{bio}[foss/2023b] GROMACS v2024.2 w/ CUDA 12.5.0 by boegel · Pull Request #20809 · easybuilders/easybuild-easyconfigs

boegel · 2024-06-12T21:09:12Z

(created using eb --new-pr)

requires:

{lib}[GCCcore/13.2.0] UCX-CUDA v1.15.0 w/ CUDA 12.5.0 #20811

boegel · 2024-06-12T21:52:04Z

Test report by @boegel
FAILED
Build succeeded for 1 out of 2 (1 easyconfigs in total)
node3306.joltik.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz, 1 x NVIDIA Tesla V100-SXM2-32GB, 545.23.08, Python 3.6.8
See https://gist.github.com/boegel/0e97c95f98a87e72fd334b973a72901f for a full test report.

edit: Timeout for MdrunCoordinationCouplingTests2Ranks because $OMP_PROC_BIND was set to TRUE in environment...

bedroge · 2024-06-14T19:44:42Z

+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
+    'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',


I was recently looking into GROMACS 2024.2 as well, and was wondering if this patch is still required. https://gitlab.com/gromacs/gromacs/-/merge_requests/4093 may solve the same or at least similar issue. Looks like @akesandgren added this patch, so maybe he knows?

GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch should still be relevant as long as it passes patching.
Especially the "Don't drop relevant PYTHONPATH and LD_LIBRARY_PATH settings." part is vital.

I haven't looked at 2024.2 but I assume they haven't fixed those parts yet.

And GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch is just an extra precaution to keep OMMP_NUM_THREADS and --ntomp in sync.

boegel · 2024-06-14T19:53:49Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node3903.accelgor.os - Linux RHEL 8.8, x86_64, AMD EPYC 7413 24-Core Processor, 1 x NVIDIA NVIDIA A100-SXM4-80GB, 545.23.08, Python 3.6.8
See https://gist.github.com/boegel/cf1254074701e06327ebcf84b832673c for a full test report.

edit: Timeout for MdrunCoordinationCouplingTests2Ranks because $OMP_PROC_BIND was set to TRUE in environment (?)

boegel · 2024-06-15T07:44:23Z

Not setting $OMP_PROC_BIND to BIND on our system is not an option, because then the GROMACS test suite doesn't finish even after 11 hours (still running)...

boegel · 2024-06-15T08:01:41Z

Maybe we should always use -DGMX_TEST_TIMEOUT_FACTOR to increase the timeout a bit, see also https://gitlab.com/gromacs/gromacs/-/issues/5062`.

I think the issue in my case is that I'm running in a Slurm job that's asking for a partial node, and I'm not getting lucky w.r.t. which cores are assigned for the job, which makes this particular tests quite slow...

bedroge · 2024-06-15T09:45:09Z

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
gpu2 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) Gold 6150 CPU @ 2.70GHz (skylake_avx512), 1 x NVIDIA GRID V100D-32Q, 535.161.07, Python 3.6.8
See https://gist.github.com/bedroge/d229b0d73d21ced263c31f40a2f15f5c for a full test report.

branfosj · 2024-06-15T09:45:23Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0208u15a - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), 1 x NVIDIA NVIDIA A100-SXM4-40GB, 535.154.05, Python 3.6.8
See https://gist.github.com/branfosj/3dd073c237e57b2305fcf41b13f9f6ba for a full test report.

bedroge · 2024-06-15T20:33:50Z

Not setting $OMP_PROC_BIND to BIND on our system is not an option, because then the GROMACS test suite doesn't finish even after 11 hours (still running)...

I'm now running it in a Slurm job on an Icelake+A100 node (the successful test report was done on an interactive node without Slurm), and that one also seems to get stuck or something. The test step of the first iteration has been running for more than an hour, while it only took 18 minutes for the interactive V100 build.

SebastianAchilles · 2024-06-19T09:11:27Z

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16

boegelbot · 2024-06-19T09:20:10Z

@SebastianAchilles: 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=20809 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20809 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4418

Test results coming soon (I hope)...

