH_PATH -- unset MESA_ARCH_PATH -- fi -- -- unset vtk_version mesa_version mesa_llvm --fi -- --#------------------------------------------------------------------------------ ---- OpenFOAM-v2006/wmake/scripts/have_readline.orig 2020-06-19 10:09:30.056141135 +0200 -+++ OpenFOAM-v2006/wmake/scripts/have_readline 2020-06-30 15:57:13.618023129 +0200 -@@ -108,7 +108,7 @@ - # Output as per search_* function - have_readline() - { -- search_readline system -+ search_readline "$EBROOTLIBREADLINE" - } - - diff --git a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006-foss-2020a.eb b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006-foss-2020a.eb deleted file mode 100644 index 3202ebc6c41..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006-foss-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -name = 'OpenFOAM' -version = 'v2006' - -homepage = 'https://www.openfoam.com/' -description = """OpenFOAM is a free, open source CFD software package. - OpenFOAM has an extensive range of features to solve anything from complex fluid flows - involving chemical reactions, turbulence and heat transfer, - to solid dynamics and electromagnetics.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'cstd': 'c++11'} - -source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] -sources = [SOURCE_TGZ] -patches = [ - 'OpenFOAM-%(version)s-cleanup.patch', - 'OpenFOAM-v1906-wmake-ompi.patch', -] -checksums = [ - '30c6376d6f403985fc2ab381d364522d1420dd58a42cb270d2ad86f8af227edc', # OpenFOAM-v2006.tgz - 'cb3c6d26569cf11d22941963acb9741238fe829f21b452506a51a71b5c42ae84', # OpenFOAM-v2006-cleanup.patch - '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch -] - -dependencies = [ - ('libreadline', '8.0'), - ('ncurses', '6.2'), - # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) - ('METIS', '5.1.0'), - ('SCOTCH', '6.0.9'), - ('CGAL', '4.14.3', '-Python-3.8.2'), - ('ParaView', '5.8.0', '-Python-3.8.2-mpi'), - ('gnuplot', '5.2.8'), -] - -builddependencies = [ - ('Bison', '3.5.3'), - ('CMake', '3.16.4'), - ('flex', '2.6.4'), -] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb deleted file mode 100644 index 0ca9926c885..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb +++ /dev/null @@ -1,45 +0,0 @@ -name = 'OpenFOAM' -version = 'v2006' - -homepage = 'https://www.openfoam.com/' -description = """OpenFOAM is a free, open source CFD software package. - OpenFOAM has an extensive range of features to solve anything from complex fluid flows - involving chemical reactions, turbulence and heat transfer, - to solid dynamics and electromagnetics.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'cstd': 'c++11'} - -source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] -sources = [SOURCE_TGZ] -patches = [ - 'OpenFOAM-%(version)s-cleanup.patch', - 'OpenFOAM-v1906-wmake-ompi.patch', - 'OpenFOAM-%(version)s_fix-setAlphaField-compilation.patch', -] -checksums = [ - '30c6376d6f403985fc2ab381d364522d1420dd58a42cb270d2ad86f8af227edc', # OpenFOAM-v2006.tgz - 'cb3c6d26569cf11d22941963acb9741238fe829f21b452506a51a71b5c42ae84', # OpenFOAM-v2006-cleanup.patch - '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch - # OpenFOAM-v2006_fix-setAlphaField-compilation.patch - 'ce7ed531f75ca9ee404963736d8140df62d766bdfeeba469777f1bf44b5aa8bc', -] - -dependencies = [ - ('libreadline', '8.0'), - ('ncurses', '6.2'), - # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) - ('METIS', '5.1.0'), - ('SCOTCH', '6.0.9'), - ('CGAL', '4.14.3', '-Python-3.8.2'), - ('ParaView', '5.8.0', '-Python-3.8.2-mpi'), - ('gnuplot', '5.2.8'), -] - -builddependencies = [ - ('Bison', '3.5.3'), - ('CMake', '3.16.4'), - ('flex', '2.6.4'), -] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006_fix-setAlphaField-compilation.patch b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006_fix-setAlphaField-compilation.patch deleted file mode 100644 index 1a099c53c4e..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2006_fix-setAlphaField-compilation.patch +++ /dev/null @@ -1,81 +0,0 @@ -fix compilation error for setAlphaField with intel/2020a -obtained via https://develop.openfoam.com/Development/openfoam/-/commit/719d3f77bea23bbdb9c530ee2dde09383f03bc71.patch - -From 719d3f77bea23bbdb9c530ee2dde09383f03bc71 Mon Sep 17 00:00:00 2001 -From: Mark Olesen -Date: Tue, 1 Sep 2020 09:32:13 +0200 -Subject: [PATCH] COMP: Intel compiler bug with inheriting constructors (fixes - #1821) - -- the compiler reports - - Internal error loop: assertion failed: - find_seq_in_lookup_table: seq_number not found - (shared/cfe/edgcpfe/il.c, line 4118) - - Seems to be the same as the bug report - https://community.intel.com/t5/Intel-C-Compiler/Internal-error-loop-assertion-failed-find-seq-in-lookup-table/td-p/1087603 - -This _should_ be fixed in icc 17.0 update 1, but appears to have -struck here as well. - -- workaround: explicitly construct member elements. ---- - .../cylinder/cylinderImplicitFunction.C | 13 ++++++------- - .../implicitFunctions/sin/sinImplicitFunction.C | 16 +++++++--------- - 2 files changed, 13 insertions(+), 16 deletions(-) - -diff --git a/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/cylinder/cylinderImplicitFunction.C b/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/cylinder/cylinderImplicitFunction.C -index 909087e473..1c68b7fef2 100644 ---- a/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/cylinder/cylinderImplicitFunction.C -+++ b/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/cylinder/cylinderImplicitFunction.C -@@ -69,13 +69,12 @@ Foam::implicitFunctions::cylinderImplicitFunction::cylinderImplicitFunction - const dictionary& dict - ) - : -- cylinderImplicitFunction -- ( -- dict.get("origin"), -- dict.get("radius"), -- dict.getOrDefault("scale", 1), -- dict.get("direction") -- ) -+ // __INTEL_COMPILER bug with inheriting constructors?? (issue #1821) -+ origin_(dict.get("origin")), -+ radius_(dict.get("radius")), -+ scale_(dict.getOrDefault("scale", 1)), -+ direction_(dict.get("direction").normalise()), -+ project_(tensor::I - direction_*direction_) // outer product - {} - - -diff --git a/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/sin/sinImplicitFunction.C b/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/sin/sinImplicitFunction.C -index a193d2b663..4256baad94 100644 ---- a/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/sin/sinImplicitFunction.C -+++ b/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/sin/sinImplicitFunction.C -@@ -72,15 +72,13 @@ Foam::implicitFunctions::sinImplicitFunction::sinImplicitFunction - const dictionary& dict - ) - : -- sinImplicitFunction -- ( -- dict.get("period"), -- dict.getOrDefault("phase", 0), -- dict.get("amplitude"), -- dict.get("direction"), -- dict.get("up"), -- dict.get("origin") -- ) -+ // __INTEL_COMPILER bug with inheriting constructors?? (issue #1821) -+ period_(dict.get("period")), -+ phase_(dict.getOrDefault("phase", 0)), -+ amplitude_(dict.get("amplitude")), -+ up_(dict.get("up").normalise()), -+ direction_(dict.get("direction").normalise()), -+ origin_(dict.get("origin")) - {} - - --- -GitLab - diff --git a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2012-foss-2020a.eb b/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2012-foss-2020a.eb deleted file mode 100644 index 4175eafa1f7..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenFOAM/OpenFOAM-v2012-foss-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -name = 'OpenFOAM' -version = 'v2012' - -homepage = 'https://www.openfoam.com/' -description = """OpenFOAM is a free, open source CFD software package. - OpenFOAM has an extensive range of features to solve anything from complex fluid flows - involving chemical reactions, turbulence and heat transfer, - to solid dynamics and electromagnetics.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'cstd': 'c++11'} - -source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] -sources = [SOURCE_TGZ] -patches = [ - ('OpenFOAM-%(version)s-cleanup.patch', 1), - 'OpenFOAM-v1906-wmake-ompi.patch', -] -checksums = [ - '3d6e39e39e7ae61d321fbc6db6c3748e6e5e1c4886454207a7f1a7321469e65a', # OpenFOAM-v2012.tgz - 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch - '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch -] - -dependencies = [ - ('libreadline', '8.0'), - ('ncurses', '6.2'), - # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) - ('METIS', '5.1.0'), - ('SCOTCH', '6.0.9'), - ('CGAL', '4.14.3', '-Python-3.8.2'), - ('ParaView', '5.8.0', '-Python-3.8.2-mpi'), - ('gnuplot', '5.2.8'), -] - -builddependencies = [ - ('Bison', '3.5.3'), - ('CMake', '3.16.4'), - ('flex', '2.6.4'), -] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/o/OpenForceField/OpenForceField-0.7.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OpenForceField/OpenForceField-0.7.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index a7effc5cd7e..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenForceField/OpenForceField-0.7.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,49 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonBundle' - -name = 'OpenForceField' -version = '0.7.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/openforcefield/openforcefield/releases' -description = """Simulation and Parameter Estimation in Geophysics -- A python package for simulation and gradient based parameter estimation in the context of geophysical applications.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('networkx', '2.4', versionsuffix), - ('ParmEd', '3.2.0', versionsuffix), - ('RDKit', '2020.03.3', versionsuffix), - ('OpenMMTools', '0.20.0', versionsuffix), - ('netcdf4-python', '1.5.3', versionsuffix), - ('AmberMini', '16.16.0'), - ('PyYAML', '5.3'), -] - -exts_list = [ - ('bson', '0.5.10', { - 'checksums': ['d6511b2ab051139a9123c184de1a04227262173ad593429d21e443d6462d6590'], - }), - ('msgpack-python', '0.5.6', { - 'modulename': 'msgpack', - 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], - }), - ('xmltodict', '0.12.0', { - 'checksums': ['50d8c638ed7ecb88d90561beedbf720c9b4e851a9fa6c47ebd64e99d166d8a21'], - }), - (name, version, { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/openforcefield/openforcefield/archive/'], - 'checksums': [('a87642d1e4dd2192602a2b4fccb6c7764cb43df51a4fd845c2c3cd2a3220389d', - 'c66d9cdf80fb2049ec7dc94394d515f87ca93963ad6db4e5e47a2515ef4d6928')], - }), -] - -runtest = "cd %(builddir)s && pytest", - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb deleted file mode 100644 index 5633288a7b4..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenImageIO' -version = '2.1.12.0' - -homepage = 'https://openimageio.org/' -description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, - and applications.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] -sources = ['Release-%(version)s.tar.gz'] -checksums = ['da27e191349ef473220c7a373921e6d4c69d9924acd87140af55ce9d00ad58f8'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('git', '2.23.0', '-nodocs'), -] -dependencies = [ - ('Boost', '1.72.0'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('OpenEXR', '2.4.1'), - ('freetype', '2.10.1'), - ('zlib', '1.2.11'), -] - -separate_build_dir = True - -configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF' - -sanity_check_paths = { - 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], - 'dirs': ['include/OpenImageIO', 'share'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb deleted file mode 100644 index 1b4a71fcf97..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenImageIO' -version = '2.1.12.0' - -homepage = 'https://openimageio.org/' -description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, - and applications.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} - -source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] -sources = ['Release-%(version)s.tar.gz'] -checksums = ['da27e191349ef473220c7a373921e6d4c69d9924acd87140af55ce9d00ad58f8'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('git', '2.23.0', '-nodocs'), -] -dependencies = [ - ('Boost', '1.72.0'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0'), - ('OpenEXR', '2.4.1'), - ('freetype', '2.10.1'), - ('zlib', '1.2.11'), -] - -separate_build_dir = True - -configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF' - -sanity_check_paths = { - 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], - 'dirs': ['include/OpenImageIO', 'share'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-9.3.0.eb deleted file mode 100644 index 03c0cff2e86..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -# easybuild easyconfig -# -# John Dey jfdey@fredhutch.org -# -# Fred Hutchenson Cancer Research Center Seattle WA -easyblock = 'CMakeMake' - -name = 'OpenJPEG' -version = '2.4.0' - -homepage = 'https://www.openjpeg.org/' -description = """OpenJPEG is an open-source JPEG 2000 codec written in - C language. It has been developed in order to promote the use of JPEG 2000, - a still-image compression standard from the Joint Photographic Experts Group - (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as - a JPEG 2000 Reference Software.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/uclouvain/openjpeg/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['8702ba68b442657f11aaeb2b338443ca8d5fb95b0d845757968a7be31ef7f16d'] - -separate_build_dir = True - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4') -] - -# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. -dependencies = [ - ('zlib', '1.2.11'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.1.0') -] - -sanity_check_paths = { - 'files': ['bin/opj_compress', - 'bin/opj_decompress', - 'bin/opj_dump', - 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', - 'lib/libopenjp2.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include', 'lib'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMM-PLUMED/OpenMM-PLUMED-1.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OpenMM-PLUMED/OpenMM-PLUMED-1.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index f986a9d2fc8..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMM-PLUMED/OpenMM-PLUMED-1.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,48 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenMM-PLUMED' -version = '1.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/openmm/openmm-plumed/' -description = """This project provides a connection between OpenMM and -PLUMED. It allows you to bias or analyze an OpenMM simulation based on -collective variables.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -# https://github.com/openmm/openmm-plumed/archive/refs/tags/v1.0.tar.gz -github_account = 'openmm' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['97cbffab7a452a3c8f0b00c301c9a796b752ee73e30dc5c1b2435678dd7c73ed'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('SWIG', '4.0.1'), -] -dependencies = [ - ('Python', '3.8.2'), - ('OpenMM', '7.4.2', versionsuffix), - ('PLUMED', '2.6.0', versionsuffix), -] - -separate_build_dir = True - -configopts = '-DPLUMED_INCLUDE_DIR="$EBROOTPLUMED/include/plumed" ' -configopts += '-DPLUMED_LIBRARY_DIR="$EBROOTPLUMED/lib" ' -configopts += '-DOPENMM_DIR="$EBROOTOPENMM" ' - -installopts = ' && make -f python/CMakeFiles/PythonInstall.dir/build.make python/PlumedPluginWrapper.cpp' -installopts += ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' - -sanity_check_paths = { - 'files': ['include/PlumedForce.h', 'include/PlumedKernels.h', - 'lib/libOpenMMPlumed.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/openmmplumed.py'], - 'dirs': [], -} - -sanity_check_commands = ['python -c "from openmmplumed import PlumedForce"'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.4.1_fix-Doxygen.patch b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.4.1_fix-Doxygen.patch deleted file mode 100644 index 735fab55324..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.4.1_fix-Doxygen.patch +++ /dev/null @@ -1,42 +0,0 @@ -fix build errors when using Doxygen 1.8.16 like: - OpenMMSwigHeaders.i:12: Error: Bad $descriptor() macro. -see https://github.com/openmm/openmm/issues/2420 and https://github.com/openmm/openmm/pull/2460 -diff --git a/plugins/amoeba/wrappers/Doxyfile.in b/plugins/amoeba/wrappers/Doxyfile.in -index a35fd31b7..1fd04e509 100644 ---- a/plugins/amoeba/wrappers/Doxyfile.in -+++ b/plugins/amoeba/wrappers/Doxyfile.in -@@ -581,7 +581,7 @@ INPUT_ENCODING = UTF-8 - # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx - # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 - --FILE_PATTERNS = -+FILE_PATTERNS = *.h - - # The RECURSIVE tag can be used to turn specify whether or not subdirectories - # should be searched for input files as well. Possible values are YES and NO. -diff --git a/wrappers/Doxyfile.in b/wrappers/Doxyfile.in -index 76f74cfc6..ce7b7a8c4 100644 ---- a/wrappers/Doxyfile.in -+++ b/wrappers/Doxyfile.in -@@ -582,7 +582,7 @@ INPUT_ENCODING = UTF-8 - # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx - # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 - --FILE_PATTERNS = -+FILE_PATTERNS = *.h - - # The RECURSIVE tag can be used to turn specify whether or not subdirectories - # should be searched for input files as well. Possible values are YES and NO. -diff --git a/wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in b/wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in -index a1e664ae6..c835beeb9 100644 ---- a/wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in -+++ b/wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in -@@ -588,7 +588,7 @@ INPUT_ENCODING = UTF-8 - # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx - # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 - --FILE_PATTERNS = -+FILE_PATTERNS = *.h - - # The RECURSIVE tag can be used to turn specify whether or not subdirectories - # should be searched for input files as well. Possible values are YES and NO. diff --git a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.4.2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.4.2-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 4a90679db20..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.4.2-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,60 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'CMakeMake' - -name = 'OpenMM' -version = '7.4.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://openmm.org' -description = "OpenMM is a toolkit for molecular simulation." - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'opt': True} - -source_urls = ['https://github.com/openmm/openmm/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['OpenMM-7.4.1_fix-Doxygen.patch'] -checksums = [ - '2e121ad5cfcc4840861032bb1b11d4d0aea2d3ca3c59baaed73b8b0b4fd069cc', # 7.4.2.tar.gz - '99d59e3106d9c9f9fbce3c3161117a37b2699e1dc09bc2a75619e0d880f29708', # OpenMM-7.4.1_fix-Doxygen.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Doxygen', '1.8.17'), -] - -separate_build_dir = True - -dependencies = [ - ('FFTW', '3.3.8'), - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('SWIG', '4.0.1'), -] - -runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ - -preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' -preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' - -# required to install the python API -installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' - -sanity_check_paths = { - 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], - 'dirs': [] -} - -sanity_check_commands = ["python -m simtk.testInstallation"] - -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 18e347268ee..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,60 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'CMakeMake' - -name = 'OpenMM' -version = '7.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://openmm.org' -description = "OpenMM is a toolkit for molecular simulation." - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'opt': True} - -source_urls = ['https://github.com/openmm/openmm/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix_path_to_nvcc.patch'] -checksums = [ - '516748b4f1ae936c4d70cc6401174fc9384244c65cd3aef27bc2c53eac6d6de5', # 7.5.0.tar.gz - '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Doxygen', '1.8.17'), -] - -separate_build_dir = True - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('SWIG', '4.0.1'), -] - -local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)|(OpenCL)" -runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern - -preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' -preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' - -# required to install the python API -installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' - -sanity_check_paths = { - 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], - 'dirs': [] -} - -sanity_check_commands = ["python -m simtk.testInstallation"] - -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 69255d00cbf..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMM/OpenMM-7.5.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,56 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'CMakeMake' - -name = 'OpenMM' -version = '7.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://openmm.org' -description = "OpenMM is a toolkit for molecular simulation." - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'strict': True} - -source_urls = ['https://github.com/openmm/openmm/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['516748b4f1ae936c4d70cc6401174fc9384244c65cd3aef27bc2c53eac6d6de5'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Doxygen', '1.8.17'), -] - -separate_build_dir = True - -dependencies = [ - ('FFTW', '3.3.8'), - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('SWIG', '4.0.1'), -] - -runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ - -preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' -preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' - -# required to install the python API -installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' - -sanity_check_paths = { - 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], - 'dirs': [] -} - -sanity_check_commands = ["python -m simtk.testInstallation"] - -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMMTools/OpenMMTools-0.20.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OpenMMTools/OpenMMTools-0.20.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 912e64c840b..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMMTools/OpenMMTools-0.20.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,74 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonBundle' - -name = 'OpenMMTools' -version = '0.20.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/choderalab/openmmtools' -description = """A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine. -openmmtools is a Python library layer that sits on top of OpenMM to provide access to a variety of useful tools -for building full-featured molecular simulation packages. -""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('OpenMM', '7.4.2', versionsuffix), - ('netcdf4-python', '1.5.3', versionsuffix), - ('MDTraj', '1.9.4', versionsuffix), - ('PyYAML', '5.3'), -] - -exts_list = [ - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('pyrsistent', '0.16.0', { - 'checksums': ['28669905fe725965daa16184933676547c5bb40a5153055a8dee2a4bd7933ad3'], - }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('jupyter_core', '4.6.3', { - 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], - }), - ('traitlets', '4.3.3', { - 'checksums': ['d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7'], - }), - ('nbformat', '5.0.7', { - 'checksums': ['54d4d6354835a936bad7e8182dcd003ca3dc0cedfee5a306090e04854343b340'], - }), - ('mpiplus', '0.0.1', { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/choderalab/mpiplus/archive/'], - 'checksums': ['a3d50157a274decab87589ad78b9e41e9f3d34eb27a7d50cc6e7ef34def98b44'], - }), - ('sortedcontainers', '2.2.2', { - 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], - }), - ('hypothesis', '5.20.0', { - 'checksums': ['50a69d6ab99e3c027c67e217654b33f41c499ba5a05e5d386ef12dd6b8f13c40'], - }), - (name, version, { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/choderalab/openmmtools/archive/'], - 'checksums': ['05cfa136b7ca16418f156724c8ab9199b89d25dd9f92133108796034563ca685'], - # import check requires use of mpirun, handled via sanity_check_commands - 'modulename': False, - }), -] - -sanity_check_paths = { - 'files': ['bin/test-openmm-platforms'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(namelower)s'"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb deleted file mode 100644 index c6e650ef6e6..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'OpenMPI' -version = '4.0.3' - -homepage = 'https://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-3 implementation.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', - 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', - 'OpenMPI-4.x_fix_pmix_discovery.patch', -] -checksums = [ - '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz - # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch - 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, - '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch -] - -dependencies = [ - ('zlib', '1.2.11'), - ('hwloc', '2.2.0'), - ('libevent', '2.1.11'), - ('UCX', '1.8.0'), - ('libfabric', '1.11.0'), - ('PMIx', '3.1.5'), -] - -# disable MPI1 compatibility for now, see what breaks... -# configopts = '--enable-mpi1-compatibility ' - -# to enable SLURM integration (site-specific) -# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb deleted file mode 100644 index 6eb936f50ad..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb +++ /dev/null @@ -1,36 +0,0 @@ -name = 'OpenMPI' -version = '4.0.3' - -homepage = 'https://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-3 implementation.""" - -toolchain = {'name': 'gcccuda', 'version': '2020a'} - -source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', - 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', - 'OpenMPI-4.x_fix_pmix_discovery.patch', -] -checksums = [ - '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz - # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch - 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, - '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch -] - -dependencies = [ - ('zlib', '1.2.11'), - ('hwloc', '2.2.0'), - ('libevent', '2.1.11'), - ('UCX', '1.8.0', '-CUDA-11.0.2'), - ('libfabric', '1.11.0'), - ('PMIx', '3.1.5'), -] - -# to enable SLURM integration (site-specific) -# configopts = '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb deleted file mode 100644 index 435d229f4f0..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'OpenMPI' -version = '4.0.3' - -homepage = 'https://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-3 implementation.""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', - 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', - 'OpenMPI-4.x_fix_pmix_discovery.patch', -] -checksums = [ - '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz - # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch - 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, - '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch -] - -dependencies = [ - ('zlib', '1.2.11'), - ('hwloc', '2.2.0'), - ('libevent', '2.1.11'), - ('UCX', '1.8.0'), - ('libfabric', '1.11.0'), - ('PMIx', '3.1.5'), -] - -# disable MPI1 compatibility for now, see what breaks... -# configopts = '--enable-mpi1-compatibility ' - -# to enable SLURM integration (site-specific) -# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb deleted file mode 100644 index 8acb43b7ce6..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb +++ /dev/null @@ -1,36 +0,0 @@ -name = 'OpenMPI' -version = '4.0.3' - -homepage = 'https://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-3 implementation.""" - -toolchain = {'name': 'iccifortcuda', 'version': '2020a'} - -source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', - 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', - 'OpenMPI-4.x_fix_pmix_discovery.patch', -] -checksums = [ - '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz - # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch - 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, - '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch -] - -dependencies = [ - ('zlib', '1.2.11'), - ('hwloc', '2.2.0'), - ('libevent', '2.1.11'), - ('UCX', '1.8.0', '-CUDA-11.0.2'), - ('libfabric', '1.11.0'), - ('PMIx', '3.1.5'), -] - -# to enable SLURM integration (site-specific) -# configopts = '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb deleted file mode 100644 index c62a1b54501..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -name = 'OpenMPI' -version = '4.0.5' - -homepage = 'https://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-3 implementation.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', - 'OpenMPI-4.x_fix_pmix_discovery.patch', - 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', - 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', -] -checksums = [ - '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz - # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch - 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch - # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch - '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', - {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, -] - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('hwloc', '2.2.0'), - ('libevent', '2.1.11'), - ('UCX', '1.8.0'), - ('libfabric', '1.11.0'), - ('PMIx', '3.1.5'), -] - -# disable MPI1 compatibility for now, see what breaks... -# configopts = '--enable-mpi1-compatibility ' - -# to enable SLURM integration (site-specific) -# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMolcas/OpenMolcas-20.10-intel-2020a-Python-3.8.2-noGA.eb b/easybuild/easyconfigs/__archive__/o/OpenMolcas/OpenMolcas-20.10-intel-2020a-Python-3.8.2-noGA.eb deleted file mode 100644 index 508aaf1ceac..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMolcas/OpenMolcas-20.10-intel-2020a-Python-3.8.2-noGA.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenMolcas' -version = '20.10' -versionsuffix = '-Python-%(pyver)s-noGA' - -homepage = "https://gitlab.com/Molcas/OpenMolcas" -description = """OpenMolcas is a quantum chemistry software package. -This build does not support MPI and can only be run on a single node.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] -sources = ["OpenMolcas-v%(version)s.tar.gz"] -# This patch avoids a forced extra copy of 'pymolcas' script -# in a local folder of the user doing the build -# The 'make install' process will already install it in -# %(installdir)s/sbin/ -patches = ["OpenMolcas-pymolcas_only_in_ebprefix.patch"] -checksums = [ - # OpenMolcas-20.10.tar.gz - '73f73beaebbcff5d02b5bb0748d07c5b8e81784fae6122729c7e7aeed730fe42', - # OpenMolcas-pymolcas_only_in_ebprefix.patch - '56165ab4a752ef7cdbe3340c8c922fca04510e8ee2e4024ea654e6bcd83198f8' -] - -dependencies = [ - ('Python', '3.8.2'), - ('HDF5', '1.10.6'), -] - -builddependencies = [('CMake', '3.16.4')] - -separate_build_dir = True - -configopts = '-DLINALG=MKL -DMKLROOT=$EBROOTIMKL/mkl ' -configopts += '-DMPI=OFF -DGA=OFF -DOPENMP=ON ' -configopts += '-DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' - -modextravars = { - 'MOLCAS': '%(installdir)s', - 'MOLCAS_DRIVER': '%(installdir)s/sbin/pymolcas', - 'MOLCAS_SOURCE': '%(installdir)s', -} - -sanity_check_paths = { - 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, - 'sbin/help_basis', 'sbin/pymolcas'], - 'dirs': ['data/', 'basis_library/'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMolcas/OpenMolcas-20.10-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OpenMolcas/OpenMolcas-20.10-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 9d88327fdd7..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMolcas/OpenMolcas-20.10-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenMolcas' -version = '20.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://gitlab.com/Molcas/OpenMolcas" -description = "OpenMolcas is a quantum chemistry software package" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] -sources = ["OpenMolcas-v%(version)s.tar.gz"] -# This patch avoids a forced extra copy of 'pymolcas' script -# in a local folder of the user doing the build -# The 'make install' process will already install it in -# %(installdir)s/sbin/ -patches = ["OpenMolcas-pymolcas_only_in_ebprefix.patch"] -checksums = [ - # OpenMolcas-20.10.tar.gz - '73f73beaebbcff5d02b5bb0748d07c5b8e81784fae6122729c7e7aeed730fe42', - # OpenMolcas-pymolcas_only_in_ebprefix.patch - '56165ab4a752ef7cdbe3340c8c922fca04510e8ee2e4024ea654e6bcd83198f8' -] - -dependencies = [ - ('GlobalArrays', '5.8'), - ('HDF5', '1.10.6'), - ('Python', '3.8.2'), -] - -builddependencies = [('CMake', '3.16.4')] - -separate_build_dir = True - -preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' -configopts = '-DLINALG=MKL -DMKLROOT=$EBROOTIMKL/mkl ' -configopts += '-DMPI=ON -DOPENMP=ON -DGA=ON ' -configopts += '-DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' - -modextravars = { - 'MOLCAS': '%(installdir)s', - 'MOLCAS_DRIVER': '%(installdir)s/sbin/pymolcas', - 'MOLCAS_SOURCE': '%(installdir)s', -} - -sanity_check_paths = { - 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, - 'sbin/help_basis', 'sbin/pymolcas'], - 'dirs': ['data/', 'basis_library/'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch b/easybuild/easyconfigs/__archive__/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch deleted file mode 100644 index 5d22621805c..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch +++ /dev/null @@ -1,26 +0,0 @@ -# Avoid a forced copy of the 'pymolcas' script in a local path -# of the user doing the build -# 'make install' will install it using the proper prefix -# by A. Lozano (ULiege) ---- a/sbin/install_pymolcas.sh 2018-09-02 09:35:13.000000000 +0200 -+++ b/sbin/install_pymolcas.sh 2019-03-11 16:53:29.224546598 +0100 -@@ -116,8 +116,8 @@ - echo "Is this OK? [Y/n] (will assume \"Yes\" in 25 seconds)" - while true ; do - if [ "$INTERACTIVE" = "0" ] ; then -- echo "Running in non-interactive mode, assuming \"Yes\"" -- answer="Yes" -+ echo "Running in non-interactive mode, assuming \"No\"" -+ answer="No" - else - read_timeout answer - fi -@@ -143,7 +143,7 @@ - echo "" - echo "*** You have to put pymolcas in any directory in your PATH" - if [ "$INTERACTIVE" = "0" ] ; then -- exit 3 -+ exit 0 - fi - break ;; - * ) echo "Please answer yes or no" diff --git a/easybuild/easyconfigs/__archive__/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb deleted file mode 100644 index 965811fad67..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OpenPGM' -version = '5.2.122' - -homepage = 'https://code.google.com/p/openpgm/' - -description = """ - OpenPGM is an open source implementation of the Pragmatic General Multicast - (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable - and scalable multicast protocol that enables receivers to detect loss, request - retransmission of lost data, or notify an application of unrecoverable loss. - PGM is a receiver-reliable protocol, which means the receiver is responsible - for ensuring all data is received, absolving the sender of reception - responsibility. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] -sources = ['libpgm-%(version)s.tar.gz'] -patches = [ - 'OpenPGM-5.2.122-pkgconfig_includes.patch', - 'OpenPGM-5.2.122-python3-compliant.patch' -] -checksums = [ - '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz - '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch - 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('Python', '3.8.2'), -] - -start_dir = 'pgm' - -sanity_check_paths = { - 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], - 'dirs': ['include'], -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/o/OpenSSL/OpenSSL-1.1.1e-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/o/OpenSSL/OpenSSL-1.1.1e-GCCcore-9.3.0.eb deleted file mode 100644 index 08b255dd980..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenSSL/OpenSSL-1.1.1e-GCCcore-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'OpenSSL' -version = '1.1.1e' - -homepage = 'https://www.openssl.org/' -description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, - and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) - protocols as well as a full-strength general purpose cryptography library. """ - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.openssl.org/source/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['694f61ac11cb51c9bf73f54e771ff6022b0327a43bbdfa1b2f19de1662a6dcbe'] - -dependencies = [('zlib', '1.2.11')] - -builddependencies = [ - ('Perl', '5.30.2'), - ('binutils', '2.34'), -] - -runtest = 'test' - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-add_Makefile_def_parallel.patch b/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-add_Makefile_def_parallel.patch deleted file mode 100644 index 3ab22006822..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-add_Makefile_def_parallel.patch +++ /dev/null @@ -1,342 +0,0 @@ -Add Makefile.def for parallel build of OpenSees - -author: Pavel Grochal (INUITS) - -diff -rub --new-file OpenSees-3.2.0.orig/Makefile.def OpenSees-3.2.0/Makefile.def ---- OpenSees-3.2.0.orig/Makefile.def 1970-01-01 01:00:00.000000000 +0100 -+++ OpenSees-3.2.0/Makefile.def 2020-11-12 14:30:33.379699348 +0100 -@@ -0,0 +1,334 @@ -+############################################################################ -+# -+# Program: OpenSees -+# -+# Purpose: A Top-level Makefile to create the libraries needed -+# to use the OpenSees framework. -+# -+# version created for Ghent University -+# -+# Written: Pavel Grochal (INUITS) -+# Created: 08/2020 -+# -+# -+############################################################################ -+ -+# %---------------------------------% -+# | SECTION 1: PROGRAM | -+# %---------------------------------% -+ -+# pass variables (such as home directory) to make as option: 'make HOME="" -+# instead of hardcoding it below -+ -+# PROGRAMMING_MODE = SEQUENTIAL | PARALLEL | PARALLEL_INTERPRETERS -+ -+# set from CMD -+# HOME="%%(installdir)s" -+# BUILDDIR="%%(builddir)s/%%(name)s-%%(version)s" -+# PROGRAMMING_MODE="%s" -+ -+BASE = -+HOME = $(BUILDDIR) -+FE = $(BUILDDIR)/SRC -+ -+OpenSees_PROGRAM = $(HOME)/bin/OpenSees -+ -+ifeq ($(PROGRAMMING_MODE), PARALLEL) -+OpenSees_PROGRAM = $(HOME)/bin/OpenSeesSP -+endif -+ifeq ($(PROGRAMMING_MODE), PARALLEL_INTERPRETERS) -+OpenSees_PROGRAM = $(HOME)/bin/OpenSeesMP -+endif -+ -+# %---------------------------------% -+# | SECTION 2: MAKEFILE CONSTANTS | -+# %---------------------------------% -+# -+# Specify the constants the are used as control structure variables in the Makefiles. -+ -+OPERATING_SYSTEM = LINUX -+ -+#DEBUG_MODE = DEBUG, NO_DEBUG -+DEBUG_MODE = NO_DEBUG -+ -+RELIABILITY = NO_RELIABILITY -+ -+GRAPHICS = NONE -+ -+BLASdir = -+CBLASdir = -+AMDdir = -+LAPACKdir = -+ARPACKdir = -+UMFPACKdir = -+METISdir = -+SRCdir = $(FE) -+SUPERLUdir = -+SUPERLU_DISTdir = -+CSPARSEdir = -+ -+DIRS = $(SRCdir) -+ -+# %-------------------------------------------------------% -+# | SECTION 3: LIBRARIES | -+# | | -+# | The following section defines the libraries that will | -+# | be created and/or linked with when the libraries are | -+# | being created or linked with. | -+# %-------------------------------------------------------% -+# -+# Note: if vendor supplied BLAS and LAPACK libraries leave the -+# libraries blank. You have to get your own copy of the tcl/tk -+# library!! -+# -+# Note: For libraries that will be created (any in DIRS above) -+# make sure the directory exsists where you want the library to go! -+ -+FE_LIBRARY = $(HOME)/lib/libOpenSees.a -+NDARRAY_LIBRARY = $(HOME)/lib/libndarray.a # BJ_UCD jeremic@@ucdavis.edu -+MATMOD_LIBRARY = $(HOME)/lib/libmatmod.a # BJ_UCD jeremic@@ucdavis.edu -+BJMISC_LIBRARY = $(HOME)/lib/libBJmisc.a # BJ_UCD jeremic@@ucdavis.edu -+ -+LAPACK_LIBRARY = -+BLAS_LIBRARY = -+CBLAS_LIBRARY = -+ -+ARPACK_LIBRARY = $(EBROOTARPACKMINNG)/lib/libarpack.a -+METIS_LIBRARY = $(EBROOTMETIS)/lib/libmetis.a -+ -+SUPERLU_LIBRARY = $(EBROOTSUPERLU)/lib64/libsuperlu.a -+DISTRIBUTED_SUPERLU_LIBRARY = $(EBROOTSUPERLU_DIST)/lib64/libsuperlu_dist.a -+ -+UMFPACK_LIBRARY = $(EBROOTSUITESPARSE)/UMFPACK/lib/libumfpack.a -+AMD_LIBRARY = $(EBROOTSUITESPARSE)/AMD/lib/libamd.a -+CSPARSE_LIBRARY = $(EBROOTSUITESPARSE)/CSparse/lib/libcsparse.a -+CAMD_LIBRARY = $(EBROOTSUITESPARSE)/CAMD/lib/libcamd.a -+COLAMD_LIBRARY = $(EBROOTSUITESPARSE)/COLAMD/lib/libcolamd.a -+CCOLAMD_LIBRARY = $(EBROOTSUITESPARSE)/CCOLAMD/lib/libccolamd.a -+CHOLMOD_LIBRARY = $(EBROOTSUITESPARSE)/CHOLMOD/lib/libcholmod.a -+SUTESPARSECONFIG_LIBRARY = $(EBROOTSUITESPARSE)/SuiteSparse_config/libsuitesparseconfig.a -+ -+ -+ifeq ($(PROGRAMMING_MODE), SEQUENTIAL) -+DISTRIBUTED_SUPERLU_LIBRARY = -+endif -+ -+TCL_LIBRARY = -ltcl8.6 -+TCL_INCLUDES = -+ -+GRAPHIC_LIBRARY = -+ -+#RELIABILITY_LIBRARY = $(HOME)/lib/libReliability.a -+RELIABILITY_LIBRARY = -+ -+# WATCH OUT .. These libraries are removed when 'make wipe' is invoked. -+ -+WIPE_LIBS = $(FE_LIBRARY) \ -+ $(NDARRAY_LIBRARY) \ -+ $(MATMOD_LIBRARY) \ -+ -+# %---------------------------------------------------------% -+# | SECTION 5: COMPILERS | -+# | | -+# | The following macros specify compilers, linker/loaders, | -+# | the archiver, and their options. You need to make sure | -+# | these are correct for your system. | -+# %---------------------------------------------------------% -+ -+# ################################################### -+# # Compilers -+# ################################################### -+ -+MPI_DIR = $(EBROOTIMPI) -+MPI_BIN = $(EBROOTIMPI)/bin -+ -+CC++ = $(CXX) -+CC = $(CC) -+FC = $(FC) -+F90 = $(FC) -+FORTRAN = $(FC) -+LINKER = $(CXX) -+ -+AR = ar -+ARCH = ar -+ -+ARFLAGS = -q -+ARCHFLAGS = -v -q -+ -+RANLIB = ranlib -+RANLIBFLAGS = -+ -+GRAPHIC_FLAG = -D_NOGRAPHICS -+ -+PROGRAMMING_FLAG = -+ -+ifeq ($(PROGRAMMING_MODE), PARALLEL) -+PROGRAMMING_FLAG = -D_PARALLEL_PROCESSING -+endif -+ -+ifeq ($(PROGRAMMING_MODE), PARALLEL_INTERPRETERS) -+PROGRAMMING_FLAG = -D_PARALLEL_INTERPRETERS -+endif -+ -+RELIABILITY_FLAG = -+DEBUG_FLAG = -+ -+MUMPS_FLAG = -+PETSC_FLAG = -+ -+# OPT_FLAG is passed from CFLAGS -+# OPT_FLAG = -O2 -+OPT_FLAG = -+ -+COMP_FLAG = -DMPICH_IGNORE_CXX_SEEK -D_USE_METIS_5p1 -+ -+C++FLAGS = -D_LINUX -D_UNIX $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(OPT_FLAG) $(COMP_FLAG)\ -+ $(PROGRAMMING_FLAG) $(PETSC_FLAG) $(MUMPS_FLAG) \ -+ -D_TCL85 -D_BLAS -+CFLAGS = $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(PROGRAMMING_FLAG) $(OPT_FLAG) $(COMP_FLAG) -D_TCL85 -D_BLAS -+FFLAGS = $(OPT_FLAG) $(COMP_FLAG) -+LINKFLAGS = -+ -+# Misc -+MKDIR = mkdir -+MAKE = make -+CD = cd -+ECHO = echo -+RM = rm -+RMFLAGS = -f -+SHELL = /bin/sh -+ -+# %---------------------------------------------------------% -+# | SECTION 6: COMPILATION | -+# | | -+# | The following macros specify the macros used in | -+# | to compile the source code into object code. | -+# %---------------------------------------------------------% -+ -+.SUFFIXES: -+.SUFFIXES: .C .c .f .f90 .cpp .o .cpp -+ -+# -+# %------------------% -+# | Default command. | -+# %------------------% -+# -+.DEFAULT: -+ @@$(ECHO) "Unknown target $@@, try: make help" -+# -+# %-----------------------------------------------% -+# | Command to build .o files from source files. | -+# %-----------------------------------------------% -+# -+ -+ -+.cpp.o: -+ @@$(ECHO) Making $@@ from $< $@@ with $(CC++) $(C++FLAGS) $(INCLUDES) -c $< -+ @@$(CC++) $(C++FLAGS) $(INCLUDES) -c $< -+ -+ -+.C.o: -+ @@$(ECHO) Making $@@ from $< -+ $(CC++) $(C++FLAGS) $(INCLUDES) -c $< -+ -+.c.o: -+ @@$(ECHO) Making $@@ from $< -+ $(CC) $(CFLAGS) -c $< -+ -+.f.o: -+ @@$(ECHO) Making $@@ from $< -+ $(FC) $(FFLAGS) -c $< -+ -+.f77.o: -+ @@$(ECHO) Making $@@ from $< -+ $(FC) $(FFLAGS) -c $< -+ -+.f90.o: -+ @@$(ECHO) Making $@@ from $< -+ $(FC90) $(FFLAGS) -c $< -+ -+# %---------------------------------------------------------% -+# | SECTION 6: OTHER LIBRARIES | -+# | | -+# | The following macros specify other libraries that must | -+# | be linked with when creating executables. These are | -+# | platform specific and typically order does matter!! | -+# %---------------------------------------------------------% -+MACHINE_LINKLIBS = \ -+ -L$(BASE)/lib \ -+ -L$(HOME)/lib -+ -+MACHINE_NUMERICAL_LIBS = -lm \ -+ $(ARPACK_LIBRARY) \ -+ $(SUPERLU_LIBRARY) \ -+ $(UMFPACK_LIBRARY) \ -+ $(CHOLMOD_LIBRARY) \ -+ $(COLAMD_LIBRARY) \ -+ $(CCOLAMD_LIBRARY) \ -+ $(CAMD_LIBRARY) \ -+ $(AMD_LIBRARY) \ -+ $(GRAPHIC_LIBRARY) \ -+ $(RELIABILITY_LIBRARY) \ -+ $(DISTRIBUTED_SUPERLU_LIBRARY) $(CSPARSE_LIBRARY) \ -+ $(METIS_LIBRARY) $(PETSC_LIB) $(MUMPS_LIB) $(CBLAS_LIBRARY) \ -+ $(SUTESPARSECONFIG_LIBRARY) -+ -+MACHINE_SPECIFIC_LIBS = -lifcore -mkl=sequential -static-intel -lifcore -+ -+HAVEMUMPS = YES -+MUMPS_INCLUDE = -+MUMPS_LIB = -+ -+ifeq ($(PROGRAMMING_MODE), SEQUENTIAL) -+HAVEMUMPS = NO -+endif -+ -+ifeq ($(HAVEMUMPS), YES) -+ -+MUMPS = YES -+MUMPS_FLAG = -D_MUMPS -+ -+MUMPS_DIR = $(EBROOTMUMPS) -+#SCALAP = $(BLACSlib) $(SCALAPlib) $(BLACSlib) -+ -+MUMPS_LIB = -L$(MUMPS_DIR)/lib \ -+ $(FE)/system_of_eqn/linearSOE/mumps/MumpsSOE.o \ -+ $(FE)/system_of_eqn/linearSOE/mumps/MumpsSolver.o \ -+ $(FE)/system_of_eqn/linearSOE/mumps/MumpsParallelSOE.o \ -+ $(FE)/system_of_eqn/linearSOE/mumps/MumpsParallelSolver.o \ -+ -lcmumps -ldmumps -lmumps_common -lpord -+ -+MUMPS_INCLUDE = -I$(MUMPS_DIR)/include \ -+ -I$(FE)/system_of_eqn/linearSOE/sparseGEN -+ -+endif -+ -+# %---------------------------------------------------------% -+# | SECTION 7: INCLUDE FILES | -+# | | -+# | The following macros specify include files needed for | -+# | compilation. | -+# %---------------------------------------------------------% -+ -+MACHINE_INCLUDES = -I$(MKLROOT)/include \ -+ -I$(EBROOTSUITESPARSE)/include \ -+ -I$(EBROOTSUITESPARSE)/SuiteSparse_config \ -+ -I$(EBROOTSUPERLU)/include \ -+ -I$(EBROOTSUPERLU_DIST)/include \ -+ -I$(EBROOTSUITESPARSE)/AMD/include \ -+ -I$(EBROOTSUITESPARSE)/COLAMD/include \ -+ -I$(EBROOTSUITESPARSE)/CHOLMOD/include \ -+ -I$(EBROOTARPACKMINNG)/include \ -+ -I$(ROOTSUITESPARSE)/UMFPACK/include \ -+ -I$(EBROOTMETIS)/include \ -+ -I$(EBROOTSUITESPARSE)/CSparse/include \ -+ -I$(HOME)/include \ -+ $(PETSC_INC) $(MUMPS_INCLUDE) -+ -+ -+# this file contains all the OpenSees/SRC includes -+include $(FE)/Makefile.incl -+ -+#TCL_INCLUDES = -I$(HOME)/include -+ -+INCLUDES = $(TCL_INCLUDES) $(FE_INCLUDES) $(MACHINE_INCLUDES) diff --git a/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-add_Makefile_def_sequential.patch b/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-add_Makefile_def_sequential.patch deleted file mode 100644 index 079f14ac6f1..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-add_Makefile_def_sequential.patch +++ /dev/null @@ -1,313 +0,0 @@ -Add Makefile.def for sequential build of OpenSees - -author: Pavel Grochal (INUITS) - -diff -rub --new-file OpenSees-3.2.0.orig/Makefile.def OpenSees-3.2.0/Makefile.def ---- OpenSees-3.2.0.orig/Makefile.def 1970-01-01 01:00:00.000000000 +0100 -+++ OpenSees-3.2.0/Makefile.def 2020-11-03 21:20:33.186140801 +0100 -@@ -0,0 +1,305 @@ -+############################################################################ -+# -+# Program: OpenSees -+# -+# Purpose: A Top-level Makefile to create the libraries needed -+# to use the OpenSees framework. -+# -+# version created for Ghent University -+# -+# Written: Pavel Grochal (INUITS) -+# Created: 08/2020 -+# -+# -+############################################################################ -+ -+# %---------------------------------% -+# | SECTION 1: PROGRAM | -+# %---------------------------------% -+ -+# pass variables (such as home directory) to make as option: 'make HOME="" -+# instead of hardcoding it below -+ -+# PROGRAMMING_MODE = SEQUENTIAL | PARALLEL | PARALLEL_INTERPRETERS -+ -+# set from CMD -+# HOME="%%(installdir)s" -+# BUILDDIR="%%(builddir)s/%%(name)s-%%(version)s" -+# PROGRAMMING_MODE="%s" -+ -+BASE = -+HOME = $(BUILDDIR) -+FE = $(BUILDDIR)/SRC -+ -+OpenSees_PROGRAM = $(HOME)/bin/OpenSees -+ -+ifeq ($(PROGRAMMING_MODE), PARALLEL) -+OpenSees_PROGRAM = $(HOME)/bin/OpenSeesSP -+endif -+ifeq ($(PROGRAMMING_MODE), PARALLEL_INTERPRETERS) -+OpenSees_PROGRAM = $(HOME)/bin/OpenSeesMP -+endif -+ -+# %---------------------------------% -+# | SECTION 2: MAKEFILE CONSTANTS | -+# %---------------------------------% -+# -+# Specify the constants the are used as control structure variables in the Makefiles. -+ -+OPERATING_SYSTEM = LINUX -+ -+#DEBUG_MODE = DEBUG, NO_DEBUG -+DEBUG_MODE = NO_DEBUG -+ -+RELIABILITY = NO_RELIABILITY -+ -+GRAPHICS = NONE -+ -+BLASdir = -+CBLASdir = -+AMDdir = -+LAPACKdir = -+ARPACKdir = -+UMFPACKdir = -+METISdir = -+SRCdir = $(FE) -+SUPERLUdir = -+SUPERLU_DISTdir = $(HOME)/OTHER/SuperLU_DIST_4.3/SRC -+CSPARSEdir = -+ -+DIRS = $(SRCdir) -+ -+# %-------------------------------------------------------% -+# | SECTION 3: LIBRARIES | -+# | | -+# | The following section defines the libraries that will | -+# | be created and/or linked with when the libraries are | -+# | being created or linked with. | -+# %-------------------------------------------------------% -+# -+# Note: if vendor supplied BLAS and LAPACK libraries leave the -+# libraries blank. You have to get your own copy of the tcl/tk -+# library!! -+# -+# Note: For libraries that will be created (any in DIRS above) -+# make sure the directory exsists where you want the library to go! -+ -+FE_LIBRARY = $(HOME)/lib/libOpenSees.a -+NDARRAY_LIBRARY = $(HOME)/lib/libndarray.a # BJ_UCD jeremic@@ucdavis.edu -+MATMOD_LIBRARY = $(HOME)/lib/libmatmod.a # BJ_UCD jeremic@@ucdavis.edu -+BJMISC_LIBRARY = $(HOME)/lib/libBJmisc.a # BJ_UCD jeremic@@ucdavis.edu -+ -+LAPACK_LIBRARY = -+BLAS_LIBRARY = -+CBLAS_LIBRARY = -+ -+ARPACK_LIBRARY = $(EBROOTARPACKMINNG)/lib/libarpack.a -+METIS_LIBRARY = $(EBROOTMETIS)/lib/libmetis.a -+ -+SUPERLU_LIBRARY = $(EBROOTSUPERLU)/lib64/libsuperlu.a -+DISTRIBUTED_SUPERLU_LIBRARY = $(HOME)/lib/libDistributedSuperLU.a -+ -+UMFPACK_LIBRARY = $(EBROOTSUITESPARSE)/UMFPACK/lib/libumfpack.a -+AMD_LIBRARY = $(EBROOTSUITESPARSE)/AMD/lib/libamd.a -+CSPARSE_LIBRARY = $(EBROOTSUITESPARSE)/CSparse/lib/libcsparse.a -+CAMD_LIBRARY = $(EBROOTSUITESPARSE)/CAMD/lib/libcamd.a -+COLAMD_LIBRARY = $(EBROOTSUITESPARSE)/COLAMD/lib/libcolamd.a -+CCOLAMD_LIBRARY = $(EBROOTSUITESPARSE)/CCOLAMD/lib/libccolamd.a -+CHOLMOD_LIBRARY = $(EBROOTSUITESPARSE)/CHOLMOD/lib/libcholmod.a -+SUTESPARSECONFIG_LIBRARY = $(EBROOTSUITESPARSE)/SuiteSparse_config/libsuitesparseconfig.a -+ -+ -+ifeq ($(PROGRAMMING_MODE), SEQUENTIAL) -+DISTRIBUTED_SUPERLU_LIBRARY = -+endif -+ -+TCL_LIBRARY = -ltcl8.6 -+TCL_INCLUDES = -+ -+GRAPHIC_LIBRARY = -+ -+#RELIABILITY_LIBRARY = $(HOME)/lib/libReliability.a -+RELIABILITY_LIBRARY = -+ -+# WATCH OUT .. These libraries are removed when 'make wipe' is invoked. -+ -+WIPE_LIBS = $(FE_LIBRARY) \ -+ $(NDARRAY_LIBRARY) \ -+ $(MATMOD_LIBRARY) \ -+ -+# %---------------------------------------------------------% -+# | SECTION 5: COMPILERS | -+# | | -+# | The following macros specify compilers, linker/loaders, | -+# | the archiver, and their options. You need to make sure | -+# | these are correct for your system. | -+# %---------------------------------------------------------% -+ -+# ################################################### -+# # Compilers -+# ################################################### -+ -+MPI_DIR = $(EBROOTIMPI) -+MPI_BIN = $(EBROOTIMPI)/bin -+ -+CC++ = $(CXX) -+CC = $(CC) -+FC = $(FC) -+F90 = $(FC) -+FORTRAN = $(FC) -+LINKER = $(CXX) -+ -+AR = ar -+ARCH = ar -+ -+ARFLAGS = -q -+ARCHFLAGS = -v -q -+ -+RANLIB = ranlib -+RANLIBFLAGS = -+ -+GRAPHIC_FLAG = -D_NOGRAPHICS -+ -+PROGRAMMING_FLAG = -+ -+ifeq ($(PROGRAMMING_MODE), PARALLEL) -+PROGRAMMING_FLAG = -D_PARALLEL_PROCESSING -+endif -+ -+ifeq ($(PROGRAMMING_MODE), PARALLEL_INTERPRETERS) -+PROGRAMMING_FLAG = -D_PARALLEL_INTERPRETERS -+endif -+ -+RELIABILITY_FLAG = -+DEBUG_FLAG = -+ -+MUMPS_FLAG = -+PETSC_FLAG = -+ -+# OPT_FLAG is passed from CFLAGS -+# OPT_FLAG = -O2 -+OPT_FLAG = -+ -+COMP_FLAG = -DMPICH_IGNORE_CXX_SEEK -+ -+C++FLAGS = -D_LINUX -D_UNIX $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(OPT_FLAG) $(COMP_FLAG)\ -+ $(PROGRAMMING_FLAG) $(PETSC_FLAG) $(MUMPS_FLAG) \ -+ -D_TCL85 -D_BLAS -+CFLAGS = $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG)$(PROGRAMMING_FLAG) $(OPT_FLAG) $(COMP_FLAG) -D_TCL85 -D_BLAS -+FFLAGS = $(OPT_FLAG) $(COMP_FLAG) -+LINKFLAGS = -+ -+# Misc -+MKDIR = mkdir -+MAKE = make -+CD = cd -+ECHO = echo -+RM = rm -+RMFLAGS = -f -+SHELL = /bin/sh -+ -+# %---------------------------------------------------------% -+# | SECTION 6: COMPILATION | -+# | | -+# | The following macros specify the macros used in | -+# | to compile the source code into object code. | -+# %---------------------------------------------------------% -+ -+.SUFFIXES: -+.SUFFIXES: .C .c .f .f90 .cpp .o .cpp -+ -+# -+# %------------------% -+# | Default command. | -+# %------------------% -+# -+.DEFAULT: -+ @@$(ECHO) "Unknown target $@@, try: make help" -+# -+# %-----------------------------------------------% -+# | Command to build .o files from source files. | -+# %-----------------------------------------------% -+# -+ -+ -+.cpp.o: -+ @@$(ECHO) Making $@@ from $< $@@ with $(CC++) $(C++FLAGS) $(INCLUDES) -c $< -+ @@$(CC++) $(C++FLAGS) $(INCLUDES) -c $< -+ -+ -+.C.o: -+ @@$(ECHO) Making $@@ from $< -+ $(CC++) $(C++FLAGS) $(INCLUDES) -c $< -+ -+.c.o: -+ @@$(ECHO) Making $@@ from $< -+ $(CC) $(CFLAGS) -c $< -+ -+.f.o: -+ @@$(ECHO) Making $@@ from $< -+ $(FC) $(FFLAGS) -c $< -+ -+.f77.o: -+ @@$(ECHO) Making $@@ from $< -+ $(FC) $(FFLAGS) -c $< -+ -+.f90.o: -+ @@$(ECHO) Making $@@ from $< -+ $(FC90) $(FFLAGS) -c $< -+ -+# %---------------------------------------------------------% -+# | SECTION 6: OTHER LIBRARIES | -+# | | -+# | The following macros specify other libraries that must | -+# | be linked with when creating executables. These are | -+# | platform specific and typically order does matter!! | -+# %---------------------------------------------------------% -+MACHINE_LINKLIBS = \ -+ -L$(BASE)/lib \ -+ -L$(HOME)/lib -+ -+MACHINE_NUMERICAL_LIBS = -lm \ -+ $(ARPACK_LIBRARY) \ -+ $(SUPERLU_LIBRARY) \ -+ $(UMFPACK_LIBRARY) \ -+ $(CHOLMOD_LIBRARY) \ -+ $(COLAMD_LIBRARY) \ -+ $(CCOLAMD_LIBRARY) \ -+ $(CAMD_LIBRARY) \ -+ $(AMD_LIBRARY) \ -+ $(GRAPHIC_LIBRARY) \ -+ $(RELIABILITY_LIBRARY) \ -+ $(DISTRIBUTED_SUPERLU_LIBRARY) $(CSPARSE_LIBRARY) \ -+ $(METIS_LIBRARY) $(PETSC_LIB) $(MUMPS_LIB) $(CBLAS_LIBRARY) \ -+ $(SUTESPARSECONFIG_LIBRARY) -+ -+MACHINE_SPECIFIC_LIBS = -lifcore -mkl=sequential -static-intel -lifcore -+ -+# %---------------------------------------------------------% -+# | SECTION 7: INCLUDE FILES | -+# | | -+# | The following macros specify include files needed for | -+# | compilation. | -+# %---------------------------------------------------------% -+ -+MACHINE_INCLUDES = -I$(MKLROOT)/include \ -+ -I$(EBROOTSUITESPARSE)/include \ -+ -I$(EBROOTSUITESPARSE)/SuiteSparse_config \ -+ -I$(EBROOTSUPERLU)/include \ -+ -I$(EBROOTSUITESPARSE)/AMD/include \ -+ -I$(EBROOTSUITESPARSE)/COLAMD/include \ -+ -I$(EBROOTSUITESPARSE)/CHOLMOD/include \ -+ -I$(EBROOTARPACKMINNG)/include \ -+ -I$(ROOTSUITESPARSE)/UMFPACK/include \ -+ -I$(EBROOTMETIS)/include \ -+ -I$(EBROOTSUITESPARSE)/CSparse/include \ -+ -I$(HOME)/include \ -+ $(PETSC_INC) $(MUMPS_INCLUDE) -+ -+ -+# this file contains all the OpenSees/SRC includes -+include $(FE)/Makefile.incl -+ -+#TCL_INCLUDES = -I$(HOME)/include -+ -+INCLUDES = $(TCL_INCLUDES) $(FE_INCLUDES) $(MACHINE_INCLUDES) diff --git a/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-fix_superlu_dist.patch b/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-fix_superlu_dist.patch deleted file mode 100644 index 1466c08c7ea..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-fix_superlu_dist.patch +++ /dev/null @@ -1,31 +0,0 @@ -Fix SuperLU_DIST options beeing renamed in 5.x.x version - -author: Pavel Grochal (INUITS) - -diff -rub --new-file OpenSees-3.2.0.after/SRC/system_of_eqn/linearSOE/sparseGEN/DistributedSuperLU.cpp OpenSees-3.2.0/SRC/system_of_eqn/linearSOE/sparseGEN/DistributedSuperLU.cpp ---- OpenSees-3.2.0.after/SRC/system_of_eqn/linearSOE/sparseGEN/DistributedSuperLU.cpp 2020-03-09 18:02:19.000000000 +0100 -+++ OpenSees-3.2.0/SRC/system_of_eqn/linearSOE/sparseGEN/DistributedSuperLU.cpp 2020-11-12 15:08:44.344103344 +0100 -@@ -41,7 +41,7 @@ - - - --superlu_options_t options; -+superlu_dist_options_t options; - SuperLUStat_t stat; - SuperMatrix A; - ScalePermstruct_t ScalePermstruct; -@@ -366,14 +366,3 @@ - opserr << "DistributedSuperLU::recvSelf(int cTag, Channel &theChannel) - END\n"; - return 0; - } -- -- -- -- -- -- -- -- -- -- -- diff --git a/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-intel-2020a-Python-3.8.2-parallel.eb b/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-intel-2020a-Python-3.8.2-parallel.eb deleted file mode 100644 index 8be0ff6a58f..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-intel-2020a-Python-3.8.2-parallel.eb +++ /dev/null @@ -1,56 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'MakeCp' - -name = 'OpenSees' -version = '3.2.0' -versionsuffix = '-Python-%(pyver)s-parallel' - -homepage = 'https://opensees.berkeley.edu/index.php' -description = "Open System for Earthquake Engineering Simulation" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -# https://github.com/OpenSees/OpenSees -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = [ - ('%(name)s-%(version)s-add_Makefile_def_parallel.patch', 1), - '%(name)s-%(version)s-fix_superlu_dist.patch', -] -checksums = [ - '200f70fc86b7c4c2978eaef1aacd206cb40791fa797e1b9cc51da9633b53eb36', # v3.2.0.tar.gz - # OpenSees-3.2.0-add_Makefile_def_parallel.patch - 'd9eca142b325b0c64d9e1db11f2eb994af86530c1262ed29eec44dc2d75b3ea1', - '438932059c2d1d02164a50d968dacc32f372bc3a7dffaeb609eabbf5cbf753d2', # OpenSees-3.2.0-fix_superlu_dist.patch -] - -dependencies = [ - ('Python', '3.8.2'), - ('METIS', '5.1.0'), - ('MUMPS', '5.2.1', '-metis'), - ('SuiteSparse', '5.7.1', '-METIS-5.1.0'), - ('arpack-ng', '3.7.0'), - ('Tk', '8.6.10'), - ('SuperLU', '5.2.2'), - # This is latest working version with smallest possible patch - ('SuperLU_DIST', '5.4.0', '-trisolve-merge'), -] - -buildopts = 'BUILDDIR="%(builddir)s/%(name)s-%(version)s" ' -buildopts += 'PROGRAMMING_MODE="PARALLEL_INTERPRETERS" CC="$CC" CC++="$CXX" FC="$FC"' - -files_to_copy = ['bin', 'lib'] - -# Testing only few scripts. Bin folder contains > 50 files -sanity_check_paths = { - 'files': ['bin/OpenSeesMP', 'lib/libOpenSees.a', 'lib/libOpenSeesTclCommands.a'], - 'dirs': [] -} -sanity_check_commands = [ - '%(mpi_cmd_prefix)s OpenSeesMP -h', -] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 5b9a9b9b8ee..00000000000 --- a/easybuild/easyconfigs/__archive__/o/OpenSees/OpenSees-3.2.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,47 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'MakeCp' - -name = 'OpenSees' -version = '3.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://opensees.berkeley.edu/index.php' -description = "Open System for Earthquake Engineering Simulation" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True} - -# https://github.com/OpenSees/OpenSees -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = [('%(name)s-%(version)s-add_Makefile_def_sequential.patch', 1)] -checksums = [ - '200f70fc86b7c4c2978eaef1aacd206cb40791fa797e1b9cc51da9633b53eb36', # v3.2.0.tar.gz - # OpenSees-3.2.0-add_Makefile_def_sequential.patch - 'cbaea5fd166a4ee126f100e4adb82dbc0add8cc882cf1dac1d3e70108c42a540', -] - -dependencies = [ - ('Python', '3.8.2'), - ('METIS', '5.1.0'), - ('MUMPS', '5.2.1', '-metis'), - ('SuiteSparse', '5.7.1', '-METIS-5.1.0'), - ('arpack-ng', '3.7.0'), - ('Tk', '8.6.10'), - ('SuperLU', '5.2.2'), -] - -buildopts = 'BUILDDIR="%(builddir)s/%(name)s-%(version)s" ' -buildopts += 'PROGRAMMING_MODE="SEQUENTIAL" CC="$CC" CC++="$CXX" FC="$FC"' - -files_to_copy = ['bin', 'lib'] - -sanity_check_paths = { - 'files': ['bin/OpenSees', 'lib/libOpenSees.a', 'lib/libOpenSeesTclCommands.a'], - 'dirs': [], -} -sanity_check_commands = ['OpenSees -h'] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/o/openCARP/openCARP-3.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/o/openCARP/openCARP-3.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 502838b61ac..00000000000 --- a/easybuild/easyconfigs/__archive__/o/openCARP/openCARP-3.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'CMakeMakeCp' - -name = 'openCARP' -version = '3.2' -versionsuffix = '-Python-3.8.2' - -homepage = 'https://opencarp.org' -description = "openCARP is an open cardiac electrophysiology simulator for in-silico experiments." - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = ['https://git.opencarp.org/openCARP/openCARP/-/archive/v%(version)s/'] -sources = ['openCARP-v%(version)s.tar.gz'] -patches = ['openCARP-%(version)s_build-info.patch'] -checksums = [ - '4029f9bb0786636380c25d995ef7be22626daaa2c76bf741dea949df11da7bf7', # openCARP-v3.2.tar.gz - '43004c7dee2981677c4316c32ce20080ad2e70760d53981aaaaba55ebc659e8c', # openCARP-3.2_build-info.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('gengetopt', '2.23'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('PETSc', '3.12.4', versionsuffix), - ('zlib', '1.2.11'), -] - -files_to_copy = ['bin'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bench', 'igbapd', 'igbextract', 'igbhead', 'igbops', 'mesher', 'openCARP']], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PAML/PAML-4.9j-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PAML/PAML-4.9j-GCCcore-9.3.0.eb deleted file mode 100644 index d4f26228669..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PAML/PAML-4.9j-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'MakeCp' - -name = 'PAML' -version = '4.9j' - -homepage = 'http://abacus.gene.ucl.ac.uk/software/paml.html' -description = """PAML is a package of programs for phylogenetic - analyses of DNA or protein sequences using maximum likelihood.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://abacus.gene.ucl.ac.uk/software'] -sources = ['%(namelower)s%(version)s.tgz'] -checksums = ['9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d'] - -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' - -builddependencies = [('binutils', '2.34')] - -start_dir = 'src' - -files_to_copy = [ - (['GeneticCode.txt', '%(builddir)s/%(namelower)s%(version)s/README.txt'], ''), - (['*.trees', '*.ctl', '*.nuc', '*.dat', 'paup*', 'stewart.aa'], ''), - (['src/baseml', 'src/basemlg', 'src/chi2', 'src/codeml', 'src/evolver'], 'bin'), - (['src/infinitesites', 'src/mcmctree', 'src/pamp', 'src/yn00'], 'bin'), - (['dat/*'], 'dat'), - (['doc/*'], 'doc'), - (['examples/*'], 'examples'), - (['Technical/*'], 'Technical'), -] - -sanity_check_paths = { - 'files': ['bin/baseml'], - 'dirs': ['bin'] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-6.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-6.0.0-GCCcore-9.3.0.eb deleted file mode 100644 index 04c0b353db8..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-6.0.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,55 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html -## - -easyblock = 'ConfigureMake' - -name = 'PAPI' -version = '6.0.0' - -homepage = 'https://icl.cs.utk.edu/projects/papi/' - -description = """ - PAPI provides the tool designer and application engineer with a consistent - interface and methodology for use of the performance counter hardware found - in most major microprocessors. PAPI enables software engineers to see, in near - real time, the relation between software performance and processor events. - In addition Component PAPI provides access to a collection of components - that expose performance measurement opportunites across the hardware and - software stack. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://icl.cs.utk.edu/projects/papi/downloads/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['3442709dae3405c2845b304c06a8b15395ecf4f3899a89ceb4d715103cb4055f'] - -builddependencies = [ - ('binutils', '2.34'), -] - -start_dir = 'src' - -# There is also "fulltest" that is a superset of "test" but hangs on some processors -# indefinitely with a defunct `make` process. So use only "test". -runtest = 'test' - -sanity_check_paths = { - 'files': ["bin/papi_%s" % x - for x in ["avail", "clockres", "command_line", "component_avail", - "cost", "decode", "error_codes", "event_chooser", - "mem_info", "multiplex_cost", "native_avail", - "version", "xml_event_info"]], - 'dirs': [], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/p/PCRE/PCRE-8.44-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PCRE/PCRE-8.44-GCCcore-9.3.0.eb deleted file mode 100644 index cdb3f57b911..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PCRE/PCRE-8.44-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PCRE' -version = '8.44' - -homepage = 'https://www.pcre.org/' - -description = """ - The PCRE library is a set of functions that implement regular expression - pattern matching using the same syntax and semantics as Perl 5. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - SOURCEFORGE_SOURCE, - 'https://ftp.pcre.org/pub/pcre/', -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aecafd4af3bd0f3935721af77b889d9024b2e01d96b58471bd91a3063fb47728'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), -] - -configopts = """\ - --enable-utf\ - --enable-unicode-properties\ - --enable-pcre16\ - --enable-pcre32\ -""" - -sanity_check_paths = { - 'files': ['bin/pcre-config', 'include/pcre.h', - 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb deleted file mode 100644 index f5d596ea476..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PCRE2' -version = '10.34' - -homepage = 'https://www.pcre.org/' -description = """ - The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['da6aba7ba2509e918e41f4f744a59fa41a2425c59a298a232e7fe85691e00379'] - -builddependencies = [('binutils', '2.34')] - -configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" - -sanity_check_paths = { - 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/PDT/PDT-3.25.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PDT/PDT-3.25.1-GCCcore-9.3.0.eb deleted file mode 100644 index 7283707bfd4..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PDT/PDT-3.25.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany -# Authors:: Bernd Mohr -# Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -name = 'PDT' -version = '3.25.1' - -homepage = 'https://www.cs.uoregon.edu/research/pdt/' -description = """ - Program Database Toolkit (PDT) is a framework for analyzing source code - written in several programming languages and for making rich program - knowledge accessible to developers of static and dynamic analysis tools. - PDT implements a standard program representation, the program database - (PDB), that can be accessed in a uniform way through a class library - supporting common PDB operations. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://www.cs.uoregon.edu/research/tau/pdt_releases/'] -sources = ['pdtoolkit-%(version)s.tar.gz'] -checksums = [ - '0b6f8a6b8769c181b2ae6cae7298f04b8e3e3d68066f598ed24574e19500bc97', # pdtoolkit-3.25.tar.gz -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.34'), -] - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/p/PEAR/PEAR-0.9.11-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PEAR/PEAR-0.9.11-GCCcore-9.3.0.eb deleted file mode 100644 index 3feb0fbe430..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PEAR/PEAR-0.9.11-GCCcore-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PEAR' -version = '0.9.11' - -homepage = 'https://cme.h-its.org/exelixis/web/software/%(namelower)s/' -description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. - It is fully parallelized and can run with as low as just a few kilobytes of memory.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -download_instructions = "Manual download via web form, see https://www.h-its.org/software/pear-paired-end-read-merger" -sources = ['%(namelower)s-src-%(version)s.tar.gz'] -checksums = ['94f4a1835cd75ec6fab83405c2545ddba6b6bb1644579222e9cc2ad57a59d654'] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), -] - -preconfigopts = 'autoreconf && ' - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PEST++/PEST++-5.0.5-foss-2020a.eb b/easybuild/easyconfigs/__archive__/p/PEST++/PEST++-5.0.5-foss-2020a.eb deleted file mode 100644 index c1c4398a666..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PEST++/PEST++-5.0.5-foss-2020a.eb +++ /dev/null @@ -1,44 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Custom -# -# Notes:: -## - -easyblock = 'CMakeMake' - -name = 'PEST++' -version = '5.0.5' - -homepage = 'https://github.com/usgs/pestpp' -description = """PEST++ is a software suite aimed at supporting - complex numerical models in the decision-support context. - Much focus has been devoted to supporting environmental models - (groundwater, surface water, etc) but these tools are readily - applicable to any computer model. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = ['https://github.com/usgs/pestpp/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['b9695724758f69c1199371608b01419973bd1475b1788039a2fab6313f6ed67c'] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -# The default target (all) fails to build all binaries, the following is equivalent to all -local_targets = ['pestpp-sen', 'pestpp-glm', 'pestpp-ies', 'pestpp-opt', 'pestpp-swp', 'pestpp-pso'] -buildopts = ' '.join(local_targets) - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_targets], - 'dirs': [], -} - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.12.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.12.4-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index fdba07a174e..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.12.4-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,49 +0,0 @@ -name = 'PETSc' -version = '3.12.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.mcs.anl.gov/petsc' -description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the - scalable (parallel) solution of scientific applications modeled by partial differential equations.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -# https:// does not work here -source_urls = [ - 'http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', - 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', -] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'PETSc_ranlib-fix.patch', -] -checksums = [ - '56a941130da93bbacb3cfa74dcacea1e3cd8e36a0341f9ced09977b1457084c3', # petsc-3.12.4.tar.gz - '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch -] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Boost', '1.72.0'), - ('METIS', '5.1.0'), - ('SCOTCH', '6.0.9'), - ('MUMPS', '5.2.1', '-metis'), - ('SuiteSparse', '5.7.1', '-METIS-5.1.0'), - ('Hypre', '2.18.2'), -] - -# enabling --with-mpi4py seems to be totally broken, leads to make errors like: -# No rule to make target 'mpi4py-build' -configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0' - -shared_libs = 1 - -# only required when building PETSc in a SLURM job environment -# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' -# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.12.4-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.12.4-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 8cd4b13ee72..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.12.4-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,49 +0,0 @@ -name = 'PETSc' -version = '3.12.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.mcs.anl.gov/petsc' -description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the - scalable (parallel) solution of scientific applications modeled by partial differential equations.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -# https:// does not work here -source_urls = [ - 'http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', - 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', -] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'PETSc_ranlib-fix.patch', -] -checksums = [ - '56a941130da93bbacb3cfa74dcacea1e3cd8e36a0341f9ced09977b1457084c3', # petsc-3.12.4.tar.gz - '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch -] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Boost', '1.72.0'), - ('METIS', '5.1.0'), - ('SCOTCH', '6.0.9'), - ('MUMPS', '5.2.1', '-metis'), - ('SuiteSparse', '5.7.1', '-METIS-5.1.0'), - ('Hypre', '2.18.2'), -] - -# enabling --with-mpi4py seems to be totally broken, leads to make errors like: -# No rule to make target 'mpi4py-build' -configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0' - -shared_libs = 1 - -# only required when building PETSc in a SLURM job environment -# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' -# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/p/PHYLIP/PHYLIP-3.697-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PHYLIP/PHYLIP-3.697-GCC-9.3.0.eb deleted file mode 100644 index 25bf7a020ea..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PHYLIP/PHYLIP-3.697-GCC-9.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'MakeCp' - -name = 'PHYLIP' -version = '3.697' - -homepage = 'https://evolution.genetics.washington.edu/phylip' -description = "PHYLIP is a free package of programs for inferring phylogenies." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://evolution.gs.washington.edu/phylip/download/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['9a26d8b08b8afea7f708509ef41df484003101eaf4beceb5cf7851eb940510c1'] - -buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' - -files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.%s' % SHLIB_EXT, 'src/libdrawtree.%s' % SHLIB_EXT], 'lib')] - -sanity_check_paths = { - 'files': ['lib/libdrawgram.%s' % SHLIB_EXT, 'lib/libdrawtree.%s' % SHLIB_EXT], - 'dirs': ['bin'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 8efe5d7405a..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,58 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PIPITS' -version = '2.7' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/hsgweon/pipits' -description = """An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences -from the Illumina sequencing platform.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), - ('h5py', '2.10.0', '-Python-%(pyver)s'), - ('VSEARCH', '2.15.0'), - ('FASTX-Toolkit', '0.0.14'), - ('ITSx', '1.1.2'), - ('HMMER', '3.3.1'), - ('RDP-Classifier', '2.13', '-Java-11', SYSTEM), - ('SeqKit', '0.13.2', '', SYSTEM), -] - -exts_list = [ - ('biom-format', '2.1.8-1', { - 'modulename': 'biom', - 'checksums': ['3711de5807e5b29d944cd2713a16f26b6148eefd5b831ccad6a10c06cbd42649'], - }), - ('python-utils', '2.4.0', { - 'checksums': ['f21fc09ff58ea5ebd1fd2e8ef7f63e39d456336900f26bdc9334a03a3f7d8089'], - }), - ('progressbar2', '3.53.1', { - 'modulename': 'progressbar', - 'checksums': ['ef72be284e7f2b61ac0894b44165926f13f5d995b2bf3cd8a8dedc6224b255a7'], - }), - ('pispino', '1.1', { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/hsgweon/pispino/archive/'], - 'checksums': ['8fb2e1c0ae38ecca7c637de9c0b655eb18fc67d7838ceb5a6902555ea12416c0'], - }), - (name, version, { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/hsgweon/pipits/archive/'], - 'checksums': ['ae2b3eca133a44c072bc0f0817af2affbcc1b2a64cc8904c326e4604cda3ecff'], - }), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['pipits_funits', 'pipits_process', - 'pispino_createreadpairslist', - 'pispino_seqprep']], - 'dirs': [] -} - -sanity_check_commands = ['pipits_process --help'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.9b5-golf-2020a.eb b/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.9b5-golf-2020a.eb deleted file mode 100644 index 6d02cc47481..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.9b5-golf-2020a.eb +++ /dev/null @@ -1,45 +0,0 @@ -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# Author: Adam Huffman -# The Francis Crick Institute -# Author: Åke Sandgren -# HPC2N, Umeå University - -easyblock = 'ConfigureMake' - -name = 'PLINK' -version = '1.9b5' - -homepage = 'https://www.cog-genomics.org/plink/1.9' -description = """ PLINK is a free, open-source whole genome association analysis toolset, - designed to perform a range of basic, large-scale analyses in a computationally efficient manner. - The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for - steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).""" - -toolchain = {'name': 'golf', 'version': '2020a'} - -source_urls = ['https://github.com/chrchang/plink-ng/archive'] -sources = [{'download_filename': 'b15c19f.tar.gz', 'filename': SOURCE_TAR_GZ}] -patches = ['%(name)s-%(version)s_fix_bad_memcmp_and_Makefile.patch'] -checksums = [ - 'e00ef16ac5abeb6b4c4d77846bd655fafc62669fbebf8cd2e941f07b3111907e', # PLINK-1.9b5.tar.gz - 'bca77c1142ef6d1cb542295e6273bb5c3719895825470fc0f01b58965a983876', # PLINK-1.9b5_fix_bad_memcmp_and_Makefile.patch -] - -dependencies = [('zlib', '1.2.11')] - -start_dir = '1.9' -skipsteps = ['configure'] - -buildopts = '-f Makefile.std CPPFLAGS="-DDYNAMIC_ZLIB" ' -buildopts += 'BLASFLAGS="$LIBLAPACK_MT $LIBBLAS_MT" ZLIB="-lz" ' - -installopts = '-f Makefile.std DESTDIR="" PREFIX="%(installdir)s" ' - -sanity_check_paths = { - 'files': ["bin/plink"], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.9b5_fix_bad_memcmp_and_Makefile.patch b/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.9b5_fix_bad_memcmp_and_Makefile.patch deleted file mode 100644 index 65aecee5a75..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.9b5_fix_bad_memcmp_and_Makefile.patch +++ /dev/null @@ -1,88 +0,0 @@ -Fix some memcmp that where stepping outside of the string. -Fix Makefile.std so the -lm -lpthread -ldl is in LIBS and added at the end of the link line. -Fix a bad #include zlib.h - -Åke Sandgren, 20201021 -diff -ru plink-ng-b15c19f.orig/1.9/dose2plink.c plink-ng-b15c19f/1.9/dose2plink.c ---- plink-ng-b15c19f.orig/1.9/dose2plink.c 2017-11-14 21:16:37.000000000 +0100 -+++ plink-ng-b15c19f/1.9/dose2plink.c 2020-10-21 16:10:16.978526654 +0200 -@@ -96,7 +96,11 @@ - #endif - #endif - --#include "../zlib-1.2.11/zlib.h" -+#ifdef DYNAMIC_ZLIB -+ #include -+#else -+ #include "../zlib-1.2.11/zlib.h" -+#endif - - #ifdef __APPLE__ - #include -diff -ru plink-ng-b15c19f.orig/1.9/Makefile.std plink-ng-b15c19f/1.9/Makefile.std ---- plink-ng-b15c19f.orig/1.9/Makefile.std 2017-11-14 21:16:37.000000000 +0100 -+++ plink-ng-b15c19f/1.9/Makefile.std 2020-10-21 16:24:14.399023402 +0200 -@@ -32,7 +32,7 @@ - CFLAGS ?= -Wall -O2 - CXXFLAGS ?= -Wall -O2 - BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lcblas -latlas --LDFLAGS ?= -lm -lpthread -ldl -+LIBS ?= -lm -lpthread -ldl - ZLIB ?= ../zlib-1.2.11/libz.so.1.2.11 - - PREFIX ?= /usr/local -@@ -73,10 +73,10 @@ - all: $(BIN) - - plink: $(OBJS) -- $(CXX) $(OBJS) $(LDFLAGS_EXTRA) $(BLASFLAGS) $(LDFLAGS) -L. $(ZLIB) -o $@ -+ $(CXX) $(OBJS) $(LDFLAGS_EXTRA) $(BLASFLAGS) $(LDFLAGS) -L. $(ZLIB) -o $@ $(LIBS) - - plinkw: $(OBJS) -- gfortran -O2 $(OBJS) $(LDFLAGS_EXTRA) -Wl,-Bstatic $(BLASFLAGS) $(LDFLAGS) -L. $(ZLIB) -o $@ -+ gfortran -O2 $(OBJS) $(LDFLAGS_EXTRA) -Wl,-Bstatic $(BLASFLAGS) $(LDFLAGS) -L. $(ZLIB) -o $@ $(LIBS) - - install: - $(INSTALL) -d $(DESTDIR)$(PREFIX)/bin -diff -ru plink-ng-b15c19f.orig/1.9/plink.c plink-ng-b15c19f/1.9/plink.c ---- plink-ng-b15c19f.orig/1.9/plink.c 2017-11-14 21:16:37.000000000 +0100 -+++ plink-ng-b15c19f/1.9/plink.c 2020-10-21 16:22:48.512204129 +0200 -@@ -6854,7 +6854,7 @@ - sprintf(g_logbuf, "Error: Invalid --flip-scan-window size '%s'.\n", argv[cur_arg + 1]); - goto main_ret_INVALID_CMDLINE_WWA; - } -- } else if (!memcmp(argptr2, "lip-scan-window-kb", 22)) { -+ } else if (!memcmp(argptr2, "lip-scan-window-kb", 19)) { - if (!(calculation_type & CALC_FLIPSCAN)) { - logerrprint("Error: --flip-scan-window-kb must be used with --flip-scan.\n"); - goto main_ret_INVALID_CMDLINE; -@@ -10816,7 +10816,7 @@ - if (retval) { - goto main_ret_1; - } -- } else if (!memcmp(argptr2, "ead-genome-list", 19)) { -+ } else if (!memcmp(argptr2, "ead-genome-list", 16)) { - logerrprint("Error: --read-genome-list flag retired. Use --parallel + Unix cat instead.\n"); - goto main_ret_INVALID_CMDLINE; - } else if (!memcmp(argptr2, "ead-genome-minimal", 19)) { -diff -ru plink-ng-b15c19f.orig/1.9/plink_glm.c plink-ng-b15c19f/1.9/plink_glm.c ---- plink-ng-b15c19f.orig/1.9/plink_glm.c 2017-11-14 21:16:37.000000000 +0100 -+++ plink-ng-b15c19f/1.9/plink_glm.c 2020-10-21 16:33:56.287029270 +0200 -@@ -7821,7 +7821,7 @@ - } - for (param_idx = 1; param_idx < param_ct; param_idx++) { - wptr = strcpya(&(outname_end[1]), &(param_names[param_idx * max_param_name_len])); -- memcpy(wptr, ".mperm.dump.all", 17); -+ memcpy(wptr, ".mperm.dump.all", 16); - if (fopen_checked(outname, "w", &outfile)) { - goto glm_linear_nosnp_ret_OPEN_FAIL; - } -@@ -8605,7 +8605,7 @@ - } - for (param_idx = 1; param_idx < param_ct; param_idx++) { - wptr = strcpya(&(outname_end[1]), &(param_names[param_idx * max_param_name_len])); -- memcpy(wptr, ".mperm.dump.all", 17); -+ memcpy(wptr, ".mperm.dump.all", 16); - if (fopen_checked(outname, "w", &outfile)) { - goto glm_logistic_nosnp_ret_OPEN_FAIL; - } diff --git a/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 07c6e727d9e..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,60 +0,0 @@ -# by Ward Poelmans - -easyblock = 'ConfigureMake' - -name = 'PLUMED' -version = '2.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.plumed.org' -description = """PLUMED is an open source library for free energy calculations in molecular systems which - works together with some of the most popular molecular dynamics engines. Free energy calculations can be - performed as a function of many order parameters with a particular focus on biological problems, using - state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. - The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': 'True'} - -source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] -sources = [SOURCE_TGZ] -checksums = ['8a760a637225eeb97e84b748e992ebc0730f71cdb4737af545445132380bfff9'] - -dependencies = [ - ('zlib', '1.2.11'), - ('GSL', '2.6'), - ('libmatheval', '1.1.11'), - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Boost', '1.72.0'), -] - -preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' -configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' -configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' -prebuildopts = 'source sourceme.sh && ' - -# make sure that ld.gold linker is used -# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" -# (problem with intel build but maintain consistency between easyconfigs) -buildopts = 'LD_RO="ld.gold -r -o"' - -# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed -preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' - -sanity_check_paths = { - 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], - 'dirs': [], -} - -sanity_check_commands = ["python -c 'import plumed'"] - -modextrapaths = { - 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, - 'PLUMED_ROOT': 'lib/plumed', - 'PYTHONPATH': 'lib/plumed/python', -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index c7b659d56d9..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,60 +0,0 @@ -# by Ward Poelmans - -easyblock = 'ConfigureMake' - -name = 'PLUMED' -version = '2.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.plumed.org' -description = """PLUMED is an open source library for free energy calculations in molecular systems which - works together with some of the most popular molecular dynamics engines. Free energy calculations can be - performed as a function of many order parameters with a particular focus on biological problems, using - state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. - The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. -""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': 'True'} - -source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] -sources = [SOURCE_TGZ] -checksums = ['8a760a637225eeb97e84b748e992ebc0730f71cdb4737af545445132380bfff9'] - -dependencies = [ - ('zlib', '1.2.11'), - ('GSL', '2.6'), - ('libmatheval', '1.1.11'), - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Boost', '1.72.0'), -] - -preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' -configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' -configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' -prebuildopts = 'source sourceme.sh && ' - -# make sure that ld.gold linker is used -# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" -# (problem with intel build but maintain consistency between easyconfigs) -buildopts = 'LD_RO="ld.gold -r -o"' - -# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed -preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' - -sanity_check_paths = { - 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], - 'dirs': [], -} - -sanity_check_commands = ["python -c 'import plumed'"] - -modextrapaths = { - 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, - 'PLUMED_ROOT': 'lib/plumed', - 'PYTHONPATH': 'lib/plumed/python', -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb deleted file mode 100644 index 59b8ab28bce..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb +++ /dev/null @@ -1,51 +0,0 @@ -# Note: -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -easyblock = 'ConfigureMake' - -name = 'PMIx' -version = '3.1.5' - -homepage = 'https://pmix.org/' -description = """Process Management for Exascale Environments -PMI Exascale (PMIx) represents an attempt to -provide an extended version of the PMI standard specifically designed -to support clusters up to and including exascale sizes. The overall -objective of the project is not to branch the existing pseudo-standard -definitions - in fact, PMIx fully supports both of the existing PMI-1 -and PMI-2 APIs - but rather to (a) augment and extend those APIs to -eliminate some current restrictions that impact scalability, and (b) -provide a reference implementation of the PMI-server that demonstrates -the desired level of scalability. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.bz2'] -patches = ['PMIx-3.1.x_lchown.patch'] -checksums = [ - {'pmix-3.1.5.tar.bz2': '88934195174455df478b996313095df25b51d0caf5a5cce01b22f0ccdc6c5cf7'}, - {'PMIx-3.1.x_lchown.patch': '9a4d5e3cb0e619f2e9ac2ffad0b8cb2b22f5c67973080724c79519fb34d55776'}, -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('libevent', '2.1.11'), - ('zlib', '1.2.11'), - ('hwloc', '2.2.0'), -] - -configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' -configopts += ' --with-hwloc=$EBROOTHWLOC' -configopts += ' --enable-pmix-binaries' - -buildopts = 'V=1' - -sanity_check_paths = { - 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], - 'dirs': ['etc', 'include', 'lib', 'share'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/PRANK/PRANK-170427-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PRANK/PRANK-170427-GCC-9.3.0.eb deleted file mode 100644 index 146ae9bf55f..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PRANK/PRANK-170427-GCC-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel - -easyblock = 'MakeCp' - -name = 'PRANK' -version = '170427' - -homepage = 'http://wasabiapp.org/software/prank/' -description = """ PRANK is a probabilistic multiple alignment program for DNA, - codon and amino-acid sequences. PRANK is based on a novel algorithm that treats - insertions correctly and avoids over-estimation of the number of deletion events.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['http://wasabiapp.org/download/prank/'] -sources = ['%(namelower)s.source.%(version)s.tgz'] -checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859'] - -# PRANK uses MAFFT as external tool to contruct guide tree -dependencies = [('MAFFT', '7.453', '-with-extensions')] - -start_dir = 'src' - -files_to_copy = [(['prank'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/prank'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb deleted file mode 100644 index 2bca330dfe8..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2014-2015 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## -easyblock = 'ConfigureMake' - -name = 'PROJ' -version = '7.0.0' - -homepage = 'https://proj.org' -description = """Program proj is a standard Unix filter function which converts -geographic longitude and latitude coordinates into cartesian coordinates""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://download.osgeo.org/proj/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['ee0e14c1bd2f9429b1a28999240304c0342ed739ebaea3d4ff44c585b1097be8'] - -builddependencies = [ - ('pkg-config', '0.29.2'), - ('binutils', '2.34'), -] - -dependencies = [ - ('SQLite', '3.31.1'), - ('LibTIFF', '4.1.0'), - ('cURL', '7.69.1'), - ('XZ', '5.2.5'), -] - -sanity_check_paths = { - 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', - 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb deleted file mode 100644 index df40dd92fe8..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen - -easyblock = 'CMakeMakeCp' - -name = 'PRSice' -version = '2.3.1' - -homepage = 'https://www.prsice.info/' -description = """PRSice (pronounced 'precise') is a Polygenic Risk -Score software for calculating, applying, evaluating and -plotting the results of polygenic risk scores (PRS) analyses.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/choishingwan/PRSice/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['b4adec078d7101d00390e529c9cb6d935c50d60ae17db6fa044295767d3131a4'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34'), - ('Eigen', '3.3.7'), -] - -files_to_copy = [(['bin/PRSice'], 'bin'), "README.md", "LICENSE"] - -sanity_check_paths = { - 'files': ['bin/PRSice'], - 'dirs': [], -} - -sanity_check_commands = ["PRSice --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PRSice/PRSice-2.3.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PRSice/PRSice-2.3.3-GCCcore-9.3.0.eb deleted file mode 100644 index ea30f4a41fa..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PRSice/PRSice-2.3.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen - -easyblock = 'CMakeMakeCp' - -name = 'PRSice' -version = '2.3.3' - -homepage = 'https://www.prsice.info/' -description = """PRSice (pronounced 'precise') is a Polygenic Risk -Score software for calculating, applying, evaluating and -plotting the results of polygenic risk scores (PRS) analyses.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/choishingwan/PRSice/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['99cac1fdff727b652969ca50be32c1aebf5393c17c2df0a1a745ce6991b69eab'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34'), - ('Eigen', '3.3.7'), -] - -files_to_copy = [(['bin/PRSice'], 'bin'), "README.md", "LICENSE"] - -sanity_check_paths = { - 'files': ['bin/PRSice'], - 'dirs': [], -} - -sanity_check_commands = ["PRSice --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/Pango/Pango-1.44.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/Pango/Pango-1.44.7-GCCcore-9.3.0.eb deleted file mode 100644 index e1854b8c461..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Pango/Pango-1.44.7-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'Pango' -version = '1.44.7' - -homepage = 'https://www.pango.org/' -description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. -Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the -context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['66a5b6cc13db73efed67b8e933584509f8ddb7b10a8a40c3850ca4a985ea1b1f'] - -builddependencies = [ - ('binutils', '2.34'), - ('Meson', '0.55.1', '-Python-3.8.2'), - ('Ninja', '1.10.0'), - ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('X11', '20200222'), - ('GLib', '2.64.1'), - ('cairo', '1.16.0'), - ('HarfBuzz', '2.6.4'), - ('FriBidi', '1.0.9'), -] - -configopts = "--default-library=both " - -sanity_check_paths = { - 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, - 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-gompi-2020a.eb deleted file mode 100644 index d49afb48f0c..00000000000 --- a/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-gompi-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'ParMETIS' -version = '4.0.3' - -homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning - unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the - functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and - large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way - graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = [ - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] - -builddependencies = [('CMake', '3.16.4')] - -# Build static and shared libraries -configopts = ['', '-DSHARED=1'] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020a.eb deleted file mode 100644 index 222ea8e853f..00000000000 --- a/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020a.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'ParMETIS' -version = '4.0.3' - -homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning - unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the - functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and - large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way - graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = [ - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] - -builddependencies = [('CMake', '3.16.4')] - -configopts = ['', '-DSHARED=1'] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/ParMGridGen/ParMGridGen-1.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/p/ParMGridGen/ParMGridGen-1.0-gompi-2020a.eb deleted file mode 100644 index 85b77436f0b..00000000000 --- a/easybuild/easyconfigs/__archive__/p/ParMGridGen/ParMGridGen-1.0-gompi-2020a.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'MakeCp' - -name = 'ParMGridGen' -version = '1.0' - -homepage = 'http://www-users.cs.umn.edu/~moulitsa/software.html' -description = """ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, - that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited - for geometric multigrid methods.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = ['https://download.sourceforge.net/foam-extend/'] -sources = [SOURCE_TAR_GZ] -patches = [ - 'ParMGridGen-%(version)s_malloc_include.patch', - 'ParMGridGen-%(version)s_gompiOpenFOAM-Extend.patch', -] -checksums = [ - '62cdb6e48cfc59124e5d5d360c2841e0fc2feecafe65bda110b74e942740b395', # ParMGridGen-1.0.tar.gz - '3e0d72f82b3b56cbfcb1e3c9afc6594eb25316a0faeb49237faa8d969b4daeaa', # ParMGridGen-1.0_malloc_include.patch - '60cc46d156e99101b21bde9d23cf6c2db3dcdef1704f1830a7baa0320003c02a', # ParMGridGen-1.0_gompiOpenFOAM-Extend.patch -] - -buildopts = 'parallel make=make CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' - -files_to_copy = [ - (['MGridGen/Programs/mgridgen', 'ParMGridGen/Programs/parmgridgen'], 'bin'), - (['mgridgen.h', 'parmgridgen.h', 'MGridGen/IMlib/IMlib.h'], 'include'), - (['libmgrid.a', 'libMGridGen.a', 'libparmgrid.a', 'MGridGen/IMlib/libIMlib.a'], 'lib'), -] - -sanity_check_paths = { - 'files': ['bin/mgridgen', 'bin/parmgridgen', 'include/mgridgen.h', 'include/parmgridgen.h', - 'include/IMlib.h', 'lib/libmgrid.a', 'lib/libMGridGen.a', 'lib/libparmgrid.a', 'lib/libIMlib.a'], - 'dirs': [], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/ParMGridGen/ParMGridGen-1.0-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/p/ParMGridGen/ParMGridGen-1.0-iimpi-2020a.eb deleted file mode 100644 index 27ad4c98c64..00000000000 --- a/easybuild/easyconfigs/__archive__/p/ParMGridGen/ParMGridGen-1.0-iimpi-2020a.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'MakeCp' - -name = 'ParMGridGen' -version = '1.0' - -homepage = 'http://www-users.cs.umn.edu/~moulitsa/software.html' -description = """ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, - that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited - for geometric multigrid methods.