{bio}[foss/2023a] GROMACS v2023.4 by bedroge · Pull Request #19728 · easybuilders/easybuild-easyconfigs

bedroge · 2024-01-26T10:58:37Z

(created using eb --new-pr)

bedroge · 2024-01-26T11:01:26Z

@boegelbot please test @ generoso
CORE_CNT=16

boegelbot · 2024-01-26T11:05:08Z

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

PR test command 'EB_PR=19728 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19728 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12736

Test results coming soon (I hope)...

Details

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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 · 2024-01-26T11:39:19Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
cnx1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/ea0f22210966a6db62f0287691f3dd94 for a full test report.

edit:

Program:     gmxapi-mpi-test, version 2023.4-EasyBuild_4.9.1.dev0_r769d5e2f3bde7897dd480e24d59852ff89da8659
Source file: src/gromacs/utility/futil.cpp (line 454)
MPI rank:    1 (out of 2)

File input/output error:
/tmp/boegelbot/GROMACS/2023.4/foss-2023a/easybuild_obj/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.trr

...

The following tests FAILED:
	  2 - GmxapiMpiTests (Failed)

bedroge · 2024-01-26T12:23:32Z

Test report by @boegelbot FAILED Build succeeded for 0 out of 1 (1 easyconfigs in total) cnx1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8 See https://gist.github.com/boegelbot/ea0f22210966a6db62f0287691f3dd94 for a full test report.

This is the same failure as in #19321. We also saw that failure for EESSI, but it seemed to work fine with 2023.4 when I just tested that interactively... Let me start some test builds with the EESSI bot.

jfgrimm · 2024-01-26T12:23:51Z

Test report by @jfgrimm
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node115.viking2.yor.alces.network - Linux Rocky Linux 8.8, x86_64, AMD EPYC 7643 48-Core Processor, Python 3.6.8
See https://gist.github.com/jfgrimm/cd3486616471cba7bb41e1adbf305f03 for a full test report.

verdurin · 2024-01-29T12:06:29Z

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/91715051c6ada39cef098144a2a728d2 for a full test report.

boegel · 2024-02-07T19:33:19Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-02-07T19:40:08Z

@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=19728 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_19728 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 3577

Test results coming soon (I hope)...

Details

- notification for comment with ID 1932733093 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 · 2024-02-07T19:58:13Z

Test report by @boegelbot FAILED Build succeeded for 0 out of 1 (1 easyconfigs in total) cnx1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8 See https://gist.github.com/boegelbot/ea0f22210966a6db62f0287691f3dd94 for a full test report.

This is the same failure as in #19321. We also saw that failure for EESSI, but it seemed to work fine with 2023.4 when I just tested that interactively... Let me start some test builds with the EESSI bot.

More info in https://gitlab.com/eessi/support/-/issues/47#note_1759974438

boegelbot · 2024-02-07T20:17:28Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/9c891c4251691bf816be2e42392bb8ce for a full test report.

ocaisa · 2024-03-13T14:07:38Z

@boegelbot please test @ generoso
CORE_CNT=16

boegelbot · 2024-03-13T14:10:11Z

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

PR test command 'EB_PR=19728 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19728 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13091

Test results coming soon (I hope)...

Details

- notification for comment with ID 1994491475 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 · 2024-03-13T14:58:41Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cnx2 - 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/0f6fd937388351e0c689bdb33c19b362 for a full test report.

ocaisa · 2024-03-13T15:05:21Z

The failure on Generoso seems to have been fixed by our bugfix to OpenMPI, this is good to merge now @boegel but I wonder if we should instead focus on 2024.1 now?

casparvl · 2024-03-20T12:35:01Z

Strange, in the CUDA build it still failed on Generoso, with the error from before... https://gist.github.com/boegelbot/53a6c09141e2998ae5db6704104f56fe

…asyconfigs into 20240126115827_new_pr_GROMACS20234

github-actions · 2024-11-13T17:11:43Z

Updated software `GROMACS-2023.4-foss-2023a.eb`

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

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

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb
index d93065bbed..e8c0d929bd 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb
@@ -15,8 +15,7 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2024.4'
-versionsuffix = '-CUDA-%(cudaver)s'
+version = '2023.4'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -24,12 +23,13 @@ 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 binaries.
+This is a CPU only build, containing both MPI and threadMPI binaries
+for both single and double precision.
 
