{bio}[foss/2025b] GROMACS v2025.3 w/ CUDA 12.9.1 by FelixBangerter · Pull Request #25215 · easybuilders/easybuild-easyconfigs

FelixBangerter · 2026-02-05T10:13:54Z

(created using eb --new-pr)

github-actions · 2026-02-05T10:14:28Z

Updated software `GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb`

Diff against GROMACS-2025.2-lmpflf-2025b.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lmpflf-2025b.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lmpflf-2025b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb
index ec5805ab48..d68458a8f6 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lmpflf-2025b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb
@@ -15,7 +15,8 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2025.2'
+version = '2025.3'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -23,13 +24,12 @@ 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.
 """
 
-toolchain = {'name': 'lmpflf', 'version': '2025b'}
+toolchain = {'name': 'foss', 'version': '2025b'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -41,17 +41,15 @@ patches = [
     'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
     'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
     'GROMACS-2025.2_workaround-arm-sve512.patch',
-    'GROMACS-2025.2_fix-sample_restraint-mpich-launch.patch',
 ]
 checksums = [
-    {'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
+    {'gromacs-2025.3.tar.gz': '8bdfca0268f3f10a7ca3c06e59b62f73ea02420c67211c0ff3912f32d7833c65'},
     {'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-2025.2_workaround-arm-sve512.patch': 'e62e075ee9328f647954365edd7979ea79e6f1d7a3b84834a2aae546cf74772c'},
-    {'GROMACS-2025.2_fix-sample_restraint-mpich-launch.patch':
-     'a910ec50cf296a6bdf8e5d425617d54c13b4ef049b61196487d7dc8a8f674e2c'},
+    {'GROMACS-2025.2_workaround-arm-sve512.patch':
+     'e62e075ee9328f647954365edd7979ea79e6f1d7a3b84834a2aae546cf74772c'},
 ]
 
 builddependencies = [
@@ -61,6 +59,8 @@ builddependencies = [
 ]
 
 dependencies = [
+    ('CUDA', '12.9.1', '', SYSTEM),
+    ('UCX-CUDA', '1.19.0', versionsuffix),
     ('Python', '3.13.5'),
     ('SciPy-bundle', '2025.07'),
     ('networkx', '3.5'),
@@ -73,21 +73,22 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"
 
 exts_defaultclass = 'PythonPackage'
 
-exts_default_options = {
-    'source_urls': [PYPI_SOURCE],
-}
+_gmxapi_source_version = version
 
 exts_list = [
-    ('gmxapi', '0.4.2', {
-        'patches': ['GROMACS-2025.2_gmxapi-remove-builddependencies.patch'],
+    ('gmxapi', '0.5.0a1', {
+        'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
         'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
                           '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+        'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
+        'start_dir': 'python_packaging/gmxapi',
         'checksums': [
-            {'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
-            {'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
-             'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
+            {'gromacs-2025.3.tar.gz': '8bdfca0268f3f10a7ca3c06e59b62f73ea02420c67211c0ff3912f32d7833c65'},
+            {'GROMACS-2024.1-fix-gmxapi-version.patch':
+                'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
         ],
     }),
 ]
 
 moduleclass = 'bio'
+

Diff against GROMACS-2025.2-lfoss-2025b.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb
index fc29744c2c..d68458a8f6 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb
@@ -15,7 +15,8 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2025.2'
+version = '2025.3'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -23,13 +24,12 @@ 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.
 """
 
-toolchain = {'name': 'lfoss', 'version': '2025b'}
+toolchain = {'name': 'foss', 'version': '2025b'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -43,12 +43,13 @@ patches = [
     'GROMACS-2025.2_workaround-arm-sve512.patch',
 ]
 checksums = [
-    {'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
+    {'gromacs-2025.3.tar.gz': '8bdfca0268f3f10a7ca3c06e59b62f73ea02420c67211c0ff3912f32d7833c65'},
     {'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-2025.2_workaround-arm-sve512.patch': 'e62e075ee9328f647954365edd7979ea79e6f1d7a3b84834a2aae546cf74772c'},
+    {'GROMACS-2025.2_workaround-arm-sve512.patch':
+     'e62e075ee9328f647954365edd7979ea79e6f1d7a3b84834a2aae546cf74772c'},
 ]
 
 builddependencies = [
@@ -58,6 +59,8 @@ builddependencies = [
 ]
 
 dependencies = [
+    ('CUDA', '12.9.1', '', SYSTEM),
+    ('UCX-CUDA', '1.19.0', versionsuffix),
     ('Python', '3.13.5'),
     ('SciPy-bundle', '2025.07'),
     ('networkx', '3.5'),
@@ -70,21 +73,22 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"
 
 exts_defaultclass = 'PythonPackage'
 
