Chimie Théorique » scripts_chimie4psmn » DockOnSurf

#!/bin/bash

#$ -S /bin/bash

#$ -cwd

#$ -V

#$ -N H2Otest

#$ -q E5-*,SSD-E5*,CLG*

#$ -pe mpi8* 8

#$ -e stderr

#$ -o stdout

#$ -m aes

#$ -M carles.marti-aliod@ens-lyon.fr 

## Set up the environment

module purge

module load cp2k/5.1_gcc7.2_avx

export OMP_NUM_THREADS=1

## Prepare /scratch to work in it, if possible.

IN_FILES="*.inp* coord.xyz *.wfn *Hessian"

HOMEDIR=$PWD

if [ -d /scratch/E5N ]; then

  WORKDIR=/scratch/E5N/$USER/$JOB_ID

elif [ -d /scratch/X5 ]; then

  WORKDIR=/scratch/X5/$USER/$JOB_ID

elif [ -d /scratch/Chimie ]; then

  WORKDIR=/scratch/Chimie/$USER/$JOB_ID

else 

  WORKDIR=$HOMEDIR/$JOB_ID

fi

mkdir $WORKDIR

cp -r $IN_FILES $WORKDIR

cd $WORKDIR

## Run the job

basename=$(ls *.inp | cut -d "." -f 1)

mpirun -np $NSLOTS cp2k.popt -i $basename.inp -o $basename.out

## Copy files back to home

cp -r * $HOMEDIR

cd $HOMEDIR

rm -r $WORKDIR