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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 · 2024-06-19T09:41:59Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 550.54.15, Python 3.9.18
See https://gist.github.com/boegelbot/bb3a1716c849cb6a6085c1b64622964e for a full test report.

akesandgren · 2024-06-19T14:06:11Z

Test report by @akesandgren
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
b-cn1611.hpc2n.umu.se - Linux Ubuntu 22.04, x86_64, AMD EPYC 7313 16-Core Processor, 1 x NVIDIA NVIDIA A100 80GB PCIe, 550.78, Python 3.10.12
See https://gist.github.com/akesandgren/446251f9d574523a8ff45149c187361b for a full test report.

akesandgren · 2024-06-20T05:46:43Z

Test report by @akesandgren
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
b-cn1502.hpc2n.umu.se - Linux Ubuntu 20.04, x86_64, Intel(R) Xeon(R) Gold 6132 CPU @ 2.60GHz, 2 x NVIDIA Tesla V100-PCIE-16GB, 545.29.06, Python 3.8.10
See https://gist.github.com/akesandgren/8236afa5668895b2c6201bce5be8e959 for a full test report.

akesandgren · 2024-06-20T06:00:27Z

Test report by @akesandgren
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
b-cn1602.hpc2n.umu.se - Linux Ubuntu 22.04, x86_64, AMD EPYC 9454 48-Core Processor, 4 x NVIDIA NVIDIA H100 80GB HBM3, 550.78, Python 3.10.12
See https://gist.github.com/akesandgren/259dc4b1f2a21ccb5103d17f61c10614 for a full test report.

akesandgren · 2024-06-20T06:24:00Z

Test report by @akesandgren
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
b-cn1604.hpc2n.umu.se - Linux Ubuntu 22.04, x86_64, AMD EPYC 9254 24-Core Processor, 2 x NVIDIA NVIDIA L40S, 550.78, Python 3.10.12
See https://gist.github.com/akesandgren/cb3dec04d82d480e9bad23a4d85f412f for a full test report.

akesandgren · 2024-06-20T08:20:37Z

I had no problem building this for an A40 on a broadwell node in a non-interactive batch job.

bedroge · 2024-06-26T09:14:25Z

-        'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+        'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
+                          '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
        'source_tmpl': 'gromacs-2023.3.tar.gz',


This should correspond to the current version (and the version of gmxapi needs to be bumped as well).

Ugh... Fixed in 5dc1057

@boegel what about the gmxapi version? I'm not completely sure what the correct version number should be. https://gitlab.com/gromacs/gromacs/-/blob/v2024.2/python_packaging/gmxapi/pyproject.toml?ref_type=tags has 0.4.1 (?!), but https://gitlab.com/gromacs/gromacs/-/blob/v2024.2/python_packaging/gmxapi/src/gmxapi/version.py?ref_type=tags and https://manual.gromacs.org/2024.2/gmxapi/index.html say 0.5.0a1. So I guess the latter??

…g for GROMACS 2024.2

boegel · 2024-06-26T11:51:58Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node3302.joltik.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz, 1 x NVIDIA Tesla V100-SXM2-32GB, 545.23.08, Python 3.6.8
See https://gist.github.com/boegel/516323bafd0a78e15c512921d7f25383 for a full test report.

boegel · 2024-06-26T11:53:53Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node3902.accelgor.os - Linux RHEL 8.8, x86_64, AMD EPYC 7413 24-Core Processor, 1 x NVIDIA NVIDIA A100-SXM4-80GB, 545.23.08, Python 3.6.8
See https://gist.github.com/boegel/0b1eca1a8e7788ef14314e1781129edb for a full test report.

…mxapi in easyconfig for GROMACS 2024.2

boegel · 2024-07-03T13:25:12Z

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16

boegelbot · 2024-07-03T13:30:10Z

@boegel: 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=20809 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20809 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4509

Test results coming soon (I hope)...

Details

- notification for comment with ID 2206073712 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).

boegel · 2024-07-04T06:57:01Z

Hmm, seems like GPU node is down in jsc-zen3 currently, that's why it's taking so long to come back with test report result...

branfosj · 2024-07-04T07:43:57Z

Test report by @branfosj
SUCCESS
Build succeeded for 7 out of 7 (1 easyconfigs in total)
bear-pg0208u15a - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), 1 x NVIDIA NVIDIA A100-SXM4-40GB, 535.154.05, Python 3.6.8
See https://gist.github.com/branfosj/bdd71ca9580e9d808e7e994b5b49b221 for a full test report.

boegelbot · 2024-08-22T11:57:24Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.18
See https://gist.github.com/boegelbot/4550d0e26ac916b65979b04ee1f2a134 for a full test report.

