Skip to content

Fix MPIEXEC and improve handling of FlexiBLAS in GROMACS easyblock#3959

Merged
smoors merged 1 commit intoeasybuilders:developfrom
jhmeinke:gromacs-easyblock-2025
Oct 15, 2025
Merged

Fix MPIEXEC and improve handling of FlexiBLAS in GROMACS easyblock#3959
smoors merged 1 commit intoeasybuilders:developfrom
jhmeinke:gromacs-easyblock-2025

Conversation

@jhmeinke
Copy link
Copy Markdown
Contributor

@jhmeinke jhmeinke commented Oct 14, 2025

CMake (>3.10) uses MPIEXEC_EXECUTABLE instead of MPIEXEC to specify the launcher used for MPI programs.

If FlexiBLAS and MKL are loaded it's reasonable to assume that MKL should be loaded through FlexiBLAS instead of always being used to build and run GROMACS.

@jhmeinke
Adjust gromacs easyblock for 2025b
6d4b4be 
CMake (>3.10) uses MPIEXEC_EXECUTABLE instead of MPIEXEC to specify
the launcher used for MPI programs.

If FlexiBLAS and MKL are loaded it's reasonable to assume that MKL
should be loaded through FlexiBLAS instead of always being used to
build and run GROMACS.
@Thyre Thyre added this to the next release (5.2.0?) milestone Oct 15, 2025
@Thyre Thyre added the bug fix label Oct 15, 2025
@Thyre
Copy link
Copy Markdown
Collaborator

Thyre commented Oct 15, 2025

@boegelbot please test @ jsc-zen3-a100
EB_ARGS="GROMACS-2025.2-foss-2025a.eb GROMACS-2025.2-foss-2025b.eb GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb --installpath=/tmp/$USER/ebpr-3959"

@boegelbot
Copy link
Copy Markdown

boegelbot commented Oct 15, 2025

@Thyre: 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=3959 EB_ARGS="GROMACS-2025.2-foss-2025a.eb GROMACS-2025.2-foss-2025b.eb GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb --installpath=/tmp/$USER/ebpr-3959" EB_CONTAINER= EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_3959 --ntasks=8 --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 8390

Test results coming soon (I hope)...

Details

- notification for comment with ID 3404991104 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
Copy link
Copy Markdown

boegelbot commented Oct 15, 2025

Test report by @boegelbot

Overview of tested easyconfigs (in order)

  • SUCCESS GROMACS-2025.2-foss-2025a.eb
  • SUCCESS GROMACS-2025.2-foss-2025b.eb
  • SUCCESS GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb
  • SUCCESS GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb

Build succeeded for 4 out of 4 (4 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 580.95.05, Python 3.9.21
See https://gist.github.com/boegelbot/4dc88bc2efc91b25ed7dd178a867207c for a full test report.

smoors
smoors approved these changes Oct 15, 2025
View reviewed changes
Copy link
Copy Markdown
Contributor

@smoors smoors left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm

@smoors
Copy link
Copy Markdown
Contributor

smoors commented Oct 15, 2025

Going in, thanks @jhmeinke!

@smoors smoors merged commit 28bb479 into easybuilders:develop Oct 15, 2025
22 checks passed
@SebastianAchilles
Copy link
Copy Markdown
Member

SebastianAchilles commented Oct 15, 2025

Test report by @SebastianAchilles

Overview of tested easyconfigs (in order)

  • SUCCESS GROMACS-2025.2-foss-2025a.eb
  • SUCCESS GROMACS-2025.2-foss-2025b.eb

Build succeeded for 2 out of 2 (2 easyconfigs in total)
skx-rockylinux-96 - Linux Rocky Linux 9.6 (Blue Onyx), x86_64, Intel(R) Xeon(R) Gold 6126 CPU @ 2.60GHz (skylake_avx512), 4 x NVIDIA Tesla V100-SXM2-32GB, 580.95.05, Python 3.9.21
See https://gist.github.com/SebastianAchilles/d351311856cabc74ff7e5c9f75e0df57 for a full test report.

@boegel boegel changed the title Fix MPIEXEC and improve handling of FlexiBLAS in gromacs.py Fix MPIEXEC and improve handling of FlexiBLAS in GROMACS easyblock Oct 22, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@smoors smoors smoors approved these changes

Assignees

No one assigned

Labels

bug fix

Projects

None yet

Milestone

5.2.0

Development

Successfully merging this pull request may close these issues.

5 participants

@jhmeinke @Thyre @boegelbot @smoors @SebastianAchilles