use generic version of RAxML v8.2.13 as dependency for bcgTree and Parsnp by ocaisa · Pull Request #23975 · easybuilders/easybuild-easyconfigs

ocaisa · 2025-09-23T13:33:13Z

A custom version of RAxML with AVX2 optimisation was being used as a dependency in some places. This doesn't work on non-x86_64 so rather switch to a more generic build but using the EasyBuild CFLAGS which allows the compiler to use native CPU optimisations.

If there is a concern about performance loss here, RAxML-NG should really be used anyway in that scenario.

…v8.2.13

ocaisa · 2025-09-23T13:37:00Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-09-23T13:40:09Z

@ocaisa: 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=23975 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23975 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8037

Test results coming soon (I hope)...

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boegelbot · 2025-09-23T13:51:36Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/7910fe6e5211446847e06a8379a16992 for a full test report.

boegel · 2025-09-24T14:43:07Z

-
-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"'


@ocaisa Did you check how these Makefiles differ from Makefile.PTHREADS.gcc and Makefile.HYBRID.gcc?

Is it really only changes in compiler options?

Yes I checked them and there are two things done differently:

avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS) $(CC) $(CFLAGS) -mavx2 -D_FMA -march=core-avx2 -c -o avxLikelihood.o avxLikelihood.c fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS) $(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

The second is only an additional compilation flag.

The first is a complete file with optimisations which gets picked up via a make flag. However, that file is 10+ years old, I'm sure it does what is was intended for (AVX2 optimisations) but if you are really looking for performance RAxML-NG claims to have the upper hand.

I don't have any way to test the performance between the two builds, but I really wonder if it is worth our while to introduce dependency branching for something that (right now) doesn't even use our standard compiler optimisations.

boegel · 2025-10-08T11:30:53Z

I totally forgot about @lexming's easyblock PR that tackles the same problem in a different way:

add easyblock for RAxML easybuild-easyblocks#2180

github-actions · 2025-10-08T11:32:05Z

Updated software `RAxML-8.2.13-gompi-2023b.eb`

Diff against RAxML-8.2.13-gompi-2023a.eb

easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023a.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023b.eb
index 405f5c6857..7f9c007e22 100644
--- a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023a.eb
+++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023b.eb
@@ -6,7 +6,7 @@ version = '8.2.13'
 homepage = 'https://github.com/stamatak/standard-RAxML'
 description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees."
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 
 source_urls = ['https://github.com/stamatak/standard-RAxML/archive/']
 sources = ['v%(version)s.tar.gz']

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-2023b.eb
index 8b13f18b2d..7f9c007e22 100644
--- a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2022b-avx2.eb
+++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.13-gompi-2023b.eb
@@ -1,32 +1,34 @@
 easyblock = 'MakeCp'
 
 name = 'RAxML'
-version = '8.2.12'
-versionsuffix = '-avx2'
+version = '8.2.13'
 
 homepage = 'https://github.com/stamatak/standard-RAxML'
 description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees."
 
-toolchain = {'name': 'gompi', 'version': '2022b'}
-toolchainopts = {'usempi': True}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 
 source_urls = ['https://github.com/stamatak/standard-RAxML/archive/']
-sources = ['v%(version)s.zip']
-checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105']
+sources = ['v%(version)s.tar.gz']
+patches = ['raxml_8.2.13_respect_eb_settings.patch']
+checksums = [
+    '28e500793324bd7d330b396ef27ea49c9186fa5e1edb3d5439036dc6c33e6067',
+    '66412303ccbb2720e3dbb5acb1179fe441a2aaa563d033c5f0292f5ba1e08c3b',
+]
+
+buildopts = '-f Makefile.gcc && rm *.o && '
+buildopts += 'make -j %(parallel)s -f  Makefile.PTHREADS.gcc && rm *.o && '
+buildopts += 'make -j %(parallel)s -f  Makefile.MPI.gcc && rm *.o && '
+buildopts += 'make -j %(parallel)s -f Makefile.HYBRID.gcc '
 
-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-AVX2", "raxmlHPC-PTHREADS-AVX2", "raxmlHPC-HYBRID-AVX2"], "bin"),
-    "usefulScripts", "README", "manual"
+    (["raxmlHPC", "raxmlHPC-PTHREADS", "raxmlHPC-HYBRID", "raxmlHPC-MPI"], "bin"),
+    "usefulScripts", "README.md", "manual",
 ]
 
-postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-AVX2 raxmlHPC"]
-
 sanity_check_paths = {
-    'files': ['bin/raxmlHPC'],
+    'files': ['bin/raxmlHPC%s' % x for x in ['', '-PTHREADS', '-HYBRID', '-MPI']],
     '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-2023b.eb
index 7be898198d..7f9c007e22 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-2023b.eb
@@ -1,27 +1,34 @@
 easyblock = 'MakeCp'
 
 name = 'RAxML'
-version = '8.2.12'
-versionsuffix = '-hybrid-avx2'
+version = '8.2.13'
 
 homepage = 'https://github.com/stamatak/standard-RAxML'
 description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees."
 
