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faq:chimie:vasp [2019/05/13 13:48] – [Submission script] tjiangfaq:chimie:vasp [2022/03/01 12:36] (Version actuelle) – [Submission script] tjiang
Ligne 9: Ligne 9:
 #$ -V #$ -V
 #$ -cwd #$ -cwd
 +
 # Choose the version of vasp by loading the module file accordingly # Choose the version of vasp by loading the module file accordingly
 module use /home/tjiang/modules/lmod/ module use /home/tjiang/modules/lmod/
-module load vasp/5.4.1 + 
-#module load vasp/5.3.5+#choose a version of vasp by uncommenting the corresponding section below 
 + 
 +# vasp 5.4.1 
 +module load vasp/5.4.1_ompi1.8.8_intel15.0.2 
 + 
 +#For vasp 5.4.4, we need to source the intel mpi mpivars script to properly set environment 
 +#module load vasp/5.4.4_intel_suite2019.5 
 +#source /applis/PSMN/debian9/software/Compiler/intel/2019.5/impi/2019.5.281/intel64/bin/mpivars.sh 
 + 
 +#For vasp 6.2.0, we need to source the intel mpi mpivars script to properly set environment 
 +#module load vasp/6.2.0_intel_suite2019.5 
 +#source /applis/PSMN/debian9/software/Compiler/intel/2019.5/impi/2019.5.281/intel64/bin/mpivars.sh 
  
 # for OpenMP + multithreaded MKL # for OpenMP + multithreaded MKL
-export OMP_NUM_THREADS=1 +export OMP_NUM_THREADS="1" 
-export MKL_NUM_THREADS=1+export MKL_NUM_THREADS="1"
 #ulimit -l unlimited #ulimit -l unlimited
 +
 # Where are we # Where are we
-HOMEDIR=$SGE_O_WORKDIR+HOMEDIR="${SGE_O_WORKDIR}"
  
 # stuff for parallel computing # stuff for parallel computing
-HOSTFILE=$TMPDIR/machines+HOSTFILE="${TMPDIR}/machines"
  
 # save nodelist (optional) # save nodelist (optional)
-#/bin/cat $TMPDIR/machines > $HOMEDIR/tmp+#/bin/cat "${TMPDIR}/machines"${HOMEDIR}/tmp
 + 
 +# Check which scratch to use 
 +if [[ -d "/scratch/Chimie" ]] 
 +then 
 +    SCRATCHDIR="/scratch/Chimie/${USER}/${JOB_ID}/" 
 +elif [[ -d "/scratch/Lake" ]] 
 +then 
 +    SCRATCHDIR="/scratch/Lake/${USER}/${JOB_ID}/" 
 +elif [[ -d "/scratch/E5N" ]] 
 +then 
 +    SCRATCHDIR="/scratch/E5N/${USER}/${JOB_ID}/" 
 + 
 +else 
 +    echo "/scratch not found, cannot create ${SCRATCHDIR}" 
 +    exit 1 
 +fi 
 +# Using /tmp as scratch instead 
 +#SCRATCHDIR="/tmp/${USER}/${JOB_ID}/" 
 +mkdir -p "${SCRATCHDIR}" 
 +echo "scratch directory is: ${SCRATCHDIR}" 
 + 
 + 
 +cd "${HOMEDIR}" || { echo "cannot cd to ${HOMEDIR}"; exit 1; } 
 +#Creating POTCAR, contribution of Stephan 
 +rm POTCAR ; for i in `awk '{if(NR==6){print $0}}' POSCAR`  ; do cat ~tjiang/vasp/PSEUDOS_DATABASIS/2013/gw/potpaw/pbe/$i/POTCAR >> POTCAR ; done:w
  
-# Copy from home to scratch 
-QUEUE=$QUEUE 
-SCRATCHDIR=/scratch/E5/$USER/$JOB_ID/ 
-# Using ramdisk as scratch instead 
-# SCRATCHDIR=/dev/shm/$USER/$JOB_ID/ 
  
-echo $SCRATCHDIR 
-/bin/mkdir -p $SCRATCHDIR 
-cd ${HOMEDIR} 
 #for normal calculation #for normal calculation
-/bin/cp -f INCAR KPOINTS POTCAR  POSCAR WAVECAR ${SCRATCHDIR}/+/bin/cp -f INCAR KPOINTS POTCAR POSCAR WAVECAR "${SCRATCHDIR}/"
 #for neb calculation, numbering depends on the number of images #for neb calculation, numbering depends on the number of images
-#/bin/cp -rf INCAR KPOINTS POTCAR  POSCAR WAVECAR  00 01 02 ${SCRATCHDIR}/+#/bin/cp -rf INCAR KPOINTS POTCAR POSCAR WAVECAR 00 01 02 "${SCRATCHDIR}/"
 # If starting wavecar and chgcar exists, uncomment the following line # If starting wavecar and chgcar exists, uncomment the following line
-#/bin/cp -f $HOMEDIR/CHG* $HOMEDIR/WAVECAR+#/bin/cp -f -- "${HOMEDIR}/CHG*" "${HOMEDIR}/WAVECAR" "${SCRATCHDIR}/"
  
