Slurm Batch

Now it is time for the fun part: submitting a job!

SLURM

First we create a job script.

mkdir -p /fsx/logs
cat << \EOF > benchRIB.sbatch
#!/bin/sh
#SBATCH --ntasks-per-node=6
#SBATCH --cpus-per-task=6
#SBATCH --exclusive
#SBATCH --job-name=GROMACS_benchRIB
#SBATCH --output=/fsx/logs/GROMACS_benchRIB.%J.txt

module load intelmpi $(module avail gromacs 2>&1 |tail -n1)

mkdir -p /fsx/jobdir/${SLURM_JOBID}
mpirun -ppn 6 gmx_mpi mdrun -ntomp 6 -s /fsx/input/gromacs/benchRIB.tpr 
EOF
sbatch -N1 benchRIB.sbatch -p c5n

This will take ~15min on one node.