{bio}[foss/2025b] GROMACS v2025.4

[bedroge]

(created using eb --new-pr)

Note: dropped GROMACS-2025.2_workaround-arm-sve512.patch, as that fix is included in 2025.4, see https://gitlab.com/gromacs/gromacs/-/merge_requests/5593.

[github-actions]

Updated software GROMACS-2025.4-foss-2025b.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-2025.4-foss-2025b.eb
index ec5805ab48..03c540fcc2 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lmpflf-2025b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.4-foss-2025b.eb
@@ -15,7 +15,7 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2025.2'
+version = '2025.4'
 
 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': 'lmpflf', 'version': '2025b'}
+toolchain = {'name': 'foss', 'version': '2025b'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -40,18 +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-2025.2_workaround-arm-sve512.patch',
-    'GROMACS-2025.2_fix-sample_restraint-mpich-launch.patch',
 ]
 checksums = [
-    {'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
+    {'gromacs-2025.4.tar.gz': 'ca17720b4a260eb73649211e9f6a940ee7543452129844213c3accb0a927a5c3'},
     {'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'},
 ]
 
 builddependencies = [

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-2025.4-foss-2025b.eb
index fc29744c2c..03c540fcc2 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.4-foss-2025b.eb
@@ -15,7 +15,7 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2025.2'
+version = '2025.4'
 
 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': 'lfoss', 'version': '2025b'}
+toolchain = {'name': 'foss', 'version': '2025b'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = [
@@ -40,15 +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-2025.2_workaround-arm-sve512.patch',
 ]
 checksums = [
-    {'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
+    {'gromacs-2025.4.tar.gz': 'ca17720b4a260eb73649211e9f6a940ee7543452129844213c3accb0a927a5c3'},
     {'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'},
 ]
 
 builddependencies = [

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-2025.4-foss-2025b.eb
index 415b6a16f9..03c540fcc2 100644
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2025.4-foss-2025b.eb
@@ -15,7 +15,7 @@
 # License::   MIT/GPL
 
 name = 'GROMACS'
-version = '2025.3'
+version = '2025.4'
 
 homepage = 'https://www.gromacs.org'
 description = """
@@ -40,16 +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-2025.2_workaround-arm-sve512.patch',
 ]
 checksums = [
-    {'gromacs-2025.3.tar.gz': '8bdfca0268f3f10a7ca3c06e59b62f73ea02420c67211c0ff3912f32d7833c65'},
+    {'gromacs-2025.4.tar.gz': 'ca17720b4a260eb73649211e9f6a940ee7543452129844213c3accb0a927a5c3'},
     {'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'},
 ]
 
 builddependencies = [

[bedroge]

@boegelbot please test @ jsc-zen3

[boegelbot]

@bedroge: 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=24956 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24956 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 9277

Test results coming soon (I hope)...

Details

- notification for comment with ID 3681949374 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]

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 51 mins 14 secs) (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/82a885f9f2ed35152be5bc490d4fb3d0 for a full test report.

[bedroge]

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 25.04 (Plucky Puffin), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.13.3
See https://gist.github.com/bedroge/7729bbb14689a9cbd7a4df448c7dc3fe for a full test report.

[Thyre]

Test report by @Thyre
FAILED
Build succeeded for 0 out of 1 (total: 39 mins 6 secs) (1 easyconfigs in total)
jrc0901.jureca - Linux Rocky Linux 9.6, AArch64, ARM UNKNOWN (neoverse_v2), 1 x NVIDIA NVIDIA GH200 480GB, 580.95.05, Python 3.9.21
See https://gist.github.com/Thyre/b9d4510c21c160f1271171577079b0c4 for a full test report.