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faq:chimie:crystal

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faq:chimie:crystal [2020/04/10 08:22] – [Submission script for crystal 17] tjiangfaq:chimie:crystal [2022/03/03 16:28] (Version actuelle) – [Submission script for Properties 17] tjiang
Ligne 13: Ligne 13:
 module load crystal/17 module load crystal/17
  
-export HOMEDIR=$SGE_O_WORKDIR +export HOMEDIR="${SGE_O_WORKDIR}" 
-cd $HOMEDIR+cd "${HOMEDIR}" || { echo "cannot cd to ${HOMEDIR}"; exit 1; }
  
-INPUT=LaTaS6+INPUT="LaTaS6"
  
 if [[ -d "/scratch/Chimie" ]] if [[ -d "/scratch/Chimie" ]]
 then then
-    export CRY17_SCRDIR=/scratch/Chimie/$USER/$JOB_ID+    export CRY17_SCRDIR="/scratch/Chimie/$USER/$JOB_ID"
 elif [[ -d "/scratch/Lake" ]] elif [[ -d "/scratch/Lake" ]]
 then then
-    export CRY17_SCRDIR=/scratch/Lake/$USER/$JOB_ID/+    export CRY17_SCRDIR="/scratch/Lake/$USER/$JOB_ID/"
 elif [[ -d "/scratch/E5N" ]] elif [[ -d "/scratch/E5N" ]]
 then then
-    export CRY17_SCRDIR=/scratch/E5N/$USER/$JOB_ID/ +    export CRY17_SCRDIR="/scratch/E5N/$USER/$JOB_ID/"
-elif [[ -d "/scratch/E5" ]] +
-then +
-    export CRY17_SCRDIR=/scratch/E5/$USER/$JOB_ID/+
 else else
-    echo "/scratch not found, cannot create ${CRY17_SCRDIR}"+    echo "/scratch not found, cannot create ${SCRATCHDIR}" 
 +    exit 1
 fi fi
  
 #Use /tmp as scratch #Use /tmp as scratch
-#export CRY17_SCRDIR=/tmp/$USER/$JOB_ID+#export CRY17_SCRDIR="/tmp/$USER/$JOB_ID"
  
-/bin/mkdir -p $CRY17_SCRDIR +echo "Creating scratch for this job: ${CRY17_SCRDIR}" 
-export CRY17P_MACH=$HOMEDIR+/bin/mkdir -p "${CRY17_SCRDIR}" 
 +export CRY17P_MACH="${HOMEDIR}"
  
-export MPIRUN=mpirun +export MPIRUN="mpirun" 
-export HOSTFILE=$TMPDIR/machines +export HOSTFILE="${TMPDIR}/machines" 
-#export hosts=$HOMEDIR/hosts_`basename $INPUT .d12` +#export hosts="${HOMEDIR}/hosts_$(basename ${INPUT} .d12)" 
-cp $HOSTFILE $HOMEDIR/machines.LINUX +cp "${HOSTFILE}" "${HOMEDIR}/machines.LINUX" 
-cp $HOSTFILE $HOMEDIR/nodes.par+cp "${HOSTFILE}" "${HOMEDIR}/nodes.par"
 #Too lazy to do a test, but the file needs to be refreshed! #Too lazy to do a test, but the file needs to be refreshed!
 #rm -f $hosts #rm -f $hosts
 #/bin/cat $TMPDIR/machines > $hosts #/bin/cat $TMPDIR/machines > $hosts
-export OMP_NUM_THREADS=1 +export OMP_NUM_THREADS="1" 
-export MKL_NUM_THREADS=1+export MKL_NUM_THREADS="1"
  
-$CRYSTALROOT/utils/runmpi17 $NSLOTS $INPUT+"${CRYSTALROOT}/utils/runmpi17" "${NSLOTS}" "${INPUT}"
 #use ramdisk as scratch, only works on one node #use ramdisk as scratch, only works on one node
-#$CRYSTALROOT/utils/runmpi17SN $NSLOTS $INPUT+#"${CRYSTALROOT}/utils/runmpi17SN" "${NSLOTS}" "${INPUT}"
  
-rm -fr $CRY17_SCRDIR+rm -fr "${CRY17_SCRDIR}"
 #rm $HOMEDIR/hosts_`basename $INPUT .d12` #rm $HOMEDIR/hosts_`basename $INPUT .d12`
 +
 </code> </code>
 ===== Submission script for Properties 17 ===== ===== Submission script for Properties 17 =====
Ligne 70: Ligne 70:
 module load crystal/17 module load crystal/17
  
-export HOMEDIR=$SGE_O_WORKDIR +export HOMEDIR="${SGE_O_WORKDIR}" 
-cd $HOMEDIR +cd "${HOMEDIR}" || { echo "cannot cd to ${HOMEDIR}"; exit 1; } 
-export CRY17_INP=$HOMEDIR +export CRY17_INP="${HOMEDIR}" 
-export CRY17_SCRDIR=/scratch/Chimie/$USER/$JOB_ID +  
-/bin/mkdir -p $CRY17_SCRDIR +if [[ -d "/scratch/Chimie" ]] 
-export EXEC=$CRYSTALROOT/utils/runprop17+then 
 +    export CRY17_SCRDIR="/scratch/Chimie/${USER}/${JOB_ID}" 
 +elif [[ -d "/scratch/Lake" ]] 
 +then 
 +    export CRY17_SCRDIR="/scratch/Lake/${USER}/${JOB_ID}/" 
 +elif [[ -d "/scratch/E5N" ]] 
 +then 
 +    export CRY17_SCRDIR="/scratch/E5N/${USER}/${JOB_ID}/" 
 +else 
 +    echo "/scratch not found, cannot create ${SCRATCHDIR}" 
 +    exit 1 
 +fi 
 + 
 +echo "Creating scratch for this job: ${CRY17_SCRDIR}" 
 +/bin/mkdir -p "${CRY17_SCRDIR}" 
 +export EXEC="${CRYSTALROOT}/utils/runprop17"
  
 # Running crystal properties # Running crystal properties
Ligne 85: Ligne 100:
  
 # Cleaning up scratch directory # Cleaning up scratch directory
-rm -fr $CRY17_SCRDIR+rm -fr "${CRY17_SCRDIR}" 
 </code> </code>
faq/chimie/crystal.1586506976.txt.gz · Dernière modification : 2020/08/25 15:58 (modification externe)
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