How to use GROMOSXX

Software	Version	Cluster
GROMOSXX	1.6.0-OMP	Dardel

Running on Dardel

The current installation of GROMOS is built with OpenMP support enabled. This means that you can run GROMOS in parallel on a single node by using multiple threads. The number of threads can be set using the OMP_NUM_THREADS environment variable.

Unfortunately, the OMP implementation allows a maximum of 16 threads.

#!/bin/bash -l
#SBATCH -A XXXX-XX-XX
#SBATCH -J gromosjob
#SBATCH -t 00:10:00
#SBATCH --nodes=1
#SBATCH -c 16 # 16 cores
#SBATCH -p main

# set the number of threads
export OMP_NUM_THREADS=16

# load the GROMOS module
ml PDC/23.03
ml gromosXX/1.6.0-cpeGNU-23.03-omp

# Run gromos
srun srun md \
@topo topology.top \
@conf input_coord.g96 \
@fin output_coord.g96 \
@refpos refpos.rpr \
@posresspec posresspec.por \
@trc output_trajectory.trc.gz \
@tre output_energy.tre.gz \
@input config.imd > log.omd

Disclaimer

PDC takes no responsibility for the correctness of results produced with the binaries. Always evaluate the binaries against known results for the systems and properties you are investigating before using the binaries for production jobs.