GROMACS simulation thread allocation

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1

Hello Galaxy Team,

I am encountering a recurring error with the GROMACS simulation tool in my workflow. My jobs are failing intermittently with the following fatal error:

“The total number of threads requested (8) is not divisible by the number of OpenMP threads requested (16).”

It appears that the job is being allocated 8 slots (cores) by the scheduler, but the tool wrapper has a hardcoded default requesting 16 OpenMP threads (-ntomp 16).

I have tried to change this setting to 0 (Auto) or 1 in the Workflow Editor, but the “Process Handling” / “OpenMP threads” parameter seems to be hidden or unavailable in my view.

Could you please advise on how I can override this thread count, or check why the tool is defaulting to 16 threads on 8-core nodes?

Thanks!

2

I switched to GPU usage, and apparently this solves the problem, but still I do not know if this is the best approach. Thank you in advance!