Gromacs on the Clusters
You can run Gromacs on the cluster by using a 'container', i.e. through 'singularity'. For development or basic gromacs work, you can login to pod-gpu and work there. once you're in, type
module load singularity
to start a Gromacs container, with the option to use the GPU (gromacs can be very efficient with the GPU), type
singularity run --nv /sw/singularity/SingularityImages/gromacs-2021.sif /bin/bash
this will drop you in a singularity / gromacs shell where you can do the typical gromacs commands, e.g. 'gmx'. once you're ready to run something that will take a long time (e.g. the dynamics), you should quit out of singularity (control-D) and then put the commands you need in a Slurm file, e.g.
#SBATCH -N 1 --partition=gpu --ntasks-per-node=6 #SBATCH --gres=gpu:1 ## will use the GPU partition cd $SLURM_SUBMIT_DIR module load singularity /bin/hostname singularity run --nv /sw/singularity/SingularityImages/gromacs-2021.sif << EOF ## Put your commands to do in gromacs in here # gmx mdrun -ntmpi 1 -ntomp $SLURM_NTASKS -nb gpu -pin on -s benchRIB.tpr -nsteps 10000 ## End of Gromacs job commands EOF # just to pause it 10 seconds... sleep 10
and then submit with the usual 'sbatch' commands and so on.