 # go to scratch (instead of SGE workdir) # go to scratch (instead of SGE workdir)
-cd ${SCRATCHDIR} +cd "${SCRATCHDIR}" || { echo "cannot cd to ${SCRATCHDIR}"; exit 1; 
-echo ${HOMEDIR} > homedir+echo "${HOMEDIR}> homedir
  
 # The line for computing # The line for computing
-mpirun  -hostfile $HOSTFILE -np ${NSLOTS} vasp_std > ${HOMEDIR}/out +mpirun  -hostfile "${HOSTFILE}" -np "${NSLOTS}vasp_std > "${HOMEDIR}/out" 
-#mpirun  -hostfile $HOSTFILE -np ${NSLOTS} vasp_gam > ${HOMEDIR}/out +#mpirun  -hostfile "${HOSTFILE}" -np "${NSLOTS}vasp_gam > "${HOMEDIR}/out" 
-#mpirun  -hostfile $HOSTFILE -np ${NSLOTS} vasp_ncl > ${HOMEDIR}/out+#mpirun  -hostfile "${HOSTFILE}" -np "${NSLOTS}vasp_ncl > "${HOMEDIR}/out"
  
 # Get back the results # Get back the results
 # Full copy back # Full copy back
-#cp WAVECAR CHG* OUTCAR POSCAR OSZICAR XDATCAR CONTCAR vasprun.xml $HOMEDIR/+#cp -- WAVECAR CHG* OUTCAR POSCAR OSZICAR XDATCAR CONTCAR vasprun.xml "${HOMEDIR}/"
 # Minimum copy back # Minimum copy back
-cp -rf OUTCAR POSCAR OSZICAR XDATCAR CONTCAR $HOMEDIR/ +
-# copy back for neb calculation, numbering depends on the number of images +
-#cp -rf OUTCAR POSCAR OSZICAR XDATCAR CONTCAR 00 01 02 $HOMEDIR/ +
-# Zip OUTCAR to save space +
-cd $HOMEDIR+
 bzip2 OUTCAR bzip2 OUTCAR
 #gzip OUTCAR #gzip OUTCAR
 +cp -rf OUTCAR.bz2 POSCAR OSZICAR XDATCAR CONTCAR "${HOMEDIR}/"
 +# copy back for neb calculation, numbering depends on the number of images
 +#cp -rf OUTCAR POSCAR OSZICAR XDATCAR CONTCAR 00 01 02 "${HOMEDIR}/"
 +# Zip OUTCAR to save space
 +cd "${HOMEDIR}/" || { echo "cannot cd to ${HOMEDIR}"; exit 1; }
  
 # Cleaning up # Cleaning up
-rm -rf ${SCRATCHDIR}+# there should be a test here, what if ${SCRATCHDIR} = ${SGE_O_WORKDIR}? 
 +rm -rf "${SCRATCHDIR}"
  
-# The following part is only useful for users from the chemistry lab of ens-lyon. +# The following part is only useful for users from the chemistry lab of ens-lyon.
 # Importing finished calculation into database # Importing finished calculation into database
-if [ ! -d /home/${USER}/.chimie_db/ ]; then +#if [ ! -d "/home/${USER}/.chimie_db/]; then 
-    mkdir /home/${USER}/.chimie_db/ +   mkdir "/home/${USER}/.chimie_db/" 
-fi +#fi 
-export PYTHONPATH=/home/tjiang/usr/lib/python2.7/site-package/:$PYTHONPATH +#export PYTHONPATH="/home/tjiang/usr/lib/python2.7/site-package/:$PYTHONPATH" 
-export PATH=/home/tjiang/chimie4psmn/database/:$PATH +#export PATH="/home/tjiang/chimie4psmn/database/:$PATH" 
-import_vasp_calc -p -u ${USER} -n 1 -d /home/${USER}/.chimie_db/${USER}.db ${HOMEDIR}+#import_vasp_calc -p -u "${USER}-n 1 -d "/home/${USER}/.chimie_db/${USER}.db" "${HOMEDIR}"
  
 </code> </code>
  
faq/chimie/vasp.1557755284.txt.gz · Dernière modification : 2020/08/25 15:58 (modification externe)