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = ['https://download.sourceforge.net/foam-extend/'] -sources = [SOURCE_TAR_GZ] -patches = ['ParMGridGen-%(version)s_malloc_include.patch'] -checksums = [ - '62cdb6e48cfc59124e5d5d360c2841e0fc2feecafe65bda110b74e942740b395', # ParMGridGen-1.0.tar.gz - '3e0d72f82b3b56cbfcb1e3c9afc6594eb25316a0faeb49237faa8d969b4daeaa', # ParMGridGen-1.0_malloc_include.patch -] - -buildopts = 'parallel make=make CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' - -files_to_copy = [ - (['MGridGen/Programs/mgridgen', 'ParMGridGen/Programs/parmgridgen'], 'bin'), - (['mgridgen.h', 'parmgridgen.h'], 'include'), - (['libmgrid.a', 'libparmgrid.a'], 'lib'), -] - -sanity_check_paths = { - 'files': ['bin/mgridgen', 'bin/parmgridgen', 'include/mgridgen.h', 'include/parmgridgen.h', - 'lib/libmgrid.a', 'lib/libparmgrid.a'], - 'dirs': [], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-5.8.0-foss-2020a-Python-3.8.2-mpi.eb b/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-5.8.0-foss-2020a-Python-3.8.2-mpi.eb deleted file mode 100644 index ba28603c3a5..00000000000 --- a/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-5.8.0-foss-2020a-Python-3.8.2-mpi.eb +++ /dev/null @@ -1,55 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'ParaView' -version = '5.8.0' -versionsuffix = '-Python-%(pyver)s-mpi' - -homepage = "https://www.paraview.org" -description = "ParaView is a scientific parallel visualizer." - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' -source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] -sources = ["ParaView-v%(version)s.tar.xz"] -checksums = ['219e4107abf40317ce054408e9c3b22fb935d464238c1c00c0161f1c8697a3f9'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-3.8.2'), - ('XZ', '5.2.5'), - ('HDF5', '1.10.6'), - ('netCDF', '4.7.4'), - ('libGLU', '9.0.1'), - ('X11', '20200222'), - ('Mesa', '20.0.2'), - ('Qt5', '5.14.1'), - ('zlib', '1.2.11'), - ('FFmpeg', '4.2.2'), - ('Szip', '2.1.1'), -] - -builddependencies = [('CMake', '3.16.4')] - -separate_build_dir = True - -# Paraview -configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' -configopts += '-DPARAVIEW_USE_MPI=ON ' -configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' -configopts += '-DPARAVIEW_USE_PYTHON=ON ' -configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' - -# OpenGL & Mesa -configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT -configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' - -sanity_check_paths = { - 'files': ['bin/paraview', 'bin/pvpython'], - 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ['python -c "import paraview"'] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-5.8.0-intel-2020a-Python-3.8.2-mpi.eb b/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-5.8.0-intel-2020a-Python-3.8.2-mpi.eb deleted file mode 100644 index b73dccf72d0..00000000000 --- a/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-5.8.0-intel-2020a-Python-3.8.2-mpi.eb +++ /dev/null @@ -1,60 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'ParaView' -version = '5.8.0' -versionsuffix = '-Python-%(pyver)s-mpi' - -homepage = "https://www.paraview.org" -description = "ParaView is a scientific parallel visualizer." - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' -source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] -sources = ["ParaView-v%(version)s.tar.xz"] -checksums = ['219e4107abf40317ce054408e9c3b22fb935d464238c1c00c0161f1c8697a3f9'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-3.8.2'), - ('XZ', '5.2.5'), - ('HDF5', '1.10.6'), - ('netCDF', '4.7.4'), - ('libGLU', '9.0.1'), - ('X11', '20200222'), - ('Mesa', '20.0.2'), - ('Qt5', '5.14.1'), - ('zlib', '1.2.11'), - ('FFmpeg', '4.2.2'), - ('Szip', '2.1.1'), -] - -builddependencies = [('CMake', '3.16.4')] - -separate_build_dir = True - -# Paraview -configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' -configopts += '-DPARAVIEW_USE_MPI=ON ' -configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' -configopts += '-DPARAVIEW_USE_PYTHON=ON ' -configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' - -# There is a problem with intel compiler. It seems that -ipo triggers some bug, which results in a -# messages like 'icpc: error #10014: problem during multi-file optimization compilation (code 4)'. -# Thus, -no-ipo is set. -configopts += '-DCMAKE_CXX_FLAGS_RELEASE="$CXXFLAGS -DNDEBUG -no-ipo" ' - -# OpenGL & Mesa -configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT -configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' - -sanity_check_paths = { - 'files': ['bin/paraview', 'bin/pvpython'], - 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ['python -c "import paraview"'] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/ParmEd/ParmEd-3.2.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/ParmEd/ParmEd-3.2.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 72220ad77dd..00000000000 --- a/easybuild/easyconfigs/__archive__/p/ParmEd/ParmEd-3.2.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'ParmEd' -version = '3.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://parmed.github.io/ParmEd' -description = """ParmEd is a general tool for aiding in investigations of biomolecular systems using popular - molecular simulation packages, like Amber, CHARMM, and OpenMM written in Python.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['0c178994af736b16df3c8eaa9c54a0ac98425129c8f0228563acc094e7c6f40f'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('OpenMM', '7.4.2', versionsuffix), -] - -sanity_check_paths = { - 'files': ['bin/parmed', 'bin/xparmed'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["parmed --help"] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb deleted file mode 100644 index fec6c89d995..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'Perl' -version = '5.30.2' -versionsuffix = '-minimal' - -homepage = 'https://www.perl.org/' -description = """Larry Wall's Practical Extraction and Report Language - -This is a minimal build without any modules. Should only be used for build dependencies. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] -checksums = [ - {'perl-5.30.2.tar.gz': '66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689'}, - {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': - '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, -] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb deleted file mode 100644 index 98e93f98b52..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,1803 +0,0 @@ -name = 'Perl' -version = '5.30.2' - -homepage = 'https://www.perl.org/' -description = """Larry Wall's Practical Extraction and Report Language""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] -checksums = [ - {'perl-5.30.2.tar.gz': '66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689'}, - {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': - '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, -] - -builddependencies = [ - ('binutils', '2.34'), - ('groff', '1.22.4'), -] - -dependencies = [ - ('zlib', '1.2.11'), # for Net::SSLeay - ('expat', '2.2.9'), # for XML::Parser - ('ncurses', '6.2'), # for Term::ReadLine::Gnu - ('libreadline', '8.0'), # for Term::ReadLine::Gnu - ('DB', '18.1.32'), # for DB_File -] - -# OpenSSL is required for Net::SSLeay -osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -# !! order of extensions is important !! -# extensions updated on Sept 13th 2019 -exts_list = [ - ('Config::General', '2.63', { - 'source_tmpl': 'Config-General-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], - 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], - }), - ('File::Listing', '6.04', { - 'source_tmpl': 'File-Listing-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], - 'checksums': ['1e0050fcd6789a2179ec0db282bf1e90fb92be35d1171588bd9c47d52d959cf5'], - }), - ('ExtUtils::InstallPaths', '0.012', { - 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], - }), - ('ExtUtils::Helpers', '0.026', { - 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], - }), - ('Test::Harness', '3.42', { - 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['0fd90d4efea82d6e262e6933759e85d27cbcfa4091b14bf4042ae20bab528e53'], - }), - ('ExtUtils::Config', '0.008', { - 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], - }), - ('Module::Build::Tiny', '0.039', { - 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], - }), - ('aliased', '0.34', { - 'source_tmpl': 'aliased-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], - }), - ('Text::Glob', '0.11', { - 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], - 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], - }), - ('Regexp::Common', '2017060201', { - 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], - 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], - }), - ('GO::Utils', '0.15', { - 'source_tmpl': 'go-perl-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], - 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], - }), - ('Module::Pluggable', '5.2', { - 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], - 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], - }), - ('Test::Fatal', '0.014', { - 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['bcdcef5c7b2790a187ebca810b0a08221a63256062cfab3c3b98685d91d1cbb0'], - }), - ('Test::Warnings', '0.029', { - 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['b55214ea50395f1ae14ac504dd3d0d21580a92c558e8049cbe7b3ac42add1792'], - }), - ('File::ShareDir', '1.116', { - 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], - 'checksums': ['59d90bfdf98c4656ff4173e62954ea8cf0de66565e35d108ecd7050596cb8328'], - }), - ('File::ShareDir::Install', '0.13', { - 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['45befdf0d95cbefe7c25a1daf293d85f780d6d2576146546e6828aad26e580f9'], - }), - ('DateTime::Locale', '1.25', { - 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['aa79746bd488b32aa4dbccccd05f1e5505642be013d8064a5d6f8a76a3c45d0b'], - }), - ('DateTime::TimeZone', '2.38', { - 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['0e5c99ef22471f4d262ac590ce5ce8177094d7a92f380d8eea6219f5a12dc0cd'], - }), - ('Test::Requires', '0.10', { - 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], - 'checksums': ['2768a391d50ab94b95cefe540b9232d7046c13ee86d01859e04c044903222eb5'], - }), - ('Module::Implementation', '0.09', { - 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], - }), - ('Module::Build', '0.4231', { - 'source_tmpl': 'Module-Build-%(version)s.tar.gz', - 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}), - ('Encode', '3.04', { - 'source_tmpl': 'Encode-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], - 'checksums': ['2a04dc334846915bdb52ef03422f4f47ce588d2edf4b8ae4e7e442748e7ae09a'], - }), - ('constant', '1.33', { - 'source_tmpl': 'constant-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], - }), - ('Data::Dumper', '2.173', { - 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], - }), - ('Cwd', '3.75', { - 'source_tmpl': 'PathTools-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], - }), - ('MIME::Base64', '3.15', { - 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], - 'checksums': ['7f863566a6a9cb93eda93beadb77d9aa04b9304d769cea3bb921b9a91b3a1eb9'], - }), - ('ExtUtils::CppGuess', '0.21', { - 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], - 'checksums': ['ff629178321a1e591b83f809712593eae4408a413aa448654bce59b156f24153'], - }), - ('XSLoader', '0.24', { - 'source_tmpl': 'XSLoader-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], - 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], - }), - ('AutoLoader', '5.74', { - 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], - 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], - }), - ('URI::Escape', '3.31', { - 'source_tmpl': 'URI-1.76.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['b2c98e1d50d6f572483ee538a6f4ccc8d9185f91f0073fd8af7390898254413e'], - }), - ('Set::IntervalTree', '0.12', { - 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], - 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], - }), - ('MCE::Mutex', '1.866', { - 'source_tmpl': 'MCE-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/'], - 'checksums': ['087ad6d6a495d823771e5bc23bcbcd31c683289b5cb45fc4e857449f9ea7aa1b'], - }), - ('Text::CSV_XS', '1.41', { - 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND/'], - 'checksums': ['0e4b7be423c02f09135a75082cb00136ff6a69cff25b012089048ea030f173ab'], - }), - ('DBD::CSV', '0.54', { - 'source_tmpl': 'DBD-CSV-%(version)s.tgz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND/'], - 'checksums': ['bc597cd7195e5a023e2b3413d8dc614602b9b3f279f436027881796464d4f0be'], - }), - ('Array::Transpose', '0.06', { - 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT/'], - 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], - }), - ('Config::Simple', '4.58', { - 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR/'], - 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], - }), - ('Business::ISBN', '3.005', { - 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], - 'checksums': ['6530fbae40c56376db4e6686c34af8da3db5c4baad0d104047b1ef3e24fe2e2a'], - }), - ('Business::ISBN::Data', '20191107', { - 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], - 'checksums': ['844c4f64f193d389340b4465a1d5bc34c60f0c8e42e5c69ac8afe3d3bbc5ca0d'], - }), - ('common::sense', '3.75', { - 'source_tmpl': 'common-sense-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], - 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], - }), - ('JSON::XS', '4.03', { - 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], - 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], - }), - ('List::MoreUtils::XS', '0.430', { - 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], - 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], - }), - ('Authen::NTLM', '1.09', { - 'source_tmpl': 'NTLM-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT/'], - 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], - }), - ('Types::Serialiser', '1.0', { - 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], - 'checksums': ['7ad3347849d8a3da6470135018d6af5fd8e58b4057cd568c3813695f2a04730d'], - }), - ('XML::SAX::Expat', '0.51', { - 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN/'], - 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], - }), - ('Inline', '0.86', { - 'source_tmpl': 'Inline-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY/'], - 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.1-FCC-4.5.0.eb deleted file mode 100644 index d70fd1c84b2..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.1-FCC-4.5.0.eb +++ /dev/null @@ -1,1789 +0,0 @@ -## -# Author: Robert Mijakovic -## -name = 'Perl' -version = '5.32.1' - -homepage = 'https://www.perl.org/' -description = """Larry Wall's Practical Extraction and Report Language""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] -checksums = [ - {'perl-5.32.1.tar.gz': '03b693901cd8ae807231b1787798cf1f2e0b8a56218d07b7da44f784a7caeb2c'}, - {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': - '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, -] - -builddependencies = [ - ('binutils', '2.36.1'), - ('groff', '1.22.4'), -] - -dependencies = [ - ('zlib', '1.2.11'), # for Net::SSLeay - ('expat', '2.2.9'), # for XML::Parser - ('ncurses', '6.2'), # for Term::ReadLine::Gnu - ('libreadline', '8.1'), # for Term::ReadLine::Gnu - ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay -] - -exts_default_options = {'buildopts': 'CC="$CC"'} - -# !! order of extensions is important !! -# extensions updated on Apr 21st 2021 -exts_list = [ - ('Config::General', '2.63', { - 'source_tmpl': 'Config-General-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], - 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], - }), - ('File::Listing', '6.14', { - 'source_tmpl': 'File-Listing-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], - 'checksums': ['15b3a4871e23164a36f226381b74d450af41f12cc94985f592a669fcac7b48ff'], - }), - ('ExtUtils::InstallPaths', '0.012', { - 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], - }), - ('ExtUtils::Helpers', '0.026', { - 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], - }), - ('Test::Harness', '3.42', { - 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['0fd90d4efea82d6e262e6933759e85d27cbcfa4091b14bf4042ae20bab528e53'], - }), - ('ExtUtils::Config', '0.008', { - 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], - }), - ('Module::Build::Tiny', '0.039', { - 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], - }), - ('aliased', '0.34', { - 'source_tmpl': 'aliased-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], - }), - ('Text::Glob', '0.11', { - 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], - 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], - }), - ('Regexp::Common', '2017060201', { - 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], - 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], - }), - ('GO::Utils', '0.15', { - 'source_tmpl': 'go-perl-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], - 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], - }), - ('Module::Pluggable', '5.2', { - 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], - 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], - }), - ('Test::Fatal', '0.016', { - 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['7283d430f2ba2030b8cd979ae3039d3f1b2ec3dde1a11ca6ae09f992a66f788f'], - }), - ('Test::Warnings', '0.030', { - 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['89a4947ddf1564ae01122275584433d7f6c4370370bcf3768922d796956ae24f'], - }), - ('File::ShareDir', '1.118', { - 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], - 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], - }), - ('File::ShareDir::Install', '0.13', { - 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['45befdf0d95cbefe7c25a1daf293d85f780d6d2576146546e6828aad26e580f9'], - }), - ('DateTime::Locale', '1.31', { - 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['c7224c7e51dce4dd9ba80d8857cd4c3b72137653da34d3ba3c3a3c20cbf438b8'], - }), - ('DateTime::TimeZone', '2.47', { - 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['41617138dbb5e255fe5ac3cab6f1cc8e09f934bc95906b8cd7077192a21ef2b9'], - }), - ('Test::Requires', '0.11', { - 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], - 'checksums': ['4b88de549597eecddf7c3c38a4d0204a16f59ad804577b671896ac04e24e040f'], - }), - ('Module::Implementation', '0.09', { - 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], - }), - ('Module::Build', '0.4231', { - 'source_tmpl': 'Module-Build-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['7e0f4c692c1740c1ac84ea14d7ea3d8bc798b2fb26c09877229e04f430b2b717'], - }), - ('Module::Runtime', '0.016', { - 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], - 'checksums': ['68302ec646833547d410be28e09676db75006f4aa58a11f3bdb44ffe99f0f024'], - }), - ('Try::Tiny', '0.30', { - 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['da5bd0d5c903519bbf10bb9ba0cb7bcac0563882bcfe4503aee3fb143eddef6b'], - }), - ('Params::Validate', '1.30', { - 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['9a3a35583d3125d07e8c802c1f92f5be7d526e76dd496e944da270b1e273d812'], - }), - ('List::MoreUtils', '0.430', { - 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], - 'checksums': ['63b1f7842cd42d9b538d1e34e0330de5ff1559e4c2737342506418276f646527'], - }), - ('Exporter::Tiny', '1.002002', { - 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], - 'checksums': ['00f0b95716b18157132c6c118ded8ba31392563d19e490433e9a65382e707101'], - }), - ('Class::Singleton', '1.6', { - 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], - 'checksums': ['27ba13f0d9512929166bbd8c9ef95d90d630fc80f0c9a1b7458891055e9282a4'], - }), - ('DateTime', '1.54', { - 'source_tmpl': 'DateTime-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['b12eda6d900713f227964dc4dc0e2efb86d294e8bc2f16be9e95b659f953b2e7'], - }), - ('File::Find::Rule::Perl', '1.15', { - 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['9a48433f86e08ce18e03526e2982de52162eb909d19735460f07eefcaf463ea6'], - 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}), - ('Net::Domain', '3.13', { - 'source_tmpl': 'libnet-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], - 'checksums': ['5a35fb1f2d4aa291680eb1af38899fab453c22c28e71f7c7bd3747b5a3db348c'], - }), - ('Scalar::Util', '1.56', { - 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], - 'checksums': ['15b8537d40fb3e6dae64b2e7e983c47a99b2c20816a180bb9c868b787a12ab5b'], - }), - ('Text::ParseWords', '3.30', { - 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], - 'checksums': ['85e0238179dd43997e58c66bd51611182bc7d533505029a2db0d3232edaff5e8'], - }), - ('Encode', '3.08', { - 'source_tmpl': 'Encode-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], - 'checksums': ['ed063d01d01a140a3a3ec0aeba2f2b4849a35c18ca96ac231a5d7c7d54d17b5b'], - }), - ('constant', '1.33', { - 'source_tmpl': 'constant-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], - }), - ('Data::Dumper', '2.173', { - 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], - }), - ('Cwd', '3.75', { - 'source_tmpl': 'PathTools-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], - 'checksums': [ - 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', - {'PathTools-3.75_fix-cwd_enoent-test.patch': - '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, - ], - }), - ('MIME::Base64', '3.16', { - 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], - 'checksums': ['77f73d6f7aeb8d33be08b0d8c2617f9b6c77fb7fc45422d507ca8bafe4246017'], - }), - ('ExtUtils::CppGuess', '0.21', { - 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], - 'checksums': ['ff629178321a1e591b83f809712593eae4408a413aa448654bce59b156f24153'], - }), - ('XSLoader', '0.24', { - 'source_tmpl': 'XSLoader-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], - 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], - }), - ('AutoLoader', '5.74', { - 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], - 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], - }), - ('URI::Escape', '5.09', { - 'source_tmpl': 'URI-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['03e63ada499d2645c435a57551f041f3943970492baa3b3338246dab6f1fae0a'], - }), - ('Set::IntervalTree', '0.12', { - 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], - 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], - }), - ('MCE::Mutex', '1.874', { - 'source_tmpl': 'MCE-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], - 'checksums': ['d809e3018475115ad7eccb8bef49bde3bf3e75abbbcd80564728bbcfab86d3d0'], - }), - ('Text::CSV_XS', '1.46', { - 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], - 'checksums': ['27e39f0d5f2322aaf78ff90eb1221f3cbed1d4c514d0956bda19407fcb98bed6'], - }), - ('DBD::CSV', '0.58', { - 'source_tmpl': 'DBD-CSV-%(version)s.tgz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], - 'checksums': ['6c26f710453b14d7b3cf5f3e1697e8ddaa48c0a66f5d811f4394bd8c32f287ef'], - }), - ('Array::Transpose', '0.06', { - 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], - 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], - }), - ('Config::Simple', '4.58', { - 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], - 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], - }), - ('Business::ISBN', '3.006', { - 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], - 'checksums': ['c1fefe68354ffb80cdbd24303ebe684b3b6828df3d5f09b429a09fc4f0919c9a'], - }), - ('Business::ISBN::Data', '20210112.006', { - 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], - 'checksums': ['98c2cfb266b5fdd016989abaa471d9dd4c1d593c508a6f01f66d184d5fee8bae'], - }), - ('common::sense', '3.75', { - 'source_tmpl': 'common-sense-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], - 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], - }), - ('IO::Compress::Bzip2', '2.102', { - 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], - 'checksums': ['d6fa7f9a5beee446452a0fbc43589a0c73fe7e925c075b98628b018048dc72a4'], - }), - ('JSON::XS', '4.03', { - 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], - 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], - }), - ('List::MoreUtils::XS', '0.430', { - 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], - 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], - }), - ('Authen::NTLM', '1.09', { - 'source_tmpl': 'NTLM-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], - 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], - }), - ('Types::Serialiser', '1.01', { - 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], - 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], - }), - ('XML::SAX::Expat', '0.51', { - 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'], - 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], - }), - ('Inline', '0.86', { - 'source_tmpl': 'Inline-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], - 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 4a0ee8e12a9..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,51 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'PhyloPhlAn' -version = '3.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/biobakery/phylophlan' -description = """ -PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of -genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method -for large-scale microbial genome characterization and phylogenetic analysis -at multiple levels of resolution. -""" - -source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] -sources = ['%(version)s.tar.gz'] -checksums = ['26d150d37159406f678165bf3d6cb06b3021fb2227b301b06095e769c87bdd9f'] - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('Biopython', '1.78', versionsuffix), - ('DendroPy', '4.4.0'), - ('matplotlib', '3.2.1', versionsuffix), - ('Seaborn', '0.10.1', versionsuffix), - ('FastTree', '2.1.11'), - ('IQ-TREE', '2.1.2'), - ('MUSCLE', '3.8.31'), - ('MAFFT', '7.453', '-with-extensions'), - ('SEPP', '4.3.10', versionsuffix), - ('trimAl', '1.4.1'), - ('BLAST+', '2.10.1'), - ('USEARCH', '11.0.667-i86linux32', '', SYSTEM), - ('DIAMOND', '2.0.4'), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], - 'dirs': ['lib'], -} -sanity_check_commands = [('%(namelower)s', '-h')] - -options = {'modulename': '%(namelower)s'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 9ef1225e1e3..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pillow-SIMD' -version = '7.1.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/uploadcare/pillow-simd' -description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. - PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['Pillow-8_CVE-2021-23437.patch'] -checksums = [ - '72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa', # 7.1.2.tar.gz - '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Python', '3.8.2'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), - ('LibTIFF', '4.1.0'), - ('freetype', '2.10.1') -] - -options = {'modulename': 'PIL'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index ad658fbc802..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pillow' -version = '7.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pillow.readthedocs.org/' -description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. - PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] -checksums = [ - '4d9ed9a64095e031435af120d3c910148067087541131e82b3e8db302f4c8946', # Pillow-7.0.0.tar.gz - '8c4195792e3a3581fef80a4cbca39f1123c0b83f74acc002bbbec7185c62baf3', # Pillow-7_CVE-2021-23437.patch -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Python', '3.8.2'), - ('libjpeg-turbo', '2.0.4'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), - ('LibTIFF', '4.1.0'), - ('freetype', '2.10.1') -] - -# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template -# (which will be empty if EasyBuild is not configured to use an alternate sysroot); -# see also https://gitlab.com/eessi/support/-/issues/9 -preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ -preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ - -# avoid that hardcoded paths like /usr/include are used in build commands -installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " - -options = {'modulename': 'PIL'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-7_CVE-2021-23437.patch b/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-7_CVE-2021-23437.patch deleted file mode 100644 index 747c20f3ae8..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Pillow/Pillow-7_CVE-2021-23437.patch +++ /dev/null @@ -1,27 +0,0 @@ -Fix for CVE-2021-23437 -author: Hugo van Kemenade (Nord Software) ---- a/src/PIL/ImageColor.py 2020-01-02 09:31:35.000000000 +0100 -+++ b/src/PIL/ImageColor.py 2022-01-18 16:42:11.359922625 +0100 -@@ -32,6 +32,8 @@ - :param color: A color string - :return: ``(red, green, blue[, alpha])`` - """ -+ if len(color) > 100: -+ raise ValueError("color specifier is too long") - color = color.lower() - - rgb = colormap.get(color, None) ---- a/Tests/test_imagecolor.py 2022-01-18 16:42:11.362700436 +0100 -+++ b/Tests/test_imagecolor.py 2022-01-18 17:43:53.880517448 +0100 -@@ -182,3 +182,11 @@ - self.assertEqual((255, 255), ImageColor.getcolor("white", "LA")) - self.assertEqual((163, 33), ImageColor.getcolor("rgba(0, 255, 115, 33)", "LA")) - Image.new("LA", (1, 1), "white") -+ -+def test_color_too_long(): -+ # Arrange -+ color_too_long = "hsl(" + "1" * 100 + ")" -+ -+ # Act / Assert -+ with pytest.raises(ValueError): -+ ImageColor.getrgb(color_too_long) diff --git a/easybuild/easyconfigs/__archive__/p/PlasmaPy/PlasmaPy-0.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PlasmaPy/PlasmaPy-0.3.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 42c060f3c3a..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PlasmaPy/PlasmaPy-0.3.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PlasmaPy' -version = '0.3.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.plasmapy.org' -description = """Open source Python ecosystem for plasma research and education""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('h5py', '2.10.0', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('mpmath', '1.1.0', versionsuffix), - ('astropy', '4.0.1', versionsuffix), - ('pybind11', '2.4.3', versionsuffix), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('colorama', '0.4.3', { - 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], - }), - ('uncertainties', '3.1.2', { - 'checksums': ['ba07c17a8a78cb58a47cd373079c7ea459f8b26cd474e29163b6ba0d72856a1e'], - }), - ('asteval', '0.9.18', { - 'checksums': ['5d64e18b8a72c2c7ae8f9b70d1f80b68bbcaa98c1c0d7047c35489d03209bc86'], - }), - ('lmfit', '1.0.1', { - 'checksums': ['d249eb756899360f4d2a544c9458f47fc8f765ac22c09e099530585fd64e286e'], - }), - ('plasmapy', version, { - 'checksums': ['d2af2dd4de77797c5d26e2ae2ca894619f18c117f61aba5ffcb8e3eaff319fed'], - }), -] - -sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/plasmapy/README.md'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.1-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.1-gompi-2020a.eb deleted file mode 100644 index 1e8e0989213..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.1-gompi-2020a.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PnetCDF' -version = "1.12.1" - -homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' -description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://parallel-netcdf.github.io/Release/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2'] - -builddependencies = [ - ('Autotools', '20180311'), - ('Perl', '5.30.2'), -] - -preconfigopts = "autoreconf -f -i && " - -configopts = ['', '--enable-shared'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', - 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + - ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -modextrapaths = { - 'PNETCDF': '', -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.1-gompic-2020a.eb b/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.1-gompic-2020a.eb deleted file mode 100644 index a57028784ce..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.1-gompic-2020a.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PnetCDF' -version = "1.12.1" - -homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' -description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" - -toolchain = {'name': 'gompic', 'version': '2020a'} - -source_urls = ['https://parallel-netcdf.github.io/Release/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2'] - -builddependencies = [ - ('Autotools', '20180311'), - ('Perl', '5.30.2'), -] - -preconfigopts = "autoreconf -f -i && " - -configopts = ['', '--enable-shared'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', - 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + - ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -modextrapaths = { - 'PNETCDF': '', -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.1-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.1-iimpi-2020a.eb deleted file mode 100644 index 21567908664..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PnetCDF/PnetCDF-1.12.1-iimpi-2020a.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PnetCDF' -version = "1.12.1" - -homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' -description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" - -toolchain = {'name': 'iimpi', 'version': '2020a'} - -source_urls = ['https://parallel-netcdf.github.io/Release/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2'] - -builddependencies = [ - ('Autotools', '20180311'), - ('Perl', '5.30.2'), -] - -preconfigopts = "autoreconf -f -i && " - -configopts = ['', '--enable-shared'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', - 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + - ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -modextrapaths = { - 'PNETCDF': '', -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-12.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-12.4-GCCcore-9.3.0.eb deleted file mode 100644 index 0279d32b6eb..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-12.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,50 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'ConfigureMake' - -name = 'PostgreSQL' -version = '12.4' - -homepage = 'https://www.postgresql.org/' -description = """PostgreSQL is a powerful, open source object-relational database system. - It is fully ACID compliant, has full support for foreign keys, - joins, views, triggers, and stored procedures (in multiple languages). - It includes most SQL:2008 data types, including INTEGER, - NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. - It also supports storage of binary large objects, including pictures, - sounds, or video. It has native programming interfaces for C/C++, Java, - .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['9749b891b9d8f984312fe510a7a3613035134cee1e634793dac5568d1e1a5852'] - -builddependencies = [ - ('binutils', '2.34'), - ('Bison', '3.5.3'), - ('flex', '2.6.4'), - ('Perl', '5.30.2'), - ('Python', '3.8.2'), -] - -dependencies = [ - ('libreadline', '8.0'), - ('zlib', '1.2.11'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.0.2h'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -configopts = '--with-python --with-openssl' - -sanity_check_paths = { - 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], - 'dirs': ['share/postgresql'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/Primer3/Primer3-2.5.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/Primer3/Primer3-2.5.0-GCC-9.3.0.eb deleted file mode 100644 index 1e27a881dc2..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Primer3/Primer3-2.5.0-GCC-9.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'Primer3' -version = '2.5.0' - -homepage = 'https://primer3.org/' -description = """Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Chain Reaction'). - PCR is an essential and ubiquitous tool in genetics and molecular biology. - Primer3 can also design hybridization probes and sequencing primers.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/primer3-org/%(namelower)s/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['7581e2fa3228ef0ee1ffa427b2aa0a18fc635d561208327471daf59d1b804da0'] - -runtest = 'test' - -sanity_check_commands = [ - 'primer3_masker -h', - # https://github.com/biobuilds/biobuilds/issues/21 - 'cd %(builddir)s/%(namelower)s-%(version)s/src && primer3_core ../example' -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/ProbABEL/ProbABEL-0.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/ProbABEL/ProbABEL-0.5.0-GCCcore-9.3.0.eb deleted file mode 100644 index 8b262cb2951..00000000000 --- a/easybuild/easyconfigs/__archive__/p/ProbABEL/ProbABEL-0.5.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ProbABEL' -version = '0.5.0' - -homepage = "https://github.com/GenABEL-Project/ProbABEL" -description = """Tool for genome-wide association analysis of imputed genetic data.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'cstd': 'c++03'} - -github_account = 'GenABEL-Project' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['883f618cce4e08f25bc90faa68d47c3e548d56c177760288fbd8368df0636917'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), -] - -# Use the bundled Eigen, as tests fail with Eigen > 3.2.1 (https://github.com/GenABEL-Project/ProbABEL/issues/11) -dependencies = [('Perl', '5.30.2')] - -preconfigopts = "autoreconf -i && " -configopts = '--disable-latex-doc' - -runtest = 'check' - -postinstallcmds = ["mv %(installdir)s/etc/probabel_config.cfg.example %(installdir)s/etc/probabel_config.cfg"] - -fix_perl_shebang_for = ['bin/probabel'] - -sanity_check_paths = { - 'files': ['bin/probabel', 'bin/pacoxph', 'bin/palinear', 'bin/palogist', 'etc/probabel_config.cfg'], - 'dirs': ['share'], -} - -sanity_check_commands = ["%s --help" % x for x in ['pacoxph', 'palinear', 'palogist', 'probabel']] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PyBerny/PyBerny-0.6.2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PyBerny/PyBerny-0.6.2-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 66ac409e381..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyBerny/PyBerny-0.6.2-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,41 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonPackage' - -name = 'PyBerny' -version = '0.6.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/jhrmnn/pyberny' -description = """PyBerny is an optimizer of molecular geometries with respect to the total energy, -using nuclear gradient information.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -# https://github.com/jhrmnn/pyberny -github_account = 'jhrmnn' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['b56867f352055614441154f776575f1b318909d2c0c15eeb89a45262f079bdd7'] - -builddependencies = [('poetry', '1.0.9', versionsuffix)] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - -options = {'modulename': 'berny'} - -sanity_check_paths = { - 'files': ['bin/berny'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["berny -h"] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/p/PyCairo/PyCairo-1.18.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PyCairo/PyCairo-1.18.2-GCCcore-9.3.0.eb deleted file mode 100644 index 4fa2a09e57f..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyCairo/PyCairo-1.18.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyCairo' -version = '1.18.2' - -homepage = 'https://pycairo.readthedocs.io/' -description = """Python bindings for the cairo library""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['dcb853fd020729516e8828ad364084e752327d4cff8505d20b13504b32b16531'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('cairo', '1.16.0'), -] - -# PyGTK needs PyCairo installed by pip - -# Don't build a wheel or the pkg-cfg file won't be installed -installopts = '--no-binary=%(namelower)s' - -sanity_check_paths = { - 'files': ['%s/%s.%s' % (p, n, e) - for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')] for n in ['py3cairo', 'pycairo']], - 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], -} - -options = {'modulename': 'cairo'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 84853ac34c6..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,24 +0,0 @@ -# This easyconfig was created by the BEAR Software team at the University of Birmingham. -easyblock = 'PythonPackage' - -name = 'PyGEOS' -version = '0.8' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pygeos.readthedocs.io" -description = """PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in - the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance - improvement when operating on arrays of geometries.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['45b7e1aaa5fc9ff53565ef089fb75c53c419ace8cee18385ec1d7c1515c17cbc'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('GEOS', '3.8.1', versionsuffix), -] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index b6a71070055..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,89 +0,0 @@ -easyblock = 'Bundle' - -name = 'PyQt5' -version = '5.15.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.riverbankcomputing.com/software/pyqt' -description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. -This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'cstd': 'c++11'} - -builddependencies = [('binutils', '2.34')] -dependencies = [ - ('Python', '3.8.2'), - ('Qt5', '5.14.1'), -] - -default_easyblock = 'PythonPackage' - -local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' - -local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" - -local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " -local_pyqtweb_configopts += "--no-stubs --no-dist-info" - -local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " -local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -local_sipver = '5.4.0' -components = [ - ('SIP', local_sipver, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], - 'start_dir': 'sip-%s' % local_sipver, - 'options': {'modulename': 'PyQt5.sip'}, - }), - ('PyQt-builder', '1.5.0', { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], - 'start_dir': 'PyQt-builder-%(version)s', - }), - ('PyQt5_sip', '12.8.1', { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], - 'start_dir': 'PyQt5_sip-%(version)s', - }), - (name, version, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], - 'easyblock': 'Binary', - 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, - }), - ('PyQtWebEngine', version, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], - 'easyblock': 'ConfigureMakePythonPackage', - 'start_dir': '%(name)s-%(version)s', - 'preconfigopts': local_setup_env, - 'configopts': local_pyqtweb_configopts, - 'options': {'modulename': 'PyQt5.QtWebEngine'}, - }), -] - -sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "python -c 'import PyQt5.QtCore'", - "sip5 --help", -] - -modextrapaths = { - 'QT_INSTALL_DATA': 'qsci', -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index c8e87d39c65..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PyRETIS' -version = '2.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.pyretis.org' -description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based - on transition interface sampling and replica exchange transition interface sampling.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('MDTraj', '1.9.4', versionsuffix), - ('tqdm', '4.47.0'), - ('PyTables', '3.6.1', versionsuffix), -] - -exts_list = [ - ('colorama', '0.4.3', { - 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], - }), - ('sphinx-bootstrap-theme', '0.7.1', { - 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], - }), - (name, version, { - 'source_tmpl': 'pyretis-%(version)s.tar.gz', - 'checksums': ['b4b842a83f39e97a9bbf2d9797f53823b9e741b479b5a6744aeb42daf1c7ad2b'], - }), -] - -sanity_check_paths = { - 'files': ['bin/pyretisanalyse', 'bin/pyretisrun'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 1a91bd446a3..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PyRETIS' -version = '2.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.pyretis.org' -description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based - on transition interface sampling and replica exchange transition interface sampling.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('MDTraj', '1.9.4', versionsuffix), - ('tqdm', '4.47.0'), - ('PyTables', '3.6.1', versionsuffix), -] - -exts_list = [ - ('colorama', '0.4.3', { - 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], - }), - ('sphinx-bootstrap-theme', '0.7.1', { - 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], - }), - (name, version, { - 'source_tmpl': 'pyretis-%(version)s.tar.gz', - 'checksums': ['b4b842a83f39e97a9bbf2d9797f53823b9e741b479b5a6744aeb42daf1c7ad2b'], - }), -] - -sanity_check_paths = { - 'files': ['bin/pyretisanalyse', 'bin/pyretisrun'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/p/PySAT/PySAT-0.1.6.dev11-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PySAT/PySAT-0.1.6.dev11-GCC-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 670ff91c34d..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PySAT/PySAT-0.1.6.dev11-GCC-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PySAT' -version = '0.1.6.dev11' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/mvcisback/py-aiger' -description = """ -PySAT is a Python toolkit, which aims at providing a simple and unified -interface to a number of state-of-art Boolean satisfiability (SAT) solvers as -well as to a variety of cardinality and pseudo-Boolean encodings.""" - -# PySAT includes solvers in C and C++ -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -dependencies = [ - ('Python', '3.8.2'), - ('py-aiger', '6.1.1', versionsuffix), -] - -exts_list = [ - ('pypblib', '0.0.4', { - 'checksums': ['71dd930bf177ca38d6eeb473702d05df07e11f20382db0c766465297eaf49062'], - }), - ('python-sat', version, { - 'checksums': ['0e68f3439841dab7b43b054fbbe5299297f549c3eba189ced722d8312ecfd5d5'], - 'modulename': name.lower(), - }), -] - -# check provided examples and solvers -local_examples = ['fm', 'genhard', 'lbx', 'lsu', 'mcsls', 'models', 'musx', 'rc2'] -local_solvers = ['Cadical', 'Glucose3', 'Glucose4', 'Lingeling', 'MapleChrono', 'MapleCM', 'Maplesat', - 'Minicard', 'Minisat22', 'MinisatGH'] - -sanity_check_paths = { - 'files': ['bin/%s.py' % x for x in local_examples], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["python -c 'from pysat.solvers import %s'" % s for s in local_solvers] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 3acad61f843..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyTables' -version = '3.6.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.pytables.org' -description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope - with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the - NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical - parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, - process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk - resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as - relational or object oriented databases.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/PyTables/PyTables/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s-fix-libs.patch'] -checksums = [ - '4cea86bab5bcb5423a07c7951b8c65e24b674e0dcec0e448d434829eff5f18d0', # v3.6.1.tar.gz - '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.6.1-fix-libs.patch -] - -dependencies = [ - ('Python', '3.8.2'), - ('numexpr', '2.7.1', versionsuffix), - ('HDF5', '1.10.6'), - ('LZO', '2.10'), - ('Blosc', '1.17.1'), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -options = {'modulename': 'tables'} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 672014df512..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyTables/PyTables-3.6.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyTables' -version = '3.6.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.pytables.org' -description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope - with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the - NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical - parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, - process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk - resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as - relational or object oriented databases.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/PyTables/PyTables/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s-fix-libs.patch'] -checksums = [ - '4cea86bab5bcb5423a07c7951b8c65e24b674e0dcec0e448d434829eff5f18d0', # v3.6.1.tar.gz - '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.6.1-fix-libs.patch -] - -dependencies = [ - ('Python', '3.8.2'), - ('numexpr', '2.7.1', versionsuffix), - ('HDF5', '1.10.6'), - ('LZO', '2.10'), - ('Blosc', '1.17.1'), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -options = {'modulename': 'tables'} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 64428626873..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,348 +0,0 @@ -name = 'PyTorch' -version = '1.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pytorch.org/' -description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. -PyTorch is a deep learning framework that puts Python first.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -# PyTorch pulls in a bunch of submodules that are not releases. -# We download the submodule revisions from their repos. -# The list is generated by easybuild-framework/easybuild/scripts/createSubmoduleDeps.sh -local_extract_cmd_pattern = 'tar -C pytorch-%%(version)s/third_party/%s --strip-components=1 -xf %%s' - -source_urls = ['https://github.com/pytorch/pytorch/archive'] -sources = [ - 'v%(version)s.tar.gz', # PyTorch - { - 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], - 'download_filename': '4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz', - 'filename': 'FP16-20200514.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'FP16', - }, - { - 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], - 'download_filename': 'b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz', - 'filename': 'FXdiv-20200417.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'FXdiv', - }, - { - 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], - 'download_filename': '24b55303f5cf65d75844714513a0d1b1409809bd.tar.gz', - 'filename': 'NNPACK-20191007.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'NNPACK', - }, - { - 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], - 'download_filename': '7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz', - 'filename': 'QNNPACK-20190828.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'QNNPACK', - }, - { - 'source_urls': ['https://github.com/google/XNNPACK/archive'], - 'download_filename': '1b354636b5942826547055252f3b359b54acff95.tar.gz', - 'filename': 'XNNPACK-20200323.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'XNNPACK', - }, - { - 'source_urls': ['https://github.com/google/benchmark/archive'], - 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', - 'filename': 'benchmark-20180606.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'benchmark', - }, - { - 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], - 'download_filename': '63b254577ed77a8004a9be6ac707f3dccc4e1fd9.tar.gz', - 'filename': 'cpuinfo-20200611.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'cpuinfo', - }, - { - 'source_urls': ['https://github.com/NVlabs/cub/archive'], - 'download_filename': 'd106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz', - 'filename': 'cub-20200512.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'cub', - }, - { - 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], - 'download_filename': 'd41dc4dd74acce21fb210e7625d5d135751fa9e5.tar.gz', - 'filename': 'eigen-20190125.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'eigen', - }, - { - 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], - 'download_filename': '1d710393d5b7588f5de3b83f51c22bbddf095229.tar.gz', - 'filename': 'fbgemm-20200914.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'fbgemm', - }, - { - 'source_urls': ['https://github.com/asmjit/asmjit/archive'], - 'download_filename': '9057aa30b620f0662ff51e2230c126a345063064.tar.gz', - 'filename': 'asmjit-20200429.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/asmjit', - }, - { - 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], - 'download_filename': 'd5e37adf1406cf899d7d9ec1d317c47506ccb970.tar.gz', - 'filename': 'cpuinfo-20190201.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/cpuinfo', - }, - { - 'source_urls': ['https://github.com/google/googletest/archive'], - 'download_filename': '0fc5466dbb9e623029b1ada539717d10bd45e99e.tar.gz', - 'filename': 'googletest-20180925.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'fbgemm/third_party/googletest', - }, - { - 'source_urls': ['https://github.com/fmtlib/fmt/archive'], - 'download_filename': 'cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz', - 'filename': 'fmt-20200806.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'fmt', - }, - { - 'source_urls': ['https://github.com/houseroad/foxi/archive'], - 'download_filename': '4aba696ec8f31794fd42880346dc586486205e0a.tar.gz', - 'filename': 'foxi-20200922.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'foxi', - }, - { - 'source_urls': ['https://github.com/google/gemmlowp/archive'], - 'download_filename': '3fb5c176c17c765a3492cd2f0321b0dab712f350.tar.gz', - 'filename': 'gemmlowp-20181126.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'gemmlowp/gemmlowp', - }, - { - 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], - 'download_filename': '3dc0328fe6a9d47bd47c0c6ca145a0d8a21845c6.tar.gz', - 'filename': 'gloo-20200918.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'gloo', - }, - { - 'source_urls': ['https://github.com/google/googletest/archive'], - 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', - 'filename': 'googletest-20180831.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'googletest', - }, - { - 'source_urls': ['https://github.com/intel/ideep/archive'], - 'download_filename': 'ba885200dbbc1f144c7b58eba487378eb324f281.tar.gz', - 'filename': 'ideep-20200915.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'ideep', - }, - { - 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], - 'download_filename': '5ef631a030a6f73131c77892041042805a06064f.tar.gz', - 'filename': 'mkl-dnn-20200909.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'ideep/mkl-dnn', - }, - { - 'source_urls': ['https://github.com/onnx/onnx/archive'], - 'download_filename': 'a82c6a7010e2e332d8f74ad5b0c726fd47c85376.tar.gz', - 'filename': 'onnx-20200531.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'onnx', - }, - { - 'source_urls': ['https://github.com/google/benchmark/archive'], - 'download_filename': 'e776aa0275e293707b6a0901e0e8d8a8a3679508.tar.gz', - 'filename': 'benchmark-20180525.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'onnx/third_party/benchmark', - }, - { - 'source_urls': ['https://github.com/onnx/onnx-tensorrt/archive'], - 'download_filename': 'c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz', - 'filename': 'onnx-tensorrt-20190916.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'onnx-tensorrt', - }, - { - 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], - 'download_filename': '072586a71b55b7f8c584153d223e95687148a900.tar.gz', - 'filename': 'psimd-20200517.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'psimd', - }, - { - 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], - 'download_filename': '029c88620802e1361ccf41d1970bd5b07fd6b7bb.tar.gz', - 'filename': 'pthreadpool-20200615.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'pthreadpool', - }, - { - 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], - 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', - 'filename': 'PeachPy-20180218.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'python-peachpy', - }, - { - 'source_urls': ['https://github.com/shibatch/sleef/archive'], - 'download_filename': '7f523de651585fe25cade462efccca647dcc8d02.tar.gz', - 'filename': 'sleef-20190730.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'sleef', - }, - { - 'source_urls': ['https://github.com/01org/tbb/archive'], - 'download_filename': 'a51a90bc609bb73db8ea13841b5cf7aa4344d4a9.tar.gz', - 'filename': 'tbb-20181009.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'tbb', - }, - { - 'source_urls': ['https://github.com/pytorch/tensorpipe/archive'], - 'download_filename': '95ff9319161fcdb3c674d2bb63fac3e94095b343.tar.gz', - 'filename': 'tensorpipe-20200928.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe', - }, - { - 'source_urls': ['https://github.com/google/googletest/archive'], - 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', - 'filename': 'googletest-20180831.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/googletest', - }, - { - 'source_urls': ['https://github.com/google/libnop/archive'], - 'download_filename': 'aa95422ea8c409e3f078d2ee7708a5f59a8b9fa2.tar.gz', - 'filename': 'libnop-20200723.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/libnop', - }, - { - 'source_urls': ['https://github.com/libuv/libuv/archive'], - 'download_filename': '02a9e1be252b623ee032a3137c0b0c94afbe6809.tar.gz', - 'filename': 'libuv-20200419.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % 'tensorpipe/third_party/libuv', - }, -] -patches = [ - 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', - 'PyTorch-1.7.0_fix_altivec_defines.patch', - 'PyTorch-1.7.0_fix_test_DistributedDataParallel.patch', - 'PyTorch-1.7.0_fix-fbgemm-not-implemented-issue.patch', - 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', - 'PyTorch-1.7.0_increase-distributed-test-timeout.patch', - 'PyTorch-1.7.0_disable-dev-shm-test.patch', - 'PyTorch-1.7.1_add-jit-support-for-cuda11.patch', - 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', - 'PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch', - 'PyTorch-1.7.1_dont-use-gpu-ccc-in-test.patch', - 'PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch', - 'PyTorch-1.7.1_complex32.patch', - 'PyTorch-1.7.1_bypass-nan-compare.patch', - 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.7.1_fix-err-variable.patch', - 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', - 'PyTorch-1.7.1_el8_ppc64le.patch', - 'PyTorch-1.7.1_run-large-tests-on-GPU.patch', - 'PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch', -] -checksums = [ - 'fc8d6aaf0bdedd4221617be8d47ac39af57605bdcc814fabc28739427b55e9c7', # v1.7.1.tar.gz - '90f20492621d5ed80b442aa682ff92d7ccf333ac8fac4a10e7e02afb159f3c13', # FP16-20200514.tar.gz - '9ccf554541666b5c089ad5dd465141d671c99971f36d72f313652f5c49ffce14', # FXdiv-20200417.tar.gz - '1f11dbbfad78d0a4c39fe94e52a28c0821cb25f9880420bb304f6302f73fe002', # NNPACK-20191007.tar.gz - '0d752bd75f46ce4d7c6f0a60b0d6c0e5918a7b4683c825284f8db3706dd24f76', # QNNPACK-20190828.tar.gz - 'b55a6ef3a0b4c0d3c39ad5578eb4fa9a7b2d7ee1ef06592b8a808a59a8e6589b', # XNNPACK-20200323.tar.gz - '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz - '18a99130ced1eaacab2ba8f75a1435f9955aab54fa0436b60468f020876ee902', # cpuinfo-20200611.tar.gz - 'd87f6737be1b544c299340b64b9303c1d6ec0447b49b3aaf6642838b4f8280d7', # cub-20200512.tar.gz - '2ec954f18cec50a7063a7358ce555f7e11788a7f6d4e7e597d83687dc2f3b989', # eigen-20190125.tar.gz - 'e7e495fee65a73fa40cf1644f5b9496a6498c7a4209ce4b6b4d7d80f3d3941a4', # fbgemm-20200914.tar.gz - '5c7ecb03ede09a38fa9bcf2527a0f1454cd67a34c0e6fd939ae4d93b276ce982', # asmjit-20200429.tar.gz - '3f2dc1970f397a0e59db72f9fca6ff144b216895c1d606f6c94a507c1e53a025', # cpuinfo-20190201.tar.gz - 'e99b904983d08ac8e9bddb5b0d21196b78ad9499e3c5d12192cee2ddd2b7515c', # googletest-20180925.tar.gz - '0654ea5a1899f373fee87ae00ca3478aef227c3cf23916572421c6ce25d274bc', # fmt-20200806.tar.gz - '10a3774a2ebef7a09dd5c9a6b7bfdc9d3e4eb153711572864d4cc560637727c3', # foxi-20200922.tar.gz - 'fdd6f08bdb33d33f4df516ffb91730fdb163479c19502cfc983083fd9cf43bfa', # gemmlowp-20181126.tar.gz - '9c6bace1c2af3ee186a84c791ba61a6ba92ecbe8a3990839d895771219a73ebc', # gloo-20200918.tar.gz - 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz - 'f205584378d9b0b6aeae9558b9d578469235f4e394e71b44ead616881e5fb210', # ideep-20200915.tar.gz - '4234ce25fd8bb64899493bb21c2473559d6bcfe098309fe74e351945475da930', # mkl-dnn-20200909.tar.gz - 'c3bf8cc8091b24c43aa205a1f2037a518d249eb5997bea7f543b7fc880e80e21', # onnx-20200531.tar.gz - 'c7682e9007ddfd94072647abab3e89ffd9084089460ae47d67060974467b58bf', # benchmark-20180525.tar.gz - '314cde420a7cf692bdb6877bc6af6bc514805f6cdb8bee90f32566ed08d94b1c', # onnx-tensorrt-20190916.tar.gz - 'f6c4dab91ae9a03b3019e7cab0572743afd0e1b6e75b97fcca50259c737c924e', # psimd-20200517.tar.gz - 'd13818a10a645d557202aa005606337b2a0cdf690e5655253800ab11abb0c076', # pthreadpool-20200615.tar.gz - '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180218.tar.gz - '8cb5fae822077ca9cbc14dcc7bba9a3a35ad519284fc5169f9a176672c63860a', # sleef-20190730.tar.gz - # checksum for original download of tbb-20181009.tar.gz from https://github.com/intel/tbb/archive - ('dc0a8d8d96cb8765782aa6ac1b509ad4db955d9bbb58fa5cc2265f0292756d72', - # checksum for download of tbb-20181009.tar.gz from https://github.com/01org/tbb/archive - 'be111cf161b587812fa3b106fe550efb6f129b8b0b702fef32fac23af9580e5e'), - '0039658ffed8d4ff21575651a6f5258853cf8e1ca8bf564822b51f94da28b7fd', # tensorpipe-20200928.tar.gz - 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz - '9ee3f3b1efc629dbc3703ece3892e7e05c7048eed7031d06020e38bb30bee3ab', # libnop-20200723.tar.gz - '5ca4e9091f3231d8ad8801862dc4e851c23af89c69141d27723157776f7291e7', # libuv-20200419.tar.gz - # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch - 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', - '98a32023292772984aa53ef739e444ec8b20617b72bd7593c62e884f5d8b2e6c', # PyTorch-1.7.0_fix_altivec_defines.patch - # PyTorch-1.7.0_fix_test_DistributedDataParallel.patch - '5e70e6aecb1916bb8369b8d3f5e4b3cbf7e2b7a015f8099eea330b42775e25c5', - # PyTorch-1.7.0_fix-fbgemm-not-implemented-issue.patch - '97febb91ae2d051db9541e1e4c5924c77555ab73ee49ad7d62ef3e4714110297', - 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch - # PyTorch-1.7.0_increase-distributed-test-timeout.patch - '95abb468a35451fbd0f864ca843f6ad15ff8bfb909c3fd580f65859b26c9691c', - '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - # PyTorch-1.7.1_add-jit-support-for-cuda11.patch - '7a5a6ca64196f5fe0dc954d387e188695a683cc37790da67f903c52a5dd5a1e7', - # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch - 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', - # PyTorch-1.7.1_detect-max-ccc-from-nvrtc.patch - '96241088dbfcd4db93bd5faadecabce6259a495ffd24b75101444cd0e164c12b', - '12be5139e4e7aeec214bb38b123b09b391cd1ca72ce5ded6e61590cfae801824', # PyTorch-1.7.1_dont-use-gpu-ccc-in-test.patch - # PyTorch-1.7.1_validate-num-gpus-in-distributed-test.patch - 'd27f7b5149632512b6fe226837df914aad35c88f8b490856dc6dd90ea1e5d7e6', - '6028bff2be720cf70acad2129db60fd10872e02c9e460c72bb274228cf90b320', # PyTorch-1.7.1_complex32.patch - '0943496231b6857801e2424e561d03897a6982d098cba5b6967017b391a7e977', # PyTorch-1.7.1_bypass-nan-compare.patch - # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch - 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', - 'abb79e7ffd10be87adfb62e79131c50079c32470031ac22b12b273cfae85ca4c', # PyTorch-1.7.1_fix-err-variable.patch - # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch - '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', - '2a94a9cc009f02469b843fc65a6ee2cb01873f783568b8bcc83c33ba8e6b1a58', # PyTorch-1.7.1_el8_ppc64le.patch - # PyTorch-1.7.1_run-large-tests-on-GPU.patch - '06651b6746a27bee1adf15af24e356e188d683241bb186343009dc69c8d5aa9b', - # PyTorch-1.7.1_disable-failing-cuda-11.2-tests.patch - '2a9df4face04798f51eee0db83d28a905ea7ac53569cf25ed9f049b0a547702e', -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('hypothesis', '5.6.0', versionsuffix), -] -dependencies = [ - ('Ninja', '1.10.0'), # Required for JIT compilation of C++ extensions - ('Python', '3.8.2'), - ('protobuf', '3.13.0'), - ('protobuf-python', '3.13.0', versionsuffix), - ('pybind11', '2.4.3', versionsuffix), - ('SciPy-bundle', '2020.03', '-Python-3.8.2'), - ('typing-extensions', '3.7.4.3', versionsuffix), - ('PyYAML', '5.3'), - ('MPFR', '4.0.2'), - ('GMP', '6.2.0'), - ('numactl', '2.0.13'), - ('FFmpeg', '4.2.2'), - ('Pillow', '7.0.0', versionsuffix), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), - ('magma', '2.5.4'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), -] - -osdependencies = [OS_PKG_IBVERBS_DEV] - -# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) -cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] - -excluded_tests = { - '': [ - # Test from this suite timeout often. The process group backend is deprecated anyway - 'distributed/rpc/test_process_group_agent', - # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! - # https://github.com/pytorch/pytorch/issues/43209 - 'test_quantization', - ] -} - -runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' - -sanity_check_commands = ["python -c 'import caffe2.python'"] -tests = ['PyTorch-check-cpp-extension.py'] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.7.1_el8_ppc64le.patch b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.7.1_el8_ppc64le.patch deleted file mode 100644 index 694b2268fc8..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-1.7.1_el8_ppc64le.patch +++ /dev/null @@ -1,27 +0,0 @@ -fix, on ppc64le and RHEL / CentOS 8, for: identifier "__ieee128" is undefined -See https://github.com/easybuilders/easybuild-easyconfigs/issues/11913 -Patch by Simon Branford (University of Birmingham), ported to PyTorch 1.7.1 by Kenneth Hoste (HPC-UGent) ---- pytorch-1.7.1/cmake/Dependencies.cmake.orig 2020-12-07 19:28:38.000000000 +0000 -+++ pytorch-1.7.1/cmake/Dependencies.cmake 2021-01-10 14:09:00.593547793 +0000 -@@ -1501,6 +1501,9 @@ - if(CMAKE_POSITION_INDEPENDENT_CODE AND NOT MSVC) - list(APPEND CUDA_NVCC_FLAGS "-Xcompiler" "-fPIC") - endif() -+ if(CMAKE_SYSTEM_PROCESSOR MATCHES "(powerpc|ppc)64le") -+ list(APPEND CUDA_NVCC_FLAGS "-Xcompiler" "-mno-float128") -+ endif() - - if(CUDA_HAS_FP16 OR NOT ${CUDA_VERSION} LESS 7.5) - message(STATUS "Found CUDA with FP16 support, compiling with torch.cuda.HalfTensor") ---- pytorch-1.7.1/third_party/gloo/cmake/Cuda.cmake.orig 2021-01-10 14:09:00.593547793 +0000 -+++ pytorch-1.7.1/third_party/gloo/cmake/Cuda.cmake 2021-01-10 14:11:36.177738536 +0000 -@@ -177,5 +177,9 @@ - gloo_list_append_if_unique(CUDA_NVCC_FLAGS "-Xcompiler" "-fPIC") - endif() - -+if(CMAKE_SYSTEM_PROCESSOR MATCHES "(powerpc|ppc)64le") -+ gloo_list_append_if_unique(CUDA_NVCC_FLAGS "-Xcompiler" "-mno-float128") -+endif() -+ - mark_as_advanced(CUDA_BUILD_CUBIN CUDA_BUILD_EMULATION CUDA_VERBOSE_BUILD) - mark_as_advanced(CUDA_SDK_ROOT_DIR CUDA_SEPARABLE_COMPILATION) diff --git a/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-2.1.0_skip-test-linalg-svd-complex.patch b/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-2.1.0_skip-test-linalg-svd-complex.patch deleted file mode 100644 index 92ea36337eb..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyTorch/PyTorch-2.1.0_skip-test-linalg-svd-complex.patch +++ /dev/null @@ -1,19 +0,0 @@ -Skip test_python_ref_meta__refs_linalg_svd_cpu_complex -Result varies depending on underlying device -see https://github.com/pytorch/pytorch/issues/105068 -author: Alex Domingo (Vrije Universiteit Brussel) ---- test/test_ops.py.orig 2024-01-16 15:37:02.596411122 +0100 -+++ test/test_ops.py 2024-01-16 15:39:02.824489395 +0100 -@@ -311,6 +311,12 @@ - return out - return x - -+ # Skip test_python_ref_meta__refs_linalg_svd_cpu_complex -+ # Result varies depending on underlying device -+ # see https://github.com/pytorch/pytorch/issues/105068 -+ if op.name == '_refs.linalg.svd' and dtype in (torch.complex64, torch.complex128): -+ self.skipTest("Unreliable on certain devices, see issue #105068") -+ - # TODO: iterate over requires_grad true/false - for sample in op.reference_inputs(device, dtype, requires_grad=False): - result = op(sample.input, *sample.args, **sample.kwargs) diff --git a/easybuild/easyconfigs/__archive__/p/PyYAML/PyYAML-5.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/PyYAML/PyYAML-5.3-GCCcore-9.3.0.eb deleted file mode 100644 index e0bfa86135d..00000000000 --- a/easybuild/easyconfigs/__archive__/p/PyYAML/PyYAML-5.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyYAML' -version = '5.3' - -homepage = "https://github.com/yaml/pyyaml" -description = """PyYAML is a YAML parser and emitter for the Python programming language.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['e9f45bd5b92c7974e59bcd2dcc8631a6b6cc380a904725fce7bc08872e691615'] - -builddependencies = [('binutils', '2.34')] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [('libyaml', '0.2.2')] - -options = {'modulename': 'yaml'} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-GCC-9.3.0.eb deleted file mode 100644 index cfbb9f7a492..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-GCC-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# 0.9.1.4: -# Modified by: Adam Huffman -# The Francis Crick Institute -# Modified by: Erich Birngruber -# Gregor Mendel Institute -# Modified by: Pavel Grochal -# INUITS - -easyblock = 'PythonPackage' - -name = 'Pysam' -version = '0.16.0.1' - -homepage = 'https://github.com/pysam-developers/pysam' -description = """Pysam is a python module for reading and manipulating Samfiles. - It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/pysam-developers/pysam/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['a61e98e299fa93ba121aab521081282b61bc978bb9052d33b26b38f8fe15573e'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [ - ('ncurses', '6.2'), - ('cURL', '7.69.1'), - ('XZ', '5.2.5'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-iccifort-2020.1.217.eb deleted file mode 100644 index 2769193f2fc..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Pysam/Pysam-0.16.0.1-iccifort-2020.1.217.eb +++ /dev/null @@ -1,36 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# 0.9.1.4: -# Modified by: Adam Huffman -# The Francis Crick Institute -# Modified by: Erich Birngruber -# Gregor Mendel Institute -# Modified by: Pavel Grochal -# INUITS - -easyblock = 'PythonPackage' - -name = 'Pysam' -version = '0.16.0.1' - -homepage = 'https://github.com/pysam-developers/pysam' -description = """Pysam is a python module for reading and manipulating Samfiles. - It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://github.com/pysam-developers/pysam/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['a61e98e299fa93ba121aab521081282b61bc978bb9052d33b26b38f8fe15573e'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [ - ('ncurses', '6.2'), - ('cURL', '7.69.1'), - ('XZ', '5.2.5'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.18-GCCcore-9.3.0-bare.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.18-GCCcore-9.3.0-bare.eb deleted file mode 100644 index 41c95013bf7..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.18-GCCcore-9.3.0-bare.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'Python' -version = '2.7.18' -versionsuffix = '-bare' - -homepage = 'https://python.org/' -description = """Python is a programming language that lets you work more quickly and integrate your systems - more effectively.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.%(namelower)s.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] -checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] - -# python needs bzip2 to build the bz2 package - -dependencies = [ - ('binutils', '2.34'), - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), - ('libreadline', '8.0'), - ('ncurses', '6.2'), - ('SQLite', '3.31.1'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.0h'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -install_pip = True - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.18-GCCcore-9.3.0.eb deleted file mode 100644 index e74994fa67e..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.18-GCCcore-9.3.0.eb +++ /dev/null @@ -1,304 +0,0 @@ -name = 'Python' -version = '2.7.18' - -homepage = 'https://python.org/' -description = """Python is a programming language that lets you work more quickly and integrate your systems - more effectively.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] -checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] - -dependencies = [ - ('binutils', '2.34'), # required for pip install that involves compilation - ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib - ('zlib', '1.2.11'), - ('libreadline', '8.0'), - ('ncurses', '6.2'), - ('SQLite', '3.31.1'), - ('GMP', '6.2.0'), # required for pycrypto - ('libffi', '3.3'), # required for cryptography - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.1e'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -install_pip = True - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - -# order is important! -# package versions updated 23 April 2020 -exts_list = [ - # setuptools 44.0.0 is the most recent version still supporting Python 2.x - ('setuptools', '44.0.0', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['e5baf7723e5bb8382fc146e33032b241efc63314211a3a120aaa55d62d2bb008'], - }), - ('wheel', '0.34.2', { - 'checksums': ['8788e9155fe14f54164c1b9eb0a319d98ef02c160725587ad60f14ddc57b6f96'], - }), - ('pip', '20.0.2', { - 'checksums': ['7db0c8ea4c7ea51c8049640e8e6e7fde949de672bfa4949920675563a5a6967f'], - }), - ('nose', '1.3.7', { - 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], - }), - ('blist', '1.3.6', { - 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], - }), - ('paycheck', '1.0.2', { - 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], - }), - ('pbr', '5.4.5', { - 'checksums': ['07f558fece33b05caf857474a366dfcc00562bca13dd8b47b2b3e22d9f9bf55c'], - }), - ('Cython', '0.29.16', { - 'checksums': ['232755284f942cbb3b43a06cd85974ef3c970a021aef19b5243c03ee2b08fa05'], - }), - ('six', '1.14.0', { - 'checksums': ['236bdbdce46e6e6a3d61a337c0f8b763ca1e8717c03b369e87a7ec7ce1319c0a'], - }), - ('toml', '0.10.0', { - 'checksums': ['229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c'], - }), - ('setuptools_scm', '3.5.0', { - 'checksums': ['5bdf21a05792903cafe7ae0c9501182ab52497614fa6b1750d9dbae7b60c1a87'], - }), - ('python-dateutil', '2.8.1', { - 'modulename': 'dateutil', - 'checksums': ['73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c'], - }), - ('decorator', '4.4.2', { - 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], - }), - ('liac-arff', '2.4.0', { - 'modulename': 'arff', - 'checksums': ['47afcd1fd248b2892f66075987422d0576fc2c2fd0811d0cbd32f2135b065df5'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], - 'checksums': [ - 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz - # pycrypto-2.6.1_remove-usr-include.patch - '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', - ], - }), - ('ecdsa', '0.15', { - 'checksums': ['8f12ac317f8a1318efa75757ef0a651abe12e51fc1af8838fb91079445227277'], - }), - ('enum34', '1.1.10', { - 'modulename': 'enum', - 'checksums': ['cce6a7477ed816bd2542d03d53db9f0db935dd013b70f336a95c73979289f248'], - }), - ('ipaddress', '1.0.23', { - 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], - }), - ('asn1crypto', '1.3.0', { - 'checksums': ['5a215cb8dc12f892244e3a113fe05397ee23c5c4ca7a69cd6e69811755efc42d'], - }), - ('idna', '2.9', { - 'checksums': ['7588d1c14ae4c77d74036e8c22ff447b26d0fde8f007354fd48a7814db15b7cb'], - }), - ('pycparser', '2.20', { - 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], - }), - ('cffi', '1.14.0', { - 'checksums': ['2d384f4a127a15ba701207f7639d94106693b6cd64173d6c8988e2c25f3ac2b6'], - }), - ('cryptography', '2.9.2', { - 'checksums': ['a0c30272fb4ddda5f5ffc1089d7405b7a71b0b0f51993cb4e5dbb4590b2fc229'], - }), - ('pyasn1', '0.4.8', { - 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], - }), - ('PyNaCl', '1.3.0', { - 'modulename': 'nacl', - 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], - }), - ('bcrypt', '3.1.7', { - 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], - }), - ('paramiko', '2.7.1', { - 'checksums': ['920492895db8013f6cc0179293147f830b8c7b21fdfc839b6bad760c27459d9f'], - }), - ('pyparsing', '2.4.7', { - 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], - }), - ('netifaces', '0.10.9', { - 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], - }), - ('netaddr', '0.7.19', { - 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], - }), - ('funcsigs', '1.0.2', { - 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], - }), - # mock 3.0.5 is the most recent version still supporting Python 2.x - ('mock', '3.0.5', { - 'checksums': ['83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3'], - }), - ('pytz', '2019.3', { - 'checksums': ['b02c06db6cf09c12dd25137e563b31700d3b80fcc4ad23abb7a315f2789819be'], - }), - ('bitstring', '3.1.6', { - 'checksums': ['c97a8e2a136e99b523b27da420736ae5cb68f83519d633794a6a11192f69f8bf'], - }), - ('appdirs', '1.4.3', { - 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], - }), - ('distlib', '0.3.0', { - 'source_tmpl': 'distlib-%(version)s.zip', - 'checksums': ['2e166e231a26b36d6dfe35a48c4464346620f8645ed0ace01ee31822b288de21'], - }), - ('filelock', '3.0.12', { - 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], - }), - ('importlib_resources', '1.4.0', { - 'checksums': ['4019b6a9082d8ada9def02bece4a76b131518866790d58fdda0b5f8c603b36c2'], - }), - ('virtualenv', '20.0.18', { - 'checksums': ['ac53ade75ca189bc97b6c1d9ec0f1a50efe33cbf178ae09452dcd9fd309013c1'], - }), - ('docopt', '0.6.2', { - 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], - }), - ('joblib', '0.14.1', { - 'checksums': ['0630eea4f5664c463f23fbf5dcfc54a2bc6168902719fa8e19daf033022786c8'], - }), - ('chardet', '3.0.4', { - 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], - }), - ('certifi', '2020.4.5.1', { - 'checksums': ['51fcb31174be6e6664c5f69e3e1691a2d72a1a12e90f872cbdb1567eb47b6519'], - }), - ('urllib3', '1.25.9', { - 'checksums': ['3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527'], - }), - ('requests', '2.23.0', { - 'checksums': ['b3f43d496c6daba4493e7c431722aeb7dbc6288f52a6e04e7b6023b0247817e6'], - }), - ('xlrd', '1.2.0', { - 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], - }), - ('py_expression_eval', '0.3.9', { - 'checksums': ['d80a948f91f78d08f789b0a7c3fb2bd9a34ad625f5ce88c262a6c91189a4abb9'], - }), - ('tabulate', '0.8.7', { - 'checksums': ['db2723a20d04bcda8522165c73eea7c300eda74e0ce852d9022e0159d7895007'], - }), - ('ujson', '2.0.3', { - 'checksums': ['bd2deffc983827510e5145fb66e4cc0f577480c62fe0b4882139f8f7d27ae9a3'], - }), - ('atomicwrites', '1.3.0', { - 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], - }), - ('py', '1.8.1', { - 'checksums': ['5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa'], - }), - ('scandir', '1.10.0', { - 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], - }), - ('pathlib2', '2.3.5', { - 'checksums': ['6cd9a47b597b37cc57de1c05e56fb1a1c9cc9fab04fe78c29acd090418529868'], - }), - # zipp 1.2.0 is the most recent version still supporting Python 2.x - ('zipp', '1.2.0', { - 'checksums': ['c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1'], - }), - # configparser 4.0.2 is the most recent version still supporting Python 2.x - ('configparser', '4.0.2', { - 'checksums': ['c7d282687a5308319bf3d2e7706e575c635b0a470342641c93bea0ea3b5331df'], - }), - ('contextlib2', '0.6.0.post1', { - 'checksums': ['01f490098c18b19d2bd5bb5dc445b2054d2fa97f09a4280ba2c5f3c394c8162e'], - }), - ('importlib_metadata', '1.6.0', { - 'checksums': ['34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e'], - }), - ('pluggy', '0.13.1', { - 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], - }), - # more-itertools 5.0.0 is the most recent version still supporting Python 2.x - ('more-itertools', '5.0.0', { - 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], - }), - ('attrs', '19.3.0', { - 'modulename': 'attr', - 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], - }), - ('wcwidth', '0.1.9', { - 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], - }), - # pytest 4.6.9 is the most recent version still supporting Python 2.x - ('pytest', '4.6.9', { - 'checksums': ['19e8f75eac01dd3f211edd465b39efbcbdc8fc5f7866d7dd49fedb30d8adf339'], - }), - ('MarkupSafe', '1.1.1', { - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('Jinja2', '2.11.2', { - 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], - }), - ('packaging', '20.3', { - 'checksums': ['3c292b474fda1671ec57d46d739d072bfd495a4f51ad01a055121d81e952b7a3'], - }), - # sphinxcontrib-websupport 1.1.2 is the most recent version still supporting Python 2.x - ('sphinxcontrib-websupport', '1.1.2', { - 'modulename': 'sphinxcontrib.websupport', - 'checksums': ['1501befb0fdf1d1c29a800fdbf4ef5dc5369377300ddbdd16d2cd40e54c6eefc'], - }), - ('Pygments', '2.5.2', { - 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], - }), - ('imagesize', '1.2.0', { - 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], - }), - ('docutils', '0.16', { - 'checksums': ['c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc'], - }), - ('snowballstemmer', '2.0.0', { - 'checksums': ['df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52'], - }), - ('Babel', '2.8.0', { - 'checksums': ['1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38'], - }), - ('alabaster', '0.7.12', { - 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], - }), - ('typing', '3.7.4.1', { - 'checksums': ['91dfe6f3f706ee8cc32d38edbbf304e9b7583fb37108fef38229617f8b3eba23'], - }), - # Sphinx 1.8.5 is the most recent version still supporting Python 2.x - ('Sphinx', '1.8.5', { - 'checksums': ['c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08'], - }), - ('click', '7.1.1', { - 'checksums': ['8a18b4ea89d8820c5d0c7da8a64b2c324b4dabb695804dbfea19b9be9d88c0cc'], - }), - ('psutil', '5.7.0', { - 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], - }), - ('future', '0.18.2', { - 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], - }), - ('singledispatch', '3.4.0.3', { - 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], - }), - ('sortedcontainers', '2.2.2', { - 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], - }), - ('intervaltree', '3.0.2', { - 'checksums': ['cb4f61c81dcb4fea6c09903f3599015a83c9bdad1f0bbd232495e6681e19e273'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/p/Python/Python-3.8.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-3.8.2-GCCcore-9.3.0.eb deleted file mode 100644 index 0d4c2260bf7..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Python/Python-3.8.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,305 +0,0 @@ -name = 'Python' -version = '3.8.2' - -homepage = 'https://python.org/' -description = """Python is a programming language that lets you work more quickly and integrate your systems - more effectively.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] -checksums = ['e634a7a74776c2b89516b2e013dda1728c89c8149b9863b8cea21946daf9d561'] - -builddependencies = [ - ('UnZip', '6.0'), - ('git', '2.23.0', '-nodocs'), # required for pbr -] - -dependencies = [ - ('binutils', '2.34'), # required for pip install that involves compilation - ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib - ('zlib', '1.2.11'), - ('libreadline', '8.0'), - ('ncurses', '6.2'), - ('SQLite', '3.31.1'), - ('XZ', '5.2.5'), - ('GMP', '6.2.0'), # required for pycrypto - ('libffi', '3.3'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) - # ('OpenSSL', '1.1.1e'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -install_pip = True - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - -# order is important! -# package versions updated 23 April 2020 -exts_list = [ - ('setuptools', '45.2.0', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['89c6e6011ec2f6d57d43a3f9296c4ef022c2cbf49bab26b407fe67992ae3397f'], - }), - ('wheel', '0.34.2', { - 'checksums': ['8788e9155fe14f54164c1b9eb0a319d98ef02c160725587ad60f14ddc57b6f96'], - }), - ('pip', '20.0.2', { - 'checksums': ['7db0c8ea4c7ea51c8049640e8e6e7fde949de672bfa4949920675563a5a6967f'], - }), - ('nose', '1.3.7', { - 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], - }), - ('blist', '1.3.6', { - 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], - }), - ('paycheck', '1.0.2', { - 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], - }), - ('pbr', '5.4.5', { - 'checksums': ['07f558fece33b05caf857474a366dfcc00562bca13dd8b47b2b3e22d9f9bf55c'], - }), - ('Cython', '0.29.16', { - 'checksums': ['232755284f942cbb3b43a06cd85974ef3c970a021aef19b5243c03ee2b08fa05'], - }), - ('six', '1.14.0', { - 'checksums': ['236bdbdce46e6e6a3d61a337c0f8b763ca1e8717c03b369e87a7ec7ce1319c0a'], - }), - ('toml', '0.10.0', { - 'checksums': ['229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c'], - }), - ('setuptools_scm', '3.5.0', { - 'checksums': ['5bdf21a05792903cafe7ae0c9501182ab52497614fa6b1750d9dbae7b60c1a87'], - }), - ('python-dateutil', '2.8.1', { - 'modulename': 'dateutil', - 'checksums': ['73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c'], - }), - ('decorator', '4.4.2', { - 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], - }), - ('liac-arff', '2.4.0', { - 'modulename': 'arff', - 'checksums': ['47afcd1fd248b2892f66075987422d0576fc2c2fd0811d0cbd32f2135b065df5'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], - 'checksums': [ - 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz - # pycrypto-2.6.1_remove-usr-include.patch - '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', - ], - }), - ('ecdsa', '0.15', { - 'checksums': ['8f12ac317f8a1318efa75757ef0a651abe12e51fc1af8838fb91079445227277'], - }), - ('ipaddress', '1.0.23', { - 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], - }), - ('asn1crypto', '1.3.0', { - 'checksums': ['5a215cb8dc12f892244e3a113fe05397ee23c5c4ca7a69cd6e69811755efc42d'], - }), - ('idna', '2.9', { - 'checksums': ['7588d1c14ae4c77d74036e8c22ff447b26d0fde8f007354fd48a7814db15b7cb'], - }), - ('pycparser', '2.20', { - 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], - }), - ('cffi', '1.14.0', { - 'checksums': ['2d384f4a127a15ba701207f7639d94106693b6cd64173d6c8988e2c25f3ac2b6'], - }), - ('cryptography', '2.9.2', { - 'checksums': ['a0c30272fb4ddda5f5ffc1089d7405b7a71b0b0f51993cb4e5dbb4590b2fc229'], - }), - ('pyasn1', '0.4.8', { - 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], - }), - ('PyNaCl', '1.3.0', { - 'modulename': 'nacl', - 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], - }), - ('bcrypt', '3.1.7', { - 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], - }), - ('paramiko', '2.7.1', { - 'checksums': ['920492895db8013f6cc0179293147f830b8c7b21fdfc839b6bad760c27459d9f'], - }), - ('pyparsing', '2.4.7', { - 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], - }), - ('netifaces', '0.10.9', { - 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], - }), - ('netaddr', '0.7.19', { - 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], - }), - ('mock', '4.0.1', { - 'checksums': ['2a572b715f09dd2f0a583d8aeb5bb67d7ed7a8fd31d193cf1227a99c16a67bc3'], - }), - ('pytz', '2019.3', { - 'checksums': ['b02c06db6cf09c12dd25137e563b31700d3b80fcc4ad23abb7a315f2789819be'], - }), - ('bitstring', '3.1.6', { - 'checksums': ['c97a8e2a136e99b523b27da420736ae5cb68f83519d633794a6a11192f69f8bf'], - }), - ('appdirs', '1.4.3', { - 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], - }), - ('distlib', '0.3.0', { - 'source_tmpl': 'distlib-%(version)s.zip', - 'checksums': ['2e166e231a26b36d6dfe35a48c4464346620f8645ed0ace01ee31822b288de21'], - }), - ('filelock', '3.0.12', { - 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], - }), - ('virtualenv', '20.0.18', { - 'checksums': ['ac53ade75ca189bc97b6c1d9ec0f1a50efe33cbf178ae09452dcd9fd309013c1'], - }), - ('docopt', '0.6.2', { - 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], - }), - ('joblib', '0.14.1', { - 'checksums': ['0630eea4f5664c463f23fbf5dcfc54a2bc6168902719fa8e19daf033022786c8'], - }), - ('chardet', '3.0.4', { - 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], - }), - ('certifi', '2020.4.5.1', { - 'checksums': ['51fcb31174be6e6664c5f69e3e1691a2d72a1a12e90f872cbdb1567eb47b6519'], - }), - ('urllib3', '1.25.9', { - 'checksums': ['3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527'], - }), - ('requests', '2.23.0', { - 'checksums': ['b3f43d496c6daba4493e7c431722aeb7dbc6288f52a6e04e7b6023b0247817e6'], - }), - ('xlrd', '1.2.0', { - 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], - }), - ('py_expression_eval', '0.3.9', { - 'checksums': ['d80a948f91f78d08f789b0a7c3fb2bd9a34ad625f5ce88c262a6c91189a4abb9'], - }), - ('tabulate', '0.8.7', { - 'checksums': ['db2723a20d04bcda8522165c73eea7c300eda74e0ce852d9022e0159d7895007'], - }), - ('ujson', '2.0.3', { - 'checksums': ['bd2deffc983827510e5145fb66e4cc0f577480c62fe0b4882139f8f7d27ae9a3'], - }), - ('atomicwrites', '1.3.0', { - 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], - }), - ('py', '1.8.1', { - 'checksums': ['5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa'], - }), - ('scandir', '1.10.0', { - 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], - }), - ('pathlib2', '2.3.5', { - 'checksums': ['6cd9a47b597b37cc57de1c05e56fb1a1c9cc9fab04fe78c29acd090418529868'], - }), - ('zipp', '1.2.0', { - 'checksums': ['c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1'], - }), - ('importlib_metadata', '1.6.0', { - 'checksums': ['34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e'], - }), - ('pluggy', '0.13.1', { - 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], - }), - ('more-itertools', '8.2.0', { - 'checksums': ['b1ddb932186d8a6ac451e1d95844b382f55e12686d51ca0c68b6f61f2ab7a507'], - }), - ('attrs', '19.3.0', { - 'modulename': 'attr', - 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], - }), - ('wcwidth', '0.1.9', { - 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], - }), - ('pytest', '5.4.1', { - 'checksums': ['84dde37075b8805f3d1f392cc47e38a0e59518fb46a431cfdaf7cf1ce805f970'], - }), - ('MarkupSafe', '1.1.1', { - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('Jinja2', '2.11.2', { - 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], - }), - ('packaging', '20.3', { - 'checksums': ['3c292b474fda1671ec57d46d739d072bfd495a4f51ad01a055121d81e952b7a3'], - }), - ('sphinxcontrib-websupport', '1.2.1', { - 'modulename': 'sphinxcontrib.websupport', - 'checksums': ['545f5da4bd7757e82b8a23ce3af9500c6ffeedbcb13429fca436ad1e80bd10cf'], - }), - ('Pygments', '2.5.2', { - 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], - }), - ('imagesize', '1.2.0', { - 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], - }), - ('docutils', '0.16', { - 'checksums': ['c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc'], - }), - ('snowballstemmer', '2.0.0', { - 'checksums': ['df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52'], - }), - ('Babel', '2.8.0', { - 'checksums': ['1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38'], - }), - ('alabaster', '0.7.12', { - 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], - }), - ('sphinxcontrib-applehelp', '1.0.2', { - 'modulename': 'sphinxcontrib.applehelp', - 'checksums': ['a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58'], - }), - ('sphinxcontrib-devhelp', '1.0.2', { - 'modulename': 'sphinxcontrib.devhelp', - 'checksums': ['ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4'], - }), - ('sphinxcontrib-htmlhelp', '1.0.3', { - 'modulename': 'sphinxcontrib.htmlhelp', - 'checksums': ['e8f5bb7e31b2dbb25b9cc435c8ab7a79787ebf7f906155729338f3156d93659b'], - }), - ('sphinxcontrib-jsmath', '1.0.1', { - 'modulename': 'sphinxcontrib.jsmath', - 'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'], - }), - ('sphinxcontrib-qthelp', '1.0.3', { - 'modulename': 'sphinxcontrib.qthelp', - 'checksums': ['4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72'], - }), - ('sphinxcontrib-serializinghtml', '1.1.4', { - 'modulename': 'sphinxcontrib.serializinghtml', - 'checksums': ['eaa0eccc86e982a9b939b2b82d12cc5d013385ba5eadcc7e4fed23f4405f77bc'], - }), - ('Sphinx', '3.0.2', { - 'checksums': ['d7c6e72c6aa229caf96af82f60a0d286a1521d42496c226fe37f5a75dcfe2941'], - }), - ('click', '7.1.1', { - 'checksums': ['8a18b4ea89d8820c5d0c7da8a64b2c324b4dabb695804dbfea19b9be9d88c0cc'], - }), - ('psutil', '5.7.0', { - 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], - }), - ('future', '0.18.2', { - 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], - }), - ('sortedcontainers', '2.2.2', { - 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], - }), - ('intervaltree', '3.0.2', { - 'checksums': ['cb4f61c81dcb4fea6c09903f3599015a83c9bdad1f0bbd232495e6681e19e273'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/p/Python/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/__archive__/p/Python/numpy-1.12.0-mkl.patch deleted file mode 100644 index 3d09924f966..00000000000 --- a/easybuild/easyconfigs/__archive__/p/Python/numpy-1.12.0-mkl.patch +++ /dev/null @@ -1,55 +0,0 @@ -fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries -by Kenneth Hoste (HPC-UGent) -diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py ---- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 -@@ -628,7 +628,10 @@ - return options - - def library_option(self, lib): -- return "-l" + lib -+ if lib[0]=='-': -+ return lib -+ else: -+ return "-l" + lib - def library_dir_option(self, dir): - return "-L" + dir - -diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py ---- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 -@@ -675,7 +675,7 @@ - if is_string(default): - return [default] - return default -- return [b for b in [a.strip() for a in libs.split(',')] if b] -+ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] - - def get_libraries(self, key='libraries'): - if hasattr(self, '_lib_names'): -@@ -756,6 +756,9 @@ - # make sure we preserve the order of libs, as it can be important - found_dirs, found_libs = [], [] - for lib in libs: -+ if lib[0] == '-': -+ found_libs.append(lib) -+ continue - for lib_dir in lib_dirs: - found_lib = self._find_lib(lib_dir, lib, exts) - if found_lib: -diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py ---- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 -@@ -123,3 +123,12 @@ - - replace_method(UnixCCompiler, 'create_static_lib', - UnixCCompiler_create_static_lib) -+ -+def UnixCCompiler_library_option(self, lib): -+ if lib[0]=='-': -+ return lib -+ else: -+ return "-l" + lib -+ -+replace_method(UnixCCompiler, 'library_option', -+ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/__archive__/p/packmol/packmol-v20.2.2-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/p/packmol/packmol-v20.2.2-iccifort-2020.1.217.eb deleted file mode 100644 index ad8516e8edc..00000000000 --- a/easybuild/easyconfigs/__archive__/p/packmol/packmol-v20.2.2-iccifort-2020.1.217.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'MakeCp' - -name = 'packmol' -version = 'v20.2.2' - -homepage = 'http://m3g.iqm.unicamp.br/packmol' -description = "Packing Optimization for Molecular Dynamics Simulations" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -source_urls = ['https://github.com/m3g/packmol/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['129cc1b7e6b00c1740c5c6f285a2c6207e18f05cdeb71af8107c3fedf48f23de'] - -buildopts = 'FORTRAN="$F90"' - -files_to_copy = [(['packmol'], 'bin'), 'AUTHORS', 'LICENSE'] - -sanity_check_paths = { - 'files': ['bin/packmol', 'AUTHORS', 'LICENSE'], - 'dirs': [], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 7c6e763149e..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pandas' -version = '1.1.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/pandas/" -description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures - and data analysis tools for the Python programming language.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['b64ffd87a2cfd31b40acd4b92cb72ea9a52a48165aec4c140e78fd69c45d1444'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('numexpr', '2.7.1', versionsuffix), - ('Bottleneck', '1.3.2', versionsuffix), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 9c5ad89b1a6..00000000000 --- a/easybuild/easyconfigs/__archive__/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,39 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonPackage' - -name = 'parallel-fastq-dump' -version = '0.6.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/rvalieris/parallel-fastq-dump' -description = "parallel fastq-dump wrapper" -docurls = ["https://github.com/rvalieris/parallel-fastq-dump"] - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -# https://github.com/rvalieris/parallel-fastq-dump/archive/ -github_account = 'rvalieris' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['38a3db72e4f87b8ca2412147a5938372098df15e839c78cddc8a7bfa3dd35b64'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Python', '3.8.2'), - ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', SYSTEM) -] - -sanity_check_paths = { - "files": ["bin/parallel-fastq-dump"], - "dirs": ["lib/python%(pyshortver)s/site-packages"], -} - -# This package doesn't produce importable module, only executable script. -options = {'modulename': False} - -sanity_check_commands = ["parallel-fastq-dump --version"] - -moduleclass = "bio" diff --git a/easybuild/easyconfigs/__archive__/p/parallel/parallel-20200422-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/parallel/parallel-20200422-GCCcore-9.3.0.eb deleted file mode 100644 index e93c91645e5..00000000000 --- a/easybuild/easyconfigs/__archive__/p/parallel/parallel-20200422-GCCcore-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'parallel' -version = '20200422' - -homepage = 'https://savannah.gnu.org/projects/parallel/' -description = """parallel: Build and execute shell commands in parallel""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['4bdebf91cc39ea54dec384ad475463cb7c2758fda2ae4a30111e7cfdb3c85530'] - -builddependencies = [('binutils', '2.34')] -dependencies = [ - ('Perl', '5.30.2'), -] - -sanity_check_paths = { - 'files': ['bin/parallel'], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/parallel/parallel-20200522-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/parallel/parallel-20200522-GCCcore-9.3.0.eb deleted file mode 100644 index 66f84f9aaa4..00000000000 --- a/easybuild/easyconfigs/__archive__/p/parallel/parallel-20200522-GCCcore-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'parallel' -version = '20200522' - -homepage = 'https://savannah.gnu.org/projects/parallel/' -description = """parallel: Build and execute shell commands in parallel""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['49b4685a8b23a9f94d3ab3dff6eae5ad2283c39bf103bf56ec8cdd56b6213a82'] - -builddependencies = [('binutils', '2.34')] -dependencies = [ - ('Perl', '5.30.2'), -] - -sanity_check_paths = { - 'files': ['bin/parallel'], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/parasail/parasail-2.4.