Example script desmond-md-gpu.sh to launch Desmond multisim on 1 node, 1 core, 1 GPU:

desmond-md-gpu.sh

#!/bin/sh                                                                        
#SBATCH --job-name=desmond_md_gpu
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --gres=gpu:1
#SBATCH --time=0-24:00:00
#SBATCH --mem=10G
#SBATCH --partition=gpu
#
# Charge resources to account
#SBATCH --account=<account>
 
test -n "$SLURM_NODELIST" || exit
 
module load cuda
module load schrodinger
 
if [ -d '/node' ]; then
  SCHRODINGER_TMPDIR='/node'
else
  SCHRODINGER_TMPDIR=$(dirname "$SCRATCH")
fi
 
export SCHRODINGER_TMPDIR
 
cd "$SLURM_SUBMIT_DIR"
 
test -n "$STAGE" || STAGE=1
 
test $STAGE -eq 1 && \
multisim \
-WAIT \
-JOBNAME "$SLURM_JOB_NAME" \
-m "${SLURM_JOB_NAME}-in.msj" \
-o "${SLURM_JOB_NAME}-out.cms" \
-maxjob $SLURM_NTASKS_PER_NODE \
-cpu $SLURM_NTASKS_PER_NODE \
-set stage[1].set_family.md.jlaunch_opt=[-gpu]
 
test $STAGE -gt 1 && \
multisim \
-WAIT \
-JOBNAME "$SLURM_JOB_NAME" \
-RESTART "${SLURM_JOB_NAME}-multisim_checkpoint:${STAGE}" \
-d "${SLURM_JOB_NAME}_$((STAGE-1))-out.tgz" \
-o "${SLURM_JOB_NAME}-out.cms" \
-maxjob $SLURM_NTASKS_PER_NODE \
-cpu $SLURM_NTASKS_PER_NODE \
-set stage[1].set_family.md.jlaunch_opt=[-gpu]

For the first stage of the Desmond multisim workflows you can use:

sbatch desmond-md-gpu.sh

To pass the value of the variable STAGE into the job script named desmond-md-gpu.sh you can use:

sbatch --export=STAGE=2 desmond-md-gpu.sh