script

#!/bin/bash 
#SBATCH --job-name="apptainer"
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=2
#SBATCH --exclusive
#SBATCH --export=ALL
#SBATCH --time=02:00:00
#SBATCH --output=apptainer.log
#SBATCH --mem=0

export STARTDIR=`pwd`
export CDIR=/nopt/nrel/apps/software/apptainer/1.1.9/examples
mkdir $SLURM_JOB_ID
cd $SLURM_JOB_ID

cat $0 >   script
printenv > env

touch warnings
touch output

module load apptainer
which apptainer >> output

echo "hostname" >> output
hostname        >> output

echo "from alpine.sif" >> output
          apptainer exec $CDIR/alpine.sif hostname  >> output
echo "from alpine.sif with srun" >> output
srun -n 1 --nodes=1 apptainer exec $CDIR/alpine.sif cat /etc/os-release  >> output


export OMP_NUM_THREADS=2

$CDIR/tymer times starting

MPI=pmix
for v in openmpi intel mpich_ch4 mpich_ch4b  mpich_ch3; do
  srun  --mpi=$MPI   apptainer  exec   $CDIR/$v.sif  /opt/examples/affinity/tds/phostone -F >  phost.$v  2>>warnings
  $CDIR/tymer times $v
  MPI=pmi2
  unset PMIX_MCA_gds
done

MPI=pmix
#skip mpich_ch3 because it is very slow
for v in openmpi intel mpich_ch4 mpich_ch4b           ; do
  srun  --mpi=$MPI   apptainer  exec   $CDIR/$v.sif  /opt/examples/affinity/tds/ppong>  ppong.$v  2>>warnings
  $CDIR/tymer times $v
  MPI=pmi2
  unset PMIX_MCA_gds
done

$CDIR/tymer times finished

mv $STARTDIR/apptainer.log .