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/parasail/parasail-2.4.2-GCC-9.3.0.eb deleted file mode 100644 index 8c472d02b40..00000000000 --- a/easybuild/easyconfigs/__archive__/p/parasail/parasail-2.4.2-GCC-9.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# Updated to v2.4.2 -# R.QIAO - -easyblock = 'CMakeMake' - -name = 'parasail' -version = '2.4.2' - -homepage = 'https://github.com/jeffdaily/parasail' -description = """parasail is a SIMD C (C99) library containing implementations - of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global - pairwise sequence alignment algorithms. """ - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -# https://github.com/jeffdaily/parasail -github_account = 'jeffdaily' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['3843055fc04743269cf22d127ae26952a7f5e6fc4f1bc29f6b6f3c156c8ca434'] - -builddependencies = [('CMake', '3.16.4')] - -sanity_check_paths = { - 'files': ['bin/parasail_aligner', 'bin/parasail_stats', - 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/parasail/parasail-2.4.2-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/p/parasail/parasail-2.4.2-iccifort-2020.1.217.eb deleted file mode 100644 index a84eba9b444..00000000000 --- a/easybuild/easyconfigs/__archive__/p/parasail/parasail-2.4.2-iccifort-2020.1.217.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'parasail' -version = '2.4.2' - -homepage = 'https://github.com/jeffdaily/parasail' -description = """parasail is a SIMD C (C99) library containing implementations - of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global - pairwise sequence alignment algorithms. """ - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} - -# https://github.com/jeffdaily/parasail -github_account = 'jeffdaily' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['3843055fc04743269cf22d127ae26952a7f5e6fc4f1bc29f6b6f3c156c8ca434'] - -builddependencies = [('CMake', '3.16.4')] - -sanity_check_paths = { - 'files': ['bin/parasail_aligner', 'bin/parasail_stats', - 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/patchelf/patchelf-0.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/patchelf/patchelf-0.12-GCCcore-9.3.0.eb deleted file mode 100644 index f114d746236..00000000000 --- a/easybuild/easyconfigs/__archive__/p/patchelf/patchelf-0.12-GCCcore-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'patchelf' -version = '0.12' - -homepage = 'https://github.com/NixOS/patchelf' -description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/NixOS/patchelf/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['3dca33fb862213b3541350e1da262249959595903f559eae0fbc68966e9c3f56'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), -] - -preconfigopts = "sh bootstrap.sh && " - -sanity_check_paths = { - 'files': ['bin/patchelf'], - 'dirs': ['share'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb deleted file mode 100644 index d4f06300b6e..00000000000 --- a/easybuild/easyconfigs/__archive__/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,57 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'phonemizer' -version = '2.2.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://github.com/bootphon/phonemizer" -description = """ -The phonemizer allows simple phonemization of words and texts in many languages. -Provides both the phonemize command-line tool and the Python function phonemizer.phonemize. -It is using four backends: espeak, espeak-mbrola, festival and segments. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('eSpeak-NG', '1.50'), - ('festival', '2.5.0'), -] - -exts_list = [ - ('regex', '2020.7.14', { - 'checksums': ['3a3af27a8d23143c49a3420efe5b3f8cf1a48c6fc8bc6856b03f638abc1833bb'], - }), - ('csvw', '1.8.0', { - 'checksums': ['1cfc8d05b6db59a0f4004c8f9c96aefbbc4888f702404ee93d12e63b874c7c47'], - }), - ('uritemplate', '3.0.1', { - 'checksums': ['5af8ad10cec94f215e3f48112de2022e1d5a37ed427fbd88652fa908f2ab7cae'], - }), - ('isodate', '0.6.0', { - 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], - }), - ('rfc3986', '1.4.0', { - 'checksums': ['112398da31a3344dc25dbf477d8df6cb34f9278a94fee2625d89e4514be8bb9d'], - }), - ('colorlog', '4.2.1', { - 'checksums': ['75e55822c3a3387d721579241e776de2cf089c9ef9528b1f09e8b04d403ad118'], - }), - ('clldutils', '3.5.2', { - 'checksums': ['4ceb6c50eafce44a83901df0de6ed5ec9de9c6c7c8514338f0f1db78f55b7ddd'], - }), - ('segments', '2.1.3', { - 'checksums': ['fb24845f8826444054dfb1605e6aa8a300fd6114420d6106faeec1a8823085af'], - }), - (name, version, { - 'checksums': ['4bf1b7a70967b69f8bb82e83b4307c8b9328ab0a8cee8e1a0606f70f8223f688'], - }), -] - -sanity_check_commands = [ - 'phonemize --version', - 'echo "hello world" | phonemize' -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 24158991c74..00000000000 --- a/easybuild/easyconfigs/__archive__/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'phonopy' -version = '2.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://phonopy.github.io/phonopy/' -description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['482c6ff29c058d091ac885e561e28ba3e516ea9e91c44a951cad11f3ae19856c'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy - ('matplotlib', '3.2.1', versionsuffix), - ('PyYAML', '5.3'), - ('h5py', '2.10.0', versionsuffix), - ('spglib-python', '1.16.0', versionsuffix), -] - -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - -sanity_check_paths = { - 'files': ['bin/phonopy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["phonopy --help"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/pigz/pigz-2.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/pigz/pigz-2.4-GCCcore-9.3.0.eb deleted file mode 100644 index 66e5f58fc86..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pigz/pigz-2.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,55 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# -# 2.4.0: -# Jonas Demeulemeester -# The Francis Crick Institute -## -easyblock = 'MakeCp' - -name = 'pigz' -version = '2.4' - -homepage = 'https://zlib.net/pigz/' - -description = """ - pigz, which stands for parallel implementation of gzip, is a fully - functional replacement for gzip that exploits multiple processors and multiple - cores to the hilt when compressing data. pigz was written by Mark Adler, and - uses the zlib and pthread libraries. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [ - 'https://zlib.net/pigz/', - 'https://zlib.net/pigz/fossils/', -] -sources = [SOURCE_TAR_GZ] -patches = ['%(name)s-%(version)s_makefile.patch'] -checksums = [ - 'a4f816222a7b4269bd232680590b579ccc72591f1bb5adafcd7208ca77e14f73', # pigz-2.4.tar.gz - '8de19216a69b6402942f73177c566791f0c7fa4649376029d30d0c537d2195c1', # pigz-2.4_makefile.patch -] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -buildopts = 'CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="-L$EBROOTZLIB/lib"' - -files_to_copy = [(["pigz", "unpigz"], "bin")] - -sanity_check_paths = { - 'files': ['bin/pigz', 'bin/unpigz'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/pixman/pixman-0.38.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/pixman/pixman-0.38.4-GCCcore-9.3.0.eb deleted file mode 100644 index 93fcba8ecbc..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pixman/pixman-0.38.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pixman' -version = '0.38.4' - -homepage = 'http://www.pixman.org/' - -description = """ - Pixman is a low-level software library for pixel manipulation, providing - features such as image compositing and trapezoid rasterization. Important - users of pixman are the cairo graphics library and the X server. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://cairographics.org/releases/'] -sources = [SOURCE_TAR_GZ] -checksums = ['da66d6fd6e40aee70f7bd02e4f8f76fc3f006ec879d346bae6a723025cfbdde7'] - -builddependencies = [ - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/pkg-config/pkg-config-0.29.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/pkg-config/pkg-config-0.29.2-GCCcore-9.3.0.eb deleted file mode 100644 index 9aca10ce415..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pkg-config/pkg-config-0.29.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pkg-config' -version = '0.29.2' - -homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' - -description = """ - pkg-config is a helper tool used when compiling applications and libraries. - It helps you insert the correct compiler options on the command line so an - application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` - for instance, rather than hard-coding values on where to find glib (or other - libraries). -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://pkg-config.freedesktop.org/releases/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] - -builddependencies = [('binutils', '2.34')] - -# don't use PAX, it might break. -tar_config_opts = True - -configopts = " --with-internal-glib" - -sanity_check_paths = { - 'files': ['bin/pkg-config'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/pkgconfig/pkgconfig-1.5.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pkgconfig/pkgconfig-1.5.1-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 26c892c9f67..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pkgconfig/pkgconfig-1.5.1-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pkgconfig' -version = '1.5.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/matze/pkgconfig' -description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f'] - -builddependencies = [ - ('binutils', '2.34'), - ('poetry', '1.0.9', versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('pkg-config', '0.29.2'), -] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/plantcv/plantcv-3.8.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/plantcv/plantcv-3.8.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index f72704a9942..00000000000 --- a/easybuild/easyconfigs/__archive__/p/plantcv/plantcv-3.8.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,55 +0,0 @@ -# This easyconfig was written by the HPC team at Agriculture Victoria Research -# http://agriculture.vic.gov.au/agriculture/innovation-and-research -# -# Author: Ben Moran -easyblock = 'PythonBundle' - -name = 'plantcv' -version = '3.8.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.org/project/plantcv/' -description = """PlantCV: Plant phenotyping using computer vision.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('Pillow', '7.0.0', versionsuffix), - ('scikit-image', '0.17.1', versionsuffix), - ('statsmodels', '0.11.1', versionsuffix), -] - -exts_list = [ - ('palettable', '3.3.0', { - 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], - }), - ('mizani', '0.7.1', { - 'checksums': ['97eea665d17fdc6c827b832925c094839e1ef7bf65b3aa47105e772b6eca9b0a'], - }), - ('descartes', '1.1.0', { - 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], - }), - ('plotnine', '0.7.0', { - 'checksums': ['8ee67cbf010ccea32670760e930b7b02177030a89ccdf85e35d156a96ce36cd3'], - }), - ('opencv-python', '3.4.10.35', { - 'source_tmpl': 'opencv_python-%(version)s-cp38-cp38-manylinux2014_x86_64.whl', - 'checksums': ['be25d76d9a104c73a0bb934894e54f2cebf5fb7aa46925fafbe2ccfcc48297cc'], - 'modulename': 'cv2', - }), - (name, version, { - 'checksums': ['4728e2ba78011cde4c7e2da2e45174bf71d9441fa58f772f25d4ad0dc9deecba'], - }), -] - -sanity_check_paths = { - 'files': ['bin/plantcv-workflow.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/plinkQC/plinkQC-0.3.3-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/p/plinkQC/plinkQC-0.3.3-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 3d201014972..00000000000 --- a/easybuild/easyconfigs/__archive__/p/plinkQC/plinkQC-0.3.3-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'Bundle' - -name = 'plinkQC' -# Listed upstream as 0.3.3 unreleased -version = '0.3.3' -versionsuffix = '-R-%(rver)s' -local_git_commit = 'b83c1ec' - -homepage = 'https://meyer-lab-cshl.github.io/plinkQC/' -description = """plinkQC is a R/CRAN package for genotype quality control in genetic association studies. - It makes PLINK basic statistics (e.g.missing genotyping rates per individual, allele frequencies per genetic - marker) and relationship functions easily accessible from within R and allows for automatic evaluation of the - results.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('R', '4.0.0'), -] - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -exts_list = [ - ('UpSetR', '1.4.0', { - 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], - }), - (name, version, { - 'source_tmpl': 'b83c1ec.tar.gz', - 'source_urls': ['https://github.com/meyer-lab-cshl/plinkQC/archive/'], - 'checksums': ['e30c10450bd9b39e3d8fad982f655efc9f96ffc30ef505f954c5efd45fc7e86e'], - }), -] - -modextrapaths = {'R_LIBS_SITE': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/plotly-orca/plotly-orca-1.3.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/plotly-orca/plotly-orca-1.3.1-GCCcore-9.3.0.eb deleted file mode 100644 index f979667d88e..00000000000 --- a/easybuild/easyconfigs/__archive__/p/plotly-orca/plotly-orca-1.3.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'Binary' - -name = 'plotly-orca' -version = '1.3.1' - -homepage = 'https://github.com/plotly/orca' -description = """Orca is an Electron app that generates images and reports of Plotly things like -plotly.js graphs, dash apps, dashboards from the command line.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/plotly/orca/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['25ebf207d75769c140dcea033a984e7a3a6d919bb8e110a14c890c8cf430f14d'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('nodejs', '12.16.1'), -] - -install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s electron@6.1.4 v%(version)s.tar.gz' - -sanity_check_paths = { - 'files': ['bin/orca'], - 'dirs': ['lib/node_modules/orca'], -} -sanity_check_commands = ['orca --help'] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/plotly.py/plotly.py-4.8.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/plotly.py/plotly.py-4.8.1-GCCcore-9.3.0.eb deleted file mode 100644 index ada2efe023b..00000000000 --- a/easybuild/easyconfigs/__archive__/p/plotly.py/plotly.py-4.8.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'plotly.py' -version = '4.8.1' - -homepage = 'https://plot.ly/python' -description = "An open-source, interactive graphing library for Python" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -exts_list = [ - ('retrying', '1.3.3', { - 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], - }), - ('plotly', version, { - 'checksums': ['d3fea527fe3dfdd55d7334318f107b05a8407474a0fffe6cd4726c9b99e624f1'], - }), -] - -builddependencies = [ - ('binutils', '2.34'), -] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.5-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.5-GCC-9.3.0.eb deleted file mode 100644 index 3a67d21dcc9..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.5-GCC-9.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'CMakeNinja' - -name = 'pocl' -version = '1.5' - -homepage = 'https://portablecl.org' -description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/pocl/pocl/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix-examples.patch'] -checksums = [ - '4fcf4618171727d165fc044d465a66e3119217bb4577a97374f94fcd8aed330e', # v1.5.tar.gz - 'be913b2157cc37fa62306b914f3a93cdaa30c98028220717a6fb4bc21d2cb33c', # pocl-1.5_fix-examples.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('Ninja', '1.10.0'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Clang', '10.0.1'), - ('hwloc', '2.2.0'), - ('libtool', '2.4.6'), - ('libxml2', '2.9.10'), -] - -separate_build_dir = True - -# disable attempt to find an ICD loader, always build libOpenCL.so -configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " -# make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config " -# avoid host CPU auto-detection (which may fail on recent CPUs) -configopts += "-DLLC_HOST_CPU=native " - -sanity_check_paths = { - 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], - 'dirs': ['include/CL', 'lib64/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.5_fix-examples.patch b/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.5_fix-examples.patch deleted file mode 100644 index d3d39ba0109..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pocl/pocl-1.5_fix-examples.patch +++ /dev/null @@ -1,22 +0,0 @@ -From 28a31079d9284215f92ace1a0f35cf161080cf59 Mon Sep 17 00:00:00 2001 -From: Matthias Diener -Date: Thu, 7 May 2020 12:50:49 -0700 -Subject: [PATCH] matrix1: add missing #define - -https://github.com/pocl/pocl/pull/818 ---- - examples/matrix1/matrix1.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/examples/matrix1/matrix1.c b/examples/matrix1/matrix1.c -index 14965b6f2..758c414d0 100644 ---- a/examples/matrix1/matrix1.c -+++ b/examples/matrix1/matrix1.c -@@ -23,6 +23,7 @@ - - /* For srandom. */ - #define _DEFAULT_SOURCE -+#define _BSD_SOURCE - - #include - #include diff --git a/easybuild/easyconfigs/__archive__/p/poetry/poetry-1.0.9-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/poetry/poetry-1.0.9-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index c7292de70dd..00000000000 --- a/easybuild/easyconfigs/__archive__/p/poetry/poetry-1.0.9-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,120 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonBundle' - -name = 'poetry' -version = '1.0.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://python-poetry.org/' -description = "Python packaging and dependency management made easy" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Python', '3.8.2'), -] - -# The order of extensions is significant! -# some dependencies can't be installed via 'pip .' - using 'use_pip: False' in those cases -exts_list = [ - ('pytoml', '0.1.21', { - 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], - }), - ('intreehooks', '1.0', { - 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], - }), - ('crashtest', '0.3.0', { - 'use_pip': False, - 'checksums': ['e9c06cc96400939ab5327123a3f699078eaad8a6283247d7b2ae0f6afffadf14'], - }), - ('pylev', '1.3.0', { - 'checksums': ['063910098161199b81e453025653ec53556c1be7165a9b7c50be2f4d57eae1c3'], - }), - ('pastel', '0.2.0', { - 'use_pip': False, - 'checksums': ['46155fc523bdd4efcd450bbcb3f2b94a6e3b25edc0eb493e081104ad09e1ca36'], - }), - ('clikit', '0.4.3', { - 'use_pip': False, - 'checksums': ['6e2d7e115e7c7b35bceb0209109935ab2f9ab50910e9ff2293f7fa0b7abf973e'], - }), - ('jeepney', '0.4.3', { - 'use_pip': False, - 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], - }), - ('SecretStorage', '3.1.2', { - 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], - }), - ('keyring', '20.0.1', { - 'checksums': ['963bfa7f090269d30bdc5e25589e5fd9dad2cf2a7c6f176a7f2386910e5d0d8d'], - }), - ('keyrings.alt', '3.4.0', { - 'checksums': ['91328ac4229e70b1d0061d21bf61d36b031a6b4828f2682e38c741812f6eb23d'], - }), - ('tomlkit', '0.5.11', { - 'use_pip': False, - 'checksums': ['f044eda25647882e5ef22b43a1688fb6ab12af2fc50e8456cdfc751c873101cf'], - }), - ('shellingham', '1.3.2', { - 'checksums': ['576c1982bea0ba82fb46c36feb951319d7f42214a82634233f58b40d858a751e'], - }), - ('requests-toolbelt', '0.8.0', { - 'checksums': ['f6a531936c6fa4c6cfce1b9c10d5c4f498d16528d2a54a22ca00011205a187b5'], - }), - ('pyrsistent', '0.14.11', { - 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], - }), - ('pkginfo', '1.5.0.1', { - 'checksums': ['7424f2c8511c186cd5424bbf31045b77435b37a8d604990b79d4e70d741148bb'], - }), - ('pexpect', '4.8.0', { - 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], - }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('webencodings', '0.5.1', { - 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], - }), - ('html5lib', '1.1', { - 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], - }), - ('cleo', '0.7.6', { - 'use_pip': False, - 'checksums': ['99cf342406f3499cec43270fcfaf93c126c5164092eca201dfef0f623360b409'], - }), - ('cachy', '0.3.0', { - 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], - }), - ('msgpack', '1.0.0', { - 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], - }), - ('CacheControl', '0.12.6', { - 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], - }), - ('ptyprocess', '0.6.0', { - 'use_pip': False, - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], - }), - ('lockfile', '0.12.2', { - 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], - }), - (name, version, { - 'checksums': ['0a4c56983546964b47cbbe0e1b49fef5662277bbf0673e3e350e1215560377ab'], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - 'poetry --help' -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/porefoam/porefoam-2021-09-21-foss-2020a.eb b/easybuild/easyconfigs/__archive__/p/porefoam/porefoam-2021-09-21-foss-2020a.eb deleted file mode 100644 index ca9ea7d9cd0..00000000000 --- a/easybuild/easyconfigs/__archive__/p/porefoam/porefoam-2021-09-21-foss-2020a.eb +++ /dev/null @@ -1,49 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'porefoam' -local_commit = 'eb02ba3' -version = '2021-09-21' - -homepage = 'https://github.com/ImperialCollegeLondon/porefoam' -description = "Direct pore-scale simulation of single- and two-phase flow through confined media" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/ImperialCollegeLondon/porefoam/archive/'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = [ - 'porefoam-2021-09-21_fix-scotch-linking.patch', - 'porefoam-2021-09-21_fix-hardcoded-mpicommand.patch', -] -checksums = [ - '61b7d23869f5cfadf001def25750576b05f13d3f117ffb409e56996a0de6d696', # porefoam-2021-09-21.tar.gz - '86b7e389b62f54bbd3c931ae3dbdc363226e250faa181e7e50ed121da9959a92', # porefoam-2021-09-21_fix-scotch-linking.patch - # porefoam-2021-09-21_fix-hardcoded-mpicommand.patch - '4cfa924c9a5d3ec38cf233312eb325ed625219644468f4b34fba8bc6ceee5ba2', -] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('SCOTCH', '6.0.9'), -] - -buildininstalldir = True -unpack_options = '--strip-components=1' - -skipsteps = ['configure', 'install'] - -prebuildopts = "export WM_COMPILER=Gcc && export WM_COMPILE_OPTION=Opt && " -# using ld.gold linker doesn't work -prebuildopts += 'export WM_CC="$CC $CFLAGS -fuse-ld=bfd" && export WM_CXX="$CXX $CXXFLAGS -fuse-ld=bfd" && ' - -sanity_check_paths = { - 'files': ['bin/interFaceFoam', 'bin/smoothMesh', 'bin/voxelToSurface'], - 'dirs': ['include', 'lib'], -} - -sanity_check_commands = ["voxelToFoam --help | grep 'convert micro-CT images to OpenFOAM mesh'"] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/p/porefoam/porefoam-2021-09-21_fix-hardcoded-mpicommand.patch b/easybuild/easyconfigs/__archive__/p/porefoam/porefoam-2021-09-21_fix-hardcoded-mpicommand.patch deleted file mode 100644 index 23c42699def..00000000000 --- a/easybuild/easyconfigs/__archive__/p/porefoam/porefoam-2021-09-21_fix-hardcoded-mpicommand.patch +++ /dev/null @@ -1,16 +0,0 @@ -# porefome hard-codes mpi command to be "mpirun.openmpi" and also fixes the "-np" switch to set the number of mpi tasks. -# I implemeted here $POREFOAM_MPIRUN_CMD variable to set the mpirun command and the switch to set the number of mpi tasks. -# for example for OpenMPI, use export POREFOAM_MPIRUN_CMD="mpirun -np" before you run porefoem -# June 21st 2022 by B. Hajgato (UGent) -diff -ru porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f.org/src/script/initbash porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f/src/script/initbash ---- porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f.org/src/script/initbash 2021-09-21 19:12:45.000000000 +0200 -+++ porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f/src/script/initbash 2022-06-21 14:24:04.255861222 +0200 -@@ -70,7 +70,7 @@ - else - echo "Running $APP_NAME $@ > $PWD/$LOG_NAME , using $np processes" - # --bind to none ( mpirun -x LD_LIBRARY_PATH -x PATH -x WM_PROJECT_DIR -x WM_PROJECT_INST_DIR -x MPI_BUFFER_SIZE --mca btl_tcp_if_exclude lo --mca btl_tcp_if_exclude eth0:avahi --hostfile machines.txt -np $np $APP_RUN -parallel "$@" < /dev/null > $LOG_NAME 2>&1 ) -- nice mpirun.openmpi -np $np $APP_RUN -parallel "$@" < /dev/null > $LOG_NAME 2>&1 -+ ${POREFOAM_MPIRUN_CMD:- nice mpirun.openmpi -np} $np $APP_RUN -parallel "$@" < /dev/null > $LOG_NAME 2>&1 - [[ $? == 0 ]] || echo "Error: $APP_RUN -parallel $@, exit status: $?, see $(pwd)/$LOG_NAME" >&2 - fi - sleep .1 diff --git a/easybuild/easyconfigs/__archive__/p/porefoam/porefoam-2021-09-21_fix-scotch-linking.patch b/easybuild/easyconfigs/__archive__/p/porefoam/porefoam-2021-09-21_fix-scotch-linking.patch deleted file mode 100644 index 17d5864d050..00000000000 --- a/easybuild/easyconfigs/__archive__/p/porefoam/porefoam-2021-09-21_fix-scotch-linking.patch +++ /dev/null @@ -1,13 +0,0 @@ -fix for: undefined reference to `SCOTCH_errorPrint' -author: Kenneth Hoste (HPC-UGent) ---- porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f/pkgs/foamx4m/applications/utilities/parallelProcessing/decomposePar/Make/options.orig 2022-02-25 16:29:05.774243797 +0100 -+++ porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f/pkgs/foamx4m/applications/utilities/parallelProcessing/decomposePar/Make/options 2022-02-25 16:29:28.484450588 +0100 -@@ -10,7 +10,7 @@ - -l:libdecompositionMethods.$(SO) \ - -l:libdecomposeReconstruct.$(SO) \ - -l:libmeshTools.$(SO) \ -- -l:libscotchDecomp.$(SO) -lscotch -+ -l:libscotchDecomp.$(SO) -lscotch -lscotcherrexit - - delsSkip = -ltetFiniteElement - delsSkip = -lfiniteArea diff --git a/easybuild/easyconfigs/__archive__/p/preCICE/preCICE-2.1.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/preCICE/preCICE-2.1.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index f12ae5482d1..00000000000 --- a/easybuild/easyconfigs/__archive__/p/preCICE/preCICE-2.1.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'preCICE' -version = '2.1.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.precice.org/' -description = """preCICE (Precise Code Interaction Coupling Environment) -is a coupling library for partitioned multi-physics simulations, -including, but not restricted to fluid-structure interaction and -conjugate heat transfer simulations. Partitioned means that preCICE -couples existing programs (solvers) capable of simulating a subpart of -the complete physics involved in a simulation. This allows for the high -flexibility that is needed to keep a decent time-to-solution for complex -multi-physics scenarios.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -# Needed to make the PETSc testing work. -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/precice/precice/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['729b7c24a7a61b3953bb70d96a954ad3a85729a29a35a288b59ba25661117064'] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('Python', '3.8.2'), - ('Boost', '1.72.0'), - ('Eigen', '3.3.7'), - ('libxml2', '2.9.10'), - ('PETSc', '3.12.4', versionsuffix), -] - -# Make sure PythonActions support is enabled -configopts = "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT -configopts += '-DPRECICE_PythonActions=ON ' - -separate_build_dir = True -build_shared_libs = True - -sanity_check_paths = { - 'files': ['bin/binprecice'] + - ['include/precice/%s' % x for x in ['SolverInterfaceC.h', 'SolverInterfaceFASTEST.hpp', - 'SolverInterfaceFortran.hpp', 'SolverInterface.hpp']] + - ['lib/libprecice.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/preCICE/preCICE-2.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/preCICE/preCICE-2.2.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index aab3c7f8764..00000000000 --- a/easybuild/easyconfigs/__archive__/p/preCICE/preCICE-2.2.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,65 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'preCICE' -version = '2.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.precice.org/' -description = """preCICE (Precise Code Interaction Coupling Environment) -is a coupling library for partitioned multi-physics simulations, -including, but not restricted to fluid-structure interaction and -conjugate heat transfer simulations. Partitioned means that preCICE -couples existing programs (solvers) capable of simulating a subpart of -the complete physics involved in a simulation. This allows for the high -flexibility that is needed to keep a decent time-to-solution for complex -multi-physics scenarios.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/precice/precice/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['f8c4e0810dcaeb6a40a0fcab64b95c899f0121c968e0730416d4d2a97d39d0c4'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('Boost', '1.72.0'), - ('Eigen', '3.3.7'), - ('libxml2', '2.9.10'), - ('PETSc', '3.12.4', versionsuffix), - ('SciPy-bundle', '2020.03', '-Python-3.8.2'), -] - -separate_build_dir = True -build_shared_libs = True - -# Tell pkg-config to keep flags available in CPATH and others because it prevents CMake from finding PETSc correctly -preconfigopts = 'PKG_CONFIG_ALLOW_SYSTEM_LIBS=1 PKG_CONFIG_ALLOW_SYSTEM_CFLAGS=1 ' -# Make sure MPI support is enabled -configopts = '-DPRECICE_MPICommunication=ON ' -# Make sure PETSc support is enabled -configopts += '-DPRECICE_PETScMapping=ON ' -# Make sure PythonActions support is enabled -configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT -configopts += '-DPRECICE_PythonActions=ON ' -# force Eigen include directory which is not found correctly otherwise -configopts += '-DEIGEN3_INCLUDE_DIR="$EBROOTEIGEN/include"' - -# Run basic tests -runtest = ' test_base' - -sanity_check_paths = { - 'files': ['bin/binprecice'] + - ['include/precice/%s' % x for x in ['SolverInterfaceC.h', 'SolverInterfaceFASTEST.hpp', - 'SolverInterfaceFortran.hpp', 'SolverInterface.hpp']] + - ['lib/libprecice.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/p/preCICE/preCICE-2.2.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/preCICE/preCICE-2.2.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 2ab8eb176ef..00000000000 --- a/easybuild/easyconfigs/__archive__/p/preCICE/preCICE-2.2.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,67 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'preCICE' -version = '2.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.precice.org/' -description = """preCICE (Precise Code Interaction Coupling Environment) -is a coupling library for partitioned multi-physics simulations, -including, but not restricted to fluid-structure interaction and -conjugate heat transfer simulations. Partitioned means that preCICE -couples existing programs (solvers) capable of simulating a subpart of -the complete physics involved in a simulation. This allows for the high -flexibility that is needed to keep a decent time-to-solution for complex -multi-physics scenarios.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/precice/precice/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['f8c4e0810dcaeb6a40a0fcab64b95c899f0121c968e0730416d4d2a97d39d0c4'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('Boost', '1.72.0'), - ('Eigen', '3.3.7'), - ('libxml2', '2.9.10'), - ('PETSc', '3.12.4', versionsuffix), - ('SciPy-bundle', '2020.03', '-Python-3.8.2'), -] - -separate_build_dir = True -build_shared_libs = True - -# Tell pkg-config to keep flags available in CPATH and others because it prevents CMake from finding PETSc correctly -preconfigopts = 'PKG_CONFIG_ALLOW_SYSTEM_LIBS=1 PKG_CONFIG_ALLOW_SYSTEM_CFLAGS=1 ' -# Make sure MPI support is enabled -configopts = '-DPRECICE_MPICommunication=ON ' -# Make sure PETSc support is enabled -configopts += '-DPRECICE_PETScMapping=ON ' -# Make sure PythonActions support is enabled -configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT -configopts += '-DPRECICE_PythonActions=ON ' -# force Eigen include directory which is not found correctly otherwise -configopts += '-DEIGEN3_INCLUDE_DIR="$EBROOTEIGEN/include"' - -# Run basic tests -# -> disabled because they fail with intel toolchain -# cf https://github.com/precice/precice/issues/966 -# runtest = ' test_base' - -sanity_check_paths = { - 'files': ['bin/binprecice'] + - ['include/precice/%s' % x for x in ['SolverInterfaceC.h', 'SolverInterfaceFASTEST.hpp', - 'SolverInterfaceFortran.hpp', 'SolverInterface.hpp']] + - ['lib/libprecice.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/p/pretty-yaml/pretty-yaml-20.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/pretty-yaml/pretty-yaml-20.4.0-GCCcore-9.3.0.eb deleted file mode 100644 index a5d71623ba4..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pretty-yaml/pretty-yaml-20.4.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pretty-yaml' -local_mod = 'pyaml' -version = '20.4.0' - -homepage = 'https://github.com/mk-fg/pretty-yaml' -description = """PyYAML-based python module to produce pretty and readable YAML-serialized data. -This module is for serialization only, see ruamel.yaml module for literate YAML -parsing (keeping track of comments, spacing, line/column numbers of values, etc).""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] -sources = ['%s-%%(version)s.tar.gz' % local_mod] -checksums = ['29a5c2a68660a799103d6949167bd6c7953d031449d08802386372de1db6ad71'] - -builddependencies = [('binutils', '2.34')] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [ - ('PyYAML', '5.3'), -] - -options = {'modulename': local_mod} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb deleted file mode 100644 index 8b65726786a..00000000000 --- a/easybuild/easyconfigs/__archive__/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exe Escobedo -# License:: GPL-v3.0 -# -# Updated: Pavel Grochal (INUITS) -# -# Notes:: -## - -easyblock = 'MakeCp' - -name = 'prodigal' -version = '2.6.3' - -homepage = 'https://github.com/hyattpd/Prodigal/' - -description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) - is a microbial (bacterial and archaeal) gene finding program developed - at Oak Ridge National Laboratory and the University of Tennessee.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] - -builddependencies = [('binutils', '2.34')] - -files_to_copy = [ - (['prodigal'], 'bin'), - (['*.h'], 'include'), - (['LICENSE'], 'license'), -] - -sanity_check_paths = { - 'files': ['bin/prodigal'], - 'dirs': ['include', 'license'], -} - -sanity_check_commands = ["prodigal -h"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/protobuf-python/protobuf-python-3.13.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/protobuf-python/protobuf-python-3.13.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 4607b52ca72..00000000000 --- a/easybuild/easyconfigs/__archive__/p/protobuf-python/protobuf-python-3.13.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'protobuf-python' -version = '3.13.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/google/protobuf/' -description = """Python Protocol Buffers runtime library.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] -sources = [{'download_filename': 'protobuf-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['6a82e0c8bb2bf58f606040cc5814e07715b2094caeba281e2e7d0b0e2e397db5'] - -dependencies = [ - ('Python', '3.8.2'), - ('protobuf', version) -] - -# Make sure protobuf is installed as a regular folder or it will not be found if -# other google packages are installed in other site-packages folders -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], -} - -options = {'modulename': 'google.protobuf'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/protobuf-python/protobuf-python-3.13.0-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/protobuf-python/protobuf-python-3.13.0-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 845f512aa63..00000000000 --- a/easybuild/easyconfigs/__archive__/p/protobuf-python/protobuf-python-3.13.0-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'protobuf-python' -version = '3.13.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/google/protobuf/' -description = """Python Protocol Buffers runtime library.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] -sources = [{'download_filename': 'protobuf-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['6a82e0c8bb2bf58f606040cc5814e07715b2094caeba281e2e7d0b0e2e397db5'] - -dependencies = [ - ('Python', '3.8.2'), - ('protobuf', version) -] - -# Make sure protobuf is installed as a regular folder or it will not be found if -# other google packages are installed in other site-packages folders -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], -} - -options = {'modulename': 'google.protobuf'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/protobuf/protobuf-3.10.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/protobuf/protobuf-3.10.0-GCCcore-9.3.0.eb deleted file mode 100644 index 702e79d7059..00000000000 --- a/easybuild/easyconfigs/__archive__/p/protobuf/protobuf-3.10.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'protobuf' -version = '3.10.0' - -homepage = 'https://github.com/google/protobuf/' -description = """Google Protocol Buffers""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['758249b537abba2f21ebc2d02555bf080917f0f2f88f4cbe2903e0e28c4187ed'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -srcdir = 'cmake' - -configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON ' - -sanity_check_paths = { - 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/protobuf/protobuf-3.13.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/protobuf/protobuf-3.13.0-GCCcore-9.3.0.eb deleted file mode 100644 index e7f522b6c01..00000000000 --- a/easybuild/easyconfigs/__archive__/p/protobuf/protobuf-3.13.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'protobuf' -version = '3.13.0' - -homepage = 'https://github.com/google/protobuf/' -description = """Google Protocol Buffers""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['9b4ee22c250fe31b16f1a24d61467e40780a3fbb9b91c3b65be2a376ed913a1a'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -srcdir = 'cmake' - -configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON ' - -sanity_check_paths = { - 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/p/psycopg2/psycopg2-2.8.6-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/psycopg2/psycopg2-2.8.6-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 83db322251c..00000000000 --- a/easybuild/easyconfigs/__archive__/p/psycopg2/psycopg2-2.8.6-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonPackage' - -name = 'psycopg2' -version = '2.8.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://initd.org/psycopg/' -description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['fb23f6c71107c37fd667cb4ea363ddeb936b348bbd6449278eb92c189699f543'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('PostgreSQL', '12.4'), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/py-aiger-bdd/py-aiger-bdd-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/py-aiger-bdd/py-aiger-bdd-3.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 182e3551131..00000000000 --- a/easybuild/easyconfigs/__archive__/p/py-aiger-bdd/py-aiger-bdd-3.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'py-aiger-bdd' -version = '3.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/mvcisback/py-aiger-bdd' -description = "Aiger to BDD bridge." - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['f91ac998ce1d2e352f522ff69937ee55ed69a20d649dcc8abcfd7cd63c955844'] - -builddependencies = [ - ('poetry', '1.0.9', versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('py-aiger', '6.1.1', versionsuffix), - ('dd', '0.5.6', versionsuffix), -] - -options = {'modulename': 'aiger_bdd'} - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/p/py-aiger/py-aiger-6.1.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/py-aiger/py-aiger-6.1.1-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 2e4ca666bd6..00000000000 --- a/easybuild/easyconfigs/__archive__/p/py-aiger/py-aiger-6.1.1-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,71 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'py-aiger' -version = '6.1.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/mvcisback/py-aiger' -description = """ -A python library for manipulating sequential and combinatorial circuits. -This module provides the py-aiger extensions: aiger_bv, aiger_cnf, aiger_ptltl, -aiger_coins, aiger_gridworld, aiger_dfa""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [ - ('binutils', '2.34'), - ('poetry', '1.0.9', versionsuffix), -] - -dependencies = [ - ('Python', '3.8.2'), - ('DFA', '0.3.4', versionsuffix), # needed by py-aiger-dfa -] - -exts_list = [ - ('bidict', '0.18.4', { - 'checksums': ['b60e16233ecb8d533afa072ad387ca0315700c6596a7ed4d576ada3418768324'], - }), - ('funcy', '1.15', { - 'checksums': ['65b746fed572b392d886810a98d56939c6e0d545abb750527a717c21ced21008'], - }), - ('parsimonious', '0.8.1', { - 'checksums': ['3add338892d580e0cb3b1a39e4a1b427ff9f687858fdd61097053742391a9f6b'], - }), - ('toposort', '1.6', { - 'checksums': ['a7428f56ef844f5055bb9e9e44b343983773ae6dce0fe5b101e08e27ffbd50ac'], - }), - ('pyrsistent', '0.15.7', { - 'checksums': ['cdc7b5e3ed77bed61270a47d35434a30617b9becdf2478af76ad2c6ade307280'], - }), - (name, version, { - 'modulename': 'aiger', - 'checksums': ['31dab44dbf5fa9e6233ef871526f341d8084c9ab3160a3544a08a193d957d187'], - }), - ('py-aiger-bv', '4.2.1', { - 'modulename': 'aiger_bv', - 'checksums': ['511722e34877171694812e562e6a3a3bf9e86b6319a3efd3260aa7581cbac4cc'], - }), - ('py-aiger-cnf', '5.0.0', { - 'modulename': 'aiger_cnf', - 'checksums': ['765bcadf0359e841fd12822ec5a9bbb2e57389be387ce3f1cec172ce96022b79'], - }), - ('py-aiger-ptltl', '3.0.0', { - 'modulename': 'aiger_ptltl', - 'checksums': ['507d2d9c1e8a49f448d950d78f9fc2471cde419382dc2022565dee6a2e1434a6'], - }), - ('py-aiger-coins', '2.2.0', { - 'modulename': 'aiger_coins', - 'checksums': ['3d04a5df212ce10c5567f9b90d68d78c319f1ba6c890e98914e0574f92d91d31'], - }), - ('py-aiger-gridworld', '0.3.0', { - 'modulename': 'aiger_gridworld', - 'checksums': ['28b1e1ef3ceef6d7bb1b2422f6dd677d7677a388f3dd4e3e991081970dc1f060'], - }), - ('py-aiger-dfa', '0.2.0', { - 'modulename': 'aiger_dfa', - 'checksums': ['808b2ca51a84fef5dbdf14fb0e000f9fc6a7f9f1a0959a1d80e8fb8278d201cb'], - }), -] - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/p/pyBigWig/pyBigWig-0.3.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/pyBigWig/pyBigWig-0.3.17-GCCcore-9.3.0.eb deleted file mode 100644 index a00dfd8a329..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pyBigWig/pyBigWig-0.3.17-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pyBigWig' -version = '0.3.17' - -github_account = 'deeptools' -homepage = 'https://github.com/%(github_account)s/%(name)s' -description = """A python extension, written in C, for quick access to bigBed - files and access to and creation of bigWig files.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['a1ccd607db0ece1553471cab3763e318609171a8219a7e0625bc80b61479f8d7'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [ - ('binutils', '2.34'), - ('cURL', '7.69.1'), -] - -options = {'modulename': name} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 957ec86b821..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pyEGA3' -version = '3.4.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/EGA-archive/ega-download-client' -description = """ A basic Python-based EGA download client """ - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Python', '3.8.2'), - ('tqdm', '4.47.0'), -] - -exts_list = [ - ('humanize', '0.5.1', { - 'checksums': ['a43f57115831ac7c70de098e6ac46ac13be00d69abbf60bdcac251344785bb19'], - }), - ('htsget', '0.2.5', { - 'checksums': ['d383dc36f699bd921f760f5500c8ed251e5f8358a7cc219c6c89c35d103e8045'], - }), - (name, version, { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/EGA-archive/ega-download-client/archive/'], - 'checksums': ['7d3756d91e7f942635f16bbe0e17221afff6d9a2b5582964ff1250d4cb81066f'], - }), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/pySCENIC/pySCENIC-0.10.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pySCENIC/pySCENIC-0.10.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index cefac3e0356..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pySCENIC/pySCENIC-0.10.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,79 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pySCENIC' -version = '0.10.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/aertslab/pySCENIC' -description = """pySCENIC is a lightning-fast python implementation of the SCENIC -pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables -biologists to infer transcription factors, gene regulatory networks and -cell types from single-cell RNA-seq data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('numba', '0.50.0', versionsuffix), - ('Arrow', '0.17.1', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('tqdm', '4.47.0'), - ('networkx', '2.4', versionsuffix), - ('h5py', '2.10.0', versionsuffix), - ('dask', '2.18.1', versionsuffix), -] - -exts_list = [ - ('cytoolz', '0.10.1', { - 'checksums': ['82f5bba81d73a5a6b06f2a3553ff9003d865952fcb32e1df192378dd944d8a5c'], - }), - ('dill', '0.3.2', { - 'source_tmpl': 'dill-%(version)s.zip', - 'checksums': ['6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e'], - }), - ('multiprocessing_on_dill', '3.5.0a4', { - 'checksums': ['d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7'], - }), - ('frozendict', '1.2', { - 'checksums': ['774179f22db2ef8a106e9c38d4d1f8503864603db08de2e33be5b778230f6e45'], - }), - ('arboreto', '0.1.5', { - 'checksums': ['a78c73b367eaae38dadeba150e52ac98aec6fc916df703ce61b79d27fe1015f9'], - }), - ('boltons', '20.2.0', { - 'checksums': ['d367506c0b32042bb1ee3bf7899f2dcc8492dceb42ce3727b89e174d85bffe6e'], - }), - ('interlap', '0.2.6', { - 'checksums': ['a8585a165bf7e94d4d262811b4cb00674059414c50afc7561c949b0feb78fa09'], - }), - ('umap-learn', '0.4.6', { - 'modulename': 'umap', - 'checksums': ['4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3'], - }), - ('numpy_groupies', '0.9.10', { - 'checksums': ['a6835c252b7bd489e0f701f8bf5bc880c647ef251e3b434998b95a8aecc9b68a'], - }), - ('loompy', '3.0.6', { - 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], - }), - ('pyscenic', version, { - 'patches': ['pySCENIC-%(version)s_fix-pyarrow-FeatherReader.patch'], - 'checksums': [ - '517c4fadf6198ba0202116f1c419d61c4d4491fc4099b611fbe738845fe4acc9', # pyscenic-0.10.3.tar.gz - # pySCENIC-0.10.3_fix-pyarrow-FeatherReader.patch - '022e69a384771a1389d176db699cc97f5a3c8ee43502a49f0335b82c1932e0e5', - ], - # strip out version restrictions for required Python packages - 'preinstallopts': "sed -i 's/[=>]=[0-9].*//g' requirements.txt && ", - }), -] - -sanity_check_paths = { - 'files': ['bin/pyscenic'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["pyscenic --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/pySCENIC/pySCENIC-0.10.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pySCENIC/pySCENIC-0.10.3-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 181a182f47a..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pySCENIC/pySCENIC-0.10.3-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,79 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pySCENIC' -version = '0.10.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/aertslab/pySCENIC' -description = """pySCENIC is a lightning-fast python implementation of the SCENIC -pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables -biologists to infer transcription factors, gene regulatory networks and -cell types from single-cell RNA-seq data.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('numba', '0.50.0', versionsuffix), - ('Arrow', '0.17.1', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('tqdm', '4.47.0'), - ('networkx', '2.4', versionsuffix), - ('h5py', '2.10.0', versionsuffix), - ('dask', '2.18.1', versionsuffix), -] - -exts_list = [ - ('cytoolz', '0.10.1', { - 'checksums': ['82f5bba81d73a5a6b06f2a3553ff9003d865952fcb32e1df192378dd944d8a5c'], - }), - ('dill', '0.3.2', { - 'source_tmpl': 'dill-%(version)s.zip', - 'checksums': ['6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e'], - }), - ('multiprocessing_on_dill', '3.5.0a4', { - 'checksums': ['d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7'], - }), - ('frozendict', '1.2', { - 'checksums': ['774179f22db2ef8a106e9c38d4d1f8503864603db08de2e33be5b778230f6e45'], - }), - ('arboreto', '0.1.5', { - 'checksums': ['a78c73b367eaae38dadeba150e52ac98aec6fc916df703ce61b79d27fe1015f9'], - }), - ('boltons', '20.2.0', { - 'checksums': ['d367506c0b32042bb1ee3bf7899f2dcc8492dceb42ce3727b89e174d85bffe6e'], - }), - ('interlap', '0.2.6', { - 'checksums': ['a8585a165bf7e94d4d262811b4cb00674059414c50afc7561c949b0feb78fa09'], - }), - ('umap-learn', '0.4.6', { - 'modulename': 'umap', - 'checksums': ['4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3'], - }), - ('numpy_groupies', '0.9.10', { - 'checksums': ['a6835c252b7bd489e0f701f8bf5bc880c647ef251e3b434998b95a8aecc9b68a'], - }), - ('loompy', '3.0.6', { - 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], - }), - ('pyscenic', version, { - 'patches': ['pySCENIC-%(version)s_fix-pyarrow-FeatherReader.patch'], - 'checksums': [ - '517c4fadf6198ba0202116f1c419d61c4d4491fc4099b611fbe738845fe4acc9', # pyscenic-0.10.3.tar.gz - # pySCENIC-0.10.3_fix-pyarrow-FeatherReader.patch - '022e69a384771a1389d176db699cc97f5a3c8ee43502a49f0335b82c1932e0e5', - ], - # strip out version restrictions for required Python packages - 'preinstallopts': "sed -i 's/[=>]=[0-9].*//g' requirements.txt && ", - }), -] - -sanity_check_paths = { - 'files': ['bin/pyscenic'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["pyscenic --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/pySCENIC/pySCENIC-0.10.3_fix-pyarrow-FeatherReader.patch b/easybuild/easyconfigs/__archive__/p/pySCENIC/pySCENIC-0.10.3_fix-pyarrow-FeatherReader.patch deleted file mode 100644 index 0362c621f19..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pySCENIC/pySCENIC-0.10.3_fix-pyarrow-FeatherReader.patch +++ /dev/null @@ -1,17 +0,0 @@ -fix compatibilty with PyArrow 0.17.1, where FeatherReader was moved from pyarrow.feather to pyarrow.lib -author: Kenneth Hoste (HPC-UGent) ---- pyscenic-0.10.3/src/pyscenic/rnkdb.py.orig 2020-08-11 14:55:53.212511866 +0200 -+++ pyscenic-0.10.3/src/pyscenic/rnkdb.py 2020-08-11 14:56:02.932604710 +0200 -@@ -9,7 +9,11 @@ - from operator import itemgetter - from .genesig import GeneSignature - from cytoolz import memoize --from pyarrow.feather import write_feather, FeatherReader -+from pyarrow.feather import write_feather -+try: -+ from pyarrow.feather import FeatherReader -+except ImportError: -+ from pyarrow.lib import FeatherReader - from tqdm import tqdm - - diff --git a/easybuild/easyconfigs/__archive__/p/pybind11/pybind11-2.4.3-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pybind11/pybind11-2.4.3-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 54ea7b78ec7..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pybind11/pybind11-2.4.3-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'pybind11' -version = '2.4.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pybind11.readthedocs.io' -description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, - mainly to create Python bindings of existing C++ code.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/pybind/pybind11/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s-fix-get-include.patch'] -checksums = [ - '1eed57bc6863190e35637290f97a20c81cfe4d9090ac0a24f3bbf08f265eb71d', # v2.4.3.tar.gz - 'b03550f05dcff97eeb3d7f4cd393b0584341ac7a310c89ee120f95e54fdc3125', # pybind11-2.4.3-fix-get-include.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('Eigen', '3.3.7'), -] -dependencies = [('Python', '3.8.2')] - -configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/pybind11/pybind11-2.4.3-fix-get-include.patch b/easybuild/easyconfigs/__archive__/p/pybind11/pybind11-2.4.3-fix-get-include.patch deleted file mode 100644 index e6d7892a517..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pybind11/pybind11-2.4.3-fix-get-include.patch +++ /dev/null @@ -1,27 +0,0 @@ -The current function doesn't take into account that a custom install prefix might have been set -at installation time which we do in EB. -Insert a quick hack to make it work as it should (fixed in 2.5.0) - -Author: Alexander Grund (TU Dresden) - -diff --git a/pybind11/__init__.py b/pybind11/__init__.py -index c625e8c..5c2e3bd 100644 ---- a/pybind11/__init__.py -+++ b/pybind11/__init__.py -@@ -27,10 +27,16 @@ def get_include(user=False): - - dist_cobj = dist.get_command_obj('install', create=True) - -+ # Very crude hack to get install prefix from /lib/python3.7/site-packages/pybind11 -+ from pathlib import Path -+ prefix = prefix = Path(__file__).resolve().parents[4] -+ - # Search for packages in user's home directory? - if user: - dist_cobj.user = user - dist_cobj.prefix = "" -+ else: -+ dist_cobj.prefix = prefix - dist_cobj.finalize_options() - - return os.path.dirname(dist_cobj.install_headers) diff --git a/easybuild/easyconfigs/__archive__/p/pycocotools/pycocotools-2.0.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pycocotools/pycocotools-2.0.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 5d1ab1329a2..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pycocotools/pycocotools-2.0.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pycocotools' -version = '2.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.org/project/pycocotools' -description = "Official APIs for the MS-COCO dataset" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['24717a12799b4471c2e54aa210d642e6cd4028826a1d49fcc2b0e3497e041f1a'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/pycocotools/pycocotools-2.0.2-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pycocotools/pycocotools-2.0.2-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 073c1d2171a..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pycocotools/pycocotools-2.0.2-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pycocotools' -version = '2.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.org/project/pycocotools' -description = "Official APIs for the MS-COCO dataset" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['24717a12799b4471c2e54aa210d642e6cd4028826a1d49fcc2b0e3497e041f1a'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/pydicom/pydicom-2.1.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pydicom/pydicom-2.1.2-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 936b855b499..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pydicom/pydicom-2.1.2-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pydicom' -version = '2.1.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pydicom.github.io/' -description = "Pure python package for DICOM medical file reading and writing." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'pydicom' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['e7cfbc4a997e327583bee047b7c9340845328373d088e776cf9565e47609a1a3'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Python', '3.8.2'), -] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/pydot/pydot-1.4.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/p/pydot/pydot-1.4.1-GCCcore-9.3.0.eb deleted file mode 100644 index f29e7803984..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pydot/pydot-1.4.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pydot' -version = '1.4.1' - -homepage = 'https://github.com/pydot/pydot' -description = "Python interface to Graphviz's Dot language." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['d49c9d4dd1913beec2a997f831543c8cbd53e535b1a739e921642fe416235f01'] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -builddependencies = [('binutils', '2.34')] - -dependencies = [('Graphviz', '2.44.1', '-Java-11')] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 28ac33f2dce..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,83 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pyiron' -version = '0.3.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pyiron/pyiron' -description = "An integrated development environment (IDE) for computational materials science." - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('h5py', '2.10.0', versionsuffix), - ('PyYAML', '5.3'), - ('phonopy', '2.7.1', versionsuffix), - ('spglib-python', '1.16.0', versionsuffix), - ('ASE', '3.20.1', versionsuffix), - ('numexpr', '2.7.1', versionsuffix), - ('PyTables', '3.6.1', versionsuffix), - ('nglview', '2.7.7', versionsuffix), - ('tqdm', '4.47.0'), - ('molmod', '1.4.5', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('yaff', '1.6.0', versionsuffix), - ('TAMkin', '1.2.6', versionsuffix), - ('QuickFF', '2.2.4', versionsuffix), -] - -check_ldshared = True - -exts_list = [ - ('h5io', '0.1.2', { - 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], - }), - ('defusedxml', '0.6.0', { - 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], - }), - ('pysqa', '0.0.11', { - 'checksums': ['b1a1995ac8b83b86046cef8b72cda962c5fdbf480c6dbba906a467a5dd1d3c81'], - }), - ('SQLAlchemy', '1.3.19', { - 'checksums': ['3bba2e9fbedb0511769780fe1d63007081008c5c2d7d715e91858c94dbaa260e'], - }), - ('dill', '0.3.2', { - 'source_tmpl': 'dill-%(version)s.zip', - 'checksums': ['6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e'], - }), - ('smmap', '3.0.4', { - 'checksums': ['9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24'], - }), - ('gitdb', '4.0.5', { - 'checksums': ['c9e1f2d0db7ddb9a704c2a0217be31214e91a4fe1dea1efad19ae42ba0c285c9'], - }), - ('GitPython', '3.1.8', { - 'checksums': ['080bf8e2cf1a2b907634761c2eaefbe83b69930c94c66ad11b65a8252959f912'], - 'modulename': 'git', - }), - ('colorama', '0.4.3', { - 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], - }), - ('pyfiglet', '0.8.post1', { - 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], - }), - ('mendeleev', '0.6.0', { - 'checksums': ['944d185e81f158e48dd394b011e6c14acb612c2ffbc3c32c4aa490cd5b4f65dd'], - }), - ('pyfileindex', '0.0.4', { - 'checksums': ['bbfbfc9372f810587917ab1a88bebb8de44d32a1210bbd436c5b88447d97dfd2'], - }), - ('seekpath', '2.0.1', { - 'checksums': ['188513ee187fbbace49066a29ecea9bbd351f23da3bea33d507d0f590856b082'], - }), - (name, version, { - 'checksums': ['6d49899c2dbec4b80299c227b04dceb9211a668c49e9d80a621448b69bb2ac65'], - # import pyiron triggers interactive configuration setup, so we disable it - 'modulename': False, - }), -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/p/pylift/pylift-0.1.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pylift/pylift-0.1.5-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 2df51d6449f..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pylift/pylift-0.1.5-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pylift' -version = '0.1.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/df-foundation/pylift' -description = """ pylift is an uplift library that provides, primarily: - (1) Fast uplift modeling implementations and (2) Evaluation tools (UpliftEval class).""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['bf855996abfd65125cde40b378393766c379694a4b814cdecb1cadd743392730'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('pretty-yaml', '20.4.0'), - ('scikit-learn', '0.23.1', versionsuffix), - ('scikit-optimize', '0.8.1', versionsuffix), - ('Seaborn', '0.10.1', versionsuffix), - ('XGBoost', '1.2.0', versionsuffix), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/pymbar/pymbar-3.0.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pymbar/pymbar-3.0.3-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 70179ad34f7..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pymbar/pymbar-3.0.3-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pymbar' -version = '3.0.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://pymbar.readthedocs.io/en/master/' -description = """The pymbar package contains the pymbar suite of tools for the analysis of -simulated and experimental data with the multistate Bennett acceptance -ratio (MBAR) estimator.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/choderalab/pymbar/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['5e59bb9f3789ae723e85d4483d7d204e39425551f30df8cefc13c6e607af6398'] - -dependencies = [ - ('Python', '3.8.2'), - ('numexpr', '2.7.1', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/p/pyobjcryst/pyobjcryst-2.1.0.post2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pyobjcryst/pyobjcryst-2.1.0.post2-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index d894ee9ec42..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pyobjcryst/pyobjcryst-2.1.0.post2-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pyobjcryst' -version = '2.1.0.post2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/diffpy/pyobjcryst' -description = "Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library." - -toolchain = {'name': 'intel', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['2ee797cf4d0ba90a7d144110b0f3295ee7fa73462c648297100bfd5eb467bb6d'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy - ('Boost.Python', '1.72.0'), - ('libobjcryst', '2017.2.3'), -] - -sanity_check_commands = ["python -m pyobjcryst.tests.run"] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/p/pyproj/pyproj-2.6.1.post1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/pyproj/pyproj-2.6.1.post1-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index e66e1713073..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pyproj/pyproj-2.6.1.post1-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pyproj' -version = '2.6.1.post1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pyproj4.github.io/pyproj' -description = "Python interface to PROJ4 library for cartographic transformations" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['4f5b02b4abbd41610397c635b275a8ee4a2b5bc72a75572b98ac6ae7befa471e'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('PROJ', '7.0.0'), -] - -preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/p/pyspoa/pyspoa-0.2.1_use-spoa-dep.patch b/easybuild/easyconfigs/__archive__/p/pyspoa/pyspoa-0.2.1_use-spoa-dep.patch deleted file mode 100644 index 37a309bd217..00000000000 --- a/easybuild/easyconfigs/__archive__/p/pyspoa/pyspoa-0.2.1_use-spoa-dep.patch +++ /dev/null @@ -1,24 +0,0 @@ -use spoa dependency provided through EasyBuild - -author: Kenneth Hoste (HPC-UGent) -updated by: Petr Král (Inuits) -diff --git a/pyspoa-0.2.1/setup.py.orig b/pyspoa-0.2.1/setup.py ---- a/pyspoa-0.2.1/setup.py.orig 2023-11-27 14:48:14.661356275 +0100 -+++ b/pyspoa-0.2.1/setup.py 2023-11-27 14:52:53.880656275 +0100 -@@ -119,14 +119,14 @@ - 'spoa', - ['pyspoa.cpp'], - include_dirs=[ -- 'src/include/spoa', -+ os.path.join(os.getenv('EBROOTSPOA'), 'include/spoa'), - 'src/vendor/cereal/include', - get_pybind_include(), - get_pybind_include(user=True), - ], - language='c++', - extra_objects=[ -- LIB_SPOA -+ os.path.join(os.getenv('EBROOTSPOA'), 'lib64/libspoa.a'), - ], - - ), diff --git a/easybuild/easyconfigs/__archive__/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb deleted file mode 100644 index af10859a5ff..00000000000 --- a/easybuild/easyconfigs/__archive__/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'python-igraph' -version = '0.8.0' - -homepage = 'https://igraph.org/python' -description = """Python interface to the igraph high performance graph library, primarily aimed at complex network - research and analysis.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('igraph', '0.8.2'), - ('PyCairo', '1.18.2'), -] - -use_pip = False - -exts_list = [ - ('texttable', '1.6.3', { - 'checksums': ['ce0faf21aa77d806bbff22b107cc22cce68dc9438f97a2df32c93e9afa4ce436'], - }), - (name, version, { - 'buildopts': '--use-pkg-config', - 'installopts': '--use-pkg-config', - 'modulename': 'igraph', - 'checksums': ['47e6bb48ec7dbfddbd89cf064a24b271783a1490fc688ebce17fbd652bcdab8e'], - }), -] - -sanity_check_paths = { - 'files': ['bin/igraph'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -# cairo must be available for proper plotting support -sanity_check_commands = ["python -c 'from igraph.drawing.utils import find_cairo; cairo = find_cairo(); cairo.Context'"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.2-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 24c27389466..00000000000 --- a/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.2-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'python-parasail' -version = '1.2.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/jeffdaily/parasail-python' -description = "Python Bindings for the Parasail C Library" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] -sources = ['parasail-%(version)s.tar.gz'] -checksums = ['ef3f7dda655f1c7d6adb14a41e226482960b2a17ea7791db41cb3e7c5dd29b08'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('parasail', '2.4.2'), -] - -# make sure setup.py finds the parasail library -preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT - -options = {'modulename': 'parasail'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 405f7cca61f..00000000000 --- a/easybuild/easyconfigs/__archive__/p/python-parasail/python-parasail-1.2.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# Updated to v1.2.3 -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'python-parasail' -version = '1.2.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/jeffdaily/parasail-python' -description = "Python Bindings for the Parasail C Library" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] -sources = ['parasail-%(version)s.tar.gz'] -checksums = ['e0eb66b15c6318724bd3c4a3c05b5a1a4b7926eb1ee79606958c98c52a32cbb3'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('parasail', '2.4.2'), -] - -# make sure setup.py finds the parasail library -preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT - -options = {'modulename': 'parasail'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 83696ced397..00000000000 --- a/easybuild/easyconfigs/__archive__/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,59 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonBundle' - -name = 'QUAST' -version = '5.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/ablab/%(namelower)s' -description = """QUAST evaluates genome assemblies by computing various metrics. - It works both with and without reference genomes. The tool accepts multiple - assemblies, thus is suitable for comparison.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -dependencies = [ - ('Python', '3.8.2'), - ('Perl', '5.30.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('Java', '11', '', SYSTEM), - ('Boost', '1.72.0'), -] - -exts_list = [ - ('simplejson', '3.17.0', { - 'checksums': ['2b4b2b738b3b99819a17feaf118265d0753d5536049ea570b3c43b51c4701e81'], - }), - (name, version, { - 'install_target': 'install_full', - 'modulename': 'quast_libs', - 'patches': ['QUAST-%(version)s_fix-Python-3.8.patch'], - 'source_tmpl': 'quast_%(version)s.tar.gz', - 'source_urls': ['https://github.com/ablab/quast/archive/'], - 'checksums': [ - '9f30c03e0bfd261492fe6b72fb07645bdee5b29d741f75fc75857b6fa095d91d', # quast_5.0.2.tar.gz - '8ae7ebf45e5368ebc058fc208822a23d32ce1052bd53fd8c3aaa4ad14d3c95aa', # QUAST-5.0.2_fix-Python-3.8.patch - ], - }), -] - -postinstallcmds = ["cd %(installdir)s/bin && ln -s quast.py quast"] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "wget quast.sf.net/test_data.tar.gz && " - "tar xzf test_data.tar.gz && " - "%(namelower)s.py --test && " - "rm ./test_data.tar.gz ./test_data -rf", - "%(namelower)s -h", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb deleted file mode 100644 index 444cbab7ef0..00000000000 --- a/easybuild/easyconfigs/__archive__/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,70 +0,0 @@ -easyblock = 'EB_Qt' - -name = 'Qt5' -version = '5.14.1' - -homepage = 'https://qt.io/' -description = "Qt is a comprehensive cross-platform C++ application framework." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) -toolchainopts = {'vectorize': False} - -source_urls = [ - 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', - 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', - 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', -] -sources = ['qt-everywhere-src-%(version)s.tar.xz'] -patches = [ - 'Qt5-5.13.1_fix-avx2.patch', - 'Qt5-5.13.1_fix-qmake-libdir.patch', - 'Qt5-5.14.1_fix-mantissatable.patch', - 'Qt5-5.14.1_fix-OF-Gentoo.patch', -] -checksums = [ - '6f17f488f512b39c2feb57d83a5e0a13dcef32999bea2e2a8f832f54a29badb8', # qt-everywhere-src-5.14.1.tar.xz - '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch - '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch - '11db32da45a003963e6abfd8ab7161d7e4ec3a8d668b54d18a3f6a713fd813a2', # Qt5-5.14.1_fix-mantissatable.patch - '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), - # deps for QtWebEngine - ('Bison', '3.5.3'), - ('flex', '2.6.4'), - ('gperf', '3.1'), - ('Ninja', '1.10.0'), - ('Python', '2.7.18'), - ('re2c', '1.3') -] - -dependencies = [ - ('double-conversion', '3.1.5'), - ('GLib', '2.64.1'), - ('PCRE2', '10.34'), - ('libpng', '1.6.37'), - # deps for QtWebEngine - ('X11', '20200222'), - ('fontconfig', '2.13.92'), - ('DBus', '1.13.12'), - ('libevent', '2.1.11'), - ('libGLU', '9.0.1'), - ('libjpeg-turbo', '2.0.4'), - ('NSS', '3.51'), - ('snappy', '1.1.8'), - ('JasPer', '2.0.14'), - ('bzip2', '1.0.8'), -] - -# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) -# qtwayland fails to build on (some) Centos 7 systems -configopts = '-skip qtgamepad -skip qtwayland' - -# make sure QtWebEngine component is being built & installed -check_qtwebengine = True - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/q/Qt5/Qt5-5.14.1_fix-mantissatable.patch b/easybuild/easyconfigs/__archive__/q/Qt5/Qt5-5.14.1_fix-mantissatable.patch deleted file mode 100644 index 6603177399f..00000000000 --- a/easybuild/easyconfigs/__archive__/q/Qt5/Qt5-5.14.1_fix-mantissatable.patch +++ /dev/null @@ -1,21 +0,0 @@ -# replaces F16C preprocessor conditional directives in gen_qfloat16_tables.cpp -# author: Jiri Furst, see also easybuild pr #10332 ---- qtbase/src/corelib/global/qfloat16tables.cpp.orig 2020-08-04 14:15:28.796162843 +0200 -+++ qtbase/src/corelib/global/qfloat16tables.cpp 2020-08-04 14:16:18.775679078 +0200 -@@ -44,7 +44,7 @@ - - QT_BEGIN_NAMESPACE - --#if !defined(__F16C__) && !defined(__ARM_FP16_FORMAT_IEEE) -+#if !defined(__ARM_FP16_FORMAT_IEEE) - - const quint32 qfloat16::mantissatable[2048] = { - 0, -@@ -3261,6 +3261,6 @@ - 0xDU, - }; - --#endif // !__F16C__ && !__ARM_FP16_FORMAT_IEEE -+#endif // !__ARM_FP16_FORMAT_IEEE - - QT_END_NAMESPACE diff --git a/easybuild/easyconfigs/__archive__/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb b/easybuild/easyconfigs/__archive__/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb deleted file mode 100644 index 69b8171bce0..00000000000 --- a/easybuild/easyconfigs/__archive__/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb +++ /dev/null @@ -1,43 +0,0 @@ -name = 'QuantumESPRESSO' -version = '6.6' - -homepage = 'https://www.quantum-espresso.org' -description = """Quantum ESPRESSO is an integrated suite of computer codes - for electronic-structure calculations and materials modeling at the nanoscale. - It is based on density-functional theory, plane waves, and pseudopotentials - (both norm-conserving and ultrasoft). -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True, 'openmp': True} - -source_urls = [ - 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', - 'https://github.com/dceresoli/qe-gipaw/archive/', - 'https://github.com/wannier-developers/wannier90/archive/' -] -sources = [ - 'qe-%(version)s-ReleasePack.tgz', - {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, -] -checksums = [ - 'de6996b9f1bf480bcd0166d24e918f5ff3c8fdb710f59f781bc9d33819280eb5', # qe-6.6-ReleasePack.tgz - '277fbe3bd10cb8f64e0f351a0c2fff1f68fb3ccdeb18107900803f4566661459', # qe-gipaw-6.6.tar.gz - '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz -] - -dependencies = [ - ('HDF5', '1.10.6'), - ('ELPA', '2019.11.001'), - ('libxc', '4.3.4'), -] - -# The third party packages should be installed separately and added as -# dependencies. The exception is w90, which is force built -buildopts = 'all gwl xspectra couple epw gipaw w90' - -# parallel build tends to fail -maxparallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb b/easybuild/easyconfigs/__archive__/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb deleted file mode 100644 index 5cfd92e0885..00000000000 --- a/easybuild/easyconfigs/__archive__/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb +++ /dev/null @@ -1,43 +0,0 @@ -name = 'QuantumESPRESSO' -version = '6.6' - -homepage = 'https://www.quantum-espresso.org' -description = """Quantum ESPRESSO is an integrated suite of computer codes - for electronic-structure calculations and materials modeling at the nanoscale. - It is based on density-functional theory, plane waves, and pseudopotentials - (both norm-conserving and ultrasoft). -""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True, 'openmp': True} - -source_urls = [ - 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', - 'https://github.com/dceresoli/qe-gipaw/archive/', - 'https://github.com/wannier-developers/wannier90/archive/' -] -sources = [ - 'qe-%(version)s-ReleasePack.tgz', - {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, -] -checksums = [ - 'de6996b9f1bf480bcd0166d24e918f5ff3c8fdb710f59f781bc9d33819280eb5', # qe-6.6-ReleasePack.tgz - '277fbe3bd10cb8f64e0f351a0c2fff1f68fb3ccdeb18107900803f4566661459', # qe-gipaw-6.6.tar.gz - '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz -] - -dependencies = [ - ('HDF5', '1.10.6'), - ('ELPA', '2019.11.001'), - ('libxc', '4.3.4'), -] - -# The third party packages should be installed separately and added as -# dependencies. The exception is w90, which is force built -buildopts = 'all gwl xspectra couple epw gipaw w90' - -# parallel build tends to fail -maxparallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/q/QuickFF/QuickFF-2.2.4-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/q/QuickFF/QuickFF-2.2.4-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 5715db0da62..00000000000 --- a/easybuild/easyconfigs/__archive__/q/QuickFF/QuickFF-2.2.4-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'QuickFF' -version = '2.2.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://molmod.github.io/QuickFF/' -description = """QuickFF is a Python package developed at the Center for -Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio -calculations.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/molmod/QuickFF/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['9c916eab890eec865985bc3e11249b0b5fee28a049206b9755081adeaf13ff60'] - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('molmod', '1.4.5', versionsuffix), - ('yaff', '1.6.0', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/q/QuickFF/QuickFF-2.2.7-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/q/QuickFF/QuickFF-2.2.7-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 685f5c48431..00000000000 --- a/easybuild/easyconfigs/__archive__/q/QuickFF/QuickFF-2.2.7-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'QuickFF' -version = '2.2.7' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://molmod.github.io/QuickFF/' -description = """QuickFF is a Python package developed at the Center for -Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio -calculations.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/molmod/QuickFF/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['a71922dd39869770b03809355f13bcabdbb8d50429f4d3574cf427ea762f4023'] - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('molmod', '1.4.5', versionsuffix), - ('yaff', '1.6.0', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/q/Qwt/Qwt-6.1.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/q/Qwt/Qwt-6.1.5-GCCcore-9.3.0.eb deleted file mode 100644 index becf844cebd..00000000000 --- a/easybuild/easyconfigs/__archive__/q/Qwt/Qwt-6.1.5-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Qwt' -version = '6.1.5' - -homepage = 'https://qwt.sourceforge.io/' -description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs - with a technical background.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_BZ2] -patches = ['Qwt-6.1.4_Fix_prefix_and_pkgconfig.patch'] -checksums = [ - '4076de63ec2b5e84379ddfebf27c7b29b8dc9074f3db7e2ca61d11a1d8adc041', # qwt-6.1.5.tar.bz2 - '82788aaa23e4bc764ab1f2769e9260d154976c7d7f043ba4e288330d6984b6a9', # Qwt-6.1.4_Fix_prefix_and_pkgconfig.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Qt5', '5.14.1'), -] - -skipsteps = ['configure'] - -prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' -prebuildopts += "qmake qwt.pro && " - -sanity_check_paths = { - 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], - 'dirs': ['doc', 'features', 'include', 'plugins'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/q/qcat/qcat-1.1.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/q/qcat/qcat-1.1.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 13cd887c88f..00000000000 --- a/easybuild/easyconfigs/__archive__/q/qcat/qcat-1.1.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonPackage' - -name = 'qcat' -version = '1.1.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/nanoporetech/qcat/releases' -description = "qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files" - -toolchain = {'name': 'intel', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] - -dependencies = [ - ('Python', '3.8.2'), - ('Biopython', '1.78', versionsuffix), - ('python-parasail', '1.2.2', versionsuffix), - ('PyYAML', '5.3'), -] - -sanity_check_paths = { - 'files': ['bin/qcat'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["qcat --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 7d09c8f8a79..00000000000 --- a/easybuild/easyconfigs/__archive__/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,883 +0,0 @@ -easyblock = 'Bundle' - -name = 'R-bundle-Bioconductor' -version = '3.11' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://bioconductor.org' -description = """Bioconductor provides tools for the analysis and coprehension - of high-throughput genomic data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -builddependencies = [('pkg-config', '0.29.2')] - -dependencies = [ - ('R', '4.0.0'), - ('Boost', '1.72.0'), # for mzR - ('GSL', '2.6'), # for flowClust - ('HDF5', '1.10.6'), # for rhdf5 - ('MariaDB-connector-c', '3.1.7'), # for RMySQL - ('ncdf4', '1.17', versionsuffix), # for mzR -] - -exts_default_options = { - 'source_urls': [ - 'https://bioconductor.org/packages/3.11/bioc/src/contrib/', - 'https://bioconductor.org/packages/3.11/bioc/src/contrib/Archive/%(name)s', - 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/', - 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz' -} - -exts_defaultclass = 'RPackage' - -# check whether correct version is installed in extension filter -# (some versions in this bundle may be newer than the ones provided by R) -local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " -local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" -exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) - -# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends -# !! order of packages is important !! -# packages updated on July 8th 2020 -exts_list = [ - ('readr', '1.3.1', { - 'checksums': ['33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3'], - }), - ('BiocGenerics', '0.34.0', { - 'checksums': ['534f5640fe0f1c165f164ebb26e312c4140e336145af3c839dbff427a0c7db96'], - }), - ('Biobase', '2.48.0', { - 'checksums': ['17dbdfd9f06a7dcca5daeb067a7acf46391f155c3321e119b20b9edaed9be38e'], - }), - ('S4Vectors', '0.26.0', { - 'checksums': ['757aaf89c177a228a0c418c1f141fffc587e115a8e6d4259bada7341a7c9131e'], - }), - ('IRanges', '2.22.1', { - 'checksums': ['72b531e0c69c584525e3812be40e7c3dcc84a30461a42be5832c859b7b49d9e5'], - }), - ('GenomeInfoDbData', '1.2.3', { - 'checksums': ['945d79fc542ce7914fc89ad95bd0ead827597cfa50f2f758cfef42a09fc78aeb'], - }), - ('GenomeInfoDb', '1.24.0', { - 'checksums': ['3be2fabf1946a16bd4d4d818c34e58c0af0b6f8c108b50ee831b6e7ab0156929'], - }), - ('AnnotationDbi', '1.50.0', { - 'checksums': ['05dca3e4bb1c3a6e3584707f58692138d518a189607f958465f0624055a7f781'], - }), - ('zlibbioc', '1.34.0', { - 'checksums': ['8026a46a06bf951481fe2281261c714f6996989dfc77176d609c892545013448'], - }), - ('XVector', '0.28.0', { - 'checksums': ['6cdf01943177f9aeba808b028ad3261d2bba91fb26a3be5ec0281db2bf860186'], - }), - ('Biostrings', '2.56.0', { - 'checksums': ['286e06883c4c230b696e89b06fba78ba418db15559def871a163a1d7ce77b046'], - }), - ('GenomicRanges', '1.40.0', { - 'checksums': ['a18bb9cddf7a147b8c8b53f0f024a3ed77637f7c54452e7eda37038c45fec172'], - }), - ('BiocParallel', '1.22.0', { - 'checksums': ['4fa0a5f777de5c9cda96cfe2e93cd34f2686df84bf4507cc2c9e0e596a2f4fd3'], - }), - ('Rhtslib', '1.20.0', { - 'checksums': ['b13d3f20f483dedc778d1a386ce1d1fe394ddbb9710c4b588836ff99593cd9a0'], - }), - ('Rsamtools', '2.4.0', { - 'checksums': ['78039e3781865d79af36bd4bd3926148e8bb94b78668abcf0c24b97034f8017c'], - }), - ('DelayedArray', '0.14.0', { - 'checksums': ['1307d776d52d837b77b9bd490bb4a3e7a7c12f9a751c6009e1633b9a3350e7d3'], - }), - ('SummarizedExperiment', '1.18.1', { - 'checksums': ['4cb0e16e9ac4506e3141ce8fe0a67b2c29555272b1ebdd88b30ddc56663a2c1f'], - }), - ('GenomicAlignments', '1.24.0', { - 'checksums': ['0dcded5d0ca3d79a3fa1f0836e23f94b25ced099f193591922b7d4ec4e33136d'], - }), - ('ShortRead', '1.46.0', { - 'checksums': ['6d804cc5dc780935c83580584a1f93ae80d76f9562c70e2c85def8642c6d9350'], - }), - ('graph', '1.66.0', { - 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}), - ('baySeq', '2.22.0', { - 'checksums': ['b27ae6bfd772caac98870a8c581119c5adce3ce0cbe95eab2d41a78d2f190df4'], - }), - ('qvalue', '2.20.0', { - 'checksums': ['6e7cb24a36939ca334b0abcd236a4c4f7eb99d836b039f495e4f459b72abcdc2'], - }), - ('impute', '1.62.0', { - 'checksums': ['10541b1c2476ab5a78e1f4d2961710db1b98a1076ff33ead6f9c8fcb02353798'], - }), - ('shinyFiles', '0.8.0', { - 'checksums': ['1ca1455c99f6559fa8a790d5f16a79485ea76ed2dc4eaf1b650665e1cee89e3f'], - }), - ('samr', '3.0', { - 'checksums': ['25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506'], - }), - ('DEGseq', '1.42.0', { - 'checksums': ['71a9ab6ce59dad67e71dd6098611c71a429acf1671cbff7806bb25311730aafc'], - }), - ('hgu133plus2.db', '3.2.3', { - 'checksums': ['a56b247b69a6b8c81d23410e9def44f8d3e7c133aedf09fb1561798dca2c0549'], - }), - ('illuminaio', '0.30.0', { - 'checksums': ['ec180c39921f8707c09e2226a2feaef80576f581fb872a012f42a9b2433ea844'], - }), - ('rtracklayer', '1.48.0', { - 'checksums': ['ae974dbc4caa4ea0ecc3a340071d63160a38a725ba26cd8f271eb6a8459a8ffd'], - }), - ('rappdirs', '0.3.1', { - 'checksums': ['2fd891ec16d28862f65bb57e4a78f77a597930abb59380e757afd8b6c6d3264a'], - }), - ('BiocFileCache', '1.12.0', { - 'checksums': ['68f7cc8d56a44c5e001783d37c2bedbebf057f8cd95fd7f2895f55c6f8cf9009'], - }), - ('biomaRt', '2.44.0', { - 'checksums': ['929f12814a1eb3f4cf38dd73b474a5f1acc343b718f54fbeabe90e241236e229'], - }), - ('GenomicFeatures', '1.40.0', { - 'checksums': ['c88d8518d4a7fa9cfca091d4db5f8b68efd9f0f04880ba6392107a31a9d3ce25'], - }), - ('bumphunter', '1.30.0', { - 'checksums': ['b891ccfd4cba0b1c2e95ff2e3a01e35355b7f46838da2eb05e4326d4dbd5c613'], - }), - ('multtest', '2.44.0', { - 'checksums': ['a243d6b5d1355bca432a133444668f5c5d9c6349401cd29dd4a33effbf3d918a'], - }), - ('scrime', '1.3.5', { - 'checksums': ['5d97d3e57d8eb30709340fe572746029fd139456d7a955421c4e3aa75d825578'], - }), - ('siggenes', '1.62.0', { - 'checksums': ['de55703763b6bffc4367c8fcb20b464a04723d62665daf8d9b5dd2801f0c9e44'], - }), - ('DynDoc', '1.66.0', { - 'checksums': ['c0fa5300ce811048aa945cacef350ca113e2bd6808784e62082f8a7de5444f8a'], - }), - ('genoset', '1.44.0', { - 'checksums': ['4615a034d2e89bc96a83dd52f0f95a849443e9b854368ca54b66b1ce7f5fd80b'], - }), - ('NOISeq', '2.31.0', { - 'checksums': ['6348b80f1a488f129fcd3ac1efdba8c6a7aeade97dbdd89ba1699b3a81fae351'], - }), - ('Rgraphviz', '2.32.0', { - 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], - 'checksums': [ - 'be7c2ef0d9cbe2d1ca3da89f2b7f49eae981e42cc32dd3893edb7cf6febe54b1', # Rgraphviz_2.32.0.tar.gz - # Rgraphviz-2.28.0_fno-tree-vectorize.patch - '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9', - ], - }), - ('RNASeqPower', '1.28.0', { - 'checksums': ['99fdfd8001330ad632ced4f987f1b7a26ef117b3c7795ae7d78b3172c3383992'], - }), - ('annotate', '1.66.0', { - 'checksums': ['9cd45c2ad1ccd08b0046ead33ffe379abded44901ffd8254b106fb6c27fe7ac7'], - }), - ('GSEABase', '1.50.0', { - 'checksums': ['be25a006e1338507b72b04cc45b28c7fd7a2dda3a817b39fd0ccf12d0220cfeb'], - }), - ('genefilter', '1.70.0', { - 'checksums': ['0f15d10ff66f1b99ffecc7476f87e15a4d23f81758991941cc0ea46bb0cd6be9'], - 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}), - ('affycoretools', '1.60.0', { - 'checksums': ['d7abdd583500b456903ba328ccda9a0e27039498eb6876633fa284e0f41bc237'], - }), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', { - 'checksums': ['063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9'], - }), - ('Homo.sapiens', '1.3.1', { - 'checksums': ['014809fc6ef6410be8dc1094c9cb083719f20d999065ae4bf388855be0913b94'], - }), - ('BSgenome.Hsapiens.UCSC.hg19', '1.4.3', { - 'checksums': ['5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a'], - }), - ('AgiMicroRna', '2.38.0', { - 'checksums': ['d949f956deb889df596e28154d5f9200cc8d96ce97397fdb5ff3f5ec01c5ac6d'], - }), - ('geneLenDataBase', '1.24.0', { - 'checksums': ['138408602210ca3c60b247842c0ff0c99e077cb71e07b3e1802b73cc4d2fa8a5'], - }), - ('goseq', '1.40.0', { - 'checksums': ['d5d32fddd1a095ea264ccdd652e7e8988d06c624b94b6e2eb2fa43963389d9c7'], - }), - ('KEGGREST', '1.28.0', { - 'checksums': ['419a4adb0a9ec14d88aa23c0f81aa5ee0088679913fa5dcf075d28ef4ee0e660'], - }), - ('KEGGgraph', '1.48.0', { - 'checksums': ['692fecf9d512793b9acc1b3875ac8cc8a759f19fd9f9c10638ca8ee9b862f881'], - }), - ('KEGGprofile', '1.30.0', { - 'checksums': ['1e7cdadea99afa73ad0dd5cebad8ffd8c83683665ff34323c6ce6b1559aaff04'], - }), - ('GEOquery', '2.56.0', { - 'checksums': ['5524ad356694c3c1c31b16bf83a2c2a82ee87b8d6cf8f2cbbe78cca1740b5769'], - }), - ('RSpectra', '0.16-0', { - 'checksums': ['aaf1cfc9ffe3a4c6684247899924e1c18306971dfef4bae1dc596a2fb42a64a9'], - }), - ('rARPACK', '0.11-0', { - 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], - }), - ('mixOmics', '6.12.0', { - 'checksums': ['85fb511b30a5f160eff89cfee9fa07b92c0c9ed03db61bb5fc75f93d3186ca10'], - }), - ('Rhdf5lib', '1.10.0', { - 'checksums': ['9c28870104b3b22ccd1b27295ea9c7144f7f99bffbf41a62cd4d2365a6e7d427'], - }), - ('rhdf5', '2.32.0', { - 'checksums': ['9e4d2d8e066b502fc0005a1f652beedcc675aa30ba63af95695bf89228b7ff24'], - }), - ('HDF5Array', '1.16.0', { - 'checksums': ['842b12d2c04f682939caf601efa698eff530d1bc450b7fda8d241a86814604bd'], - 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}), - ('venn', '1.9', { - 'checksums': ['19c96cd7daad83267c666106ceea742dbc1eed917922ce61b2088b9198e45b34'], - }), - ('maSigPro', '1.60.0', { - 'checksums': ['9c24f59fe9d04e7854d5656bd637ea787abb266325f0bc1025f76d8e31595afa'], - }), - ('SPIA', '2.40.0', { - 'checksums': ['55df5ea662127c89994a44dfa56e095deed9cf5e6e408493ef833cf30a1bb34c'], - }), - ('Gviz', '1.32.0', { - 'checksums': ['0a814fff55b1513ea4b65240c9d4d69bacd46bb97f0ff8f0f458781f19b8f331'], - }), - ('cummeRbund', '2.30.0', { - 'checksums': ['4cf6cd3f653032e6cd2e8fe1847979d3b8597e54ec7c861d5e9c07ccbaf367ab'], - }), - ('GenomicFiles', '1.24.0', { - 'checksums': ['c412b082e788a9201487e2b0cc6cbd4bd5810539e233b3d9c6cd25f72f1168cc'], - }), - ('derfinderHelper', '1.22.0', { - 'checksums': ['b3aae9cca8208efbf1b897623f934730fbaa9845c3a8fbded26c7cc0d96342b1'], - }), - ('derfinder', '1.22.0', { - 'checksums': ['3eb0ebaa22c6fa09627e2b81ad0dfe146716a1e18226c20af0aafe07b240a9bc'], - }), - ('polyester', '1.24.0', { - 'checksums': ['a1d90df0fd84b0615b86c23472e7110778923d2ad94ecac58fbafd9699ff2fd1'], - }), - ('Rsubread', '2.2.1', { - 'checksums': ['cb611902cc51b68b96b6c046546fa90b2ddf872866ae9c0c7ac808d6f71c0a1d'], - }), - ('pcaMethods', '1.80.0', { - 'checksums': ['d1bed9d51bc660d0e8f33abe862004320ca6b8250075bd56e7d37adf25e19c81'], - }), - ('marray', '1.66.0', { - 'checksums': ['6d9a67bd20587f08d8d57163e43f437fd71440ee03d9285601efe3a2a31dd5eb'], - }), - ('CGHbase', '1.48.0', { - 'checksums': ['6ed26f4b6bc0185740d1471a0d7eef3cbf6631427e5218476911169d93c2d83d'], - }), - ('sigaR', '1.35.0', { - 'checksums': ['ee437c98a498f15ce2b8181a24893af3f3202fc480a4aa28d4b5e6755a939515'], - }), - ('Wrench', '1.6.0', { - 'checksums': ['a67382302dfb76de97669195703e09993bc75353e8c5b16ddc3fe3b5fd98be15'], - }), - ('lpsymphony', '1.16.0', { - 'checksums': ['c43a0e1324c029296c49705c81a48dadac1d6e2337b6233344c11e235a9d511c'], - }), - ('IHW', '1.16.0', { - 'checksums': ['929c9a8ccd51cb139f9f19f8ff3dcd2d43db5b6e40f1e57980edf91726c83199'], - }), - ('metagenomeSeq', '1.30.0', { - 'checksums': ['fd5785d8891db9ecf310b2d72cb831bdc16ab3f2ce7b0b96f8cbd7009c238d44'], - }), - ('gdsfmt', '1.24.0', { - 'checksums': ['e6a69a92853aff56cfbd9b39dfd9c44b8e54c41620cb14fb00bc8408547d0f02'], - }), - ('SNPRelate', '1.22.0', { - 'checksums': ['235b5e3b7742f20fb5ce4a541ad592810b51448978f54d446cedfe6ece2f1e92'], - }), - ('biomformat', '1.16.0', { - 'checksums': ['687898a1a3779f6386c87985bff25f7f2536b52dbe264847273d56199a3522d0'], - }), - ('phyloseq', '1.32.0', { - 'checksums': ['eeed32aea371efd4f5ba8b47f593b2d8cebf24b73e000b96882fb6c50d85fb48'], - }), - ('NADA', '1.6-1.1', { - 'checksums': ['670ff6595ba074ed0a930b7a09624d5ef20616379a20e768c1a7b37332aee44a'], - }), - ('truncnorm', '1.0-8', { - 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], - }), - ('zCompositions', '1.3.4', { - 'checksums': ['ae22c86fe92368a26265933f42eecc518b9b69e7d9b698bc31bfaabfc3c48e95'], - }), - ('ALDEx2', '1.20.0', { - 'checksums': ['f0c20c02b855293fb28ca1114b9ae4d93a083f95702ce333e48645f6da43dab2'], - }), - ('RcppParallel', '5.0.1', { - 'checksums': ['6d3a4ef1ae93ac057d8f4f9378f9ed078616310fb0f3af5aabf8bd1eadf43e09'], - }), - ('dada2', '1.16.0', { - 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], - 'checksums': [ - '20f1215fc67cf00d5019993fb3d6397c1ef418736996e15eecf36cec3cfecdc5', # dada2_1.16.0.tar.gz - # dada2-1.16.0-remove-sse-on-aarch64.patch - 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', - ], - }), - ('LEA', '3.0.0', { - 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], - 'checksums': [ - '802821ac1dbe27c6cfc4523fe6ec37155be3df21fb47e4d8f83a79df26d8dffa', # LEA_3.0.0.tar.gz - # LEA-3.0.0_support_aarch64_and_ppc64le.patch - 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', - ], - }), - ('tximport', '1.16.0', { - 'checksums': ['b5f35cea2b9746ba92bc66f23c9566c2e565681e6527071e66d401072b5a2446'], - }), - ('SingleCellExperiment', '1.10.1', { - 'checksums': ['d77d019c1c1fb6455587f4eaf0edd26392d8dea81d72bac910ea1e1bc2dc5c24'], - }), - ('beachmat', '2.4.0', { - 'checksums': ['b1c37ff8bf490dc30c00b1bc0dbf218b6c49c0df68b5194965e8a898dc9286ee'], - }), - ('RcppAnnoy', '0.0.16', { - 'checksums': ['d98d5f239039a0f82c19b44abf37c26388bc40e96d573f2058846d736919ca2d'], - }), - ('RcppHNSW', '0.2.0', { - 'checksums': ['1b8fd5368b27209079822f4deed67fde0cf4e885e015f23321a5b2b90f9f0d3f'], - }), - ('BiocNeighbors', '1.6.0', { - 'checksums': ['be634e66d00e3a12f74e3c4b7e0ca5428cf7cd09612de379a95da0d879f69e91'], - }), - ('rsvd', '1.0.3', { - 'checksums': ['13560e0fc3ae6927c4cc4d5ad816b1f640a2a445b712a5a612ab17ea0ce179bb'], - }), - ('BiocSingular', '1.4.0', { - 'checksums': ['301651a659c3bade336e4183a368b72f61432c1501c2da27667133227b52c80c'], - }), - ('scater', '1.16.0', { - 'checksums': ['7b280bf9b8633fadab31d06a7c7c794c30df0eb0f6162e360fa8cfb5d813ffa4'], - }), - ('sitmo', '2.0.1', { - 'checksums': ['0c90d357af334d5c99c8956739dc12623ddd87dda5efa59f4a43f7393c87ed2a'], - }), - ('dqrng', '0.2.1', { - 'checksums': ['e149c105b1db31e7f46b1aebf31d911a109e380923f3696fc56a53197fc1e866'], - }), - ('scran', '1.16.0', { - 'checksums': ['5befdd893492babcfa9b88eff86329ce4b4ed0983d875988bd0122ac88f6a4be'], - }), - ('SC3', '1.16.0', { - 'checksums': ['29918e7a78858ef6602c0f461bf33e32af5d384448029ba1368be41118c2a797'], - }), - ('ComplexHeatmap', '2.4.2', { - 'checksums': ['14e4f92155aaf8d5c92aeab47b890641942b52599928f9ba5ac826073bef5d06'], - }), - ('GENIE3', '1.10.0', { - 'checksums': ['47e336ae8442f6da38ca5bd954d75bd7c137f5867c706579785e3395fb0355af'], - }), - ('dupRadar', '1.18.0', { - 'checksums': ['aad44271649c5f81457b790435e14f5c9595022fd8ac5fff488d099fbad761a1'], - }), - ('DNAcopy', '1.62.0', { - 'checksums': ['eac3dd8f4896c54798c43a6871854a49ee94fa99f5b07160d1eee73650a6e849'], - }), - ('sva', '3.36.0', { - 'checksums': ['24caa3a13cef2933a3c98d055af4ca0859fa08ec66a90ad28bd6a83041a54175'], - }), - ('ballgown', '2.20.0', { - 'checksums': ['0d8a9f5b08c4f8a53215d5c2573c3b83ee99bb6cf1beffb83b6eeaf17a4cfe46'], - }), - ('DropletUtils', '1.8.0', { - 'checksums': ['c2a733226c9f848d018f6163183c03faaa9e4dbbfc1e52eb1d5c679714e81c7f'], - }), - ('DeconRNASeq', '1.30.0', { - 'checksums': ['5f1b20fe266bc1a7528af053845b1ec41da9377b3d8e34d992db4e5b7ab8a36a'], - }), - ('GSVA', '1.36.0', { - 'checksums': ['8df5efe40511b3633488d0e5e310f181d141bb31a85fb38a2767fffb174ae08e'], - }), - ('PureCN', '1.18.0', { - 'checksums': ['9ff934b69a707b0899bc299b14e2a165246a10fe58ad0d1e66b09a63ffefd2d5'], - }), - ('globaltest', '5.42.0', { - 'checksums': ['201484a6209410384deb00aa587594a6038031e8aed5efc59ee5d78622bfb359'], - }), - ('GlobalAncova', '4.6.0', { - 'checksums': ['b19f6946b006524e8652b9525658bd32ccb98a72034940a6207bb1be3f86237d'], - }), - ('SSPA', '2.28.0', { - 'checksums': ['7a09f978d2f075462bd69b48bf804c1b183851494c23a54d712f2a353e45a9d5'], - }), - ('vsn', '3.56.0', { - 'checksums': ['a84094c6603d2e205eb3965029bed87d867f1e0f23045f98f5ec859d676c02cd'], - }), - ('MALDIquant', '1.19.3', { - 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], - }), - ('mzID', '1.26.0', { - 'checksums': ['c5962909033d5fb9d13b34ca5ad5ba5d6343c485bc64e38ef97756d5e6a7a078'], - }), - ('mzR', '2.22.0', { - 'patches': ['mzR-2.22.0_use-external-boost.patch'], - 'checksums': [ - '9509d6d831584af8866aa3d1dd1b22f4333e85fafa0c48e4b18ad1f2a34712e5', # mzR_2.22.0.tar.gz - '8b5ba4f0c4efbbab9b4801d7da3fb04a490a5d95af1cefb489f209afa4d14fb4', # mzR-2.22.0_use-external-boost.patch - ], - }), - ('MSnbase', '2.14.0', { - 'checksums': ['f35b9d023047dfd5ae32bf43fa166e7e3d245c4d5708fac08f84270713f3d7d2'], - }), - ('MassSpecWavelet', '1.54.0', { - 'checksums': ['d80efa84988d0db0c8854bf94d274f21824e2c698c29ac8dbe39b8f390c9615b'], - }), - ('xcms', '3.10.0', { - 'checksums': ['c23e3d50f9836f206ffe69eb0ee1a310d4fc94c105e183437e7afe57734fd58c'], - }), - ('CAMERA', '1.44.0', { - 'checksums': ['be27c1df60d9a9c1c373b39286ca23867b550642d478fab83f8cc7924e63ff00'], - }), - ('fgsea', '1.14.0', { - 'checksums': ['6cf995d603e07616f56b77618e77afb7ae4dd12b56f7d86b8d47df401592727d'], - }), - ('GWASExactHW', '1.01', { - 'checksums': ['e850ed40fbf14b02eb3798603cfb111fe3718bb69d74c0ff4cb6f679209a15a7'], - }), - ('quantsmooth', '1.54.0', { - 'checksums': ['8526ab1273d61be79aa2617330f709c5ebf766a610c73408266ef66035a1a63f'], - }), - ('GWASTools', '1.34.0', { - 'checksums': ['972bd093aed22910d7a7e2771395bb8d68418fb6c5fd4b04008f055af6735da2'], - }), - ('SeqArray', '1.28.0', { - 'checksums': ['f62193159377dc9f3ec75026359a9da819452ac441561a696a544bc9f2650cf5'], - }), - ('SeqVarTools', '1.26.0', { - 'checksums': ['bf7e1502ca8b9695f391c19f150bcda59991d74087891af9eff06c4543e30ac5'], - }), - ('GENESIS', '2.18.0', { - 'checksums': ['aa7fd97214a385ea76e7b5741e16052a95047d2308c8dfaccf293ad30ffaea4b'], - }), - ('MLInterfaces', '1.68.0', { - 'checksums': ['d87a5efc69f9527cd38c6a56f811f0359d2d40af8e035e3089791a55d6b67574'], - }), - ('pRoloc', '1.28.0', { - 'checksums': ['64cf300eb4f869986756e2fd6c3adb9e28e8ceb5c10b9745b4bbf3d15989523c'], - }), - ('pRolocdata', '1.26.0', { - 'checksums': ['ff68cdd66f24521a7260c1483dee243b22c3baa6f685de7f8b1213b9442c879b'], - }), - ('pRolocGUI', '1.22.0', { - 'checksums': ['0a88a6f3eef7512fe52ecd8ce0c759d8be73422f2f7257d381847334a7fb42b0'], - }), - ('EBImage', '4.30.0', { - 'checksums': ['3bf1734a17a6f650654292d34f811715a8cbcff6bfd9e7f5991c1652e0ca558d'], - }), - ('GenomicScores', '2.0.0', { - 'checksums': ['6b9994e58dea839bd912a92f766487ba76e496c001839438816ad633d8a3226a'], - }), - ('BSgenome.Mmusculus.UCSC.mm10', '1.4.0', { - 'checksums': ['6e2eb3bce208cc7766f0e0ef1e14465289d5463b34d94c9a9279256545b5408b'], - }), - ('TxDb.Mmusculus.UCSC.mm10.knownGene', '3.10.0', { - 'checksums': ['696281749d01737c94894564d62093433045bc007a4528cc3d94f205edb54977'], - }), - ('regioneR', '1.20.0', { - 'checksums': ['30ea4e83bf0db8f564bd0347e2490cfe47d9c5314a1609a9cbf458b0fb0b2282'], - }), - ('RcppZiggurat', '0.1.5', { - 'checksums': ['db6d5fd3a77ac9473bf21f84b65da3c6e485f9ed33f5313bbf0ec852b71db97e'], - }), - ('Rfast', '1.9.9', { - 'checksums': ['c0932398a4783a33586d5cc47b79592cd2b8220cb76d7530e4cf4f221eeca8a2'], - }), - ('ChIPpeakAnno', '3.22.0', { - 'checksums': ['980389b98b05b5b88337e41fafb23207a33fc8fafc5be14bccf8852d398f391b'], - }), - ('seqLogo', '1.54.1', { - 'checksums': ['61cc237ad648c86be451450d2128120dcec969b4b1e574e0730d233307ab1c57'], - }), - ('rGADEM', '2.36.0', { - 'checksums': ['e86b6271cb57f63db101c3bb21321061dddab96c9ab65fc01a2e4908f9a2ae92'], - }), - ('MotIV', '1.43.0', { - 'checksums': ['06d2884741f79b29b1fa1a53dcc57842a41476a41e203ea0d997729b59f518fb'], - }), - ('MotifDb', '1.30.0', { - 'checksums': ['752ea5904f4e37594a555c24a4d0a43f6bbd568e5cd882b24abb030d2e6eb547'], - }), - ('motifStack', '1.32.0', { - 'checksums': ['45d3d1bd4527729c2dc1f93d0947ba54f8be39be8dea4c23413f7acf64150e01'], - }), - ('ATACseqQC', '1.12.0', { - 'checksums': ['e75a11b1559af0e0c153396652aa6b69740b6cfa0052a7a1f73a02a5b940d294'], - }), - ('batchelor', '1.4.0', { - 'checksums': ['913eb386120cb8fb6ca500a91b59918d5c8ba76ef403f749c69d668687558885'], - }), - ('gsmoothr', '0.1.7', { - 'checksums': ['b75ffd2a4a0f357762e02e46e355b45cc90ea637830f0a1b01f216bb4541e903'], - }), - ('Ringo', '1.52.0', { - 'checksums': ['c9bf40f67a0c23e18d48b968ca285bc844ca5108f6e8f963bf9b41e5f638ed83'], - }), - ('R.devices', '2.16.1', { - 'checksums': ['adedb928e6e6d1951d512f13688aa8ad4558a8fbc5b3e58cc0901ff106b6f497'], - }), - ('R.filesets', '2.13.0', { - 'checksums': ['cf1597227bc2cc4b3f4a2bdf087e1ed33330a8450655d6a72236d105f0f39988'], - }), - ('aroma.light', '3.18.0', { - 'checksums': ['ccb305b421b10425b9a59c213a9fef6a5e3e71d883c0f6c7b957741bab70c5a7'], - }), - ('PSCBS', '0.65.0', { - 'checksums': ['3365065d5375c599eb024bfff12c5f6b10a6b1a4fe4ba6f200f7e83618dd399a'], - }), - ('aroma.core', '3.2.1', { - 'checksums': ['2f815d4a0b2e0fec89006e6a07e1322cd6df529f725b22fd7f4b49380f4488d9'], - }), - ('R.huge', '0.9.0', { - 'checksums': ['f12d113a965603cfdbbb46e1a57331d267916235555b22f2bbc06caa302ae58e'], - }), - ('aroma.apd', '0.6.0', { - 'checksums': ['87513774baeed8e1d43f819e615c85278aef748ebc842f1ee50686c3392e37d1'], - }), - ('R.utils', '2.9.2', { - 'checksums': ['ac6b3b8e814fbb855c38fbdb89a4f0cf0ed65ce7fa308445bd74107fbc0d32cf'], - }), - ('aroma.affymetrix', '3.2.0', { - 'checksums': ['d279cf13cf6ed8369cfdf6682ace12924379bad578003453449aa1ccec31b0a7'], - }), - ('Rsolnp', '1.16', { - 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], - }), - ('Repitools', '1.34.0', { - 'checksums': ['4580abf755bef3e16c60a04debace613ee8cffafc6d3001d14743b6b4465d586'], - }), - ('BSgenome.Hsapiens.UCSC.hg38', '1.4.3', { - 'checksums': ['c29911ca93935e3b9aa6a67e894337dc2ad707405da1500c9898bd0578519ecc'], - }), - ('MEDIPS', '1.40.0', { - 'checksums': ['08edf0812c4c419bcf51c586773dd6d5495e09b6d03a6e10539ded6ad5f2c293'], - }), - ('RProtoBufLib', '2.0.0', { - 'checksums': ['fa6e04f9196fa0df55f4a886d8f00ef99d525a140371553b2e31b0bf93b3d14d'], - }), - ('cytolib', '2.0.0', { - 'checksums': ['5b5ff0a82cc09c255ad5c3a2a0c9ad81c12e2106412292c499b9207c7c2d482d'], - }), - ('flowCore', '2.0.0', { - 'checksums': ['832b9bdbc89549c6084814150a5fa197869aff1e8c9f9573811394172ad588bb'], - }), - ('mutoss', '0.1-12', { - 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], - }), - ('metap', '1.3', { - 'checksums': ['7fcf148bfd77f445b2ee68cbd2367caaf991028d9843020c755dd11965adb5ca'], - }), - ('uwot', '0.1.8', { - 'checksums': ['ede6e061b43f9e1337c0132a5334082f4565ec1623bbb0eee1f738034346f0cb'], - }), - ('Seurat', '3.1.5', { - 'checksums': ['757ef0e7697734aac5769705bef80dc7b95f006cdf52ae7034309a05f11578d1'], - }), - ('ALL', '1.30.0', { - 'checksums': ['1fa870db73c1c113c1613518d0829f74ea90390030f8f3d92a87e8689ec820bf'], - }), - ('ConsensusClusterPlus', '1.52.0', { - 'checksums': ['98fddf86255dc641beb3ccd8fd9b1c8ace430146ea87be3e0c750258921af819'], - }), - ('flowViz', '1.52.0', { - 'checksums': ['d883feadc65cae7d3bc44d59b366a249b05b5f99749d71e8cb3c61551b777238'], - }), - ('ncdfFlow', '2.34.0', { - 'checksums': ['2ec9c135940c8d0f300ac353504705a9edf7b93cbf6766e70bd311b894b07d2b'], - }), - ('flowWorkspace', '4.0.0', { - 'checksums': ['a06ca759ba998ad2287183eca8f6cba99889e32a44caf4a39a9680c56b7c110e'], - }), - ('fda', '5.1.4', { - 'checksums': ['5ddc723dba4019f72c11bab556f5306bdacfa017e7f36bcdc49a4735e87b444b'], - }), - ('flowStats', '4.0.0', { - 'checksums': ['39b69ff7248f3832ad018f206e02642ef0cd1bf37040e00f48571a7fdaeefbf9'], - }), - ('flowClust', '3.26.0', { - 'installopts': "--configure-args='--with-gsl=${EBROOTGSL} --enable-bundled-gsl=false'", - 'checksums': ['abe01b47e7692f335b5f0418cef6dd0dbf99df871bda49fa015dc9407cc2b31a'], - }), - ('openCyto', '2.0.0', { - 'checksums': ['3521a9d76414f35060a0fb39a0e688695db41ad6cbf10b37387bead69a69be81'], - }), - ('isoband', '0.2.1', { - 'checksums': ['18883606bea8352e04a4618bea4e5c9833269e73a46b50bc006dddf4c8b6b4d9'], - }), - ('ggcyto', '1.16.0', { - 'checksums': ['e012f204a01c6b3427a5b29050e37c8034f44a9a5a30ba50b75dcae3d57b06c6'], - }), - ('CytoML', '2.0.0', { - 'checksums': ['38804bfff42ef82db35022eb16cd01e34a8ce8d5840b3983a6b4c4e48914f87e'], - }), - ('FlowSOM', '1.20.0', { - 'checksums': ['e84069bef95e4b748e64171fac38ea99dfbfd982c9cb2b0f616cb580c99627dc'], - }), - ('HMMcopy', '1.30.0', { - 'checksums': ['94513a4a3398e8526cdd3d77a5525380d3dcdcab6c996b0d68a88d262d9fffdc'], - }), - ('diffcyt', '1.8.0', { - 'checksums': ['4bef82e672959efa88b124d5c6d73b02e06f1af8f9cfc52c29a269824daac8e7'], - }), - ('blme', '1.0-4', { - 'checksums': ['c2bfc6b7804cdc1f1b95cd6ce215a13a7c7aa5833ad9cfe8900e4c44045842b1'], - }), - ('colorRamps', '2.3', { - 'checksums': ['3f10eab0602a42a2e5a79c7c04638be06cbf1e6f23979a1bd95d853e10940b6a'], - }), - ('variancePartition', '1.18.0', { - 'checksums': ['b589a1479b314374cfcc448ad6254a047d07853f3690d6c25c50b7837129c6e6'], - }), - ('muscat', '1.2.0', { - 'checksums': ['83c4a88e1cd87fcbe5395655fe02a07f9d00f211a46d547b11543d993436e1f7'], - }), - ('IlluminaHumanMethylation450kmanifest', '0.4.0', { - 'checksums': ['41b2e54bac3feafc7646fe40bce3aa2b92c10871b0a13657c5736517792fa763'], - }), - ('IlluminaHumanMethylationEPICmanifest', '0.3.0', { - 'checksums': ['e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a'], - }), - ('IlluminaHumanMethylation450kanno.ilmn12.hg19', '0.6.0', { - 'checksums': ['249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15'], - }), - ('IlluminaHumanMethylationEPICanno.ilm10b2.hg19', '0.6.0', { - 'checksums': ['4decdbc78a6a8d02bf8aecb0d6e1d81134ae9dbc2375add52574f07829e8cd69'], - }), - ('IlluminaHumanMethylationEPICanno.ilm10b4.hg19', '0.6.0', { - 'checksums': ['2c8128126b63e7fa805a5f3b02449367dca9c3be3eb5f6300acc718826590719'], - }), - ('conumee', '1.22.0', { - 'checksums': ['cdbbf1ee7e87422b21e2d938559c1b30ce81cc4ccf0bbd9f06a74f5cb162f972'], - }), - ('BSgenome.Cfamiliaris.UCSC.canFam3', '1.4.0', { - 'checksums': ['99c55b6f7808822a3dae6679e60ecfb88a2b618159484bc35303c000bd4820c7'], - }), - ('ExperimentHub', '1.14.0', { - 'checksums': ['8d59046604917b1d6e45714aff3414df8a3f1b8c74cdfb9239abf8ad9c9ca6a1'], - }), - ('SingleR', '1.2.4', { - 'checksums': ['371fd11ed0ab8d6be7353267061d5210d788f9efa4b50d2c22c21467225a82aa'], - }), - ('FlowSorted.Blood.EPIC', '1.6.1', { - 'checksums': ['be13359127cfba5973ac86b41455cc705770bfe846c0813325c671605e0d7cc2'], - }), - ('FlowSorted.CordBloodCombined.450k', '1.4.1', { - 'checksums': ['f57308a0bc1f7c7e25564e1ea3da521fa04ff010f6359fad065eb0cf5089d277'], - }), - ('DRIMSeq', '1.16.0', { - 'checksums': ['c1842cbd875de8572e8349faf211c5403ca681696102c38973c69590c43ad6c4'], - }), - ('stageR', '1.10.0', { - 'checksums': ['34c31e771fa76cb474966121baaef52eefc5a4f66b9c8e86889b7318d159353f'], - }), - ('isva', '1.9', { - 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], - }), - ('org.Mm.eg.db', '3.11.4', { - 'checksums': ['12c6abb3060a85112e5061840f7845895ef29be8440eebcbfa4f4c1d73195aeb'], - }), - ('org.Rn.eg.db', '3.11.4', { - 'checksums': ['b662c9130692aa6e5a42b4e3a8e0626ff24dbfa991090f64e2fbb45a5833e42e'], - }), - ('ROC', '1.64.0', { - 'checksums': ['09f5e7fa18df843e89494860611a2e47c7653daf0a0a5964c6ae507f4e1ebd3e'], - }), - ('wateRmelon', '1.32.0', { - 'checksums': ['96f737823c3646dcd24fedad2cff63393e6e4d56f165d7ea44bbbe37f0326ab0'], - }), - ('GLAD', '2.52.0', { - 'checksums': ['9cf6e391c1f2da12b723c5122e5183e83e4869d106e25c071700a391c187e4cd'], - }), - ('missMethyl', '1.22.0', { - 'checksums': ['afb73e54037abb93db3f8a594aa3fde97c55afe825d387d6096a080d7621b540'], - }), - ('MethylSeekR', '1.28.0', { - 'checksums': ['47852110485865f5582d7a59bb62dfe268f1a65f71ead93ea31b69776bc993df'], - }), - ('affxparser', '1.60.0', { - 'checksums': ['d8a3f876e5d60a9b34b6d5754a5f5ac78bbd32e6676b9cde22b50d0578c09034'], - }), - ('ccdata', '1.14.0', { - 'checksums': ['29cef251d129c84d79d95a1ea30fdbc277b1ca9cf1ec6c4802360783f3cf1f9a'], - }), - ('xgboost', '1.2.0.1', { - 'checksums': ['44472e673e4f346c05257ec78a260e0148285a79819d0fd2f3ec370ec5de179a'], - }), - ('lsa', '0.73.2', { - 'checksums': ['cb0017bbda9b0eb1d05b451e0f557d02f789f65b2f8bf005606b63a3708e63a8'], - }), - ('ccmap', '1.14.0', { - 'checksums': ['40b5d5de9be2a77ce1ae386fa75ef2a7d88df1e87bc97566d75c2c49c79457e2'], - }), - ('oligo', '1.52.1', { - 'checksums': ['8d4f07d7218a0fc6f0f2000320e5eefe2c7a99dc3732a93e7de17f7ec7c8fbbe'], - }), - ('SMVar', '1.3.3', { - 'checksums': ['17625e89eb8be7a6dbb77e6bd9daca1ea1acff69026049f213e30edf2325999f'], - }), - ('metaMA', '3.1.2', { - 'checksums': ['01851d9632cdf1988d6a43ba44500e51477b9b25d5df1e1da488cd800df85ed6'], - }), - ('crossmeta', '1.14.0', { - 'checksums': ['0ced79094cd3d2aea3f9745efe26de967d5225b01706ded7b528f633ba6226c5'], - }), - ('snpStats', '1.38.0', { - 'checksums': ['98a3ccb30f5e6b150b9b5bb2457242b49544574b0d73558db1a3819131b663e3'], - }), - ('coloc', '3.2-1', { - 'checksums': ['b01c8fd81e4c4d766606e546482482d07ebe9e46e12538a1661bc685a2aca26a'], - }), - ('SCANVIS', '1.2.0', { - 'checksums': ['cdaaa3d4382ccce7ad539e00fff1cf1d296c1bcb3918bacb8e9a810ece610ae3'], - }), - ('EnsDb.Hsapiens.v86', '2.99.0', { - 'checksums': ['552c07bcc2a1420089d4330deafaeb5303e03d0fa75c96b78075dfd67eeee7be'], - }), -] - -modextrapaths = {'R_LIBS_SITE': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/R-opencv/R-opencv-0.2.0-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/r/R-opencv/R-opencv-0.2.0-foss-2020a-R-4.0.0.eb deleted file mode 100644 index da503b91dc8..00000000000 --- a/easybuild/easyconfigs/__archive__/r/R-opencv/R-opencv-0.2.0-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'RPackage' - -name = 'R-opencv' -local_rpkg = 'opencv' -version = '0.2.0' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/web/packages/opencv/' -description = """ -Experimenting with computer vision and machine learning in R. This package -exposes some of the available OpenCV algorithms, such as edge, body or face -detection. These can either be applied to analyze static images, or to filter -live video footage from a camera device.