Différences

Ci-dessous, les différences entre deux révisions de la page.

--- faq:chimie:crystal [2018/11/15 10:02] – [Submission script for crystal 17] tjiang
+++ faq:chimie:crystal [2022/03/03 16:28] (Version actuelle) – [Submission script for Properties 17] tjiang
@@ Ligne 13: / Ligne 13: @@
 module load crystal/17
-export HOMEDIR=$SGE_O_WORKDIR
+export HOMEDIR="${SGE_O_WORKDIR}"
-cd $HOMEDIR
+cd "${HOMEDIR}" || { echo "cannot cd to ${HOMEDIR}"; exit 1; }
-INPUT=LaTaS6
+INPUT="LaTaS6"
-export CRY17_SCRDIR=/scratch/$USER/$JOB_ID
+if [[ -d "/scratch/Chimie" ]]
-#Use ramdisk as scratch
+then
-#export CRY17_SCRDIR=/dev/shm/$USER/$JOB_ID
+    export CRY17_SCRDIR="/scratch/Chimie/$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
-/bin/mkdir -p $CRY17_SCRDIR
+#Use /tmp as scratch
-export CRY17P_MACH=$HOMEDIR
+#export CRY17_SCRDIR="/tmp/$USER/$JOB_ID"
-export MPIRUN=mpirun
+echo "Creating scratch for this job: ${CRY17_SCRDIR}"
-export HOSTFILE=$TMPDIR/machines
+/bin/mkdir -p "${CRY17_SCRDIR}"
-#export hosts=$HOMEDIR/hosts_`basename $INPUT .d12`
+export CRY17P_MACH="${HOMEDIR}"
-cp $HOSTFILE $HOMEDIR/machines.LINUX
-cp $HOSTFILE $HOMEDIR/nodes.par
+export MPIRUN="mpirun"
+export HOSTFILE="${TMPDIR}/machines"
+#export hosts="${HOMEDIR}/hosts_$(basename ${INPUT} .d12)"
+cp "${HOSTFILE}" "${HOMEDIR}/machines.LINUX"
+cp "${HOSTFILE}" "${HOMEDIR}/nodes.par"
 #Too lazy to do a test, but the file needs to be refreshed!
 #rm -f $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
-#$CRYSTALROOT/utils/runmpi17SN $NSLOTS $INPUT
+#"${CRYSTALROOT}/utils/runmpi17SN" "${NSLOTS}" "${INPUT}"
-rm -fr $CRY17_SCRDIR
+rm -fr "${CRY17_SCRDIR}"
 #rm $HOMEDIR/hosts_`basename $INPUT .d12`
 </code>
 ===== Submission script for Properties 17 =====
@@ Ligne 55: / Ligne 70: @@
 module load crystal/17
-export HOMEDIR=$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="${HOMEDIR}"
-export CRY17_SCRDIR=/scratch/$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
@@ Ligne 70: / Ligne 100: @@
 # Cleaning up scratch directory
-rm -fr $CRY17_SCRDIR
+rm -fr "${CRY17_SCRDIR}"
 </code>

faq/chimie/crystal.1542276120.txt.gz · Dernière modification : 2020/08/25 15:58 (modification externe)

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