{bio}[foss/2023a,gompi/2023a] bcgTree v1.2.1, RAxML v8.2.13 w/ avx2 by PetrKralCZ · Pull Request #22540 · easybuilders/easybuild-easyconfigs

PetrKralCZ · 2025-03-12T13:51:42Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#522

…023a-avx2.eb

github-actions · 2025-03-12T13:52:13Z

Updated software `RAxML-8.2.13-gompi-2023a-avx2.eb`

Diff against RAxML-8.2.13-gompi-2023b-avx2.eb

easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023b-avx2.eb

diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023b-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023a-avx2.eb
index 35faf662fe..83738b8140 100644
--- a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023b-avx2.eb
+++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023a-avx2.eb
@@ -7,7 +7,7 @@ versionsuffix = '-avx2'
 homepage = 'https://github.com/stamatak/standard-RAxML'
 description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees."
 
-toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://github.com/stamatak/standard-RAxML/archive/']

Diff against RAxML-8.2.12-gompi-2022b-avx2.eb

easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2022b-avx2.eb

diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2022b-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023a-avx2.eb
index 8b13f18b2d..83738b8140 100644
--- a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2022b-avx2.eb
+++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023a-avx2.eb
@@ -1,18 +1,18 @@
 easyblock = 'MakeCp'
 
 name = 'RAxML'
-version = '8.2.12'
+version = '8.2.13'
 versionsuffix = '-avx2'
 
 homepage = 'https://github.com/stamatak/standard-RAxML'
 description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees."
 
-toolchain = {'name': 'gompi', 'version': '2022b'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://github.com/stamatak/standard-RAxML/archive/']
-sources = ['v%(version)s.zip']
-checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105']
+sources = ['v%(version)s.tar.gz']
+checksums = ['28e500793324bd7d330b396ef27ea49c9186fa5e1edb3d5439036dc6c33e6067']
 
 buildopts = '-f Makefile.AVX2.gcc CC="$CC" && rm *.o && '
 buildopts += 'make -j %(parallel)s -f Makefile.AVX2.PTHREADS.gcc CC="$CC" && rm *.o && '
@@ -20,13 +20,17 @@ buildopts += 'make -j %(parallel)s -f Makefile.AVX2.HYBRID.gcc CC="$CC"'
 
 files_to_copy = [
     (["raxmlHPC-AVX2", "raxmlHPC-PTHREADS-AVX2", "raxmlHPC-HYBRID-AVX2"], "bin"),
-    "usefulScripts", "README", "manual"
+    "usefulScripts", "README.md", "manual",
 ]
 
-postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-AVX2 raxmlHPC"]
+postinstallcmds = [
+    "ln -s raxmlHPC-AVX2 %(installdir)s/bin/raxmlHPC",
+    "ln -s raxmlHPC-PTHREADS-AVX2 %(installdir)s/bin/raxmlHPC-PTHREADS",
+    "ln -s raxmlHPC-HYBRID-AVX2 %(installdir)s/bin/raxmlHPC-HYBRID",
+]
 
 sanity_check_paths = {
-    'files': ['bin/raxmlHPC'],
+    'files': ['bin/raxmlHPC%s' % x for x in ['', '-PTHREADS', '-HYBRID']],
     'dirs': [],
 }

Diff against RAxML-8.2.12-gompi-2021b-hybrid-avx2.eb

easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021b-hybrid-avx2.eb

diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021b-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023a-avx2.eb
index 7be898198d..83738b8140 100644
--- a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021b-hybrid-avx2.eb
+++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023a-avx2.eb
@@ -1,27 +1,36 @@
 easyblock = 'MakeCp'
 
 name = 'RAxML'
-version = '8.2.12'
-versionsuffix = '-hybrid-avx2'
+version = '8.2.13'
+versionsuffix = '-avx2'
 
 homepage = 'https://github.com/stamatak/standard-RAxML'
 description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees."
 
-toolchain = {'name': 'gompi', 'version': '2021b'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://github.com/stamatak/standard-RAxML/archive/']
-sources = ['v%(version)s.zip']
-checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105']
+sources = ['v%(version)s.tar.gz']
+checksums = ['28e500793324bd7d330b396ef27ea49c9186fa5e1edb3d5439036dc6c33e6067']
 
-buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"'
+buildopts = '-f Makefile.AVX2.gcc CC="$CC" && rm *.o && '
+buildopts += 'make -j %(parallel)s -f Makefile.AVX2.PTHREADS.gcc CC="$CC" && rm *.o && '
+buildopts += 'make -j %(parallel)s -f Makefile.AVX2.HYBRID.gcc CC="$CC"'
 
-files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"]
+files_to_copy = [
+    (["raxmlHPC-AVX2", "raxmlHPC-PTHREADS-AVX2", "raxmlHPC-HYBRID-AVX2"], "bin"),
+    "usefulScripts", "README.md", "manual",
+]
 
-postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"]
+postinstallcmds = [
+    "ln -s raxmlHPC-AVX2 %(installdir)s/bin/raxmlHPC",
+    "ln -s raxmlHPC-PTHREADS-AVX2 %(installdir)s/bin/raxmlHPC-PTHREADS",
+    "ln -s raxmlHPC-HYBRID-AVX2 %(installdir)s/bin/raxmlHPC-HYBRID",
+]
 
 sanity_check_paths = {
-    'files': ['bin/raxmlHPC'],
+    'files': ['bin/raxmlHPC%s' % x for x in ['', '-PTHREADS', '-HYBRID']],
     'dirs': [],
 }

PetrKralCZ · 2025-03-12T14:18:24Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-03-12T14:20:09Z

@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=22540 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22540 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5925

Test results coming soon (I hope)...

Details

- notification for comment with ID 2718054899 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 · 2025-03-12T14:21:28Z

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 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/0a11e069a74fba581d259d841b4153eb for a full test report.

…asyconfigs into 20250312145137_new_pr_bcgTree121

laraPPr · 2025-03-31T15:19:45Z

Test report by @laraPPr
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3615.doduo.os - Linux RHEL 9.4 (Plow), x86_64, AMD EPYC 7552 48-Core Processor, Python 3.9.18
See https://gist.github.com/laraPPr/2dc3b628d29f970cc72aefa36261ddea for a full test report.

laraPPr

lgtm

laraPPr · 2025-03-31T15:24:00Z

Going in, thanks @PetrKralCZ!

adding easyconfigs: bcgTree-1.2.1-foss-2023a.eb, RAxML-8.2.13-gompi-2…

6b9f218

…023a-avx2.eb

PetrKralCZ added the update label Mar 12, 2025

PetrKralCZ mentioned this pull request Mar 12, 2025

bcgTree vscentrum/vsc-software-stack#522

Closed

2 tasks

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

1429499

…asyconfigs into 20250312145137_new_pr_bcgTree121

github-actions Bot added the new label Mar 31, 2025

laraPPr added this to the release after 5.0.0 milestone Mar 31, 2025

laraPPr approved these changes Mar 31, 2025

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laraPPr merged commit f787801 into easybuilders:develop Mar 31, 2025
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{bio}[foss/2023a,gompi/2023a] bcgTree v1.2.1, RAxML v8.2.13 w/ avx2#22540

{bio}[foss/2023a,gompi/2023a] bcgTree v1.2.1, RAxML v8.2.13 w/ avx2#22540
laraPPr merged 2 commits intoeasybuilders:developfrom
PetrKralCZ:20250312145137_new_pr_bcgTree121

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Updated software RAxML-8.2.13-gompi-2023a-avx2.eb

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Updated software `RAxML-8.2.13-gompi-2023a-avx2.eb`