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://cran.r-project.org/src/contrib/'] -sources = ['%s_%%(version)s.tar.gz' % local_rpkg] -checksums = ['1b4d840d5a6ed75973622d396c04f909303643ab231dbbfc3e415c6d08d73452'] - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('R', '4.0.0'), - ('OpenCV', '4.2.0', '-Python-3.8.2-contrib'), -] - -preinstallopts = "CPATH=${EBROOTOPENCV}/include/opencv4:${CPATH}" - -sanity_check_paths = { - 'files': ['%s/R/%s' % (local_rpkg, local_rpkg)], - 'dirs': ['%s' % local_rpkg], -} - -options = {'modulename': local_rpkg} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.6.3-foss-2020a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.6.3-foss-2020a.eb deleted file mode 100644 index 70c106c7363..00000000000 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.6.3-foss-2020a.eb +++ /dev/null @@ -1,2413 +0,0 @@ -name = 'R' -version = '3.6.3' - -homepage = 'https://www.r-project.org/' -description = """R is a free software environment for statistical computing - and graphics.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] -sources = [SOURCE_TAR_GZ] -patches = ['R-4.x_fix-CVE-2024-27322.patch'] -checksums = [ - {'R-3.6.3.tar.gz': '89302990d8e8add536e12125ec591d6951022cf8475861b3690bc8bf1cefaa8f'}, - {'R-4.x_fix-CVE-2024-27322.patch': 'd8560e15c3c5716f99e852541901014d406f2a73136b0b74f11ba529f7a7b00d'}, -] - -builddependencies = [ - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('X11', '20200222'), - ('Mesa', '20.0.2'), - ('libGLU', '9.0.1'), - ('cairo', '1.16.0'), - ('libreadline', '8.0'), - ('ncurses', '6.2'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('zlib', '1.2.11'), - ('SQLite', '3.31.1'), - ('PCRE', '8.44'), - ('libpng', '1.6.37'), # for plotting in R - ('libjpeg-turbo', '2.0.4'), # for plottting in R - ('LibTIFF', '4.1.0'), - ('Java', '11', '', SYSTEM), - ('Tk', '8.6.10'), # for tcltk - ('cURL', '7.69.1'), # for RCurl - ('libxml2', '2.9.10'), # for XML - ('GMP', '6.2.0'), # for igraph - ('NLopt', '2.6.1'), # for nloptr - ('FFTW', '3.3.8'), # for fftw - ('libsndfile', '1.0.28'), # for seewave - ('ICU', '66.1'), # for rJava & gdsfmt - ('HDF5', '1.10.6'), # for hdf5r - ('UDUNITS', '2.2.26'), # for units - ('GSL', '2.6'), # for RcppGSL - ('ImageMagick', '7.0.10-1'), # for animation - # OS dependency should be preferred if the os version is more recent then - # this version, it's nice to have an up to date openssl for security - # reasons - # ('OpenSSL', '1.1.1e'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -configopts = "--with-pic --enable-threads --enable-R-shlib" -# some recommended packages may fail in a parallel build (e.g. Matrix), and -# we're installing them anyway below -configopts += " --with-recommended-packages=no" - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -# !! order of packages is important !! -# packages updated on 25 March 2020 -exts_list = [ - # include packages that are part of the base installation of R, - # both to make sure they are available (via sanity check), - # and to be able to pass the check for required dependencies when installing extensions in parallel - 'base', - 'compiler', - 'datasets', - 'graphics', - 'grDevices', - 'grid', - 'methods', - 'parallel', - 'splines', - 'stats', - 'stats4', - 'tcltk', - 'tools', - 'utils', - ('Rmpi', '0.6-9', { - 'checksums': ['b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6'], - }), - ('abind', '1.4-5', { - 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], - }), - ('magic', '1.5-9', { - 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], - }), - ('Rcpp', '1.0.4', { - 'checksums': ['d992fe8f7480606a0790be94948a6b667f37aa607ccd5e5613e88af861bb00d5'], - }), - ('RcppProgress', '0.4.2', { - 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], - }), - ('lpSolve', '5.6.15', { - 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], - }), - ('linprog', '0.9-2', { - 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], - }), - ('geometry', '0.4.5', { - 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], - }), - ('bit', '1.1-15.2', { - 'checksums': ['0b83e78385293d6cdc0189a07fcc3f9f9db286c8c4af3288467f5257e79cb28b'], - }), - ('filehash', '2.4-2', { - 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], - }), - ('ff', '2.2-14.2', { - 'checksums': [ - 'f8c06ac333ffe3545cdf56531619865176e1827728f7aeeba82d135d5c5e37e4', - 'beae9b31d7962b035329e07f4dc09308ca3a527327885d1c4ba9a1dd105e0bbd' # ff_2.2-14.2_aarch64_support.patch - 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'checksums': [ - '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', - # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch - '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', - ], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', - }), - ('oddsratio', '2.0.0', { - 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], - }), - ('mltools', '0.3.5', { - 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], - }), - ('h2o', '3.28.0.4', { - 'checksums': ['580dc6115b9ac21352eab2f94fa88eca2b7480a5886f0c3c18f247be1ce14bdb'], - }), - ('mlegp', '3.1.7', { - 'checksums': ['d4845eaf9260f8b8112726dd7ceb5c2f5ce75125fa313191db9de121f2ee15e0'], - }), - ('itertools', '0.1-3', { - 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], - }), - ('missForest', '1.4', { - 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], - }), - ('bartMachineJARs', '1.1', { - 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], - }), - ('bartMachine', '1.2.4.2', { - 'checksums': ['28a5f7363325021bd93f9bd060cc48f20c689dae2f2f6f7100faae66d7651f80'], - }), - ('lqa', '1.0-3', { - 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], - }), - ('PresenceAbsence', '1.1.9', { - 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], - }), - ('GUTS', '1.1.1', { - 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], - }), - ('GenSA', '1.1.7', { - 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], - }), - ('rematch2', '2.1.0', { - 'checksums': ['78677071bd44b40e562df1da6f0c6bdeae44caf973f97ff8286b8c994db59f01'], - }), - ('parsedate', '1.2.0', { - 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], - }), - ('circular', '0.4-93', { - 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], - }), - ('cobs', '1.3-4', { - 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], - }), - ('resample', '0.4', { - 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], - }), - ('MIIVsem', '0.5.4', { - 'checksums': ['de918d6b1820c59a7d4324342ad15444c2370ce1d843397a136c307397ed64b9'], - }), - ('medflex', '0.6-6', { - 'checksums': ['b9d04fb5281d0ea0555ec4f327a0ee951a7f312a3af944578dc175183dc49211'], - }), - ('Rserve', '1.7-3.1', { - 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], - }), - ('spls', '2.2-3', { - 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], - }), - ('Boruta', '6.0.0', { - 'checksums': ['1c9a7aabe09f040e147f6c614f5fe1d0b951d3b0f0024161fbb4c31da8fae8de'], - }), - ('dr', '3.0.10', { - 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], - }), - ('CovSel', '1.2.1', { - 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], - }), - ('tmle', '1.4.0.1', { - 'checksums': ['075e7b7fe0496e02785eb35aed0db84476db756c6f14a0047808af2565b33501'], - }), - ('ctmle', '0.1.2', { - 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], - }), - ('BayesPen', '1.0', { - 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], - }), - ('inline', '0.3.15', { - 'checksums': ['ff043fe13c1991a3b285bed256ff4a9c0ba10bee764225a34b285875b7d69c68'], - }), - ('BMA', '3.18.12', { - 'checksums': ['cbabb77d92b09a11a986ad03950322e78dff743f82ff67fda51d32e44135dd79'], - }), - ('BCEE', '1.2', { - 'checksums': ['0b1183458d625ef5dd0962fc77ca1326e77754a2c04be11fb002057abcb65a22'], - }), - ('bacr', '1.0.1', { - 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], - }), - ('clue', '0.3-57', { - 'checksums': ['6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17'], - }), - ('bdsmatrix', '1.3-4', { - 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], - }), - ('fftwtools', '0.9-8', { - 'checksums': ['4641c8cd70938c2a8bde0b6da6cf7f83e96175ef52f1ca42ec3920a1dabf1bdb'], - }), - ('imagerExtra', '1.3.2', { - 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], - }), - ('MALDIquant', '1.19.3', { - 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], - }), - ('threejs', '0.3.3', { - 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], - }), - ('LaplacesDemon', '16.1.4', { - 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], - }), - ('rda', '1.0.2-2.1', { - 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', - 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], - }), - ('sampling', '2.8', { - 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], - }), - ('lda', '1.4.2', { - 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], - }), - ('jiebaRD', '0.1', { - 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], - }), - ('jiebaR', '0.11', { - 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], - }), - ('hdm', '0.3.1', { - 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], - }), - ('abe', '3.0.1', { - 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], - }), - ('SignifReg', '2.1', { - 'checksums': ['d21959ce5b1ee20efd1483f6020b57e5f6616bd525af77a7bd325501cc670606'], - }), - ('bbmle', '1.0.23.1', { - 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], - }), - ('emdbook', '1.3.12', { - 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], - }), - ('SOAR', '0.99-11', { - 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], - }), - ('rasterVis', '0.47', { - 'checksums': ['123ebe870895c2ba3a4b64d8a18bccab5287c831fa14bb0fe07f0d7de61e51d3'], - }), - ('tictoc', '1.0', { - 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], - }), - ('ISOcodes', '2020.03.16', { - 'checksums': ['160eb4ea23be53305e4e728002c8f5d3852d89155f538deccb734e7c8ad4e1c3'], - }), - ('stopwords', '1.0', { - 'checksums': ['9b727a5d827ac8dcfa6329140d294dcf964a06d80132b4ca434330d0ee02b1da'], - }), - ('janeaustenr', '0.1.5', { - 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], - }), - ('SnowballC', '0.6.0', { - 'checksums': ['61617d344444235940f5b9ac1cd6b86938e74a8c76791235724b16b755c3f72c'], - }), - ('tokenizers', '0.2.1', { - 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], - }), - ('hunspell', '3.0', { - 'checksums': ['01fb9c87f7cf094aaad3b7098378134f2e503286224351e91d08c00b6ee19857'], - }), - ('topicmodels', '0.2-9', { - 'checksums': ['40770fb7de6ab6bd6e3ef6a0c777fa6db65d0322e67503c26c84ea857ac9a79c'], - }), - ('tidytext', '0.2.3', { - 'checksums': ['c103f98f5cbbb5a4ea4c893520ea5eb38b9c5097e5325d7efd4f7e3afe71068b'], - }), - ('splitstackshape', '1.4.8', { - 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], - }), - ('grImport2', '0.2-0', { - 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], - }), - ('preseqR', '4.0.0', { - 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], - }), - ('idr', '1.2', { - 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], - }), - ('entropy', '1.2.1', { - 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], - }), - ('kedd', '1.0.3', { - 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], - }), - ('HiddenMarkov', '1.8-11', { - 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], - }), - ('lmerTest', '3.1-1', { - 'checksums': ['520ef83e9a7c58e3c5b7175fbda902b747b2e01c24b53714ede81a6a87de5b64'], - }), - ('loo', '2.2.0', { - 'checksums': ['466df60953a89fcb135b32909197c3ff26ecea719c191667faa5747324fb01c3'], - }), - ('StanHeaders', '2.21.0-1', { - 'checksums': ['4e94148af2960f203b208c2b725d8be628ca282c7a1e967a7e6e78aa5eb90d3f'], - }), - ('rstan', '2.19.3', { - 'checksums': ['d7025dccdc2337fd0cf3b9689c3e0a07558a47a08b7cbc370e0b3998256f1689'], - }), - ('Rborist', '0.2-3', { - 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], - }), - ('VSURF', '1.1.0', { - 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], - }), - ('mRMRe', '2.1.0', { - 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], - }), - ('dHSIC', '2.1', { - 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], - }), - ('ggsci', '2.9', { - 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], - }), - ('ggsignif', '0.6.0', { - 'checksums': ['6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e'], - }), - ('corrplot', '0.84', { - 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], - }), - ('rstatix', '0.5.0', { - 'checksums': ['06b2ba1b16698c93203474eb67e59169fa4127283d46cf694e032a5472956b46'], - }), - ('ggfan', '0.1.3', { - 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], - }), - ('ggpubr', '0.3.0', { - 'checksums': ['b82ffc6bd5974c3036d08393fa1f2bafeaf6f567e0b3faf43e38226b19399eb6'], - }), - ('yaImpute', '1.0-32', { - 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], - }), - ('intrinsicDimension', '1.2.0', { - 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], - }), - ('patchwork', '1.0.0', { - 'checksums': ['8bfb59b91775781848f39eedcaaaf92c147e2637f384085fcdd41fc8355b3c63'], - }), - ('leiden', '0.3.3', { - 'checksums': ['c2b5e1c061c8bbea494639a0d7f0fa22f5b41ff5fd911409e5f832f3575d06c2'], - }), - ('future.apply', '1.4.0', { - 'checksums': ['737e5a8e2d0ce2678835f5be15c96d491f690d307662ed6719be41937633f8cd'], - }), - ('sctransform', '0.2.1', { - 'checksums': ['d6430a81a66c93da770b1a7c55344df42187321038b4eee80b7066cdd8a7631f'], - }), - ('packrat', '0.5.0', { - 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], - }), - ('shinyjs', '1.1', { - 'checksums': ['8986181baa68fb2863eea65b9df1b04b9b4e1293685298531d42de3bc2f06892'], - }), - ('colourpicker', '1.0', { - 'checksums': ['f1dacbafb05c09f61b9bdd0fdcee5344409759b042a71ec46d7c9e3710107b7c'], - }), - ('ggExtra', '0.9', { - 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], - }), - ('findpython', '1.0.5', { - 'checksums': ['3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145'], - }), - ('argparse', '2.0.1', { - 'checksums': ['949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab'], - }), - ('intergraph', '2.0-2', { - 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], - }), - ('ggnetwork', '0.5.8', { - 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], - }), - ('qqman', '0.1.4', { - 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/r/R/R-4.0.0-foss-2020a.eb deleted file mode 100644 index d0fcc5867f5..00000000000 --- a/easybuild/easyconfigs/__archive__/r/R/R-4.0.0-foss-2020a.eb +++ /dev/null @@ -1,2719 +0,0 @@ -name = 'R' -version = '4.0.0' - -homepage = 'https://www.r-project.org/' -description = """R is a free software environment for statistical computing - and graphics.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] -sources = [SOURCE_TAR_GZ] -patches = [ - 'R-%(version)s_ppc64le-build-fix.patch', - 'R-4.x_fix-CVE-2024-27322.patch', -] -checksums = [ - {'R-4.0.0.tar.gz': '06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940'}, - {'R-4.0.0_ppc64le-build-fix.patch': 'ae14b063be40ba2f2e73d95ae1ee0b8630ac7bbc8ec2d64830016c8d62f672ad'}, - {'R-4.x_fix-CVE-2024-27322.patch': 'd8560e15c3c5716f99e852541901014d406f2a73136b0b74f11ba529f7a7b00d'}, -] - -builddependencies = [ - ('pkg-config', '0.29.2'), - ('Xvfb', '1.20.9'), -] -dependencies = [ - ('X11', '20200222'), - ('Mesa', '20.0.2'), - ('libGLU', '9.0.1'), - ('cairo', '1.16.0'), - ('libreadline', '8.0'), - ('ncurses', '6.2'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('zlib', '1.2.11'), - ('SQLite', '3.31.1'), - ('PCRE2', '10.34'), - ('libpng', '1.6.37'), # for plotting in R - ('libjpeg-turbo', '2.0.4'), # for plottting in R - ('LibTIFF', '4.1.0'), - ('Java', '11', '', SYSTEM), - ('Tk', '8.6.10'), # for tcltk - ('cURL', '7.69.1'), # for RCurl - ('libxml2', '2.9.10'), # for XML - ('GMP', '6.2.0'), # for igraph - ('NLopt', '2.6.1'), # for nloptr - ('FFTW', '3.3.8'), # for fftw - ('libsndfile', '1.0.28'), # for seewave - ('ICU', '66.1'), # for rJava & gdsfmt - ('HDF5', '1.10.6'), # for hdf5r - ('UDUNITS', '2.2.26'), # for units - ('GSL', '2.6'), # for RcppGSL - ('ImageMagick', '7.0.10-1'), # for animation - ('GLPK', '4.65'), # for Rglpk - # OS dependency should be preferred if the os version is more recent then - # this version, it's nice to have an up to date openssl for security - # reasons - # ('OpenSSL', '1.1.1e'), -] - -osdependencies = [OS_PKG_OPENSSL_DEV] - -configopts = "--with-pic --enable-threads --enable-R-shlib" -# some recommended packages may fail in a parallel build (e.g. Matrix), and -# we're installing them anyway below -configopts += " --with-recommended-packages=no" - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -# !! order of packages is important !! -# packages updated on 23 July 2020 -exts_list = [ - # include packages that are part of the base installation of R, - # both to make sure they are available (via sanity check), - # and to be able to pass the check for required dependencies when installing extensions in parallel - 'base', - 'compiler', - 'datasets', - 'graphics', - 'grDevices', - 'grid', - 'methods', - 'parallel', - 'splines', - 'stats', - 'stats4', - 'tcltk', - 'tools', - 'utils', - ('Rmpi', '0.6-9', { - 'checksums': ['b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6'], - }), - ('abind', '1.4-5', { - 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], - }), - ('magic', '1.5-9', { - 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], - }), - ('Rcpp', '1.0.4.6', { - 'checksums': ['45af675ddbbe155e671453b2e84fe32250bb98d4ccb4342b61c1e25cff10b302'], - }), - ('RcppProgress', '0.4.2', { - 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], - }), - ('lpSolve', '5.6.15', { - 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], - }), - ('linprog', '0.9-2', { - 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], - }), - ('geometry', '0.4.5', { - 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}), - ('npsurv', '0.4-0', { - 'checksums': ['404cf7135dc40a04e9b81224a543307057a8278e11109ba1fcaa28e87c6204f3'], - }), - ('fitdistrplus', '1.0-14', { - 'checksums': ['85082590f62aa08d99048ea3414c5cc1e5b780d97b3779d2397c6cb435470083'], - }), - ('rappdirs', '0.3.1', { - 'checksums': ['2fd891ec16d28862f65bb57e4a78f77a597930abb59380e757afd8b6c6d3264a'], - }), - ('reticulate', '1.15', { - 'checksums': ['47db3e9c9424263ade15287da8e74f6ba261a936b644b197dba6772853b7b50d'], - }), - ('hdf5r', '1.3.2', { - 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', - 'preinstallopts': "unset LIBS && ", - 'checksums': ['31493d9dde9705543e5474c937fa5b4b64895ae1dd6ee51d7039dd95a6015730'], - }), - ('DTRreg', '1.5', { - 'checksums': ['eb9b4d98b25eec304a447db302f618a75180f8d8fe0f5728ecd7e85957613456'], - }), - ('pulsar', '0.3.6', { - 'checksums': ['b5851bf365003ace07542fd21ccff015c4b21ffd73e21ec3a539563e9ef53564'], - }), - ('bayesm', '3.1-4', { - 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], - }), - ('energy', '1.7-7', { - 'checksums': ['67b88fb33ee6e7bec2e4fe356a4efd36f70c3cf9b0ebe2f6d9da9ec96de9968f'], - }), - ('compositions', '1.40-5', { - 'checksums': ['879e296037b0b3c52cfe48556820500b94d4eea16ec2b40f85988b65c5f72a51'], - }), - ('clustree', '0.4.2', { - 'checksums': ['5d6b8ee3cbbcdd235a7abe4107429e45847ed09ec1cdb572ad6efb9d88dff82e'], - }), - ('plotly', '4.9.2.1', { - 'checksums': ['f45eae325ab7e7924b0be098bad866ce003d657cf63e137104401c2dd4401db8'], - }), - ('tweedie', '2.3.2', { - 'checksums': ['9a6226e64e3d56eb7eb2a408f8b825c2ad6ee0ea203a9220e85e7789514adb81'], - }), - ('RcppGSL', '0.3.7', { - 'checksums': ['45e95c4170fc8421ae9b32134b3a402f76ea9657030969723a3563c7ce14dc32'], - }), - ('mvabund', '4.1.3', { - 'checksums': ['4b98049026fcc5a262163f6801d5b98b8543267cf7b0edac8382d5311b81a8fc'], - }), - ('fishMod', '0.29', { - 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], - }), - ('gllvm', '1.2.1', { - 'checksums': ['a9dca68227a8f89c61950f6411de3b988e6e067d97fadc589f69ddd731c2e1ff'], - }), - ('grpreg', '3.2.2', { - 'checksums': ['e59f576ee5d794444917e0fbdab0d1ebf4aa71967c9a35ec196899ed5b168388'], - }), - ('trust', '0.1-8', { - 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], - }), - ('ergm', '3.10.4', { - 'checksums': ['885f0b1a23c5a2c1947962350cfab66683dfdfd1db173c115e90396d00831f22'], - }), - ('networkDynamic', '0.10.1', { - 'checksums': ['22eed8d9dea8d70877c1619eb2bc3f1ac5142ce3db6fd6eb3e0879ca56b76ca0'], - }), - ('tergm', '3.6.1', { - 'checksums': ['21de2eca943d89ba63af14951655d626f241bafccc4b2709fa39aa130625cd0f'], - }), - ('ergm.count', '3.4.0', { - 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], - }), - ('tsna', '0.3.1', { - 'checksums': ['bba4b5e04ba647784581a2137f653f60b4c83cfd726c399556054c5a6d2cbd95'], - }), - ('statnet', '2019.6', { - 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], - }), - ('aggregation', '1.0.1', { - 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], - }), - ('ComICS', '1.0.4', { - 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], - }), - ('dtangle', '2.0.9', { - 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], - }), - ('mcmc', '0.9-7', { - 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], - }), - ('MCMCpack', '1.4-6', { - 'checksums': ['6bcd018d6fa589a6854ee1bcea18b9d6c4095f3deae9058f69afbb09cba873c7'], - }), - ('shinythemes', '1.1.2', { - 'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'], - }), - ('csSAM', '1.2.4', { - 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], - }), - ('bridgedist', '0.1.0', { - 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], - }), - ('asnipe', '1.1.12', { - 'checksums': ['3a1f166f1c71b5877a2acca1384ec6c9b430b67af67ef26125f2abbb53c66206'], - }), - ('liquidSVM', '1.2.4', { - 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - 'checksums': [ - '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz - # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch - '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', - ], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', - }), - ('oddsratio', '2.0.0', { - 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], - }), - ('mltools', '0.3.5', { - 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], - }), - ('h2o', '3.30.0.1', { - 'checksums': ['cb11ef58a7d7dfd3a9193686ddd9c8a9f988b33a69656d8b3e8f59082068b0f5'], - }), - ('mlegp', '3.1.7', { - 'checksums': ['d4845eaf9260f8b8112726dd7ceb5c2f5ce75125fa313191db9de121f2ee15e0'], - }), - ('itertools', '0.1-3', { - 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], - }), - ('missForest', '1.4', { - 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], - }), - ('bartMachineJARs', '1.1', { - 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], - }), - ('bartMachine', '1.2.4.2', { - 'checksums': ['28a5f7363325021bd93f9bd060cc48f20c689dae2f2f6f7100faae66d7651f80'], - }), - ('lqa', '1.0-3', { - 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], - }), - ('PresenceAbsence', '1.1.9', { - 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], - }), - ('GUTS', '1.1.1', { - 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], - }), - ('GenSA', '1.1.7', { - 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], - }), - ('parsedate', '1.2.0', { - 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], - }), - ('circular', '0.4-93', { - 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], - }), - ('cobs', '1.3-4', { - 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], - }), - ('resample', '0.4', { - 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], - }), - ('MIIVsem', '0.5.4', { - 'checksums': ['de918d6b1820c59a7d4324342ad15444c2370ce1d843397a136c307397ed64b9'], - }), - ('medflex', '0.6-6', { - 'checksums': ['b9d04fb5281d0ea0555ec4f327a0ee951a7f312a3af944578dc175183dc49211'], - }), - ('Rserve', '1.7-3.1', { - 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], - }), - ('spls', '2.2-3', { - 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], - }), - ('Boruta', '6.0.0', { - 'checksums': ['1c9a7aabe09f040e147f6c614f5fe1d0b951d3b0f0024161fbb4c31da8fae8de'], - }), - ('dr', '3.0.10', { - 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], - }), - ('CovSel', '1.2.1', { - 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], - }), - ('tmle', '1.4.0.1', { - 'checksums': ['075e7b7fe0496e02785eb35aed0db84476db756c6f14a0047808af2565b33501'], - }), - ('ctmle', '0.1.2', { - 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], - }), - ('BayesPen', '1.0', { - 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], - }), - ('inline', '0.3.15', { - 'checksums': ['ff043fe13c1991a3b285bed256ff4a9c0ba10bee764225a34b285875b7d69c68'], - }), - ('BMA', '3.18.12', { - 'checksums': ['cbabb77d92b09a11a986ad03950322e78dff743f82ff67fda51d32e44135dd79'], - }), - ('BCEE', '1.3.0', { - 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], - }), - ('bacr', '1.0.1', { - 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], - }), - ('clue', '0.3-57', { - 'checksums': ['6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17'], - }), - ('bdsmatrix', '1.3-4', { - 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], - }), - ('fftwtools', '0.9-8', { - 'checksums': ['4641c8cd70938c2a8bde0b6da6cf7f83e96175ef52f1ca42ec3920a1dabf1bdb'], - }), - ('imagerExtra', '1.3.2', { - 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], - }), - ('MALDIquant', '1.19.3', { - 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], - }), - ('threejs', '0.3.3', { - 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], - }), - ('LaplacesDemon', '16.1.4', { - 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], - }), - ('rda', '1.0.2-2.1', { - 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', - 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], - }), - ('sampling', '2.8', { - 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], - }), - ('lda', '1.4.2', { - 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], - }), - ('jiebaRD', '0.1', { - 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], - }), - ('jiebaR', '0.11', { - 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], - }), - ('hdm', '0.3.1', { - 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], - }), - ('abe', '3.0.1', { - 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], - }), - ('SignifReg', '3.0', { - 'checksums': ['ada4e1f8cbb08ba8ff16275ec5f9a453857e0cab63b70d42753989ab4c716b7b'], - }), - ('bbmle', '1.0.23.1', { - 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], - }), - ('emdbook', '1.3.12', { - 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], - }), - ('SOAR', '0.99-11', { - 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], - }), - ('rasterVis', '0.47', { - 'checksums': ['123ebe870895c2ba3a4b64d8a18bccab5287c831fa14bb0fe07f0d7de61e51d3'], - }), - ('tictoc', '1.0', { - 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], - }), - ('ISOcodes', '2020.03.16', { - 'checksums': ['160eb4ea23be53305e4e728002c8f5d3852d89155f538deccb734e7c8ad4e1c3'], - }), - ('stopwords', '2.0', { - 'checksums': ['5cca60ce9f44406486e0dca2e36cec2488096c3558b45fc3bd0e7b6d1500af94'], - }), - ('janeaustenr', '0.1.5', { - 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], - }), - ('SnowballC', '0.7.0', { - 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], - }), - ('tokenizers', '0.2.1', { - 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], - }), - ('hunspell', '3.0', { - 'checksums': ['01fb9c87f7cf094aaad3b7098378134f2e503286224351e91d08c00b6ee19857'], - }), - ('topicmodels', '0.2-11', { - 'checksums': ['9c26b4d967be6ec26834a39f04aa92b059ea9503eb70c700e1c0a7a43637b74a'], - }), - ('tidytext', '0.2.4', { - 'checksums': ['46ff59063b6a519c9eb606ae135ef31d7073ac729e4a912c9f77e234801b933d'], - }), - ('splitstackshape', '1.4.8', { - 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], - }), - ('grImport2', '0.2-0', { - 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], - }), - ('preseqR', version, { - 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], - }), - ('idr', '1.2', { - 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], - }), - ('entropy', '1.2.1', { - 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], - }), - ('kedd', '1.0.3', { - 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], - }), - ('HiddenMarkov', '1.8-11', { - 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], - }), - ('lmerTest', '3.1-2', { - 'checksums': ['385870873fd303c2caa4ac43e2df0ca5aa36ddb484bfb4eefbc5c4ac4bef6de2'], - }), - ('loo', '2.2.0', { - 'checksums': ['466df60953a89fcb135b32909197c3ff26ecea719c191667faa5747324fb01c3'], - }), - ('StanHeaders', '2.21.0-1', { - 'checksums': ['4e94148af2960f203b208c2b725d8be628ca282c7a1e967a7e6e78aa5eb90d3f'], - }), - ('rstan', '2.19.3', { - 'checksums': ['d7025dccdc2337fd0cf3b9689c3e0a07558a47a08b7cbc370e0b3998256f1689'], - }), - ('Rborist', '0.2-3', { - 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], - }), - ('VSURF', '1.1.0', { - 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], - }), - ('mRMRe', '2.1.0', { - 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], - }), - ('dHSIC', '2.1', { - 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], - }), - ('ggsci', '2.9', { - 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], - }), - ('ggsignif', '0.6.0', { - 'checksums': ['6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e'], - }), - ('corrplot', '0.84', { - 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], - }), - ('rstatix', '0.5.0', { - 'checksums': ['06b2ba1b16698c93203474eb67e59169fa4127283d46cf694e032a5472956b46'], - }), - ('ggfan', '0.1.3', { - 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], - }), - ('ggpubr', '0.3.0', { - 'checksums': ['b82ffc6bd5974c3036d08393fa1f2bafeaf6f567e0b3faf43e38226b19399eb6'], - }), - ('yaImpute', '1.0-32', { - 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], - }), - ('intrinsicDimension', '1.2.0', { - 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], - }), - ('patchwork', '1.0.0', { - 'checksums': ['8bfb59b91775781848f39eedcaaaf92c147e2637f384085fcdd41fc8355b3c63'], - }), - ('leiden', '0.3.3', { - 'checksums': ['c2b5e1c061c8bbea494639a0d7f0fa22f5b41ff5fd911409e5f832f3575d06c2'], - }), - ('future.apply', '1.4.0', { - 'checksums': ['737e5a8e2d0ce2678835f5be15c96d491f690d307662ed6719be41937633f8cd'], - }), - ('sctransform', '0.2.1', { - 'checksums': ['d6430a81a66c93da770b1a7c55344df42187321038b4eee80b7066cdd8a7631f'], - }), - ('packrat', '0.5.0', { - 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], - }), - ('shinyjs', '1.1', { - 'checksums': ['8986181baa68fb2863eea65b9df1b04b9b4e1293685298531d42de3bc2f06892'], - }), - ('colourpicker', '1.0', { - 'checksums': ['f1dacbafb05c09f61b9bdd0fdcee5344409759b042a71ec46d7c9e3710107b7c'], - }), - ('ggExtra', '0.9', { - 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], - }), - ('findpython', '1.0.5', { - 'checksums': ['3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145'], - }), - ('argparse', '2.0.1', { - 'checksums': ['949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab'], - }), - ('intergraph', '2.0-2', { - 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], - }), - ('ggnetwork', '0.5.8', { - 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], - }), - ('qqman', '0.1.4', { - 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], - }), - ('rstantools', '2.0.0', { - 'checksums': [('4ae78aa39c3d4897f453e621a09961d6f2cda27a1b5657d4d4b32d3d89bd80c6', - 'd200a4d8c62d8577fdba819bf770e7abb11c57c3332f4498e1d30ce824598b3a')], - }), - ('bayesplot', '1.7.1', { - 'checksums': ['820ca9ca3258fc68333e75fd60898c0d0f08f513b66c161ca6159a54ad54006b'], - }), - ('dygraphs', '1.1.1.6', { - 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], - }), - ('rsconnect', '0.8.16', { - 'checksums': ['3f728c6a5153dca28f69b9355ae9d18c5f7e70d12495c0c047eef673c1053116'], - }), - ('shinystan', '2.5.0', { - 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'], - }), - ('brms', '2.12.0', { - 'checksums': ['fa21505dca65d027f1cf1c573258de5f3c51ca8b94abd6dcf9123a3a27a72999'], - }), - ('drgee', '1.1.10', { - 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], - }), - ('stdReg', '3.4.0', { - 'checksums': ['b423df43e9c4bb8ffafe2de88b93fdcf3a90f964f136580ea1b849a83dba7400'], - }), - ('mcmcse', '1.4-1', { - 'checksums': ['6b181f56d60ddf55c9c08a2468ef9ffe3ec8a1b16cfa9a7742c3872597f85d17'], - }), - ('copCAR', '2.0-3', { - 'checksums': ['e626380d3f11ca6c756381f2423ef3661efb52667147114253416cc6151a71b8'], - }), - ('batchmeans', '1.0-4', { - 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], - }), - ('ngspatial', '1.2-2', { - 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], - }), - ('BIGL', '1.4.3', { - 'checksums': ['7ef7edd5c1852409f1da176e810a9a2a7f0b9441e0e6459d4d16179f3eb000f4'], - }), - ('drugCombo', '1.1.1', { - 'checksums': ['9fdc3a7cf63552c32f1c7573258fc4ceacdaf5c475fe79aa4ca8c9226b9f8a38'], - }), - ('betareg', '3.1-3', { - 'checksums': ['cc19387ec516492d11cf59cdfa07e1733950a2af8196c1e155bc95939bc76246'], - }), - ('unmarked', '1.0.1', { - 'checksums': ['a3bb9bdc7a4a79ea38482df3f8cbb6e9082332a0d894eeb4b3dc816344cec0e4'], - }), - ('maxlike', '0.1-8', { - 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], - }), - ('coxme', '2.2-16', { - 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], - }), - ('AICcmodavg', '2.3-0', { - 'checksums': ['4d6bcff3c549be9dcefdd849b239659618fdaf9ba0d27b9d0589620d104e5e24'], - }), - ('pacman', '0.5.1', { - 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], - }), - ('spaa', '0.2.2', { - 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], - }), - ('maxnet', '0.1.2', { - 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], - }), - ('ENMeval', '0.3.0', { - 'checksums': ['1c924098a27c82a9bf75408173b47429c40cc41cae3aba18c86ba217bb45ba60'], - }), - ('plotmo', '3.5.7', { - 'checksums': ['aa366a49a63cabfd5d799a1524e23a4faed022f10ee60f8407d70ab70731b38c'], - }), - ('earth', '5.1.2', { - 'checksums': ['326f98e8c29365ca3cd5584cf2bd6529358f5ef81664cbd494162f92b6c3488d'], - }), - ('mda', '0.5-2', { - 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], - }), - ('biomod2', '3.4.6', { - 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], - }), - ('poLCA', '1.4.1', { - 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], - }), - ('PermAlgo', '1.1', { - 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], - }), - ('coxed', '0.3.3', { - 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], - }), - ('testit', '0.11', { - 'checksums': ['12fb24f0c7b032ae0d146d22161efc676ef4cdf604b81f6345e8d9dfd125388e'], - }), - ('data.tree', '1.0.0', { - 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], - }), - ('NISTunits', '1.0.1', { - 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], - }), - ('celestial', '1.4.6', { - 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], - }), - ('fasterize', '1.0.3', { - 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], - }), - ('RPMM', '1.25', { - 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], - }), - ('RefFreeEWAS', '2.2', { - 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], - }), - ('wordcloud', '2.6', { - 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], - }), - ('JADE', '2.0-3', { - 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], - }), - ('gsl', '2.1-6', { - 'checksums': ['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], - }), - ('awsMethods', '1.1-1', { - 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], - }), - ('aws', '2.4-3', { - 'checksums': ['8582dc7669242eb0e6bee204bdc87ff1c344e2e74912931da47e21279d439531'], - }), - ('ruv', '0.9.7.1', { - 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], - }), - ('mhsmm', '0.4.16', { - 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], - }), - ('dbarts', '0.9-18', { - 'patches': ['dbarts-0.9-18_fix-simd-on-non-x86.patch'], - 'checksums': [ - 'fd99f99d1a24c16596767246618cf240ebd8d86fa82b0e5ce65b737b9afb4ac4', # dbarts_0.9-18.tar.gz - # dbarts-0.9-18_fix-simd-on-non-x86.patch - '80a7e84c691d418da4e90a38db1caebed31d01771e4e7f64d24676ee8d84c104', - ], - }), - ('proftools', '0.99-3', { - 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], - }), - ('NCmisc', '1.1.6', { - 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], - }), - ('reader', '1.0.6', { - 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], - }), - ('gnumeric', '0.7-8', { - 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], - }), - ('tcltk2', '1.2-11', { - 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], - }), - ('readODS', '1.7.0', { - 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], - }), - ('nortest', '1.0-4', { - 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], - }), - ('EnvStats', '2.3.1', { - 'checksums': ['d753d42b42ff28c1cd25c63916fb2aa9e325941672fb16f7dfd97e218416cf2a'], - }), - ('outliers', '0.14', { - 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], - }), - ('elementR', '1.3.7', { - 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], - }), - ('gWidgets2', '1.0-8', { - 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], - }), - ('gWidgets2tcltk', '1.0-6', { - 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... - 'modulename': False, - }), - ('mgsub', '1.7.2', { - 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], - }), - ('ie2misc', '0.8.6', { - 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], - }), - ('assertive.base', '0.0-7', { - 'checksums': ['f02d4eca849f512500abb266a2a751d1fa2cf064f7142e5161a77c20b7f643f7'], - }), - ('assertive.properties', '0.0-4', { - 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], - }), - ('assertive.types', '0.0-3', { - 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], - }), - ('assertive.numbers', '0.0-2', { - 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], - }), - ('assertive.strings', '0.0-3', { - 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], - }), - ('assertive.datetimes', '0.0-3', { - 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], - }), - ('assertive.files', '0.0-2', { - 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], - }), - ('assertive.sets', '0.0-3', { - 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], - }), - ('assertive.matrices', '0.0-2', { - 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], - }), - ('assertive.models', '0.0-2', { - 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], - }), - ('assertive.data', '0.0-3', { - 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], - }), - ('assertive.data.uk', '0.0-2', { - 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], - }), - ('assertive.data.us', '0.0-2', { - 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], - }), - ('assertive.reflection', '0.0-5', { - 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], - }), - ('assertive.code', '0.0-3', { - 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], - }), - ('assertive', '0.3-6', { - 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], - }), - ('rdrop2', '0.8.2.1', { - 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], - }), - ('Exact', '2.1', { - 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], - }), - ('lmom', '2.8', { - 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], - }), - ('gld', '2.6.2', { - 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], - }), - ('DescTools', '0.99.38', { - 'checksums': ['bd8edce64a8f9e295611959295b85cf8d7bbf915093158016169bd334e0e1104'], - }), - ('orthopolynom', '1.0-5', { - 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], - }), - ('gaussquad', '1.0-2', { - 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], - }), - ('nlsem', '0.8', { - 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], - }), - ('mitools', '2.4', { - 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], - }), - ('survey', '4.0', { - 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], - }), - ('tableone', '0.12.0', { - 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], - }), - ('jstable', '1.0.1', { - 'checksums': ['2e4cfce264a2353e4655d0faafc93969222d67a21c0c9cc61a2454abd99c5cdc'], - }), - ('RCAL', '2.0', { - 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], - }), - ('stargazer', '5.2.2', { - 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], - }), - ('sensemakr', '0.1.3', { - 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], - }), - ('origami', '1.0.3', { - 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], - }), - ('hal9001', '0.2.7', { - 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-4.0.0-fosscuda-2020a.eb b/easybuild/easyconfigs/__archive__/r/R/R-4.0.0-fosscuda-2020a.eb deleted file mode 100644 index b17cffac654..00000000000 --- a/easybuild/easyconfigs/__archive__/r/R/R-4.0.0-fosscuda-2020a.eb +++ /dev/null @@ -1,2733 +0,0 @@ -name = 'R' -version = '4.0.0' - -homepage = 'https://www.r-project.org/' -description = """R is a free software environment for statistical computing - and graphics.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] -sources = [SOURCE_TAR_GZ] -patches = ['%(name)s-%(version)s_ppc64le-build-fix.patch'] -checksums = [ - '06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940', # R-4.0.0.tar.gz - 'ae14b063be40ba2f2e73d95ae1ee0b8630ac7bbc8ec2d64830016c8d62f672ad', # R-4.0.0_ppc64le-build-fix.patch -] - -builddependencies = [ - ('pkg-config', '0.29.2'), - ('Xvfb', '1.20.9'), -] -dependencies = [ - ('X11', '20200222'), - ('Mesa', '20.0.2'), - ('libGLU', '9.0.1'), - ('cairo', '1.16.0'), - ('libreadline', '8.0'), - ('ncurses', '6.2'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('zlib', '1.2.11'), - ('SQLite', '3.31.1'), - ('PCRE2', '10.34'), - ('libpng', '1.6.37'), # for plotting in R - ('libjpeg-turbo', '2.0.4'), # for plottting in R - ('LibTIFF', '4.1.0'), - ('Java', '11', '', SYSTEM), - ('Tk', '8.6.10'), # for tcltk - ('cURL', '7.69.1'), # for RCurl - ('libxml2', '2.9.10'), # for XML - ('GMP', '6.2.0'), # for igraph - ('NLopt', '2.6.1'), # for nloptr - ('FFTW', '3.3.8'), # for fftw - ('libsndfile', '1.0.28'), # for seewave - ('ICU', '66.1'), # for rJava & gdsfmt - ('HDF5', '1.10.6'), # for hdf5r - ('UDUNITS', '2.2.26'), # for units - ('GSL', '2.6'), # for RcppGSL - ('ImageMagick', '7.0.10-1'), # for animation - ('GLPK', '4.65'), # for Rglpk - ('pocl', '1.5'), # for OpenCL support (particularly on POWER) - # OS dependency should be preferred if the os version is more recent then - # this version, it's nice to have an up to date openssl for security - # reasons - # ('OpenSSL', '1.1.1e'), -] - -osdependencies = [OS_PKG_OPENSSL_DEV] - -# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) -cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0'] - -# replace hardcoded CUDA compute capabilitites in liquidSVM -local_cuda_cc = [c.replace('.', '') for c in cuda_compute_capabilities] -local_cuda_arch = "-arch sm_%s" % local_cuda_cc[0] -local_cuda_gencode = ' '.join(['-gencode=arch=compute_%s,code=sm_%s' % (c, c) for c in local_cuda_cc]) -local_liquidSVM_sed = "sed -i 's/-arch sm_30/%s %s/' src/Makevars.in" % (local_cuda_arch, local_cuda_gencode) - -configopts = "--with-pic --enable-threads --enable-R-shlib" -# some recommended packages may fail in a parallel build (e.g. Matrix), and -# we're installing them anyway below -configopts += " --with-recommended-packages=no" - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -# !! order of packages is important !! -# packages updated on 23 July 2020 -exts_list = [ - # include packages that are part of the base installation of R, - # both to make sure they are available (via sanity check), - # and to be able to pass the check for required dependencies when installing extensions in parallel - 'base', - 'compiler', - 'datasets', - 'graphics', - 'grDevices', - 'grid', - 'methods', - 'parallel', - 'splines', - 'stats', - 'stats4', - 'tcltk', - 'tools', - 'utils', - ('Rmpi', '0.6-9', { - 'checksums': ['b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6'], - }), - ('abind', '1.4-5', { - 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], - }), - ('magic', '1.5-9', { - 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], - 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}), - ('tweedie', '2.3.2', { - 'checksums': ['9a6226e64e3d56eb7eb2a408f8b825c2ad6ee0ea203a9220e85e7789514adb81'], - }), - ('RcppGSL', '0.3.7', { - 'checksums': ['45e95c4170fc8421ae9b32134b3a402f76ea9657030969723a3563c7ce14dc32'], - }), - ('mvabund', '4.1.3', { - 'checksums': ['4b98049026fcc5a262163f6801d5b98b8543267cf7b0edac8382d5311b81a8fc'], - }), - ('fishMod', '0.29', { - 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], - }), - ('gllvm', '1.2.1', { - 'checksums': ['a9dca68227a8f89c61950f6411de3b988e6e067d97fadc589f69ddd731c2e1ff'], - }), - ('grpreg', '3.2.2', { - 'checksums': ['e59f576ee5d794444917e0fbdab0d1ebf4aa71967c9a35ec196899ed5b168388'], - }), - ('trust', '0.1-8', { - 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], - }), - ('ergm', '3.10.4', { - 'checksums': ['885f0b1a23c5a2c1947962350cfab66683dfdfd1db173c115e90396d00831f22'], - }), - ('networkDynamic', '0.10.1', { - 'checksums': ['22eed8d9dea8d70877c1619eb2bc3f1ac5142ce3db6fd6eb3e0879ca56b76ca0'], - }), - ('tergm', '3.6.1', { - 'checksums': ['21de2eca943d89ba63af14951655d626f241bafccc4b2709fa39aa130625cd0f'], - }), - ('ergm.count', '3.4.0', { - 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], - }), - ('tsna', '0.3.1', { - 'checksums': ['bba4b5e04ba647784581a2137f653f60b4c83cfd726c399556054c5a6d2cbd95'], - }), - ('statnet', '2019.6', { - 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], - }), - ('aggregation', '1.0.1', { - 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], - }), - ('ComICS', '1.0.4', { - 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], - }), - ('dtangle', '2.0.9', { - 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], - }), - ('mcmc', '0.9-7', { - 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], - }), - ('MCMCpack', '1.4-6', { - 'checksums': ['6bcd018d6fa589a6854ee1bcea18b9d6c4095f3deae9058f69afbb09cba873c7'], - }), - ('shinythemes', '1.1.2', { - 'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'], - }), - ('csSAM', '1.2.4', { - 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], - }), - ('bridgedist', '0.1.0', { - 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], - }), - ('asnipe', '1.1.12', { - 'checksums': ['3a1f166f1c71b5877a2acca1384ec6c9b430b67af67ef26125f2abbb53c66206'], - }), - ('liquidSVM', '1.2.4', { - 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - 'checksums': [ - '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz - # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch - '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', - ], - # Replace hardcoded CUDA compute capabilities with settings from EB - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC - 'preinstallopts': local_liquidSVM_sed + " && LIQUIDSVM_TARGET='empty'", - }), - ('oddsratio', '2.0.0', { - 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], - }), - ('mltools', '0.3.5', { - 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], - }), - ('h2o', '3.30.0.1', { - 'checksums': ['cb11ef58a7d7dfd3a9193686ddd9c8a9f988b33a69656d8b3e8f59082068b0f5'], - }), - ('mlegp', '3.1.7', { - 'checksums': ['d4845eaf9260f8b8112726dd7ceb5c2f5ce75125fa313191db9de121f2ee15e0'], - }), - ('itertools', '0.1-3', { - 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], - }), - ('missForest', '1.4', { - 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], - }), - ('bartMachineJARs', '1.1', { - 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], - }), - ('bartMachine', '1.2.4.2', { - 'checksums': ['28a5f7363325021bd93f9bd060cc48f20c689dae2f2f6f7100faae66d7651f80'], - }), - ('lqa', '1.0-3', { - 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], - }), - ('PresenceAbsence', '1.1.9', { - 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], - }), - ('GUTS', '1.1.1', { - 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], - }), - ('GenSA', '1.1.7', { - 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], - }), - ('parsedate', '1.2.0', { - 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], - }), - ('circular', '0.4-93', { - 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], - }), - ('cobs', '1.3-4', { - 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], - }), - ('resample', '0.4', { - 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], - }), - ('MIIVsem', '0.5.4', { - 'checksums': ['de918d6b1820c59a7d4324342ad15444c2370ce1d843397a136c307397ed64b9'], - }), - ('medflex', '0.6-6', { - 'checksums': ['b9d04fb5281d0ea0555ec4f327a0ee951a7f312a3af944578dc175183dc49211'], - 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}), - ('SnowballC', '0.7.0', { - 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], - }), - ('tokenizers', '0.2.1', { - 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], - }), - ('hunspell', '3.0', { - 'checksums': ['01fb9c87f7cf094aaad3b7098378134f2e503286224351e91d08c00b6ee19857'], - }), - ('topicmodels', '0.2-11', { - 'checksums': ['9c26b4d967be6ec26834a39f04aa92b059ea9503eb70c700e1c0a7a43637b74a'], - }), - ('tidytext', '0.2.4', { - 'checksums': ['46ff59063b6a519c9eb606ae135ef31d7073ac729e4a912c9f77e234801b933d'], - }), - ('splitstackshape', '1.4.8', { - 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], - }), - ('grImport2', '0.2-0', { - 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], - }), - ('preseqR', version, { - 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], - }), - ('idr', '1.2', { - 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], - 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}), - ('maxnet', '0.1.2', { - 'checksums': ['dfa02ca1031b369415d8b16863ca5fd115c7bf96b1f8fc24f91719b017f5cce5'], - }), - ('ENMeval', '0.3.0', { - 'checksums': ['1c924098a27c82a9bf75408173b47429c40cc41cae3aba18c86ba217bb45ba60'], - }), - ('plotmo', '3.5.7', { - 'checksums': ['aa366a49a63cabfd5d799a1524e23a4faed022f10ee60f8407d70ab70731b38c'], - }), - ('earth', '5.1.2', { - 'checksums': ['326f98e8c29365ca3cd5584cf2bd6529358f5ef81664cbd494162f92b6c3488d'], - }), - ('mda', '0.5-2', { - 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], - }), - ('biomod2', '3.4.6', { - 'checksums': ['41fd7745f4d0af3f799e9cf4fa5484a427de6854db84c6476fde7a7414787d5b'], - }), - ('poLCA', '1.4.1', { - 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], - }), - ('PermAlgo', '1.1', { - 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], - }), - ('coxed', '0.3.3', { - 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], - }), - ('testit', '0.11', { - 'checksums': ['12fb24f0c7b032ae0d146d22161efc676ef4cdf604b81f6345e8d9dfd125388e'], - }), - ('data.tree', '1.0.0', { - 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], - }), - ('NISTunits', '1.0.1', { - 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], - }), - ('celestial', '1.4.6', { - 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], - }), - ('fasterize', '1.0.3', { - 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], - }), - ('RPMM', '1.25', { - 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], - }), - ('RefFreeEWAS', '2.2', { - 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], - }), - ('wordcloud', '2.6', { - 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], - }), - ('JADE', '2.0-3', { - 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], - }), - ('gsl', '2.1-6', { - 'checksums': ['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], - }), - ('awsMethods', '1.1-1', { - 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], - }), - ('aws', '2.4-3', { - 'checksums': ['8582dc7669242eb0e6bee204bdc87ff1c344e2e74912931da47e21279d439531'], - }), - ('ruv', '0.9.7.1', { - 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], - }), - ('mhsmm', '0.4.16', { - 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], - }), - ('dbarts', '0.9-18', { - 'patches': ['dbarts-0.9-18_fix-simd-on-non-x86.patch'], - 'checksums': [ - 'fd99f99d1a24c16596767246618cf240ebd8d86fa82b0e5ce65b737b9afb4ac4', # dbarts_0.9-18.tar.gz - # dbarts-0.9-18_fix-simd-on-non-x86.patch - '80a7e84c691d418da4e90a38db1caebed31d01771e4e7f64d24676ee8d84c104', - ], - }), - ('proftools', '0.99-3', { - 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], - }), - ('NCmisc', '1.1.6', { - 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], - }), - ('reader', '1.0.6', { - 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], - }), - ('gnumeric', '0.7-8', { - 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], - }), - ('tcltk2', '1.2-11', { - 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], - }), - ('readODS', '1.7.0', { - 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], - }), - ('nortest', '1.0-4', { - 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], - }), - ('EnvStats', '2.3.1', { - 'checksums': ['d753d42b42ff28c1cd25c63916fb2aa9e325941672fb16f7dfd97e218416cf2a'], - }), - ('outliers', '0.14', { - 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], - }), - ('elementR', '1.3.7', { - 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], - }), - ('gWidgets2', '1.0-8', { - 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], - }), - ('gWidgets2tcltk', '1.0-6', { - 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... - 'modulename': False, - }), - ('mgsub', '1.7.2', { - 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], - }), - ('ie2misc', '0.8.6', { - 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], - }), - ('assertive.base', '0.0-7', { - 'checksums': ['f02d4eca849f512500abb266a2a751d1fa2cf064f7142e5161a77c20b7f643f7'], - }), - ('assertive.properties', '0.0-4', { - 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], - }), - ('assertive.types', '0.0-3', { - 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], - }), - ('assertive.numbers', '0.0-2', { - 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], - }), - ('assertive.strings', '0.0-3', { - 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], - }), - ('assertive.datetimes', '0.0-3', { - 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], - }), - ('assertive.files', '0.0-2', { - 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], - }), - ('assertive.sets', '0.0-3', { - 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], - }), - ('assertive.matrices', '0.0-2', { - 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], - }), - ('assertive.models', '0.0-2', { - 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], - }), - ('assertive.data', '0.0-3', { - 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], - }), - ('assertive.data.uk', '0.0-2', { - 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], - }), - ('assertive.data.us', '0.0-2', { - 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], - }), - ('assertive.reflection', '0.0-5', { - 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], - }), - ('assertive.code', '0.0-3', { - 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], - }), - ('assertive', '0.3-6', { - 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], - }), - ('rdrop2', '0.8.2.1', { - 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], - }), - ('Exact', '2.1', { - 'checksums': ['088d291339a4d8d9396cdb956889ac571fd9e834c6e3c3d51621a8c3f0eb9f32'], - }), - ('lmom', '2.8', { - 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], - }), - ('gld', '2.6.2', { - 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], - }), - ('DescTools', '0.99.38', { - 'checksums': ['bd8edce64a8f9e295611959295b85cf8d7bbf915093158016169bd334e0e1104'], - }), - ('orthopolynom', '1.0-5', { - 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], - }), - ('gaussquad', '1.0-2', { - 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], - }), - ('nlsem', '0.8', { - 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], - }), - ('mitools', '2.4', { - 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], - }), - ('survey', '4.0', { - 'checksums': ['b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1'], - }), - ('tableone', '0.12.0', { - 'checksums': ['6a5cc16f7d2303c8f42b8adcad0fc41e1ba74f24ada4e7ad3a16effb63d3575e'], - }), - ('jstable', '1.0.1', { - 'checksums': ['2e4cfce264a2353e4655d0faafc93969222d67a21c0c9cc61a2454abd99c5cdc'], - }), - ('RCAL', '2.0', { - 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], - }), - ('stargazer', '5.2.2', { - 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], - }), - ('sensemakr', '0.1.3', { - 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], - }), - ('origami', '1.0.3', { - 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], - }), - ('hal9001', '0.2.7', { - 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], - }), - # Specific packages for GPUs - ('OpenCL', '0.2-1', { - 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], - }), - ('RViennaCL', '1.7.1.8', { - 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-4.0.0_ppc64le-build-fix.patch b/easybuild/easyconfigs/__archive__/r/R/R-4.0.0_ppc64le-build-fix.patch deleted file mode 100644 index 411d54f1108..00000000000 --- a/easybuild/easyconfigs/__archive__/r/R/R-4.0.0_ppc64le-build-fix.patch +++ /dev/null @@ -1,55 +0,0 @@ -R build gets stuck in an infinite loop on ppc64le (https://stat.ethz.ch/pipermail/r-devel/2020-April/079382.html) -Upstream fix: https://github.com/wch/r-source/commit/2159f0296056693da2d25a4fb9d2635f769836c3 -Patch prepared for EasyBuild by Simon Branford, University of Birmingham -diff --git a/src/main/machar.c b/src/main/machar.c -index 8db54f1350f..cede6e6d582 100644 ---- a/src/main/machar.c -+++ b/src/main/machar.c -@@ -98,21 +98,22 @@ MACH_NAME(int *ibeta, int *it, int *irnd, int *ngrd, int *machep, int *negep, - { - volatile DTYPE a, b, beta, betain, betah, one, - t, temp, tempa, temp1, two, y, z, zero; -- int i, itemp, iz, j, k, mx, nxres; -+ int i, iz, j, k, mx, nxres; - - one = 1; - two = one+one; - zero = one-one; - - /* determine ibeta, beta ala malcolm. */ -- -- a = one; -+ a = one; // a = = 9.0072e+15 for 'double' is used later - do { - a = a + a; - temp = a + one; - temp1 = temp - a; - } - while(temp1 - one == zero); -+#ifdef _no_longer___did_overflow_ // on IBM PowerPPC ('Power 8') -+ int itemp; - b = one; - do { - b = b + b; -@@ -121,6 +122,9 @@ MACH_NAME(int *ibeta, int *it, int *irnd, int *ngrd, int *machep, int *negep, - } - while (itemp == 0); - *ibeta = itemp; -+#else -+ *ibeta = (int) FLT_RADIX; -+#endif - beta = *ibeta; - - /* determine it, irnd */ -diff --git a/src/main/platform.c b/src/main/platform.c -index 2cdaeed05a5..ef93c0b0e5f 100644 ---- a/src/main/platform.c -+++ b/src/main/platform.c -@@ -43,6 +43,7 @@ - #include - #include - #include /* toupper */ -+#include // -> FLT_RADIX - #include - #include - #include /* for realpath */ diff --git a/easybuild/easyconfigs/__archive__/r/R/ff-2.2-14.2_aarch64_support.patch b/easybuild/easyconfigs/__archive__/r/R/ff-2.2-14.2_aarch64_support.patch deleted file mode 100644 index 0da84016a4a..00000000000 --- a/easybuild/easyconfigs/__archive__/r/R/ff-2.2-14.2_aarch64_support.patch +++ /dev/null @@ -1,16 +0,0 @@ -# ff does not recognize aarch64 as a valid architecture. -# Patch by Terje Kvernes -# Pushed upstream: https://github.com/truecluster/ff/pull/4 -diff --git a/src/utk_platform_macros.hpp b/src/utk_platform_macros.hpp -index d82ad4f..027b685 100644 ---- a/src/utk_platform_macros.hpp -+++ b/src/utk_platform_macros.hpp -@@ -134,6 +134,8 @@ - #define UTK__Arch_ARM_ARM - #elif defined(__arm__) && defined(__thumb__) - #define UTK__Arch_ARM_THUMB -+ #elif defined(__aarch64__) -+ #define UTK__Aarch_AARCH64 - #elif defined(__sh__) - #define UTK__Arch_SuperH - #else diff --git a/easybuild/easyconfigs/__archive__/r/R/protolite-2.3.0_use-c++17.patch b/easybuild/easyconfigs/__archive__/r/R/protolite-2.3.0_use-c++17.patch deleted file mode 100644 index a73741e3a1e..00000000000 --- a/easybuild/easyconfigs/__archive__/r/R/protolite-2.3.0_use-c++17.patch +++ /dev/null @@ -1,14 +0,0 @@ -make sure that protolite using -std=gnu++17 instead of -std=gnu++14 (default in R 4.2.2) -required to fix compilation problems like: -error: string_view in namespace std does not name a type -author: Kenneth Hoste (HPC-UGent) ---- protolite/configure.orig 2024-01-10 10:50:16.030350785 +0100 -+++ protolite/configure 2024-01-10 10:50:52.847841896 +0100 -@@ -87,6 +87,7 @@ - - # Write to Makevars - sed -e "s|@cflags@|$PKG_CFLAGS|" -e "s|@libs@|$PKG_LIBS|" src/Makevars.in > src/Makevars -+echo 'CXX_STD = CXX17' >> src/Makevars - - # Look for 'protoc' compiler - if [ `command -v protoc` ]; then diff --git a/easybuild/easyconfigs/__archive__/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb deleted file mode 100644 index 7302501b9c3..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: GNU GPLv1 -# -# Notes:: -## - -easyblock = 'MakeCp' - -name = 'RAPSearch2' -version = '2.24' - -homepage = 'https://omics.informatics.indiana.edu/mg/RAPSearch2' -description = """ -RAPSearch stands for Reduced Alphabet based Protein similarity Search -""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'cstd': 'c++11', 'extra_cxxflags': '-D_GLIBCXX_USE_CXX11_ABI=0'} - -source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] -sources = ['%(name)s.%(version_minor)s_64bits.tar.gz'] -checksums = ['85db4573f4c768b6c3c73bb44ff2611ba48dc6c8d188feb40f44bf7c55de36ce'] - -skipsteps = ['configure'] -build_cmd = './install' -maxparallel = 1 - -files_to_copy = ['bin'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ('rapsearch', 'prerapsearch')], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/RAxML/RAxML-8.2.12-gompi-2020a-hybrid-avx2.eb b/easybuild/easyconfigs/__archive__/r/RAxML/RAxML-8.2.12-gompi-2020a-hybrid-avx2.eb deleted file mode 100644 index c863451d483..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RAxML/RAxML-8.2.12-gompi-2020a-hybrid-avx2.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Custom -# -# Notes:: -## - -easyblock = 'MakeCp' - -name = 'RAxML' -version = '8.2.12' -versionsuffix = '-hybrid-avx2' - -homepage = 'https://github.com/stamatak/standard-RAxML' -description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] -sources = ['v%(version)s.zip'] -checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105'] - -buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"' - -files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] - -postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"] - -sanity_check_paths = { - 'files': ['bin/raxmlHPC'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index ce6b1bfcfa8..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,74 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'RDKit' -version = '2020.03.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.rdkit.org' -description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." - -toolchain = {'name': 'foss', 'version': '2020a'} -# avoid failing tests on skylake CPUs. comment out this line when building on CPUs that don't support AVX2 -# see also: https://github.com/rdkit/rdkit/issues/1674 -toolchainopts = {'optarch': 'mavx2', 'cstd': 'c++11'} - -source_urls = ['https://github.com/rdkit/rdkit/archive/'] -sources = ['Release_%s.tar.gz' % version.replace('.', '_')] -patches = [ - '%(name)s-%(version)s_skip_tests.patch', -] -checksums = [ - 'f25529dd80795a499907b90625c4d107ad10211aaf138a07e1a0d8e3426d78c4', # Release_2020_03_3.tar.gz - 'f7c42749c9b198226125c353b934a49340b132e5a03cfbfa0fd344e501f544f7', # RDKit-2020.03.3_skip_tests.patch -] - -# Dependencies varies from version to version -# https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source -builddependencies = [ - ('CMake', '3.16.4'), - ('Eigen', '3.3.7'), - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('SQLite', '3.31.1'), - ('matplotlib', '3.2.1', versionsuffix), - ('Pillow', '7.0.0', versionsuffix), - ('Boost.Python', '1.72.0'), - ('cairo', '1.16.0'), -] - -separate_build_dir = True - -configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " -configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " -configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " -configopts += "-DBoost_NO_BOOST_CMAKE=ON " - -# merge source directory into build directory in order to run the tests -buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' -buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' - -# 'ctest' allows to pass additional arguments opposed to 'make test' -buildopts += 'ctest --output-on-failure' - -local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs', - 'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers', - 'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol', - 'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D', - 'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost', - 'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib', - 'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs', - 'SubstructLibrary', 'SubstructMatch', 'Trajectory'] - -sanity_check_paths = { - 'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs], - 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], -} - -sanity_check_commands = [ - "python -c 'import rdkit.rdBase'", -] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index df38efd4f3b..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,75 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'RDKit' -version = '2020.03.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.rdkit.org' -description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." - -toolchain = {'name': 'intel', 'version': '2020a'} -# avoid failing tests on skylake CPUs. comment out this line when building on CPUs that don't support AVX2 -# see also: https://github.com/rdkit/rdkit/issues/1674 -toolchainopts = {'optarch': 'mavx2', 'cstd': 'c++11'} - -source_urls = ['https://github.com/rdkit/rdkit/archive/'] -sources = ['Release_%s.tar.gz' % version.replace('.', '_')] -patches = [ - '%(name)s-%(version)s_skip_tests.patch', -] -checksums = [ - 'f25529dd80795a499907b90625c4d107ad10211aaf138a07e1a0d8e3426d78c4', # Release_2020_03_3.tar.gz - 'f7c42749c9b198226125c353b934a49340b132e5a03cfbfa0fd344e501f544f7', # RDKit-2020.03.3_skip_tests.patch -] - -# Dependencies varies from version to version -# https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source -builddependencies = [ - ('CMake', '3.16.4'), - ('Eigen', '3.3.7'), - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('SQLite', '3.31.1'), - ('matplotlib', '3.2.1', versionsuffix), - ('Pillow', '7.0.0', versionsuffix), - ('Boost.Python', '1.72.0'), - ('cairo', '1.16.0'), -] - -separate_build_dir = True - -configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " -configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " -configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " -configopts += "-DBoost_NO_BOOST_CMAKE=ON " - -# merge source directory into build directory in order to run the tests -buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' -buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' - -# 'ctest' allows to pass additional arguments opposed to 'make test' -# Exclude RGroup test on intel - https://github.com/rdkit/rdkit/issues/3291 -buildopts += 'ctest --output-on-failure -E RGroup' - -local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs', - 'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers', - 'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol', - 'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D', - 'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost', - 'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib', - 'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs', - 'SubstructLibrary', 'SubstructMatch', 'Trajectory'] - -sanity_check_paths = { - 'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs], - 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], -} - -sanity_check_commands = [ - "python -c 'import rdkit.rdBase'", -] - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/r/RDKit/RDKit-2020.03.3_skip_tests.patch b/easybuild/easyconfigs/__archive__/r/RDKit/RDKit-2020.03.3_skip_tests.patch deleted file mode 100644 index ef3572b0344..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RDKit/RDKit-2020.03.3_skip_tests.patch +++ /dev/null @@ -1,57 +0,0 @@ -Skip failing (*broken*) tests - -Tests are broken and probably never been run on Python until Python 3.8? -Find more about tests on following issues on GitHub: -https://github.com/rdkit/rdkit/issues/3185 -https://github.com/rdkit/rdkit/issues/3278 -https://github.com/rdkit/rdkit/issues/3291 -Author: Pavel Grochal (INUITS) -diff -rub --new-file rdkit-Release_2020_03_3.orig/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py rdkit-Release_2020_03_3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py ---- rdkit-Release_2020_03_3.orig/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py 2020-06-10 05:59:48.000000000 +0200 -+++ rdkit-Release_2020_03_3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py 2020-07-08 13:17:22.320695386 +0200 -@@ -617,6 +617,7 @@ - nTPSA = rdMD.CalcTPSA(mol, force=True, includeSandP=True) - self.assertAlmostEqual(nTPSA, new_tpsa[i], 2) - -+ @unittest.skip("Broken test - skipping") - @unittest.skipIf(not haveBCUT, "BCUT descriptors not present") - def testBCUT(self): - smiles = ("c1ccccc1S", "c1cscc1", "CC(=S)C", "CSC", "CS(=O)C", "CP(C)C", "CP=O", "CP(C)(C)=O", -diff -rub --new-file rdkit-Release_2020_03_3.orig/rdkit/Chem/EnumerateStereoisomers.py rdkit-Release_2020_03_3/rdkit/Chem/EnumerateStereoisomers.py ---- rdkit-Release_2020_03_3.orig/rdkit/Chem/EnumerateStereoisomers.py 2020-06-10 05:59:48.000000000 +0200 -+++ rdkit-Release_2020_03_3/rdkit/Chem/EnumerateStereoisomers.py 2020-07-08 09:35:11.297909322 +0200 -@@ -280,11 +280,12 @@ - - Or randomly sample a small subset: - -- >>> m = Chem.MolFromSmiles('Br' + '[CH](Cl)' * 20 + 'F') -- >>> opts = StereoEnumerationOptions(maxIsomers=3) -- >>> isomers = EnumerateStereoisomers(m, options=opts) -- >>> for smi in sorted(Chem.MolToSmiles(x, isomericSmiles=True) for x in isomers): -- ... print(smi) -+ # This is skipped test below -+ >> m = Chem.MolFromSmiles('Br' + '[CH](Cl)' * 20 + 'F') -+ >> opts = StereoEnumerationOptions(maxIsomers=3) -+ >> isomers = EnumerateStereoisomers(m, options=opts) -+ >> for smi in sorted(Chem.MolToSmiles(x, isomericSmiles=True) for x in isomers): -+ .. print(smi) - F[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)Br - F[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)Br - F[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)Br -@@ -345,5 +346,3 @@ - break - elif verbose: - print("%s failed to embed" % (Chem.MolToSmiles(isomer, isomericSmiles=True))) -- -- -diff -rub --new-file rdkit-Release_2020_03_3.orig/rdkit/Chem/UnitTestMol3D.py rdkit-Release_2020_03_3/rdkit/Chem/UnitTestMol3D.py ---- rdkit-Release_2020_03_3.orig/rdkit/Chem/UnitTestMol3D.py 2020-06-10 05:59:48.000000000 +0200 -+++ rdkit-Release_2020_03_3/rdkit/Chem/UnitTestMol3D.py 2020-07-08 09:35:53.666235177 +0200 -@@ -207,6 +207,7 @@ - smiles = set(Chem.MolToSmiles(i, isomericSmiles=True) for i in AllChem.EnumerateStereoisomers(mol, opts)) - self.assertEqual(len(smiles), 13) - -+ @unittest.skip("Broken test - skipping") - def testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable(self): - mol = Chem.MolFromSmiles('CC(F)=CC(Cl)C=C(Br)C(I)N') - opts = AllChem.StereoEnumerationOptions(maxIsomers=2) diff --git a/easybuild/easyconfigs/__archive__/r/RSeQC/RSeQC-4.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/r/RSeQC/RSeQC-4.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 64e30eb625a..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RSeQC/RSeQC-4.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,47 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Adam Huffman -# The Francis Crick Institute - -easyblock = 'PythonPackage' - -name = 'RSeQC' -version = '4.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://rseqc.sourceforge.net/' -description = """RSeQC provides a number of useful modules that can - comprehensively evaluate high throughput sequence data especially RNA-seq - data. Some basic modules quickly inspect sequence quality, nucleotide - composition bias, PCR bias and GC bias, while RNA-seq specific modules - evaluate sequencing saturation, mapped reads distribution, coverage - uniformity, strand specificity, transcript level RNA integrity etc.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['5b44932bad669c6d9190c5c111d181e868fb40077ed20c16c0881f67fbcc669b'] - -dependencies = [ - ('Python', '3.8.2'), - ('Pysam', '0.16.0.1'), - ('bx-python', '0.8.9', versionsuffix), - ('pyBigWig', '0.3.17'), -] - -fix_python_shebang_for = ['bin/*.py'] - -options = {'modulename': 'qcmodule'} - -sanity_check_paths = { - 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', 'bin/split_paired_bam.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - -sanity_check_commands = [ - 'bam_stat.py --help', - 'overlay_bigwig.py --help', - 'split_bam.py --help', -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.2.1335-fix_env.patch b/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.2.1335-fix_env.patch deleted file mode 100644 index 9f965ed2e9a..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.2.1335-fix_env.patch +++ /dev/null @@ -1,17 +0,0 @@ -commit https://github.com/ComputeCanada/easybuild-easyconfigs/commit/7c6171057562a68086bcb81362f1e997ba4aaeba -Author: @cmd-ntrf -Date: May 4 2019 - -Without this patch, RStudio does not inherits environment variables set before launching it. Since R is provided by a separate module, it means RStudio has no idea where R is nor any other library or executables that were loaded before launching RStudio. - -diff -Nru rstudio-1.2.1335.orig/src/cpp/core/system/PosixSystem.cpp rstudio-1.2.1335/src/cpp/core/system/PosixSystem.cpp ---- rstudio-1.2.1335.orig/src/cpp/core/system/PosixSystem.cpp 2019-03-28 05:08:20.000000000 +0000 -+++ rstudio-1.2.1335/src/cpp/core/system/PosixSystem.cpp 2019-05-04 19:23:19.014327797 +0000 -@@ -2195,6 +2195,7 @@ - - // setup environment - core::system::Options env; -+ core::system::environment(&env); - copyEnvironmentVar("PATH", &env); - copyEnvironmentVar("MANPATH", &env); - copyEnvironmentVar("LANG", &env); diff --git a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb deleted file mode 100644 index 80dfe9052a9..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb +++ /dev/null @@ -1,74 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'RStudio-Server' -version = '1.3.1093' -versionsuffix = '-Java-%(javaver)s-R-%(rver)s' - -homepage = 'https://www.rstudio.com/' -description = """This is the RStudio Server version. -RStudio is a set of integrated tools designed to help you be more productive with R. - -The server can be started with: - rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/rstudio/rstudio/archive'] -sources = ['v%(version)s.tar.gz'] -patches = [ - 'RStudio-Server-1.3.1093_fix-use-of-var.patch', - 'RStudio-Server-1.2.1335-fix_env.patch', -] -checksums = [ - 'af8dc5e71ee934043856938af2e2065d1f1efef08aba37962ed03f6ccb8201bb', # v1.3.1093.tar.gz - '36e22c34d07095522ed570492c047296e782fe3519fdb1dc491bcf820d3aa343', # RStudio-Server-1.3.1093_fix-use-of-var.patch - 'a7b6edab4f5605f5695b5a987f2f1b229e90dbcfcb7a85cc2ea9341e8766941b', # RStudio-Server-1.2.1335-fix_env.patch -] - -builddependencies = [ - ('pkg-config', '0.29.2'), - ('CMake', '3.16.4'), - ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), -] - -dependencies = [ - ('Boost', '1.72.0'), - ('R', '4.0.0'), - ('Java', '11', '', SYSTEM), -] - -osdependencies = [ - ('pam-devel', 'libpam0g-dev') -] - -start_dir = "%(builddir)s/rstudio-%(version)s" -separate_build_dir = False -build_type = "Release" - -preconfigopts = " && ".join([ - "cd %(builddir)s/rstudio-%(version)s/dependencies/common", - "./install-cef", - "./install-dictionaries", - "./install-mathjax", - "./install-pandoc", - "./install-packages", - "cd ../..", - "", # To append && -]) - -configopts = "-DRSTUDIO_TARGET=Server -DRSTUDIO_BOOST_SIGNALS_VERSION=2" - -sanity_check_paths = { - 'files': ["bin/rstudio-server", "bin/rsession", "bin/rserver", "bin/rserver-pam", "bin/rpostback"], - 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], -} - -sanity_check_commands = [ - # This command requires environment variables R_HOME and R_DOC_DIR - "R_HOME=$EBROOTR/lib64/R R_DOC_DIR=$R_HOME/doc rsession --verify-installation=1", - "rserver --verify-installation=1", - "rstudio-server verify-installation", -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.3.1093_fix-use-of-var.patch b/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.3.1093_fix-use-of-var.patch deleted file mode 100644 index 153104111a4..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.3.1093_fix-use-of-var.patch +++ /dev/null @@ -1,26 +0,0 @@ -commit https://github.com/ComputeCanada/easybuild-easyconfigs/commit/77ecdad8fc629078d106fba250951c5c8c22ae52 -Author: @ccoulombe -Date: Nov. 5 2020 - - Patch Rstudio to use /tmp by default for data-dir and pid file -diff -Nru rstudio-1.3.1093.orig/src/cpp/server/ServerOptions.cpp rstudio-1.3.1093/src/cpp/server/ServerOptions.cpp ---- rstudio-1.3.1093.orig/src/cpp/server/ServerOptions.cpp 2021-04-19 12:42:58.217742905 -0400 -+++ rstudio-1.3.1093/src/cpp/server/ServerOptions.cpp 2021-04-19 13:00:06.787497937 -0400 -@@ -214,7 +214,7 @@ - core::system::effectiveUserIsRoot()), - "run program as daemon") - ("server-pid-file", -- value(&serverPidFile_)->default_value("/var/run/rstudio-server.pid"), -+ value(&serverPidFile_)->default_value("/tmp/rstudio-server.pid"), - "location of pid file to write (only in daemon mode)") - ("server-app-armor-enabled", - value(&serverAppArmorEnabled_)->default_value(0), -@@ -226,7 +226,7 @@ - value(&secureCookieKeyFile_)->default_value(""), - "path override for secure cookie key") - ("server-data-dir", -- value(&serverDataDir_)->default_value("/var/run/rstudio-server"), -+ value(&serverDataDir_)->default_value("/tmp/rstudio-server"), - "path to data directory where rstudio server will write run-time state") - ("server-add-header", - value>(&serverAddHeaders_)->default_value(std::vector{})->multitoken(), diff --git a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb deleted file mode 100644 index 2ef5e389064..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'RStudio-Server' -version = '1.3.959' -versionsuffix = '-Java-%(javaver)s-R-%(rver)s' - -homepage = 'https://www.rstudio.com/' -description = """This is the RStudio Server version. -RStudio is a set of integrated tools designed to help you be more productive with R. - -The server can be started with: - rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/rstudio/rstudio/archive'] -sources = ['v%(version)s.tar.gz'] -patches = ['rstudio-%(version)s_fix-rslave.patch'] -checksums = [ - '5c89fe18e3d5ead0e7921c88e5fb42ed816823238e84135f5e9e3a364d35fcc1', # v1.3.959.tar.gz - 'e6ab9c3df3035e502fa855c33cfb6085b11bf65094de469257a76ceb2b5b329a', # rstudio-1.3.959_fix-rslave.patch -] - -builddependencies = [ - ('pkg-config', '0.29.2'), - ('CMake', '3.16.4'), - ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), -] - -dependencies = [ - ('Boost', '1.72.0'), - ('R', '4.0.0'), - ('Java', '11', '', SYSTEM), -] - -osdependencies = [ - ('pam-devel', 'libpam0g-dev') -] - -build_type = "Release" -local_dep_dir = "%(builddir)s/rstudio-%(version)s/dependencies/common" -preconfigopts = ("(cd %s && ./install-dictionaries && " - "./install-pandoc && ./install-mathjax) && ") % local_dep_dir -configopts = "-DRSTUDIO_TARGET=Server -DRSTUDIO_BOOST_SIGNALS_VERSION=2" - -sanity_check_paths = { - 'files': ["bin/rstudio-server"], - 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch b/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch deleted file mode 100644 index f57b688b6a5..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch +++ /dev/null @@ -1,46 +0,0 @@ -From 9b7ac4b2952a47568d23f6cbfed4a797798ee161 Mon Sep 17 00:00:00 2001 -From: Kevin Ushey -Date: Fri, 19 Aug 2022 10:01:14 -0700 -Subject: [PATCH] make it possible to control QUARTO_ENABLED from command line - ---- - CMakeGlobals.txt | 26 ++++++++++++++------------ - 1 file changed, 14 insertions(+), 12 deletions(-) - -diff --git a/CMakeGlobals.txt b/CMakeGlobals.txt -index 6dfe1017a9a..cbd8e865672 100644 ---- a/CMakeGlobals.txt -+++ b/CMakeGlobals.txt -@@ -244,18 +244,20 @@ if(LINUX AND EXISTS "/etc/centos-release") - endif() - - # quarto support --if(LINUX AND UNAME_M STREQUAL aarch64) -- # disabled on linux aarch64 -- message(STATUS "quarto does not yet support aarch64 builds of Linux; disabling quarto") -- set(QUARTO_ENABLED FALSE CACHE INTERNAL "") --elseif(IS_CENTOS7) -- # disable quarto on Centos 7 -- message(STATUS "quarto is not supported on Centos7; disabling quarto") -- set(QUARTO_ENABLED FALSE CACHE INTERNAL "") --else() -- # enable by default -- set(QUARTO_ENABLED TRUE CACHE INTERNAL "") -- add_definitions(-DQUARTO_ENABLED) -+if(NOT DEFINED QUARTO_ENABLED) -+ if(LINUX AND UNAME_M STREQUAL aarch64) -+ # disabled on linux aarch64 -+ message(STATUS "quarto does not yet support aarch64 builds of Linux; disabling quarto") -+ set(QUARTO_ENABLED FALSE CACHE INTERNAL "") -+ elseif(IS_CENTOS7) -+ # disable quarto on Centos 7 -+ message(STATUS "quarto is not supported on Centos7; disabling quarto") -+ set(QUARTO_ENABLED FALSE CACHE INTERNAL "") -+ else() -+ # enable by default -+ set(QUARTO_ENABLED TRUE CACHE INTERNAL "") -+ add_definitions(-DQUARTO_ENABLED) -+ endif() - endif() - - # install freedesktop integration files if we are installing into /usr diff --git a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch b/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch deleted file mode 100644 index 25cae4ea6db..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch +++ /dev/null @@ -1,27 +0,0 @@ -Allow to find system SOCI_* libraries - -Add a second `find_library` call which will find the SOCI libraries in default locations if it hasn't been found already in `SOCI_LIBRARY_DIR` -See https://github.com/rstudio/rstudio/pull/11691 - -Author: Alexander Grund (TU Dresden) - -diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt -index d2be417b40..6a42b4614d 100644 ---- a/src/cpp/CMakeLists.txt -+++ b/src/cpp/CMakeLists.txt -@@ -467,12 +467,12 @@ endif() - # find SOCI libraries - if(UNIX) - set(SOCI_LIBRARY_DIR "${RSTUDIO_TOOLS_SOCI}/build/lib") -- if(NOT APPLE AND RSTUDIO_USE_SYSTEM_SOCI) -- set(SOCI_LIBRARY_DIR "/usr/lib") -- endif() - find_library(SOCI_CORE_LIB NAMES "libsoci_core.a" "soci_core" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) -+ find_library(SOCI_CORE_LIB NAMES "libsoci_core.a" "soci_core") - find_library(SOCI_SQLITE_LIB NAMES "libsoci_sqlite3.a" "soci_sqlite3" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) -+ find_library(SOCI_SQLITE_LIB NAMES "libsoci_sqlite3.a" "soci_sqlite3") - find_library(SOCI_POSTGRESQL_LIB NAMES "libsoci_postgresql.a" "soci_postgresql" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) -+ find_library(SOCI_POSTGRESQL_LIB NAMES "libsoci_postgresql.a" "soci_postgresql") - find_library(DL_LIB "dl") - find_library(SQLITE_LIB "sqlite3") - get_filename_component(SQLITE_LIB "${SQLITE_LIB}" REALPATH) diff --git a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch b/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch deleted file mode 100644 index 9df3a006a82..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch +++ /dev/null @@ -1,71 +0,0 @@ -From https://github.com/rstudio/rstudio/pull/11976 - -From c131989e8ecb19733fe274fe7ad8a18d490fdcf9 Mon Sep 17 00:00:00 2001 -From: Jonathan McPherson -Date: Mon, 19 Sep 2022 14:34:18 -0700 -Subject: [PATCH] use XDG_CACHE_HOME for secure cookie key in low privilege - mode - ---- - src/cpp/core/include/core/system/Xdg.hpp | 7 +++++++ - src/cpp/core/system/Xdg.cpp | 15 +++++++++++++++ - src/cpp/server_core/SecureKeyFile.cpp | 2 +- - 3 files changed, 23 insertions(+), 1 deletion(-) - -diff --git a/src/cpp/core/include/core/system/Xdg.hpp b/src/cpp/core/include/core/system/Xdg.hpp -index 71cb2a8d50f..ed848ca2476 100644 ---- a/src/cpp/core/include/core/system/Xdg.hpp -+++ b/src/cpp/core/include/core/system/Xdg.hpp -@@ -66,6 +66,13 @@ FilePath userDataDir(const boost::optional& user = boost::none, - // Returns the user-specific logging directory underneath the userDataDir - FilePath userLogDir(); - -+// Returns the RStudio XDG user cache directory. -+// -+// On Unix-alikes, this is ~/.cache, or XDG_CACHE_HOME. -+// On Windows, this is 'FOLDERID_InternetCache' (typically 'AppData/Local/Microsoft/Windows/Temporary Files') -+FilePath userCacheDir(const boost::optional& user = boost::none, -+ const boost::optional& homeDir = boost::none); -+ - // This function verifies that the userConfigDir() and userDataDir() exist and are owned by the running user. - // - // It should be invoked once. Any issues with these directories will be emitted to the session log. -diff --git a/src/cpp/core/system/Xdg.cpp b/src/cpp/core/system/Xdg.cpp -index 3866f286437..ca1e7923ac5 100644 ---- a/src/cpp/core/system/Xdg.cpp -+++ b/src/cpp/core/system/Xdg.cpp -@@ -218,6 +218,21 @@ FilePath userDataDir( - ); - } - -+FilePath userCacheDir( -+ const boost::optional& user, -+ const boost::optional& homeDir) -+{ -+ return resolveXdgDir("RSTUDIO_CACHE_HOME", -+ "XDG_CACHE_HOME", -+#ifdef _WIN32 -+ FOLDERID_InternetCache, -+#endif -+ "~/.cache", -+ user, -+ homeDir -+ ); -+} -+ - FilePath userLogDir() - { - return userDataDir().completePath("log"); -diff --git a/src/cpp/server_core/SecureKeyFile.cpp b/src/cpp/server_core/SecureKeyFile.cpp -index d3a5e37c1bd..cbc3a91a44c 100644 ---- a/src/cpp/server_core/SecureKeyFile.cpp -+++ b/src/cpp/server_core/SecureKeyFile.cpp -@@ -113,7 +113,7 @@ core::Error readSecureKeyFile(const std::string& filename, - } - else - { -- secureKeyPath = core::FilePath("/tmp/rstudio-server").completePath(filename); -+ secureKeyPath = core::system::xdg::userCacheDir().completePath(filename); - if (secureKeyPath.exists()) - { - LOG_INFO_MESSAGE("Running without privilege; using secure key at " + secureKeyPath.getAbsolutePath()); diff --git a/easybuild/easyconfigs/__archive__/r/RStudio-Server/rstudio-1.3.959_fix-rslave.patch b/easybuild/easyconfigs/__archive__/r/RStudio-Server/rstudio-1.3.959_fix-rslave.patch deleted file mode 100644 index a85c9e1aa78..