…asyconfigs into 20240612230908_new_pr_GROMACS20242

github-actions · 2024-11-13T17:33:16Z

Updated software `GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb`

Diff against GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb
index 9a950353a4..866dacc867 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb
@@ -15,9 +15,8 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2024.4'
-local_plumedver = '2.9.2'
-versionsuffix = '-PLUMED-%s' % local_plumedver
+version = '2024.2'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -25,8 +24,7 @@ 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 binaries
-for both single and double precision.
+This is a GPU enabled build, containing both MPI and threadMPI binaries.
 
 It also contains the gmxapi extension for the single precision MPI build.
 """
@@ -42,15 +40,13 @@ sources = [SOURCELOWER_TAR_GZ]
 patches = [
     'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
     'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
-    'GROMACS-2023.3_skip_test_for_plumed.patch',
 ]
 checksums = [
-    {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
+    {'gromacs-2024.2.tar.gz': '802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'},
     {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
      '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
     {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
      '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'},
-    {'GROMACS-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'},
 ]
 
 builddependencies = [
@@ -59,16 +55,14 @@ builddependencies = [
 ]
 
 dependencies = [
+    ('CUDA', '12.5.0', '', SYSTEM),
+    ('UCX-CUDA', '1.15.0', versionsuffix),
     ('Python', '3.11.5'),
     ('SciPy-bundle', '2023.11'),
     ('networkx', '3.2.1'),
     ('mpi4py', '3.1.5'),
-    ('PLUMED', local_plumedver),
 ]
 
-# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.4 seems to work fine too
-ignore_plumed_version_check = True
-
 # be a bit more forgiving w.r.t. timeouts for GROMACS test suite,
 # see also https://gitlab.com/gromacs/gromacs/-/issues/5062
 configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"
@@ -83,8 +77,9 @@ exts_list = [
     ('gmxapi', '0.4.2', {
         'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
                           '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
-        'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
+        'sources': ['gromacs-%s.tar.gz' % version],
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'],
     }),
 ]
-
 moduleclass = 'bio'

Diff against GROMACS-2024.4-foss-2023b.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb
index cf8db688ea..866dacc867 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb
@@ -15,7 +15,8 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2024.4'
+version = '2024.2'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -23,8 +24,7 @@ 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 binaries
-for both single and double precision.
+This is a GPU enabled build, containing both MPI and threadMPI binaries.
 
 It also contains the gmxapi extension for the single precision MPI build.
 """
@@ -42,7 +42,7 @@ patches = [
     'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
 ]
 checksums = [
-    {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
+    {'gromacs-2024.2.tar.gz': '802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'},
     {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
      '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
     {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
@@ -55,6 +55,8 @@ builddependencies = [
 ]
 
 dependencies = [
+    ('CUDA', '12.5.0', '', SYSTEM),
+    ('UCX-CUDA', '1.15.0', versionsuffix),
     ('Python', '3.11.5'),
     ('SciPy-bundle', '2023.11'),
     ('networkx', '3.2.1'),
@@ -75,8 +77,9 @@ exts_list = [
     ('gmxapi', '0.4.2', {
         'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
                           '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
-        'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
+        'sources': ['gromacs-%s.tar.gz' % version],
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'],
     }),
 ]
-
 moduleclass = 'bio'

Diff against GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb
index dc77aa2914..866dacc867 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb
@@ -15,9 +15,8 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2024.4'
-local_plumedver = '2.9.2'
-versionsuffix = '-CUDA-%%(cudaver)s-PLUMED-%s' % local_plumedver
+version = '2024.2'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -41,15 +40,13 @@ sources = [SOURCELOWER_TAR_GZ]
 patches = [
     'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
     'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
-    'GROMACS-2023.3_skip_test_for_plumed.patch',
 ]
 checksums = [
-    {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
+    {'gromacs-2024.2.tar.gz': '802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'},
     {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
      '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
     {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
      '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'},
-    {'GROMACS-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'},
 ]
 
 builddependencies = [
@@ -58,22 +55,18 @@ builddependencies = [
 ]
 
 dependencies = [
-    ('CUDA', '12.4.0', '', SYSTEM),
-    ('UCX-CUDA', '1.15.0', '-CUDA-%(cudaver)s'),
+    ('CUDA', '12.5.0', '', SYSTEM),
+    ('UCX-CUDA', '1.15.0', versionsuffix),
     ('Python', '3.11.5'),
     ('SciPy-bundle', '2023.11'),
     ('networkx', '3.2.1'),
     ('mpi4py', '3.1.5'),
-    ('PLUMED', local_plumedver),
 ]
 
