module load gromacs/version

See the other server examples for additional tips to get good performance.

Batch jobs

To run jobs in the compute nodes, use a script of the following type (you can also load the module before submitting the job and then omit it from the script):

A serial batch job would use:

#!/bin/csh
#SBATCH -J my_jobname
#SBATCH -e my_output_err_%j
#SBATCH -o my_output_%j
#SBATCH --mem-per-cpu=1000
#SBATCH -t 04:02:00
#SBATCH -n 1

module load gromacs

srun mdrun -s topol.tpr -n index.ndx

The script is submitted with:

sbatch script_name

A parallel batch job:

#!/bin/csh
#SBATCH -J my_jobname
#SBATCH -e my_output_%j
#SBATCH -o my_output_%j
#SBATCH -t 11:00:00
#SBATCH -n 12
#SBATCH -p parallel

module load gromacs

srun mdrun_mpi -s topol.tpr -n index.ndx

The script requests 12 cores (one full node) and 11 hours of running time. If you don't want to use module, you can add the full path to the mdrun_mpi yourself.

All parallel computations must be done through the queuing system and in the compute nodes. Small parallel interactive jobs can be run e.g. with a command like:

You can use the same way to run long analysis jobs or initial geometry optimizations. You can also request an x-terminal on a computing node (you will need linux, mac  or an x-emulator on your windows-computer):

Additional details can be asked from Atte. A lot of useful information can be found also in the Gromacs home page www.gromacs.org and its mailing lists.

Back to CSC Gromacs page.