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RStudio-Server/rstudio-1.3.959_fix-rslave.patch +++ /dev/null @@ -1,32 +0,0 @@ -commit 3fb2397c2f208bb8ace0bbaf269481ccb96b5b20 -Author: Kevin Ushey -Date: Wed Apr 1 10:43:13 2020 -0700 - - R_Slave -> R_NoEcho for non-Windows - -diff --git a/src/cpp/r/session/REmbeddedPosix.cpp b/src/cpp/r/session/REmbeddedPosix.cpp -index dc8ea49b16..3ec265cb4d 100644 ---- a/src/cpp/r/session/REmbeddedPosix.cpp -+++ b/src/cpp/r/session/REmbeddedPosix.cpp -@@ -13,6 +13,8 @@ - * - */ - -+#include -+ - #include - - #include -@@ -104,7 +106,11 @@ void runEmbeddedR(const core::FilePath& /*rHome*/, // ignored on posix - structRstart rp; - Rstart Rp = &rp; - R_DefParams(Rp) ; -- Rp->R_Slave = FALSE ; -+#if R_VERSION < R_Version(4, 0, 0) -+ Rp->R_Slave = FALSE; -+#else -+ Rp->R_NoEcho = FALSE; -+#endif - Rp->R_Quiet = quiet ? TRUE : FALSE; - Rp->R_Interactive = TRUE ; - Rp->SaveAction = defaultSaveAction ; diff --git a/easybuild/easyconfigs/__archive__/r/Racon/Racon-1.4.13-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/r/Racon/Racon-1.4.13-GCCcore-9.3.0.eb deleted file mode 100644 index 37a280d605a..00000000000 --- a/easybuild/easyconfigs/__archive__/r/Racon/Racon-1.4.13-GCCcore-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Racon' -version = '1.4.13' - -homepage = 'https://github.com/lbcb-sci/racon' -description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/lbcb-sci/racon/releases/download/%(version)s/'] -sources = ['%(namelower)s-v%(version)s.tar.gz'] -checksums = ['4220e98bf84768483bd94eef62a0821cffc74f4e7139c74685c08161909263b0'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ['bin/racon'], - 'dirs': [], -} - -sanity_check_commands = ['racon --help'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/RapidJSON/RapidJSON-1.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/r/RapidJSON/RapidJSON-1.1.0-GCCcore-9.3.0.eb deleted file mode 100644 index 187b4f5e6b6..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RapidJSON/RapidJSON-1.1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'RapidJSON' -version = '1.1.0' - -homepage = 'https://rapidjson.org' -description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix-compiler-errors.patch'] -checksums = [ - 'bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e', # v1.1.0.tar.gz - # %(name)s-%(version_major_minor)s.0_fix-compiler-errors.patch - '2e40ef6c46bf355feac16cd84faad5b7aca0ad54273117b85534b1b781f411c7', -] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -# strip out hardcoded use of -march=native, EasyBuild should be in control of this -preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " - -sanity_check_paths = { - 'files': ['lib/pkgconfig/%(name)s.pc'], - 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/r/RnBeads/RnBeads-2.6.0-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/r/RnBeads/RnBeads-2.6.0-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 8d54608b3cf..00000000000 --- a/easybuild/easyconfigs/__archive__/r/RnBeads/RnBeads-2.6.0-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -easyblock = 'Bundle' - -name = 'RnBeads' -version = '2.6.0' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://rnbeads.org' -description = """RnBeads is an R package for comprehensive analysis of DNA methylation data obtained with any -experimental protocol that provides single-CpG resolution.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('R', '4.0.0'), - ('R-bundle-Bioconductor', '3.11', versionsuffix), - ('Ghostscript', '9.52'), - ('Zip', '3.0'), -] - -exts_default_options = { - 'source_urls': [ - 'https://bioconductor.org/packages/3.11/bioc/src/contrib/', - 'https://bioconductor.org/packages/3.11/bioc/src/contrib/Archive/%(name)s', - 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/', - 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/', - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz' -} - -exts_defaultclass = 'RPackage' - -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -exts_list = [ - ('RnBeads', '2.6.0', { - 'checksums': ['5c7f1f3f3a6ecf3efc199723950f02d6ffb8460e2bc3e964266c5bdb1b369186'], - }), - ('RnBeads.hg19', '1.20.0', { - 'checksums': ['8fbda7e67661994791d8986f8d54cd3ae7495299dfe56fd2069396cdaa75e089'], - }), - ('RnBeads.mm10', '1.20.0', { - 'checksums': ['7aeff709a3669476240727a36da0cb21c138729ee41d3188527c74c9fc2dc0f2'], - }), - ('RnBeads.hg38', '1.20.0', { - 'checksums': ['7e3d625b98876a49ecd31406a73feeaebd1b0fb9fb3b6fd371a5962aaca3e8a2'], - }), -] - -modextrapaths = {'R_LIBS_SITE': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/Roary/Roary-3.13.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/r/Roary/Roary-3.13.0-foss-2020a.eb deleted file mode 100644 index 027bd1b0661..00000000000 --- a/easybuild/easyconfigs/__archive__/r/Roary/Roary-3.13.0-foss-2020a.eb +++ /dev/null @@ -1,48 +0,0 @@ -easyblock = 'Tarball' - -name = 'Roary' -version = '3.13.0' - -homepage = 'https://github.com/sanger-pathogens/Roary' -description = "Rapid large-scale prokaryote pan genome analysis" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/sanger-pathogens/Roary/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['Roary-3.13.0_fix-CD-HIT-regexp.patch'] -checksums = [ - '375f83c8750b0f4dea5b676471e73e94f3710bc3a327ec88b59f25eae1c3a1e8', # v3.13.0.tar.gz - '28b4176ebf20c7bc6f38fdf1cf7e71cae8bd823297543f93fbc28a0c1c3cf791', # Roary-3.13.0_fix-CD-HIT-regexp.patch -] - -dependencies = [ - ('Perl', '5.30.2'), - ('CD-HIT', '4.8.1'), - ('BLAST+', '2.10.1'), - ('MCL', '14.137'), - ('BEDTools', '2.29.2'), - ('PRANK', '170427'), - ('parallel', '20200522'), - ('FastTree', '2.1.11'), - ('Kraken', '1.1.1'), - ('BioPerl', '1.7.7'), - ('R', '4.0.0'), -] - -sanity_check_paths = { - 'files': ['bin/roary', 'lib/Bio/Roary.pm'], - 'dirs': ['lib/Bio/Roary'], -} - -modextrapaths = {'PERL5LIB': 'lib'} - -sanity_check_commands = [ - "perldoc -lm Bio::Roary", - "roary -a", - # make sure all (optional) dependencies are found - # grep exits with '1' if no matches are found, hence we need to test the exit code ($?) - "roary -a 2>&1 | grep 'not found'; test $? -eq 1", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/r/Ruby/Ruby-2.7.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/r/Ruby/Ruby-2.7.2-GCCcore-9.3.0.eb deleted file mode 100644 index de1202ad0e0..00000000000 --- a/easybuild/easyconfigs/__archive__/r/Ruby/Ruby-2.7.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,161 +0,0 @@ -name = 'Ruby' -version = '2.7.2' - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6e5706d0d4ee4e1e2f883db9d768586b4d06567debea353c796ec45e8321c3d4'] - -builddependencies = [('binutils', '2.34')] - -exts_default_options = { - 'source_urls': ['https://rubygems.org/downloads/'], - 'source_tmpl': '%(name)s-%(version)s.gem', -} - -# !! order of packages is important !! -# some packages have dependencies with minimum and maximum version requirements -# each version is picked as high as possible to fullfill all requirements -# packages updated on 12 Oct 2020 -exts_list = [ - ('ffi', '1.13.1', { - 'checksums': ['4e15f52ee45af7c5674d656041855448adbb5022618be252cd602d81b8e2978a'], - }), - ('childprocess', '4.0.0', { - 'checksums': ['72bc4c3e63b88d29e5faebb981e809562ba643c1939b46b465294447451b0d22'], - }), - ('json', '2.3.1', { - 'checksums': ['3f9ebb42fcd46ec3ecad16c89c7b174dc539bdd353610c39c15aecca1d570e95'], - }), - ('cabin', '0.9.0', { - 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], - }), - ('backports', '3.18.2', { - 'checksums': ['691c8f82907bbb4f0f72958c2b80385a73fa5345822ba4e8e7faab3fdd311387'], - }), - ('arr-pm', '0.0.10', { - 'checksums': ['0fa2d425a84eeeaf8f95268568e826723b41aeefa14511d1f0ed1368c30bdd1f'], - }), - ('clamp', '1.3.2', { - 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], - }), - ('multipart-post', '2.1.1', { - 'checksums': ['d2dd7aa957650e0d99e0513cd388401b069f09528441b87d884609c8e94ffcfd'], - }), - ('faraday', '1.0.1', { - 'checksums': ['381aee04fcc9effbe5fa7cc703d8f5f20293722f987ded4f958f77514cd29373'], - }), - ('faraday_middleware', '1.0.0', { - 'checksums': ['19e808539681bbf2e65df30dfbe27bb402bde916a1dceb4c7496dbe8de14334a'], - }), - ('highline', '2.0.3', { - 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], - }), - ('net-http-pipeline', '1.0.1', { - 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], - }), - ('connection_pool', '2.2.3', { - 'checksums': ['8e5bf44b6bfa96f5c94a5c30ae2447fce3dbcc0828a855a6c513fdb015a133e2'], - }), - ('net-http-persistent', '2.9.4', { - 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], - }), - ('multi_json', '1.15.0', { - 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], - }), - ('public_suffix', '4.0.6', { - 'checksums': ['a99967c7b2d1d2eb00e1142e60de06a1a6471e82af574b330e9af375e87c0cf7'], - }), - ('addressable', '2.7.0', { - 'checksums': ['5e9b62fe1239091ea9b2893cd00ffe1bcbdd9371f4e1d35fac595c98c5856cbb'], - }), - ('concurrent-ruby', '1.1.7', { - 'checksums': ['ff4befc88d522ccb2109596da26309f4b0b041683ca62d3cb903b313e1caddee'], - }), - ('i18n', '1.8.5', { - 'checksums': ['f3bb7c9e89804cde8264b89f47f4746527f7293e7b5e4c74e66a9b70cfe97a94'], - }), - ('minitest', '5.14.2', { - 'checksums': ['9b401338e287c50cd2354353b4b781d3766d863cae413b2a1bf585d237131e9c'], - }), - ('thread_safe', '0.3.6', { - 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], - }), - ('tzinfo', '1.2.7', { - 'checksums': ['3945d8a57c62a59e691d527ae4daaf562d6e07a3c0d032876c6b066e108072c4'], - }), - ('zeitwerk', '2.4.0', { - 'checksums': ['135470596c845bd8073af4774f1095004c9d9c6e90cceaaf23814e732628764b'], - }), - ('activesupport', '5.2.4.4', { - 'checksums': ['8d3ddc9b86431f4e2df3c641c2f534c4c244621e57a7efa4f98e94a38198f636'], - }), - ('gh', '0.18.0', { - 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], - }), - ('launchy', '2.5.0', { - 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], - }), - ('ethon', '0.12.0', { - 'checksums': ['e99d3095e89f82c5a7e63d9261ddf4a21f28ae5d12a9d3abaa6920cce6cbef3d'], - }), - ('typhoeus', '1.4.0', { - 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], - }), - ('websocket', '1.2.8', { - 'checksums': ['1d8155c1cdaab8e8e72587a60e08423c9dd84ee44e4e827358ce3d4c2ccb2138'], - }), - ('pusher-client', '0.6.2', { - 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], - }), - ('diff-lcs', '1.4.4', { - 'checksums': ['bf3a658875f70c1467fe7a3b302b795f074c84b28db6e4a2bd6b1ad6d12a2255'], - }), - ('rspec-support', '3.9.3', { - 'checksums': ['394a0402aa187bb05b830640b8904946d5b5be223b3989a69cae05ef046c5635'], - }), - ('rspec-mocks', '3.9.1', { - 'checksums': ['b9820ed35afbc552b4448ccb98984ffe20e92bff6760dbd60f4fec503d6e75a7'], - }), - ('rspec-expectations', '3.9.2', { - 'checksums': ['6ba5bcf1e21e9e2a29958946a5f5c4443c00f873ab8cde329669f88a8bd8b3af'], - }), - ('rspec-core', '3.9.3', { - 'checksums': ['704f3af166bb8d763199742d94f0be3027c0f26d61a2f2156d99d0444248082d'], - }), - ('rspec', '3.9.0', { - 'checksums': ['90a037a7cc02365d7c112201881839aafbc875a88094423bc8cba778c98bfac3'], - }), - ('rack', '2.2.3', { - 'checksums': ['2638e7eb6689a5725c7e16f30cc4aa4e31694dc3ca30d790952526781bd0bb44'], - }), - ('rack-protection', '2.1.0', { - 'checksums': ['1f523c16e5b32f139c8f6f1e3b3eb53aaa7a69bc79a30f3e80f8a93c89242a95'], - }), - ('tilt', '2.0.10', { - 'checksums': ['9b664f0e9ae2b500cfa00f9c65c34abc6ff1799cf0034a8c0a0412d520fac866'], - }), - ('ruby2_keywords', '0.0.2', { - 'checksums': ['145c91edd2ef4c509403328ed05ae4387a8841b7a3ae93679e71c0fd3860ec9e'], - }), - ('mustermann', '1.1.1', { - 'checksums': ['0a21cfe505869cce9ce17998db5260344e78df81ae857c07a62143fd30299531'], - }), - ('sinatra', '2.1.0', { - 'checksums': ['f323e4446f3e2a132dcaaa134f89caddb29dd88370317f4f32faf5797f1ea535'], - }), - ('rack-test', '1.1.0', { - 'checksums': ['154161f40f162b1c009a655b7b0c5de3a3102cc6d7d2e94b64e1f46ace800866'], - }), - ('bundler', '2.1.4', { - 'checksums': ['50014d21d6712079da4d6464de12bb93c278f87c9200d0b60ba99f32c25af489'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb deleted file mode 100644 index 821af75b032..00000000000 --- a/easybuild/easyconfigs/__archive__/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Rust' -version = '1.42.0' - -homepage = 'https://www.rust-lang.org' -description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, - and guarantees thread safety.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://static.rust-lang.org/dist/'] -sources = ['rustc-%(version)s-src.tar.gz'] -checksums = ['d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('Python', '2.7.18', '-bare'), -] - -configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" - -# Use ./x.py to bootstrap so that options like -j N are correctly passed through -# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy -# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) -build_cmd = "./x.py build" -install_cmd = "./x.py install -j %(parallel)s" - -sanity_check_paths = { - 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], - 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/r/rMATS-turbo/rMATS-turbo-4.1.1_bamtools_as_dependency.patch b/easybuild/easyconfigs/__archive__/r/rMATS-turbo/rMATS-turbo-4.1.1_bamtools_as_dependency.patch deleted file mode 100644 index 94041816293..00000000000 --- a/easybuild/easyconfigs/__archive__/r/rMATS-turbo/rMATS-turbo-4.1.1_bamtools_as_dependency.patch +++ /dev/null @@ -1,36 +0,0 @@ -# author: Denis Kristak -# this patch makes rMATS take bamtools from official dependencies, not from the downloaded folder -diff -ruN rmats-turbo-4.1.1_orig/rMATS_pipeline/setup.py rmats-turbo-4.1.1/rMATS_pipeline/setup.py ---- rmats-turbo-4.1.1_orig/rMATS_pipeline/setup.py 2021-05-27 11:08:08.467275054 +0200 -+++ rmats-turbo-4.1.1/rMATS_pipeline/setup.py 2021-05-28 16:18:06.005617527 +0200 -@@ -4,15 +4,16 @@ - from Cython.Build import cythonize - from Cython.Distutils import build_ext - --bamtools_include = [os.path.abspath('../bamtools/include'),] --bamtools_lib = [os.path.abspath('../bamtools/lib'),] -+bamtools_root = os.environ['EBROOTBAMTOOLS'] -+bamtools_include = bamtools_root + '/include/bamtools' -+bamtools_lib = bamtools_root + '/lib' - source_pattern = 'rmatspipeline/%s.pyx' - - asevent_ext = [ -- Extension('rmats.rmatspipeline', sources=[source_pattern % "rmatspipeline"], -- include_dirs=bamtools_include, -+ Extension('rmatspipeline', sources=[source_pattern % "rmatspipeline"], -+ include_dirs=[bamtools_include,], - libraries=['m','stdc++','bamtools','z'], -- library_dirs=bamtools_lib, -+ library_dirs=[bamtools_lib,], - extra_compile_args = ['-O3', '-funroll-loops', - '-std=c++11', '-fopenmp', - '-D__STDC_CONSTANT_MACROS', -@@ -25,7 +26,7 @@ - ] - - setup( -- name = 'rmats.rmatspipeline', -+ name = 'rmatspipeline', - ext_modules = cythonize(asevent_ext), - cmdclass = {'build_ext': build_ext}, - ) diff --git a/easybuild/easyconfigs/__archive__/r/rMATS-turbo/rMATS-turbo-4.2.0_bamtools_as_dependency.patch b/easybuild/easyconfigs/__archive__/r/rMATS-turbo/rMATS-turbo-4.2.0_bamtools_as_dependency.patch deleted file mode 100644 index a1d613184c2..00000000000 --- a/easybuild/easyconfigs/__archive__/r/rMATS-turbo/rMATS-turbo-4.2.0_bamtools_as_dependency.patch +++ /dev/null @@ -1,37 +0,0 @@ -# author: Denis Kristak -# this patch makes rMATS take bamtools from official dependencies, not from the downloaded folder -# updated for new version by Samuel Moors (Vrije Universiteit Brussel) -diff -ur rmats-turbo-4.2.0.orig/rMATS_pipeline/setup.py rmats-turbo-4.2.0/rMATS_pipeline/setup.py ---- rmats-turbo-4.2.0.orig/rMATS_pipeline/setup.py 2023-10-18 18:33:06.000000000 +0200 -+++ rmats-turbo-4.2.0/rMATS_pipeline/setup.py 2024-01-16 10:59:40.272152202 +0100 -@@ -5,15 +5,16 @@ - from Cython.Build import cythonize - from Cython.Distutils import build_ext - --bamtools_include = [os.path.abspath('../bamtools/include'),] --bamtools_lib = [os.path.abspath('../bamtools/lib'),] -+bamtools_root = os.environ['EBROOTBAMTOOLS'] -+bamtools_include = bamtools_root + '/include/bamtools' -+bamtools_lib = bamtools_root + '/lib' - source_pattern = 'rmatspipeline/%s.pyx' - - asevent_ext = [ -- Extension('rmats.rmatspipeline', sources=[source_pattern % "rmatspipeline"], -- include_dirs=bamtools_include, -+ Extension('rmatspipeline', sources=[source_pattern % "rmatspipeline"], -+ include_dirs=[bamtools_include,], - libraries=['m','stdc++','bamtools','z'], -- library_dirs=bamtools_lib, -+ library_dirs=[bamtools_lib,], - extra_compile_args = ['-O3', '-funroll-loops', - '-std=c++11', '-fopenmp', - '-D__STDC_CONSTANT_MACROS', -@@ -31,7 +32,7 @@ - compiler_directives['legacy_implicit_noexcept'] = True - - setup( -- name = 'rmats.rmatspipeline', -+ name = 'rmatspipeline', - ext_modules = cythonize(asevent_ext, compiler_directives=compiler_directives), - cmdclass = {'build_ext': build_ext}, - ) diff --git a/easybuild/easyconfigs/__archive__/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 366ae381991..00000000000 --- a/easybuild/easyconfigs/__archive__/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,68 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'rasterio' -version = '1.1.7' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/mapbox/rasterio' -description = "Rasterio reads and writes geospatial raster data." - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy - ('matplotlib', '3.2.1', versionsuffix), - ('GDAL', '3.0.4', versionsuffix), -] - -exts_list = [ - ('affine', '2.3.0', { - 'checksums': ['2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102'], - }), - ('attrs', '20.2.0', { - 'modulename': 'attr', - 'checksums': ['26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594'], - }), - ('jmespath', '0.10.0', { - 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], - }), - ('botocore', '1.18.16', { - 'checksums': ['f0616d2c719691b94470307cee8adf89ceb1657b7b6f9aa1bf61f9de5543dbbb'], - }), - ('s3transfer', '0.3.3', { - 'checksums': ['921a37e2aefc64145e7b73d50c71bb4f26f46e4c9f414dc648c6245ff92cf7db'], - }), - ('boto3', '1.15.16', { - 'checksums': ['454a8dfb7b367a058c7967ef6b4e2a192c318f10761769fd1003cf7f2f5a7db9'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('click-plugins', '1.1.1', { - 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], - }), - ('cligj', '0.5.0', { - 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], - }), - ('snuggs', '1.4.7', { - 'checksums': ['501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b'], - }), - (name, version, { - 'checksums': ['8418c024f9bf7350d03855039d2700064532bae33a3c6ee885c8b6c8fc13415a'], - }), -] - -fix_python_shebang_for = ['bin/jp.py', 'bin/rio'] - -sanity_check_paths = { - 'files': ['bin/rio'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "jp.py --help", - "rio --help", -] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index a3037cd8c08..00000000000 --- a/easybuild/easyconfigs/__archive__/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'rasterstats' -version = '0.15.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/perrygeo/python-rasterstats' -description = "rasterstats is a Python module for summarizing geospatial raster datasets based on vector geometries." - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy - ('Shapely', '1.7.1', versionsuffix), - ('Fiona', '1.8.16', versionsuffix), - ('rasterio', '1.1.7', versionsuffix), -] - -exts_list = [ - ('affine', '2.3.0', { - 'checksums': ['2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102'], - }), - ('cligj', '0.5.0', { - 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], - }), - ('simplejson', '3.17.2', { - 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], - }), - (name, version, { - 'checksums': ['d554fbc7e749e5649dfcdbd7ea8e21c7388437bc66ef13fde9ef3662a258b277'], - }), -] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/r/re2c/re2c-1.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/r/re2c/re2c-1.3-GCCcore-9.3.0.eb deleted file mode 100644 index d7ce53e3165..00000000000 --- a/easybuild/easyconfigs/__archive__/r/re2c/re2c-1.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 're2c' -version = '1.3' - -homepage = 'https://re2c.org/' -description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating -fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using -traditional table-driven approach, re2c encodes the generated finite state automata directly in the form -of conditional jumps and comparisons.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] -sources = ['%(name)s-%(version)s.tar.xz'] -checksums = ['f37f25ff760e90088e7d03d1232002c2c2672646d5844fdf8e0d51a5cd75a503'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/re2c'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/r/regionmask/regionmask-0.9.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/r/regionmask/regionmask-0.9.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index a1a8e11ba95..00000000000 --- a/easybuild/easyconfigs/__archive__/r/regionmask/regionmask-0.9.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'regionmask' -version = '0.9.0' -versionsuffix = "-Python-%(pyver)s" - -homepage = 'https://regionmask.readthedocs.io' -description = """regionmask creates masks of geographical regions. It determines to which -geographic region each grid point belongs.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('geopandas', '0.8.1', versionsuffix), - ('rasterio', '1.1.7', versionsuffix), - ('Shapely', '1.7.1', versionsuffix), - ('xarray', '0.16.1', versionsuffix), -] - -exts_list = [ - ('pooch', '1.3.0', { - 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], - }), - (name, version, { - 'checksums': ['8da1b6359756241867c4e967097810ef86b9dff4e06d11ca648fe1d607e9cf14'], - }), -] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/r/rgdal/rgdal-1.4-8-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/r/rgdal/rgdal-1.4-8-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 722634b62a0..00000000000 --- a/easybuild/easyconfigs/__archive__/r/rgdal/rgdal-1.4-8-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -easyblock = 'RPackage' - -name = 'rgdal' -version = '1.4-8' -versionsuffix = '-R-%(rver)s' - -homepage = "http://rgdal.r-forge.r-project.org/" -description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and - access to projection/transformation operations from the 'PROJ.4' library.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['5a0da53aedc9e1fc2ca9e5d04b6711d36c43e17e25d458b0fdf00d575548a6c9'] - -dependencies = [ - ('R', '4.0.0'), - ('GDAL', '3.0.4', '-Python-3.8.2'), -] - -sanity_check_paths = { - 'files': ['rgdal/R/rgdal'], - 'dirs': [], -} - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/r/rgdal/rgdal-1.5-16-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/r/rgdal/rgdal-1.5-16-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 0aabffa5847..00000000000 --- a/easybuild/easyconfigs/__archive__/r/rgdal/rgdal-1.5-16-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -easyblock = 'RPackage' - -name = 'rgdal' -version = '1.5-16' -versionsuffix = '-R-%(rver)s' - -homepage = "https://rgdal.r-forge.r-project.org/" -description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and - access to projection/transformation operations from the 'PROJ.4' library.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['f7c5bfd0ebeda1522456904688f873e5b8f171522a32d2a2a30ebf8e9dd29467'] - -dependencies = [ - ('R', '4.0.0'), - ('GDAL', '3.0.4', '-Python-3.8.2'), -] - -sanity_check_paths = { - 'files': ['rgdal/R/rgdal'], - 'dirs': [], -} - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/r/rgeos/rgeos-0.5-5-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/r/rgeos/rgeos-0.5-5-foss-2020a-R-4.0.0.eb deleted file mode 100644 index a1817cc9a56..00000000000 --- a/easybuild/easyconfigs/__archive__/r/rgeos/rgeos-0.5-5-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'RPackage' - -name = 'rgeos' -version = '0.5-5' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/web/packages/rgeos/' -description = """R interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations - on geometries""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['4baa0dfe6ff76e87ddb67a030fc14fe963d28b518485a4d71058923b2606d420'] - -dependencies = [ - ('R', '4.0.0'), - ('GEOS', '3.8.1', '-Python-3.8.2'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['%(namelower)s'], -} - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/r/rioxarray/rioxarray-0.1.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/r/rioxarray/rioxarray-0.1.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index fbf868d8c1a..00000000000 --- a/easybuild/easyconfigs/__archive__/r/rioxarray/rioxarray-0.1.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'rioxarray' -version = '0.1.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/corteva/rioxarray' -description = "geospatial xarray extension powered by rasterio" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['635bf755beaae9414f5a19cc6dd5bde7a04dfbf38b7a02d152754653f79e4330'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('rasterio', '1.1.7', versionsuffix), - ('pyproj', '2.6.1.post1', versionsuffix), - ('xarray', '0.16.1', versionsuffix), -] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/r/rjags/rjags-4-10-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/r/rjags/rjags-4-10-foss-2020a-R-4.0.0.eb deleted file mode 100644 index e06d1a1f83d..00000000000 --- a/easybuild/easyconfigs/__archive__/r/rjags/rjags-4-10-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'RPackage' - -name = 'rjags' -version = '4-10' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/web/packages/rjags' -description = """The rjags package is an interface to the JAGS library.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/rjags/', -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] - -dependencies = [ - ('R', '4.0.0'), - ('JAGS', '4.3.0'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['rjags'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/r/rnaQUAST/rnaQUAST-2.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/r/rnaQUAST/rnaQUAST-2.2.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 78763f9b2f1..00000000000 --- a/easybuild/easyconfigs/__archive__/r/rnaQUAST/rnaQUAST-2.2.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,65 +0,0 @@ -easyblock = 'Tarball' - -name = 'rnaQUAST' -version = '2.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://cab.spbu.ru/software/rnaquast/' -description = """rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. -In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality -assessment using third-party software.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/ablab/rnaquast/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['117dff9d9c382ba74b7b0ff24bc7b95b9ca6aa701ebf8afd22943aa54e382334'] - -dependencies = [ - ('Python', '3.8.2'), - ('GMAP-GSNAP', '2020-12-17'), - ('Biopython', '1.78', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('BLAST+', '2.10.1'), -] - -postinstallcmds = [ - 'chmod -x %(installdir)s/VERSION' -] - -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - -exts_list = [ - ('joblib', '1.0.0', { - 'checksums': ['7ad866067ac1fdec27d51c8678ea760601b70e32ff1881d4dc8e1171f2b64b24'], - }), - ('simplejson', '3.17.2', { - 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], - }), - ('argh', '0.26.2', { - 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], - }), - ('argcomplete', '1.12.2', { - 'checksums': ['de0e1282330940d52ea92a80fea2e4b9e0da1932aaa570f84d268939d1897b04'], - }), - ('pyfaidx', '0.5.9.2', { - 'checksums': ['73e740eaa45c097a09e543450f88d5ed06c0ece4b6936dad7e71077f67797b74'], - }), - ('gffutils', '0.10.1', { - 'checksums': ['a8fc39006d7aa353147238160640e2210b168f7849cb99896be3fc9441e351cb'], - }), -] - -modextrapaths = { - 'PATH': '', -} - -sanity_check_paths = { - 'files': ['rnaQUAST.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.10-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.10-GCC-9.3.0.eb deleted file mode 100644 index 8d9459be9fa..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.10-GCC-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: MIT -# -# Notes:: -## - -name = 'SAMtools' -version = '1.10' - -homepage = 'https://www.htslib.org/' -description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating alignments in a per-position format.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585'] - -# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. -# The latter is currently provided by XZ. -dependencies = [ - ('ncurses', '6.2'), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('cURL', '7.69.1'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.11-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.11-GCC-9.3.0.eb deleted file mode 100644 index b62fa3d6562..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.11-GCC-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: MIT -# -# Notes:: -## - -name = 'SAMtools' -version = '1.11' - -homepage = 'https://www.htslib.org/' -description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating alignments in a per-position format.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['e283cebd6c1c49f0cf8a3ca4fa56e1d651496b4d2e42f80ab75991a9ece4e5b6'] - -# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. -# The latter is currently provided by XZ. -dependencies = [ - ('ncurses', '6.2'), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('cURL', '7.69.1'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.12-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.12-GCC-9.3.0.eb deleted file mode 100644 index 8afe7bfb7ae..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.12-GCC-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: MIT -# -# Notes:: -## - -name = 'SAMtools' -version = '1.12' - -homepage = 'https://www.htslib.org/' -description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating alignments in a per-position format.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['6da3770563b1c545ca8bdf78cf535e6d1753d6383983c7929245d5dba2902dcb'] - -# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. -# The latter is currently provided by XZ. -dependencies = [ - ('ncurses', '6.2'), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('cURL', '7.69.1'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SBCL/SBCL-2.0.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SBCL/SBCL-2.0.9-GCCcore-9.3.0.eb deleted file mode 100644 index ca40e8a4c42..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SBCL/SBCL-2.0.9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'ConfigureMake' -name = 'SBCL' -version = '2.0.9' - -homepage = 'http://sbcl.sourceforge.net/' -description = """ -Steel Bank Common Lisp (SBCL) is a high performance Common Lisp compiler. It is -open source / free software, with a permissive license. In addition to the -compiler and runtime system for ANSI Common Lisp, it provides an interactive -environment including a debugger, a statistical profiler, a code coverage tool, -and many other extensions.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(namelower)s-%(version)s-source.tar.bz2'] -checksums = ['c4f700350c113fe003ee93a9922146209d6fa50b63c6accc4abf90fb38cb9b9f'] - -builddependencies = [ - ('binutils', '2.34'), - ('CCL', '1.12'), -] - -maxparallel = 1 -skipsteps = ['configure'] -local_prefixarg = '--prefix=%(installdir)s' - -# Build SBCL with Clozure CL -# Using the binary distribution of SBCL to build SBCL is not trivial because -# it needs GLIBC v2.28 -build_cmd = "sh make.sh" -buildopts = "%s --xc-host=ccl" % local_prefixarg - -install_cmd = "sh install.sh" -installopts = local_prefixarg - -sanity_check_paths = { - 'files': ['bin/sbcl'], - 'dirs': ['lib/sbcl'], -} - -sanity_check_commands = ["sbcl --help"] - -modextrapaths = {'SBCL_HOME': 'lib/sbcl'} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb deleted file mode 100644 index 6a312d8ebca..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb +++ /dev/null @@ -1,20 +0,0 @@ -name = 'SCOTCH' -version = '6.0.9' - -homepage = 'https://gforge.inria.fr/projects/scotch/' -description = """Software package and libraries for sequential and parallel graph partitioning, -static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://gforge.inria.fr/frs/download.php/file/38187/'] -sources = ['%(namelower)s_%(version)s.tar.gz'] -checksums = ['622b4143cf01c480bb15708b3651b29c25e4aeb00c8c6447ff196aca2eca5c93'] -threadedmpi = False - -dependencies = [ - ('zlib', '1.2.11'), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.0.9-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.0.9-iimpi-2020a.eb deleted file mode 100644 index c0223a3e754..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.0.9-iimpi-2020a.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'SCOTCH' -version = '6.0.9' - -homepage = 'https://gforge.inria.fr/projects/scotch/' -description = """Software package and libraries for sequential and parallel graph partitioning, -static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://gforge.inria.fr/frs/download.php/file/38187/'] -sources = ['%(namelower)s_%(version)s.tar.gz'] -checksums = ['622b4143cf01c480bb15708b3651b29c25e4aeb00c8c6447ff196aca2eca5c93'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/SCons/SCons-3.0.4_fix-pip-install.patch b/easybuild/easyconfigs/__archive__/s/SCons/SCons-3.0.4_fix-pip-install.patch deleted file mode 100644 index ba45cdf7cd6..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SCons/SCons-3.0.4_fix-pip-install.patch +++ /dev/null @@ -1,36 +0,0 @@ -fix installation with pip by using setuptools.{install,setup} rather than distutils.* -author: Kenneth Hoste (HPC-UGent) -loosely inspired by https://bitbucket.org/scons/scons/pull-requests/113 -cfr. https://github.com/SCons/scons/issues/2769 ---- scons-3.0.4/setup.py.orig 2019-01-23 18:30:57.000000000 +0100 -+++ scons-3.0.4/setup.py 2019-02-27 14:07:50.139560710 +0100 -@@ -27,9 +27,8 @@ - import distutils.command.install_scripts - import distutils.command.install_lib - import distutils.command.install_data --import distutils.command.install --import distutils.core --import distutils -+import setuptools.command.install -+import setuptools - # import setuptools - """ - NOTE: Installed SCons is not importable like usual Python packages. It is -@@ -77,7 +76,7 @@ - is_win32 = 1 - - --_install = distutils.command.install.install -+_install = setuptools.command.install.install - _install_data = distutils.command.install_data.install_data - _install_lib = distutils.command.install_lib.install_lib - _install_scripts = distutils.command.install_scripts.install_scripts -@@ -510,7 +509,7 @@ - 'build_scripts': build_scripts}, - } - --distutils.core.setup(**arguments) -+setuptools.setup(**arguments) - - if Installed: - for i in Installed: diff --git a/easybuild/easyconfigs/__archive__/s/SCons/SCons-3.1.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SCons/SCons-3.1.2-GCCcore-9.3.0.eb deleted file mode 100644 index fd61e70e204..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SCons/SCons-3.1.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'SCons' -version = '3.1.2' - -homepage = 'https://www.scons.org/' -description = "SCons is a software construction tool." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -patches = ['SCons-3.0.4_fix-pip-install.patch'] -checksums = [ - '7801f3f62f654528e272df780be10c0e9337e897650b62ddcee9f39fde13f8fb', # scons-3.1.2.tar.gz - 'c632a50184edbb0dc032943fd717e832577d4ad407eb7743e5331eddb842a69f', # SCons-3.0.4_fix-pip-install.patch -] - -builddependencies = [('binutils', '2.34')] - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -sanity_check_paths = { - 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], - 'dirs': [], -} - -# no Python module to import during sanity check -options = {'modulename': False} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 4f8791fe0f8..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# Updated to v4.3.10 by: -# R.QIAO -# DeepThought, Flinders University - -name = 'SEPP' -version = '4.3.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/smirarab/sepp' -description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic -placement of short reads into reference alignments and trees.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -# https://github.com/smirarab/sepp -github_account = 'smirarab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['24d8d410138563017e6f2f1263d5e34427f5bbddb875b72a036f7c879cef203b'] - -dependencies = [ - ('Python', '3.8.2'), - ('DendroPy', '4.4.0'), -] - -fix_python_shebang_for = ['bin/*.py'] - -local_bin_files = [ - 'run_abundance.py', 'run_sepp.py', 'run_tipp.py', - 'run_tipp_tool.py', 'run_upp.py', 'split_sequences.py' -] - -sanity_check_paths = { - 'files': ['bin/%s' % f for f in local_bin_files], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] -} - -sanity_check_commands = ["%s --help" % f for f in local_bin_files] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020a.eb deleted file mode 100644 index b2121ed7d7d..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2020a.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = "MakeCp" - -name = 'SHAPEIT4' -version = '4.2.0' - -homepage = 'https://odelaneau.github.io/shapeit4/' -description = """ -SHAPEIT4 is a fast and accurate method for estimation of haplotypes -(aka phasing) for SNP array and high coverage sequencing data. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'opt': True, 'cstd': 'c++11'} - -github_account = 'odelaneau' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] -checksums = [ - '329aa920be49b085c96b420d4f42ade7ba92eae8a202ecb2f71ca32a61955588', # v4.2.0.tar.gz - 'c4a5a5d280463a7e39435239284702e0d13feb2eb10f902434874176c884516e', # SHAPEIT4_4.2.0_use_EB_settings.patch -] - -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('Boost', '1.72.0'), - ('HTSlib', '1.10.2'), -] - -buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts ' -buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options ' -buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS" ' - -files_to_copy = [(['bin/shapeit4.2'], 'bin'), 'maps'] - -sanity_check_paths = { - 'files': ["bin/shapeit4.2"], - 'dirs': ['maps'] -} - -sanity_check_commands = ['shapeit4.2 --help'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SICER2/SICER2-1.0.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SICER2/SICER2-1.0.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 2173f807fee..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SICER2/SICER2-1.0.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,26 +0,0 @@ -# This easyconfig was created by the BEAR Software team at the University of Birmingham. -easyblock = 'PythonPackage' - -name = 'SICER2' -version = '1.0.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://zanglab.github.io/SICER2/" -description = """Redesigned and improved ChIP-seq broad peak calling tool SICER""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('BEDTools', '2.29.2'), -] - -sources = [SOURCE_TAR_GZ] -checksums = ['003e0f46fb45717fa6b1c94b2c21416161f5b3a4896fbb335cf2024daf2560dd'] - -options = {'modulename': 'sicer'} - -sanity_check_commands = ['sicer -h'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SIONlib/SIONlib-1.7.6-GCCcore-9.3.0-tools.eb b/easybuild/easyconfigs/__archive__/s/SIONlib/SIONlib-1.7.6-GCCcore-9.3.0-tools.eb deleted file mode 100644 index b3e654f5b31..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SIONlib/SIONlib-1.7.6-GCCcore-9.3.0-tools.eb +++ /dev/null @@ -1,54 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany -# Authors:: Markus Geimer -# Modified 2017 by Andreas Henkel -# License:: 3-clause BSD -## - -easyblock = 'ConfigureMake' - -name = 'SIONlib' -version = '1.7.6' -# Provide a stripped-down version with renamed symbols for tools, -# see description for further details -versionsuffix = '-tools' - -homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' -description = """ - SIONlib is a scalable I/O library for parallel access to task-local files. - The library not only supports writing and reading binary data to or from - several thousands of processors into a single or a small number of physical - files, but also provides global open and close functions to access SIONlib - files in parallel. This package provides a stripped-down installation of - SIONlib for use with performance tools (e.g., Score-P), with renamed symbols - to avoid conflicts when an application using SIONlib itself is linked against - a tool requiring a different SIONlib version. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)sl'] -sources = ['sionlib-%(version)sl.tar.gz'] -checksums = [ - '2c220390ef63d001f8ab02c380087187ea02ad2bfc5956e05ecaa0725a6f9942', # sionlib-1.7.6.tar.gz -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.34'), -] - -configopts = '--disable-cxx --disable-fortran --disable-ompi ' - -# Comment it out if you have Xeon Phi: -configopts += '--disable-mic ' - -sanity_check_paths = { - 'files': ['bin/sionconfig'] + - ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], - 'dirs': [] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/SLEPc/SLEPc-3.12.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SLEPc/SLEPc-3.12.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index cc636474cd6..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SLEPc/SLEPc-3.12.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'SLEPc' -version = '3.12.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://slepc.upv.es/' -description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution - of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for - either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a - partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True, 'openmp': True} - -source_urls = ['https://slepc.upv.es/download/distrib'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['a586ce572a928ed87f04961850992a9b8e741677397cbaa3fb028323eddf4598'] - -dependencies = [ - ('Python', '3.8.2'), - ('PETSc', '3.12.4', versionsuffix), -] - -petsc_arch = 'installed-arch-linux-c-opt' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/SLEPc/SLEPc-3.12.2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SLEPc/SLEPc-3.12.2-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index f5daf576cc5..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SLEPc/SLEPc-3.12.2-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'SLEPc' -version = '3.12.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://slepc.upv.es/' -description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution - of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for - either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a - partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True, 'openmp': True} - -source_urls = ['https://slepc.upv.es/download/distrib'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['a586ce572a928ed87f04961850992a9b8e741677397cbaa3fb028323eddf4598'] - -dependencies = [ - ('Python', '3.8.2'), - ('PETSc', '3.12.4', versionsuffix), -] - -petsc_arch = 'installed-arch-linux-c-opt' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/SLiM/SLiM-3.4-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SLiM/SLiM-3.4-GCC-9.3.0.eb deleted file mode 100644 index a6a6b3b9873..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SLiM/SLiM-3.4-GCC-9.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'SLiM' -version = '3.4' - -homepage = 'https://messerlab.org/slim' -description = """SLiM is an evolutionary simulation framework that combines a powerful engine for population - genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/MesserLab/%(name)s/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['b25a39109e7dbacb847ce4241a59788db645d199eacb607d002295d0a369d798'] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -sanity_check_paths = { - 'files': ['bin/eidos', 'bin/slim'], - 'dirs': [], -} - -sanity_check_commands = [ - "eidos -usage", - "eidos -testEidos", - "slim -usage", - "slim -testSLiM", -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/s/SNPomatic/SNPomatic-1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SNPomatic/SNPomatic-1.0-GCCcore-9.3.0.eb deleted file mode 100644 index df732575a6c..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SNPomatic/SNPomatic-1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'MakeCp' - -name = 'SNPomatic' -version = '1.0' - -homepage = 'https://github.com/magnusmanske/snpomatic' - -description = """ - High throughput sequencing technologies generate large amounts of short reads. - Mapping these to a reference sequence consumes large amounts of processing - time and memory, and read mapping errors can lead to noisy or incorrect - alignments. SNP-o-matic is a fast, memory-efficient, and stringent read - mapping tool offering a variety of analytical output functions, with an - emphasis on genotyping. -""" - -source_urls = ['https://github.com/magnusmanske/snpomatic/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['b90123226e24edfa5c2ca296f9414b5aa005d3da77ad80b5c576adddbb38a094'] - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [('binutils', '2.34')] - -prebuildopts = "" -prebuildopts += "sed -i 's/CXX=g++/CXX:=g++/' Makefile && " -prebuildopts += "sed -i 's/CXXFLAGS=/CXXFLAGS+=/' Makefile && " -prebuildopts += "sed -i 's/LIBS=/LIBS+=/' Makefile && " -prebuildopts += 'make reassemble && make variety && make mapcontigs &&' - -local_executables = ['findknownsnps', 'reassemble', 'variety', 'mapcontigs'] - -files_to_copy = [(local_executables, 'bin')] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_executables], - 'dirs': [], -} - -sanity_check_commands = ['findknownsnps'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SOCI/SOCI-4.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SOCI/SOCI-4.0.1-GCCcore-9.3.0.eb deleted file mode 100644 index dffee229660..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SOCI/SOCI-4.0.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,53 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'SOCI' -version = '4.0.1' - -homepage = 'http://soci.sourceforge.net/' -description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the - regular C++ code, staying entirely within the Standard C++.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/SOCI/soci/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['1979b4084ba644125da29dbfbd132798f7742a56caf5a0edb16756a5dbad0f31'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -dependencies = [ - ('Boost', '1.72.0', '-no_mpi'), - ('SQLite', '3.31.1'), - ('PostgreSQL', '12.4'), -] - -# Matches RStudio (1.4.1101) install options -# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci -configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " -configopts += "-DSOCI_TESTS=OFF " -configopts += "-DSOCI_CXX11=ON " -configopts += "-DSOCI_EMPTY=OFF " -configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' -configopts += "-DBoost_USE_STATIC_LIBS=ON " -configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' -configopts += "-DWITH_BOOST=ON " -configopts += "-DWITH_POSTGRESQL=ON " -configopts += "-DWITH_SQLITE3=ON " -configopts += "-DWITH_DB2=OFF " -configopts += "-DWITH_MYSQL=OFF " -configopts += "-DWITH_ORACLE=OFF " -configopts += "-DWITH_FIREBIRD=OFF " -configopts += "-DWITH_ODBC=OFF " -configopts += "-DBoost_DEBUG=1 " - -_dbs = ['postgresql', 'sqlite3'] - -sanity_check_paths = { - 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in _dbs + ['core']], - 'dirs': ['include/soci/%s' % x for x in _dbs], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SPAdes/SPAdes-3.14.1-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SPAdes/SPAdes-3.14.1-GCC-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 24ec86b9fb0..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SPAdes/SPAdes-3.14.1-GCC-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,48 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# 3.9.0: -# Modified by: -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'CMakeMake' - -name = 'SPAdes' -version = '3.14.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/ablab/spades' -description = "Genome assembler for single-cell and isolates data sets" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['d629b78f7e74c82534ac20f5b3c2eb367f245e6840a67b9ef6a76f6fac5323ca'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34'), -] -dependencies = [ - ('Python', '3.8.2'), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('libreadline', '8.0'), -] - -start_dir = 'src' - -configopts = " -DBoost_NO_BOOST_CMAKE=ON" - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', - 'spades-ionhammer', 'spades-kmercount', 'spades.py']], - 'dirs': [], -} - -sanity_check_commands = [('%(namelower)s.py', '--test')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb deleted file mode 100644 index facc79c8f9b..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -# # -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the -# policy: https://hpcbios.readthedocs.org/en/latest/ -# # - -easyblock = 'ConfigureMake' - -name = 'SQLite' -version = '3.31.1' -local_filename_version = '3310100' - -homepage = 'https://www.sqlite.org/' -description = "SQLite: SQL Database Engine in a C Library" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.%(namelower)s.org/2020/'] -sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] -checksums = ['62284efebc05a76f909c580ffa5c008a7d22a1287285d68b7825a2b6b51949ae'] - -builddependencies = [ - ('binutils', '2.34'), -] -dependencies = [ - ('libreadline', '8.0'), - ('Tcl', '8.6.10'), -] - -# enable additional APIs that provide access to meta-data about tables and queries -# needed for GDAL when it used as a dep for QGIS -buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' - - -sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', - 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -sanity_check_commands = [ - 'sqlite3 --version | grep ^%(version)s', -] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/NCBI-VDB-2.10.8_fix-LD_LIBRARY_PATH.patch b/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/NCBI-VDB-2.10.8_fix-LD_LIBRARY_PATH.patch deleted file mode 100644 index 2c318352d7b..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/NCBI-VDB-2.10.8_fix-LD_LIBRARY_PATH.patch +++ /dev/null @@ -1,25 +0,0 @@ -don't blindly overwrite $LD_LIBRARY_PATH (which breaks ld.gold linker because it requires a sufficiently recent libstdc++.so) -author: Kenneth Hoste (HPC-UGent) -+++ ncbi-vdb-2.10.7/build/ld.linux.exe.sh 2020-06-08 16:42:51.922658824 +0200 -@@ -91,8 +91,7 @@ - done - - # update LD_LIBRARY_PATH -- unset LD_LIBRARY_PATH -- export LD_LIBRARY_PATH="$LDIRS:$XDIRS" -+ export LD_LIBRARY_PATH="$LDIRS:$XDIRS:$LD_LIBRARY_PATH" - - # tack on libraries, finding as we go - for LIB in $LIBS ---- ncbi-vdb-2.10.7/build/ld.linux.dlib.sh.orig 2020-05-22 16:58:49.000000000 +0200 -+++ ncbi-vdb-2.10.7/build/ld.linux.dlib.sh 2020-06-08 16:43:13.663013183 +0200 -@@ -83,8 +83,7 @@ - done - - # update LD_LIBRARY_PATH -- unset LD_LIBRARY_PATH -- export LD_LIBRARY_PATH="$LDIRS:$XDIRS" -+ export LD_LIBRARY_PATH="$LDIRS:$XDIRS:$LD_LIBRARY_PATH" - - # tack on libraries, finding as we go - for LIB in $LIBS diff --git a/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/SRA-Toolkit-2.10.8-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/SRA-Toolkit-2.10.8-gompi-2020a.eb deleted file mode 100644 index 6349cd152a8..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/SRA-Toolkit-2.10.8-gompi-2020a.eb +++ /dev/null @@ -1,104 +0,0 @@ -easyblock = 'Bundle' - -name = 'SRA-Toolkit' -version = '2.10.8' - -homepage = 'https://github.com/ncbi/sra-tools' -description = """The SRA Toolkit, and the source-code SRA System Development - Kit (SDK), will allow you to programmatically access data housed within SRA - and convert it from the SRA format""" -github_account = 'ncbi' - -toolchain = {'name': 'gompi', 'version': '2020a'} - -builddependencies = [ - ('Perl', '5.30.2'), - ('Python', '3.8.2'), -] - -dependencies = [ - ('NGS', '2.10.5'), - ('file', '5.38'), # provides libmagic - ('HDF5', '1.10.6'), - ('libxml2', '2.9.10'), -] - -# Add addtional libraries needed to statically link HDF5 from EB -local_base_preconfig = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl && " - -# Change default build directory and add paths to dependencies in EB -local_base_config = '--build-prefix=%(builddir)s --with-ngs-sdk-prefix=$EBROOTNGS ' -local_base_config += '--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2' -local_vdb_config = local_base_config + ' --with-ngs-java-prefix=$EBROOTNGS/jar/ngs-java.jar' -# SRA-Tools need the source and build directory of NCBI-VDB -local_sra_config = local_base_config + ' --with-ncbi-vdb-sources=%(builddir)s/ncbi-vdb-%(version)s' -local_sra_config += ' --with-ncbi-vdb-build=%(builddir)s/ncbi-vdb ' - -# Replace hardcoded optimization flags with flags from EB -local_base_prebuild = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && " -local_base_prebuild += 'EBFLAGS="$CFLAGS" ' -local_base_preinstall = 'EBFLAGS="$CFLAGS" ' - -# Standalone compilation of utf8proc to ensure that its shared objects are available -local_sra_prebuild = "make -C tools/driver-tool/utf8proc && " -# Add addtional libraries needed to statically link HDF5 from EB -local_sra_prebuild += "sed -i 's/-sm/-sm -lmpi -lsz/' tools/pacbio-load/Makefile && " -# Add additional libraries needed to statically link libxml2 from EB -local_sra_prebuild += "find build/ -name \"ld*.sh\" -exec sed -i 's/-lxml2/-lxml2 -lz -llzma/g' {} + && " -local_sra_prebuild += local_base_prebuild - -default_easyblock = 'ConfigureMake' -default_component_specs = { - 'source_urls': [GITHUB_LOWER_SOURCE], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'start_dir': '%(namelower)s-%(version)s', - 'preconfigopts': local_base_preconfig, - 'preinstallopts': local_base_preinstall, -} - -components = [ - # NCBI-VDB has to be installed as component instead of dependency because SRA-Tools needs its sources - ('NCBI-VDB', version, { - 'patches': ['NCBI-VDB-%(version)s_fix-LD_LIBRARY_PATH.patch'], - 'checksums': [ - '7a593aa22584db9443bb56ac01409707bca01b8f9601fe530dac81b73f1a44df', # NCBI-VDB-2.10.8.tar.gz - # NCBI-VDB-2.10.8_fix-LD_LIBRARY_PATH.patch - 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', - ], - 'configopts': local_vdb_config, - 'prebuildopts': local_base_prebuild, - }), - ('SRA-Tools', version, { - 'patches': ['SRA-Toolkit-%(version)s_fix-LD_LIBRARY_PATH.patch'], - 'checksums': [ - '4adb969a9a998f6a50020f99aa66f6ae27916f7dc83ddf6722fc0fea4a3a4d17', # SRA-Tools-2.10.8.tar.gz - # SRA-Toolkit-2.10.8_fix-LD_LIBRARY_PATH.patch - 'cac8e8db25c25ce2e06c3354b27c31dcad613beda3d76e70074f446dff84e63f', - ], - 'configopts': local_sra_config, - 'prebuildopts': local_sra_prebuild, - }), -] - -local_bin = ['abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', - 'fastq-dump', 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'kget', - 'latf-load', 'magic', 'pacbio-load', 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', - 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', 'sratools', 'srf-load', 'test-sra', 'vdb-config', - 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock', 'vdb-passwd', 'vdb-unlock', - 'vdb-validate'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_bin] + - ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + - [('lib/libncbi-%s.%s' % (x, e), 'lib64/libncbi-%s.%s' % (x, e)) - for x in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], - 'dirs': [] -} - -sanity_check_commands = [ - "abi-dump --help", - "kar --help", - "sra-sort --help", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/SRA-Toolkit-2.10.8_fix-LD_LIBRARY_PATH.patch b/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/SRA-Toolkit-2.10.8_fix-LD_LIBRARY_PATH.patch deleted file mode 100644 index 66d48a74251..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SRA-Toolkit/SRA-Toolkit-2.10.8_fix-LD_LIBRARY_PATH.patch +++ /dev/null @@ -1,33 +0,0 @@ -don't blindly overwrite $LD_LIBRARY_PATH (which breaks ld.gold linker because it requires a sufficiently recent libstdc++.so) -author: Kenneth Hoste (HPC-UGent) ---- sra-tools-2.10.8/build/ld.linux.exe.sh.orig 2020-07-01 18:47:00.699575027 +0200 -+++ sra-tools-2.10.8/build/ld.linux.exe.sh 2020-07-01 18:49:35.803226644 +0200 -@@ -96,8 +96,7 @@ - done - - # update LD_LIBRARY_PATH -- unset LD_LIBRARY_PATH -- export LD_LIBRARY_PATH="$LDIRS:$XDIRS" -+ export LD_LIBRARY_PATH="$LDIRS:$XDIRS:$LD_LIBRARY_PATH" - - # tack on libraries, finding as we go - for LIB in $LIBS ---- sra-tools-2.10.8/build/ld.linux.dlib.sh.orig 2020-07-01 18:48:46.122057124 +0200 -+++ sra-tools-2.10.8/build/ld.linux.dlib.sh 2020-07-01 18:48:57.662328498 +0200 -@@ -83,8 +83,7 @@ - done - - # update LD_LIBRARY_PATH -- unset LD_LIBRARY_PATH -- export LD_LIBRARY_PATH="$LDIRS:$XDIRS" -+ export LD_LIBRARY_PATH="$LDIRS:$XDIRS:$LD_LIBRARY_PATH" - - # tack on libraries, finding as we go - for LIB in $LIBS -@@ -308,4 +307,4 @@ - echo "$MSG" >> $LOGFILE - - "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" --fi -\ No newline at end of file -+fi diff --git a/easybuild/easyconfigs/__archive__/s/SSW/SSW-1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SSW/SSW-1.1-GCCcore-9.3.0.eb deleted file mode 100644 index 29d94fb7c6e..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SSW/SSW-1.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -# Author: Jasper Grimm (UoY) - -easyblock = 'MakeCp' - -name = 'SSW' -version = '1.1' - -homepage = 'https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library' -description = """SSW is a fast implementation of the Smith-Waterman algorithm, which uses the - Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the - instruction level. SSW library provides an API that can be flexibly used by programs written in - C, C++ and other languages. We also provide a software that can do protein and genome alignment - directly. Current version of our implementation is ~50 times faster than an ordinary - Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path - (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and - location heuristically. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/archive'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-1.1_build-cpp-lib.patch'] -checksums = [ - 'cdbc20740daeb188ed39413ea5ff9ae4cf72c4d7ccff1d2de2cac0446d64d99f', # v1.1.tar.gz - 'fe0d1f536ecd526dda8879b2f41b62c3c82b39d236f023ee735c1c18d584f06a', # SSW-1.1_build-cpp-lib.patch -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('zlib', '1.2.11')] - -start_dir = 'src' - -buildopts = 'default' - -files_to_copy = [ - (['ssw_test'], 'bin'), - (['*.%s*' % SHLIB_EXT], 'lib'), - (['*.h'], 'include/ssw'), -] - -sanity_check_paths = { - 'files': ['bin/ssw_test', 'lib/libssw.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.5.3a-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.5.3a-GCC-9.3.0.eb deleted file mode 100644 index 6ef843cdfef..00000000000 --- a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.5.3a-GCC-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# Modified by: -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'MakeCp' - -name = 'STAR' -version = '2.5.3a' - -homepage = 'https://github.com/alexdobin/STAR' -description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/alexdobin/STAR/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['2a258e77cda103aa293e528f8597f25dc760cba188d0a7bc7c9452f4698e7c04'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -start_dir = 'source' - -buildopts = ' STAR && make STARlong' - -maxparallel = 1 - -files_to_copy = [ - (['source/STAR', 'source/STARlong'], 'bin'), - 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', -] - -sanity_check_paths = { - 'files': ["bin/STAR", "bin/STARlong"], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.3a-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.3a-GCC-9.3.0.eb deleted file mode 100644 index 1839974f9e4..00000000000 --- a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.3a-GCC-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'MakeCp' - -name = 'STAR' -version = '2.7.3a' - -homepage = 'https://github.com/alexdobin/STAR' -description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/alexdobin/STAR/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['de204175351dc5f5ecc40cf458f224617654bdb8e00df55f0bb03a5727bf26f9'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -start_dir = 'source' - -buildopts = ' STAR && make STARlong' - -maxparallel = 1 - -files_to_copy = [ - (['source/STAR', 'source/STARlong'], 'bin'), - 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', -] - -sanity_check_paths = { - 'files': ['bin/STAR', 'bin/STARlong'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.4a-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.4a-GCC-9.3.0.eb deleted file mode 100644 index edb5d03908f..00000000000 --- a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.4a-GCC-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'MakeCp' - -name = 'STAR' -version = '2.7.4a' - -homepage = 'https://github.com/alexdobin/STAR' -description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/alexdobin/STAR/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['91273b6b2f8305282fea67f88bc39c24516e6e6b01f8293bca63b7375d5f672c'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -start_dir = 'source' - -buildopts = ' STAR && make STARlong' - -maxparallel = 1 - -files_to_copy = [ - (['source/STAR', 'source/STARlong'], 'bin'), - 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', -] - -sanity_check_paths = { - 'files': ['bin/STAR', 'bin/STARlong'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.5b-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.5b-GCC-9.3.0.eb deleted file mode 100644 index a0ad5e5a879..00000000000 --- a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.5b-GCC-9.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: MIT License -# -# Notes:: -## - -easyblock = 'MakeCp' - -name = 'STAR' -version = '2.7.5b' - -homepage = 'https://github.com/alexdobin/STAR' -description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/alexdobin/STAR/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['8d50ad715e1204b69ff155bb97af8358bdfb564879e23654d4edb8ec28e598d0'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -start_dir = 'source' - -buildopts = ' STAR && make STARlong' - -maxparallel = 1 - -files_to_copy = [ - (['source/STAR', 'source/STARlong'], 'bin'), - 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', -] - -sanity_check_paths = { - 'files': ['bin/STAR', 'bin/STARlong'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.6a-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.6a-GCC-9.3.0.eb deleted file mode 100644 index 7a08382e10a..00000000000 --- a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.6a-GCC-9.3.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# Based on STAR-2.7.3a-GCC-8.3.0.eb -# uploaded by J. Sassmannshausen - - -easyblock = 'MakeCp' - -name = 'STAR' -version = '2.7.6a' - -homepage = 'https://github.com/alexdobin/STAR' -description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/alexdobin/STAR/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['9320797c604673debea0fe8f2e3762db364915cc59755de1a0d87c8018f97d51'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -start_dir = 'source' - -buildopts = ' STAR && make STARlong' - -maxparallel = 1 - -files_to_copy = [ - (['source/STAR', 'source/STARlong'], 'bin'), - 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', -] - -sanity_check_paths = { - 'files': ['bin/STAR', 'bin/STARlong'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.7a-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.7a-GCC-9.3.0.eb deleted file mode 100644 index a1405644596..00000000000 --- a/easybuild/easyconfigs/__archive__/s/STAR/STAR-2.7.7a-GCC-9.3.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# Based on STAR-2.7.3a-GCC-8.3.0.eb -# uploaded by J. Sassmannshausen - - -easyblock = 'MakeCp' - -name = 'STAR' -version = '2.7.7a' - -homepage = 'https://github.com/alexdobin/STAR' -description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/alexdobin/STAR/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['a4be87223816f2a34b98ae89470d89caff60ecc8e6d49b5ae6c917b3cadf31bb'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -start_dir = 'source' - -buildopts = ' STAR && make STARlong' - -maxparallel = 1 - -files_to_copy = [ - (['source/STAR', 'source/STARlong'], 'bin'), - 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', -] - -sanity_check_paths = { - 'files': ['bin/STAR', 'bin/STARlong'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/STREAM/STREAM-5.10-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/STREAM/STREAM-5.10-GCC-9.3.0.eb deleted file mode 100644 index eeb11f69171..00000000000 --- a/easybuild/easyconfigs/__archive__/s/STREAM/STREAM-5.10-GCC-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'CmdCp' - -name = 'STREAM' -version = '5.10' - -homepage = 'https://www.cs.virginia.edu/stream/' -description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable - memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] -sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c', 'extract_cmd': "cp %s ."}] -checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] - -# 10 million array elements (1000 runs): requires ~224MB of memory -local_cmds = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " -# 100 million array elements (1000 runs): requires ~2.2GiB of memory -local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " -# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory -local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " -# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory -local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " -# 5 billion array elements (1000 runs): requires ~111 GiB of memory -local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " - -cmds_map = [('stream-%(version)s.c', local_cmds)] - -files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], - 'dirs': [], -} - -tests = ['%(installdir)s/bin/stream_1Kx10M'] - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/s/STREAM/STREAM-5.10-iccifort-2020.1.217.eb b/easybuild/easyconfigs/__archive__/s/STREAM/STREAM-5.10-iccifort-2020.1.217.eb deleted file mode 100644 index 2c192e46653..00000000000 --- a/easybuild/easyconfigs/__archive__/s/STREAM/STREAM-5.10-iccifort-2020.1.217.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'CmdCp' - -name = 'STREAM' -version = '5.10' - -homepage = 'https://www.cs.virginia.edu/stream/' -description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable - memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" - -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -toolchainopts = {'openmp': True} - -source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] -sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c', 'extract_cmd': "cp %s ."}] -checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] - -# 10 million array elements (1000 runs): requires ~224MB of memory -local_cmds = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " -# 100 million array elements (1000 runs): requires ~2.2GiB of memory -local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " -# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory -local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " -# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory -local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " -# 5 billion array elements (1000 runs): requires ~111 GiB of memory -local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " - -cmds_map = [('stream-%(version)s.c', local_cmds)] - -files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], - 'dirs': [], -} - -tests = ['%(installdir)s/bin/stream_1Kx10M'] - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index df977f9ea2b..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,58 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'SUMO' -version = '1.7.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.eclipse.org/sumo/' -description = """Simulation of Urban MObility" (SUMO) is an open source, highly portable, -microscopic and continuous traffic simulation package designed to handle large -networks. It allows for intermodal simulation including pedestrians and comes -with a large set of tools for scenario creation.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/eclipse/sumo/archive/'] -sources = ['v%s.tar.gz' % version.replace('.', '_')] -patches = ['SUMO-1.0.0_fix-link-flags.patch'] -checksums = [ - 'db0868318f2a602475a15ba8b83d30b686e6283b3ff753b9d112217529f2893b', # v1_7_0.tar.gz - 'fe7ef229baeba8a4ea2608f18f531ffbe31da16a274f7383e0d8e30d99e63e87', # SUMO-1.0.0_fix-link-flags.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), - ('SWIG', '4.0.1'), - ('Java', '11', '', SYSTEM), -] - -dependencies = [ - ('Python', '3.8.2'), - ('Xerces-C++', '3.2.3'), - ('FOX-Toolkit', '1.6.57'), - ('GL2PS', '1.4.2'), - ('GDAL', '3.0.4', versionsuffix), - ('PROJ', '7.0.0'), -] - -local_sumo_home = 'share/sumo' -local_pythonpath = 'lib/python%(pyshortver)s/site-packages' -local_bins = ['activitygen', 'dfrouter', 'duarouter', 'emissionsDrivingCycle', 'emissionsMap', 'jtrrouter', - 'marouter', 'netconvert', 'netgenerate', 'od2trips', 'polyconvert', 'sumo', 'sumo-gui'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_bins] + - ['%s/libsumo/_libsumo.%s' % (local_pythonpath, SHLIB_EXT)], - 'dirs': [local_sumo_home, local_pythonpath], -} - -sanity_check_commands = [ - 'sumo --help', - "python -c 'import libsumo'", -] - -modextrapaths = { - 'SUMO_HOME': local_sumo_home, -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/SWAT+/SWAT+-60.4.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SWAT+/SWAT+-60.4.1-GCC-9.3.0.eb deleted file mode 100644 index 54dbf262de0..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SWAT+/SWAT+-60.4.1-GCC-9.3.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'SWAT+' -version = '60.4.1' -local_commit = '0f4dc3e4701d' - -homepage = 'https://swatplus.gitbook.io' -description = """ -The Soil & Water Assessment Tool (SWAT) is a small watershed to river -basin-scale model used to simulate the quality and quantity of surface and -ground water and predict the environmental impact of land use, land management -practices, and climate change. In order to face present and future challenges -in water resources modeling SWAT code has undergone major modifications over -the past few years, resulting in SWAT+, a completely revised version of the -model. SWAT+ provides a more flexible spatial representation of interactions -and processes within a watershed.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://bitbucket.org/blacklandgrasslandmodels/modular_swatplus/get/'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}] -patches = [ - ('SWAT+_add-cmakelists.patch', 0), - 'SWAT+-%(version)s_fix-implicits.patch', -] -checksums = [ - '3c4f9f30ef6b50a5553d9b68074cf88e1a56be98a88a7f25856855996eb3c1a4', # SWAT+-60.4.1.tar.gz - '777be052b815f48b4c448636bb9e4e7bd8a0bc6e4691ddcd0363fc7116d632ae', # SWAT+_add-cmakelists.patch - 'b424232b482b5be96462e036835672696e04e41ea03cca883cd10b5c0aba3b5f', # SWAT+-60.4.1_fix-implicits.patch -] - -builddependencies = [('CMake', '3.16.4')] - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['bin/swatplus'], - 'dirs': ['share/%s' % d for d in ['data', 'database_files', 'documentation', 'example_data_descriptions', - 'modular_database_table', 'revision_notes']], -} - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/s/SWIG/SWIG-4.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SWIG/SWIG-4.0.1-GCCcore-9.3.0.eb deleted file mode 100644 index 406cb6f2d89..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SWIG/SWIG-4.0.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'SWIG' -version = '4.0.1' - -homepage = 'http://www.swig.org/' -description = """SWIG is a software development tool that connects programs written in C and C++ with - a variety of high-level programming languages.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['7a00b4d0d53ad97a14316135e2d702091cd5f193bb58bcfcd8bc59d41e7887a9'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('zlib', '1.2.11'), - ('PCRE', '8.44'), -] - -configopts = '--without-alllang --with-boost=no' - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-1.3.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-1.3.0-gompi-2020a.eb deleted file mode 100644 index 9d600a075dc..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-1.3.0-gompi-2020a.eb +++ /dev/null @@ -1,61 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: GLPv2 -# -# Notes:: -## -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen -# Thanks to people like Simon Brandord, Mikael Oehmann and Kenneth Hoste -# for their help with the ICE - -easyblock = 'CMakeMake' - -name = 'Salmon' -version = '1.3.0' - -homepage = 'https://github.com/COMBINE-lab/salmon' -description = """Salmon is a wicked-fast program to produce a highly-accurate, - transcript-level quantification estimates from RNA-seq data.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True, 'openmp': True} - -github_account = 'COMBINE-lab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['c105be481630d57e7022bf870eb040857834303abff05fe0e971dda5ed6f0236'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('pkg-config', '0.29.2'), - ('jemalloc', '5.2.1'), -] - -dependencies = [ - ('Boost', '1.72.0'), - ('tbb', '2020.1'), -] - -# Disable link-time optimizations (-flto) because it triggers a segfault/internal compiler error (ICE) with GCC 9.3.0 -# This problem might be solved with a newer version of either GCC or Salmon. -configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC -DNO_IPO=1' - -# need to unset the $LD_PRELOAD set be jemalloc to avoid hanging 'make test' -# since jemalloc is statically linked in Salmon (and hence only a build dep), -# this only affects the tests -pretestopts = "unset LD_PRELOAD && " -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'] + ['lib/lib%s.a' % x for x in ['graphdump', 'ntcard', 'salmon_core', 'twopaco']], - 'dirs': [], -} - -sanity_check_commands = ["salmon --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020a.eb b/easybuild/easyconfigs/__archive__/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020a.eb deleted file mode 100644 index 99337960764..00000000000 --- a/easybuild/easyconfigs/__archive__/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ScaFaCoS' -version = '1.0.1' - -homepage = 'http://www.scafacos.de/' -description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = [ - '2b125f313795c81b0e87eb920082e91addf94c17444f9486d979e691aaded99b', # scafacos-1.0.1.tar.gz -] - -builddependencies = [ - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('GMP', '6.2.0'), - ('GSL', '2.6'), -] - -preconfigopts = 'unset F77 && ' - -configopts = '--enable-shared --enable-static --disable-doc ' -# tell it where to find provided FFTW -configopts += '--without-internal-fftw --with-fftw3-includedir=$EBROOTFFTW/include --with-fftw3-libdir=$EBROOTFFTW/lib ' -# only include the solvers supported for LAMMPS -# (for p2nfft we need an additonal dependency) -configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' - -sanity_check_paths = { - 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], - 'dirs': [], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/ScaFaCoS/ScaFaCoS-1.0.1-intel-2020a.eb b/easybuild/easyconfigs/__archive__/s/ScaFaCoS/ScaFaCoS-1.0.1-intel-2020a.eb deleted file mode 100644 index 5dd1d679921..00000000000 --- a/easybuild/easyconfigs/__archive__/s/ScaFaCoS/ScaFaCoS-1.0.1-intel-2020a.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ScaFaCoS' -version = '1.0.1' - -homepage = 'http://www.scafacos.de/' -description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = [ - '2b125f313795c81b0e87eb920082e91addf94c17444f9486d979e691aaded99b', # scafacos-1.0.1.tar.gz -] - -builddependencies = [ - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('GMP', '6.2.0'), - ('GSL', '2.6'), - ('FFTW', '3.3.8'), -] - -preconfigopts = 'unset F77 && ' - -configopts = '--enable-shared --enable-static --disable-doc ' -# tell it where to find provided FFTW -configopts += '--without-internal-fftw --with-fftw3-includedir=$EBROOTFFTW/include --with-fftw3-libdir=$EBROOTFFTW/lib ' -# only include the solvers supported for LAMMPS -# (for p2nfft we need an additonal dependency) -configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' - -sanity_check_paths = { - 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], - 'dirs': [], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb deleted file mode 100644 index 17c53d6a060..00000000000 --- a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'ScaLAPACK' -version = '2.1.0' -versionsuffix = '-bf' - -homepage = 'https://www.netlib.org/scalapack/' -description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines - redesigned for distributed memory MIMD parallel computers.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} - -source_urls = [homepage] -sources = [SOURCELOWER_TGZ] -checksums = ['61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6'] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('BLIS', '0.8.0'), - ('libFLAME', '5.2.0'), -] - -# Config Opts based on AOCL User Guide: -# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf - -configopts = '-DBUILD_SHARED_LIBS=ON ' -configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' -configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' - -sanity_check_paths = { - 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], - 'dirs': ["lib", "lib64"], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a.eb deleted file mode 100644 index 5ed0ad1f454..00000000000 --- a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'ScaLAPACK' -version = '2.1.0' - -homepage = 'https://www.netlib.org/scalapack/' -description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines - redesigned for distributed memory MIMD parallel computers.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = [SOURCELOWER_TGZ] -checksums = ['61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6'] - -dependencies = [('OpenBLAS', '0.3.9')] - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020a.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020a.eb deleted file mode 100644 index 2ce571f666f..00000000000 --- a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020a.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'ScaLAPACK' -version = '2.1.0' - -homepage = 'https://www.netlib.org/scalapack/' -description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines - redesigned for distributed memory MIMD parallel computers.""" - -toolchain = {'name': 'gompic', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = [SOURCELOWER_TGZ] -checksums = ['61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6'] - -dependencies = [('OpenBLAS', '0.3.9')] - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.2-gompi-2020a-amd.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.2-gompi-2020a-amd.eb deleted file mode 100644 index 4176455a27a..00000000000 --- a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.2-gompi-2020a-amd.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'ScaLAPACK' -version = '2.2' -versionsuffix = '-amd' - -homepage = 'https://www.netlib.org/scalapack/' -description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines -redesigned for distributed memory MIMD parallel computers.""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True} - -# https://github.com/amd/scalapack/archive/2.2.tar.gz -source_urls = ['https://github.com/amd/scalapack/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['2d64926864fc6d12157b86e3f88eb1a5205e7fc157bf67e7577d0f18b9a7484c'] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('BLIS', '2.2', versionsuffix), - ('libFLAME', '2.2', versionsuffix), -] - -# Config Opts based on AOCL User Guide: -# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf - -configopts = '-DBUILD_SHARED_LIBS=ON ' -configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis-mt.a" ' -configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DUSE_OPTIMIZED_LAPACK_BLAS=ON ' -configopts += '-DUSE_F2C=ON ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' - -sanity_check_paths = { - 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], - 'dirs': ["lib", "lib64"], -} - - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-2.5-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-2.5-gompi-2020a.eb deleted file mode 100644 index 0c70213a945..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-2.5-gompi-2020a.eb +++ /dev/null @@ -1,53 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany -# Authors:: Bernd Mohr -# Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_Score_minus_P' - -name = 'Scalasca' -version = '2.5' - -homepage = 'https://www.scalasca.org/' -description = """ - Scalasca is a software tool that supports the performance optimization of - parallel programs by measuring and analyzing their runtime behavior. The - analysis identifies potential performance bottlenecks -- in particular - those concerning communication and synchronization -- and offers guidance - in exploring their causes. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] -sources = [SOURCELOWER_TAR_GZ] -checksums = [ - '7dfa01e383bfb8a4fd3771c9ea98ff43772e415009d9f3c5f63b9e05f2dde0f6', # scalasca-2.5.tar.gz -] - -builddependencies = [ - ('CubeWriter', '4.4.3'), -] - -dependencies = [ - ('CubeGUI', '4.4.4'), - ('CubeLib', '4.4.4'), - ('OTF2', '2.2'), - ('Score-P', '6.0'), -] - -sanity_check_paths = { - 'files': ['bin/scalasca', 'lib/libpearl.replay.a'], - 'dirs': [], -} - -# Ensure that local metric documentation is found by CubeGUI -modextrapaths = {'CUBE_DOCPATH': 'share/doc/scalasca/patterns'} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-foss-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-foss-2020a-Python-2.7.18.eb deleted file mode 100644 index 3b8f9bd2ac8..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-foss-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'SciPy-bundle' -version = '2020.03' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://python.org/' -description = "Bundle of Python packages for scientific software" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'lowopt': True} - -dependencies = [ - ('Python', '2.7.18'), -] - -# order is important! -exts_list = [ - ('numpy', '1.16.6', { - 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': [ - 'e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff', # numpy-1.16.6.zip - # numpy-1.16.2_relax-long-complex-test.patch - '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb', - ], - }), - ('scipy', '1.2.3', { - 'patches': ['scipy-1.2.3_fix_nan_problem_in_vi.patch'], - 'checksums': [ - 'ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57', # scipy-1.2.3.tar.gz - # scipy-1.2.3_fix_nan_problem_in_vi.patch - '0513c5d0491a3f062ed024b6aa7b382706e8c42b3a3fdd26ff7a4d305ac9a30d', - ], - }), - ('mpi4py', '3.0.3', { - 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], - }), - ('pandas', '0.24.2', { - 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], - }), - ('mpmath', '1.1.0', { - 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], - }), - ('deap', '1.3.1', { - 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index e2a99b7d2ae..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'SciPy-bundle' -version = '2020.03' -versionsuffix = '-Python-3.8.2' - -homepage = 'https://python.org/' -description = "Bundle of Python packages for scientific software" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'lowopt': True} - -dependencies = [ - ('Python', '3.8.2'), - ('pybind11', '2.4.3', versionsuffix), # required by scipy -] - -# order is important! -exts_list = [ - ('numpy', '1.18.3', { - 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': [ - 'e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8', # numpy-1.18.3.zip - # numpy-1.16.2_relax-long-complex-test.patch - '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb', - ], - }), - ('scipy', '1.4.1', { - 'patches': ['scipy-1.4.1-fix-pthread.patch'], - 'checksums': [ - 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz - '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch - ], - }), - ('mpi4py', '3.0.3', { - 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], - }), - ('pandas', '1.0.3', { - 'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'], - }), - ('mpmath', '1.1.0', { - 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], - }), - ('deap', '1.3.1', { - 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-fosscuda-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-fosscuda-2020a-Python-2.7.18.eb deleted file mode 100644 index 784d2c16197..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-fosscuda-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'SciPy-bundle' -version = '2020.03' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://python.org/' -description = "Bundle of Python packages for scientific software" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'pic': True, 'lowopt': True} - -dependencies = [ - ('Python', '2.7.18'), -] - -# order is important! -exts_list = [ - ('numpy', '1.16.6', { - 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': [ - 'e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff', # numpy-1.16.6.zip - # numpy-1.16.2_relax-long-complex-test.patch - '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb', - ], - }), - ('scipy', '1.2.3', { - 'patches': ['scipy-1.2.3_fix_nan_problem_in_vi.patch'], - 'checksums': [ - 'ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57', # scipy-1.2.3.tar.gz - # scipy-1.2.3_fix_nan_problem_in_vi.patch - '0513c5d0491a3f062ed024b6aa7b382706e8c42b3a3fdd26ff7a4d305ac9a30d', - ], - }), - ('mpi4py', '3.0.3', { - 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], - }), - ('pandas', '0.24.2', { - 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], - }), - ('mpmath', '1.1.0', { - 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], - }), - ('deap', '1.3.1', { - 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 6866ab8e876..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'SciPy-bundle' -version = '2020.03' -versionsuffix = '-Python-3.8.2' - -homepage = 'https://python.org/' -description = "Bundle of Python packages for scientific software" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'pic': True, 'lowopt': True} - -dependencies = [ - ('Python', '3.8.2'), - ('pybind11', '2.4.3', versionsuffix), # required by scipy -] - -# order is important! -exts_list = [ - ('numpy', '1.18.3', { - 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': [ - 'e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8', # numpy-1.18.3.zip - # numpy-1.16.2_relax-long-complex-test.patch - '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb', - ], - }), - ('scipy', '1.4.1', { - 'patches': ['scipy-1.4.1-fix-pthread.patch'], - 'checksums': [ - 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz - '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch - ], - }), - ('mpi4py', '3.0.3', { - 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], - }), - ('pandas', '1.0.3', { - 'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'], - }), - ('mpmath', '1.1.0', { - 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], - }), - ('deap', '1.3.1', { - 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-2.7.18.eb deleted file mode 100644 index 4c0efedf416..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'SciPy-bundle' -version = '2020.03' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://python.org/' -description = "Bundle of Python packages for scientific software" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'lowopt': True} - -dependencies = [ - ('Python', '2.7.18'), -] - -# order is important! -exts_list = [ - ('numpy', '1.16.6', { - 'patches': ['numpy-1.12.0-mkl.patch'], - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': [ - 'e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff', # numpy-1.16.6.zip - 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch - ], - }), - ('scipy', '1.2.3', { - 'checksums': ['ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57'], - }), - ('mpi4py', '3.0.3', { - 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], - }), - ('pandas', '0.24.2', { - 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], - }), - ('mpmath', '1.1.0', { - 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], - }), - ('deap', '1.3.1', { - 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 157fa1fe435..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,49 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'SciPy-bundle' -version = '2020.03' -versionsuffix = '-Python-3.8.2' - -homepage = 'https://python.org/' -description = "Bundle of Python packages for scientific software" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'lowopt': True} - -dependencies = [ - ('Python', '3.8.2'), - ('pybind11', '2.4.3', versionsuffix), # required by scipy -] - -# order is important! -exts_list = [ - ('numpy', '1.18.3', { - 'patches': ['numpy-1.18.2-mkl.patch'], - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': [ - 'e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8', # numpy-1.18.2.zip - 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch - ], - }), - ('scipy', '1.4.1', { - 'patches': ['scipy-1.4.1-fix-pthread.patch'], - 'checksums': [ - 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz - '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch - ], - }), - ('mpi4py', '3.0.3', { - 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], - }), - ('pandas', '1.0.3', { - 'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'], - }), - ('mpmath', '1.1.0', { - 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], - }), - ('deap', '1.3.1', { - 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-intelcuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-intelcuda-2020a-Python-3.8.2.eb deleted file mode 100644 index dbca921c3b1..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/SciPy-bundle-2020.03-intelcuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,49 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'SciPy-bundle' -version = '2020.03' -versionsuffix = '-Python-3.8.2' - -homepage = 'https://python.org/' -description = "Bundle of Python packages for scientific software" - -toolchain = {'name': 'intelcuda', 'version': '2020a'} -toolchainopts = {'pic': True, 'lowopt': True} - -dependencies = [ - ('Python', '3.8.2'), - ('pybind11', '2.4.3', versionsuffix), # required by scipy -] - -# order is important! -exts_list = [ - ('numpy', '1.18.3', { - 'patches': ['numpy-1.18.2-mkl.patch'], - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': [ - 'e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8', # numpy-1.18.2.zip - 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch - ], - }), - ('scipy', '1.4.1', { - 'patches': ['scipy-1.4.1-fix-pthread.patch'], - 'checksums': [ - 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz - '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch - ], - }), - ('mpi4py', '3.0.3', { - 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], - }), - ('pandas', '1.0.3', { - 'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'], - }), - ('mpmath', '1.1.0', { - 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], - }), - ('deap', '1.3.1', { - 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/numpy-1.12.0-mkl.patch deleted file mode 100644 index 3d09924f966..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/numpy-1.12.0-mkl.patch +++ /dev/null @@ -1,55 +0,0 @@ -fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries -by Kenneth Hoste (HPC-UGent) -diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py ---- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 -@@ -628,7 +628,10 @@ - return options - - def library_option(self, lib): -- return "-l" + lib -+ if lib[0]=='-': -+ return lib -+ else: -+ return "-l" + lib - def library_dir_option(self, dir): - return "-L" + dir - -diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py ---- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 -@@ -675,7 +675,7 @@ - if is_string(default): - return [default] - return default -- return [b for b in [a.strip() for a in libs.split(',')] if b] -+ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] - - def get_libraries(self, key='libraries'): - if hasattr(self, '_lib_names'): -@@ -756,6 +756,9 @@ - # make sure we preserve the order of libs, as it can be important - found_dirs, found_libs = [], [] - for lib in libs: -+ if lib[0] == '-': -+ found_libs.append(lib) -+ continue - for lib_dir in lib_dirs: - found_lib = self._find_lib(lib_dir, lib, exts) - if found_lib: -diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py ---- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 -+++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 -@@ -123,3 +123,12 @@ - - replace_method(UnixCCompiler, 'create_static_lib', - UnixCCompiler_create_static_lib) -+ -+def UnixCCompiler_library_option(self, lib): -+ if lib[0]=='-': -+ return lib -+ else: -+ return "-l" + lib -+ -+replace_method(UnixCCompiler, 'library_option', -+ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/scipy-1.4.1-fix-pthread.patch b/easybuild/easyconfigs/__archive__/s/SciPy-bundle/scipy-1.4.1-fix-pthread.patch deleted file mode 100644 index d399b2ba412..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SciPy-bundle/scipy-1.4.1-fix-pthread.patch +++ /dev/null @@ -1,39 +0,0 @@ -From https://github.com/scipy/scipy/pull/11324 -Author: Peter Bell -diff --git a/scipy/fft/_pocketfft/setup.py b/scipy/fft/_pocketfft/setup.py -index a4411bdedb1..493387d9719 100644 ---- a/scipy/fft/_pocketfft/setup.py -+++ b/scipy/fft/_pocketfft/setup.py -@@ -5,20 +5,28 @@ def pre_build_hook(build_ext, ext): - cc = build_ext._cxx_compiler - args = ext.extra_compile_args - -- std_flag = get_cxx_std_flag(build_ext._cxx_compiler) -+ std_flag = get_cxx_std_flag(cc) - if std_flag is not None: - args.append(std_flag) - - if cc.compiler_type == 'msvc': - args.append('/EHsc') - else: -- try_add_flag(args, cc, '-fvisibility=hidden') -- -+ # Use pthreads if available - has_pthreads = try_compile(cc, code='#include \n' - 'int main(int argc, char **argv) {}') - if has_pthreads: - ext.define_macros.append(('POCKETFFT_PTHREADS', None)) -- -+ if has_flag(cc, '-pthread'): -+ args.append('-pthread') -+ ext.extra_link_args.append('-pthread') -+ else: -+ raise RuntimeError("Build failed: System has pthreads header " -+ "but could not compile with -pthread option") -+ -+ # Don't export library symbols -+ try_add_flag(args, cc, '-fvisibility=hidden') -+ # Set min macOS version - min_macos_flag = '-mmacosx-version-min=10.9' - import sys - if sys.platform == 'darwin' and has_flag(cc, min_macos_flag): diff --git a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0-gompi-2020a.eb deleted file mode 100644 index 91cbda21537..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0-gompi-2020a.eb +++ /dev/null @@ -1,61 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany -# Authors:: Bernd Mohr -# Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -name = 'Score-P' -version = '6.0' - -homepage = 'https://www.score-p.org' -description = """ - The Score-P measurement infrastructure is a highly scalable and easy-to-use - tool suite for profiling, event tracing, and online analysis of HPC - applications. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://www.vi-hps.org/cms/upload/packages/scorep/'] -sources = ['scorep-%(version)s.tar.gz'] -patches = [ - 'Score-P-6.0_binutils_2.34_api_change.patch', - 'Score-P-6.0_no_PDT_for_CUDA.patch', -] -checksums = [ - '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8', # scorep-6.0.tar.gz - 'c64a3c0b666a75b114e29a48c8d1f5e420be3674a0fba2b37ecd50630ba2d45c', # Score-P-6.0_binutils_2.34_api_change.patch - '93e3fc5d19a89d14ce98fb772b4d9ddde4191df3ce321c9965602aa12d43fa93', # Score-P-6.0_no_PDT_for_CUDA.patch -] - -dependencies = [ - ('CubeLib', '4.4.4'), - ('CubeWriter', '4.4.3'), - # Unwinding/sampling support (optional): - ('libunwind', '1.3.1'), - ('OPARI2', '2.0.5'), - ('OTF2', '2.2'), - # Hardware counter support (optional): - ('PAPI', '6.0.0'), - # PDT source-to-source instrumentation support (optional): - ('PDT', '3.25.1'), -] - -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/scorep', 'include/scorep/SCOREP_User.h', - 'lib/libscorep_adapter_mpi_event.a', - 'lib/libscorep_adapter_mpi_event.%s' % SHLIB_EXT], - 'dirs': [], -} - -# Ensure that local metric documentation is found by CubeGUI -modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0-gompic-2020a.eb b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0-gompic-2020a.eb deleted file mode 100644 index 53b2cfb994f..