 # be a bit more forgiving w.r.t. timeouts for GROMACS test suite,
 # see also https://gitlab.com/gromacs/gromacs/-/issues/5062
 configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"
 
-# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.4 seems to work fine too
-ignore_plumed_version_check = True
-
 exts_defaultclass = 'PythonPackage'
 
 exts_default_options = {
@@ -84,8 +77,9 @@ exts_list = [
     ('gmxapi', '0.4.2', {
         'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
                           '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
-        'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
+        'sources': ['gromacs-%s.tar.gz' % version],
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'],
     }),
 ]
-
 moduleclass = 'bio'

boegel · 2024-11-13T19:17:55Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3303.joltik.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz (cascadelake), 1 x NVIDIA Tesla V100-SXM2-32GB, 555.42.06, Python 3.9.18
See https://gist.github.com/boegel/e2f488ffe24619eb323ed7bf68a7c3af for a full test report.

boegel · 2024-11-13T19:31:29Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3902.accelgor.os - Linux RHEL 9.4, x86_64, AMD EPYC 7413 24-Core Processor (zen3), 1 x NVIDIA NVIDIA A100-SXM4-80GB, 555.42.06, Python 3.9.18
See https://gist.github.com/boegel/129eb7c62ff352b2df3aa34ffddf8463 for a full test report.

…asyconfigs into 20240612230908_new_pr_GROMACS20242

…-12.5.0.eb

…asyconfigs into 20240612230908_new_pr_GROMACS20242

boegel · 2025-06-16T19:54:17Z

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16

boegelbot · 2025-06-16T20:00:12Z

@boegel: 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=20809 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20809 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6818

Test results coming soon (I hope)...

Details

- notification for comment with ID 2977921570 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 · 2025-06-16T20:25:05Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.21
See https://gist.github.com/boegelbot/6b7e6e74a56c8d007473d45e0b72fab4 for a full test report.

adding easyconfigs: GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb

d3d32a1

boegel added the update label Jun 12, 2024

boegel added this to the 4.x milestone Jun 12, 2024

bedroge reviewed Jun 14, 2024

View reviewed changes

boegel added 2 commits June 25, 2024 23:00

Merge branch 'develop' into 20240612230908_new_pr_GROMACS20242

8400034

fix long line in GROMACS 2024.2 easyconfig

f45673c

bedroge reviewed Jun 26, 2024

View reviewed changes

fix version of GROMACS tarball used for gmxapi extension in easyconfi…

5dc1057

…g for GROMACS 2024.2

boegel added 2 commits July 3, 2024 13:54

replace scikit-build with scikit-build-core as build dependency for g…

6da26ec

…mxapi in easyconfig for GROMACS 2024.2

increase test timeout by factor 3 for GROMACS 2024.2

387edbe

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

6e150b0

…asyconfigs into 20240612230908_new_pr_GROMACS20242

boegel requested a review from bedroge November 15, 2024 21:33

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

d5ce4b3

…asyconfigs into 20240612230908_new_pr_GROMACS20242

Micket reviewed Jun 11, 2025

View reviewed changes

Comment thread easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb Outdated

Update easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA…

8536291

…-12.5.0.eb

Micket reviewed Jun 11, 2025

View reviewed changes

Comment thread easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb Outdated

Micket and others added 2 commits June 11, 2025 14:10

Update easybuild/easyconfigs/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA…

f1a55b5

…-12.5.0.eb

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

51f44c5

…asyconfigs into 20240612230908_new_pr_GROMACS20242

Thyre added the 2023b label Aug 18, 2025

gkaf89 mentioned this pull request Feb 2, 2026

[BUGFIX:GROMACS] Build with gmxapi distributed with the GROMACS source code #25188

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