High Performance Computing

Run KIMMDY on HPC clusters

Setup

You need an installation of python (>= 3.10) and (possibly PLUMED patched) GROMACS in your HPC environment.

Example setup:

srun -t 1400:00 --mem=16000 -n20 --pty /bin/bash
ml EasyBuild
eb ./assets/Python-3.10.8.eb

Prepare a bash script _modules.sh that loads the required modules and activates the python environment in which KIMMDY is installed.

Run

kimmdy --generate-jobscript

to generate a file jobscript.sh that can be submitted to the HPC cluster.

This commands generates a kimmdy checkpoint and prepares the output folder. KIMMDY can then be started and re-started from the checkpoint via the jobscript, which uses

# -c = continue, same  as --from-latest-checkpoint
kimmdy -c
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