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0-gompic-2020a.eb +++ /dev/null @@ -1,64 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany -# Authors:: Bernd Mohr -# Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -name = 'Score-P' -version = '6.0' - -homepage = 'https://www.score-p.org' -description = """ - The Score-P measurement infrastructure is a highly scalable and easy-to-use - tool suite for profiling, event tracing, and online analysis of HPC - applications. -""" - -toolchain = {'name': 'gompic', 'version': '2020a'} - -source_urls = ['https://www.vi-hps.org/cms/upload/packages/scorep/'] -sources = ['scorep-%(version)s.tar.gz'] -patches = [ - 'Score-P-6.0_binutils_2.34_api_change.patch', - 'Score-P-6.0_no_PDT_for_CUDA.patch', -] -checksums = [ - '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8', # scorep-6.0.tar.gz - 'c64a3c0b666a75b114e29a48c8d1f5e420be3674a0fba2b37ecd50630ba2d45c', # Score-P-6.0_binutils_2.34_api_change.patch - '93e3fc5d19a89d14ce98fb772b4d9ddde4191df3ce321c9965602aa12d43fa93', # Score-P-6.0_no_PDT_for_CUDA.patch -] - -dependencies = [ - ('CubeLib', '4.4.4'), - ('CubeWriter', '4.4.3'), - # Unwinding/sampling support (optional): - ('libunwind', '1.3.1'), - ('OPARI2', '2.0.5'), - ('OTF2', '2.2'), - # Hardware counter support (optional): - ('PAPI', '6.0.0'), - # PDT source-to-source instrumentation support (optional): - ('PDT', '3.25.1'), -] - -configopts = '--enable-shared' - -local_adapters = [ - 'compiler_event', 'compiler_mgmt', 'cuda_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' -] -sanity_check_paths = { - 'files': - ['bin/scorep', 'include/scorep/SCOREP_User.h'] + - ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], - 'dirs': [], -} - -# Ensure that local metric documentation is found by CubeGUI -modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0_binutils_2.34_api_change.patch b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0_binutils_2.34_api_change.patch deleted file mode 100644 index b8d22fd1c53..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0_binutils_2.34_api_change.patch +++ /dev/null @@ -1,37 +0,0 @@ -Support libbfd API change introduced with binutils 2.34. Patch backported -from upstream repo; fix will be included in releases after v6.0. ---- a/src/services/unwinding/scorep_unwinding_unify.c -+++ b/src/services/unwinding/scorep_unwinding_unify.c -@@ -28,6 +28,19 @@ - - #if HAVE( LIBBFD ) - #include -+ -+#ifndef bfd_get_section_size -+#define bfd_get_section_size( asection ) bfd_section_size( asection ) -+#endif -+ -+#ifndef bfd_get_section_vma -+#define bfd_get_section_vma( abfd, asection ) bfd_section_vma( asection ) -+#endif -+ -+#ifndef bfd_get_section_flags -+#define bfd_get_section_flags( abfd, asection ) bfd_section_flags( asection ) -+#endif -+ - #endif - - #include "scorep_unwinding_region.h" ---- a/src/adapters/compiler/scorep_compiler_symbol_table_libbfd.c -+++ b/src/adapters/compiler/scorep_compiler_symbol_table_libbfd.c -@@ -43,6 +43,10 @@ - - #include - -+#ifndef bfd_get_section -+#define bfd_get_section( asymbol ) bfd_asymbol_section( asymbol ) -+#endif -+ - #include - #define SCOREP_DEBUG_MODULE_NAME COMPILER - #include diff --git a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0_no_PDT_for_CUDA.patch b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0_no_PDT_for_CUDA.patch deleted file mode 100644 index 24d90a4184a..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-6.0_no_PDT_for_CUDA.patch +++ /dev/null @@ -1,16 +0,0 @@ -Prevent PDT from instrumenting .cu files; fixes 'make installcheck' when both -PDT and CUDA are enabled. Patch backported from upstream repo; fix will be -included in releases after v6.0. ---- a/src/tools/instrumenter/scorep_instrumenter_pdt.cpp -+++ b/src/tools/instrumenter/scorep_instrumenter_pdt.cpp -@@ -74,6 +74,10 @@ SCOREP_Instrumenter_PdtAdapter::precompile( SCOREP_Instrumenter& instrum - SCOREP_Instrumenter_CmdLine& cmdLine, - const std::string& source_file ) - { -+ if ( is_cuda_file( source_file ) ) -+ { -+ return source_file; -+ } - std::string extension = get_extension( source_file ); - if ( is_fortran_file( source_file ) ) - { diff --git a/easybuild/easyconfigs/__archive__/s/Scythe/Scythe-0.994-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/Scythe/Scythe-0.994-GCCcore-9.3.0.eb deleted file mode 100644 index 0416ac72d02..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Scythe/Scythe-0.994-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'MakeCp' - -name = 'Scythe' -version = '0.994' - -homepage = 'https://github.com/ucdavis-bioinformatics/scythe' - -description = """ - Scythe uses a Naive Bayesian approach to classify contaminant substrings in - sequence reads. It considers quality information, which can make it robust in - picking out 3'-end adapters, which often include poor quality bases. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/ucdavis-bioinformatics/scythe/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['943467cbc59e7438b1db4a8e7d0e777f584ce6dbcf582053128f2924710959fc'] - -builddependencies = [('binutils', '2.34')] - -prebuildopts = "sed -i 's/CC = gcc/CC := gcc/' Makefile && " -prebuildopts += "sed -i 's/CFLAGS = -Wall/CFLAGS += -Wall/' Makefile && " - -files_to_copy = [(['scythe'], 'bin'), 'adap.fa', 'adapter_templates.txt'] - -sanity_check_paths = { - 'files': ['adap.fa', 'bin/scythe'], - 'dirs': [] -} - -sanity_check_commands = ['scythe --version'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.10.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.10.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 269773cec93..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.10.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics (SIB) -# Biozentrum - University of Basel -easyblock = 'PythonPackage' - -name = 'Seaborn' -version = '0.10.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://seaborn.pydata.org/' -description = """ Seaborn is a Python visualization library based on matplotlib. - It provides a high-level interface for drawing attractive statistical graphics. """ - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['2d1a0c9d6bd1bc3cadb0364b8f06540f51322a670cf8438d0fde1c1c7317adc0'] - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.10.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.10.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 11a5f3828d6..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Seaborn/Seaborn-0.10.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics (SIB) -# Biozentrum - University of Basel -easyblock = 'PythonPackage' - -name = 'Seaborn' -version = '0.10.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://seaborn.pydata.org/' -description = """ Seaborn is a Python visualization library based on matplotlib. - It provides a high-level interface for drawing attractive statistical graphics. """ - -toolchain = {'name': 'intel', 'version': '2020a'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['2d1a0c9d6bd1bc3cadb0364b8f06540f51322a670cf8438d0fde1c1c7317adc0'] - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SentencePiece/SentencePiece-0.1.94-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SentencePiece/SentencePiece-0.1.94-GCC-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 11ee0e8a4de..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SentencePiece/SentencePiece-0.1.94-GCC-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,56 +0,0 @@ -easyblock = 'Bundle' - -name = 'SentencePiece' -version = '0.1.94' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/google/sentencepiece' -description = "Unsupervised text tokenizer for Neural Network-based text generation." -github_account = 'google' - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('gperftools', '2.8'), -] - -default_component_specs = { - 'source_urls': [GITHUB_LOWER_SOURCE], - 'sources': ['v%(version)s.tar.gz'], - 'checksums': ['a23133caa67c38c3bf7f978fcea07947072783b32554a034cbbe99a8cf776192'], -} - -components = [ - (name, version, { - 'easyblock': 'CMakeMake', - 'separate_build_dir': True, - 'start_dir': '%(namelower)s-%(version)s', - }), - ('sentencepiece', version, { - 'easyblock': 'PythonPackage', - 'start_dir': '%(namelower)s-%(version)s/python', - 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', - 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', - }), -] - -postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] - -sanity_check_paths = { - 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + - ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + - ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], - 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], -} - -sanity_check_commands = [ - 'spm_train --help', - "python -c 'import sentencepiece'", -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/SeqAn/SeqAn-2.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SeqAn/SeqAn-2.4.0-GCCcore-9.3.0.eb deleted file mode 100644 index 2819cf0763b..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SeqAn/SeqAn-2.4.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,50 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'CMakeMake' - -name = 'SeqAn' -version = '2.4.0' - -homepage = 'https://github.com/seqan/seqan' - -description = """ - SeqAn is an open source C++ library of efficient algorithms and data structures - for the analysis of sequences with the focus on biological data. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/seqan/seqan/archive/'] -sources = ['%(namelower)s-v%(version)s.tar.gz'] -checksums = ['d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('Python', '3.8.2'), -] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), -] - -separate_build_dir = True - -postinstallcmds = [ - "mkdir -p %(installdir)s/util/cmake", - "cp -a %(builddir)s/seqan-*/util/cmake/seqan-config.cmake %(installdir)s/util/cmake/", - "cp -a %(builddir)s/seqan-*/include %(installdir)s", -] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["gustaf_mate_joining", "mason_materializer", "mason_variator", - "rabema_prepare_sam", "razers3", "seqan_tcoffee", "s4_join", "samcat", "splazers", - "yara_mapper"]] + ['util/cmake/seqan-config.cmake'], - 'dirs': ['include/seqan'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SeqLib/SeqLib-1.2.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SeqLib/SeqLib-1.2.0-GCC-9.3.0.eb deleted file mode 100644 index f437ba0bbb1..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SeqLib/SeqLib-1.2.0-GCC-9.3.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -# Author: Jasper Grimm (UoY) - -easyblock = 'ConfigureMake' - -name = 'SeqLib' -version = '1.2.0' - -homepage = 'https://github.com/walaj/SeqLib' -description = """C++ interface to HTSlib, BWA-MEM and Fermi.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -github_account = 'walaj' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version_major_minor)s.0_avoid-bwa-fml-namespace-conflict.patch', - '%(name)s-%(version_major_minor)s.0_use-external-deps.patch', -] -checksums = [ - '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz - # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch - '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', - '413f0ad8e0963d8922205d31e0c361cfa98a10f93e7d3e0506e0bed539ec70eb', # SeqLib-1.2.0_use-external-deps.patch -] - -builddependencies = [('Autotools', '20180311')] - -dependencies = [ - ('zlib', '1.2.11'), - ('XZ', '5.2.5'), - ('bzip2', '1.0.8'), - ('JsonCpp', '1.9.4'), - ('BWA', '0.7.17'), - ('HTSlib', '1.10.2'), - ('fermi-lite', '20190320'), - ('SSW', '1.1'), - ('PCRE', '8.44'), -] - -preconfigopts = "autoreconf -i -f && " - -sanity_check_paths = { - 'files': ['bin/seqtools', 'lib/libseqlib.%s' % SHLIB_EXT], - 'dirs': [], -} -sanity_check_commands = ["seqtools"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb deleted file mode 100644 index df419a78c7f..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'SCons' -name = 'Serf' -version = '1.3.9' - -homepage = 'https://serf.apache.org/' -description = """The serf library is a high performance C-based HTTP client library - built upon the Apache Portable Runtime (APR) library""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://archive.apache.org/dist/%(namelower)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc'] - -builddependencies = [ - ('binutils', '2.34'), - ('Python', '2.7.18'), # Serfs build scripts are python 2 only - ('SCons', '3.1.2'), -] - -dependencies = [ - ('APR', '1.7.0'), - ('APR-util', '1.6.1'), - # OS dependency should be preferred if the os version is more recent then this version, - # it is nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.0.1p'), -] - -osdependencies = [OS_PKG_OPENSSL_DEV] - -buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" - -sanity_check_paths = { - 'files': ['include/serf-1/serf.h'] + - ['lib/libserf-1.%s' % x for x in ['a', 'so']], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/s/Seurat/Seurat-3.1.5-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/s/Seurat/Seurat-3.1.5-foss-2020a-R-4.0.0.eb deleted file mode 100644 index f26b738cfcc..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Seurat/Seurat-3.1.5-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'RPackage' - -name = 'Seurat' -version = '3.1.5' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://satijalab.org/seurat' -description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['757ef0e7697734aac5769705bef80dc7b95f006cdf52ae7034309a05f11578d1'] - -dependencies = [ - ('R', '4.0.0'), - ('R-bundle-Bioconductor', '3.11', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.7.1-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.7.1-GCC-9.3.0-Python-3.8.2.eb deleted file mode 100644 index e2b5a9d004a..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Shapely/Shapely-1.7.1-GCC-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Shapely' -version = '1.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Toblerity/Shapely' -description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. -It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['1641724c1055459a7e2b8bbe47ba25bdc89554582e62aec23cb3f3ca25f9b129'] - -dependencies = [ - ('Python', '3.8.2'), - ('GEOS', '3.8.1', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/SiNVICT/SiNVICT-1.0-20180817-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SiNVICT/SiNVICT-1.0-20180817-GCC-9.3.0.eb deleted file mode 100644 index d91fc6fc749..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SiNVICT/SiNVICT-1.0-20180817-GCC-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'MakeCp' - -name = 'SiNVICT' -local_commit = 'b4d091e' -version = '1.0-20180817' - -homepage = 'https://github.com/sfu-compbio/sinvict' -description = """SiNVICT is a tool for the detection of SNVs and indels from cfDNA/ctDNA samples obtained - by ultra-deep sequencing.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/sfu-compbio/%(namelower)s/archive'] -sources = ['%s.tar.gz' % local_commit] -checksums = ['b597b7743695f83e55decfa6c376b7785b18877b2e7e22a9270a0e919ff39097'] - -builddependencies = [ - ('CMake', '3.16.4'), -] -dependencies = [ - ('ABRA2', '2.23'), - ('bam-readcount', '0.8.0'), - ('BWA', '0.7.17'), - ('FASTX-Toolkit', '0.0.14'), -] - -files_to_copy = [(['sinvict'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/sinvict'], - 'dirs': [], -} - -sanity_check_commands = ["sinvict --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Siesta/Siesta-4.1.5-foss-2020a.eb b/easybuild/easyconfigs/__archive__/s/Siesta/Siesta-4.1.5-foss-2020a.eb deleted file mode 100644 index 5eff815b77c..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Siesta/Siesta-4.1.5-foss-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'Siesta' -version = '4.1.5' - -homepage = 'http://departments.icmab.es/leem/siesta' -description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic - structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True, 'precise': True} - -source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['518df31aa6213af5e24cc73abb537b2c89a925b487171f5339d743d0c7140b3f'] - -dependencies = [ - ('netCDF-Fortran', '4.5.2'), - ('METIS', '5.1.0'), - ('ELPA', '2019.11.001'), -] - -# transiesta is now siesta --electrode -with_transiesta = False - -runtest = 'check' - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/s/Siesta/Siesta-4.1.5-intel-2020a.eb b/easybuild/easyconfigs/__archive__/s/Siesta/Siesta-4.1.5-intel-2020a.eb deleted file mode 100644 index 50527cd229e..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Siesta/Siesta-4.1.5-intel-2020a.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'Siesta' -version = '4.1.5' - -homepage = 'http://departments.icmab.es/leem/siesta' -description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic - structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True, 'precise': True} - -source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['518df31aa6213af5e24cc73abb537b2c89a925b487171f5339d743d0c7140b3f'] - -dependencies = [ - ('netCDF-Fortran', '4.5.2'), - ('METIS', '5.1.0'), - ('ELPA', '2019.11.001'), -] - -# transiesta is now siesta --electrode -with_transiesta = False - -runtest = 'check' - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index b91fd64347f..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,55 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'PythonBundle' - -name = 'SimPEG' -version = '0.14.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://simpeg.xyz/' -description = """Simulation and Parameter Estimation in Geophysics -- A python package for simulation and gradient based parameter estimation in the context of geophysical applications.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('numba', '0.50.0', versionsuffix), -] - -exts_list = [ - ('pyMKL', '0.0.3', { - 'modulename': '%(name)s', - 'checksums': ['5a24f63f510007d908506c88aa5b6b720a0d9201b8222d14805aca1f771b6afa'], - }), - ('pymatsolver', '0.1.2', { - 'checksums': ['3ea58d5de6b0a05f646359766932f186d74d46b23730613f9fbff1482b2dde51'], - }), - ('properties', '0.6.1', { - 'checksums': ['b119ce4c53f4717fa29371c1bb929f422dda7ed90a4559b3583ea77389177263'], - }), - ('vectormath', '0.2.2', { - 'checksums': ['f9f9209d350ec89dc11e2548e0e6397c1b9489c8468eb50ce33788ee4322a7b8'], - }), - ('discretize', '0.4.12', { - 'checksums': ['b90ba8ab32c4009c4b6af1962f27a15bc69d47b4d752eaf71c033be0551d2387'], - }), - ('utm', '0.5.0', { - 'checksums': ['07e55707ed660eec1ae983bd54a406c437962618a6261b38d70592fe30f5f508'], - }), - ('geoana', '0.0.6', { - 'checksums': ['7f37a72a722f5f0690fdefe0cbafc59d613143962e154c87210a0b4f6d1d3730'], - }), - ('empymod', '2.0.1', { - 'checksums': ['f78eb017be4e65b6994b6c07007b1754ccba7e20a547e1670afcd844ad6dad70'], - }), - (name, version, { - 'modulename': '%(name)s', - 'checksums': ['ef74c2434840c5a8027898fb724aa12b7343b4b11a32f488353a7d0f8ed33255'], - }), -] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/s/SortMeRNA/SortMeRNA-2.1-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SortMeRNA/SortMeRNA-2.1-GCC-9.3.0.eb deleted file mode 100644 index 710019073e2..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SortMeRNA/SortMeRNA-2.1-GCC-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -# # -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Cedric Laczny , Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -# # -easyblock = 'ConfigureMake' - -name = 'SortMeRNA' -version = '2.1' - -homepage = 'https://bioinfo.lifl.fr/RNA/sortmerna/' -description = "SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads." - -toolchain = {'name': 'GCC', 'version': '9.3.0'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = ['https://github.com/biocore/%(namelower)s/archive/'] -sources = ['%(version)s.tar.gz'] -# Patch for double includes of header files in Makefile.in -patches = ['%(name)s-%(version)s_Makefile.in.patch'] -checksums = [ - '44a3b29570e339da235acc00a35cde18f4fff03b7087b0fa8100f6c3826385d5', # 2.1.tar.gz - '0137ee3d4c583f3c4a4b18aadd1029e8a9cf0ff1748d364d993b82482777d4d5', # SortMeRNA-2.1_Makefile.in.patch -] - -sanity_check_paths = { - 'files': ['bin/indexdb_rna', 'bin/%(namelower)s'], - 'dirs': ['include', '%(namelower)s'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SortMeRNA/SortMeRNA-2.1_Makefile.in.patch b/easybuild/easyconfigs/__archive__/s/SortMeRNA/SortMeRNA-2.1_Makefile.in.patch deleted file mode 100644 index 14b80c8523d..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SortMeRNA/SortMeRNA-2.1_Makefile.in.patch +++ /dev/null @@ -1,13 +0,0 @@ -# Remove double includes of header files in Makefile.in -# Author: Fokke Dijkstra - University of Groningen ---- Makefile.in 2014-10-30 23:24:56.000000000 +0100 -+++ Makefile.in 2015-03-09 15:42:14.213220762 +0100 -@@ -340,7 +340,7 @@ - top_builddir = @top_builddir@ - top_srcdir = @top_srcdir@ - include_HEADERS = ./alp/gumbel_params.hpp ./alp/njn_dynprogprob.hpp ./alp/njn_dynprogproblim.hpp ./alp/njn_dynprogprobproto.hpp ./alp/njn_ioutil.hpp ./alp/njn_localmaxstat.hpp ./alp/njn_localmaxstatmatrix.hpp ./alp/njn_localmaxstatutil.hpp ./alp/njn_random.hpp ./alp/sls_alp.hpp ./alp/sls_alp_data.hpp ./alp/sls_alp_regression.hpp ./alp/sls_alp_sim.hpp ./alp/sls_pvalues.hpp \ -- ./alp/gumbel_params.hpp ./alp/njn_approx.hpp ./alp/njn_doubletype.hpp ./alp/njn_dynprogprob.hpp ./alp/njn_dynprogproblim.hpp ./alp/njn_dynprogprobproto.hpp ./alp/njn_function.hpp ./alp/njn_integer.hpp ./alp/njn_ioutil.hpp ./alp/njn_localmaxstat.hpp ./alp/njn_localmaxstatmatrix.hpp ./alp/njn_localmaxstatutil.hpp ./alp/njn_matrix.hpp ./alp/njn_memutil.hpp ./alp/njn_random.hpp ./alp/njn_root.hpp ./alp/njn_stringutil.hpp ./alp/njn_uniform.hpp ./alp/njn_vector.hpp ./alp/sls_alp.hpp ./alp/sls_alp_data.hpp ./alp/sls_alp_regression.hpp ./alp/sls_alp_sim.hpp ./alp/sls_normal_distr_array.hpp ./alp/sls_pvalues.hpp \ -+ ./alp/njn_approx.hpp ./alp/njn_doubletype.hpp ./alp/njn_function.hpp ./alp/njn_integer.hpp ./alp/njn_matrix.hpp ./alp/njn_memutil.hpp ./alp/njn_root.hpp ./alp/njn_stringutil.hpp ./alp/njn_uniform.hpp ./alp/njn_vector.hpp ./alp/sls_normal_distr_array.hpp \ - ./cmph/bdz.h ./cmph/bdz_ph.h ./cmph/bdz_structs.h ./cmph/bdz_structs_ph.h ./cmph/bitbool.h ./cmph/bmz.h ./cmph/bmz8.h ./cmph/bmz8_structs.h ./cmph/bmz_structs.h ./cmph/brz.h ./cmph/brz_structs.h ./cmph/buffer_entry.h ./cmph/buffer_manager.h ./cmph/chd.h ./cmph/chd_ph.h ./cmph/chd_structs.h ./cmph/chd_structs_ph.h ./cmph/chm.h ./cmph/chm_structs.h ./cmph/cmph.h ./cmph/cmph_structs.h ./cmph/cmph_time.h ./cmph/cmph_types.h ./cmph/compressed_rank.h ./cmph/compressed_seq.h ./cmph/debug.h ./cmph/fch.h ./cmph/fch_buckets.h ./cmph/fch_structs.h ./cmph/graph.h ./cmph/hash.h ./cmph/hash_state.h ./cmph/jenkins_hash.h ./cmph/miller_rabin.h ./cmph/select.h ./cmph/select_lookup_tables.h ./cmph/vqueue.h ./cmph/vstack.h \ - ./include/bitvector.hpp ./include/common.hpp ./include/indexdb.hpp ./include/loadgenome.hpp ./include/paralleltraversal.hpp ./include/ssw.h ./include/outputformats.hpp - diff --git a/easybuild/easyconfigs/__archive__/s/SpaceRanger/SpaceRanger-1.1.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SpaceRanger/SpaceRanger-1.1.0-GCC-9.3.0.eb deleted file mode 100644 index a18b3a26af7..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SpaceRanger/SpaceRanger-1.1.0-GCC-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'Tarball' - -name = 'SpaceRanger' -version = '1.1.0' - -homepage = 'https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger' -description = """ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output -and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, -perform clustering and gene expression analysis, and place spots in spatial context on the slide image. """ - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5de5fe46b8d6c71057e079ea65f9359b69e589b19cb91f6bf902a00606c3d999'] -download_instructions = f"{name} requires manual download from " -download_instructions += "https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest" -download_instructions += f"\nRequired downloads: {' '.join(sources)}""" - -dependencies = [ - ('bcl2fastq2', '2.20.0'), -] - -allow_prepend_abs_path = True -# prepend reference databases GRCh38 and mm10 to PATH -# modextrapaths = {'PATH': '/path/to/databases/%(namelower)s-%(version)s'} - -sanity_check_paths = { - 'files': ['bin/spaceranger'], - 'dirs': ['external', 'lib', 'mro'], -} - -sanity_check_commands = ['spaceranger -h'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/SpaceRanger/SpaceRanger-1.2.2-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/SpaceRanger/SpaceRanger-1.2.2-GCC-9.3.0.eb deleted file mode 100644 index 067aece38b2..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SpaceRanger/SpaceRanger-1.2.2-GCC-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'Tarball' - -name = 'SpaceRanger' -version = '1.2.2' - -homepage = 'https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger' -description = """ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output -and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, -perform clustering and gene expression analysis, and place spots in spatial context on the slide image. """ - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['379b4cf63f0c37a6cc7d3e530788605cda5fdb52328d9b2b1604f753c8e60d3f'] -download_instructions = f"{name} requires manual download from " -download_instructions += "https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest" -download_instructions += f"\nRequired downloads: {' '.join(sources)}""" - -dependencies = [ - ('bcl2fastq2', '2.20.0'), -] - -allow_prepend_abs_path = True -# prepend reference databases GRCh38 and mm10 to PATH -# modextrapaths = {'PATH': '/path/to/databases/%(namelower)s-%(version)s'} - -sanity_check_paths = { - 'files': ['bin/spaceranger'], - 'dirs': ['external', 'lib', 'mro'], -} - -sanity_check_commands = ['spaceranger -h'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index fea58961e79..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,53 +0,0 @@ -# Author: Denis Krišťák (INUITS) - -easyblock = 'Tarball' - -name = 'Spark' -version = '3.1.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://spark.apache.org' -description = """Spark is Hadoop MapReduce done in memory""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', - 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' -] -sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] -checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] - -dependencies = [ - ('Python', '3.8.2'), - ('Java', '11', '', SYSTEM), - # ('Hadoop', '2.10.0', '-native'), - ('Arrow', '0.17.1', versionsuffix), -] - -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - -exts_list = [ - ('py4j', '0.10.9.2', { - 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], - }), -] - -sanity_check_paths = { - 'files': ['bin/pyspark', 'bin/spark-shell'], - 'dirs': ['python'] -} - -sanity_check_commands = [ - "pyspark -h", - "python -c 'import pyspark'", -] - -modextrapaths = {'PYTHONPATH': 'python'} - -modextravars = {'SPARK_HOME': '%(installdir)s'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/s/SplAdder/SplAdder-2.4.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/SplAdder/SplAdder-2.4.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index e7ab6d7d71d..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SplAdder/SplAdder-2.4.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'SplAdder' -version = '2.4.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/ratschlab/spladder' -description = """ -Splicing Adder is a toolbox for alternative splicing analysis based on RNA-Seq -alignment data. Briefly, the software takes a given annotation and RNA-Seq read -alignments in standardized formats, transforms the annotation into a splicing -graph representation, augments the splicing graph with additional information -extracted from the read data, extracts alternative splicing events from the -graph and quantifies the events based on the alignment data.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -github_account = 'ratschlab' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['58764ab11cce15236cb07c456bc06dafc49b68fd621e91962bc32b84629c8267'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('h5py', '2.10.0', versionsuffix), - ('statsmodels', '0.11.1', versionsuffix), - ('Pysam', '0.16.0.1'), -] - -sanity_check_paths = { - 'files': ['bin/spladder'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 521d3006f6a..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,207 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Spyder' -version = '4.1.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/spyder-ide/spyder' -description = """Spyder is an interactive Python development environment providing MATLAB-like features in a simple - and light-weighted software.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'cstd': 'c++11'} - -builddependencies = [ - ('CMake', '3.16.4'), -] -dependencies = [ - ('Python', '3.8.2'), - ('ZeroMQ', '4.3.2'), - ('PyQt5', '5.15.1', versionsuffix), - ('IPython', '7.15.0', versionsuffix), - ('geopandas', '0.8.1', versionsuffix), -] - -# strip out (too strict version) requirements for pyqt5 and pyqtwebengine, -# because they are not installed with pip, but are provided via the PyQt5 dependency -local_spyder_preinstallopts = ( - """sed -i "s/'pyqt5.*,//g" setup.py && """ - """sed -i "s/'pyqtwebengine.*,//g" setup.py && """ -) - -exts_list = [ - ('astroid', '2.4.2', { - 'checksums': ['2f4078c2a41bf377eea06d71c9d2ba4eb8f6b1af2135bec27bbbb7d8f12bb703'], - }), - ('async_generator', '1.10', { - 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], - }), - ('autopep8', '1.5.4', { - 'checksums': ['d21d3901cb0da6ebd1e83fc9b0dfbde8b46afc2ede4fe32fbda0c7c6118ca094'], - }), - ('binaryornot', '0.4.4', { - 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], - }), - ('bleach', '3.2.1', { - 'checksums': ['52b5919b81842b1854196eaae5ca29679a2f2e378905c346d3ca8227c2c66080'], - }), - ('cloudpickle', '1.6.0', { - 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], - }), - ('cookiecutter', '1.7.2', { - 'checksums': ['efb6b2d4780feda8908a873e38f0e61778c23f6a2ea58215723bcceb5b515dac'], - }), - ('decorator', '4.4.2', { - 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], - }), - ('diff-match-patch', '20200713', { - 'checksums': ['da6f5a01aa586df23dfc89f3827e1cafbb5420be9d87769eeb079ddfd9477a18'], - }), - ('flake8', '3.8.4', { - 'checksums': ['aadae8761ec651813c24be05c6f7b4680857ef6afaae4651a4eccaef97ce6c3b'], - }), - ('helpdev', '0.7.1', { - 'checksums': ['bb62a79acbac141dadf42cadeb92bb7450dd18b9824a62043b6a0b149190db3d'], - }), - ('isort', '5.6.3', { - 'use_pip': False, - 'checksums': ['3820dd92c3214290cda6351f2ae2cedd5170759bc434af600eaad4f7a82a6ade'], - }), - ('jedi', '0.17.1', { - 'checksums': ['807d5d4f96711a2bcfdd5dfa3b1ae6d09aa53832b182090b222b5efb81f52f63'], - }), - ('jeepney', '0.4.3', { - 'use_pip': False, - 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], - }), - ('arrow', '0.17.0', { - 'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'], - }), - ('jinja2-time', '0.2.0', { - 'checksums': ['d14eaa4d315e7688daa4969f616f226614350c48730bfa1692d2caebd8c90d40'], - }), - ('jupyterlab_pygments', '0.1.2', { - 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], - }), - ('keyring', '21.4.0', { - 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], - }), - ('keyrings.alt', '4.0.0', { - 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], - }), - ('lazy-object-proxy', '1.4.3', { - 'checksums': ['f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0'], - }), - ('mccabe', '0.6.1', { - 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], - }), - ('jupyter_client', '6.1.7', { - 'checksums': ['49e390b36fe4b4226724704ea28d9fb903f1a3601b6882ce3105221cd09377a1'], - }), - ('nbclient', '0.5.1', { - 'checksums': ['01e2d726d16eaf2cde6db74a87e2451453547e8832d142f73f72fddcd4fe0250'], - }), - ('nest_asyncio', '1.4.1', { - 'checksums': ['b86c3193abda5b2eeccf8c79894bc71c680369a178f4b068514ac00720b14e01'], - }), - ('numpydoc', '1.1.0', { - 'checksums': ['c36fd6cb7ffdc9b4e165a43f67bf6271a7b024d0bb6b00ac468c9e2bfc76448e'], - }), - ('pathtools', '0.1.2', { - 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], - }), - ('poyo', '0.5.0', { - 'checksums': ['e26956aa780c45f011ca9886f044590e2d8fd8b61db7b1c1cf4e0869f48ed4dd'], - }), - ('pycodestyle', '2.6.0', { - 'checksums': ['c58a7d2815e0e8d7972bf1803331fb0152f867bd89adf8a01dfd55085434192e'], - }), - ('pydocstyle', '5.1.1', { - 'checksums': ['19b86fa8617ed916776a11cd8bc0197e5b9856d5433b777f51a3defe13075325'], - }), - ('pyflakes', '2.2.0', { - 'checksums': ['35b2d75ee967ea93b55750aa9edbbf72813e06a66ba54438df2cfac9e3c27fc8'], - }), - ('pylint', '2.6.0', { - 'checksums': ['bb4a908c9dadbc3aac18860550e870f58e1a02c9f2c204fdf5693d73be061210'], - }), - ('ujson', '4.0.1', { - 'checksums': ['26cf6241b36ff5ce4539ae687b6b02673109c5e3efc96148806a7873eaa229d3'], - }), - ('python-language-server', '0.35.1', { - 'checksums': ['6e0c9a3b2ae98e0eb22e98ed6b3c4e190a6bf9e27af53efd2396da60cd92b221'], - 'modulename': 'pyls', - }), - ('pyrsistent', '0.17.3', { - 'checksums': ['2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e'], - }), - ('python-jsonrpc-server', '0.4.0', { - 'checksums': ['62c543e541f101ec5b57dc654efc212d2c2e3ea47ff6f54b2e7dcb36ecf20595'], - 'modulename': 'pyls_jsonrpc', - }), - ('python-slugify', '4.0.1', { - 'checksums': ['69a517766e00c1268e5bbfc0d010a0a8508de0b18d30ad5a1ff357f8ae724270'], - 'modulename': 'slugify', - }), - ('pyxdg', '0.26', { - 'checksums': ['fe2928d3f532ed32b39c32a482b54136fe766d19936afc96c8f00645f9da1a06'], - 'modulename': 'xdg', - }), - ('rope', '0.18.0', { - 'checksums': ['786b5c38c530d4846aa68a42604f61b4e69a493390e3ca11b88df0fbfdc3ed04'], - }), - ('QDarkStyle', '2.8.1', { - 'checksums': ['d53b0120bddd9e3efba9801731e22ef86ed798bb5fc6a802f5f7bb32dedf0321'], - }), - ('QtAwesome', '1.0.1', { - 'checksums': ['d612a313e531966d17f5a8fb7604faba961cf7ce3c77a9168c6f60e60140b767'], - }), - ('qtconsole', '4.7.7', { - 'checksums': ['f236ead8711dba0702507dd8fad473c7216a86eefa6098eff8ec4b54f57d7804'], - }), - ('QtPy', '1.9.0', { - 'checksums': ['2db72c44b55d0fe1407be8fba35c838ad0d6d3bb81f23007886dc1fc0f459c8d'], - }), - ('SecretStorage', '3.1.2', { - 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], - 'modulename': 'secretstorage', - }), - ('spyder', version, { - 'checksums': ['d467f020b694193873a237ce6744ae36bd5a59f4d2b7ffbeb15dda68b03f5aa1'], - 'preinstallopts': local_spyder_preinstallopts, - }), - ('spyder-kernels', '1.9.4', { - 'checksums': ['ca9d997c475b714b54d2fd67aa140837ec3630e91cbbc2e0cd190f1b0bd9fe9d'], - 'modulename': 'spyder_kernels', - }), - ('text-unidecode', '1.3', { - 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], - }), - ('traitlets', '5.0.4', { - 'checksums': ['86c9351f94f95de9db8a04ad8e892da299a088a64fd283f9f6f18770ae5eae1b'], - }), - ('typed_ast', '1.4.1', { - 'checksums': ['8c8aaad94455178e3187ab22c8b01a3837f8ee50e09cf31f1ba129eb293ec30b'], - }), - ('watchdog', '0.10.3', { - 'checksums': ['4214e1379d128b0588021880ccaf40317ee156d4603ac388b9adcf29165e0c04'], - }), - ('wurlitzer', '2.0.1', { - 'checksums': ['d08f0728a998441aac3d7a0f8cd6dfed2ba2525144878fb49599b719085b7543'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('yapf', '0.30.0', { - 'checksums': ['3000abee4c28daebad55da6c85f3cd07b8062ce48e2e9943c8da1b9667d48427'], - }), -] - -sanity_check_paths = { - 'files': ['bin/spyder3'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["spyder3 --help"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/s/Stacks/Stacks-2.54-foss-2020a.eb b/easybuild/easyconfigs/__archive__/s/Stacks/Stacks-2.54-foss-2020a.eb deleted file mode 100644 index ea834dd2873..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Stacks/Stacks-2.54-foss-2020a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Stacks' -version = '2.54' - -homepage = 'https://catchenlab.life.illinois.edu/stacks/' -description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, - for the purpose of building genetic maps and conducting population genomics and phylogeography. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['1278bf006cfd4c1c654b1d353ce453358436e306f88f2f0e80af7f3829c08894'] - -dependencies = [ - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', - 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', - 'bin/tsv2bam', 'bin/ustacks'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Statistics-R/Statistics-R-0.34-foss-2020a.eb b/easybuild/easyconfigs/__archive__/s/Statistics-R/Statistics-R-0.34-foss-2020a.eb deleted file mode 100644 index bb8a8f65acb..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Statistics-R/Statistics-R-0.34-foss-2020a.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PerlModule' - -name = 'Statistics-R' -version = '0.34' - -homepage = 'https://metacpan.org/pod/Statistics::R' -description = "Perl interface with the R statistical program" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://cpan.metacpan.org/authors/id/F/FA/FANGLY'] -sources = [SOURCE_TAR_GZ] -checksums = ['782dd064876ac94680d97899f24fb0e727df42c05ba474ec096a9116438fbed4'] - -dependencies = [ - ('Perl', '5.30.2'), - ('R', '4.0.0'), -] - -options = {'modulename': 'Statistics::R'} - -sanity_check_paths = { - 'files': ['lib/perl5/site_perl/%(perlver)s/Statistics/R.pm'], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/Statistics/R'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/StringTie/StringTie-2.1.3-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/StringTie/StringTie-2.1.3-GCC-9.3.0.eb deleted file mode 100644 index f6f060f6473..00000000000 --- a/easybuild/easyconfigs/__archive__/s/StringTie/StringTie-2.1.3-GCC-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'MakeCp' - -name = 'StringTie' -version = '2.1.3' - -homepage = 'https://ccb.jhu.edu/software/stringtie/' -description = 'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts' - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://ccb.jhu.edu/software/stringtie/dl/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['bd57c76069f6d0447623236ef49a64da7d023f233815781f16fe7fb4bd89c664'] - -builddependencies = [('binutils', '2.34')] -dependencies = [ - ('zlib', '1.2.11'), -] - -# the test script downloads some test data from the internet -buildopts = 'release && ./run_tests.sh' - -files_to_copy = [ - (['stringtie', 'prepDE.py'], 'bin'), - 'README.md', - 'LICENSE' -] - -sanity_check_paths = { - 'files': ['bin/stringtie'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/StringTie/StringTie-2.1.4-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/StringTie/StringTie-2.1.4-GCC-9.3.0.eb deleted file mode 100644 index 1cee82d2237..00000000000 --- a/easybuild/easyconfigs/__archive__/s/StringTie/StringTie-2.1.4-GCC-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'MakeCp' - -name = 'StringTie' -version = '2.1.4' - -homepage = 'https://ccb.jhu.edu/software/stringtie/' -description = 'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts' - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://ccb.jhu.edu/software/stringtie/dl/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['a08383edc9d41340b2c932084f64ea09280ce53f758ec3464fc9a8cf6f7eb6b1'] - -builddependencies = [('binutils', '2.34')] -dependencies = [ - ('zlib', '1.2.11'), -] - -# the test script downloads some test data from the internet -buildopts = 'release && ./run_tests.sh' - -files_to_copy = [ - (['stringtie', 'prepDE.py'], 'bin'), - 'README.md', - 'LICENSE' -] - -sanity_check_paths = { - 'files': ['bin/stringtie'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Subread/Subread-2.0.3-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/Subread/Subread-2.0.3-GCC-9.3.0.eb deleted file mode 100644 index a9ad4aecc98..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Subread/Subread-2.0.3-GCC-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'MakeCp' - -name = 'Subread' -version = '2.0.3' - -# HTTPS is not valid -homepage = 'http://subread.sourceforge.net/' -description = """High performance read alignment, quantification and mutation discovery""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(namelower)s-%(version)s-source.tar.gz'] - -checksums = ['56cef3a2f914d432713069d5c282f48831c3a1ecc89432ad5580caa322a5f56b'] - -start_dir = 'src' - -prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && " -prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && " - -buildopts = " -f Makefile.Linux" - -files_to_copy = ['bin'] - -local_binaries_list = [ - 'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', 'subread-align', 'subread-buildindex', -] -sanity_check_paths = { - 'files': ['bin/%s' % f for f in local_binaries_list], - 'dirs': ['bin/utilities'], -} - -sanity_check_commands = [ - 'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh' -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb deleted file mode 100644 index a4767edbe52..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Subversion' -version = '1.14.0' - -homepage = 'https://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [ - 'https://apache.belnet.be/%(namelower)s', - 'http://www.eu.apache.org/dist/%(namelower)s', - 'http://www.us.apache.org/dist/%(namelower)s', - 'https://archive.apache.org/dist/%(namelower)s', -] -sources = [SOURCELOWER_TAR_BZ2] -patches = ['Subversion-1.12.0-no_swig.patch'] -checksums = [ - '6ba8e218f9f97a83a799e58a3c6da1221d034b18d9d8cbbcb6ec52ab11722102', # subversion-1.14.0.tar.bz2 - '539ea2118f958d152d78438c81649eb727ff0b2e8491295702ee98e1f922041f', # Subversion-1.12.0-no_swig.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), -] - -dependencies = [ - ('APR', '1.7.0'), - ('APR-util', '1.6.1'), - ('SQLite', '3.31.1'), - ('zlib', '1.2.11'), - ('lz4', '1.9.2'), - ('utf8proc', '2.5.0'), - ('Serf', '1.3.9'), -] - -preconfigopts = './autogen.sh && ' - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-lz4=$EBROOTLZ4 --with-serf=$EBROOTSERF" - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-5.7.1-foss-2020a-METIS-5.1.0.eb b/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-5.7.1-foss-2020a-METIS-5.1.0.eb deleted file mode 100644 index 8a64e2ae146..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-5.7.1-foss-2020a-METIS-5.1.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'SuiteSparse' -version = '5.7.1' -local_metis_ver = '5.1.0' -versionsuffix = '-METIS-%s' % local_metis_ver - -homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' -description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['5ba5add1663d51a1b6fb128b50fe869b497f3096765ff7f8212f0ede044b9557'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('M4', '1.4.18'), -] - -dependencies = [('METIS', local_metis_ver)] - -# make sure that bin/demo can find libsuitesparseconfig.so.5 during build -prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-5.7.1-intel-2020a-METIS-5.1.0.eb b/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-5.7.1-intel-2020a-METIS-5.1.0.eb deleted file mode 100644 index e90f6e3ca4f..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-5.7.1-intel-2020a-METIS-5.1.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'SuiteSparse' -version = '5.7.1' -local_metis_ver = '5.1.0' -versionsuffix = '-METIS-%s' % local_metis_ver - -homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' -description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['5ba5add1663d51a1b6fb128b50fe869b497f3096765ff7f8212f0ede044b9557'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('M4', '1.4.18'), -] - -dependencies = [('METIS', local_metis_ver)] - -# make sure that bin/demo can find libsuitesparseconfig.so.5 during build -prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/SuperLU/SuperLU-5.2.2-foss-2020a.eb b/easybuild/easyconfigs/__archive__/s/SuperLU/SuperLU-5.2.2-foss-2020a.eb deleted file mode 100644 index efd83d01aa4..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SuperLU/SuperLU-5.2.2-foss-2020a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'SuperLU' -version = '5.2.2' - -homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems - of linear equations on high performance machines.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'openmp': True} - -github_account = 'xiaoyeli' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ["v%(version)s.tar.gz"] -checksums = ['470334a72ba637578e34057f46948495e601a5988a602604f5576367e606a28c'] - -builddependencies = [('CMake', '3.16.4')] - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/SuperLU/SuperLU-5.2.2-intel-2020a.eb b/easybuild/easyconfigs/__archive__/s/SuperLU/SuperLU-5.2.2-intel-2020a.eb deleted file mode 100644 index 19d231672f3..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SuperLU/SuperLU-5.2.2-intel-2020a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'SuperLU' -version = '5.2.2' - -homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems - of linear equations on high performance machines.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'openmp': True} - -github_account = 'xiaoyeli' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ["v%(version)s.tar.gz"] -checksums = ['470334a72ba637578e34057f46948495e601a5988a602604f5576367e606a28c'] - -builddependencies = [('CMake', '3.16.4')] - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/SuperLU_DIST/SuperLU_DIST-5.4.0-intel-2020a-trisolve-merge.eb b/easybuild/easyconfigs/__archive__/s/SuperLU_DIST/SuperLU_DIST-5.4.0-intel-2020a-trisolve-merge.eb deleted file mode 100644 index 428aca4110d..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SuperLU_DIST/SuperLU_DIST-5.4.0-intel-2020a-trisolve-merge.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = "EB_SuperLU" - -name = 'SuperLU_DIST' -version = '5.4.0' -versionsuffix = '-trisolve-merge' - -homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems - of linear equations on high performance machines.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'openmp': True} - -github_account = 'xiaoyeli' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ["v%(version)s%(versionsuffix)s.tar.gz"] -checksums = ['ba6ffd45246727f79510ff1f5fcccaf5ae1221165ac37213373c4c017ed2cc69'] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('ParMETIS', '4.0.3'), -] - -configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" ' -configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" ' - -# tests on this version of SuperLU_DIST are broken on intel mpi. -# HYD_spawn (../../../../../src/pm/i_hydra/libhydra/spawn/intel/hydra_spawn.c:128): -# execvp error on file pdtest (No such file or directory) -# disabling tests as this version is created as dependency for OpenSees easyconfigs -runtest = False - -postinstallcmds = [ - "rm %(installdir)s/lib64/libsuperlu.a", # remove broken symlink to libsuperlu.a - "ln -s %(installdir)s/lib64 %(installdir)s/lib", -] - -sanity_check_paths = { - 'files': ['lib64/libsuperlu_dist.a'], - 'dirs': ['include'], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/SuperLU_DIST/SuperLU_DIST-6.4.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/s/SuperLU_DIST/SuperLU_DIST-6.4.0-foss-2020a.eb deleted file mode 100644 index 4a9350da064..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SuperLU_DIST/SuperLU_DIST-6.4.0-foss-2020a.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = "EB_SuperLU" - -name = 'SuperLU_DIST' -version = '6.4.0' - -homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems - of linear equations on high performance machines.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'openmp': True} - -github_account = 'xiaoyeli' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ["v%(version)s.tar.gz"] -checksums = ['cb9c0b2ba4c28e5ed5817718ba19ae1dd63ccd30bc44c8b8252b54f5f04a44cc'] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('ParMETIS', '4.0.3'), -] - -configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" ' -configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" ' - -# Some tests run longer than default 1500s timeout on fairly big machine (36 cores). -# Include only first four tests, which should be fairly small to run -pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && ' - -postinstallcmds = [ - "rm %(installdir)s/lib64/libsuperlu.a", # remove broken symlink to libsuperlu.a - "ln -s %(installdir)s/lib64 %(installdir)s/lib", -] - -sanity_check_paths = { - 'files': ['lib64/libsuperlu_dist.a'], - 'dirs': ['include'] -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/SuperLU_DIST/SuperLU_DIST-6.4.0-intel-2020a.eb b/easybuild/easyconfigs/__archive__/s/SuperLU_DIST/SuperLU_DIST-6.4.0-intel-2020a.eb deleted file mode 100644 index 2e915dc2792..00000000000 --- a/easybuild/easyconfigs/__archive__/s/SuperLU_DIST/SuperLU_DIST-6.4.0-intel-2020a.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = "EB_SuperLU" - -name = 'SuperLU_DIST' -version = '6.4.0' - -homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems - of linear equations on high performance machines.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'pic': True, 'openmp': True} - -github_account = 'xiaoyeli' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ["v%(version)s.tar.gz"] -checksums = ['cb9c0b2ba4c28e5ed5817718ba19ae1dd63ccd30bc44c8b8252b54f5f04a44cc'] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('ParMETIS', '4.0.3'), -] - -configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" ' -configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" ' - -# Some tests run longer than default 1500s timeout on fairly big machine (36 cores). -# First two tests (pdtest_1x1_[13]_2_8_20_SP) in intel fails -# see: https://github.com/xiaoyeli/superlu_dist/issues/66 -# On intel include only second two tests, which should be fairly small to run -pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_2x1_[13]_2_8_20_SP" && ' - -postinstallcmds = [ - "rm %(installdir)s/lib64/libsuperlu.a", # remove broken symlink to libsuperlu.a - "ln -s %(installdir)s/lib64 %(installdir)s/lib", -] - -sanity_check_paths = { - 'files': ['lib64/libsuperlu_dist.a'], - 'dirs': ['include'] -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb deleted file mode 100644 index 822080c60fe..00000000000 --- a/easybuild/easyconfigs/__archive__/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1.1' - -homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' - -description = """ - Szip compression software, providing lossless compression of scientific data -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] - -builddependencies = [ - ('binutils', '2.34'), -] - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/s/samclip/samclip-0.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/samclip/samclip-0.4.0-GCCcore-9.3.0.eb deleted file mode 100644 index dde39779b92..00000000000 --- a/easybuild/easyconfigs/__archive__/s/samclip/samclip-0.4.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'Tarball' - -name = 'samclip' -version = '0.4.0' - -homepage = 'https://github.com/tseemann/samclip' -description = """Filter SAM file for soft and hard clipped alignments.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'tseemann' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127'] - -dependencies = [('Perl', '5.30.2')] - -sanity_check_paths = { - 'files': [name], - 'dirs': [], -} - -sanity_check_commands = ["%(name)s --help"] - -modextrapaths = {'PATH': ''} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-allel/scikit-allel-1.2.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-allel/scikit-allel-1.2.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 317ccfd6a64..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-allel/scikit-allel-1.2.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = "PythonBundle" - -name = 'scikit-allel' -version = '1.2.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scikit-allel.readthedocs.io/en/latest/' -description = """This package provides utilities for exploratory analysis of large scale genetic variation data. - It is based on numpy, scipy and other general-purpose Python scientific libraries.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('Seaborn', '0.10.1', versionsuffix), - ('h5py', '2.10.0', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('numexpr', '2.7.1', versionsuffix), - ('dask', '2.18.1', versionsuffix), - ('bcolz', '1.2.1', versionsuffix), - ('zarr', '2.4.0', versionsuffix), -] - -exts_list = [ - ('pytoml', '0.1.21', { - 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], - }), - ('flit-core', '2.3.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', - 'checksums': ['a50bcd8bf5785e3a7d95434244f30ba693e794c5204ac1ee908fc07c4acdbf80'], - }), - ('flit', '2.3.0', { - 'checksums': ['017012b809ec489918afd68af7a70bd7c8c770c87b60159d875c126866e97a4b'], - }), - ('threadpoolctl', '2.1.0', { - 'checksums': ['ddc57c96a38beb63db45d6c159b5ab07b6bced12c45a1f07b2b92f272aebfa6b'], - }), - (name, version, { - 'modulename': 'allel', - 'checksums': ['193ad7be829a4e155fbe68357fa3dba7af509de9673c1c94302cb23e18550297'], - }), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-bio/scikit-bio-0.5.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-bio/scikit-bio-0.5.6-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 7af3cf4942f..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-bio/scikit-bio-0.5.6-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scikit-bio' -version = '0.5.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://scikit-bio.org' -description = """scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms -and educational resources for bioinformatics.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('IPython', '7.15.0', versionsuffix), -] - -exts_list = [ - ('msgpack', '1.0.0', { - 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], - }), - ('CacheControl', '0.12.6', { - 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], - }), - ('hdmedians', '0.14.1', { - 'checksums': ['ccefaae26302afd843c941b3b662f1119d5a36dec118077310f811a7a1ed8871'], - }), - ('lockfile', '0.12.2', { - 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], - }), - ('natsort', '7.0.1', { - 'checksums': ['a633464dc3a22b305df0f27abcb3e83515898aa1fd0ed2f9726c3571a27258cf'], - }), - (name, version, { - 'checksums': ['48b73ec53ce0ff2c2e3e05f3cfcf93527c1525a8d3e9dd4ae317b4219c37f0ea'], - 'modulename': 'skbio', - }), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.10.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.10.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index c8090a74e2f..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.10.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'scikit-build' -version = '0.10.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scikit-build.readthedocs.io/en/latest' -description = """Scikit-Build, or skbuild, is an improved build system generator -for CPython C/C++/Fortran/Cython extensions.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['7342017cc82dd6178e3b19377389b8a8d1f8b429d9cdb315cfb1094e34a0f526'] - -dependencies = [ - ('Python', '3.8.2'), -] - -options = {'modulename': 'skbuild'} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.10.0-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.10.0-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index d4a71bc9ac4..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-build/scikit-build-0.10.0-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'scikit-build' -version = '0.10.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scikit-build.readthedocs.io/en/latest' -description = """Scikit-Build, or skbuild, is an improved build system generator -for CPython C/C++/Fortran/Cython extensions.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['7342017cc82dd6178e3b19377389b8a8d1f8b429d9cdb315cfb1094e34a0f526'] - -dependencies = [ - ('Python', '3.8.2'), -] - -options = {'modulename': 'skbuild'} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.17.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.17.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index b27cbe2b4cb..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-image/scikit-image-0.17.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scikit-image' -version = '0.17.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scikit-image.org/' -description = "scikit-image is a collection of algorithms for image processing." - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('Pillow', '7.0.0', versionsuffix), - ('dask', '2.18.1', versionsuffix), -] - -exts_list = [ - ('networkx', '2.4', { - 'checksums': ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'], - }), - ('PyWavelets', '1.1.1', { - 'modulename': 'pywt', - 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], - }), - ('imageio', '2.9.0', { - 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], - }), - ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], - }), - ('pooch', '1.1.1', { - 'checksums': ['a19fa11d46ddfd72e272e111ed165394b5875b7948425bc9c1df8b1a3a93ba68'], - }), - ('tifffile', '2020.7.17', { - 'checksums': ['5bcad7e2e1d88c7923da662bf85ca2a1302ceaea04198d4ca696e0f7e7908576'], - }), - (name, version, { - 'modulename': 'skimage', - 'checksums': ['1e2e2cf2572549bdb20b88a0f0ac275eea9f04f78b2b6973afdc3f329a73c75c'], - }), -] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 1c3d920d8df..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scikit-learn' -version = '0.23.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scikit-learn.org/stable/index.html' -description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, -building upon numpy, scipy, and matplotlib. As a machine-learning module, -it provides versatile tools for data mining and analysis in any field of science and engineering. -It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix) -] - -exts_list = [ - ('pytoml', '0.1.21', { - 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], - }), - ('flit-core', '2.3.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', - 'checksums': ['a50bcd8bf5785e3a7d95434244f30ba693e794c5204ac1ee908fc07c4acdbf80'], - }), - ('flit', '2.3.0', { - 'checksums': ['017012b809ec489918afd68af7a70bd7c8c770c87b60159d875c126866e97a4b'], - }), - ('threadpoolctl', '2.1.0', { - 'checksums': ['ddc57c96a38beb63db45d6c159b5ab07b6bced12c45a1f07b2b92f272aebfa6b'], - }), - (name, version, { - 'modulename': 'sklearn', - 'checksums': ['e3fec1c8831f8f93ad85581ca29ca1bb88e2da377fb097cf8322aa89c21bc9b8'], - }), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 4cfab77f332..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scikit-learn' -version = '0.23.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scikit-learn.org/stable/index.html' -description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, -building upon numpy, scipy, and matplotlib. As a machine-learning module, -it provides versatile tools for data mining and analysis in any field of science and engineering. -It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix) -] - -exts_list = [ - ('pytoml', '0.1.21', { - 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], - }), - ('flit-core', '2.3.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', - 'checksums': ['a50bcd8bf5785e3a7d95434244f30ba693e794c5204ac1ee908fc07c4acdbf80'], - }), - ('flit', '2.3.0', { - 'checksums': ['017012b809ec489918afd68af7a70bd7c8c770c87b60159d875c126866e97a4b'], - }), - ('threadpoolctl', '2.1.0', { - 'checksums': ['ddc57c96a38beb63db45d6c159b5ab07b6bced12c45a1f07b2b92f272aebfa6b'], - }), - (name, version, { - 'modulename': 'sklearn', - 'checksums': ['e3fec1c8831f8f93ad85581ca29ca1bb88e2da377fb097cf8322aa89c21bc9b8'], - }), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index e7c7bb7e122..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scikit-learn' -version = '0.23.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scikit-learn.org/stable/index.html' -description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, -building upon numpy, scipy, and matplotlib. As a machine-learning module, -it provides versatile tools for data mining and analysis in any field of science and engineering. -It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix) -] - -exts_list = [ - ('pytoml', '0.1.21', { - 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], - }), - ('flit-core', '2.3.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', - 'checksums': ['a50bcd8bf5785e3a7d95434244f30ba693e794c5204ac1ee908fc07c4acdbf80'], - }), - ('flit', '2.3.0', { - 'checksums': ['017012b809ec489918afd68af7a70bd7c8c770c87b60159d875c126866e97a4b'], - }), - ('threadpoolctl', '2.1.0', { - 'checksums': ['ddc57c96a38beb63db45d6c159b5ab07b6bced12c45a1f07b2b92f272aebfa6b'], - }), - (name, version, { - 'modulename': 'sklearn', - 'checksums': ['e3fec1c8831f8f93ad85581ca29ca1bb88e2da377fb097cf8322aa89c21bc9b8'], - }), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-intelcuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-intelcuda-2020a-Python-3.8.2.eb deleted file mode 100644 index 748c03276fe..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-learn/scikit-learn-0.23.1-intelcuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scikit-learn' -version = '0.23.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scikit-learn.org/stable/index.html' -description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, -building upon numpy, scipy, and matplotlib. As a machine-learning module, -it provides versatile tools for data mining and analysis in any field of science and engineering. -It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" - -toolchain = {'name': 'intelcuda', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix) -] - -exts_list = [ - ('pytoml', '0.1.21', { - 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], - }), - ('flit-core', '2.3.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', - 'checksums': ['a50bcd8bf5785e3a7d95434244f30ba693e794c5204ac1ee908fc07c4acdbf80'], - }), - ('flit', '2.3.0', { - 'checksums': ['017012b809ec489918afd68af7a70bd7c8c770c87b60159d875c126866e97a4b'], - }), - ('threadpoolctl', '2.1.0', { - 'checksums': ['ddc57c96a38beb63db45d6c159b5ab07b6bced12c45a1f07b2b92f272aebfa6b'], - }), - (name, version, { - 'modulename': 'sklearn', - 'checksums': ['e3fec1c8831f8f93ad85581ca29ca1bb88e2da377fb097cf8322aa89c21bc9b8'], - }), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-optimize/scikit-optimize-0.8.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-optimize/scikit-optimize-0.8.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 8e530ab7cf9..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-optimize/scikit-optimize-0.8.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'scikit-optimize' -version = '0.8.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scikit-optimize.github.io' -description = """Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive - and noisy black-box functions.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['ed5c47818959c91490120b89240527cf5ef36dc3e350dc79e5dbc22edc4ee186'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('pretty-yaml', '20.4.0'), -] - -options = {'modulename': 'skopt'} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/scikit-uplift/scikit-uplift-0.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/scikit-uplift/scikit-uplift-0.2.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index b316333bc8c..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scikit-uplift/scikit-uplift-0.2.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scikit-uplift' -version = '0.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/maks-sh/scikit-uplift' -description = """ -scikit-uplift is a Python module for classic approaches for uplift modeling built on top of scikit-learn. -Uplift prediction aims to estimate the causal impact of a treatment at the individual level. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), -] - -# pypi source has missing Readme.rst file, using github source instead -exts_list = [ - (name, version, { - 'modulename': 'sklift', - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/maks-sh/scikit-uplift/archive'], - 'checksums': ['88870b8456754eeb99f1e0582e802df178a56ec648ad74d147aedb601846a571'], - }), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/s/scipy/scipy-1.4.1-fix-pthread.patch b/easybuild/easyconfigs/__archive__/s/scipy/scipy-1.4.1-fix-pthread.patch deleted file mode 100644 index d399b2ba412..00000000000 --- a/easybuild/easyconfigs/__archive__/s/scipy/scipy-1.4.1-fix-pthread.patch +++ /dev/null @@ -1,39 +0,0 @@ -From https://github.com/scipy/scipy/pull/11324 -Author: Peter Bell -diff --git a/scipy/fft/_pocketfft/setup.py b/scipy/fft/_pocketfft/setup.py -index a4411bdedb1..493387d9719 100644 ---- a/scipy/fft/_pocketfft/setup.py -+++ b/scipy/fft/_pocketfft/setup.py -@@ -5,20 +5,28 @@ def pre_build_hook(build_ext, ext): - cc = build_ext._cxx_compiler - args = ext.extra_compile_args - -- std_flag = get_cxx_std_flag(build_ext._cxx_compiler) -+ std_flag = get_cxx_std_flag(cc) - if std_flag is not None: - args.append(std_flag) - - if cc.compiler_type == 'msvc': - args.append('/EHsc') - else: -- try_add_flag(args, cc, '-fvisibility=hidden') -- -+ # Use pthreads if available - has_pthreads = try_compile(cc, code='#include \n' - 'int main(int argc, char **argv) {}') - if has_pthreads: - ext.define_macros.append(('POCKETFFT_PTHREADS', None)) -- -+ if has_flag(cc, '-pthread'): -+ args.append('-pthread') -+ ext.extra_link_args.append('-pthread') -+ else: -+ raise RuntimeError("Build failed: System has pthreads header " -+ "but could not compile with -pthread option") -+ -+ # Don't export library symbols -+ try_add_flag(args, cc, '-fvisibility=hidden') -+ # Set min macOS version - min_macos_flag = '-mmacosx-version-min=10.9' - import sys - if sys.platform == 'darwin' and has_flag(cc, min_macos_flag): diff --git a/easybuild/easyconfigs/__archive__/s/seqtk/seqtk-1.3-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/seqtk/seqtk-1.3-GCC-9.3.0.eb deleted file mode 100644 index 098086d30eb..00000000000 --- a/easybuild/easyconfigs/__archive__/s/seqtk/seqtk-1.3-GCC-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'seqtk' -version = '1.3' - -homepage = 'https://github.com/lh3/seqtk/' -description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. - It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -github_account = 'lh3' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563'] - -dependencies = [('zlib', '1.2.11')] - -skipsteps = ['configure'] - -buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' - -preinstallopts = "mkdir %(installdir)s/bin && " -installopts = 'BINDIR=%(installdir)s/bin/' - -sanity_check_paths = { - 'files': ['bin/seqtk'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/sf/sf-0.9-5-foss-2020a-R-4.0.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/sf/sf-0.9-5-foss-2020a-R-4.0.0-Python-3.8.2.eb deleted file mode 100644 index 3c9a55c5048..00000000000 --- a/easybuild/easyconfigs/__archive__/s/sf/sf-0.9-5-foss-2020a-R-4.0.0-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'RPackage' - -name = 'sf' -version = '0.9-5' -local_pyver = '3.8.2' -versionsuffix = '-R-%%(rver)s-Python-%s' % local_pyver - -homepage = 'https://cran.r-project.org/package=sf' -description = """Support for simple features, a standardized way to encode spatial vector data. Binds to GDAL for -reading and writing data, to GEOS for geometrical operations, and to PROJ for projection conversions and datum -transformations.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['8e3f3bf0b967c213c495e0a7d17abd832cced0e77f52b0669b37fc9db156a830'] - -dependencies = [ - ('R', '4.0.0'), - ('Python', local_pyver), - ('GDAL', '3.0.4', '-Python-%s' % local_pyver), # required for sf - ('GEOS', '3.8.1', '-Python-%s' % local_pyver), # required for sf - ('PROJ', '7.0.0'), # required for sf -] - -modextrapaths = {'R_LIBS_SITE': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/smithwaterman/smithwaterman-20160702-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/smithwaterman/smithwaterman-20160702-GCCcore-9.3.0.eb deleted file mode 100644 index a93cddd94f5..00000000000 --- a/easybuild/easyconfigs/__archive__/s/smithwaterman/smithwaterman-20160702-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'smithwaterman' -version = '20160702' -local_commit = '2610e25' - -homepage = 'https://github.com/ekg/smithwaterman' -description = """smith-waterman-gotoh alignment algorithm.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'ekg' -source_urls = [GITHUB_SOURCE] -sources = ['%s.tar.gz' % local_commit] -patches = ['%(name)s-20160702_build-shared-lib.patch'] -checksums = [ - '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz - '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch -] - -builddependencies = [('binutils', '2.34')] - -skipsteps = ['configure'] - -installopts = 'PREFIX=%(installdir)s ' - -sanity_check_paths = { - 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], - 'dirs': [], -} - -sanity_check_commands = ["%(name)s --help"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/snakemake/snakemake-5.26.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/snakemake/snakemake-5.26.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index ca92f3fa92d..00000000000 --- a/easybuild/easyconfigs/__archive__/s/snakemake/snakemake-5.26.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,78 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'snakemake' -version = '5.26.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://snakemake.readthedocs.io' -description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('PyYAML', '5.3'), - ('GitPython', '3.1.9', versionsuffix), -] - -exts_list = [ - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('ratelimiter', '1.2.0.post0', { - 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], - }), - ('ConfigArgParse', '1.2.3', { - 'checksums': ['edd17be986d5c1ba2e307150b8e5f5107aba125f3574dddd02c85d5cdcfd37dc'], - }), - ('datrie', '0.8.2', { - 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], - }), - ('pyrsistent', '0.17.3', { - 'checksums': ['2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e'], - }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('traitlets', '5.0.5', { - 'checksums': ['178f4ce988f69189f7e523337a3e11d91c786ded9360174a3d9ca83e79bc5396'], - }), - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('jupyter-core', '4.6.3', { - 'modulename': 'jupyter_core', - 'source_tmpl': 'jupyter_core-%(version)s.tar.gz', - 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], - }), - ('nbformat', '5.0.8', { - 'checksums': ['f545b22138865bfbcc6b1ffe89ed5a2b8e2dc5d4fe876f2ca60d8e6f702a30f8'], - }), - ('toposort', '1.5', { - 'checksums': ['dba5ae845296e3bf37b042c640870ffebcdeb8cd4df45adaa01d8c5476c557dd'], - }), - ('amply', '0.1.4', { - 'checksums': ['cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38'], - }), - ('PuLP', '2.3', { - 'checksums': ['9d8ecf532868cc31fa9ff59ee5d5b2049600c5c902c18c794a2bad677c1f92e5'], - }), - (name, version, { - 'checksums': ['94cfed2f47f6441cca6cf9d53cffdc11eb78dd1758d96c0af9cd5e453247363e'], - }), -] - -# site-specific: the line below is the command for loading this module with the (default) EB module naming scheme -# if necessary, change this command to match your cluster setup -local_snakemake_load = 'module load %(module_name)s' -modextravars = {'SNAKEMAKE_LOAD_MODULE': local_snakemake_load} - -sanity_check_paths = { - 'files': ['bin/snakemake'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], -} - -sanity_check_commands = ['snakemake --help'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb deleted file mode 100644 index 2313fa31373..00000000000 --- a/easybuild/easyconfigs/__archive__/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'snappy' -version = '1.1.8' - -homepage = 'https://github.com/google/snappy' -description = """Snappy is a compression/decompression library. It does not aim -for maximum compression, or compatibility with any other compression library; -instead, it aims for very high speeds and reasonable compression.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/google/snappy/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['16b677f07832a612b0836178db7f374e414f94657c138e6993cbfc5dcc58651f'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code -_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' -configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] - -sanity_check_paths = { - 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], - 'dirs': [''] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb deleted file mode 100644 index aba93468232..00000000000 --- a/easybuild/easyconfigs/__archive__/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb +++ /dev/null @@ -1,61 +0,0 @@ -# Author: Jasper Grimm (UoY) - -easyblock = 'CmdCp' - -name = 'snippy' -version = '4.6.0' -local_pyversuffix = '-Python-%(pyver)s' -local_javaversuffix = '-Java-%(javaver)s' -versionsuffix = local_javaversuffix + local_pyversuffix - -homepage = 'https://github.com/tseemann/snippy' -description = """Snippy finds SNPs between a haploid reference genome and your NGS sequence - reads. It will find both substitutions (snps) and insertions/deletions (indels). - Rapid haploid variant calling and core genome alignment.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -github_account = 'tseemann' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['7264e3819e249387effd3eba170ff49404b1cf7347dfa25944866f5aeb6b11c3'] - -dependencies = [ - ('Java', '13', '', SYSTEM), - ('Python', '3.8.2'), - ('Perl', '5.30.2'), - ('BioPerl', '1.7.7'), - ('any2fasta', '0.4.2'), - ('BWA', '0.7.17'), - ('BCFtools', '1.10.2'), - ('BEDTools', '2.29.2'), - ('freebayes', '1.3.5', local_pyversuffix), - ('gzip', '1.10'), - ('minimap2', '2.17'), - ('parallel', '20200522'), - ('samclip', '0.4.0'), - ('SAMtools', '1.11'), - ('SeqLib', '1.2.0'), - ('seqtk', '1.3'), - ('snp-sites', '2.5.1'), - ('snpEff', '5.0', versionsuffix), - ('vcflib', '1.0.2', local_pyversuffix), - ('vt', '0.57721'), -] - -skipsteps = ['configure', 'build'] - -pretestopts = "cd test && " -runtest = ' ' - -files_to_copy = ['bin', 'etc', 'perl5', 'LICENSE', 'README.md'] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'etc/snpeff.config'], - 'dirs': [], -} -sanity_check_commands = ["%(namelower)s --check"] - -modextrapaths = {'PERL5LIB': 'perl5/%(name)s'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/snp-sites/snp-sites-2.5.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/snp-sites/snp-sites-2.5.1-GCCcore-9.3.0.eb deleted file mode 100644 index 3b9c97a9623..00000000000 --- a/easybuild/easyconfigs/__archive__/s/snp-sites/snp-sites-2.5.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -# Author: Jasper Grimm (UoY) - -easyblock = 'ConfigureMake' - -name = 'snp-sites' -version = '2.5.1' - -homepage = 'https://sanger-pathogens.github.io/snp-sites/' -description = """Finds SNP sites from a multi-FASTA alignment file.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'sanger-pathogens' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['913f79302e5d3127aea382756abc9ffeb05e26ce00022f43a6ea16a55cdd7a7e'] - -builddependencies = [ - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), - ('binutils', '2.34'), - ('Check', '0.15.2'), -] - -dependencies = [('zlib', '1.2.11')] - -preconfigopts = 'autoreconf -i -f &&' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['bin/snp-sites'], - 'dirs': [], -} -sanity_check_commands = ["snp-sites -h"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb deleted file mode 100644 index e05db5008e7..00000000000 --- a/easybuild/easyconfigs/__archive__/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'Tarball' - -name = 'snpEff' -version = '5.0' -versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' - -homepage = 'https://pcingola.github.io/SnpEff/' -description = """SnpEff is a variant annotation and effect prediction tool. - It annotates and predicts the effects of genetic variants (such as amino acid changes).""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://snpeff.blob.core.windows.net/versions/'] -sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] -checksums = ['2b177440eb4a2c3bbfc8f50d4adf9e405f3dcfc05a31a55c96f773f07832af34'] - -dependencies = [ - ('Java', '13', '', SYSTEM), - ('Python', '3.8.2'), - ('Perl', '5.30.2'), -] - -fix_perl_shebang_for = ['scripts/*.pl'] -fix_python_shebang_for = ['scripts/*.py'] - -sanity_check_paths = { - 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], - 'dirs': [], -} - -sanity_check_commands = ["%(name)s -version"] - -modextrapaths = {'PATH': 'scripts'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/s/sonic/sonic-20180202-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/s/sonic/sonic-20180202-gompi-2020a.eb deleted file mode 100644 index 1cbaef14976..00000000000 --- a/easybuild/easyconfigs/__archive__/s/sonic/sonic-20180202-gompi-2020a.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'MakeCp' - -name = 'sonic' -local_commit = '134074f' -version = '20180202' - -homepage = 'https://github.com/espeak-ng/sonic' -description = """ -Sonic is a simple algorithm for speeding up or slowing down speech. However, -it's optimized for speed ups of over 2X, unlike previous algorithms for changing -speech rate. The Sonic library is a very simple ANSI C library that is designed -to easily be integrated into streaming voice applications, like TTS back ends. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/espeak-ng/sonic/archive'] -sources = [{ - 'download_filename': '%s.tar.gz' % local_commit, - 'filename': SOURCE_TAR_GZ, -}] -patches = ['%(name)s-%(version)s.patch'] -checksums = [ - 'ace1ef03ab095cb73066e57b2467faddef0356579099ba64e917bf9dab072709', # sonic-20180202.tar.gz - '1e767c98286e13231d01ec7ae2ec2ea9b9c0ce074d4f8034b9d92ee2854d1be9', # sonic-20180202.patch -] - -dependencies = [('FFTW', '3.3.8')] - -keepsymlinks = True - -files_to_copy = [ - (['sonic'], 'bin'), - (['sonic.h'], 'include'), - (['libsonic*'], 'lib'), -] - -sanity_check_paths = { - 'files': ['bin/sonic', 'include/sonic.h'] + - ['lib/libsonic.%s' % x for x in ['a'] + [SHLIB_EXT + '%s' % y for y in ['', '.0', '.0.3.0']]], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/s/sparsehash/sparsehash-2.0.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/sparsehash/sparsehash-2.0.4-GCCcore-9.3.0.eb deleted file mode 100644 index cabdc34d6b0..00000000000 --- a/easybuild/easyconfigs/__archive__/s/sparsehash/sparsehash-2.0.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -# Updated from previous easyconfig -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'ConfigureMake' - -name = 'sparsehash' -version = '2.0.4' - -homepage = 'https://github.com/sparsehash/sparsehash' -description = """ - An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! - The SparseHash library contains several hash-map implementations, including - implementations that optimize for space or speed. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GITHUB_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['8cd1a95827dfd8270927894eb77f62b4087735cbede953884647f16c521c7e58'] - -builddependencies = [ - ('binutils', '2.34'), -] - - -sanity_check_paths = { - 'files': ['include/google/type_traits.h'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb deleted file mode 100644 index 6666e62d45a..00000000000 --- a/easybuild/easyconfigs/__archive__/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,63 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'speech_tools' -version = '2.5.0' - -homepage = ['http://festvox.org/festival/'] - -description = """ -The Edinburgh Speech Tools Library is a collection of C++ class, -functions and related programs for manipulating the sorts of objects -used in speech processing. It includes support for reading and writing -waveforms, parameter files (LPC, Ceptra, F0) in various formats -and converting between them. -It also includes support for linguistic type objects and support -for various label files and ngrams (with smoothing). -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://festvox.org/packed/festival/%(version_major_minor)s'] -sources = ['%(name)s-%(version)s-release.tar.gz'] -patches = ['%(name)s-%(version)s_easybuild.patch'] -checksums = [ - 'e4fd97ed78f14464358d09f36dfe91bc1721b7c0fa6503e04364fb5847805dcc', # speech_tools-2.5.0-release.tar.gz - '192012d97a671b151f084e0423042e03446a6031a8d7718354f2a56022210921', # speech_tools-2.5.0_easybuild.patch -] - -unpack_options = '--strip-components=1' - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('ncurses', '6.2'), - ('Perl', '5.30.2'), -] - -# LIBS environmental variable interfers with libs/Makefile line 61: LIBS_ABS=$(subst $(TOP),$$(EST_HOME),$(LIBS)) -prebuildopts = 'unset LIBS &&' - -# If g++ used for compiling c++ files, then some extra link-time libraries detrmined wrongly -# and the binary creation fails -buildopts = 'CXX="${CC}"' - -buildininstalldir = True - -maxparallel = 1 - -local_sanity = [ - 'align', 'bcat', 'ch_lab', 'ch_track', 'ch_utt', 'ch_wave', 'design_filter', 'est_program', 'na_play', - 'na_record', 'ngram_build', 'ols', 'pda', 'pitchmark', 'raw_to_xgraph', 'resynth', 'scfg_make', 'scfg_parse', - 'scfg_train', 'sig2fv', 'sigfilter', 'siod', 'spectgen', 'tex_to_images', 'tilt_analysis', 'tilt_synthesis', - 'viterbi', 'wagon', 'wfst_build', 'wfst_run', 'wfst_train', 'xml_parser', -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_sanity + ['Makefile', 'pm']] + - ['lib/lib%s.a' % x for x in ['estbase', 'estools', 'eststring']], - 'dirs': [] -} - -sanity_check_commands = ['%s -h' % x for x in local_sanity] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index d143012579c..00000000000 --- a/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'spglib-python' -version = '1.16.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/spglib' -description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] -sources = ['spglib-%(version)s.tar.gz'] -checksums = ['94d056e48e7e6fe2e6fe4161471e774ac03221a6225fd83d551d3184220c1edf'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -options = {'modulename': 'spglib'} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index e1d95951b12..00000000000 --- a/easybuild/easyconfigs/__archive__/s/spglib-python/spglib-python-1.16.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'spglib-python' -version = '1.16.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/spglib' -description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] -sources = ['spglib-%(version)s.tar.gz'] -checksums = ['94d056e48e7e6fe2e6fe4161471e774ac03221a6225fd83d551d3184220c1edf'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - -options = {'modulename': 'spglib'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/s/stars/stars-0.4-3-foss-2020a-R-4.0.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/stars/stars-0.4-3-foss-2020a-R-4.0.0-Python-3.8.2.eb deleted file mode 100644 index 8fa82d979bd..00000000000 --- a/easybuild/easyconfigs/__archive__/s/stars/stars-0.4-3-foss-2020a-R-4.0.0-Python-3.8.2.eb +++ /dev/null @@ -1,58 +0,0 @@ -easyblock = 'Bundle' - -name = 'stars' -version = '0.4-3' -local_pyver = '3.8.2' -versionsuffix = '-R-%%(rver)s-Python-%s' % local_pyver - -homepage = 'https://cran.r-project.org/package=stars' -description = """Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) - in R, using GDAL bindings provided by sf, and NetCDF bindings by ncmeta and RNetCDF.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('R', '4.0.0'), - ('Python', local_pyver), - ('GDAL', '3.0.4', '-Python-%s' % local_pyver), # required for sf - ('GEOS', '3.8.1', '-Python-%s' % local_pyver), # required for sf - ('PROJ', '7.0.0'), # required for sf - ('netCDF', '4.7.4'), - ('sf', '0.9-5', versionsuffix), -] - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -exts_list = [ - ('RNetCDF', '2.3-1', { - 'checksums': ['7537196ee4a2ae71dd4c0e3bb4d35d2220349d82afb019a1477ed2eba06344c6'], - }), - ('ncmeta', '0.3.0', { - 'checksums': ['4b34fd27a7bfaee87ddfbc0387ed2b45956f6bbc04652649f29c311d16053766'], - }), - ('lwgeom', '0.2-5', { - 'checksums': ['4a1d93f96c10c2aac173d8186cf7d7bef7febcb3cf066a7f45da32251496d02f'], - }), - (name, version, { - 'checksums': ['a2f38d5ed4130ea36b20597ffdcc2dc0619df13804c69d72486cf93528eac279'], - }), -] - -modextrapaths = {'R_LIBS_SITE': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lwgeom', name], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.11.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.11.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 6decbc53402..00000000000 --- a/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.11.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'statsmodels' -version = '0.11.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.statsmodels.org/' -description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, -and perform statistical tests.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('patsy', '0.5.1', { - 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], - }), - (name, version, { - 'checksums': ['5bde3fa0a35a91b45dba7cbc28270b5b649ff1d721c89290883f6e831672d5f0'], - }), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.11.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.11.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 14d44ebce2e..00000000000 --- a/easybuild/easyconfigs/__archive__/s/statsmodels/statsmodels-0.11.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'statsmodels' -version = '0.11.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.statsmodels.org/' -description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, -and perform statistical tests.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('patsy', '0.5.1', { - 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], - }), - (name, version, { - 'checksums': ['5bde3fa0a35a91b45dba7cbc28270b5b649ff1d721c89290883f6e831672d5f0'], - }), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.6.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.6.2-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index a1f637c5454..00000000000 --- a/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.6.2-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'sympy' -version = '1.6.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://sympy.org/' -description = """SymPy is a Python library for symbolic mathematics. It aims to - become a full-featured computer algebra system (CAS) while keeping the code as - simple as possible in order to be comprehensible and easily extensible. SymPy - is written entirely in Python and does not require any external libraries.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -patches = ['%(name)s-%(version)s_allpython.patch'] -checksums = [ - '1cfadcc80506e4b793f5b088558ca1fcbeaec24cd6fc86f1fdccaa3ee1d48708', # sympy-1.6.2.tar.gz - '605f4f1aadbbfd3d44f1cfeae34ed920323a408efb5b43737b0458e9a90e447f', # sympy-1.6.2_allpython.patch -] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('gmpy2', '2.1.0b5'), -] - -runtest = 'python setup.py test' - -sanity_check_paths = { - 'files': ['bin/isympy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.6.2_allpython.patch b/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.6.2_allpython.patch deleted file mode 100644 index bd3676e70a6..00000000000 --- a/easybuild/easyconfigs/__archive__/s/sympy/sympy-1.6.2_allpython.patch +++ /dev/null @@ -1,138 +0,0 @@ -Updated patch file sympy-1.5.1_allpython.patch for version 1.6.2 -Author: Samuel Moors, Vrije Universiteit Brussel (VUB) -# this patch contains fixes for two different problems: -# -# *** IOError: [Errno 39] aka "Directory not empty" FIX *** -# -# - 22.1.2019, J. Dvoracek (Institute of Physics | Czech Academy of Sciences, www.fzu.cz -# -# While running test step on NFS share, it fails with: -# File "(...)sympy/utilities/_compilation/tests/test_compilation.py", line 61 -# in test_compile_link_import_strings -# shutil.rmtree(info['build_dir']) -# File "(...)lib/python3.6/shutil.py", line 484, in rmtree -# onerror(os.rmdir, path, sys.exc_info()) -# File "(...)lib/python3.6/shutil.py", line 482, in rmtree -# os.rmdir(path) -# OSError: [Errno 39] Directory not empty: '(...)sympy-1.3/tmp695y36rc' -# -# shmem.rmtree() is called when file inside is stil being used, so files are renamed to .nfsXXXXX -# and rmtee fails with Errno 39 (Directory not empty) error. -# As we're running the tests in Easybuild, we can assume that the buil_dir will be deleted by EasyBuild, -# so we can safely skip the delete operation -# -# *** IOError: [Errno 2] aka "No such file or directory" FIX *** -# -# - original (1.10.2018, B. Hajgato (Free Ubiversity Brussels - VUB) -# -# During some test jobs, an error -# IOError: [Errno 2] No such file or directory: '/tmp/hajgato/link/eb-Tfchx1/tmpx5Z16m/_newton.c' -# occured, if the tmpdir was a symlink or any of its subdir was a symlink. Therefore, realpath is used. -# -# - update (22.1.2019, J. Dvoracek (Institute of Physics | Czech Academy of Sciences, www.fzu.cz ) -# -# fix above deals just with the occurence in Python2. Now we use the same trick for Python3 too. - ---- sympy-1.3/sympy/utilities/_compilation/tests/test_compilation.py_orig 2019-01-21 21:47:46.552355000 +0100 -+++ sympy-1.3/sympy/utilities/_compilation/tests/test_compilation.py 2019-01-21 21:48:16.358586000 +0100 -@@ -58,4 +58,4 @@ - assert numpy.allclose(res_mod, res_npy) - finally: - if info and info['build_dir']: -- shutil.rmtree(info['build_dir']) -+ pass - -diff -ur sympy-1.6.2.orig/sympy/codegen/tests/test_algorithms.py sympy-1.6.2/sympy/codegen/tests/test_algorithms.py ---- sympy-1.6.2.orig/sympy/codegen/tests/test_algorithms.py 2020-08-09 18:58:47.000000000 +0200 -+++ sympy-1.6.2/sympy/codegen/tests/test_algorithms.py 2020-09-07 14:27:54.479107000 +0200 -@@ -8,7 +8,8 @@ - from sympy.external import import_module - from sympy.printing.ccode import ccode - from sympy.utilities._compilation import compile_link_import_strings, has_c, has_fortran --from sympy.utilities._compilation.util import TemporaryDirectory, may_xfail -+from sympy.utilities._compilation.util import may_xfail -+from sympy.utilities._compilation.util import TemporaryDirectory_DND as TemporaryDirectory - from sympy.testing.pytest import skip, raises - - cython = import_module('cython') -diff -ur sympy-1.6.2.orig/sympy/codegen/tests/test_applications.py sympy-1.6.2/sympy/codegen/tests/test_applications.py ---- sympy-1.6.2.orig/sympy/codegen/tests/test_applications.py 2020-08-09 18:58:47.000000000 +0200 -+++ sympy-1.6.2/sympy/codegen/tests/test_applications.py 2020-09-07 14:30:30.424309000 +0200 -@@ -3,7 +3,8 @@ - from sympy.external import import_module - from sympy.printing.ccode import ccode - from sympy.utilities._compilation import compile_link_import_strings, has_c --from sympy.utilities._compilation.util import TemporaryDirectory, may_xfail -+from sympy.utilities._compilation.util import may_xfail -+from sympy.utilities._compilation.util import TemporaryDirectory_DND as TemporaryDirectory - from sympy.testing.pytest import skip - from sympy.codegen.ast import ( - FunctionDefinition, FunctionPrototype, Variable, Pointer, real, Assignment, -diff -ur sympy-1.6.2.orig/sympy/codegen/tests/test_fnodes.py sympy-1.6.2/sympy/codegen/tests/test_fnodes.py ---- sympy-1.6.2.orig/sympy/codegen/tests/test_fnodes.py 2020-08-09 18:58:47.000000000 +0200 -+++ sympy-1.6.2/sympy/codegen/tests/test_fnodes.py 2020-09-07 14:29:15.151121000 +0200 -@@ -14,7 +14,8 @@ - from sympy.external import import_module - from sympy.printing.fcode import fcode - from sympy.utilities._compilation import has_fortran, compile_run_strings, compile_link_import_strings --from sympy.utilities._compilation.util import TemporaryDirectory, may_xfail -+from sympy.utilities._compilation.util import may_xfail -+from sympy.utilities._compilation.util import TemporaryDirectory_DND as TemporaryDirectory - from sympy.testing.pytest import skip - - cython = import_module('cython') - ---- sympy-1.3/sympy/utilities/_compilation/compilation.py.orig 2019-01-21 17:28:36.327899000 +0100 -+++ sympy-1.3/sympy/utilities/_compilation/compilation.py 2019-01-21 17:31:32.197254000 +0100 -@@ -535,7 +535,8 @@ - return mod - - def _write_sources_to_build_dir(sources, build_dir): -- build_dir = build_dir or tempfile.mkdtemp() -+ #build_dir = build_dir or tempfile.mkdtemp() -+ build_dir = build_dir or tempfile.mkdtemp(prefix=os.path.realpath(tempfile.gettempprefix())) - if not os.path.isdir(build_dir): - raise OSError("Non-existent directory: ", build_dir) - ---- sympy-1.3/sympy/utilities/_compilation/util.py.orig 2018-09-06 21:27:21.000000000 +0200 -+++ sympy-1.3/sympy/utilities/_compilation/util.py 2019-01-21 20:19:25.030436000 +0100 -@@ -25,21 +25,26 @@ - return func - - --if sys.version_info[0] == 2: -- class FileNotFoundError(IOError): -- pass -+class FileNotFoundError(IOError): -+ pass - -- class TemporaryDirectory(object): -- def __init__(self): -- self.path = tempfile.mkdtemp() -- def __enter__(self): -- return self.path -- def __exit__(self, exc, value, tb): -- shutil.rmtree(self.path) --else: -- FileNotFoundError = FileNotFoundError -- TemporaryDirectory = tempfile.TemporaryDirectory -+class TemporaryDirectory(object): -+ def __init__(self): -+ # self.path = tempfile.mkdtemp() -+ self.path = tempfile.mkdtemp(prefix=os.path.realpath(tempfile.gettempprefix())) -+ def __enter__(self): -+ return self.path -+ def __exit__(self, exc, value, tb): -+ shutil.rmtree(self.path) - -+class TemporaryDirectory_DND(object): -+ def __init__(self): -+ # self.path = tempfile.mkdtemp() -+ self.path = tempfile.mkdtemp(prefix=os.path.realpath(tempfile.gettempprefix())) -+ def __enter__(self): -+ return self.path -+ def __exit__(self, exc, value, tb): -+ pass - - class CompilerNotFoundError(FileNotFoundError): - pass diff --git a/easybuild/easyconfigs/__archive__/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb deleted file mode 100644 index 680897efbc7..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -# Author: Jasper Grimm (UoY) -easyblock = 'CmdCp' - -name = 'TALYS' -version = '1.95' - -homepage = 'https://tendl.web.psi.ch/tendl_2019/talys.html' -description = "TALYS is a nuclear reaction program." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'noopt': True} - -source_urls = ['https://tendl.web.psi.ch/tendl_2019/talys/'] -sources = ['%(namelower)s%(version)s.tar'] -checksums = ['f7efe1e07cdc072394b2b9ec5801ba70957d4f1be1eaee22c4975cc9840a57c6'] - -builddependencies = [('binutils', '2.34')] - -start_dir = 'source' - -# Use environment variable to set structure directory path -local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' -local_sed += ' -e "s|character*132 path|character*256 path|g" ' -local_sed += ' -e "s|//\'abundance|//\'/abundance|g" machine.f && ' -# Also strip hardcoded talys path in verify script -local_sed += 'sed -i "/talys=.*/d" ../samples/verify ' - -cmds_map = [('.*', '%s && $FC $FFLAGS $FCFLAGS -o talys *.f' % local_sed)] - -files_to_copy = [(['%(namelower)s'], 'bin'), 'structure', 'samples'] - -sanity_check_paths = { - 'files': ['bin/talys'], - 'dirs': ['samples', 'structure'], -} - -sanity_check_commands = ["cd %(builddir)s/%(namelower)s/samples && ./verify"] - -modextravars = {'TALYS_STRUCTURE_DIR': '%(installdir)s/structure'} - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index f440c8f7169..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'TAMkin' -version = '1.2.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://molmod.github.io/tamkin/' -description = """TAMkin is a post-processing toolkit for normal mode analysis, - thermochemistry and reaction kinetics. It uses a Hessian computation from a - standard computational chemistry program as its input.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -patches = [ - 'TAMkin-1.2.6_fix-python38.patch', - 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', -] -checksums = [ - {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, - {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, - {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, -] - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('molmod', '1.4.5', versionsuffix), -] - -# disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' -runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.2.6-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.2.6-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 6d43a85793b..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.2.6-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'TAMkin' -version = '1.2.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://molmod.github.io/tamkin/' -description = """TAMkin is a post-processing toolkit for normal mode analysis, - thermochemistry and reaction kinetics. It uses a Hessian computation from a - standard computational chemistry program as its input.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -patches = ['TAMkin-1.2.6_fix-python38.patch'] -checksums = [ - '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd', # TAMkin-1.2.6.tar.gz - '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b', # TAMkin-1.2.6_fix-python38.patch -] - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('molmod', '1.4.5', versionsuffix), -] - -# disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' -runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/t/TCLAP/TCLAP-1.2.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/TCLAP/TCLAP-1.2.4-GCCcore-9.3.0.eb deleted file mode 100644 index 0ef17e1c4e0..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TCLAP/TCLAP-1.2.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'TCLAP' -version = '1.2.4' - -homepage = 'http://tclap.sourceforge.net/' -description = """TCLAP is a small, flexible library that provides a simple interface for defining and accessing -command line arguments. It was initially inspired by the user friendly CLAP library.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['634c5b59dbb1ccbc9d6a5f6de494a257e29a3f59dcb6fc30445ff39b45188574'] - -builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -preconfigopts = "autoreconf -i -f && " - -runtest = 'check' - -sanity_check_paths = { - 'files': ['include/tclap/CmdLine.h'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/TEtranscripts/TEtranscripts-2.2.0-foss-2020a.eb b/easybuild/easyconfigs/__archive__/t/TEtranscripts/TEtranscripts-2.2.0-foss-2020a.eb deleted file mode 100644 index 777918771b1..