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--- hpc:numericserveruser:hpc_numericserver:batch_job_scripts:job_scripts_examples:script_gaussian [2018/08/24 17:44] – kraus
+++ hpc:numericserveruser:hpc_numericserver:batch_job_scripts:job_scripts_examples:script_gaussian [2020/02/14 18:08] (aktuell) – kraus
@@ Zeile 1: / Zeile 1: @@
+====== Gaussian ======
+Launch this script shown below by typing: \\
+<file>qsub jobscript_gaussian16.sh [name_of_your_job]</file> \\
+OR substitute <file> NAME=$1 </file> by <file>NAME=[name_of_your_job]</file> and launch as: \\
+<file>qsub jobscript_gaussian16.sh</file> \\
+**Remark:**
+<html>
+<span style="color:red;font-size:110%;">Please ensure <span style="color:blue;font-family:monospace;font-size:130%;">the value for NProcShared</span> within the Gaussian input equals <span style="color:blue;font-family:monospace;font-size:130%;">the number of threads</span> you demand by <span style="color:blue;font-family:monospace;font-size:130%;">-pe mp [no_threads]</span> </span>
+</html> \\
+\\
+<code bash jobscript_gaussian16.sh>
+#!/bin/bash --login
+##### example for an OpenMP Gaussian run with 4 CPU
+#$ -cwd
+##### please define your own job resources
+# time in hh:mm:ss
+#$ -l h_rt=00:30:00
+#$ -l mem_free=4G
+# IMPORTANT: ensure that %NProcShared within
+# gaussian input is set to same value
+#$ -pe mp 4
+#$ -N jobname
+#$ -e jobname_err.out
+#$ -o jobname_stdout.out
+#$ -j n
+#$ -m n
+##########
+# saves current directory; where output goes
+STOREDIR=$PWD
+NAME=$1
+# strip off file extension
+COMNAME=${1/.*/}
+if [ ! -s $STOREDIR/$NAME ]; then
+ echo "Error: Job input file $STOREDIR/$NAME does not exist!"
+ exit 1
+fi
+# create temporary directory for .rwf and .chk files
+# create unique tmpdir with random name
+#SCRATCHDIR=$(mktemp -d /scratch/$USER/gaussian.XXXXXXX)
+# tmpdir per job ID
+if [ -n "$TASK_ID" ]
+then
+SCRATCHDIR=/scratch/$USER/gaussian_${JOB_ID}_$TASK_ID
+else
+SCRATCHDIR=/scratch/$USER/gaussian_$JOB_ID
+fi
+# don't forget to create recursively
+mkdir -p $SCRATCHDIR
+# export location for Gaussian scratch directory
+export GAUSS_SCRDIR=$SCRATCHDIR
+# copy job files to tmpdir
+# in case of one .chk file with same name, uncomment this
+#if [ -e $STOREDIR/$COMNAME.chk ] ; then
+#cp $STOREDIR/$COMNAME.chk $SCRATCHDIR
+#fi
+# if several .chk files need to be copied
+cp $STOREDIR/*.chk $SCRATCHDIR
+# copy the job input file
+cp $STOREDIR/$NAME $SCRATCHDIR
+# job starts
+# change to tmpdir
+cd $SCRATCHDIR
+# and start of job run
+module load g16
+g16 < $NAME > $STOREDIR/$COMNAME.out
+# job ends
+# gives some info about the space left on scratch
+if [ -n "$TASK_ID" ]
+then
+df -B GB /scratch > scratch_info_${JOB_ID}_$TASK_ID.out
+else
+df -B GB /scratch > scratch_info_$JOB_ID.out
+fi
+# copy files and chdir to job directory
+mv -f $SCRATCHDIR/*.chk $STOREDIR ; cd $STOREDIR
+# creation of formatted chk (if needed), use with caution for big chk files
+# formchk $COMNAME.chk
+#clean up
+rm -fr $SCRATCHDIR
+</code>
+\\
+<WRAP rightalign>
+date of revision: 02-14-2020 © kraus
+</WRAP>