Updated rp-basic-ensemble.py example - Githubissues

SCALE-MS / workshop

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Updated rp-basic-ensemble.py example #7

Closed eirrgang closed 1 year ago

eirrgang commented 1 year ago

Summary

The original example had mdrun arguments hard coded in the python script that made the script only valid for thread-MPI GROMACS installations.

Add some flexibility to account for different possible GROMACS back-end.
Defer GROMACS resource assignment flags to user, via new --mdrun-arg.

Validation

In a Docker container with 4 cores, I installed gmxapi 0.4.0 with an MPI-enabled GROMACS 2023, and ran the following.

python rp_basic_ensemble.py --resource docker.login --access ssh --venv $VIRTUAL_ENV/ --pilot-option cores=4 --procs-per-sim 2 --size 2 --mdrun-arg maxh 0.01 --log-level DEBUG

Based on the terminal output, I then checked the MD log to confirm the simulation ran successfully with 2 MPI ranks.

cat  /home/rp/radical.pilot.sandbox/rp.session.2c419e24-bcec-11ed-9770-0242ac120003/pilot.e6f81a7e-d847-4e28-810e-24c632616aef/rp-basic-ensemble-1/mdrun_6d00f4b07eabc852c23b016d1c2ca339_i0_0/md.log

eirrgang commented 1 year ago

I believe this has now been confirmed with MPI-gromacs on bridges2. @wehs7661 do you have any feedback or requested changes or should this be merged?