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TEtranscripts/TEtranscripts-2.2.0-foss-2020a.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'TEtranscripts' -version = '2.2.0' - -homepage = 'https://github.com/mhammell-laboratory/TEtranscripts' -description = """TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads -to both genes & transposable elements. -TEtranscripts then performs differential analysis using DESeq2.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -multi_deps = {'Python': ['3.8.2', '2.7.18']} - -dependencies = [ - ('Pysam', '0.16.0.1'), - ('R-bundle-Bioconductor', '3.11', '-R-4.0.0'), -] - -exts_list = [ - ('argparse', '1.4.0', { - 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], - }), - (name, version, { - 'source_urls': ['https://github.com/mhammell-laboratory/TEtranscripts/archive/'], - 'source_tmpl': '%(version)s.tar.gz', - 'checksums': ['9060f284ca20d598cfb6cc6895d5708afdd7850b353359fbe32e893f29bda98e'], - 'modulename': 'TEToolkit', - }), -] - -fix_python_shebang_for = ['bin/*'] - -sanity_check_paths = { - 'files': ['bin/TEtranscripts', 'bin/TEcount'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - 'TEtranscripts --version', - 'TEcount --version', -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/TINKER/TINKER-8.8.1-foss-2020a.eb b/easybuild/easyconfigs/__archive__/t/TINKER/TINKER-8.8.1-foss-2020a.eb deleted file mode 100644 index 02797e394cd..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TINKER/TINKER-8.8.1-foss-2020a.eb +++ /dev/null @@ -1,20 +0,0 @@ -name = 'TINKER' -version = '8.8.1' - -homepage = 'https://dasher.wustl.edu/tinker' -description = """The TINKER molecular modeling software is a complete and general package for molecular mechanics - and dynamics, with some special features for biopolymers.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://dasher.wustl.edu/tinker/downloads/'] -sources = [SOURCELOWER_TAR_GZ] - -checksums = ['8477afb51a0dcbba421948645eb77df3d071de984440b2e2d14063f9477e6d2e'] - -runtest = True - - -# sanity_check_commands is not possible since all the programs require multiple other inputs - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/t/TRF/TRF-4.09.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/TRF/TRF-4.09.1-GCCcore-9.3.0.eb deleted file mode 100644 index 81b41527d96..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TRF/TRF-4.09.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'TRF' -version = '4.09.1' - -homepage = 'https://tandem.bu.edu/trf/trf.html' -description = """Tandem Repeats Finder: a program to analyze DNA sequences.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'Benson-Genomics-Lab' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), -] - -preconfigopts = "autoreconf -i -f && " - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [], -} - -sanity_check_commands = ["%(namelower)s -v"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/TRIQS-cthyb/TRIQS-cthyb-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/TRIQS-cthyb/TRIQS-cthyb-3.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 0b3c6cdeb87..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TRIQS-cthyb/TRIQS-cthyb-3.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,62 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'TRIQS-cthyb' -version = '3.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://triqs.github.io/cthyb/' -description = """ - TRIQS (Toolbox for Research on Interacting Quantum Systems) is a - scientific project providing a set of C++ and Python libraries to - develop new tools for the study of interacting quantum systems. - - cthyb = continuous-time hybridisation-expansion quantum Monte Carlo - - The TRIQS-based hybridization-expansion solver allows to solve the - generic problem of a quantum impurity embedded in a conduction bath - for an arbitrary local interaction vertex. The “impurity” can be any - set of orbitals, on one or several atoms. -""" - -docurls = ['https://triqs.github.io/cthyb/%(version_major_minor)s.x/'] -software_license = 'LicenseGPLv3' - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/TRIQS/cthyb/releases/download/%(version)s/'] -sources = ['cthyb-%(version)s.tar.gz'] -checksums = ['64970bfc73f5be819a87044411b4cc9e1f7996d122158c5c011046b7e1aec4e5'] - -dependencies = [ - ('Python', '3.8.2'), - ('TRIQS', '3.0.0', versionsuffix), - ('NFFT', '3.5.2') -] - -builddependencies = [ - ('CMake', '3.16.4') -] - -separate_build_dir = True - -runtest = 'test' - -sanity_check_paths = { - 'files': ['lib/libtriqs_cthyb_c.a'], - 'dirs': ['include', 'include/triqs_cthyb', 'lib', - 'lib/python%(pyshortver)s/site-packages', 'share'], -} - -sanity_check_commands = ["python -c 'import triqs_cthyb'"] - -modextrapaths = { - 'CPLUS_INCLUDE_PATH': 'include', - 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_cthyb', -} -modextravars = { - 'TRIQS_CTHYB_ROOT': '%(installdir)s', - 'TRIQS_CTHYB_VERSION': '%(version)s', -} - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/t/TRIQS-dft_tools/TRIQS-dft_tools-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/TRIQS-dft_tools/TRIQS-dft_tools-3.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 9bb34618509..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TRIQS-dft_tools/TRIQS-dft_tools-3.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,63 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'TRIQS-dft_tools' -version = '3.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://triqs.github.io/dft_tools/' -description = """ - TRIQS (Toolbox for Research on Interacting Quantum Systems) is a - scientific project providing a set of C++ and Python libraries to - develop new tools for the study of interacting quantum systems. - - This TRIQS-based-based application is aimed at ab-initio calculations - for correlated materials, combining realistic DFT band-structure calculation - with the dynamical mean-field theory. Together with the necessary tools to - perform the DMFT self-consistency loop for realistic multi-band problems, - the package provides a full-fledged charge self-consistent interface to the - Wien2K package. In addition, if Wien2k is not available, it provides a generic - interface for one-shot DFT+DMFT calculations, where only the single-particle - Hamiltonian in orbital space has to be provided. -""" - -docurls = ['https://triqs.github.io/dft_tools/%(version_major_minor)s.x/'] -software_license = 'LicenseGPLv3' - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/TRIQS/dft_tools/releases/download/%(version)s/'] -sources = ['dft_tools-%(version)s.tar.gz'] -checksums = ['646d1d2dca5cf6ad90e18d0706124f701aa94ec39c5236d8fcf36dc5c628a3f6'] - -dependencies = [ - ('Python', '3.8.2'), - ('TRIQS', '3.0.0', versionsuffix), -] - -builddependencies = [ - ('CMake', '3.16.4') -] - -separate_build_dir = True - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/dmftproj', 'lib/libtriqs_dft_tools_c.a'], - 'dirs': ['include/triqs_dft_tools', 'bin', 'lib', 'share', - 'lib/python%(pyshortver)s/site-packages/triqs_dft_tools'], -} - -sanity_check_commands = ["python -c 'import triqs_dft_tools'"] - -modextrapaths = { - 'CPLUS_INCLUDE_PATH': 'include', - 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_dft_tools', -} -modextravars = { - 'TRIQS_DFT_TOOLS_ROOT': '%(installdir)s', - 'TRIQS_DFT_TOOLS_VERSION': '%(version)s', -} - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/t/TRIQS-tprf/TRIQS-tprf-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/TRIQS-tprf/TRIQS-tprf-3.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index b4e4d5be446..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TRIQS-tprf/TRIQS-tprf-3.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,63 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'TRIQS-tprf' -version = '3.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://triqs.github.io/tprf' -description = """ - TRIQS (Toolbox for Research on Interacting Quantum Systems) is a - scientific project providing a set of C++ and Python libraries to - develop new tools for the study of interacting quantum systems. - - TPRF is a TRIQS-based two-particle response function tool box that - implements basic operations for higher order response functions such - as inversion, products, the random phase approximation, the bethe - salpeter equation (in the local vertex approximation), etc.. - - The aim is to provide efficient (C++/OpenMP/MPI) implementations of - the basic operations needed to compute the two-particle response in - the different two-particle channels (particle-hole, particle-particle). -""" - -docurls = ['https://triqs.github.io/tprf/%(version_major_minor)s.x/'] -software_license = 'LicenseGPLv3' - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/TRIQS/tprf/releases/download/%(version)s/'] -sources = ['tprf-%(version)s.tar.gz'] -checksums = ['8e20620145bb8cbcc187f4637884457c0cacaed79ba6e1709a951046ee5ffc4b'] - -dependencies = [ - ('Python', '3.8.2'), - ('TRIQS', '3.0.0', versionsuffix) -] - -builddependencies = [ - ('CMake', '3.16.4') -] - -separate_build_dir = True - -runtest = 'test' - -sanity_check_paths = { - 'files': ['lib/libtriqs_tprf_c.a'], - 'dirs': ['include/triqs_tprf', 'lib', 'share', - 'lib/python%(pyshortver)s/site-packages/triqs_tprf'], -} - -sanity_check_commands = ["python -c 'import triqs_tprf'"] - -modextrapaths = { - 'CPLUS_INCLUDE_PATH': 'include', - 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_tprf', -} -modextravars = { - 'TRIQS_TPRF_ROOT': '%(installdir)s', - 'TRIQS_TPRF_VERSION': '%(version)s' -} - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index de76530e80f..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,70 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'TRIQS' -version = '3.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://triqs.github.io/triqs' -description = """ - TRIQS (Toolbox for Research on Interacting Quantum Systems) is a - scientific project providing a set of C++ and Python libraries to - develop new tools for the study of interacting quantum systems. -""" - -docurls = ['https://triqs.github.io/triqs/%(version_major_minor)s.x/'] -software_license = 'LicenseGPLv3' - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/TRIQS/triqs/releases/download/%(version)s/'] -sources = ['triqs-%(version)s.tar.gz'] -checksums = ['21239fb42ba73f84a77b63abce84c0d2b9162277233d5839aaf39e22e1be8128'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), - ('Boost', '1.72.0'), - ('Clang', '10.0.1'), - ('Clang-Python-bindings', '10.0.1', '-Python-%(pyver)s'), - ('GMP', '6.2.0'), - ('HDF5', '1.10.6'), - ('Mako', '1.1.2') -] - -builddependencies = [ - ('CMake', '3.16.4') -] - -separate_build_dir = True - -# Remove installation directory before building. This fixes problems with -# failing builds in the presence of preexisting installation. -preconfigopts = "rm -rf %(installdir)s && " - -configopts = "-DBuild_Deps=Always" - -runtest = 'test' - -sanity_check_paths = { - 'files': ['lib/libtriqs.%s' % SHLIB_EXT], - 'dirs': ['include/triqs', 'include/itertools', 'include/mpi', 'include/cpp2py', - 'lib/python%(pyshortver)s/site-packages', 'share'], -} - -sanity_check_commands = [ - "triqs++ --help", - "c++2py --help", - "python -c 'import triqs'" -] - -modextrapaths = { - 'CPLUS_INCLUDE_PATH': 'include', - 'CMAKE_PREFIX_PATH': ['lib/cmake/triqs', 'lib/cmake/cpp2py'] -} -modextravars = { - 'TRIQS_ROOT': '%(installdir)s', - 'TRIQS_VERSION': '%(version)s' -} - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/t/Tcl/Tcl-8.6.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/Tcl/Tcl-8.6.10-GCCcore-9.3.0.eb deleted file mode 100644 index 6bccbe04ae5..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Tcl/Tcl-8.6.10-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.10' - -homepage = 'https://www.tcl.tk/' -description = """ - Tcl (Tool Command Language) is a very powerful but easy to learn dynamic - programming language, suitable for a very wide range of uses, including web - and desktop applications, networking, administration, testing and many more. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -sources = ['%(namelower)s%(version)s-src.tar.gz'] -checksums = ['5196dbf6638e3df8d5c87b5815c8c2b758496eb6f0e41446596c9a4e638d87ed'] - -builddependencies = [ - ('binutils', '2.34'), -] -dependencies = [ - ('zlib', '1.2.11'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] - -sanity_check_paths = { - 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', - 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, - 'lib/tclConfig.sh', 'man/man1/tclsh.1'], - 'dirs': ['share'], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/t/Teneto/Teneto-0.5.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/Teneto/Teneto-0.5.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 1b7bca2be1b..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Teneto/Teneto-0.5.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,60 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Teneto' -version = '0.5.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://teneto.readthedocs.io' -description = """Teneto is package for deriving, analysing and plotting temporal network representations. -Additional tools for temporal network analysis with neuroimaging contexts.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('statsmodels', '0.11.1', versionsuffix), - ('networkx', '2.4', versionsuffix), - ('Nilearn', '0.7.0', versionsuffix), - ('tqdm', '4.47.0'), -] - -exts_list = [ - ('templateflow', '0.7.1', { - 'patches': ['templateflow-0.7.1_fix_egg_version.patch'], - 'checksums': [ - 'c6e8282d1ffbb5dca7bd704a12e02bd00021860b71a043c35716861910c7187f', # templateflow-0.7.1.tar.gz - # templateflow-0.7.1_fix_egg_version.patch - '2464eadf55f4523af10056fbf62562fa69608583b476336017ec910c5a5ade3d', - ], - }), - ('bids-validator', '1.5.8', { - 'checksums': ['5b8c3b9047d2e00e25746d55f56f62071f0a82dd2de59371a1ee589fe28b2852'], - }), - ('num2words', '0.5.10', { - 'checksums': ['37cd4f60678f7e1045cdc3adf6acf93c8b41bf732da860f97d301f04e611cc57'], - }), - ('SQLAlchemy', '1.3.22', { - 'checksums': ['758fc8c4d6c0336e617f9f6919f9daea3ab6bb9b07005eda9a1a682e24a6cacc'], - }), - ('pybids', '0.12.4', { - 'modulename': 'bids', - 'checksums': ['830f3f518ab0d2e058e9ba6d6ff9a942792909c874433b3ad58a3339a23f46bf'], - }), - ('python-louvain', '0.15', { - 'modulename': 'community', - 'checksums': ['2a856edfbe29952a60a5538a84bb78cca18f6884a88b9325e85a11c8dd4917eb'], - }), - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['62041cacd9d2ae95258d11a754c8937107c67ef4603f7a702f809337920efa4a'], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/Teneto/templateflow-0.7.1_fix_egg_version.patch b/easybuild/easyconfigs/__archive__/t/Teneto/templateflow-0.7.1_fix_egg_version.patch deleted file mode 100644 index 035614d54d1..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Teneto/templateflow-0.7.1_fix_egg_version.patch +++ /dev/null @@ -1,12 +0,0 @@ -Fix templateflow so that it installs the templateflow-.dist-info dir with the correct version instead of 0.0.0 - -Åke sandgren, 2021-01-27 -diff -ru templateflow-0.7.1.orig/setup.py templateflow-0.7.1/setup.py ---- templateflow-0.7.1.orig/setup.py 2020-12-09 18:13:21.000000000 +0100 -+++ templateflow-0.7.1/setup.py 2021-01-27 21:51:29.682057978 +0100 -@@ -4,4 +4,4 @@ - - if __name__ == "__main__": - """ Install entry-point """ -- setup() -+ setup(use_scm_version=True) diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-json-include-style.patch b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-json-include-style.patch deleted file mode 100644 index 8e2429a01fc..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-json-include-style.patch +++ /dev/null @@ -1,137 +0,0 @@ -From 20a00a0328fe1ad08ef51311b93d72d939c142e7 Mon Sep 17 00:00:00 2001 -From: Alexander Grund -Date: Thu, 20 Aug 2020 16:39:40 +0200 -Subject: [PATCH] Include jsonCPP headers via #include "json/json.h" - -Don't use #include "include/json/json.h" which is unusual and therefore confusing -This allows to remove the header symlinking done for the system lib version - -Closes #42303 ---- - .../core/platform/cloud/gcs_file_system.cc | 2 +- - .../platform/cloud/google_auth_provider.cc | 2 +- - tensorflow/core/platform/cloud/oauth_client.h | 2 +- - .../profiler/convert/trace_events_to_json.cc | 2 +- - .../convert/trace_events_to_json_test.cc | 2 +- - .../core/profiler/internal/tfprof_timeline.h | 2 +- - third_party/systemlibs/jsoncpp.BUILD | 27 ------------------- - 9 files changed, 8 insertions(+), 35 deletions(-) - -diff --git a/tensorflow/core/platform/cloud/gcs_file_system.cc b/tensorflow/core/platform/cloud/gcs_file_system.cc -index f0d2138b379ea..59eb610fc5377 100644 ---- a/tensorflow/core/platform/cloud/gcs_file_system.cc -+++ b/tensorflow/core/platform/cloud/gcs_file_system.cc -@@ -30,7 +30,7 @@ limitations under the License. - #include // for _mktemp - #endif - #include "absl/base/macros.h" --#include "include/json/json.h" -+#include "json/json.h" - #include "tensorflow/core/lib/gtl/map_util.h" - #include "tensorflow/core/platform/cloud/curl_http_request.h" - #include "tensorflow/core/platform/cloud/file_block_cache.h" -diff --git a/tensorflow/core/platform/cloud/google_auth_provider.cc b/tensorflow/core/platform/cloud/google_auth_provider.cc -index e8546ca022f22..57240fa2494b8 100644 ---- a/tensorflow/core/platform/cloud/google_auth_provider.cc -+++ b/tensorflow/core/platform/cloud/google_auth_provider.cc -@@ -24,7 +24,7 @@ limitations under the License. - #include - - #include "absl/strings/match.h" --#include "include/json/json.h" -+#include "json/json.h" - #include "tensorflow/core/platform/base64.h" - #include "tensorflow/core/platform/env.h" - #include "tensorflow/core/platform/errors.h" -diff --git a/tensorflow/core/platform/cloud/oauth_client.h b/tensorflow/core/platform/cloud/oauth_client.h -index ed8bf2572535e..97af3ecaf1785 100644 ---- a/tensorflow/core/platform/cloud/oauth_client.h -+++ b/tensorflow/core/platform/cloud/oauth_client.h -@@ -18,7 +18,7 @@ limitations under the License. - - #include - --#include "include/json/json.h" -+#include "json/json.h" - #include "tensorflow/core/platform/cloud/http_request.h" - #include "tensorflow/core/platform/env.h" - #include "tensorflow/core/platform/status.h" -diff --git a/tensorflow/core/profiler/convert/trace_events_to_json.cc b/tensorflow/core/profiler/convert/trace_events_to_json.cc -index ba3e4516c8cae..ad40292ceffb3 100644 ---- a/tensorflow/core/profiler/convert/trace_events_to_json.cc -+++ b/tensorflow/core/profiler/convert/trace_events_to_json.cc -@@ -21,7 +21,7 @@ limitations under the License. - - #include "absl/strings/str_cat.h" - #include "absl/strings/str_format.h" --#include "include/json/json.h" -+#include "json/json.h" - #include "tensorflow/core/platform/types.h" - #include "tensorflow/core/profiler/protobuf/trace_events.pb.h" - -diff --git a/tensorflow/core/profiler/convert/trace_events_to_json_test.cc b/tensorflow/core/profiler/convert/trace_events_to_json_test.cc -index dc985f2f76feb..bf08a19e0221e 100644 ---- a/tensorflow/core/profiler/convert/trace_events_to_json_test.cc -+++ b/tensorflow/core/profiler/convert/trace_events_to_json_test.cc -@@ -15,7 +15,7 @@ limitations under the License. - - #include "tensorflow/core/profiler/convert/trace_events_to_json.h" - --#include "include/json/json.h" -+#include "json/json.h" - #include "tensorflow/core/platform/protobuf.h" - #include "tensorflow/core/platform/test.h" - #include "tensorflow/core/profiler/protobuf/trace_events.pb.h" -diff --git a/tensorflow/core/profiler/internal/tfprof_timeline.h b/tensorflow/core/profiler/internal/tfprof_timeline.h -index 834e3c9be911e..fb9ff8012e06f 100644 ---- a/tensorflow/core/profiler/internal/tfprof_timeline.h -+++ b/tensorflow/core/profiler/internal/tfprof_timeline.h -@@ -17,7 +17,7 @@ limitations under the License. - #define TENSORFLOW_CORE_PROFILER_INTERNAL_TFPROF_TIMELINE_H_ - - #include "absl/strings/str_cat.h" --#include "include/json/json.h" -+#include "json/json.h" - #include "tensorflow/core/framework/graph.pb.h" - #include "tensorflow/core/framework/step_stats.pb.h" - #include "tensorflow/core/profiler/internal/tfprof_node_show.h" -diff --git a/third_party/systemlibs/jsoncpp.BUILD b/third_party/systemlibs/jsoncpp.BUILD -index 7d54f9289bfc7..b5951e3a3404f 100644 ---- a/third_party/systemlibs/jsoncpp.BUILD -+++ b/third_party/systemlibs/jsoncpp.BUILD -@@ -5,35 +5,8 @@ filegroup( - visibility = ["//visibility:public"], - ) - --HEADERS = [ -- "include/json/allocator.h", -- "include/json/assertions.h", -- "include/json/autolink.h", -- "include/json/config.h", -- "include/json/features.h", -- "include/json/forwards.h", -- "include/json/json.h", -- "include/json/reader.h", -- "include/json/value.h", -- "include/json/version.h", -- "include/json/writer.h", --] -- --genrule( -- name = "link_headers", -- outs = HEADERS, -- cmd = """ -- for i in $(OUTS); do -- i=$${i##*/} -- ln -sf $(INCLUDEDIR)/jsoncpp/json/$$i $(@D)/include/json/$$i -- done -- """, --) -- - cc_library( - name = "jsoncpp", -- hdrs = HEADERS, -- includes = ["."], - linkopts = ["-ljsoncpp"], - visibility = ["//visibility:public"], - ) diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-protoc-build.patch b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-protoc-build.patch deleted file mode 100644 index d9c98c14dcb..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-protoc-build.patch +++ /dev/null @@ -1,37 +0,0 @@ -commit c8231eb55bdbff94c44e4b554321017fbd01bda9 -Author: Alexander Grund -Date: Wed Jul 29 16:57:39 2020 +0200 - - Fix environment for protobuf compilation - - Patch using upstream https://github.com/grpc/grpc/pull/23664 - -https://github.com/tensorflow/tensorflow/pull/41889 -diff --git a/tensorflow/workspace.bzl b/tensorflow/workspace.bzl -index 24446d846c..ee63c4a811 100755 ---- a/tensorflow/workspace.bzl -+++ b/tensorflow/workspace.bzl -@@ -687,6 +687,7 @@ def tf_repositories(path_prefix = "", tf_repo_name = ""): - sha256 = "b956598d8cbe168b5ee717b5dafa56563eb5201a947856a6688bbeac9cac4e1f", - strip_prefix = "grpc-b54a5b338637f92bfcf4b0bc05e0f57a5fd8fadd", - system_build_file = clean_dep("//third_party/systemlibs:grpc.BUILD"), -+ patch_file = clean_dep("//third_party/grpc:generate_cc_env_fix.patch"), - system_link_files = { - "//third_party/systemlibs:BUILD": "bazel/BUILD", - "//third_party/systemlibs:grpc.BUILD": "src/compiler/BUILD", -diff --git a/third_party/grpc/generate_cc_env_fix.patch b/third_party/grpc/generate_cc_env_fix.patch -new file mode 100644 -index 0000000000..51832fe962 ---- /dev/null -+++ b/third_party/grpc/generate_cc_env_fix.patch -@@ -0,0 +1,10 @@ -+--- a/bazel/generate_cc.bzl -++++ b/bazel/generate_cc.bzl -+@@ -141,6 +141,7 @@ def generate_cc_impl(ctx): -+ outputs = out_files, -+ executable = ctx.executable._protoc, -+ arguments = arguments, -++ use_default_shell_env = True, -+ ) -+ -+ return struct(files = depset(out_files)) diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch deleted file mode 100644 index f7447d6300e..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch +++ /dev/null @@ -1,119 +0,0 @@ -From ab6c3bf9d98d7627509865e91913c25a1f8cc693 Mon Sep 17 00:00:00 2001 -From: Steven Clarkson -Date: Sat, 22 Aug 2020 16:57:25 -0700 -Subject: [PATCH] Add missing systemlib protobuf libraries - ---- - third_party/systemlibs/protobuf.BUILD | 83 +++++++++++++++++++++++++++ - 1 file changed, 83 insertions(+) - -diff --git a/third_party/systemlibs/protobuf.BUILD b/third_party/systemlibs/protobuf.BUILD -index 118135d129005..ef3e0c93c6483 100644 ---- a/third_party/systemlibs/protobuf.BUILD -+++ b/third_party/systemlibs/protobuf.BUILD -@@ -15,8 +15,13 @@ filegroup( - HEADERS = [ - "google/protobuf/any.pb.h", - "google/protobuf/any.proto", -+ "google/protobuf/api.pb.h", -+ "google/protobuf/api.proto", - "google/protobuf/arena.h", - "google/protobuf/compiler/importer.h", -+ "google/protobuf/compiler/plugin.h", -+ "google/protobuf/compiler/plugin.pb.h", -+ "google/protobuf/compiler/plugin.proto", - "google/protobuf/descriptor.h", - "google/protobuf/descriptor.pb.h", - "google/protobuf/descriptor.proto", -@@ -32,9 +37,15 @@ HEADERS = [ - "google/protobuf/io/zero_copy_stream_impl_lite.h", - "google/protobuf/map.h", - "google/protobuf/repeated_field.h", -+ "google/protobuf/source_context.pb.h", -+ "google/protobuf/source_context.proto", -+ "google/protobuf/struct.pb.h", -+ "google/protobuf/struct.proto", - "google/protobuf/text_format.h", - "google/protobuf/timestamp.pb.h", - "google/protobuf/timestamp.proto", -+ "google/protobuf/type.pb.h", -+ "google/protobuf/type.proto", - "google/protobuf/util/json_util.h", - "google/protobuf/util/type_resolver_util.h", - "google/protobuf/wrappers.pb.h", -@@ -102,3 +113,75 @@ py_library( - srcs_version = "PY2AND3", - visibility = ["//visibility:public"], - ) -+ -+proto_library( -+ name = "any_proto", -+ srcs = ["google/protobuf/any.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "api_proto", -+ srcs = ["google/protobuf/api.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "compiler_plugin_proto", -+ srcs = ["google/protobuf/compiler/plugin.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "descriptor_proto", -+ srcs = ["google/protobuf/descriptor.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "duration_proto", -+ srcs = ["google/protobuf/duration.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "empty_proto", -+ srcs = ["google/protobuf/empty.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "field_mask_proto", -+ srcs = ["google/protobuf/field_mask.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "source_context_proto", -+ srcs = ["google/protobuf/source_context.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "struct_proto", -+ srcs = ["google/protobuf/struct.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "timestamp_proto", -+ srcs = ["google/protobuf/timestamp.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "type_proto", -+ srcs = ["google/protobuf/type.proto"], -+ visibility = ["//visibility:public"], -+) -+ -+proto_library( -+ name = "wrappers_proto", -+ srcs = ["google/protobuf/wrappers.proto"], -+ visibility = ["//visibility:public"], -+) diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf2.patch b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf2.patch deleted file mode 100644 index 4eac729e655..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf2.patch +++ /dev/null @@ -1,103 +0,0 @@ -From 32c2048560940dcc3c475eefdc857bb6202d18e0 Mon Sep 17 00:00:00 2001 -From: Alexander Grund -Date: Fri, 11 Sep 2020 17:14:34 +0200 -Subject: [PATCH] Do not symlink system protobuf headers but only required - .proto files - -Symlinking the system headers has proven to be problematic as newer -versions of protobuf add or remove headers which makes having a static -array of header files hard to impossible. Turns out the headers don't -need to be symlinked at all but only the .proto files used as inputs -need to be present. ---- - third_party/systemlibs/protobuf.BUILD | 35 +++------------------------ - 1 file changed, 3 insertions(+), 32 deletions(-) - -diff --git a/third_party/systemlibs/protobuf.BUILD b/third_party/systemlibs/protobuf.BUILD -index ef3e0c93c6483..ccf2ab4dc7d8b 100644 ---- a/third_party/systemlibs/protobuf.BUILD -+++ b/third_party/systemlibs/protobuf.BUILD -@@ -12,49 +12,24 @@ filegroup( - visibility = ["//visibility:public"], - ) - --HEADERS = [ -- "google/protobuf/any.pb.h", -+PROTO_FILES = [ - "google/protobuf/any.proto", -- "google/protobuf/api.pb.h", - "google/protobuf/api.proto", -- "google/protobuf/arena.h", -- "google/protobuf/compiler/importer.h", -- "google/protobuf/compiler/plugin.h", -- "google/protobuf/compiler/plugin.pb.h", - "google/protobuf/compiler/plugin.proto", -- "google/protobuf/descriptor.h", -- "google/protobuf/descriptor.pb.h", - "google/protobuf/descriptor.proto", -- "google/protobuf/duration.pb.h", - "google/protobuf/duration.proto", -- "google/protobuf/dynamic_message.h", -- "google/protobuf/empty.pb.h", - "google/protobuf/empty.proto", -- "google/protobuf/field_mask.pb.h", - "google/protobuf/field_mask.proto", -- "google/protobuf/io/coded_stream.h", -- "google/protobuf/io/zero_copy_stream.h", -- "google/protobuf/io/zero_copy_stream_impl_lite.h", -- "google/protobuf/map.h", -- "google/protobuf/repeated_field.h", -- "google/protobuf/source_context.pb.h", - "google/protobuf/source_context.proto", -- "google/protobuf/struct.pb.h", - "google/protobuf/struct.proto", -- "google/protobuf/text_format.h", -- "google/protobuf/timestamp.pb.h", - "google/protobuf/timestamp.proto", -- "google/protobuf/type.pb.h", - "google/protobuf/type.proto", -- "google/protobuf/util/json_util.h", -- "google/protobuf/util/type_resolver_util.h", -- "google/protobuf/wrappers.pb.h", - "google/protobuf/wrappers.proto", - ] - - genrule( -- name = "link_headers", -- outs = HEADERS, -+ name = "link_proto_files", -+ outs = PROTO_FILES, - cmd = """ - for i in $(OUTS); do - f=$${i#$(@D)/} -@@ -66,14 +41,12 @@ genrule( - - cc_library( - name = "protobuf", -- hdrs = HEADERS, - linkopts = ["-lprotobuf"], - visibility = ["//visibility:public"], - ) - - cc_library( - name = "protobuf_headers", -- hdrs = HEADERS, - linkopts = ["-lprotobuf"], - visibility = ["//visibility:public"], - ) -@@ -94,7 +67,6 @@ genrule( - - cc_proto_library( - name = "cc_wkt_protos", -- hdrs = HEADERS, - internal_bootstrap_hack = 1, - protoc = ":protoc", - visibility = ["//visibility:public"], -@@ -109,7 +81,6 @@ proto_gen( - - py_library( - name = "protobuf_python", -- data = [":link_headers"], - srcs_version = "PY2AND3", - visibility = ["//visibility:public"], - ) diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-system_absl_py.patch b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-system_absl_py.patch deleted file mode 100644 index abe1835f0ba..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_fix-system_absl_py.patch +++ /dev/null @@ -1,55 +0,0 @@ -From fda56a4c619d093108cd2778e74073d65fb0e407 Mon Sep 17 00:00:00 2001 -From: Balint Cristian -Date: Wed, 24 Jun 2020 12:10:23 +0300 -Subject: [PATCH] [EXT-SYSLIB] Add absl_py logging submodule to build flow. - -From https://github.com/tensorflow/tensorflow/pull/40749 - ---- - tensorflow/opensource_only.files | 1 + - tensorflow/workspace.bzl | 1 + - third_party/systemlibs/absl_py.absl.logging.BUILD | 11 +++++++++++ - 3 files changed, 13 insertions(+) - create mode 100644 third_party/systemlibs/absl_py.absl.logging.BUILD - -diff --git a/tensorflow/opensource_only.files b/tensorflow/opensource_only.files -index 3d57e5f2089c5..cddf018bb21f7 100644 ---- a/tensorflow/opensource_only.files -+++ b/tensorflow/opensource_only.files -@@ -170,6 +170,7 @@ tensorflow/third_party/systemlibs/BUILD.tpl - tensorflow/third_party/systemlibs/absl_py.BUILD - tensorflow/third_party/systemlibs/absl_py.absl.flags.BUILD - tensorflow/third_party/systemlibs/absl_py.absl.testing.BUILD -+tensorflow/third_party/systemlibs/absl_py.absl.logging.BUILD - tensorflow/third_party/systemlibs/astor.BUILD - tensorflow/third_party/systemlibs/boringssl.BUILD - tensorflow/third_party/systemlibs/build_defs.bzl.tpl -diff --git a/tensorflow/workspace.bzl b/tensorflow/workspace.bzl -index f2d0c028c5fa7..d142910619c09 100755 ---- a/tensorflow/workspace.bzl -+++ b/tensorflow/workspace.bzl -@@ -535,6 +535,7 @@ def tf_repositories(path_prefix = "", tf_repo_name = ""): - "//third_party/systemlibs:absl_py.absl.BUILD": "absl/BUILD", - "//third_party/systemlibs:absl_py.absl.flags.BUILD": "absl/flags/BUILD", - "//third_party/systemlibs:absl_py.absl.testing.BUILD": "absl/testing/BUILD", -+ "//third_party/systemlibs:absl_py.absl.logging.BUILD": "absl/logging/BUILD", - }, - urls = [ - "https://storage.googleapis.com/mirror.tensorflow.org/github.com/abseil/abseil-py/archive/pypi-v0.9.0.tar.gz", -diff --git a/third_party/systemlibs/absl_py.absl.logging.BUILD b/third_party/systemlibs/absl_py.absl.logging.BUILD -new file mode 100644 -index 0000000000000..71cfc7a247c8a ---- /dev/null -+++ b/third_party/systemlibs/absl_py.absl.logging.BUILD -@@ -0,0 +1,11 @@ -+licenses(["notice"]) # Apache 2.0 -+ -+package(default_visibility = ["//visibility:public"]) -+ -+filegroup( -+ name = "LICENSE", -+) -+ -+py_library( -+ name = "logging", -+) diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch deleted file mode 100644 index 0791910e124..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch +++ /dev/null @@ -1,56 +0,0 @@ -This reverts the following commit. That change caused action_env variables to not be -passed through breaking build using system dependencies. -Author: Alexander Grund (TU Dresden) - -From f827c023906e7d30f0e5f2992b111ab34153310a Mon Sep 17 00:00:00 2001 -From: "A. Unique TensorFlower" -Date: Wed, 4 Mar 2020 22:27:03 -0800 -Subject: [PATCH] Use `exec_tools` rather than `tools` in tensorflow.bzl to - allow transitive dependencies to use python3 tools and deps in genrules - -PiperOrigin-RevId: 299023196 -Change-Id: I99981272330b060e9581c5c2a2f3992d524ae287 ---- - tensorflow/tensorflow.bzl | 12 ++++++------ - 1 file changed, 6 insertions(+), 6 deletions(-) - -diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl -index b77b923cd4d4e..e4b3fa9ae90e5 100644 ---- a/tensorflow/tensorflow.bzl -+++ b/tensorflow/tensorflow.bzl -@@ -767,7 +767,7 @@ def tf_gen_op_wrapper_cc( - out_ops_file + "_internal.cc", - ], - srcs = srcs, -- exec_tools = [":" + tool] + tf_binary_additional_srcs(), -+ tools = [":" + tool] + tf_binary_additional_srcs(), - cmd = ("$(location :" + tool + ") $(location :" + out_ops_file + ".h) " + - "$(location :" + out_ops_file + ".cc) " + - str(include_internal_ops) + " " + api_def_args_str), -@@ -969,7 +969,7 @@ def tf_gen_op_wrapper_py( - name = name + "_pygenrule", - outs = [out], - srcs = api_def_srcs + [hidden_file], -- exec_tools = [tool_name] + tf_binary_additional_srcs(), -+ tools = [tool_name] + tf_binary_additional_srcs(), - cmd = ("$(location " + tool_name + ") " + api_def_args_str + - " @$(location " + hidden_file + ") > $@"), - ) -@@ -978,7 +978,7 @@ def tf_gen_op_wrapper_py( - name = name + "_pygenrule", - outs = [out], - srcs = api_def_srcs, -- exec_tools = [tool_name] + tf_binary_additional_srcs(), -+ tools = [tool_name] + tf_binary_additional_srcs(), - cmd = ("$(location " + tool_name + ") " + api_def_args_str + " " + - op_list_arg + " " + - ("1" if op_list_is_whitelist else "0") + " > $@"), -@@ -2430,7 +2430,7 @@ def tf_generate_proto_text_sources(name, srcs_relative_dir, srcs, protodeps = [] - cmd = - "$(location //tensorflow/tools/proto_text:gen_proto_text_functions) " + - "$(@D) " + srcs_relative_dir + " $(SRCS)", -- exec_tools = [ -+ tools = [ - clean_dep("//tensorflow/tools/proto_text:gen_proto_text_functions"), - ], - ) diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 627d54a1e24..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,171 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'TensorFlow' -version = '2.3.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.tensorflow.org/' -description = "An open-source software library for Machine Intelligence" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -builddependencies = [ - ('Bazel', '3.6.0'), - ('protobuf', '3.13.0'), - # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 - ('git', '2.23.0', '-nodocs'), - ('pybind11', '2.4.3', versionsuffix), -] -dependencies = [ - ('Python', '3.8.2'), - ('h5py', '2.10.0', versionsuffix), - ('cURL', '7.69.1'), - ('double-conversion', '3.1.5'), - ('flatbuffers', '1.12.0'), - ('giflib', '5.2.1'), - ('hwloc', '2.2.0'), - ('ICU', '66.1'), - ('JsonCpp', '1.9.4'), - ('libjpeg-turbo', '2.0.4'), - ('LMDB', '0.9.24'), - ('NASM', '2.14.02'), - ('nsync', '1.24.0'), - ('SQLite', '3.31.1'), - ('PCRE', '8.44'), - ('protobuf-python', '3.13.0', versionsuffix), - ('libpng', '1.6.37'), - ('snappy', '1.1.8'), - ('SWIG', '4.0.1'), - ('zlib', '1.2.11'), -] - -# Dependencies created and updated using findPythonDeps.sh: -# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d -exts_list = [ - ('Markdown', '3.2.2', { - 'checksums': ['1fafe3f1ecabfb514a5285fca634a53c1b32a81cb0feb154264d55bf2ff22c17'], - }), - ('pyasn1-modules', '0.2.8', { - 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], - }), - ('rsa', '4.6', { - 'checksums': ['109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa'], - }), - ('cachetools', '4.1.1', { - 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], - }), - ('google-auth', '1.22.1', { - 'modulename': 'google.auth', - 'checksums': ['9c0f71789438d703f77b94aad4ea545afaec9a65f10e6cc1bc8b89ce242244bb'], - }), - ('oauthlib', '3.1.0', { - 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], - }), - ('requests-oauthlib', '1.3.0', { - 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], - }), - ('google-auth-oauthlib', '0.4.1', { - 'checksums': ['88d2cd115e3391eb85e1243ac6902e76e77c5fe438b7276b297fbe68015458dd'], - }), - ('Werkzeug', '1.0.1', { - 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], - }), - ('absl-py', '0.10.0', { - 'modulename': 'absl', - 'checksums': ['b20f504a7871a580be5268a18fbad48af4203df5d33dbc9272426cb806245a45'], - }), - ('astunparse', '1.6.3', { - 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], - }), - ('grpcio', '1.33.1', { - 'modulename': 'grpc', - 'checksums': ['f19782ec5104599382a0f73f2dfea465d0e65f6818bb3c49ca672b97034c64c3'], - 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", - }), - ('gviz-api', '1.9.0', { - 'source_tmpl': 'gviz_api-%(version)s.tar.gz', - 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], - }), - ('tensorboard', '2.3.0', { - 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['d34609ed83ff01dd5b49ef81031cfc9c166bba0dabd60197024f14df5e8eae5e'], - }), - ('tensorboard-plugin-wit', '1.7.0', { - 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['ee775f04821185c90d9a0e9c56970ee43d7c41403beb6629385b39517129685b'], - }), - ('tensorboard-plugin-profile', '2.3.0', { - 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', - 'checksums': ['7fea73dd591297a0d75604e9be61c35c693ead4ecfce1df4bb6f0e3d33677e0f'], - }), - ('google-pasta', '0.2.0', { - 'modulename': 'pasta', - 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], - }), - ('termcolor', '1.1.0', { - 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], - }), - ('tensorflow-estimator', '2.3.0', { - 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['b75e034300ccb169403cf2695adf3368da68863aeb0c14c3760064c713d5c486'], - }), - ('astor', '0.8.1', { - 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], - }), - ('gast', '0.3.3', { - 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], - }), - ('opt-einsum', '3.3.0', { - 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', - 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('Keras-Preprocessing', '1.1.2', { - 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', - 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], - }), - (name, version, { - 'patches': [ - 'TensorFlow-2.1.0_fix-cuda-build.patch', - 'TensorFlow-2.1.0_fix-system-nasm.patch', - 'TensorFlow-2.3.0_fix-json-include-style.patch', - 'TensorFlow-2.3.0_fix-system_absl_py.patch', - 'TensorFlow-2.3.0_fix-system-protobuf.patch', - 'TensorFlow-2.3.0_fix-system-protobuf2.patch', - 'TensorFlow-2.3.0_fix-protoc-build.patch', - 'TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch', - 'TensorFlow-2.3.1_fix-aarch64.patch', - ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], - 'test_script': 'TensorFlow-2.x_mnist-test.py', - 'checksums': [ - 'ee534dd31a811f7a759453567257d1e643f216d8d55a25c32d2fbfff8153a1ac', # v2.3.1.tar.gz - '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch - # TensorFlow-2.1.0_fix-system-nasm.patch - '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', - # TensorFlow-2.3.0_fix-json-include-style.patch - 'e04f5d9aa4c1222393b2cad4b84cd63128ef56eb5cc732d2afbc5d98dfa596a4', - # TensorFlow-2.3.0_fix-system_absl_py.patch - '04e53b637ca64c4804a4a8d636d75e3c09257034b143b70a33bfee09e6ab4b10', - # TensorFlow-2.3.0_fix-system-protobuf.patch - '4407c3f126eb9d3c1658ef8d6ab3a26e7ed2a40ac869dd194d8a1282f6432c1d', - # TensorFlow-2.3.0_fix-system-protobuf2.patch - '74718e007acb7f5f016848218421895a33e9e894620154482deb75408225577d', - # TensorFlow-2.3.0_fix-protoc-build.patch - '78a8390ea5e06dfcfb25f6434721abbe678e37c4ad7f052aad766c4df399bd53', - # TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch - '1a72f072a764bf66733445ce027c0bad7de7c88092363c0e2a7b91a422608d56', - # TensorFlow-2.3.1_fix-aarch64.patch - '3407fe6ffdeba5168e14e529101c58cf6f1feefb943fe8188b21234bfa674982', - ], - }), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index b768888f131..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,170 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'TensorFlow' -version = '2.3.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.tensorflow.org/' -description = "An open-source software library for Machine Intelligence" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'usempi': True, 'pic': True} - -builddependencies = [ - ('Bazel', '3.6.0'), - ('protobuf', '3.13.0'), - # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 - ('git', '2.23.0', '-nodocs'), - ('pybind11', '2.4.3', versionsuffix), -] -dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), - ('Python', '3.8.2'), - ('h5py', '2.10.0', versionsuffix), - ('cURL', '7.69.1'), - ('double-conversion', '3.1.5'), - ('flatbuffers', '1.12.0'), - ('giflib', '5.2.1'), - ('hwloc', '2.2.0'), - ('ICU', '66.1'), - ('JsonCpp', '1.9.4'), - ('libjpeg-turbo', '2.0.4'), - ('LMDB', '0.9.24'), - ('NASM', '2.14.02'), - ('nsync', '1.24.0'), - ('SQLite', '3.31.1'), - ('PCRE', '8.44'), - ('protobuf-python', '3.13.0', versionsuffix), - ('libpng', '1.6.37'), - ('snappy', '1.1.8'), - ('SWIG', '4.0.1'), - ('zlib', '1.2.11'), -] - -# Dependencies created and updated using findPythonDeps.sh: -# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d -exts_list = [ - ('Markdown', '3.2.2', { - 'checksums': ['1fafe3f1ecabfb514a5285fca634a53c1b32a81cb0feb154264d55bf2ff22c17'], - }), - ('pyasn1-modules', '0.2.8', { - 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], - }), - ('rsa', '4.6', { - 'checksums': ['109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa'], - }), - ('cachetools', '4.1.1', { - 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], - }), - ('google-auth', '1.21.3', { - 'modulename': 'google.auth', - 'checksums': ['31941bf019fb242c04d0de32845da10180788bfddb0de87d78c4bdf55555dda1'], - }), - ('oauthlib', '3.1.0', { - 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], - }), - ('requests-oauthlib', '1.3.0', { - 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], - }), - ('google-auth-oauthlib', '0.4.1', { - 'checksums': ['88d2cd115e3391eb85e1243ac6902e76e77c5fe438b7276b297fbe68015458dd'], - }), - ('Werkzeug', '1.0.1', { - 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], - }), - ('absl-py', '0.10.0', { - 'modulename': 'absl', - 'checksums': ['b20f504a7871a580be5268a18fbad48af4203df5d33dbc9272426cb806245a45'], - }), - ('astunparse', '1.6.3', { - 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], - }), - ('grpcio', '1.32.0', { - 'modulename': 'grpc', - 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], - 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", - }), - ('gviz-api', '1.9.0', { - 'source_tmpl': 'gviz_api-%(version)s.tar.gz', - 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], - }), - ('tensorboard', '2.3.0', { - 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['d34609ed83ff01dd5b49ef81031cfc9c166bba0dabd60197024f14df5e8eae5e'], - }), - ('tensorboard-plugin-wit', '1.7.0', { - 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['ee775f04821185c90d9a0e9c56970ee43d7c41403beb6629385b39517129685b'], - }), - ('tensorboard-plugin-profile', '2.3.0', { - 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', - 'checksums': ['7fea73dd591297a0d75604e9be61c35c693ead4ecfce1df4bb6f0e3d33677e0f'], - }), - ('google-pasta', '0.2.0', { - 'modulename': 'pasta', - 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], - }), - ('termcolor', '1.1.0', { - 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], - }), - ('tensorflow-estimator', '2.3.0', { - 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['b75e034300ccb169403cf2695adf3368da68863aeb0c14c3760064c713d5c486'], - }), - ('astor', '0.8.1', { - 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], - }), - ('gast', '0.3.3', { - 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], - }), - ('opt-einsum', '3.3.0', { - 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', - 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('Keras-Preprocessing', '1.1.2', { - 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', - 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], - }), - (name, version, { - 'patches': [ - 'TensorFlow-2.1.0_fix-cuda-build.patch', - 'TensorFlow-2.1.0_fix-system-nasm.patch', - 'TensorFlow-2.3.0_fix-json-include-style.patch', - 'TensorFlow-2.3.0_fix-system_absl_py.patch', - 'TensorFlow-2.3.0_fix-system-protobuf.patch', - 'TensorFlow-2.3.0_fix-system-protobuf2.patch', - 'TensorFlow-2.3.0_fix-protoc-build.patch', - 'TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch', - ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], - 'test_script': 'TensorFlow-2.x_mnist-test.py', - 'checksums': [ - 'ee534dd31a811f7a759453567257d1e643f216d8d55a25c32d2fbfff8153a1ac', # v2.3.1.tar.gz - '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch - # TensorFlow-2.1.0_fix-system-nasm.patch - '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', - # TensorFlow-2.3.0_fix-json-include-style.patch - 'e04f5d9aa4c1222393b2cad4b84cd63128ef56eb5cc732d2afbc5d98dfa596a4', - # TensorFlow-2.3.0_fix-system_absl_py.patch - '04e53b637ca64c4804a4a8d636d75e3c09257034b143b70a33bfee09e6ab4b10', - # TensorFlow-2.3.0_fix-system-protobuf.patch - '4407c3f126eb9d3c1658ef8d6ab3a26e7ed2a40ac869dd194d8a1282f6432c1d', - # TensorFlow-2.3.0_fix-system-protobuf2.patch - '74718e007acb7f5f016848218421895a33e9e894620154482deb75408225577d', - # TensorFlow-2.3.0_fix-protoc-build.patch - '78a8390ea5e06dfcfb25f6434721abbe678e37c4ad7f052aad766c4df399bd53', - # TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch - '1a72f072a764bf66733445ce027c0bad7de7c88092363c0e2a7b91a422608d56', - ], - }), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.1_fix-aarch64.patch b/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.1_fix-aarch64.patch deleted file mode 100644 index c020e42592d..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TensorFlow/TensorFlow-2.3.1_fix-aarch64.patch +++ /dev/null @@ -1,19 +0,0 @@ -fix installation on Arm64 (aarch64) - -./tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h:132:58: error: cannot convert 'int32x2_t' {aka '__vector(2) int'} to 'int8x8_t' {aka '__vector(8) signed char'} - -see also https://github.com/tensorflow/tensorflow/issues/26731 + https://github.com/tensorflow/tensorflow/pull/29515 - ---- tensorflow-2.3.1/tensorflow/lite/build_def.bzl.orig 2020-11-04 13:06:26.056496930 -0000 -+++ tensorflow-2.3.1/tensorflow/lite/build_def.bzl 2020-11-04 13:07:38.265751478 -0000 -@@ -19,6 +19,10 @@ - clean_dep("//tensorflow:ios_x86_64"): [ - "-msse4.1", - ], -+ clean_dep("//tensorflow:linux_aarch64"): [ -+ "-flax-vector-conversions", -+ "-fomit-frame-pointer", -+ ], - clean_dep("//tensorflow:windows"): [ - "/DTFL_COMPILE_LIBRARY", - "/wd4018", # -Wno-sign-compare diff --git a/easybuild/easyconfigs/__archive__/t/TensorFlow/scipy-1.4.1-fix-pthread.patch b/easybuild/easyconfigs/__archive__/t/TensorFlow/scipy-1.4.1-fix-pthread.patch deleted file mode 100644 index d399b2ba412..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TensorFlow/scipy-1.4.1-fix-pthread.patch +++ /dev/null @@ -1,39 +0,0 @@ -From https://github.com/scipy/scipy/pull/11324 -Author: Peter Bell -diff --git a/scipy/fft/_pocketfft/setup.py b/scipy/fft/_pocketfft/setup.py -index a4411bdedb1..493387d9719 100644 ---- a/scipy/fft/_pocketfft/setup.py -+++ b/scipy/fft/_pocketfft/setup.py -@@ -5,20 +5,28 @@ def pre_build_hook(build_ext, ext): - cc = build_ext._cxx_compiler - args = ext.extra_compile_args - -- std_flag = get_cxx_std_flag(build_ext._cxx_compiler) -+ std_flag = get_cxx_std_flag(cc) - if std_flag is not None: - args.append(std_flag) - - if cc.compiler_type == 'msvc': - args.append('/EHsc') - else: -- try_add_flag(args, cc, '-fvisibility=hidden') -- -+ # Use pthreads if available - has_pthreads = try_compile(cc, code='#include \n' - 'int main(int argc, char **argv) {}') - if has_pthreads: - ext.define_macros.append(('POCKETFFT_PTHREADS', None)) -- -+ if has_flag(cc, '-pthread'): -+ args.append('-pthread') -+ ext.extra_link_args.append('-pthread') -+ else: -+ raise RuntimeError("Build failed: System has pthreads header " -+ "but could not compile with -pthread option") -+ -+ # Don't export library symbols -+ try_add_flag(args, cc, '-fvisibility=hidden') -+ # Set min macOS version - min_macos_flag = '-mmacosx-version-min=10.9' - import sys - if sys.platform == 'darwin' and has_flag(cc, min_macos_flag): diff --git a/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.0.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.0.4-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 3717ac42426..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Theano/Theano-1.0.4-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Theano' -version = '1.0.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://deeplearning.net/software/theano' -description = """Theano is a Python library that allows you to define, optimize, -and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] - -sanity_check_paths = { - 'files': ['bin/theano-cache', 'bin/theano-nose'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/t/Tk/Tk-8.6.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/Tk/Tk-8.6.10-GCCcore-9.3.0.eb deleted file mode 100644 index cadac1ca545..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Tk/Tk-8.6.10-GCCcore-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tk' -version = '8.6.10' - -homepage = 'https://www.tcl.tk/' -description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for - building a graphical user interface (GUI) in many different programming languages.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ["https://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] -patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] -checksums = [ - '63df418a859d0a463347f95ded5cd88a3dd3aaa1ceecaeee362194bc30f3e386', # tk8.6.10-src.tar.gz - '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch -] - -builddependencies = [('binutils', '2.34')] -dependencies = [ - ('Tcl', version), - ('X11', '20200222'), - ('zlib', '1.2.11'), -] - -configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' - -installopts = "&& make install-private-headers" - -postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] - -sanity_check_paths = { - 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], - 'dirs': [], -} - -start_dir = 'unix' - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-2.7.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-2.7.18-GCCcore-9.3.0.eb deleted file mode 100644 index 63794a7c9c4..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-2.7.18-GCCcore-9.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'Tkinter' -version = '2.7.18' - -homepage = 'https://python.org/' -description = """Tkinter module, built with the Python buildsystem""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.python.org/ftp/python/%(version)s/'] -sources = ['Python-%(version)s.tgz'] -checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Python', version), - ('Tk', '8.6.10'), - ('zlib', '1.2.11'), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-3.8.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-3.8.2-GCCcore-9.3.0.eb deleted file mode 100644 index e14f4742215..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Tkinter/Tkinter-3.8.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'Tkinter' -version = '3.8.2' - -homepage = 'https://python.org/' -description = """Tkinter module, built with the Python buildsystem""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.python.org/ftp/python/%(version)s/'] -sources = ['Python-%(version)s.tgz'] -checksums = ['e634a7a74776c2b89516b2e013dda1728c89c8149b9863b8cea21946daf9d561'] - -builddependencies = [ - ('binutils', '2.34'), - ('libffi', '3.3'), -] - -dependencies = [ - ('Python', version), - ('Tk', '8.6.10'), - ('zlib', '1.2.11'), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.1.2-gompi-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.1.2-gompi-2020a-Python-2.7.18.eb deleted file mode 100644 index 5650df12484..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.1.2-gompi-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,49 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# Modified by: Adam Huffman -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'TopHat' -version = '2.1.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' -description = "TopHat is a fast splice junction mapper for RNA-Seq reads." - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'cstd': 'gnu++98', 'pic': True} - -github_account = 'infphilo' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = ['%(namelower)s-2.0.13-zlib.patch'] -checksums = [ - '15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1', # v2.1.2.tar.gz - 'a33075c2affda995ddbd250933dbcaf94f68768b1eebead58a69705fc40306ef', # tophat-2.0.13-zlib.patch -] - -builddependencies = [('Autotools', '20180311')] - -dependencies = [ - ('Boost', '1.72.0'), - ('zlib', '1.2.11'), - ('Python', '2.7.18'), -] - -preconfigopts = './autogen.sh && ' -configopts = '--with-boost=$EBROOTBOOST' - -maxparallel = 1 - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [], -} - -sanity_check_commands = ["tophat --help 2>&1 | grep 'TopHat maps short sequences'"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.1.2-iimpi-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.1.2-iimpi-2020a-Python-2.7.18.eb deleted file mode 100644 index fed2f58716b..00000000000 --- a/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.1.2-iimpi-2020a-Python-2.7.18.eb +++ /dev/null @@ -1,51 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# Modified by: Adam Huffman -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'TopHat' -version = '2.1.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' -description = "TopHat is a fast splice junction mapper for RNA-Seq reads." - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'cstd': 'gnu++98', 'pic': True} - -github_account = 'infphilo' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] - -patches = ['%(namelower)s-2.0.13-zlib.patch'] - -checksums = [ - '15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1', # v2.1.2.tar.gz - 'a33075c2affda995ddbd250933dbcaf94f68768b1eebead58a69705fc40306ef', # tophat-2.0.13-zlib.patch -] - -builddependencies = [('Autotools', '20180311')] - -dependencies = [ - ('Boost', '1.72.0'), - ('zlib', '1.2.11'), - ('Python', '2.7.18'), -] - -preconfigopts = './autogen.sh && ' -configopts = '--with-boost=$EBROOTBOOST' - -maxparallel = 1 - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [], -} - -sanity_check_commands = ["tophat --help 2>&1 | grep 'TopHat maps short sequences'"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/Transformers/Transformers-4.2.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/Transformers/Transformers-4.2.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 0843b11de08..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Transformers/Transformers-4.2.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Transformers' -version = '4.2.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/huggingface/transformers' -description = """ -State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('tqdm', '4.47.0'), -] - -exts_list = [ - ('regex', '2020.4.4', { - 'checksums': ['295badf61a51add2d428a46b8580309c520d8b26e769868b922750cf3ce67142'], - }), - ('sacremoses', '0.0.43', { - 'checksums': ['123c1bf2664351fb05e16f87d3786dbe44a050cfd7b85161c09ad9a63a8e2948'], - }), - ('tokenizers', '0.9.4', { - 'source_tmpl': 'tokenizers-0.9.4-cp38-cp38-manylinux2010_x86_64.whl', - 'checksums': ['31184c4691aed1e84088d7a18c1000bbc59f7bedeec95774ec4027129ea16272'], - }), - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['73ca51a4b923108651e1fd8f944f526a6ae345ea548651e4a61cfc1717141cb6'], - }), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb deleted file mode 100644 index a1773acd90b..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'MakeCp' - -name = 'Triangle' -version = '1.6' - -homepage = 'https://www.cs.cmu.edu/~quake/triangle.html' -description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, - conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. - The latter can be generated with no small or large angles, - and are thus suitable for finite element analysis.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.netlib.org/voronoi/'] -sources = ['%(namelower)s.zip'] -checksums = [ - '1766327add038495fa3499e9b7cc642179229750f7201b94f8e1b7bee76f8480', # triangle.zip - '38fc1395c2392f627068b669275c30da0c25b1a6db8ed8b80d6bf05a98971568', # Triangle-1.6_makefile.patch -] - -patches = ['%(name)s-%(version)s_makefile.patch'] - -builddependencies = [('binutils', '2.34')] - -buildopts = 'triangle trilibrary' - -files_to_copy = [ - (['triangle', 'tricall'], 'bin'), - (['triangle.h'], 'include'), - (['libtriangle.a'], 'lib'), -] - -sanity_check_paths = { - 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], - 'dirs': [] -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 48d1f2c85a2..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,52 +0,0 @@ -# Contribution from the Crick HPC team -# uploaded by J. Sassmannshausen -# -# Updated to version 0.6.2: Pavel Grochal (INUITS) -# Updated to version 0.6.5: Alex Domingo (VUB) -# - -easyblock = 'Tarball' - -name = 'Trim_Galore' -version = '0.6.6' -versionsuffix = '-Python-%(pyver)s' - - -homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' -description = """Trim Galore is a wrapper around Cutadapt and FastQC to -consistently apply adapter and quality trimming to FastQ files, with extra -functionality for RRBS data.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['b8db8ffd131d9d9e7c8532a5a1f1caee656c0c58d3eafd460fee3c39b9fcab5e'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('Python', '3.8.2'), - ('Java', '11', '', SYSTEM), - ('pigz', '2.4'), - ('Perl', '5.30.2'), - ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), - ('cutadapt', '2.10', '-Python-%(pyver)s'), -] - -postinstallcmds = [ - "chmod +x %(installdir)s/%(namelower)s", - "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s", - "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", -] - -sanity_check_paths = { - 'files': ["bin/trim_galore"], - 'dirs': [], -} - -sanity_check_commands = [ - "trim_galore --help" -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/Trycycler/Trycycler-0.3.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/Trycycler/Trycycler-0.3.3-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 3b9cecbd137..00000000000 --- a/easybuild/easyconfigs/__archive__/t/Trycycler/Trycycler-0.3.3-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Trycycler' -version = '0.3.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/rrwick/Trycycler' -description = "Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes." - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/rrwick/Trycycler/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['fa79c9d8b5ca4696b660faa9a438ecd41a2f2ea59e17280e72e24be613f461d5'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('edlib', '1.3.8.post1', versionsuffix), -] - -sanity_check_paths = { - 'files': ['bin/trycycler'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["trycycler --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/tabixpp/tabixpp-1.1.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/tabixpp/tabixpp-1.1.0-GCC-9.3.0.eb deleted file mode 100644 index 1c7562561a5..00000000000 --- a/easybuild/easyconfigs/__archive__/t/tabixpp/tabixpp-1.1.0-GCC-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -# Author: Jasper Grimm (UoY) - -easyblock = 'ConfigureMake' - -name = 'tabixpp' -version = '1.1.0' - -homepage = 'https://github.com/ekg/tabixpp' -description = """C++ wrapper to tabix indexer""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -github_account = 'ekg' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-1.1.0_use-external-HTSlib.patch'] -checksums = [ - '56c8f1b07190aba5e1d0b738e380e726d380f0ad8b2d0df133200b0ab1f8ed88', # v1.1.0.tar.gz - '65496b6e042cf54290386a33cf0de26cb1160b3ddb35216765999d790b99cab4', # tabixpp-1.1.0_use-external-HTSlib.patch -] - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('HTSlib', '1.10.2'), - ('PCRE', '8.44'), -] - -skipsteps = ['configure'] - -preinstallopts = 'PREFIX=%(installdir)s' - -sanity_check_paths = { - 'files': ['bin/tabix++', 'lib/libtabixpp.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/tbb/tbb-2020.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/tbb/tbb-2020.1-GCCcore-9.3.0.eb deleted file mode 100644 index de41bbee243..00000000000 --- a/easybuild/easyconfigs/__archive__/t/tbb/tbb-2020.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'tbb' -version = '2020.1' - -homepage = 'https://01.org/tbb/' -description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that - take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/oneapi-src/oneTBB/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['7c96a150ed22bc3c6628bc3fef9ed475c00887b26d37bca61518d76a56510971'] - -builddependencies = [ - ('binutils', '2.34') -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.22.02-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.22.02-GCCcore-9.3.0.eb deleted file mode 100644 index 73e0100cebf..00000000000 --- a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.22.02-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -# Authors:: Valentin Plugaru -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html -## -easyblock = 'ConfigureMake' - -name = 'tcsh' -version = '6.22.02' - -homepage = 'https://www.tcsh.org' -description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). - It is a command language interpreter usable both as an interactive login shell and a shell script command - processor. It includes a command-line editor, programmable word completion, spelling correction, a history - mechanism, job control and a C-like syntax.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [ - 'https://astron.com/pub/%(namelower)s', - 'https://astron.com/pub/%(namelower)s/old', - 'ftp://ftp.astron.com/pub/%(namelower)s', - 'ftp://ftp.astron.com/pub/%(namelower)s/old', -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['ed287158ca1b00ba477e8ea57bac53609838ebcfd05fcb05ca95021b7ebe885b'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('ncurses', '6.2')] - -postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] - -sanity_check_paths = { - 'files': ["bin/tcsh", "bin/csh"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/texinfo/texinfo-6.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/texinfo/texinfo-6.7-GCCcore-9.3.0.eb deleted file mode 100644 index d5523aa7fde..00000000000 --- a/easybuild/easyconfigs/__archive__/t/texinfo/texinfo-6.7-GCCcore-9.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exe Escobedo -# License:: -# -# Notes:: -## - -easyblock = 'ConfigureMake' - -name = 'texinfo' -version = '6.7' - -homepage = 'https://www.gnu.org/software/texinfo/' -description = """Texinfo is the official documentation format of the GNU project.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] - -builddependencies = [('binutils', '2.34')] - -osdependencies = ['texlive'] - -preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " - -# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency -modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} -modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" -modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" -modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" -modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" -modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" - -sanity_check_paths = { - 'files': [ - 'texmf/tex/texinfo/texinfo.tex', - 'bin/install-info', 'bin/makeinfo', 'bin/pdftexi2dvi', 'bin/pod2texi', 'bin/texi2pdf' - ], - 'dirs': ['bin', 'share', 'texmf'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/t/tidybayes/tidybayes-2.1.1-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/t/tidybayes/tidybayes-2.1.1-foss-2020a-R-4.0.0.eb deleted file mode 100644 index d8be9288b03..00000000000 --- a/easybuild/easyconfigs/__archive__/t/tidybayes/tidybayes-2.1.1-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,77 +0,0 @@ -easyblock = 'Bundle' - -name = 'tidybayes' -version = '2.1.1' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/package=tidybayes' -description = """ Compose data for and extract, manipulate, and visualize -posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', -'MCMCglmm', 'coda', ...) in a tidy data format. """ - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [('R', '4.0.0')] - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -# we need a separate bundle as some dependencies are required newer than included on R-4.0.0 easyconfig -# on a newer R release this should be easily ingested - -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -exts_list = [ - ('spelling', '2.1', { - 'checksums': ['570e3803a7cc97dc43068fed16cad842794044afb00f71426c43fd24705e22c9'], - }), - ('svGUI', '1.0.0', { - 'checksums': ['ccf5167cc2423ba90003e5744bde7c7ac217e691150a20df0018654f2e58eae4'], - }), - ('svUnit', '1.0.3', { - 'checksums': ['bc059c8c49eccdaf27c485174570f942f8237d31381b6c9347c9060ff44c9f2b'], - }), - ('arrayhelpers', '1.1-0', { - 'checksums': ['5fddd5dd4fb8237bcb24465ef823bc8715ba53e6e5fd7a716c31c48ec128340b'], - }), - ('HDInterval', '0.2.2', { - 'checksums': ['047eeb08c3dba21dc1cba8e35e3191cde6cdc98c77ee3a3496e045f7937565ed'], - }), - ('rlang', '0.4.7', { - 'checksums': ['78a3d927f46f71a0b1ad7f9de6a66f986d232340f57b40c9413b3fe8a1859938'], - }), - ('vctrs', '0.3.4', { - 'checksums': ['eb47411c9e980a555f5819a7bce46896775df2ca7c9eaa7bf0a9c16f067b7877'], - }), - ('tidyselect', '1.1.0', { - 'checksums': ['e635ed381fb53f7a53c3fa36bb33e134a3273d272367de2a8d909c821be93893'], - }), - ('dplyr', '1.0.2', { - 'checksums': ['7cb1329fbf5c9609ca300f695fdfae67198b6b7273cf81b71cfc01c12d0adc4a'], - }), - ('distributional', '0.2.0', { - 'checksums': ['94c8c761f9afa5e83ed950dba73b4f6299b933d876ade94ddddf7377581529d0'], - }), - ('ggdist', '2.2.0', { - 'checksums': ['03856440b52400c4fa03bfe0a6ea403c6f453ed6772087ac200c80f8896336b3'], - }), - (name, version, { - 'checksums': ['7178abd5b5b508f0f88542552978169ec7fa3bd684466af3315d30a18e83e773'], - }), -] - -modextrapaths = {'R_LIBS_SITE': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': ['tidybayes'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/tidymodels/tidymodels-0.1.0-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/t/tidymodels/tidymodels-0.1.0-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 373d179d34f..00000000000 --- a/easybuild/easyconfigs/__archive__/t/tidymodels/tidymodels-0.1.0-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,93 +0,0 @@ -easyblock = 'Bundle' - -name = 'tidymodels' -version = '0.1.0' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/package=tidymodels' -description = """The tidy modeling "verse" is a collection of packages for -modeling and statistical analysis that share the underlying design philosophy, -grammar, and data structures of the tidyverse.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [('R', '4.0.0')] - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -# as some extensions require 'vctrs >= 0.3.0' we have to make this separate bundle to override -# the lower version included on R-4.0.0 easyconfig, on a newer R release this bundle should -# be easily ingested on it - -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -exts_list = [ - ('GPfit', '1.0-8', { - 'checksums': ['7e4dfc28c49cad67afbd9c018255234c57a4baadc10a412ee660f72da28fb716'], - }), - ('vctrs', '0.3.1', { - 'checksums': ['17e6358735504166ecb1aab581e5fa5e565ffb6f10e8a12c4d476a8e1f8aba08'], - }), - ('hardhat', '0.1.4', { - 'checksums': ['7a4b0707b031344fbed7521972f0a6f7c61dd587609fab959247c8463224523d'], - }), - ('yardstick', '0.0.6', { - 'checksums': ['0aa7be3b2ec35e15bf3329057f31f89f20bf50b35c1f32672d945b06d85e7be2'], - }), - ('furrr', version, { - 'checksums': ['dd2937f7cad1bc69e7a512b2a777f82d6cb7e40fe99afa2049ca360f9352a9d1'], - }), - ('rsample', '0.0.7', { - 'checksums': ['a832e978edde276d79e513bfa75e289c174fc64f76e016bd55716c96017ed068'], - }), - ('RcppParallel', '5.0.2', { - 'checksums': ['8ca200908c6365aafb2063be1789f0894969adc03c0f523c6cc45434b8236f81'], - }), - ('rstanarm', '2.19.3', { - 'checksums': ['7ae06e19a193f6d1eaa722d893cd004bb5ea6917e1c236ec44ad6dda16c2b23f'], - }), - ('tidyposterior', '0.0.3', { - 'checksums': ['0ff24ae844f2ac32f801bd655f2c439112df2ab3872a6e178edf14c001405b73'], - }), - ('tidypredict', '0.4.5', { - 'checksums': ['e4d578bb43f44b814d06595134201e93bd8fee8ce92736ebbc8b9b2fb9a1dfc4'], - }), - ('parsnip', '0.1.2', { - 'checksums': ['33772a0cae462ff64895fc821281ed8bcfeba4cb126b9d8d6a4272906db49f23'], - }), - ('workflows', '0.1.1', { - 'checksums': ['143bdc14e986da692fb4a81bf53de72ba315107430f05f14fe6ef9f3bf5e9f92'], - }), - ('infer', '0.5.2', { - 'checksums': ['7580f1308f9e786b34ca04531ffd4d76c70f3b9f8a592e89e453d79d3fec0054'], - }), - ('DiceDesign', '1.8-1', { - 'checksums': ['7717e77531daf181bc84a672a793d4c7d800ef351fc1aac87ea6f53948a94187'], - }), - ('dials', '0.0.7', { - 'checksums': ['00bfaf3ffceacfd46965ee9042bd383fda857f7eca037344b4f5f2c61f6d1d3b'], - }), - ('tune', version, { - 'checksums': ['107d0d273b61f8276f5d8991c3c7f0af7123de9c6207288f036d4140e76f3176'], - }), - (name, version, { - 'checksums': ['a84a28113d2b175a416446ee2208ea73d6800fb5ef2ae5e18ac2190710dc25ae'], - }), -] - -modextrapaths = {'R_LIBS_SITE': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': ['tidymodels'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/time/time-1.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/time/time-1.9-GCCcore-9.3.0.eb deleted file mode 100644 index a401c1f6118..00000000000 --- a/easybuild/easyconfigs/__archive__/t/time/time-1.9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'time' -version = '1.9' - -homepage = 'https://www.gnu.org/software/time/' -description = """The `time' command runs another program, then displays information about the resources used by that - program, collected by the system while the program was running.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] - -builddependencies = [('binutils', '2.34')] - -postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] - -sanity_check_paths = { - 'files': ['bin/gtime', 'bin/%(name)s'], - 'dirs': [], -} - -sanity_check_commands = ["time echo test"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/tiny-cuda-nn/tiny-cuda-nn-1.6_use_external_fmt+cutlass.patch b/easybuild/easyconfigs/__archive__/t/tiny-cuda-nn/tiny-cuda-nn-1.6_use_external_fmt+cutlass.patch deleted file mode 100644 index cfe7171ed17..00000000000 --- a/easybuild/easyconfigs/__archive__/t/tiny-cuda-nn/tiny-cuda-nn-1.6_use_external_fmt+cutlass.patch +++ /dev/null @@ -1,67 +0,0 @@ -Use external fmt and CUTLASS - -Åke Sandgren, 2023-11-23 -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 600bc41..c1bfba9 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -44,14 +44,6 @@ if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) - set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "RelWithDebInfo") - endif() - --if (NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/dependencies/cutlass/CMakeLists.txt") -- message(FATAL_ERROR -- "Some tiny-cuda-nn dependencies are missing. " -- "If you forgot the \"--recursive\" flag when cloning this project, " -- "this can be fixed by calling \"git submodule update --init --recursive\"." -- ) --endif() -- - if (APPLE) - set(CMAKE_MACOSX_RPATH ON) - endif() -@@ -187,7 +179,6 @@ find_library( - ) - - set(BUILD_SHARED_LIBS OFF) --add_subdirectory("dependencies/fmt") - - ############################################################################### - # tiny-cuda-nn library, samples, and benchmarks -@@ -225,9 +216,6 @@ target_compile_options(tiny-cuda-nn PUBLIC $<$:${CUDA_NVC - target_include_directories(tiny-cuda-nn PUBLIC - "include" - "dependencies" -- "dependencies/cutlass/include" -- "dependencies/cutlass/tools/util/include" -- "dependencies/fmt/include" - ) - target_link_libraries(tiny-cuda-nn PUBLIC ${CUDA_LIBRARIES} cuda cublas fmt) - -diff --git a/bindings/torch/setup.py b/bindings/torch/setup.py -index 351a2ed..5a2886f 100644 ---- a/bindings/torch/setup.py -+++ b/bindings/torch/setup.py -@@ -89,8 +89,6 @@ bindings_dir = os.path.dirname(__file__) - root_dir = os.path.abspath(os.path.join(bindings_dir, "../..")) - source_files = [ - "tinycudann/bindings.cpp", -- "../../dependencies/fmt/src/format.cc", -- "../../dependencies/fmt/src/os.cc", - "../../src/cpp_api.cu", - "../../src/common.cu", - "../../src/common_device.cu", -@@ -115,12 +113,9 @@ ext = CUDAExtension( - include_dirs=[ - "%s/include" % root_dir, - "%s/dependencies" % root_dir, -- "%s/dependencies/cutlass/include" % root_dir, -- "%s/dependencies/cutlass/tools/util/include" % root_dir, -- "%s/dependencies/fmt/include" % root_dir, - ], - extra_compile_args={"cxx": cflags, "nvcc": nvcc_flags}, -- libraries=["cuda", "cudadevrt", "cudart_static"], -+ libraries=["cuda", "cudadevrt", "cudart_static", "fmt"], - ) - ext_modules = [ext] - diff --git a/easybuild/easyconfigs/__archive__/t/tmux/tmux-3.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/tmux/tmux-3.2-GCCcore-9.3.0.eb deleted file mode 100644 index c5111b05a4f..00000000000 --- a/easybuild/easyconfigs/__archive__/t/tmux/tmux-3.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'tmux' -version = '3.2' - -homepage = 'https://github.com/tmux/tmux/' -description = """tmux is a terminal multiplexer: it enables a number of -terminals to be created, accessed, and controlled from a single screen. tmux -may be detached from a screen and continue running in the background, then -later reattached.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'optarch': True} - -source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['664d345338c11cbe429d7ff939b92a5191e231a7c1ef42f381cebacb1e08a399'] - -builddependencies = [ - ('binutils', '2.34'), - ('Bison', '3.5.3'), - ('make', '4.3'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('libevent', '2.1.11'), - ('ncurses', '6.2'), -] - -sanity_check_paths = { - 'files': ['bin/tmux'], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.47.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.47.0-GCCcore-9.3.0.eb deleted file mode 100644 index 915f2212259..00000000000 --- a/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.47.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,18 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'tqdm' -version = '4.47.0' - -homepage = "https://github.com/tqdm/tqdm" -description = """A fast, extensible progress bar for Python and CLI""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['63ef7a6d3eb39f80d6b36e4867566b3d8e5f1fe3d6cb50c5e9ede2b3198ba7b7'] - -builddependencies = [('binutils', '2.34')] - -multi_deps = {'Python': ['2.7.18', '3.8.2']} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.51.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.51.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index de23b521a43..00000000000 --- a/easybuild/easyconfigs/__archive__/t/tqdm/tqdm-4.51.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'tqdm' -version = '4.51.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/tqdm/tqdm' -description = """Instantly make your loops show a smart progress meter.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['ef54779f1c09f346b2b5a8e5c61f96fbcb639929e640e59f8cf810794f406432'] - -dependencies = [ - ('Python', '3.8.2'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/t/treatSens/treatSens-3.0-20201002-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/t/treatSens/treatSens-3.0-20201002-foss-2020a-R-4.0.0.eb deleted file mode 100644 index f293fc01b93..00000000000 --- a/easybuild/easyconfigs/__archive__/t/treatSens/treatSens-3.0-20201002-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'RPackage' - -name = 'treatSens' -local_commit = '328551e' -version = '3.0-20201002' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://github.com/vdorie/treatSens' -description = """Utilities to investigate sensitivity to unmeasured confounding in parametric models - with either binary or continuous treatment.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/vdorie/%(name)s/archive'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['994ff5b4ae61b4629cb4f015062bb7742277ad8511df222b4e2e604b2035c803'] - -dependencies = [ - ('R', '4.0.0'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb deleted file mode 100644 index 52c4b51c8b1..00000000000 --- a/easybuild/easyconfigs/__archive__/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Updated by: Robert QIAO, Flinders University -# -easyblock = 'MakeCp' - -name = 'trimAl' -version = '1.4.1' - -homepage = 'https://github.com/scapella/trimal' -description = """EVB, FEP and LIE simulator.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'scapella' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] -builddependencies = [('binutils', '2.34', '', SYSTEM)] -start_dir = 'source' - -files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/trimal', 'bin/readal', 'bin/statal'], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb b/easybuild/easyconfigs/__archive__/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb deleted file mode 100644 index 0fa522cb25d..00000000000 --- a/easybuild/easyconfigs/__archive__/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'CmdCp' - -name = 'turbinesFoam' -version = '20220516' -_openfoamver = '8' -_commit = '480eeef' -versionsuffix = '-OpenFOAM-%s' % _openfoamver - -homepage = 'https://github.com/turbinesFoam/turbinesFoam' -description = """ -turbinesFoam is a library for simulating wind and marine hydrokinetic turbines -in OpenFOAM using the actuator line method. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -github_account = 'turbinesFoam' -source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['2e13faec8b2489e91108ea3fc8eb31b1b32bb1478e608853c9cfa9b78a3206d1'] - -dependencies = [ - ('OpenFOAM', _openfoamver), -] - -cmds_map = [('.*', 'source "$FOAM_BASH" && FOAM_USER_LIBBIN="$PWD/lib" ./Allwmake')] - -files_to_copy = ['lib'] - -sanity_check_paths = { - 'files': ['lib/libturbinesFoam.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'cae' diff --git a/easybuild/easyconfigs/__archive__/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 79c16192ab6..00000000000 --- a/easybuild/easyconfigs/__archive__/t/typing-extensions/typing-extensions-3.7.4.3-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'typing-extensions' -version = '3.7.4.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' -description = "Typing Extensions – Backported and Experimental Type Hints for Python" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -sources = ['typing_extensions-%(version)s.tar.gz'] -checksums = ['99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c'] - -builddependencies = [ - ('binutils', '2.34'), -] -dependencies = [ - ('Python', '3.8.2'), -] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch b/easybuild/easyconfigs/__archive__/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch deleted file mode 100644 index a29251bbc50..00000000000 --- a/easybuild/easyconfigs/__archive__/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch +++ /dev/null @@ -1,149 +0,0 @@ -Fix hsa and hip include path - -Åke Sandgren, 2023-01-03 -diff -ru ucx-1.11.2.orig/config/m4/rocm.m4 ucx-1.11.2/config/m4/rocm.m4 ---- ucx-1.11.2.orig/config/m4/rocm.m4 2021-02-27 02:18:15.000000000 +0100 -+++ ucx-1.11.2/config/m4/rocm.m4 2023-01-03 09:23:39.310360596 +0100 -@@ -84,9 +84,9 @@ - - rocm_happy=yes - AS_IF([test "x$rocm_happy" = xyes], -- [AC_CHECK_HEADERS([hsa.h], [rocm_happy=yes], [rocm_happy=no])]) -+ [AC_CHECK_HEADERS([hsa/hsa.h], [rocm_happy=yes], [rocm_happy=no])]) - AS_IF([test "x$rocm_happy" = xyes], -- [AC_CHECK_HEADERS([hsa_ext_amd.h], [rocm_happy=yes], [rocm_happy=no])]) -+ [AC_CHECK_HEADERS([hsa/hsa_ext_amd.h], [rocm_happy=yes], [rocm_happy=no])]) - AS_IF([test "x$rocm_happy" = xyes], - [AC_CHECK_LIB([hsa-runtime64], [hsa_init], [rocm_happy=yes], [rocm_happy=no])]) - -@@ -111,7 +111,7 @@ - hip_happy=no - AC_CHECK_LIB([hip_hcc], [hipFree], [AC_MSG_WARN([Please install ROCm-3.7.0 or above])], [hip_happy=yes]) - AS_IF([test "x$hip_happy" = xyes], -- [AC_CHECK_HEADERS([hip_runtime.h], [hip_happy=yes], [hip_happy=no])]) -+ [AC_CHECK_HEADERS([hip/hip_runtime.h], [hip_happy=yes], [hip_happy=no])]) - AS_IF([test "x$hip_happy" = xyes], - [AC_CHECK_LIB([amdhip64], [hipFree], [hip_happy=yes], [hip_happy=no])]) - AS_IF([test "x$hip_happy" = xyes], [HIP_CXXFLAGS="--std=gnu++11"], []) -diff -ru ucx-1.11.2.orig/src/ucm/rocm/rocmmem.h ucx-1.11.2/src/ucm/rocm/rocmmem.h ---- ucx-1.11.2.orig/src/ucm/rocm/rocmmem.h 2021-02-27 02:18:15.000000000 +0100 -+++ ucx-1.11.2/src/ucm/rocm/rocmmem.h 2023-01-03 09:25:40.289314597 +0100 -@@ -7,7 +7,7 @@ - #define UCM_ROCMMEM_H_ - - #include --#include -+#include - - /* hsa_amd_memory_pool_allocate */ - hsa_status_t ucm_override_hsa_amd_memory_pool_allocate( -diff -ru ucx-1.11.2.orig/src/uct/rocm/base/rocm_base.h ucx-1.11.2/src/uct/rocm/base/rocm_base.h ---- ucx-1.11.2.orig/src/uct/rocm/base/rocm_base.h 2021-07-10 09:59:16.000000000 +0200 -+++ ucx-1.11.2/src/uct/rocm/base/rocm_base.h 2023-01-03 09:24:10.206096620 +0100 -@@ -9,8 +9,8 @@ - - #include - #include --#include --#include -+#include -+#include - - - hsa_status_t uct_rocm_base_init(void); -diff -ru ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_ep.c ucx-1.11.2/src/uct/rocm/copy/rocm_copy_ep.c ---- ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_ep.c 2021-09-23 22:36:08.000000000 +0200 -+++ ucx-1.11.2/src/uct/rocm/copy/rocm_copy_ep.c 2023-01-03 09:25:35.457356174 +0100 -@@ -19,7 +19,7 @@ - #include - #include - --#include -+#include - - #define uct_rocm_memcpy_h2d(_d,_s,_l) memcpy((_d),(_s),(_l)) - #define uct_rocm_memcpy_d2h(_d,_s,_l) ucs_memcpy_nontemporal((_d),(_s),(_l)) -diff -ru ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_iface.h ucx-1.11.2/src/uct/rocm/copy/rocm_copy_iface.h ---- ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_iface.h 2021-02-27 02:18:15.000000000 +0100 -+++ ucx-1.11.2/src/uct/rocm/copy/rocm_copy_iface.h 2023-01-03 09:24:33.245895073 +0100 -@@ -8,7 +8,7 @@ - - #include - --#include -+#include - - #define UCT_ROCM_COPY_TL_NAME "rocm_cpy" - -diff -ru ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_md.c ucx-1.11.2/src/uct/rocm/copy/rocm_copy_md.c ---- ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_md.c 2021-09-23 22:36:08.000000000 +0200 -+++ ucx-1.11.2/src/uct/rocm/copy/rocm_copy_md.c 2023-01-03 09:25:33.073376690 +0100 -@@ -20,7 +20,7 @@ - #include - #include - --#include -+#include - - static ucs_config_field_t uct_rocm_copy_md_config_table[] = { - {"", "", NULL, -diff -ru ucx-1.11.2.orig/src/uct/rocm/gdr/rocm_gdr_md.c ucx-1.11.2/src/uct/rocm/gdr/rocm_gdr_md.c ---- ucx-1.11.2.orig/src/uct/rocm/gdr/rocm_gdr_md.c 2021-09-23 22:36:08.000000000 +0200 -+++ ucx-1.11.2/src/uct/rocm/gdr/rocm_gdr_md.c 2023-01-03 09:25:37.569338002 +0100 -@@ -18,7 +18,7 @@ - #include - #include - --#include -+#include - - static ucs_config_field_t uct_rocm_gdr_md_config_table[] = { - {"", "", NULL, -diff -ru ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_iface.h ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_iface.h ---- ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_iface.h 2021-02-27 02:18:15.000000000 +0100 -+++ ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_iface.h 2023-01-03 09:24:27.741943217 +0100 -@@ -9,7 +9,7 @@ - - #include - --#include -+#include - - #define UCT_ROCM_IPC_TL_NAME "rocm_ipc" - -diff -ru ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_md.h ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_md.h ---- ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_md.h 2021-02-27 02:18:15.000000000 +0100 -+++ ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_md.h 2023-01-03 09:25:30.109402193 +0100 -@@ -7,7 +7,7 @@ - #define ROCM_IPC_MD_H - - #include --#include -+#include - - - extern uct_component_t uct_rocm_ipc_component; -diff -ru ucx-1.11.2.orig/test/gtest/common/mem_buffer.cc ucx-1.11.2/test/gtest/common/mem_buffer.cc ---- ucx-1.11.2.orig/test/gtest/common/mem_buffer.cc 2021-09-23 22:36:08.000000000 +0200 -+++ ucx-1.11.2/test/gtest/common/mem_buffer.cc 2023-01-03 09:32:23.085955061 +0100 -@@ -31,7 +31,7 @@ - #endif - - #if HAVE_ROCM --# include -+# include - - #define ROCM_CALL(_code) \ - do { \ -diff -ru ucx-1.11.2.orig/test/gtest/ucm/rocm_hooks.cc ucx-1.11.2/test/gtest/ucm/rocm_hooks.cc ---- ucx-1.11.2.orig/test/gtest/ucm/rocm_hooks.cc 2021-09-23 22:36:08.000000000 +0200 -+++ ucx-1.11.2/test/gtest/ucm/rocm_hooks.cc 2023-01-03 09:32:26.177929298 +0100 -@@ -5,7 +5,7 @@ - */ - #include - #include --#include -+#include - - static ucm_event_t alloc_event, free_event; - diff --git a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.7.0_binutils_2.34_api_fix.patch b/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.7.0_binutils_2.34_api_fix.patch deleted file mode 100644 index 8e7e359bbb3..00000000000 --- a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.7.0_binutils_2.34_api_fix.patch +++ /dev/null @@ -1,102 +0,0 @@ -commit 93bdcb84b707078431c8ddffbfd7a188173cc3f3 -Author: Sergey Oblomov -Date: Mon Mar 23 21:53:10 2020 +0200 - - BUILD/DEBUG: added new API of binutils - - - enables support of new API provided by binutils 2.34+ - -diff --git a/config/m4/ucs.m4 b/config/m4/ucs.m4 -index f329e50..6722a70 100644 ---- a/config/m4/ucs.m4 -+++ b/config/m4/ucs.m4 -@@ -43,6 +43,29 @@ AS_IF([test "x$enable_backtrace_detail" = xyes], - AC_CHECK_TYPES([struct dl_phdr_info], [], [AC_MSG_WARN([struct dl_phdr_info not defined])];BT=0, - [#define _GNU_SOURCE 1 - #include ]) -+ AC_CHECK_DECLS([bfd_get_section_flags, bfd_section_flags, bfd_get_section_vma, bfd_section_vma], -+ [], [], [#include ]) -+ -+ AC_MSG_CHECKING([bfd_section_size API version]) -+ AC_LANG_PUSH([C]) -+ SAVE_CFLAGS="$CFLAGS" -+ AC_COMPILE_IFELSE([AC_LANG_SOURCE([[ -+ #include -+ int main(int argc, char** argv) { -+ asection *sec = malloc(sizeof(*sec)); -+ bfd_section_size(sec); -+ free(sec); -+ return 0; -+ } ]])], -+ [AC_MSG_RESULT([1-arg API]) -+ AC_DEFINE([HAVE_1_ARG_BFD_SECTION_SIZE], [1], -+ [bfd_section_size 1-arg version])], -+ [AC_MSG_RESULT([2-args API]) -+ AC_DEFINE([HAVE_1_ARG_BFD_SECTION_SIZE], [0], -+ [bfd_section_size 2-args version])]) -+ CFLAGS="$SAVE_CFLAGS" -+ AC_LANG_POP([C]) -+ - if test "x$BT" = "x1"; then - AC_CHECK_FUNCS([cplus_demangle]) - AC_DEFINE([HAVE_DETAILED_BACKTRACE], 1, [Enable detailed backtrace]) -diff --git a/src/ucs/debug/debug.c b/src/ucs/debug/debug.c -index b5bd4a9..d7d6d46 100644 ---- a/src/ucs/debug/debug.c -+++ b/src/ucs/debug/debug.c -@@ -55,6 +55,34 @@ struct dl_address_search { - - #ifdef HAVE_DETAILED_BACKTRACE - -+#if HAVE_DECL_BFD_GET_SECTION_FLAGS -+# define ucs_debug_bfd_section_flags(_abfd, _section) \ -+ bfd_get_section_flags(_abfd, _section) -+#elif HAVE_DECL_BFD_SECTION_FLAGS -+# define ucs_debug_bfd_section_flags(_abfd, _section) \ -+ bfd_section_flags(_section) -+#else -+# error "Unsupported BFD API" -+#endif -+ -+#if HAVE_DECL_BFD_GET_SECTION_VMA -+# define ucs_debug_bfd_section_vma(_abfd, _section) \ -+ bfd_get_section_vma(_abfd, _section) -+#elif HAVE_DECL_BFD_SECTION_VMA -+# define ucs_debug_bfd_section_vma(_abfd, _section) \ -+ bfd_section_vma(_section) -+#else -+# error "Unsupported BFD API" -+#endif -+ -+#if HAVE_1_ARG_BFD_SECTION_SIZE -+# define ucs_debug_bfd_section_size(_abfd, _section) \ -+ bfd_section_size(_section) -+#else -+# define ucs_debug_bfd_section_size(_abfd, _section) \ -+ bfd_section_size(_abfd, _section); -+#endif -+ - struct backtrace_line { - unsigned long address; - char *file; -@@ -287,17 +315,17 @@ static void find_address_in_section(bfd *abfd, asection *section, void *data) - int found; - - if ((search->count > 0) || (search->max_lines == 0) || -- ((bfd_get_section_flags(abfd, section) & SEC_ALLOC) == 0)) { -+ ((ucs_debug_bfd_section_flags(abfd, section) & SEC_ALLOC) == 0)) { - return; - } - - address = search->file->dl.address - search->file->dl.base; -- vma = bfd_get_section_vma(abfd, section); -+ vma = ucs_debug_bfd_section_vma(abfd, section); - if (address < vma) { - return; - } - -- size = bfd_section_size(abfd, section); -+ size = ucs_debug_bfd_section_size(abfd, section); - if (address >= vma + size) { - return; - } diff --git a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb deleted file mode 100644 index bfafd2ff9cd..00000000000 --- a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb +++ /dev/null @@ -1,63 +0,0 @@ -# Note: -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -easyblock = 'ConfigureMake' - -name = 'UCX' -version = '1.8.0' -local_cudaversion = '11.0.2' -versionsuffix = '-CUDA-%s' % local_cudaversion - -homepage = 'http://www.openucx.org/' -description = """Unified Communication X -An open-source production grade communication framework for data centric -and high-performance applications -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.gz'] -patches = [ - 'UCX-1.7.0_binutils_2.34_api_fix.patch', - 'UCX-1.8.0_fix-undefined-symbol.patch', -] -checksums = [ - 'e400f7aa5354971c8f5ac6b881dc2846143851df868088c37d432c076445628d', # ucx-1.8.0.tar.gz - 'c09ebe4d734d520ae23f56d95ba0b91e464a42ccbaf435675424515ebd3fa3a9', # UCX-1.7.0_binutils_2.34_api_fix.patch - 'eb757242ab3eecd8a851f329cb4baf3c64d46788ab61675f29ab4cc6a0274a45', # UCX-1.8.0_fix-undefined-symbol.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -osdependencies = [OS_PKG_IBVERBS_DEV] - -dependencies = [ - ('numactl', '2.0.13'), - ('CUDAcore', local_cudaversion, '', SYSTEM), - ('GDRCopy', '2.1', versionsuffix), -] - -# CUDA_CFLAGS set by EB toolchain but also used differently in UCX makefiles -# unset LIBS from EB toolchain to avoid unconditional linking to libcudart: -# it only needs to be linked by the CUDA run-time plugins -preconfigopts = 'autoreconf && unset CUDA_CFLAGS && unset LIBS && ' -configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' -configopts += '--without-java --disable-doxygen-doc ' -configopts += '--with-cuda=$EBROOTCUDACORE --with-gdrcopy=$EBROOTGDRCOPY ' - -prebuildopts = 'unset CUDA_CFLAGS && unset LIBS && ' -buildopts = 'V=1' - -sanity_check_paths = { - 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], - 'dirs': ['include', 'lib', 'share'] -} - -sanity_check_commands = ["ucx_info -d"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb deleted file mode 100644 index e029f5e98cc..00000000000 --- a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,54 +0,0 @@ -# Note: -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -easyblock = 'ConfigureMake' - -name = 'UCX' -version = '1.8.0' - -homepage = 'http://www.openucx.org/' -description = """Unified Communication X -An open-source production grade communication framework for data centric -and high-performance applications -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.gz'] -patches = [ - 'UCX-1.7.0_binutils_2.34_api_fix.patch', - 'UCX-1.8.0_fix-undefined-symbol.patch', -] -checksums = [ - 'e400f7aa5354971c8f5ac6b881dc2846143851df868088c37d432c076445628d', # ucx-1.8.0.tar.gz - 'c09ebe4d734d520ae23f56d95ba0b91e464a42ccbaf435675424515ebd3fa3a9', # UCX-1.7.0_binutils_2.34_api_fix.patch - 'eb757242ab3eecd8a851f329cb4baf3c64d46788ab61675f29ab4cc6a0274a45', # UCX-1.8.0_fix-undefined-symbol.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), - ('pkg-config', '0.29.2'), -] - -osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] - -dependencies = [ - ('numactl', '2.0.13'), -] - -preconfigopts = 'autoreconf && ' -configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' -configopts += '--without-java --disable-doxygen-doc ' - -buildopts = 'V=1' - -sanity_check_paths = { - 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], - 'dirs': ['include', 'lib', 'share'] -} - -sanity_check_commands = ["ucx_info -d"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.8.0_fix-undefined-symbol.patch b/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.8.0_fix-undefined-symbol.patch deleted file mode 100644 index 2778984e3ff..00000000000 --- a/easybuild/easyconfigs/__archive__/u/UCX/UCX-1.8.0_fix-undefined-symbol.patch +++ /dev/null @@ -1,30 +0,0 @@ -fix for "libuct_ib.so.0: undefined symbol: uct_ib_exp_qp_fill_attr" - -see https://github.com/openucx/ucx/issues/4883 + https://github.com/openucx/ucx/pull/4900 - -From 40d6991eca6b36c6bc2c557dccfbad7a48ce5f62 Mon Sep 17 00:00:00 2001 -From: Artemy Kovalyov -Date: Tue, 17 Mar 2020 13:34:19 +0200 -Subject: [PATCH] UCT/IB/MLX5: Fix EXP accel compilation - ---- - src/uct/ib/mlx5/exp/ib_exp.h | 6 +++++- - 1 file changed, 5 insertions(+), 1 deletion(-) - -diff --git a/src/uct/ib/mlx5/exp/ib_exp.h b/src/uct/ib/mlx5/exp/ib_exp.h -index ab1d9237e1..e97f574b17 100644 ---- a/src/uct/ib/mlx5/exp/ib_exp.h -+++ b/src/uct/ib/mlx5/exp/ib_exp.h -@@ -7,7 +7,11 @@ - #ifndef UCT_IB_MLX5_EXP_H_ - #define UCT_IB_MLX5_EXP_H_ - --#if HAVE_VERBS_EXP_H -+#ifdef HAVE_CONFIG_H -+# include "config.h" -+#endif -+ -+#if HAVE_MLX5_HW && HAVE_VERBS_EXP_H - void uct_ib_exp_qp_fill_attr(uct_ib_iface_t *iface, uct_ib_qp_attr_t *attr); - #else - static inline void uct_ib_exp_qp_fill_attr(uct_ib_iface_t *iface, uct_ib_qp_attr_t *attr) { } diff --git a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb deleted file mode 100644 index 5a8a792af5f..00000000000 --- a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University -# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html -## - -easyblock = 'ConfigureMake' - -name = 'UDUNITS' -version = '2.2.26' - -homepage = 'https://www.unidata.ucar.edu/software/udunits/' -description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, - arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/', - 'https://sources.easybuild.io/u/UDUNITS/', -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('expat', '2.2.9')] - -sanity_check_paths = { - 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', - 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], - 'dirs': ['share'], -} - -maxparallel = 1 - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.2.26-foss-2020a.eb b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.2.26-foss-2020a.eb deleted file mode 100644 index ff515fd92bc..00000000000 --- a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.2.26-foss-2020a.eb +++ /dev/null @@ -1,42 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University -# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html -## - -easyblock = 'ConfigureMake' - -name = 'UDUNITS' -version = '2.2.26' - -homepage = 'https://www.unidata.ucar.edu/software/udunits/' -description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, - arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True} - -source_urls = [ - 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/', - 'https://sources.easybuild.io/u/UDUNITS/', -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] - -dependencies = [('expat', '2.2.9')] - -sanity_check_paths = { - 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', - 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], - 'dirs': ['share'], -} - -maxparallel = 1 - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/u/UMI-tools/UMI-tools-1.0.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/u/UMI-tools/UMI-tools-1.0.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index efac0cbd2a2..00000000000 --- a/easybuild/easyconfigs/__archive__/u/UMI-tools/UMI-tools-1.0.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'UMI-tools' -version = '1.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://umi-tools.readthedocs.io' -description = "Tools for handling Unique Molecular Identifiers in NGS data sets" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('matplotlib', '3.2.1', versionsuffix), - ('Pysam', '0.16.0.1'), -] - -exts_list = [ - ('regex', '2020.4.4', { - 'checksums': ['295badf61a51add2d428a46b8580309c520d8b26e769868b922750cf3ce67142'], - }), - (name, version, { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/CGATOxford/UMI-tools/archive/'], - 'checksums': ['f27e23d6c51f97239547d7093ddb5c039d0e13301e25cc4b1c568b9029e20649'], - }), -] - -sanity_check_paths = { - 'files': ['bin/umi_tools'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/u/UnZip/UnZip-6.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/u/UnZip/UnZip-6.0-GCCcore-9.3.0.eb deleted file mode 100644 index 947ade8ed55..00000000000 --- a/easybuild/easyconfigs/__archive__/u/UnZip/UnZip-6.