Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

{lib,tools}[foss/2023a] sdsl-lite v2.1.1, libdivsufsort v2.0.1 #21848

Open
wants to merge 1 commit into
base: develop
Choose a base branch
from

Conversation

PetrKralCZ
Copy link
Collaborator

@PetrKralCZ PetrKralCZ commented Nov 13, 2024

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#412

Copy link

Updated software libdivsufsort-2.0.1-foss-2023a.eb

Diff against libdivsufsort-2.0.1-foss-2018b.eb

easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb

diff --git a/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb b/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2023a.eb
index 114f4c6225..2ad493ff64 100644
--- a/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb
+++ b/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2023a.eb
@@ -1,6 +1,7 @@
 # Author: Iñaki Mtz de Ilarduya <[email protected]>
 # sciCORE - University of Basel
 # SIB Swiss Institute of Bioinformatics
+# Update: Petr Král (INUITS)
 
 easyblock = 'CMakeMake'
 
@@ -11,18 +12,22 @@ homepage = 'https://github.com/y-256/libdivsufsort'
 description = """libdivsufsort is a software library that implements a lightweight suffix
  array construction algorithm."""
 
-toolchain = {'name': 'foss', 'version': '2018b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 source_urls = ['https://github.com/y-256/libdivsufsort/archive/refs/tags/']
 sources = ['%(version)s.tar.gz']
 checksums = ['9164cb6044dcb6e430555721e3318d5a8f38871c2da9fd9256665746a69351e0']
 
 builddependencies = [
-    ('CMake', '3.12.1'),
+    ('CMake', '3.26.3'),
 ]
 
 unpack_options = '--strip-components=1'
 
+# For `divsufsort64.h` to be available.
+# See https://github.com/y-256/libdivsufsort/blob/2.0.1/include/CMakeLists.txt#L161
+configopts = '-DBUILD_DIVSUFSORT64=ON'
+
 sanity_check_paths = {
     'files': ['lib/libdivsufsort.%s' % SHLIB_EXT],
     'dirs': [],

Updated software sdsl-lite-2.1.1-foss-2023a.eb

Diff against sdsl-lite-2.0.3-GCCcore-12.2.0.eb

easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.1.1-foss-2023a.eb
index d4bda3a4a9..46cba5e14f 100644
--- a/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.1.1-foss-2023a.eb
@@ -1,8 +1,9 @@
 # This easyconfig was created by the BEAR Software team at the University of Birmingham.
+# Update: Petr Král (INUITS)
 easyblock = "CMakeMake"
 
 name = 'sdsl-lite'
-version = '2.0.3'
+version = '2.1.1'
 
 homepage = "https://github.com/simongog/sdsl-lite"
 description = """The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing
@@ -12,19 +13,27 @@ description = """The Succinct Data Structure Library (SDSL) is a powerful and fl
  complexity of an operation performed on the classical data structure and the equivalent succinct data structure
  are (most of the time) identical."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 source_urls = ['https://github.com/simongog/%(name)s/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['08ece40ce44041906bfa425af81a20a8071d187285f674debd8816c2e3113c2f']
+checksums = ['e36591338c390184760dbdddbb653d972d9c1986c8819f462e7e73ddd28b992b']
 
 builddependencies = [
-    ('CMake', '3.24.3'),
-    ('binutils', '2.39'),
+    ('CMake', '3.26.3'),
+    ('binutils', '2.40'),
+    ('googletest', '1.13.0'),
 ]
 
+dependencies = [
+    ('libdivsufsort', '2.0.1'),
+]
+
+# Use our `googletest` and `libdivsufsort`.
+preconfigopts = "sed -i '/external/d' %(builddir)s/%(name)s-%(version)s/CMakeLists.txt && "
+
 sanity_check_paths = {
-    'files': ['lib/libdivsufsort64.a', 'lib/libdivsufsort.a', 'lib/libsdsl.a', 'include/divsufsort64.h'],
+    'files': ['lib/libsdsl.a'],
     'dirs': ['include/sdsl'],
 }
 

@PetrKralCZ
Copy link
Collaborator Author

@boegelbot please test @ generoso

@boegelbot
Copy link
Collaborator

@PetrKralCZ: Request for testing this PR well received on login1

PR test command 'EB_PR=21848 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21848 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14703

Test results coming soon (I hope)...

- notification for comment with ID 2473667884 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

@boegelbot
Copy link
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/b61a12201fb9cf80280ad5646f8bc6b2 for a full test report.

@PetrKralCZ
Copy link
Collaborator Author

@boegelbot please test @ jsc-zen3

@boegelbot
Copy link
Collaborator

@PetrKralCZ: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21848 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21848 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5267

Test results coming soon (I hope)...

- notification for comment with ID 2473798392 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

@boegelbot
Copy link
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/df5d01aa400a6bf27353963bb6aadb25 for a full test report.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging this pull request may close these issues.

SDSL-lite
2 participants