subvREOPT.sh

#!/bin/bash

dir=`pwd`
PGM_NAME="subv VASP submit script"
PGM_VERSION="1.0"
#BINARY_LOCATION="/cm/shared/apps/vasp/5.4.1/vasp.5.4.1/bin/vasp_std"
BINARY="vasp_ncl"
MODULE="vasp/mkl/intelmpi/intel/5.4.4-SuperHeavy-D3"

### SET DEFAULT VARIABLES

ncores_default=4
nnodes_default=1
#memory_default=4 ###default memory set to 2*ncores
jobtime_default=72

jobhold=""
holdid=""
debug=""
gpu=0
mpir="srun"

function usage
{
    cat <<-EOF
$PGM_NAME $PGM_VERSION
Usage: $PGM_NAME [-j JOB_ID] [-m SIZE] [-N NAME] [-p CPUS] [-n NODES] [-a COPY BACK ALL FILES] INPUT_FILE

EOF

    exit 2

}

function printExit
{
    case $1 in
        [iI]) echo INFO: "$2" ;;
        [wW]) echo WARNING: "$2" ;;
        [eE]) echo ERROR: "$2" ; exit 1 ;;
           *) echo "$1" ;;
    esac
}




### PROCESS OPTIONS

while getopts dg:hj:m:N:p:c:n:q:t: options ; do
      case $options in
         
         g) gpu=1
            ngpu=$OPTARG
            #mpir="mpiexec.hydra -n $ncores"
            BINARY="vasp_gpu"
            MODULE="vasp-gpu/mkl/intelmpi/intel/5.4.1"
            ;;
         N) jobname=$OPTARG
            ;;
         p) ncores=$OPTARG
	    ;;
	 c) actual_ncores=$OPTARG
            ;;
         n) nnodes=$OPTARG
            ;;
         m) memory=$OPTARG
            ;;
         j) holdid=$OPTARG
            jobhold=1
            echo "Jobhold not yet implemented."
            exit 1
            ;;
         d) debug=1
            ;;
         q) queue=$OPTARG
            ;;
         t) jobtime=$OPTARG
            ;;
         h) usage
            exit 0
            ;;
         \?)
            echo "Invalid option: -$OPTARG" 
            exit 1
            ;;
         \:)
            echo "Option -$OPTARG requires an argument." 
            exit 1
            ;;
         *) usage
            exit 1
            ;;
      esac
   done


shift $((OPTIND-1))



### CREATE DEFAULT JOBNAME

jobname_default="`echo $dir | sed "s/\/data\/$USER\//d/" | sed "s/\/home\/$USER\//h/ ; s/\//./g"`.$myname"

### PROCESS VARIABLES

if [ -z "$jobname" ]; then
   jobname=$jobname_default
fi
if [ -z "$ncores" ]; then
   ncores=$ncores_default
fi
if [ -z "$actual_ncores" ] ; then
   actual_ncores=$ncores
fi
if [ -z "$nnodes" ]; then
   nnodes=$nnodes_default
fi
if [ -z "$memory" ]; then
   memory=2
fi
if [ -z "$jobtime" ]; then
   jobtime=$jobtime_default
fi

### CONSTRUCT OUTPUT FILENAME



### CREATE OPTION STRING FOR QSUB

if [ -z "$holdid" ]; then
   optionstring=""
else
   optionstring=""

fi

### SET QUEUE TO DEFAULT IF $QUEUE IS EMPTY

if [ -z "$queue" ]; then
   queue="short"
fi

### GET MAIL

mail=`cat /home/${USER}/.forward`


### CREATE INPUT SCRIPT FOR QSUB

cat <<EOT >> submit.sh
#!/bin/sh

#SBATCH --job-name=$jobname
#SBATCH -t 0-${jobtime}:00
#SBATCH -N $nnodes
#SBATCH -n $ncores
#SBATCH --mem-per-cpu=${memory}G
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL
#SBATCH -o /home/${USER}/err/vasp-%j
#SBATCH --mail-user=$mail
#SBATCH -p $queue
EOT
if [ "$gpu" -eq "1" ]; then
    cat <<EOT >> submit.sh
#SBATCH --gres=gpu:$ngpu
EOT
fi
cat <<EOT >> submit.sh
echo This job was submitted from the computer:
echo \$SLURM_SUBMIT_HOST
echo and the directory:
echo \$SLURM_SUBMIT_DIR
echo
echo It is running on the compute node:
echo \$SLURM_CLUSTER_NAME
echo
echo The local scratch directory "(located on the compute node)" is:
echo \$SCRATCH
echo

module load $MODULE
module list 2>&1
echo


echo "---- The Job is executed at \$(date) on \$(hostname) ----"

# Execute the program
cp -v /home/mewes/bin/vasp_tools/vdw_kernel.bindat \$SLURM_SUBMIT_DIR
cd \$SLURM_SUBMIT_DIR
[ -e output_OLD ] && cp output_OLD output_OLDER
[ -e output ] && cp output output_OLD
[ -e XDATCAR_OLD ] && cp XDATCAR_OLD XDATCAR_OLDER
[ -e XDATCAR ] && cp XDATCAR XDATCAR_OLD
srun -n $actual_ncores $BINARY > output
echo "---- First opt finished at \$(date) ----"

#How many steps to converge?
nsteps=\$(egrep "^   [1-9] F=" output | awk '{print \$1}' | tail -n 1)
nopt=0

touch first_cycle_converged_in_\${nsteps}_steps
cp POSCAR POSCAR.start

#Repeat optimization until converged in one step
while [ \$nsteps -gt 1 ] && [ \$nopt -lt 18 ] ; do
  mv output output_\$nopt
  cp CONTCAR POSCAR
  rm *_of_optimization__used_*
  srun -n $actual_ncores $BINARY > output
  nsteps=\$(egrep "^   [1-9] F=" output | awk '{print \$1}' | tail -n 1)
  echo "Took \$nsteps to converge..."
  nopt=\$((nopt+1))
  touch meta_cycle_\$((nopt+1))__converged_in_\${nsteps}_steps
done

rm  *bindat
touch optimization_concluded_after_\$((nopt+1))_meta_cycles

EOT


if [ -z $debug ]; then
   sbatch $optionstring submit.sh
   rm submit.sh

   cat <<EOT

Job has been submitted.
Name: $jobname, #CPU_RESERVED: $ncores, #CPUS_USED: $actual_ncores, #Nodes: $nnodes, mem: $((${memory}*${ncores}))GB.
EOT

else
   cat <<EOT

Job has been created. Submit file will be saved. 
Name: $jobname, #CPU: $ncores, #Nodes: $nnodes, mem: $((${memory}*${ncores}))GB.
Submit with sbatch submit.sh!
EOT
fi


exit 0