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'UnZip' -version = '6.0' - -homepage = 'http://www.info-zip.org/UnZip.html' -description = """UnZip is an extraction utility for archives compressed -in .zip format (also called "zipfiles"). Although highly compatible both -with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's -own Zip program, our primary objectives have been portability and -non-MSDOS functionality.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://download.sourceforge.net/infozip'] -sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] -patches = [ - 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', -] -checksums = [ - '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz - # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch - '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', -] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('bzip2', '1.0.8'), -] - -skipsteps = ['configure'] - -buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' -buildopts += 'LF2="$LDFLAGS" ' -# Note: CF is multiple lines -buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' -buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' -buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' - -installopts = '-f unix/Makefile prefix=%(installdir)s ' - -sanity_check_paths = { - 'files': ['bin/unzip', 'bin/zipinfo'], - 'dirs': ['man/man1'] -} - -sanity_check_commands = ["unzip -v"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb deleted file mode 100644 index b80796afef9..00000000000 --- a/easybuild/easyconfigs/__archive__/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Unicycler' -version = '0.4.8' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/rrwick/Unicycler' -description = """ Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets - where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) - where it runs a miniasm+Racon pipeline. """ - -toolchain = {'name': 'gompi', 'version': '2020a'} - -source_urls = ['https://github.com/rrwick/Unicycler/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['e948871e4de9db5964c9ca6f8f877c3cbe6a46f62052dfab52ffe0f45bbbd203'] - -dependencies = [ - ('Python', '3.8.2'), - ('Java', '11', '', SYSTEM), - ('Bowtie2', '2.4.1'), - ('SAMtools', '1.10'), - ('SPAdes', '3.14.1', versionsuffix), - ('Racon', '1.4.13'), - ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), - ('BLAST+', '2.10.1'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/u/umi4cPackage/umi4cPackage-20200116-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/u/umi4cPackage/umi4cPackage-20200116-foss-2020a-R-4.0.0.eb deleted file mode 100644 index 17ff83f9d26..00000000000 --- a/easybuild/easyconfigs/__archive__/u/umi4cPackage/umi4cPackage-20200116-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'RPackage' - -name = 'umi4cPackage' -local_commit = '926c982' -# there doesn't seem to be a proper version, so use datestamp of commit -version = '20200116' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://github.com/tanaylab/umi4cpackage' -description = "umi4cPackage is a processing and analysis pipeline for UMI-4C experiment." - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/tanaylab/umi4cpackage/archive'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['6daa4f8907d64a2a23ab6bd9dfa5811531ec9528e685f9e778e613bc738560b5'] - -dependencies = [ - ('R', '4.0.0'), # include 'zoo' package - ('Perl', '5.30.2'), - ('Bowtie2', '2.4.1'), - ('misha', '4.0.10', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb deleted file mode 100644 index 849f979c8d6..00000000000 --- a/easybuild/easyconfigs/__archive__/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'utf8proc' -version = '2.5.0' - -homepage = 'https://github.com/JuliaStrings/utf8proc' -description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, -and other operations for data in the UTF-8 encoding.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['d4e8dfc898cfd062493cb7f42d95d70ccdd3a4cd4d90bec0c71b47cca688f1be'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -separate_build_dir = True - -configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] - -sanity_check_paths = { - 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/u/util-linux/util-linux-2.35-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/u/util-linux/util-linux-2.35-GCCcore-9.3.0.eb deleted file mode 100644 index f124a23240f..00000000000 --- a/easybuild/easyconfigs/__archive__/u/util-linux/util-linux-2.35-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'util-linux' -version = '2.35' - -homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' - -description = "Set of Linux utilities" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['%s/v%%(version_major_minor)s' % homepage] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98acab129a8490265052e6c1e033ca96d68758a13bb7fcd232c06bf16cc96238'] - -# disable account related utilities (they need OS dependent pam-devel files) -# disable wall and friends (requires group changing permissions for install user) -# install systemd service files in install dir -# install bash completion files in install dir -configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " -configopts += "--disable-wall --disable-use-tty-group " -configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " -configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " -configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " -# disable building Python bindings (since we don't include Python as a dep) -configopts += "--without-python " - -builddependencies = [('binutils', '2.34')] - -dependencies = [ - ('ncurses', '6.2'), - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], - 'dirs': ['include', 'bin', 'share', 'sbin'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/v/V8/V8-3.4.0-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/__archive__/v/V8/V8-3.4.0-foss-2020a-R-4.0.0.eb deleted file mode 100644 index d4578e7f994..00000000000 --- a/easybuild/easyconfigs/__archive__/v/V8/V8-3.4.0-foss-2020a-R-4.0.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'RPackage' - -name = 'V8' -version = '3.4.0' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/web/packages/V8/' -description = """R interface to Google's open source JavaScript engine""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/%(name)s'] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'] - -dependencies = [ - ('R', '4.0.0'), - ('nodejs', '12.16.1'), -] - -preinstallopts = 'export CPATH="$CPATH:$EBROOTNODEJS/include/node" && ' -installopts = '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"' - -sanity_check_paths = { - 'files': ['%(name)s/R/%(name)s'], - 'dirs': ['%(name)s'], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/v/VCFtools/VCFtools-0.1.16-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/v/VCFtools/VCFtools-0.1.16-GCC-9.3.0.eb deleted file mode 100644 index 7d183d2cb45..00000000000 --- a/easybuild/easyconfigs/__archive__/v/VCFtools/VCFtools-0.1.16-GCC-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'VCFtools' -version = '0.1.16' - -homepage = "https://vcftools.github.io" -description = """The aim of VCFtools is to provide - easily accessible methods for working with complex - genetic variation data in the form of VCF files.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Perl', '5.30.2'), - ('HTSlib', '1.10.2'), - ('zlib', '1.2.11'), -] - -modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/v/VSEARCH/VSEARCH-2.15.0-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/v/VSEARCH/VSEARCH-2.15.0-GCC-9.3.0.eb deleted file mode 100644 index 54308d8be3e..00000000000 --- a/easybuild/easyconfigs/__archive__/v/VSEARCH/VSEARCH-2.15.0-GCC-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'VSEARCH' -version = '2.15.0' - -homepage = 'https://github.com/torognes/vsearch' -description = """VSEARCH supports de novo and reference based chimera detection, - clustering, full-length and prefix dereplication, rereplication, - reverse complementation, masking, all-vs-all pairwise global alignment, - exact and global alignment searching, shuffling, subsampling and sorting. - It also supports FASTQ file analysis, filtering, - conversion and merging of paired-end reads.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/torognes/vsearch/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['c5d6eca1e4bf0c6e28221356b806c1d2322b51c39f40888636ab094c4df2e231'] - -builddependencies = [ - ('Autotools', '20180311'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), -] - -preconfigopts = './autogen.sh &&' - -configopts = '--disable-pdfman ' - -sanity_check_paths = { - 'files': ['bin/vsearch'], - 'dirs': [], -} - -sanity_check_commands = ['vsearch --help'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 22bac0c5732..00000000000 --- a/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,99 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html -## - -easyblock = 'CMakeMake' - -name = 'VTK' -version = '8.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.vtk.org' -description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for - 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several - interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization - algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques - such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] -sources = [ - SOURCE_TAR_GZ, - '%(name)sData-%(version)s.tar.gz', -] -patches = ['VTK-8.2.0_python_3.8_compatibility.patch', ('vtk-version.egg-info', '.')] -checksums = [ - '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz - 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz - 'a7586f60501de145d4c31e48aa0589547d9fe7a39f96ab31dae8e82aa5fb4403', # VTK-8.2.0_python_3.8_compatibility.patch - '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info -] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('XZ', '5.2.5'), - ('HDF5', '1.10.6'), - ('netCDF', '4.7.4'), - ('libGLU', '9.0.1'), - ('X11', '20200222'), -] - -separate_build_dir = True - -# Third party modules -configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " -configopts += "-DVTK_USE_SYSTEM_LZMA=ON " -configopts += "-DVTK_USE_SYSTEM_HDF5=ON " -configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " -configopts += "-DVTK_USE_SYSTEM_PNG=ON " -# OpenGL -configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT -configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " -# Python -configopts += "-DVTK_WRAP_PYTHON=ON " -configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " -configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT -# Other -configopts += "-DVTK_Group_MPI:BOOL=ON " - -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -# Install a egg-info file so VTK is more python friendly, required for mayavi -local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' -local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' -postinstallcmds = [ - 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), -] - -local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x - for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] -local_vtk_exec += ['vtkpython', 'pvtkpython'] -local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelMPI', 'RenderingOpenGL2'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_vtk_exec] + - ['lib/libvtk%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in local_vtk_libs], - 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], -} - -sanity_check_commands = [ - ('python', "-c 'import %(namelower)s'"), - ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), -] - - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index f8f71f1eb59..00000000000 --- a/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,108 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html -## - -easyblock = 'CMakeMake' - -name = 'VTK' -version = '8.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.vtk.org' -description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for - 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several - interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization - algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques - such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] -sources = [ - SOURCE_TAR_GZ, - '%(name)sData-%(version)s.tar.gz', -] -patches = [ - 'VTK-8.2.0_vtkm-cmake-read-cuda-cc.patch', - 'VTK-8.2.0_python_3.8_compatibility.patch', - ('vtk-version.egg-info', '.'), -] -checksums = [ - '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz - 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz - 'd519d63d6f1c4b4125d05e1be8b23a474a48d83a887efc832e61c3a75ac09f35', # VTK-8.2.0_vtkm-cmake-read-cuda-cc.patch - 'a7586f60501de145d4c31e48aa0589547d9fe7a39f96ab31dae8e82aa5fb4403', # VTK-8.2.0_python_3.8_compatibility.patch - '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info -] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('XZ', '5.2.5'), - ('HDF5', '1.10.6'), - ('netCDF', '4.7.4'), - ('libGLU', '9.0.1'), - ('X11', '20200222'), -] - -# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) -cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] - -# Third party modules -configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " -configopts += "-DVTK_USE_SYSTEM_LZMA=ON " -configopts += "-DVTK_USE_SYSTEM_HDF5=ON " -configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " -configopts += "-DVTK_USE_SYSTEM_PNG=ON " -# OpenGL -configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT -configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " -# VTK-m with CUDA -configopts += "-DModule_vtkVTKm:BOOL=ON -DModule_vtkAcceleratorsVTKm:BOOL=ON " -configopts += "-DVTKm_ENABLE_CUDA:BOOL=ON -DVTKm_CUDA_Architecture=%(cuda_compute_capabilities)s " -# Python -configopts += "-DVTK_WRAP_PYTHON=ON " -configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " -configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT -# Other -configopts += "-DVTK_Group_MPI:BOOL=ON " - -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -# Install a egg-info file so VTK is more python friendly, required for mayavi -local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' -local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' -postinstallcmds = [ - 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), -] - -local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x - for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] -local_vtk_exec += ['vtkpython', 'pvtkpython'] -local_vtk_libs = ['AcceleratorsVTKm', 'CommonCore', 'IONetCDF', 'ParallelMPI', 'RenderingOpenGL2'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_vtk_exec] + - ['lib/libvtk%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in local_vtk_libs], - 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], -} - -sanity_check_commands = [ - ('python', "-c 'import %(namelower)s'"), - ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), -] - - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index bc5c2030b79..00000000000 --- a/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,94 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html -## - -easyblock = 'CMakeMake' - -name = 'VTK' -version = '8.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.vtk.org' -description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for - 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several - interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization - algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques - such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] -sources = [ - SOURCE_TAR_GZ, - '%(name)sData-%(version)s.tar.gz', -] -patches = ['VTK-8.2.0_python_3.8_compatibility.patch', ('vtk-version.egg-info', '.')] -checksums = [ - '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz - 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz - 'a7586f60501de145d4c31e48aa0589547d9fe7a39f96ab31dae8e82aa5fb4403', # VTK-8.2.0_python_3.8_compatibility.patch - '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info -] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('XZ', '5.2.5'), - ('HDF5', '1.10.6'), - ('netCDF', '4.7.4'), - ('libGLU', '9.0.1'), - ('X11', '20200222'), -] - -separate_build_dir = True - -# Third party modules -configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " -configopts += "-DVTK_USE_SYSTEM_LZMA=ON " -configopts += "-DVTK_USE_SYSTEM_HDF5=ON " -configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " -# OpenGL -configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT -configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " -# Python -configopts += "-DVTK_WRAP_PYTHON=ON " -configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " -configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT -# Other -configopts += "-DVTK_Group_MPI:BOOL=ON " - -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -# Install a egg-info file so VTK is more python friendly, required for mayavi -local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' -local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' -postinstallcmds = [ - 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), -] - -sanity_check_paths = { - 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in - ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] + - ['bin/pvtkpython', 'bin/vtkpython'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], -} - -sanity_check_commands = [ - ('python', "-c 'import %(namelower)s'"), - ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), -] - - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0_vtkm-cmake-read-cuda-cc.patch b/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0_vtkm-cmake-read-cuda-cc.patch deleted file mode 100644 index d564487140e..00000000000 --- a/easybuild/easyconfigs/__archive__/v/VTK/VTK-8.2.0_vtkm-cmake-read-cuda-cc.patch +++ /dev/null @@ -1,78 +0,0 @@ -Allow VTKm_CUDA_Architecture to be defined with a comma separated list of -either architecture names or CUDA compute capabilities version numbers -author: Alex Domingo (Vrije Universiteit Brussel) ---- ThirdParty/vtkm/vtk-m/CMake/VTKmDeviceAdapters.cmake.orig 2021-01-14 16:23:26.117392000 +0100 -+++ ThirdParty/vtkm/vtk-m/CMake/VTKmDeviceAdapters.cmake 2021-01-14 21:23:12.635520314 +0100 -@@ -245,31 +245,49 @@ - - #since when we are native we can fail, and fall back to "kepler" these have - #to happen after, and separately of the native check -- if(VTKm_CUDA_Architecture STREQUAL "fermi") -- set(arch_flags --generate-code=arch=compute_20,code=sm_20) -- elseif(VTKm_CUDA_Architecture STREQUAL "kepler") -- set(arch_flags --generate-code=arch=compute_30,code=sm_30 -- --generate-code=arch=compute_35,code=sm_35) -- elseif(VTKm_CUDA_Architecture STREQUAL "maxwell") -- set(arch_flags --generate-code=arch=compute_50,code=sm_50) -- elseif(VTKm_CUDA_Architecture STREQUAL "pascal") -- set(arch_flags --generate-code=arch=compute_60,code=sm_60) -- elseif(VTKm_CUDA_Architecture STREQUAL "volta") -- set(arch_flags --generate-code=arch=compute_70,code=sm_70) -- elseif(VTKm_CUDA_Architecture STREQUAL "turing") -- set(arch_flags --generate-code=arch=compute_75,code=sm_75) -- elseif(VTKm_CUDA_Architecture STREQUAL "all") -- set(arch_flags --generate-code=arch=compute_30,code=sm_30 -- --generate-code=arch=compute_35,code=sm_35 -- --generate-code=arch=compute_50,code=sm_50 -- --generate-code=arch=compute_60,code=sm_60 -- --generate-code=arch=compute_70,code=sm_70 -- --generate-code=arch=compute_75,code=sm_75) -+ set(CUDA_ARCH_FLAGS "") -+ if(VTKm_CUDA_Architecture MATCHES "fermi") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_20,code=sm_20") - endif() -+ if(VTKm_CUDA_Architecture MATCHES "kepler") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_30,code=sm_30") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_35,code=sm_35") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_37,code=sm_37") -+ endif() -+ if(VTKm_CUDA_Architecture MATCHES "maxwell") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_50,code=sm_50") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_52,code=sm_52") -+ endif() -+ if(VTKm_CUDA_Architecture MATCHES "pascal") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_60,code=sm_60") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_61,code=sm_61") -+ endif() -+ if(VTKm_CUDA_Architecture MATCHES "volta") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_70,code=sm_70") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_72,code=sm_72") -+ endif() -+ if(VTKm_CUDA_Architecture MATCHES "turing") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_75,code=sm_75") -+ endif() -+ if(VTKm_CUDA_Architecture STREQUAL "all") -+ set(CUDA_ARCH_FLAGS "--generate-code=arch=compute_30,code=sm_30 -+ --generate-code=arch=compute_35,code=sm_35 -+ --generate-code=arch=compute_50,code=sm_50 -+ --generate-code=arch=compute_60,code=sm_60 -+ --generate-code=arch=compute_70,code=sm_70 -+ --generate-code=arch=compute_75,code=sm_75") -+ endif() -+ -+ #check for CUDA compute capabilities specific versions -+ string( REGEX MATCHALL "[0-9].[0-9]" cuda_cc "${VTKm_CUDA_Architecture}" ) -+ list( SORT cuda_cc ) # To make output easier to reason about -+ foreach (cc IN LISTS cuda_cc) -+ string( REPLACE "." "" cc "${cc}") -+ set(CUDA_ARCH_FLAGS "${CUDA_ARCH_FLAGS} --generate-code=arch=compute_${cc},code=sm_${cc}") -+ endforeach() - -- string(REPLACE ";" " " arch_flags "${arch_flags}") -- set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} ${arch_flags}") -+ set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} ${CUDA_ARCH_FLAGS}") - -- set_target_properties(vtkm::cuda PROPERTIES VTKm_CUDA_Architecture_Flags "${arch_flags}") -+ set_target_properties(vtkm::cuda PROPERTIES VTKm_CUDA_Architecture_Flags "${CUDA_ARCH_FLAGS}") - - endif() diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.16.1-gompi-2020a.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.16.1-gompi-2020a.eb deleted file mode 100644 index 157ea2abe61..00000000000 --- a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.16.1-gompi-2020a.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Valgrind' -version = '3.16.1' - -homepage = 'https://valgrind.org' -description = "Valgrind: Debugging and profiling tools" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'optarch': True} - -source_urls = [ - 'ftp://sourceware.org/pub/valgrind/', - 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', -] -sources = [SOURCELOWER_TAR_BZ2] -patches = ['Valgrind-3.15.0-no-MPI-1.patch'] -checksums = [ - 'c91f3a2f7b02db0f3bc99479861656154d241d2fdb265614ba918cc6720a33ca', # valgrind-3.16.1.tar.bz2 - 'e99464ad9f2d2e74c5c50d2fa1bcf8637295b11cd841102035f8601b01afd85f', # Valgrind-3.15.0-no-MPI-1.patch -] - -configopts = ' --with-mpicc="$MPICC"' - -local_binaries = [ - 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', - 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_binaries] + - ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.16.1-iimpi-2020a.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.16.1-iimpi-2020a.eb deleted file mode 100644 index cfe4c331435..00000000000 --- a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.16.1-iimpi-2020a.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Valgrind' -version = '3.16.1' - -homepage = 'https://valgrind.org' -description = "Valgrind: Debugging and profiling tools" - -toolchain = {'name': 'iimpi', 'version': '2020a'} -toolchainopts = {'optarch': False} - -source_urls = [ - 'ftp://sourceware.org/pub/valgrind/', - 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', -] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['c91f3a2f7b02db0f3bc99479861656154d241d2fdb265614ba918cc6720a33ca'] - -configopts = ' --with-mpicc="$MPICC"' - -local_binaries = [ - 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', - 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_binaries] + - ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/__archive__/v/VirtualGL/VirtualGL-2.6.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/v/VirtualGL/VirtualGL-2.6.2-GCCcore-9.3.0.eb deleted file mode 100644 index 538dbf0eda2..00000000000 --- a/easybuild/easyconfigs/__archive__/v/VirtualGL/VirtualGL-2.6.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -# Contribution from the Crick HPC team -# uploaded by J. Sassmannshausen -# updated by Valentin Plugaru 2019-09-26 - -easyblock = 'CMakeMake' - -name = 'VirtualGL' -version = '2.6.2' - -homepage = 'https://virtualgl.org/' -description = """VirtualGL is an open source toolkit that gives any Linux or -Unix remote display software the ability to run OpenGL applications with full -hardware acceleration.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['9679f4510ab3042618bf35eae3be8945db9463fde947719ce295ec8ea38755cb'] - -builddependencies = [ - ('CMake', '3.16.4'), - ('binutils', '2.34'), -] - -dependencies = [ - ('libjpeg-turbo', '2.0.4'), - ('Mesa', '20.0.2'), - ('libGLU', '9.0.1'), -] - -local_binaries = [ - 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', - 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', - 'vglserver_config' -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_binaries], - 'dirs': ['lib64', 'share', 'include'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb deleted file mode 100644 index 10720c28f50..00000000000 --- a/easybuild/easyconfigs/__archive__/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ - -easyblock = 'ConfigureMake' - -name = 'Voro++' -version = '0.4.6' - -homepage = 'http://math.lbl.gov/voro++/' -description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi -tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, -computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that -rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used -to analyze a system of particles.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'http://math.lbl.gov/voro++/download/dir/', - 'https://download.lammps.org/thirdparty', -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] -builddependencies = [('binutils', '2.34')] - - -# No configure -skipsteps = ['configure'] - -# Override CXX and CFLAGS variables from Makefile -buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' - -# Override PREFIX variable from Makefile -installopts = "PREFIX=%(installdir)s" - -sanity_check_paths = { - 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], - 'dirs': [], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb deleted file mode 100644 index c5cca78049f..00000000000 --- a/easybuild/easyconfigs/__archive__/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,69 +0,0 @@ -# Author: Jasper Grimm (UoY) - -easyblock = 'CMakeMake' - -name = 'vcflib' -version = '1.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/vcflib/vcflib' -description = """vcflib provides methods to manipulate and interpret sequence variation as it can be - described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended - to concisely describe reference-indexed genetic variations between individuals.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = [ - 'vcflib-1.0.2_use-external-deps.patch', - 'vcflib-1.0.2_fix-shared-linking.patch', -] -checksums = [ - 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz - '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch - '3904fb7ad5d144bf1b6500c985c84c15a5e4ba5299763628de7965cb4efa97f7', # vcflib-1.0.2_fix-shared-linking.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('Perl', '5.30.2'), - ('XZ', '5.2.5'), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('HTSlib', '1.10.2'), - ('tabixpp', '1.1.0'), - ('intervaltree', '0.1'), - ('fastahack', '1.0.0'), - ('filevercmp', '20141119'), - ('fsom', '20141119'), - ('multichoose', '1.0.3'), - ('smithwaterman', '20160702'), -] - -preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f " -preconfigopts += r"-regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" -preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" -preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" -preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" -preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" -preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " - -postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] - -modextrapaths = {'PATH': ['scripts']} - -sanity_check_paths = { - 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': ['scripts'], -} - -sanity_check_commands = ["vcfremap"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/v/velocyto/velocyto-0.17.17-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/v/velocyto/velocyto-0.17.17-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 8019d4043f4..00000000000 --- a/easybuild/easyconfigs/__archive__/v/velocyto/velocyto-0.17.17-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'velocyto' -version = '0.17.17' -versionsuffix = "-Python-%(pyver)s" - -homepage = 'https://velocyto.org/velocyto.py/' -description = "Velocyto is a library for the analysis of RNA velocity." - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('numba', '0.50.0', versionsuffix), - ('scikit-learn', '0.23.1', versionsuffix), - ('h5py', '2.10.0', versionsuffix), - ('Pysam', '0.16.0.1'), - -] - -exts_list = [ - ('numpy_groupies', '0.9.13', { - 'checksums': ['7b17b291322353f07c51598512d077e3731da0a048cfa8f738f3460d1ef0658d'], - }), - ('loompy', '3.0.6', { - 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], - }), - (name, version, { - 'checksums': ['1ad65fc53292ce1970a70bc742d73491b370038e0b0065761303e787bf7ffe39'], - }), -] - -sanity_check_paths = { - 'files': ['bin/velocyto'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - 'velocyto', -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/v/vt/vt-0.57721-GCC-9.3.0.eb b/easybuild/easyconfigs/__archive__/v/vt/vt-0.57721-GCC-9.3.0.eb deleted file mode 100644 index 7b0d2a1d9b8..00000000000 --- a/easybuild/easyconfigs/__archive__/v/vt/vt-0.57721-GCC-9.3.0.eb +++ /dev/null @@ -1,62 +0,0 @@ -# Author: Jasper Grimm (UoY) - -easyblock = 'MakeCp' - -name = 'vt' -version = '0.57721' - -homepage = 'https://genome.sph.umich.edu/wiki/Vt' -description = """A tool set for short variant discovery in genetic sequence data.""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -github_account = 'atks' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -patches = [ - '%(name)s-0.57721_use-external-libs.patch', - '%(name)s-0.57721_fix-Rmath-includes.patch', - '%(name)s-0.57721_avoid-implicit-conversion.patch', - '%(name)s-0.57721_update-faidx.patch', - '%(name)s-0.57721_fail-on-test-error.patch', -] -checksums = [ - '8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17', # 0.57721.tar.gz - '5a31713ae7c5febf850eec294dbba45b6b240d832cb94bdfe9ee695fd13e45bb', # vt-0.57721_use-external-libs.patch - '663525f5180a66d8817f271a69de1884576e2414d46b7ba93029d78f71d5b14c', # vt-0.57721_fix-Rmath-includes.patch - '56d874d5c7d488761f25afb4ee3717c88dfd959ed76efb75a8531b8428d30ccd', # vt-0.57721_avoid-implicit-conversion.patch - 'ba2cfc24a88a4291b2da634db49e18199c379eb95d3b3acac59556bc68c292df', # vt-0.57721_update-faidx.patch - '4146282eb6ec852485f5a16e647da9c3b210450ceb5519b9b4a98bc52124469a', # vt-0.57721_fail-on-test-error.patch -] - -builddependencies = [ - ('binutils', '2.34'), - ('TCLAP', '1.2.4'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('cURL', '7.69.1'), - ('PCRE', '8.44'), - ('PCRE2', '10.34'), - ('libdeflate', '1.7'), - ('libRmath', '4.0.0'), - ('LIBSVM', '3.24'), - ('HTSlib', '1.10.2'), -] - -runtest = 'test' - -files_to_copy = [ - (['vt'], 'bin'), - (['*.h'], 'include/vt'), - 'test', 'README.md', 'LICENSE', -] - -sanity_check_paths = { - 'files': ['bin/vt'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/w/WHAM/WHAM-2.0.10.2-intel-2020a-kj_mol.eb b/easybuild/easyconfigs/__archive__/w/WHAM/WHAM-2.0.10.2-intel-2020a-kj_mol.eb deleted file mode 100644 index 6f0c4a4ed8a..00000000000 --- a/easybuild/easyconfigs/__archive__/w/WHAM/WHAM-2.0.10.2-intel-2020a-kj_mol.eb +++ /dev/null @@ -1,54 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'MakeCp' - -name = 'WHAM' -version = '2.0.10.2' -# Boltzmann’s constant is by default defined in 'kcal/mol' -# Easyconfigs with versionsuffix 'kj_mol' change energy units at build time to 'kJ/mol' -versionsuffix = "-kj_mol" - -# No valid HTTPS - Let's Encrypt Cert expired loong time ago -homepage = 'http://membrane.urmc.rochester.edu/?page_id=126' -description = "An implementation of WHAM: the Weighted Histogram Analysis Method" - -toolchain = {'name': 'intel', 'version': '2020a'} - -# No valid https -source_urls = ['http://membrane.urmc.rochester.edu/sites/default/files/wham/'] -sources = [{ - # source tarball is not actually zipped... - 'download_filename': '%(namelower)s-release-%(version)s.tgz', - 'filename': '%(namelower)s-release-%(version)s.tar', -}] -checksums = ['44635a429ded5892950271fa58e97691628ad7a3be21d09f86ca2830e2b679f7'] - -# change energy units to kJ/mol -prebuildopts = "sed -i 's@^#define k_B @////#define k_B @g' wham/wham.h && " -prebuildopts += "sed -i 's@^//#define k_B @#define k_B @g' wham/wham.h && " -prebuildopts += "sed -i 's@^#define k_B @////#define k_B @g' wham-2d/wham-2d.h && " -prebuildopts += "sed -i 's@^//#define k_B @#define k_B @g' wham-2d/wham-2d.h && " - -prebuildopts += "cd wham && " -buildopts = 'CC="$CC" CFLAGS="$CFLAGS" && cd ../wham-2d && make CC="$CC" CFLAGS="$CFLAGS"' - -files_to_copy = [(['wham/wham', 'wham-2d/wham-2d'], 'bin'), 'doc', 'nr'] - -sanity_check_paths = { - 'files': ['bin/wham', 'bin/wham-2d'], - 'dirs': ['doc', 'nr'], -} -# exits with non-zero -sanity_check_commands = [ - ("wham 2>&1 | grep 'Command line: wham'", ''), - # Yep, there is double space below. - ("wham-2d 2>&1 | grep 'Command line: wham-2d'", ''), -] - -modloadmsg = """ -Boltzmann’s constant is defined in 'kJ/mol' -(use default module of %(name)s to use energy units in kcal/mol) -""" - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/w/WHAM/WHAM-2.0.10.2-intel-2020a.eb b/easybuild/easyconfigs/__archive__/w/WHAM/WHAM-2.0.10.2-intel-2020a.eb deleted file mode 100644 index 17617255c71..00000000000 --- a/easybuild/easyconfigs/__archive__/w/WHAM/WHAM-2.0.10.2-intel-2020a.eb +++ /dev/null @@ -1,47 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'MakeCp' - -name = 'WHAM' -version = '2.0.10.2' -# Boltzmann’s constant is by default defined in 'kcal/mol' -# Easyconfigs with versionsuffix 'kj_mol' change energy units at build time to 'kJ/mol' - -# No valid HTTPS - Let's Encrypt Cert expired loong time ago -homepage = 'http://membrane.urmc.rochester.edu/?page_id=126' -description = "An implementation of WHAM: the Weighted Histogram Analysis Method" - -toolchain = {'name': 'intel', 'version': '2020a'} - -# No valid https -source_urls = ['http://membrane.urmc.rochester.edu/sites/default/files/wham/'] -sources = [{ - # source tarball is not actually zipped... - 'download_filename': '%(namelower)s-release-%(version)s.tgz', - 'filename': '%(namelower)s-release-%(version)s.tar', -}] -checksums = ['44635a429ded5892950271fa58e97691628ad7a3be21d09f86ca2830e2b679f7'] - -prebuildopts = "cd wham && " -buildopts = 'CC="$CC" CFLAGS="$CFLAGS" && cd ../wham-2d && make CC="$CC" CFLAGS="$CFLAGS"' - -files_to_copy = [(['wham/wham', 'wham-2d/wham-2d'], 'bin'), 'doc', 'nr'] - -sanity_check_paths = { - 'files': ['bin/wham', 'bin/wham-2d'], - 'dirs': ['doc', 'nr'], -} -# exits with non-zero -sanity_check_commands = [ - ("wham 2>&1 | grep 'Command line: wham'", ''), - # Yep, there is double space below. - ("wham-2d 2>&1 | grep 'Command line: wham-2d'", ''), -] - -modloadmsg = """ -Boltzmann’s constant is defined in 'kcal/mol' -(use module of %(name)s ending in 'kj_mol' to use energy units in kJ/mol) -""" - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-foss-2020a-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-foss-2020a-dmpar.eb deleted file mode 100644 index ab3b0c4bf94..00000000000 --- a/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-foss-2020a-dmpar.eb +++ /dev/null @@ -1,50 +0,0 @@ -name = 'WRF' -version = '3.9.1.1' -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -homepage = 'https://www.mmm.ucar.edu/weather-research-and-forecasting-model' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -source_urls = [ - 'https://www2.mmm.ucar.edu/wrf/src/', - 'https://www.mmm.ucar.edu/wrf/src/', -] -sources = ['%(name)sV%(version)s.TAR.gz'] -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', - 'WRF-%(version)s_libtirpc.patch', -] -checksums = [ - 'e2c503c1b5adc2d3409b39d37df29d60188ff1de8c870eca15197a86d3538299', # WRFV3.9.1.1.TAR.gz - 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch - # WRF-3.9.1.1_netCDF-Fortran_separate_path.patch - '49ae0eb4c5bacd3b932be14ccb9ac2d28cbd70828b633d9f13860c92d92b1eb7', - '9a8547d6c68b0f318f74063b690c5c8cfcd3437ebebe837dbd1d4a2dc1ad2427', # WRF-3.9.1.1_libtirpc.patch -] - -# csh is used by WRF install scripts -builddependencies = [ - ('Autotools', '20180311'), - ('tcsh', '6.22.02'), - ('time', '1.9'), - ('Perl', '5.30.2'), -] - -dependencies = [ - ('libtirpc', '1.2.6'), - ('JasPer', '2.0.14'), - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), -] - -# limit parallel build to 20 -maxparallel = 20 - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-intel-2020a-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-intel-2020a-dmpar.eb deleted file mode 100644 index 2cf14260f61..00000000000 --- a/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.9.1.1-intel-2020a-dmpar.eb +++ /dev/null @@ -1,50 +0,0 @@ -name = 'WRF' -version = '3.9.1.1' -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -homepage = 'https://www.mmm.ucar.edu/weather-research-and-forecasting-model' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -source_urls = [ - 'https://www2.mmm.ucar.edu/wrf/src/', - 'https://www.mmm.ucar.edu/wrf/src/', -] -sources = ['%(name)sV%(version)s.TAR.gz'] -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', - 'WRF-%(version)s_libtirpc.patch', -] -checksums = [ - 'e2c503c1b5adc2d3409b39d37df29d60188ff1de8c870eca15197a86d3538299', # WRFV3.9.1.1.TAR.gz - 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch - # WRF-3.9.1.1_netCDF-Fortran_separate_path.patch - '49ae0eb4c5bacd3b932be14ccb9ac2d28cbd70828b633d9f13860c92d92b1eb7', - '9a8547d6c68b0f318f74063b690c5c8cfcd3437ebebe837dbd1d4a2dc1ad2427', # WRF-3.9.1.1_libtirpc.patch -] - -# csh is used by WRF install scripts -builddependencies = [ - ('Autotools', '20180311'), - ('tcsh', '6.22.02'), - ('time', '1.9'), - ('Perl', '5.30.2'), -] - -dependencies = [ - ('libtirpc', '1.2.6'), - ('JasPer', '2.0.14'), - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), -] - -# limit parallel build to 20 -maxparallel = 20 - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/w/WRF/WRF-4.1.3-foss-2020a-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-4.1.3-foss-2020a-dmpar.eb deleted file mode 100644 index d0281f2318f..00000000000 --- a/easybuild/easyconfigs/__archive__/w/WRF/WRF-4.1.3-foss-2020a-dmpar.eb +++ /dev/null @@ -1,43 +0,0 @@ -name = 'WRF' -version = '4.1.3' -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -homepage = 'https://www.wrf-model.org' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -source_urls = ['https://github.com/wrf-model/WRF/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRFv4_netCDF-Fortran_separate_path.patch', -] -checksums = [ - 'a020e83e8a7a927fb080075031630e2af592e9fa802293ad72caa7ee50d6968d', # v4.1.3.tar.gz - 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch - 'a431159180757a895c07fc193fe93bb69c4c9d25d31adcc7c2adfa7c1edb04ad', # WRFv4_netCDF-Fortran_separate_path.patch -] - -# csh is used by WRF install scripts -builddependencies = [ - ('Autotools', '20180311'), - ('tcsh', '6.22.02'), - ('time', '1.9'), - ('Perl', '5.30.2'), -] - -dependencies = [ - ('JasPer', '2.0.14'), - ('netCDF', '4.7.4'), - ('netCDF-Fortran', '4.5.2'), -] - -# limit parallel build to 20 -maxparallel = 20 - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/w/WRF/WRFv4_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/__archive__/w/WRF/WRFv4_netCDF-Fortran_separate_path.patch deleted file mode 100644 index a7527b42d44..00000000000 --- a/easybuild/easyconfigs/__archive__/w/WRF/WRFv4_netCDF-Fortran_separate_path.patch +++ /dev/null @@ -1,262 +0,0 @@ -# Allow netCDF library with separate directories for C and Fortran -# ============================================================================ -# This patch has been around in EasyBuild since WRF3.5; it was committed by -# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain - -diff -uNr WRF-4.0.1.orig/arch/Config.pl WRF-4.0.1/arch/Config.pl ---- WRF-4.0.1.orig/arch/Config.pl 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/arch/Config.pl 2018-11-19 14:20:04.776144494 +0100 -@@ -8,6 +8,7 @@ - select((select(STDOUT), $|=1)[0]); - $sw_perl_path = perl ; - $sw_netcdf_path = "" ; -+$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib might be in a different path - $sw_pnetcdf_path = "" ; - $sw_hdf5_path=""; - $sw_phdf5_path=""; -@@ -90,6 +91,10 @@ - } - } - } -+ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) -+ { -+ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; -+ } - if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) - { - $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; -@@ -117,6 +122,7 @@ - if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) - { - $sw_usenetcdff = substr( $ARGV[0], 12 ) ; -+ $sw_usenetcdff =~ s/!/ /g ; - } - if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) - { -@@ -439,6 +445,7 @@ - { - $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; - $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; -+ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; - $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; - $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; - $_ =~ s/CONFIGURE_PHDF5_PATH/$sw_phdf5_path/g ; -@@ -485,7 +492,7 @@ - } elsif ( $sw_os eq "Interix" ) { - $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; - } else { -- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; -+ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; - } - } - else -diff -uNr WRF-4.0.1.orig/arch/configure.defaults WRF-4.0.1/arch/configure.defaults ---- WRF-4.0.1.orig/arch/configure.defaults 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/arch/configure.defaults 2018-10-19 17:57:23.437418176 +0200 -@@ -1598,6 +1598,7 @@ - - LIB_EXTERNAL = \ - ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ -+ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ - ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a - ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a - LIB_BUNDLED = \ -diff -uNr WRF-4.0.1.orig/arch/conf_tokens WRF-4.0.1/arch/conf_tokens ---- WRF-4.0.1.orig/arch/conf_tokens 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/arch/conf_tokens 2018-10-23 10:19:00.867135754 +0200 -@@ -5,6 +5,7 @@ - CONFIGURE_DMPARALLEL - CONFIGURE_RWORDSIZE - CONFIGURE_NETCDF_FLAG -+CONFIGURE_NETCDFF_FLAG - CONFIGURE_GRIB2_FLAG - CONFIGURE_NETCDF_LIB_PATH - CONFIGURE_GRIB2_LIB -@@ -13,4 +14,5 @@ - CONFIGURE_WRFIO_NF - CONFIGURE_WRFIO_GRIB2 - CONFIGURE_NETCDF_PATH -+CONFIGURE_NETCDFF_PATH - CONFIGURE_GRIB2_INC -diff -uNr WRF-4.0.1.orig/arch/postamble WRF-4.0.1/arch/postamble ---- WRF-4.0.1.orig/arch/postamble 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/arch/postamble 2018-10-24 08:53:53.042677598 +0200 -@@ -47,7 +47,7 @@ - -I$(WRF_SRC_ROOT_DIR)/phys \ - -I$(WRF_SRC_ROOT_DIR)/wrftladj \ - -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ -- -I$(NETCDFPATH)/include \ -+ -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \ - CONFIGURE_RTTOV_INC - REGISTRY = Registry - CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE -@@ -70,6 +70,7 @@ - ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS - CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE - NETCDFPATH = CONFIGURE_NETCDF_PATH -+NETCDFFPATH = CONFIGURE_NETCDFF_PATH - HDF5PATH = CONFIGURE_HDF5_PATH - WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH - RTTOVPATH = CONFIGURE_RTTOV_PATH -@@ -101,13 +102,13 @@ - - wrfio_nf : - ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ -- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ -+ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ - CC="$(SCC)" CFLAGS="$(CFLAGS)" \ - FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) - - wrfio_pnf : - ( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \ -- make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ -+ make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ - FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) - - wrfio_grib_share : -diff -uNr WRF-4.0.1.orig/configure WRF-4.0.1/configure ---- WRF-4.0.1.orig/configure 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/configure 2018-11-20 12:08:49.040926889 +0100 -@@ -183,10 +183,14 @@ - if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" ] ; then - USENETCDFF="-lnetcdff" - else -- USENETCDFF=" " -+ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then -+ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space -+ else -+ USENETCDFF=" " -+ fi - fi -- if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" ] ; then -- USENETCDF="-lnetcdf" -+ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then -+ USENETCDF="-lnetcdf" - else - USENETCDF=" " - fi -@@ -549,7 +553,7 @@ - srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` - if [ -n "$srch" ] ; then - $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ -- -netcdf=$NETCDF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ -+ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ - -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ - -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ - -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" -@@ -629,14 +633,14 @@ - echo "If you wish to change the default options, edit the file:" - echo " arch/configure.defaults" - --if test -n "$NETCDF" ; then -- if [ ! -f $NETCDF/include/netcdf.inc ] ; then -+if test -n "$NETCDFF" ; then -+ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then - echo -- echo "Error : Not found $NETCDF/include/netcdf.inc" -+ echo "Error : Not found $NETCDFF/include/netcdf.inc" - echo " Please check this installation of NetCDF and re-run this configure script" - exit -1 - fi -- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null -+ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null - configure_aaaa=$? ; export configure_aaaa - if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then - echo "NetCDF users note:" -diff -uNr WRF-4.0.1.orig/external/io_netcdf/makefile WRF-4.0.1/external/io_netcdf/makefile ---- WRF-4.0.1.orig/external/io_netcdf/makefile 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/external/io_netcdf/makefile 2018-10-19 18:11:19.135941823 +0200 -@@ -3,9 +3,9 @@ - OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o - OBJS = $(OBJSL) - CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code --FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share --LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf --LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) -+FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share -+LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf -+LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) - CPP1 = $(CPP) -P $(TRADFLAG) - M4 = m4 -Uinclude -Uindex -Ulen - AR = ar -@@ -24,7 +24,7 @@ - $(RANLIB) $@ - - wrf_io.o: wrf_io.F90 $(CODE) -- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ -+ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ - a=$$? ; export a ; \ - if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ - $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ -@@ -43,14 +43,14 @@ - x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ - if [ $$x = "gfortran" ] ; then \ - echo removing external declaration of iargc for gfortran ; \ -- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ -+ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ - else \ -- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ -+ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ - fi - $(FC) -c $(FFLAGS) diffwrf.f - @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ - echo "diffwrf io_netcdf is being built now. " ; \ -- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so \) ] ; then \ -+ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so \) ] ; then \ - $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ - else \ - $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ -diff -uNr WRF-4.0.1.orig/external/io_pnetcdf/Makefile WRF-4.0.1/external/io_pnetcdf/Makefile ---- WRF-4.0.1.orig/external/io_pnetcdf/Makefile 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/external/io_pnetcdf/Makefile 2018-10-19 18:11:49.369236552 +0200 -@@ -9,8 +9,8 @@ - ext_pnc_put_var_td.code \ - ext_pnc_put_var_ti.code \ - transpose.code --FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share --LIBS = -L$(NETCDFPATH)/lib -lpnetcdf -+FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share -+LIBS = -L$(NETCDFFPATH)/lib -lpnetcdf - CPP1 = $(CPP) -P $(TRADFLAG) - M4 = m4 -Uinclude -Uindex -Ulen - AR = ar -@@ -25,15 +25,15 @@ - $(RANLIB) libwrfio_pnf.a - - wrf_io.o: wrf_io.F90 $(CODE) -- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f -+ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f - $(FC) $(FFLAGS) -c wrf_io.f - - module_wrfsi_static.o: module_wrfsi_static.F90 -- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f -+ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f - $(FC) $(FFLAGS) -c module_wrfsi_static.f - - field_routines.o: field_routines.F90 wrf_io.o -- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f -+ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f - $(FC) $(FFLAGS) -c field_routines.f - - superclean: -diff -uNr WRF-4.0.1.orig/Makefile WRF-4.0.1/Makefile ---- WRF-4.0.1.orig/Makefile 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/Makefile 2018-10-19 18:23:30.857876650 +0200 -@@ -906,7 +906,7 @@ - @ echo '--------------------------------------' - ( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \ - cd ../external/io_netcdf ; \ -- $(MAKE) NETCDFPATH="$(NETCDFPATH)" \ -+ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \ - FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \ - CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ - LIB_LOCAL="$(LIB_LOCAL)" \ -@@ -1036,7 +1036,7 @@ - - # rule used by configure to test if this will compile with netcdf4 - nc4_test: -- @cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib $(USENETCDF) ; cd .. -+ @cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 $(USENETCDF) ; cd .. - - # rule used by configure to test if Fortran 2003 IEEE signaling is available - fortran_2003_ieee_test: diff --git a/easybuild/easyconfigs/__archive__/w/Wannier90/Wannier90-3.1.0-intel-2020a.eb b/easybuild/easyconfigs/__archive__/w/Wannier90/Wannier90-3.1.0-intel-2020a.eb deleted file mode 100644 index 62a8e4a0ad3..00000000000 --- a/easybuild/easyconfigs/__archive__/w/Wannier90/Wannier90-3.1.0-intel-2020a.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'MakeCp' - -name = 'Wannier90' -version = '3.1.0' - -homepage = 'http://www.wannier.org' -description = """A tool for obtaining maximally-localised Wannier functions""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -github_account = 'wannier-developers' -source_urls = [GITHUB_LOWER_SOURCE] -sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] -checksums = [ - '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz - '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch -] - -buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' -buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' -buildopts += 'COMMS=mpi' - -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] - -sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], - 'dirs': [] -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/w/WisecondorX/WisecondorX-1.1.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/w/WisecondorX/WisecondorX-1.1.6-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 028915ff199..00000000000 --- a/easybuild/easyconfigs/__archive__/w/WisecondorX/WisecondorX-1.1.6-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'WisecondorX' -version = '1.1.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/CenterForMedicalGeneticsGhent/WisecondorX' -description = "WisecondorX -- an evolved WISECONDOR" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/CenterForMedicalGeneticsGhent/%(name)s/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['555757a186ffeb7352f8c6b9af3037dfbd676dcfd2b54bfcaa1db7ffcc43df07'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('R', '4.0.0'), # includes jsonlite - ('R-bundle-Bioconductor', '3.11', '-R-%(rver)s'), - ('Pysam', '0.16.0.1'), - ('scikit-learn', '0.23.1', versionsuffix), -] - -options = {'modulename': 'wisecondorX'} - -sanity_check_paths = { - 'files': ['bin/WisecondorX'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["WisecondorX --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/w/wget/wget-1.20.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/w/wget/wget-1.20.3-GCCcore-9.3.0.eb deleted file mode 100644 index 43dc36af7e7..00000000000 --- a/easybuild/easyconfigs/__archive__/w/wget/wget-1.20.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'wget' -version = '1.20.3' - -homepage = 'https://www.gnu.org/software/wget' -description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, - the most widely-used Internet protocols. It is a non-interactive commandline tool, - so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['31cccfc6630528db1c8e3a06f6decf2a370060b982841cfab2b8677400a5092e'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('PCRE', '8.44'), - ('libidn2', '2.3.0'), - ('zlib', '1.2.11'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.1e'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date gnutls for security reasons - # ('GnuTLS', '3.6.14'), -] - -# make sure pkg-config picks up system packages (OpenSSL & co) -local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" -local_pc += "%(sysroot)s/usr/lib/pkgconfig:" -local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" -preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc -configopts = '--with-ssl=openssl ' - -osdependencies = [OS_PKG_OPENSSL_DEV] -# Optionally, you can use gnutls (default) instead of OpenSSL. -# Do not forget to comment out configopts in that case. -# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/w/wtdbg2/wtdbg2-2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/w/wtdbg2/wtdbg2-2.5-GCCcore-9.3.0.eb deleted file mode 100644 index 4d858e57d89..00000000000 --- a/easybuild/easyconfigs/__archive__/w/wtdbg2/wtdbg2-2.5-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'MakeCp' - -name = 'wtdbg2' -version = '2.5' - -homepage = 'https://github.com/ruanjue/wtdbg2' - -description = """ - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio - or Oxford Nanopore Technologies (ONT). It assembles raw reads without error - correction and then builds the consensus from intermediate assembly output. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/ruanjue/wtdbg2/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['a2ffc8503d29f491a9a38ef63230d5b3c96db78377b5d25c91df511d0df06413'] - -builddependencies = [('binutils', '2.34')] - -dependencies = [('Perl', '5.30.2')] - -prebuildopts = "sed -i 's/CFLAGS=-g3/CFLAGS+=-g3/g' Makefile && " - -local_executables = ['wtdbg2', 'wtdbg2.pl', 'wtpoa-cns', 'kbm2', 'wtdbg-cns', 'pgzf'] - -files_to_copy = [(local_executables, 'bin'), 'README-ori.md', 'README.md', 'scripts'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_executables], - 'dirs': ['scripts'], -} - -modextrapaths = { - 'PATH': 'scripts', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/x/X11/X11-20200222-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/X11/X11-20200222-GCCcore-9.3.0.eb deleted file mode 100644 index ae81bf67362..00000000000 --- a/easybuild/easyconfigs/__archive__/x/X11/X11-20200222-GCCcore-9.3.0.eb +++ /dev/null @@ -1,209 +0,0 @@ -easyblock = 'Bundle' - -name = 'X11' -version = '20200222' - -homepage = 'https://www.x.org' -description = "The X Window System (X11) is a windowing system for bitmap displays" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [ - XORG_LIB_SOURCE, - XORG_PROTO_SOURCE, - 'https://xcb.freedesktop.org/dist/', - 'https://xkbcommon.org/download/', - XORG_DATA_SOURCE + '/xkeyboard-config', - XORG_DATA_SOURCE, -] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), - ('Bison', '3.5.3'), - ('gettext', '0.20.1'), - ('pkg-config', '0.29.2'), - ('intltool', '0.51.0'), - ('Meson', '0.55.1', '-Python-3.8.2'), - ('Ninja', '1.10.0'), - ('Doxygen', '1.8.17'), -] -dependencies = [ - ('bzip2', '1.0.8'), - ('fontconfig', '2.13.92'), - ('freetype', '2.10.1'), - ('zlib', '1.2.11'), - ('xorg-macros', '1.19.2'), - ('libpciaccess', '0.16'), -] - -default_easyblock = 'ConfigureMake' - -default_component_specs = { - 'sources': [SOURCE_TAR_GZ], - 'start_dir': '%(name)s-%(version)s', -} -components = [ - ('libpthread-stubs', '0.4', { # 2017-03-14 - 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], - }), - ('xorgproto', '2019.2', { # 2019-10-17 - 'checksums': ['ebfcfce48b66bec25d5dff0e9510e04053ef78e51a8eabeeee4c00e399226d61'], - }), - ('libXau', '1.0.9', { # 2019-02-10 - 'checksums': ['1f123d8304b082ad63a9e89376400a3b1d4c29e67e3ea07b3f659cccca690eea'], - }), - ('libXdmcp', '1.1.3', { # 2019-03-16 - 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], - }), - ('xcb-proto', '1.14', { # 2020-02-22 - 'checksums': ['1c3fa23d091fb5e4f1e9bf145a902161cec00d260fabf880a7a248b02ab27031'], - }), - ('libxcb', '1.14', { # 2020-02-22 - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['2c7fcddd1da34d9b238c9caeda20d3bd7486456fc50b3cc6567185dbd5b0ad02'], - }), - ('xtrans', '1.4.0', { # 2019-03-16 - 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], - }), - ('libxkbcommon', '0.10.0', { # 2020-01-18 - 'easyblock': 'MesonNinja', - 'sources': ['libxkbcommon-%(version)s.tar.xz'], - 'checksums': ['57c3630cdc38fb4734cd57fa349e92244f5ae3862813e533cedbd86721a0b6f2'], - 'preconfigopts': '', - 'configopts': '-Denable-wayland=false -Denable-docs=false ', - }), - ('libX11', '1.6.9', { # 2019-10-09 - 'checksums': ['b8c0930a9b25de15f3d773288cacd5e2f0a4158e194935615c52aeceafd1107b'], - }), - ('libXext', '1.3.4', { # 2019-03-16 - 'checksums': ['8ef0789f282826661ff40a8eef22430378516ac580167da35cc948be9041aac1'], - }), - ('libFS', '1.0.8', { # 2019-03-10 - 'checksums': ['e3da723257f4f4c0c629aec402e0a36fbec66a9418f70d24a159cb0470ec83d2'], - }), - ('libICE', '1.0.10', { # 2019-07-14 - 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], - }), - ('libSM', '1.2.3', { # 2018-10-10 - 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], - }), - ('libXScrnSaver', '1.2.3', { # 2018-07-05 - 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], - }), - ('libXt', '1.2.0', { # 2019-06-21 - 'checksums': ['d4bee88898fc5e1dc470e361430c72fbc529b9cdbbb6c0ed3affea3a39f97d8d'], - }), - ('libXmu', '1.1.3', { # 2019-03-16 - 'checksums': ['5bd9d4ed1ceaac9ea023d86bf1c1632cd3b172dce4a193a72a94e1d9df87a62e'], - }), - ('libXpm', '3.5.13', { # 2019-12-13 - 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], - }), - ('libXaw', '1.0.13', { # 2015-05-01 - 'checksums': ['7e74ac3e5f67def549722ff0333d6e6276b8becd9d89615cda011e71238ab694'], - }), - ('libXfixes', '5.0.3', { # 2016-10-04 - 'checksums': ['9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570'], - }), - ('libXcomposite', '0.4.5', { # 2019-03-11 - 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], - }), - ('libXrender', '0.9.10', { # 2016-10-04 - 'checksums': ['770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf'], - }), - ('libXcursor', '1.2.0', { # 2019-03-11 - 'checksums': ['ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8'], - }), - ('libXdamage', '1.1.5', { # 2019-03-11 - 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], - }), - ('libfontenc', '1.1.4', { # 2019-02-20 - 'checksums': ['895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41'], - }), - ('libXfont', '1.5.4', { # 2017-11-28 - 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], - }), - ('libXfont2', '2.0.3', { # 2019-09-14 - 'checksums': ['a4b761a37528353a2b83dba364d7c1fd6aef2d554a1a019815f24f7f8866890e'], - }), - ('libXft', '2.3.3', { # 2019-03-16 - 'checksums': ['3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701'], - }), - ('libXi', '1.7.10', { # 2019-06-19 - 'checksums': ['b51e106c445a49409f3da877aa2f9129839001b24697d75a54e5c60507e9a5e3'], - }), - ('libXinerama', '1.1.4', { # 2018-07-05 - 'checksums': ['64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18'], - }), - ('libXrandr', '1.5.2', { # 2019-03-16 - 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], - }), - ('libXres', '1.2.0', { # 2017-10-11 - 'checksums': ['5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a'], - }), - ('libXtst', '1.2.3', { # 2016-10-04 - 'checksums': ['a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2'], - }), - ('libXv', '1.0.11', { # 2016-10-04 - 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], - }), - ('libXvMC', '1.0.12', { # 2019-09-24 - 'checksums': ['024c9ec4f001f037eeca501ee724c7e51cf287eb69ced8c6126e16e7fa9864b5'], - }), - ('libXxf86dga', '1.1.5', { # 2019-03-16 - 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], - }), - ('libXxf86vm', '1.1.4', { # 2015-02-24 - 'checksums': ['5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99'], - }), - ('libdmx', '1.1.4', { # 2018-05-14 - 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], - }), - ('libxkbfile', '1.1.0', { # 2019-03-16 - 'checksums': ['2a92adda3992aa7cbad758ef0b8dfeaedebb49338b772c64ddf369d78c1c51d3'], - }), - ('libxshmfence', '1.3', { # 2018-02-26 - 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], - }), - ('xcb-util', '0.4.0', { # 2014-10-15 - 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], - }), - ('xcb-util-image', '0.4.0', { # 2014-10-15 - 'checksums': ['cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42'], - }), - ('xcb-util-keysyms', '0.4.0', { # 2014-10-01 - 'checksums': ['0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96'], - }), - ('xcb-util-renderutil', '0.3.9', { # 2014-06-13 - 'checksums': ['55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5'], - }), - ('xcb-util-wm', '0.4.1', { # 2014-02-19 - 'checksums': ['038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334'], - }), - ('xcb-util-cursor', '0.1.3', { # 2016-05-12 - 'checksums': ['a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8'], - }), - ('xkeyboard-config', '2.28', { # 2019-10-19 - 'checksums': ['4424ffaafdf9f09dea69a317709353c4e2b19f69b2405effadce0bac3bdebdff'], - }), - ('printproto', '1.0.5', { # 2011-01-06 - 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], - }), - ('libXp', '1.0.3', { # 2015-02-21 - 'checksums': ['f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c'], - }), - ('xbitmaps', '1.1.2', { # 2018-03-10 - 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], - }), -] - -preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " - -sanity_check_paths = { - 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], - 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', - 'share/pkgconfig', 'share/X11/xkb'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/XCFun/XCFun-2.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/XCFun/XCFun-2.1.0-GCCcore-9.3.0.eb deleted file mode 100644 index 962ea747cfe..00000000000 --- a/easybuild/easyconfigs/__archive__/x/XCFun/XCFun-2.1.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'XCFun' -version = '2.1.0' - -homepage = 'https://xcfun.readthedocs.io' -description = """Arbitrary order exchange-correlation functional library""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/dftlibs/xcfun/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['64aac8c933cc129ce6326f3827e342abfd10b94ea4a302aaca9f10d342ad7656'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4') -] - -modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} - -sanity_check_paths = { - 'files': ['lib/libxcfun.%s' % SHLIB_EXT], - 'dirs': ['include/XCFun'] -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/x/XGBoost/XGBoost-1.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/x/XGBoost/XGBoost-1.2.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 4cff7b5dee9..00000000000 --- a/easybuild/easyconfigs/__archive__/x/XGBoost/XGBoost-1.2.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'XGBoost' -version = '1.2.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/dmlc/xgboost' -description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, - flexible and portable.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e5f4abcd5df6767293f31b7c58d67ea38b2689641a95b2cd8ca8935295097a36'] - -builddependencies = [('CMake', '3.16.4')] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb deleted file mode 100644 index 0f45289211b..00000000000 --- a/easybuild/easyconfigs/__archive__/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -# Contribution from Imperial College London, UK -# uploaded by J. Sassmannshausen - -easyblock = 'ConfigureMake' - -name = 'XGrafix' -version = '2.41' - -homepage = 'https://ptsg.egr.msu.edu/' -description = """A graphics library and controller for physics simulation programs. -3-d surface plots, scatter plots, 2-d line plots.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://ptsg.egr.msu.edu/pub/codes'] -sources = ['%(namelower)s.tar.gz'] -checksums = ['20daa8f47cb83888e933bb2f451bc8d2b376946b2e7b1ce2252b6e3da0c3b583'] - -builddependencies = [ - ('binutils', '2.34'), - ('Bison', '3.5.3'), - ('M4', '1.4.18'), -] - -dependencies = [ - ('X11', '20200222'), - ('Tcl', '8.6.10'), - ('Tk', '8.6.10'), - ('ImageMagick', '7.0.10-1'), - ('libpng', '1.6.37'), -] - -# We need to specify where things are, unfortunately. -configopts = '--enable-fulloptimize --with-xpm=$EBROOTX11/lib ' -configopts += '--with-tclconfig=$EBROOTTCL/lib --with-tkconfig=$EBROOTTK/lib ' -configopts += '--with-X11-include=$EBROOTX11/include --with-X11_LIBDIR=$EBROOTX11/lib ' -configopts += '--enable-fortran LIBPNG_PATH=$EBROOTLIBPNG/lib ' - -sanity_check_paths = { - 'files': ['bin/ps6to1', 'bin/xgmovie', 'bin/xgmreduce', 'bin/xtest'] + - ['lib/libXGC.a', 'lib/libXGCmini.a', 'lib/libXGF.a'], - 'dirs': ['include'], -} - -sanity_check_commands = ["xtest -h"] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb deleted file mode 100644 index 78769aba0ee..00000000000 --- a/easybuild/easyconfigs/__archive__/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'Bundle' - -name = 'XML-LibXML' -version = '2.0205' - -homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' -description = "Perl binding for libxml2" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [('binutils', '2.34')] -dependencies = [ - ('Perl', '5.30.2'), - ('libxml2', '2.9.10'), -] - -exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") - -exts_list = [ - ('File::chdir', '0.1010', { - 'source_tmpl': 'File-chdir-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], - 'checksums': ['efc121f40bd7a0f62f8ec9b8bc70f7f5409d81cd705e37008596c8efc4452b01'], - }), - ('Alien::Base', '2.23', { - 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], - 'checksums': ['a6a37a01c78b39da802ca53061e1273a15d74f9d3daf523d72d3518d5015a1df'], - }), - ('Alien::Libxml2', '0.16', { - 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], - 'checksums': ['56f06a58054f788dcef8d3b6669fb47d172e9ca0b7a12d0241d9cf7835a53b97'], - }), - ('XML::LibXML', version, { - 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], - 'checksums': ['3a25002714b13f192d0baef5dc25ad2fbf09f8ec4ad1f793dec8fe6e2f5b2278'], - }), -] - -modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', -} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb b/easybuild/easyconfigs/__archive__/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb deleted file mode 100644 index 2b89d679b49..00000000000 --- a/easybuild/easyconfigs/__archive__/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb +++ /dev/null @@ -1,54 +0,0 @@ -# Contribution from Imperial College London, UK -# uploaded by J. Sassmannshausen - -easyblock = 'ConfigureMake' - -name = 'XOOPIC' -version = '20210302' -local_commit = '3fa6670' - -homepage = 'https://github.com/rinku-mishra/xoopic' -description = """XOOPIC is a two-dimensional 3-velocity particle-in-cell simulator. -It can handle electrostatic and electromagnetic models, has a large variety of -boundary conditions, supports multiple gasses and gas chemistry, and is easily -reconfigurable via an input file.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/rinku-mishra/xoopic/archive/%s' % local_commit] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['e81a2b7a527b905fd58afd080f45690963079b0a0493a55929d2a0ef1246d4e3'] - -builddependencies = [ - ('M4', '1.4.18'), - ('Bison', '3.5.3'), -] - -dependencies = [ - ('X11', '20200222'), - ('Tcl', '8.6.10'), - ('Tk', '8.6.10'), - ('ImageMagick', '7.0.10-1'), - ('XGrafix', '2.41'), - ('HDF5', '1.10.6'), - ('FFTW', '3.3.8'), -] - -# We need to specify where things are, unfortunately. -configopts = '--enable-MPI --enable-fulloptimize --with-xpm=$EBROOTX11/lib ' -configopts += '--with-tclconfig=$EBROOTTCL/lib --with-tkconfig=$EBROOTTK/lib ' -configopts += '--with-XGRAFIX-lib=$EBROOTXGRAFIX/lib --with-XGRAFIX-include=$EBROOTXGRAFIX/include ' -configopts += '--with-X11-include=$EBROOTX11/include --with-X11_LIBDIR=$EBROOTX11/lib ' -configopts += '--with-hdf5-incdir=$EBROOTHDF5/include ' -# This does not seem to be used, so for now we leave it out: -# configopts += '--with-dfftw-incdir=$EBROOTFFTW/include --with-dfftw-libdir=$EBROOTFFTW/lib ' - -sanity_check_paths = { - 'files': ['bin/xoopic'] + - ['lib/libadvisor.a', 'lib/libotools.a', 'lib/libphysics.a', 'lib/libxg.a'], - 'dirs': ['include'], -} - -sanity_check_commands = ["xoopic -h"] - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb deleted file mode 100644 index f797b8b490a..00000000000 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'XZ' -version = '5.2.5' - -homepage = 'https://tukaani.org/xz/' -description = "xz: XZ utilities" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://tukaani.org/xz/'] -sources = [SOURCELOWER_TAR_BZ2] -patches = [ - 'xz-5.2.5_fix-symbols.patch', - 'xz-5.2.5-cve-2022-1271.patch', -] -checksums = [ - {'xz-5.2.5.tar.bz2': '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df'}, - {'xz-5.2.5_fix-symbols.patch': 'ce80545e7bd88466fd9561a8abb9da87e62ebc71a1531c909a492fa2844da6d0'}, - {'xz-5.2.5-cve-2022-1271.patch': '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec'}, -] - -builddependencies = [ - # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.20.1', '', SYSTEM), - # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency - ('Autotools', '20220317', '', SYSTEM), - ('binutils', '2.34'), -] - -# may become useful in non-x86 archs -# configopts = ' --disable-assembler ' - -sanity_check_paths = { - 'files': ["bin/xz", "bin/lzmainfo"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-9.3.0.eb deleted file mode 100644 index 2775ce66948..00000000000 --- a/easybuild/easyconfigs/__archive__/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Xerces-C++' -version = '3.2.3' - -homepage = 'https://xerces.apache.org/xerces-c/' - -description = """Xerces-C++ is a validating XML parser written in a portable -subset of C++. Xerces-C++ makes it easy to give your application the ability to -read and write XML data. A shared library is provided for parsing, generating, -manipulating, and validating XML documents using the DOM, SAX, and SAX2 -APIs.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] -sources = ['xerces-c-%(version)s.tar.gz'] -checksums = ['fb96fc49b1fb892d1e64e53a6ada8accf6f0e6d30ce0937956ec68d39bd72c7e'] - -builddependencies = [ - ('pkg-config', '0.29.2'), - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -dependencies = [ - ('cURL', '7.69.1'), -] - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/XInclude', - 'include/xercesc/xinclude/XIncludeUtils.hpp', - 'lib/libxerces-c-3.2.so'], - 'dirs': ['bin', 'include', 'lib'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb deleted file mode 100644 index 94aa35864b6..00000000000 --- a/easybuild/easyconfigs/__archive__/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,112 +0,0 @@ -easyblock = 'Bundle' - -name = 'Xvfb' -version = '1.20.9' - -homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' -description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. - It emulates a dumb framebuffer using virtual memory.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), - ('Python', '3.8.2'), -] - -dependencies = [ - ('X11', '20200222'), - ('pixman', '0.38.4'), - ('libdrm', '2.4.100'), - ('Mesa', '20.0.2'), - ('nettle', '3.6'), - ('libunwind', '1.3.1'), - ('XZ', '5.2.5'), -] - -default_easyblock = 'ConfigureMake' - -local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " -local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " -local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" - -# use 'make V=1' to see compiler commands -local_xvfb_buildopts = "V=1 " - -# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" -local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' -local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' - -default_component_specs = { - 'source_urls': ['https://www.x.org/archive//individual/font/'], - 'sources': [SOURCE_TAR_GZ], - 'start_dir': '%(name)s-%(version)s', -} - -local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " -local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " - -components = [ - ('mkfontscale', '1.2.1', { - 'source_urls': ['https://www.x.org/archive//individual/app/'], - 'checksums': ['e5b687029e44d0bd3ccd254a4da6a5cbfc40350aa8b43fcca16ef6e9b9bb9f22'], - }), - ('mkfontdir', '1.0.7', { - 'source_urls': ['https://www.x.org/archive//individual/app/'], - 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], - }), - ('bdftopcf', '1.1', { - 'source_urls': ['https://www.x.org/archive//individual/app/'], - 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], - }), - ('font-util', '1.3.2', { - 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], - }), - ('font-misc-misc', '1.1.2', { - 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], - 'preconfigopts': local_font_misc_preconfigopts, - }), - ('xkbcomp', '1.4.3', { - 'source_urls': ['https://www.x.org/archive//individual/app/'], - 'checksums': ['c518a321ca98577c04d3b9a3ff0f3e7d96297b82ac65015b1f0e69627b4b598a'], - }), - ('xkeyboard-config', '2.31', { - 'source_urls': ['https://www.x.org/archive//individual/data/xkeyboard-config/'], - 'checksums': ['5ac6b5b661aeb9d0ea84ad961cbbdd8fdf2503d6e8ca65ca1b1c5d9aea2ddc52'], - 'configopts': '--with-xkb-rules-symlink=xorg', - }), - ('xauth', '1.1', { - 'source_urls': ['https://www.x.org/releases/individual/app/'], - 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], - }), - (name, version, { - 'source_urls': ['https://www.x.org/releases/individual//xserver/'], - 'sources': ['xorg-server-%(version)s.tar.gz'], - 'patches': [('xvfb-run', '.')], - 'checksums': [ - '067c348fe1a86a1924010354c1c7cf1eaa9e43866e48540aa56a465f2a341ddc', # xorg-server-1.20.9.tar.gz - 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run - ], - 'start_dir': 'xorg-server-%(version)s', - 'configopts': local_xvfb_configopts, - 'buildopts': local_xvfb_buildopts, - 'installopts': local_xvfb_buildopts, - }), -] - -# enable exec permissions for xvfb-run after copying; -# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works -postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] - -sanity_check_paths = { - 'files': ['bin/Xvfb', 'bin/xvfb-run'], - 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], -} - -sanity_check_commands = [ - "xvfb-run --help", - "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", -] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/x264/x264-20191217-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/x264/x264-20191217-GCCcore-9.3.0.eb deleted file mode 100644 index c91126155e0..00000000000 --- a/easybuild/easyconfigs/__archive__/x/x264/x264-20191217-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'x264' -version = '20191217' - -homepage = 'https://www.videolan.org/developers/x264.html' - -description = """ - x264 is a free software library and application for encoding video streams - into the H.264/MPEG-4 AVC compression format, and is released under the - terms of the GNU GPL. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'https://download.videolan.org/pub/videolan/x264/snapshots/', - 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', -] -sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] -checksums = ['b2495c8f2930167d470994b1ce02b0f4bfb24b3317ba36ba7f112e9809264160'] - -builddependencies = [ - ('binutils', '2.34'), - ('NASM', '2.14.02'), -] - -configopts = " --enable-shared --enable-static" - -sanity_check_paths = { - 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', - 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/x265/x265-3.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/x265/x265-3.3-GCCcore-9.3.0.eb deleted file mode 100644 index b98754281ad..00000000000 --- a/easybuild/easyconfigs/__archive__/x/x265/x265-3.3-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'x265' -version = '3.3' - -homepage = 'https://x265.org/' - -description = """ - x265 is a free software library and application for encoding video streams - into the H.265 AVC compression format, and is released under the terms of - the GNU GPL. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [ - 'https://bitbucket.org/multicoreware/x265_git/downloads/', - 'https://download.videolan.org/pub/videolan/x265/', -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = [( - # checksum for new source tarball (from https://bitbucket.org/multicoreware/x265_git/downloads) - 'c6d744a87eda55560da715f56f878640554ddc06e2d0fcbd822fa330affc22cc', - # checksum for original source tarball (from https://bitbucket.org/multicoreware/x265/downloads) - 'f26e148ed1f4dfb33fd1eb3ff5e60e08078d1b2017e88bcbb045b3fb58300b9c', -)] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('Yasm', '1.3.0'), -] - -start_dir = 'source' - -sanity_check_paths = { - 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/xESMF/xESMF-0.3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/x/xESMF/xESMF-0.3.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index b35721cfb35..00000000000 --- a/easybuild/easyconfigs/__archive__/x/xESMF/xESMF-0.3.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'xESMF' -version = '0.3.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://xesmf.readthedocs.io' -description = "xESMF: Universal Regridder for Geospatial Data" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['66b6deb37f43749df06819fc2003bbd394207617cf7d8fd9dafe655d7af7b94c'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy, scipy - ('ESMPy', '8.0.1', versionsuffix), - ('xarray', '0.16.1', versionsuffix), -] - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index b8de3fd29a9..00000000000 --- a/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'xarray' -version = '0.16.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pydata/xarray' -description = """xarray (formerly xray) is an open source project and Python package that aims to bring - the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the - core pandas data structures.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['5e1af056ff834bf62ca57da917159328fab21b1f8c25284f92083016bb2d92a5'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # required for numpy, pandas -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.1-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 2ff8b8ab851..00000000000 --- a/easybuild/easyconfigs/__archive__/x/xarray/xarray-0.16.1-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'xarray' -version = '0.16.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pydata/xarray' -description = """xarray (formerly xray) is an open source project and Python package that aims to bring - the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the - core pandas data structures.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['5e1af056ff834bf62ca57da917159328fab21b1f8c25284f92083016bb2d92a5'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # required for numpy, pandas -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.3.0.eb deleted file mode 100644 index 35d18f46f79..00000000000 --- a/easybuild/easyconfigs/__archive__/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Custom -# -# Notes:: -## - -easyblock = 'ConfigureMake' - -name = 'xorg-macros' -version = '1.19.2' - -homepage = 'https://cgit.freedesktop.org/xorg/util/macros' -description = """X.org macros utilities.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] -sources = ['macros-util-macros-%(version)s.tar.gz'] -checksums = ['326e51a5d673e3d9cc7f139aee469a11e18ea060b1d06c22694612e68a2089b1'] - -builddependencies = [ - ('binutils', '2.34'), - ('Autotools', '20180311'), -] - -preconfigopts = './autogen.sh && ' - -sanity_check_paths = { - 'files': ['share/pkgconfig/xorg-macros.pc'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/x/xprop/xprop-1.2.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/xprop/xprop-1.2.4-GCCcore-9.3.0.eb deleted file mode 100644 index 9a54190e8dc..00000000000 --- a/easybuild/easyconfigs/__archive__/x/xprop/xprop-1.2.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xprop' -version = '1.2.4' - -homepage = "https://www.x.org/wiki/" -description = """The xprop utility is for displaying window and font properties in an X server. - One window or font is selected using the command line arguments or possibly - in the case of a window, by clicking on the desired window. A list of - properties is then given, possibly with formatting information.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://ftp.x.org/archive/individual/app/'] -sources = [SOURCE_TAR_GZ] -checksums = ['dddb6e208ffa515e68f001c22077a465f1365a4bcf91d9b37f336a6c0d15400d'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('X11', '20200222'), -] - -sanity_check_paths = { - 'files': ['bin/xprop'], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.31-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.31-GCCcore-9.3.0.eb deleted file mode 100644 index 0a2078907fa..00000000000 --- a/easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.31-GCCcore-9.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xproto' -version = '7.0.31' - -homepage = 'https://www.freedesktop.org/wiki/Software/xlibs' -description = "X protocol and ancillary headers" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = [XORG_PROTO_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] - -builddependencies = [ - ('binutils', '2.34'), - ('xorg-macros', '1.19.2'), -] - -sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', - 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', - 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', - 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/y/YANK/YANK-0.25.2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/y/YANK/YANK-0.25.2-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 0f3c8455a85..00000000000 --- a/easybuild/easyconfigs/__archive__/y/YANK/YANK-0.25.2-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,103 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'YANK' -version = '0.25.2' -versionsuffix = "-Python-%(pyver)s" - -homepage = 'http://getyank.org/' -description = "A GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations" - -toolchain = {'name': 'intel', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('OpenMM', '7.4.2', versionsuffix), - ('MDTraj', '1.9.4', versionsuffix), - ('OpenMMTools', '0.20.0', versionsuffix), - ('pymbar', '3.0.3', versionsuffix), - ('PyYAML', '5.3'), - ('IPython', '7.15.0', versionsuffix), - ('PyTables', '3.6.1', versionsuffix), - ('packmol', 'v20.2.2'), - ('libxslt', '1.1.34'), - ('libxml2', '2.9.10'), - ('ParmEd', '3.2.0', versionsuffix), - ('AmberTools', '20', versionsuffix), -] - -exts_list = [ - ('docopt', '0.6.2', { - 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], - }), - ('six', '1.15.0', { - 'checksums': ['30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259'], - }), - ('lxml', '4.6.1', { - 'checksums': ['c152b2e93b639d1f36ec5a8ca24cde4a8eefb2b6b83668fcd8e83a67badcb367'], - }), - ('numpydoc', '1.1.0', { - 'checksums': ['c36fd6cb7ffdc9b4e165a43f67bf6271a7b024d0bb6b00ac468c9e2bfc76448e'], - }), - ('openmoltools', '0.8.7', { - 'modulename': False, - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/choderalab/openmoltools/archive'], - 'checksums': ['dae37dc1136cbc6175b1935e2b4352cc7cc9c9e4d441968178c9e90ec674a1df'], - }), - ('mpiplus', '0.0.1', { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/choderalab/mpiplus/archive'], - 'checksums': ['a3d50157a274decab87589ad78b9e41e9f3d34eb27a7d50cc6e7ef34def98b44'], - }), - ('clusterutils', '0.3.1', { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/choderalab/clusterutils/archive'], - 'checksums': ['2c841215d1a93af5c61fac2ff52cdc8a286f05af219bca84a76a7a7380f3ee96'], - }), - ('sphinxcontrib-bibtex', '1.0.0', { - 'modulename': 'sphinxcontrib.bibtex', - 'checksums': ['629612b001f86784669d65e662377a482052decfd9a0a17c46860878eef7b9e0'], - }), - ('Cerberus', '1.3.2', { - 'checksums': ['302e6694f206dd85cb63f13fd5025b31ab6d38c99c50c6d769f8fa0b0f299589'], - }), - ('oset', '0.1.3', { - 'checksums': ['4c1fd7dec96eeff9d3260995a8e37f9f415d0bdb79975f57824e68716ac8f904'], - }), - ('latexcodec', '2.0.1', { - 'checksums': ['2aa2551c373261cefe2ad3a8953a6d6533e68238d180eb4bb91d7964adb3fe9a'], - }), - ('pybtex', '0.23.0', { - 'checksums': ['b92be18ccd5e9a37895949dcf359a1f6890246b73646dddf1129178ee12e4bef'], - }), - ('pybtex-docutils', '0.2.2', { - 'checksums': ['ea90935da188a0f4de2fe6b32930e185c33a0e306154322ccc12e519ebb5fa7d'], - }), - ('pdbfixer', '1.6', { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/openmm/pdbfixer/archive'], - 'checksums': ['8dc928d1a57dded981835a6175760f3407c52664b6204053636f7754787a655e'], - }), - (name, version, { - 'modulename': False, - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/choderalab/yank/archive'], - 'checksums': ['6a1c91f8afb1d99eac67ef4a22a137f2fd755275f1a614d1ec267cb36b8960d5'], - }), -] - -sanity_check_paths = { - 'files': ['bin/yank'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -# sanity check commands must be run with mpi run since they trigger MPI_Init and -# the impi version in intel/2020a requires that everything that triggers MPI_Init is run via mpirun -sanity_check_commands = [ - '%(mpi_cmd_prefix)s %(namelower)s selftest', - "%(mpi_cmd_prefix)s python -c 'import openmoltools'", -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb deleted file mode 100644 index f0ce46c5d3f..00000000000 --- a/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of -# the policy: # https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html -## - -easyblock = 'ConfigureMake' - -name = 'Yasm' -version = '1.3.0' - -homepage = 'https://www.tortall.net/projects/yasm/' - -description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] - -builddependencies = [('binutils', '2.34')] - -sanity_check_paths = { - 'files': ['bin/yasm'], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 9a68aadd6be..00000000000 --- a/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# -# Building this in interactive Slurm session will result in freeze during either -# runtest phase or sanity_check_commands phase (python -c 'import yaff') -# -# If you submit this as non-interactive Slurm job, it will build just fine. -# Possibly root cause: https://github.com/h5py/h5py/issues/917 -# -easyblock = 'PythonPackage' - -name = 'yaff' -version = '1.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://molmod.github.io/yaff/' -description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] - -dependencies = [ - ('Python', '3.8.2'), - ('h5py', '2.10.0', versionsuffix), - ('molmod', '1.4.5', versionsuffix), -] - -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - -runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -runtest += "python setup.py build_ext -i; nosetests -v" - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 5d76d5b9517..00000000000 --- a/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,38 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# -# Building this in interactive Slurm session will result in freeze during either -# runtest phase or sanity_check_commands phase (python -c 'import yaff') -# -# If you submit this as non-interactive Slurm job, it will build just fine. -# Possibly root cause: https://github.com/h5py/h5py/issues/917 -# -easyblock = 'PythonPackage' - -name = 'yaff' -version = '1.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://molmod.github.io/yaff/' -description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] - -dependencies = [ - ('Python', '3.8.2'), - ('h5py', '2.10.0', versionsuffix), - ('molmod', '1.4.5', versionsuffix), -] - -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - -runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -runtest += "python setup.py build_ext -i; nosetests -v" - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/__archive__/z/Z3/Z3-4.8.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/z/Z3/Z3-4.8.9-GCCcore-9.3.0.eb deleted file mode 100644 index 541189b8b01..00000000000 --- a/easybuild/easyconfigs/__archive__/z/Z3/Z3-4.8.9-GCCcore-9.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Z3' -version = '4.8.9' - -homepage = 'https://github.com/Z3Prover/z3' -description = """ - Z3 is a theorem prover from Microsoft Research. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/Z3Prover/z3/archive/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c9fd04b9b33be74fffaac3ec2bc2c320d1a4cc32e395203c55126b12a14ff3f4'] - -builddependencies = [ - ('CMake', '3.16.4'), - # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.34'), -] - -dependencies = [ - ('GMP', '6.2.0'), -] - -configopts = '-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON ' - -sanity_check_paths = { - 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-4.3.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-4.3.2-GCCcore-9.3.0.eb deleted file mode 100644 index be81e3d64a2..00000000000 --- a/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-4.3.2-GCCcore-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ZeroMQ' -version = '4.3.2' - -homepage = 'https://www.zeromq.org/' -description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. - It gives you sockets that carry atomic messages across various transports like in-process, - inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, - pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered - products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous - message-processing tasks. It has a score of language APIs and runs on most operating systems.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['ebd7b5c830d6428956b67a0454a7f8cbed1de74b3b01e5c33c5378e22740f763'] - -builddependencies = [ - ('binutils', '2.34'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('OpenPGM', '5.2.122'), - ('libsodium', '1.0.18'), - ('util-linux', '2.35'), -] - -configopts = '--with-pic --with-pgm --with-libsodium ' - -sanity_check_paths = { - 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], - 'dirs': ['include', 'lib'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/__archive__/z/Zip/Zip-3.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/z/Zip/Zip-3.0-GCCcore-9.3.0.eb deleted file mode 100644 index 70f710266a7..00000000000 --- a/easybuild/easyconfigs/__archive__/z/Zip/Zip-3.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Zip' -version = '3.0' - -homepage = 'http://www.info-zip.org/Zip.html' -description = """Zip is a compression and file packaging/archive utility. -Although highly compatible both with PKWARE's PKZIP and PKUNZIP -utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives -have been portability and other-than-MSDOS functionality""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://download.sourceforge.net/infozip'] -sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] -checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] - -builddependencies = [ - ('binutils', '2.34'), -] -dependencies = [ - ('bzip2', '1.0.8'), -] - -skipsteps = ['configure'] - -buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' -buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' -buildopts += 'generic_gcc' - -installopts = '-f unix/Makefile prefix=%(installdir)s ' - -sanity_check_paths = { - 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], - 'dirs': ['man/man1'] -} - -sanity_check_commands = ["zip --version"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/z/zarr/zarr-2.4.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/__archive__/z/zarr/zarr-2.4.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 4118ac3cb7c..00000000000 --- a/easybuild/easyconfigs/__archive__/z/zarr/zarr-2.4.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = "PythonBundle" - -name = 'zarr' -version = '2.4.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://zarr.readthedocs.io/en/stable/' -description = """Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, - designed for use in parallel computing.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), -] - -exts_list = [ - ('asciitree', '0.3.3', { - 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], - }), - ('fasteners', '0.15', { - 'checksums': ['3a176da6b70df9bb88498e1a18a9e4a8579ed5b9141207762368a1017bf8f5ef'], - }), - ('monotonic', '1.5', { - 'checksums': ['23953d55076df038541e648a53676fb24980f7a1be290cdda21300b3bc21dfb0'], - }), - ('numcodecs', '0.6.4', { - 'checksums': ['ef4843d5db4d074e607e9b85156835c10d006afc10e175bda62ff5412fca6e4d'], - }), - (name, version, { - 'checksums': ['53aa21b989a47ddc5e916eaff6115b824c0864444b1c6f3aaf4f6cf9a51ed608'], - }), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/__archive__/z/zfp/zfp-1.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/z/zfp/zfp-1.0.0-GCCcore-9.3.0.eb deleted file mode 100644 index 0923191cade..00000000000 --- a/easybuild/easyconfigs/__archive__/z/zfp/zfp-1.0.0-GCCcore-9.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'MakeCp' - -name = 'zfp' -version = '1.0.0' - -homepage = 'https://github.com/LLNL/zfp' -description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. -zfp provides compressed-array classes that support high throughput read and write random access to individual array -elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications -that read and write large data sets to and from disk.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/LLNL/zfp/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['fe13b03141ee9b571692aed42ff76cf37c9dcda40f9a43a808870dca3558a57c'] - -builddependencies = [ - ('binutils', '2.34'), -] - -prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " -buildopts = 'ZFP_WITH_OPENMP=1' - -runtest = 'test' - -files_to_copy = ['bin', 'include', 'lib'] - -sanity_check_paths = { - 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], - 'dirs': ['include/zfp'], -} - -sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-FCC-4.5.0.eb deleted file mode 100644 index 7ec5802a20d..00000000000 --- a/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-FCC-4.5.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.11' - -homepage = 'https://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'FCC', 'version': '4.5.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://zlib.net/fossils'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] - -# use binutils from the OS, since zlib is itself a dependency of the easybuilt binutils -osdependencies = [('binutils')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb deleted file mode 100644 index 090662b5e71..00000000000 --- a/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.11' - -homepage = 'https://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://zlib.net/fossils'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] - -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.34', '', SYSTEM)] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/__archive__/z/zstd/zstd-1.4.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/__archive__/z/zstd/zstd-1.4.4-GCCcore-9.3.0.eb deleted file mode 100644 index fe0ca0bee72..00000000000 --- a/easybuild/easyconfigs/__archive__/z/zstd/zstd-1.4.4-GCCcore-9.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zstd' -version = '1.4.4' - -homepage = 'https://facebook.github.io/zstd' -description = """Zstandard is a real-time compression algorithm, providing high compression ratios. - It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. - It also offers a special mode for small data, called dictionary compression, and can create dictionaries - from any sample set.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -github_account = 'facebook' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['a364f5162c7d1a455cc915e8e3cf5f4bd8b75d09bc0f53965b0c9ca1383c52c8'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('gzip', '1.10'), - ('XZ', '5.2.5'), - ('lz4', '1.9.2'), -] - -skipsteps = ['configure'] - -runtest = 'check' - -installopts = "PREFIX=%(installdir)s" - -sanity_check_paths = { - 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], - 'dirs': ["lib/pkgconfig"] -} - -moduleclass = 'lib'