Job Desmond []

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==== Job Desmond ====

=== Job Desmond GPU ===

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

<code bash 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]
</code>

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

<code>
sbatch desmond-md-gpu.sh
</code>

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

<code>
sbatch --export=STAGE=2 desmond-md-gpu.sh
</code>

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