sherlock-submit.sh

#!/bin/bash
#SBATCH --job-name=seg/{wd}
#SBATCH --output=stdout.%j
#SBATCH --error=stderr.%j
#SBATCH --time=12:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2048
#SBATCH --gres gpu:1
##SBATCH --gres-flags=enforce-binding
##SBATCH --constraint=gpu_shared
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=xxx@stanford.edu
#SBATCH --no-requeue


cd $SLURM_SUBMIT_DIR
sbatch --dependency=afterok:$SLURM_JOB_ID submit.sbatch
pmemd.cuda \
    -i mdin.production \
    -p prmtop \
    -c restrt.in \
    -suffix $SLURM_JOB_ID 
ec="$?"

if [ $ec -eq 0 ]
then
    cp restrt.$SLURM_JOB_ID restrt.in \
        && python trjtime.py mdcrd.$SLURM_JOB_ID
else
    mkdir -p fail.$SLURM_JOB_ID && mv *.$SLURM_JOB_ID fail.$SLURM_JOB_ID/
    exit $ec
fi