Différences

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

--- faq:chimie:gaussian [2018/07/23 13:42] – créée tjiang
+++ faq:chimie:gaussian [2021/10/08 13:50] – [Submission script Gaussian 16] tjiang
@@ Ligne 1: / Ligne 1: @@
 ====== GAUSSIAN ======
+===== Submission script Gaussian 16 =====
+<code bash sub_gaussian16.sh>
+#!/bin/bash
+#$ -S /bin/bash
+#$ -N test
+#$ -o $JOB_NAME.batch-log
+#$ -j y
+#$ -cwd
+#$ -V
+#$ -q E5*
+##$ -pe gaussian8 8
+#$ -pe openmp8 8
+# trace script (debug purpose, not mandatory)
+#set -x
+# set globals
+job="structure11"
+ExtIn="com"
+ExtOut="log"
+# Environment setting for gaussian
+module use /home/tjiang/modules/lmod
+# Automatically decide which binary to use, depending on the cpu architecture
+cpu_arch="$(sed '20q;d' /proc/cpuinfo)"
+module use /home/tjiang/modules/lmod
+if  [[ $cpu_arch = *"avx2"* ]]; then
+    module load gaussian/g16-avx2
+elif  [[ $cpu_arch = *"avx"* ]]; then
+    module load gaussian/g16-avx
+else
+    echo ""
+    echo "#########################################################"
+    echo "This queue (${QUEUE}) is too old for running Gaussian 16!!!"
+    echo "#########################################################"
+    echo ""
+    exit
+fi
+source "$g16root/g16/bsd/g16.profile"
+export Gaussian="$g16root/g16/g16"
+#cd "${SGE_O_WORKDIR}" || { echo "cannot cd to ${SGE_O_WORKDIR}"; exit 1; }
+#echo "########## begin env##################"
+#env
+#echo "########## end env ##################"
+echo "########## Hostname ##################"
+hostname
+HOMEDIR="${SGE_O_WORKDIR}"
+# Replace 'home' by 'scratch', from SGE_O_WORKDIR, store to SCRATCHDIR
+# check if scratch exist, create or complain
+if [[ -d "/scratch/Chimie" ]]
+then
+    SCRATCHDIR="/scratch/Chimie/${USER}/${JOB_ID}/"
+    mkdir -p "${SCRATCHDIR}"
+elif [[ -d "/scratch/Lake" ]]
+then
+    SCRATCHDIR=/scratch/Lake/${USER}/${JOB_ID}/
+    mkdir -p "${SCRATCHDIR}"
+elif [[ -d "/scratch/E5N" ]]
+then
+    SCRATCHDIR=/scratch/E5N/${USER}/${JOB_ID}/
+    mkdir -p "${SCRATCHDIR}"
+else
+    echo "/scratch not found, cannot create ${SCRATCHDIR}"
+    exit 1
+fi
+CalcDir="${SCRATCHDIR}"
+mkdir -p "${CalcDir}"
+# Gaussian specific ScratchDir
+export GAUSS_SCRDIR="${CalcDir}"
+Machine=$(hostname)
+# check if there is a chk or chk.gz
+# TODO/FIXME there's a problem here, watching the trace: if no chk, it create a .chk.chk
+NChk=$(grep -i "chk" ${job}.${ExtIn} | head -1 | sed 's/=/ /g' | awk '{print $2}')
+if [ "$NChk" != "" ]
+then
+NChk=$(basename "$NChk" .chk).chk
+fi
+if [[ -s "${HOMEDIR}/${NChk}" ]]
+then
+    cp "${HOMEDIR}/${NChk}" "${CalcDir}/${NChk}"
+fi
+if [[ -s "${HOMEDIR}/${NChk}.gz" ]]
+then
+    cp "${HOMEDIR}/${NChk}.gz" "${CalcDir}/${NChk}.gz"
+    gunzip "${CalcDir}/${NChk}.gz"
+fi
+cp "${HOMEDIR}/${job}.${ExtIn}" "${CalcDir}/"
+# logrotate old logs
+if [[ -s "${HOMEDIR}/${job}.${ExtOut}" ]]
+then
+    Ext=1
+    while [[ -s "${HOMEDIR}/${job}.${ExtOut}_${Ext}" ]]
+    do
+        #let Ext=Ext+1
+        Ext=$(( Ext+1 ))
+    done
+    mv "${HOMEDIR}/${job}.${ExtOut}" "${HOMEDIR}/${job}.${ExtOut}_${Ext}"
+fi
+cd "${CalcDir}" || { echo "cannot cd to ${CalcDir}"; exit 1; }
+echo "${CalcDir}"
+ls -al
+#echo "time ${Gaussian} < ${job}.${ExtIn} > ${HOMEDIR}/${job}.${ExtOut}"
+#/usr/bin/time ${Gaussian} < ${job}.${ExtIn} > ${HOMEDIR}/${job}.${ExtOut}
+"${Gaussian}" < "${job}.${ExtIn}" > "${HOMEDIR}/${job}.${ExtOut}"
+if [[ -s "${NChk}" ]]
+then
+    gzip -9 "${NChk}"
+    cp "${NChk}.gz" "${HOMEDIR}/"
+fi
+#copy back everything including the huge rwf files, normally we don't need it
+#cp -- * "${HOMEDIR}/"
+# final cleanup (commented during debug)
+rm -r "${GAUSS_SCRDIR}"
+</code>

faq/chimie/gaussian.txt · Dernière modification : 2022/03/03 16:29 de tjiang

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