-exts_default_options = {
-    'source_urls': [PYPI_SOURCE],
-}
+_gmxapi_source_version = version
 
 exts_list = [
-    ('gmxapi', '0.4.2', {
-        'patches': ['GROMACS-2025.2_gmxapi-remove-builddependencies.patch'],
+    ('gmxapi', '0.5.0a1', {
+        'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
         'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
                           '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+        'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
+        'start_dir': 'python_packaging/gmxapi',
         'checksums': [
-            {'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
-            {'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
-             'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
+            {'gromacs-2025.3.tar.gz': '8bdfca0268f3f10a7ca3c06e59b62f73ea02420c67211c0ff3912f32d7833c65'},
+            {'GROMACS-2024.1-fix-gmxapi-version.patch':
+                'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
         ],
     }),
 ]
 
 moduleclass = 'bio'
+

Diff against GROMACS-2025.3-foss-2025b.eb

easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb
index 415b6a16f9..d68458a8f6 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb
@@ -16,6 +16,7 @@
 
 name = 'GROMACS'
 version = '2025.3'
+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.
 """
@@ -59,6 +59,8 @@ builddependencies = [
 ]
 
 dependencies = [
+    ('CUDA', '12.9.1', '', SYSTEM),
+    ('UCX-CUDA', '1.19.0', versionsuffix),
     ('Python', '3.13.5'),
     ('SciPy-bundle', '2025.07'),
     ('networkx', '3.5'),
@@ -71,21 +73,22 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"
 
 exts_defaultclass = 'PythonPackage'
 
-exts_default_options = {
-    'source_urls': [PYPI_SOURCE],
-}
+_gmxapi_source_version = version
 
 exts_list = [
-    ('gmxapi', '0.4.2', {
-        'patches': ['GROMACS-2025.2_gmxapi-remove-builddependencies.patch'],
+    ('gmxapi', '0.5.0a1', {
+        'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
         'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
                           '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+        'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
+        'start_dir': 'python_packaging/gmxapi',
         'checksums': [
-            {'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
-            {'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
-             'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
+            {'gromacs-2025.3.tar.gz': '8bdfca0268f3f10a7ca3c06e59b62f73ea02420c67211c0ff3912f32d7833c65'},
+            {'GROMACS-2024.1-fix-gmxapi-version.patch':
+                'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
         ],
     }),
 ]
 
 moduleclass = 'bio'
+

FelixBangerter · 2026-02-08T20:10:09Z

Test report by @FelixBangerter
SUCCESS
Build succeeded for 1 out of 1 (total: 37 mins 42 secs) (1 easyconfigs in total)
genoa-hopper-02.clusterurz - Linux AlmaLinux 8.9, x86_64, AMD EPYC 9554 64-Core Processor, Python 3.6.8
See https://gist.github.com/FelixBangerter/32c32f53eaea31986066ae6515f83b74 for a full test report.

FelixBangerter · 2026-02-08T20:12:23Z

Note, the contirbuted EasyConfig includes the patch introduced in PR #25188, so this PR should be merged first since the included patch is used in the updated EasyConfig here.

adding easyconfigs: GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb

96caed3

github-actions bot added 2025b issues & PRs related to 2025b common toolchains update labels Feb 5, 2026

Update PR with gmxapi change from PR easybuilders#25188

3d7dcb4

bedroge mentioned this pull request Mar 13, 2026

{bio}[foss/2025b] GROMACS v2025.3 w/ CUDA 12.9.1 #25552

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{bio}[foss/2025b] GROMACS v2025.3 w/ CUDA 12.9.1#25215

{bio}[foss/2025b] GROMACS v2025.3 w/ CUDA 12.9.1#25215
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Updated software `GROMACS-2025.3-foss-2025b-CUDA-12.9.1.eb`