-toolchain = {'name': 'gompi', 'version': '2021b'}
-toolchainopts = {'usempi': True}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 
 source_urls = ['https://github.com/stamatak/standard-RAxML/archive/']
-sources = ['v%(version)s.zip']
-checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105']
+sources = ['v%(version)s.tar.gz']
+patches = ['raxml_8.2.13_respect_eb_settings.patch']
+checksums = [
+    '28e500793324bd7d330b396ef27ea49c9186fa5e1edb3d5439036dc6c33e6067',
+    '66412303ccbb2720e3dbb5acb1179fe441a2aaa563d033c5f0292f5ba1e08c3b',
+]
 
-buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"'
+buildopts = '-f Makefile.gcc && rm *.o && '
+buildopts += 'make -j %(parallel)s -f  Makefile.PTHREADS.gcc && rm *.o && '
+buildopts += 'make -j %(parallel)s -f  Makefile.MPI.gcc && rm *.o && '
+buildopts += 'make -j %(parallel)s -f Makefile.HYBRID.gcc '
 
-files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"]
 
-postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"]
+files_to_copy = [
+    (["raxmlHPC", "raxmlHPC-PTHREADS", "raxmlHPC-HYBRID", "raxmlHPC-MPI"], "bin"),
+    "usefulScripts", "README.md", "manual",
+]
 
 sanity_check_paths = {
-    'files': ['bin/raxmlHPC'],
+    'files': ['bin/raxmlHPC%s' % x for x in ['', '-PTHREADS', '-HYBRID', '-MPI']],
     'dirs': [],
 }

ocaisa · 2025-10-08T11:34:18Z

@boegelbot please test @ jsc-zen3

ocaisa · 2025-10-08T11:40:10Z

This is (I believe) more correct than what was there before. We now build 4 versions of the package:

serial
threaded
mpi-enabled
hybrid (MPI/threaded)

boegelbot · 2025-10-08T11:40:14Z

@ocaisa: 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=23975 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23975 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8212

Test results coming soon (I hope)...

Details

- notification for comment with ID 3381101862 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 · 2025-10-08T11:52:02Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/df9e2e464af857d4189d8d9462697fe0 for a full test report.

boegel · 2025-10-22T13:45:03Z

@lexming Can you take a look at this?

ocaisa · 2025-10-22T14:01:52Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-10-22T14:20:12Z

@ocaisa: 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=23975 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23975 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8525

Test results coming soon (I hope)...

Details

- notification for comment with ID 3432523235 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 · 2025-10-22T14:32:20Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/9ff0ce54b70a301a4509f29b9fa0a00a for a full test report.

lexming

LGTM

lexming · 2025-11-18T08:52:17Z

Merging, thanks @ocaisa !

{bio}[foss/2023a,foss/2023b] Create and use generic version of RAxML …

1219d5d

…v8.2.13

github-actions Bot added the change label Sep 23, 2025

ocaisa mentioned this pull request Sep 23, 2025

{2023.06}[2023b] RAxML 8.2.13 EESSI/software-layer#1196

Merged

Thyre added 2023a 2023b labels Sep 24, 2025

boegel added this to the release after 5.1.2 (5.2.0?) milestone Sep 24, 2025

boegel changed the title ~~{bio}[foss/2023a,foss/2023b] Create and use generic version of RAxML v8.2.13~~ {bio}[foss/2023a,foss/2023b] Create and use generic version of RAxML v8.2.13 as dependency for bcgTree and Parsnp Sep 24, 2025

boegel reviewed Sep 24, 2025

View reviewed changes

boegel changed the title ~~{bio}[foss/2023a,foss/2023b] Create and use generic version of RAxML v8.2.13 as dependency for bcgTree and Parsnp~~ use generic version of RAxML v8.2.13 as dependency for bcgTree and Parsnp Sep 24, 2025

boegel mentioned this pull request Oct 8, 2025

add easyblock for RAxML easybuilders/easybuild-easyblocks#2180

Closed

Make changes a patch on existing makefiles

a556fdc

github-actions Bot added the update label Oct 8, 2025

Make sure CFLAGS is always added to

1e8c66f

ocaisa commented Oct 22, 2025

View reviewed changes

Comment thread easybuild/easyconfigs/r/RAxML/raxml_8.2.13_respect_eb_settings.patch Outdated

lexming approved these changes Nov 18, 2025

View reviewed changes

lexming merged commit 347d5c2 into easybuilders:develop Nov 18, 2025
8 checks passed

ocaisa deleted the RAxML_update branch November 18, 2025 10:37

Micket mentioned this pull request Nov 18, 2025

Remove -avx2 suffix from RAxML dependency in Gubbins #24607

Merged

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Updated software `RAxML-8.2.13-gompi-2023b.eb`