 It also contains the gmxapi extension for the single precision MPI build.
 """
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -42,7 +42,7 @@ patches = [
     'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
 ]
 checksums = [
-    {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
+    {'gromacs-2023.4.tar.gz': 'e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'},
     {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
      '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
     {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
@@ -50,23 +50,17 @@ checksums = [
 ]
 
 builddependencies = [
-    ('CMake', '3.27.6'),
-    ('scikit-build-core', '0.9.3'),
+    ('CMake', '3.26.3'),
+    ('scikit-build', '0.17.6'),
 ]
 
 dependencies = [
-    ('CUDA', '12.4.0', '', SYSTEM),
-    ('UCX-CUDA', '1.15.0', versionsuffix),
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('networkx', '3.2.1'),
-    ('mpi4py', '3.1.5'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('networkx', '3.1'),
+    ('mpi4py', '3.1.4'),
 ]
 
-# 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"
-
 exts_defaultclass = 'PythonPackage'
 
 exts_default_options = {
@@ -80,7 +74,9 @@ 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'],
+        'source_tmpl': 'gromacs-2023.4.tar.gz',
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'],
     }),
 ]

Diff against GROMACS-2024.3-foss-2023b-PLUMED-2.9.2.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-PLUMED-2.9.2.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb
index 9743e8a09a..e8c0d929bd 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-PLUMED-2.9.2.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb
@@ -15,9 +15,7 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2024.3'
-_plumedver = '2.9.2'
-versionsuffix = '-PLUMED-%s' % _plumedver
+version = '2023.4'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -31,7 +29,7 @@ for both single and double precision.
 It also contains the gmxapi extension for the single precision MPI build.
 """
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -42,33 +40,27 @@ 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-2024.3.tar.gz': 'bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029'},
+    {'gromacs-2023.4.tar.gz': 'e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'},
     {'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 = [
-    ('CMake', '3.27.6'),
-    ('scikit-build-core', '0.9.3'),
+    ('CMake', '3.26.3'),
+    ('scikit-build', '0.17.6'),
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('networkx', '3.2.1'),
-    ('mpi4py', '3.1.5'),
-    ('PLUMED', _plumedver),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('networkx', '3.1'),
+    ('mpi4py', '3.1.4'),
 ]
 
-# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.3 seems to work fine too
-ignore_plumed_version_check = True
-
 exts_defaultclass = 'PythonPackage'
 
 exts_default_options = {
@@ -82,7 +74,9 @@ 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'],
+        'source_tmpl': 'gromacs-2023.4.tar.gz',
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'],
     }),
 ]

Diff against GROMACS-2024.3-foss-2023b.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb
index a5ece3769b..e8c0d929bd 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb
@@ -15,7 +15,7 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2024.3'
+version = '2023.4'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -29,7 +29,7 @@ for both single and double precision.
 It also contains the gmxapi extension for the single precision MPI build.
 """
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -42,7 +42,7 @@ patches = [
     'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
 ]
 checksums = [
-    {'gromacs-2024.3.tar.gz': 'bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029'},
+    {'gromacs-2023.4.tar.gz': 'e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'},
     {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
      '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
     {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
@@ -50,15 +50,15 @@ checksums = [
 ]
 
 builddependencies = [
-    ('CMake', '3.27.6'),
-    ('scikit-build-core', '0.9.3'),
+    ('CMake', '3.26.3'),
+    ('scikit-build', '0.17.6'),
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('networkx', '3.2.1'),
-    ('mpi4py', '3.1.5'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('networkx', '3.1'),
+    ('mpi4py', '3.1.4'),
 ]
 
 exts_defaultclass = 'PythonPackage'
@@ -74,7 +74,9 @@ 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'],
+        'source_tmpl': 'gromacs-2023.4.tar.gz',
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'],
     }),
 ]

boegel · 2024-11-13T20:08:29Z

@boegelbot please test @ generoso
CORE_CNT=16

boegelbot · 2024-11-13T20:10:07Z

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

PR test command 'EB_PR=19728 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19728 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14709

Test results coming soon (I hope)...

Details

- notification for comment with ID 2474684866 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 · 2024-11-13T20:47:06Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cnx1 - 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/65137d0cce09bb635616cd84e4a39790 for a full test report.

boegel

lgtm

boegel · 2024-11-15T21:02:37Z

Going in, thanks @bedroge!

adding easyconfigs: GROMACS-2023.4-foss-2023a.eb

bdd2cc2

bedroge added the update label Jan 26, 2024

split long line

47ce27b

branfosj mentioned this pull request Mar 13, 2024

{bio,tools}[foss/2023b] GROMACS v2024.1, networkx v3.2.1 #20102

Merged

casparvl mentioned this pull request Mar 20, 2024

{bio}[foss/2023a] GROMACS v2023.4 w/ CUDA 12.1.1 #20154

Closed

boegel added this to the 4.x milestone Oct 4, 2024

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

ee6e069

…asyconfigs into 20240126115827_new_pr_GROMACS20234

boegel modified the milestones: 4.x, release after 4.9.4 Nov 15, 2024

boegel approved these changes Nov 15, 2024

View reviewed changes

boegel merged commit 158ab0e into easybuilders:develop Nov 15, 2024

bedroge deleted the 20240126115827_new_pr_GROMACS20234 branch November 16, 2024 14:30

boegel modified the milestones: release after 4.9.4, 5.0.0 Mar 18, 2025

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Updated software GROMACS-2023.4-foss-2023a.eb

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Updated software `GROMACS-2023.4-foss-2023a.eb`