Submit w/ SARUS

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

Pull Image

sarus pull public.ecr.aws/a4y4t9s0/spack/gromacs-2020.4:latest

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

mkdir -p /fsx/jobdir/${SLURM_JOBID}
mpirun -ppn 6 sarus run --mpi --workdir=/fsx/jobdir/${SLURM_JOBID} \
    public.ecr.aws/a4y4t9s0/spack/gromacs-2020.4:latest \
    gmx_mpi mdrun -s /fsx/input/gromacs/benchRIB.tpr -ntomp 6
EOF
sbatch -N1 benchRIB.sbatch -p c5n

This will take ~15min on one node.