[gmx_mdrun.sh]: Exit When gmx mdrun Fails

[andthum]

[gmx_mdrun.sh]: Exit When gmx mdrun Fails

Type of Change

• Bug fix.
• New feature.
• Code refactoring.
• Dependency update.
• Documentation update.
• Maintenance.
• Other: Description.

• Non-breaking (backward-compatible) change.
• Breaking (non-backward-compatible) change.

Motivation and Context

By now, gmx_mdrun.sh is not terminated when the call of gmx mdrun fails. The reason behind this was that the Slurm job script should not be terminated when gmx mdrun was terminated by the INT signal to allow for cleanup steps. However, the Slurm job script should be terminated if gmx mdrun indeed fails (without having received the INT signal).

Proposed Changes

Check the exit code of the gmx mdrun command and exit the Slurm job script if the exit code is not 0 (successful mdrun) and not 1 (mdrun terminated by INT signal).

PR Checklist

• I followed the guidelines in the Developer's Guide.
• New/changed code is properly tested.
• [~] New/changed code is properly documented.
• New/changed features are tracked in CHANGELOG.rst.
• The CI workflow is passing.