Skip to content

Debug GROMACS issue on Snellius #245

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
bedroge wants to merge 5 commits into
base: main
Choose a base branch
from
+8 −0
Draft

Debug GROMACS issue on Snellius #245

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
f61d7c2
run ulimit and env in pretestopts
bedroge Jun 3, 2026
e33572d
add easystack
bedroge Jun 3, 2026
d9d8dfb
also run numactl --show
bedroge Jun 3, 2026
abc0421
fix filename
bedroge Jun 3, 2026
7a1a386
print ulimit at start
bedroge Jun 3, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions bot/build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,9 @@
# stop as soon as something fails
set -e

echo "ULIMITS:"
ulimit -a

# Make sure we are referring to software-layer as working directory
software_layer_dir=$(dirname $(dirname $(realpath $0)))
# source utils.sh and cfg_files.sh
Expand Down
4 changes: 4 additions & 0 deletions easystacks/software.eessi.io/2025.06/accel/nvidia/eessi-2025.06-eb-5.3.0-2025b.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
easyconfigs:
- GROMACS-2025.4-foss-2025b-CUDA-12.9.1.eb:
options:
from-commit: 23228c21d24b49a10bd5a51f09e14f5484d7b67d
1 change: 1 addition & 0 deletions eb_hooks.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1526,6 +1526,7 @@ def pre_test_hook_gromacs(self, *args, **kwargs):
"""
cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
if self.name == 'GROMACS':
self.cfg['pretestopts'] = 'env && ulimit -a && numactl --show && '
if self.version < '2026.3' and cpu_target == CPU_TARGET_NVIDIA_GRACE:
self.cfg['pretestopts'] = 'export HWLOC_KEEP_NVIDIA_GPU_NUMA_NODES=0 && '
else:
Expand Down
Loading