Ci-dessous, les différences entre deux révisions de la page.
Les deux révisions précédentesRévision précédenteProchaine révision | Révision précédenteProchaine révisionLes deux révisions suivantes | ||
faq:chimie:amber [2018/11/15 10:04] – [Submission script] tjiang | faq:chimie:amber [2021/10/08 13:49] – [Submission script] tjiang | ||
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Ligne 22: | Ligne 22: | ||
# | # | ||
- | export MODULEPATH=/ | + | export MODULEPATH="/ |
- | module use ${MODULEPATH} | + | module use "${MODULEPATH}" |
#module file for gpu version of amber | #module file for gpu version of amber | ||
Ligne 31: | Ligne 31: | ||
#module load amber/ | #module load amber/ | ||
- | ambermod=$(basename $AMBERHOME) | + | ambermod=$(basename |
- | echo $ambermod | + | echo "${ambermod}" |
- | if [ $ambermod = " | + | if [ "${ambermod}" |
amberexe=" | amberexe=" | ||
else | else | ||
amberexe=" | amberexe=" | ||
fi | fi | ||
- | echo $amberexe | + | echo "${amberexe}" |
ulimit -v unlimited | ulimit -v unlimited | ||
Ligne 44: | Ligne 44: | ||
######################" | ######################" | ||
- | HOMEDIR=$SGE_O_WORKDIR | + | HOMEDIR="${SGE_O_WORKDIR}" |
- | HOSTFILE=$TMPDIR/ | + | HOSTFILE="${TMPDIR}/machines" |
- | cd $SGE_O_WORKDIR | + | cd "${SGE_O_WORKDIR}" || { echo " |
- | echo NSLOTS=$NSLOTS | + | echo NSLOTS="${NSLOTS}" |
- | SCRATCHDIR=/ | + | if [[ -d "/ |
- | # Using ramdisk | + | then |
- | # SCRATCHDIR=/ | + | |
+ | elif [[ -d "/ | ||
+ | then | ||
+ | SCRATCHDIR="/ | ||
+ | elif [[ -d "/ | ||
+ | then | ||
+ | SCRATCHDIR="/ | ||
+ | else | ||
+ | echo "/ | ||
+ | exit 1 | ||
+ | fi | ||
+ | # Using /tmp as scratch instead | ||
+ | # SCRATCHDIR="/tmp/${USER}/${JOB_ID}/" | ||
- | echo $SCRATCHDIR | + | echo "${SCRATCHDIR}" |
- | /bin/mkdir -p $SCRATCHDIR | + | /bin/mkdir -p "${SCRATCHDIR}" |
################### | ################### | ||
- | Mac=`hostname | awk ' | + | Mac=$(hostname | awk ' |
- | NbMac=`wc $PE_HOSTFILE | awk ' | + | NbMac=$(wc "${PE_HOSTFILE}" |
rm ./machines | rm ./machines | ||
- | for i in `seq 1 $NbMac` | + | for i in $(seq 1 "$NbMac") |
do | do | ||
- | Mac=` head -n $i $PE_HOSTFILE | tail -1 | awk ' | + | Mac=$(head -n "$i" "${PE_HOSTFILE}" |
- | Nb=` head -n $i $PE_HOSTFILE | tail -1 | awk ' | + | Nb=$(head -n "$i" "${PE_HOSTFILE}" |
- | for j in `seq 1 $Nb` | + | for j in $(seq 1 "$Nb" |
do | do | ||
- | echo $Mac >> ./machines | + | |
done | done | ||
done | done | ||
- | cp $PE_HOSTFILE ./ | + | cp "${PE_HOSTFILE}" |
- | cd $SCRATCHDIR | + | cd "${SCRATCHDIR}" || { echo " |
echo "start at" | echo "start at" | ||
Ligne 81: | Ligne 93: | ||
echo -n " | echo -n " | ||
date | date | ||
- | $amberexe -O -i $HOMEDIR/ | + | |
- | -o $HOMEDIR/ | + | -o "$HOMEDIR/ |
- | -p $HOMEDIR/ | + | -p "$HOMEDIR/ |
- | -c $HOMEDIR/ | + | -c "$HOMEDIR/ |
- | -r $HOMEDIR/ | + | -r "$HOMEDIR/ |
- | -x $HOMEDIR/ | + | -x "$HOMEDIR/ |
echo "done at" | echo "done at" | ||
date | date | ||
- | cp -rf * $HOMEDIR | + | cp -rf -- * "${HOMEDIR}" |
+ | rm -rf " | ||
+ | |||
</ | </ |