Révision 9
| submit/adf/run_adf.sh (revision 9) | ||
|---|---|---|
| 1 |
#!/bin/bash |
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| 2 |
#$ -S /bin/bash |
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| 3 |
#$ -N TO_CHANGE |
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| 4 |
#$ -q E5-2670deb64* |
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| 5 |
#$ -pe mpi16_debian 16 |
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| 6 |
#$ -m be |
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| 7 |
#$ -cwd |
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| 8 |
#$ -V |
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| 9 |
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| 10 |
# Version: $Id$ |
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| 11 |
|
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| 12 |
# env first |
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| 13 |
source /usr/share/modules/init/bash |
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| 14 |
module use /applis/PSMN/Modules |
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| 15 |
module load Base/psmn |
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| 16 |
module load ADF/2014.10 |
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| 17 |
# also add the SCMLICENCE line to ~/.cshrc or ~/.bashrc |
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| 18 |
export SCMLICENCE=/applis/PSMN/generic/adf/license.2016.txt |
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| 19 |
export SCM_TMPDIR=/scratch/LOGIN |
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| 20 |
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| 21 |
DATADIR="/home/LOGIN/path/to" |
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| 22 |
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| 23 |
# Declaration used by the batch system |
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| 24 |
HOSTFILE=${TMPDIR}/machines
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| 25 |
export SCM_MACHINEFILE=${TMPDIR}/machines
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| 26 |
export NSCM=${NSLOTS}
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| 27 |
# |
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| 28 |
cd ${DATADIR}
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| 29 |
# |
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| 30 |
${ADFBIN}/adf < ${DATADIR}/input_adf.run
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| 31 |
# |
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| 0 | 32 | |
| submit/gaussian/old/run_g09d-PFL.sh (revision 9) | ||
|---|---|---|
| 1 |
#!/bin/bash |
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| 2 |
# $Id$ |
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| 3 |
#$ -S /bin/bash |
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| 4 |
#$ -N A_CHANGER |
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| 5 |
#$ -o A_CHANGER.batch-log |
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| 6 |
#$ -j y |
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| 7 |
#$ -q E5-2670deb* |
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| 8 |
#$ -pe mpi8_debian 8 |
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| 9 |
#$ -cwd |
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| 10 |
#$ -V |
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| 11 |
|
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| 12 |
set -x |
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| 13 |
job=A_CHANGER |
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| 14 |
ExtIn=com |
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| 15 |
ExtOut=log |
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| 16 |
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| 17 |
HOMEDIR=$SGE_O_WORKDIR |
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| 18 |
export g09root=/softs/gaussian/g09d01 |
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| 19 |
source $g09root/g09/bsd/g09.profile |
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| 20 |
export Gaussian=$g09root/g09/g09 |
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| 21 |
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| 22 |
cd $SGE_O_WORKDIR |
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| 23 |
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| 24 |
echo "########## debut env##################" |
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| 25 |
env |
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| 26 |
echo "########## fin env ##################" |
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| 27 |
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| 28 |
echo "########## Hostname ##################" |
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| 29 |
hostname |
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| 30 |
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| 31 |
# Files definitions |
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| 32 |
SCRATCHDIR=`echo $SGE_O_WORKDIR | awk -F "/" '{$2="scratch"; for(j=2;j<=NF;j++) {printf("/%s",$j);} print ""} ' `
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|
| 33 |
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| 34 |
mkdir -p $SCRATCHDIR |
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| 35 |
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| 36 |
echo "ok" > $SCRATCHDIR/toto |
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| 37 |
Ok=`cat $SCRATCHDIR/toto ` |
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| 38 |
if [ "$Ok" != "ok" ]; then |
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| 39 |
# should not do that, should exit with error |
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| 40 |
CalcDir=$SGE_O_WORKDIR |
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| 41 |
export GAUSS_SCRDIR=$SGE_O_WORKDIR"/Scratch_"${job}_`date +%s`
|
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| 42 |
else |
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| 43 |
CalcDir=$SCRATCHDIR |
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| 44 |
export GAUSS_SCRDIR=$SCRATCHDIR"/"${job}_`date +%s`
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| 45 |
fi |
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| 46 |
|
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| 47 |
# Gaussian Scratch Dir |
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| 48 |
mkdir -p $CalcDir |
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| 49 |
mkdir -p $GAUSS_SCRDIR |
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| 50 |
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| 51 |
Machine=`hostname` |
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| 52 |
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| 53 |
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| 54 |
HDir=$PWD # !! we are using SGE_O_WORKDIR/HOMEDIR, why new one ? |
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| 55 |
#we check if there is a chk |
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| 56 |
NChk=` grep -i "chk" ${job}.${ExtIn} | head -1 | sed 's/=/ /g' | awk '{print $2}' `
|
|
| 57 |
NChk=` basename $NChk .chk`.chk |
|
| 58 |
if [ -s $HDir/$NChk ]; then |
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| 59 |
cp $HDir/$NChk $CalcDir/$NChk |
|
| 60 |
fi |
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| 61 |
if [ -s $HDir/$NChk.gz ]; then |
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| 62 |
cp $HDir/$NChk.gz $CalcDir/$NChk.gz |
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| 63 |
gunzip $CalcDir/$NChk.gz |
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| 64 |
fi |
|
| 65 |
|
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| 66 |
cp $HDir/${job}.${ExtIn} $CalcDir/.
|
|
| 67 |
|
|
| 68 |
# must simplify |
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| 69 |
echo "ssh ${SGE_O_LOGNAME}@${Machine} gzip $CalcDir/*.chk " > $HDir/${job}_${Machine}.${ExtOut}
|
|
| 70 |
echo "scp ${SGE_O_LOGNAME}@${Machine}:$CalcDir/* ." > $HDir/${job}_${Machine}.${ExtOut}
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| 71 |
echo "ssh ${SGE_O_LOGNAME}@${Machine} rm -fr $CalcDir" >> $HDir/${job}_${Machine}.${ExtOut}
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| 72 |
echo "rm ${job}_${Machine}.${ExtOut}" >> $HDir/${job}_${Machine}.${ExtOut}
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|
| 73 |
chmod u+x $HDir/${job}_${Machine}.${ExtOut}
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|
| 74 |
|
|
| 75 |
# why ? |
|
| 76 |
cd $CalcDir |
|
| 77 |
ls -al |
|
| 78 |
|
|
| 79 |
if [ -s $HDir/${job}.${ExtOut} ]; then
|
|
| 80 |
Ext=1 |
|
| 81 |
while [ -s $HDir/${job}.${ExtOut}_${Ext} ]
|
|
| 82 |
do |
|
| 83 |
let Ext=Ext+1 |
|
| 84 |
done |
|
| 85 |
mv $HDir/${job}.${ExtOut} $HDir/${job}.${ExtOut}_${Ext}
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|
| 86 |
fi |
|
| 87 |
echo "time ${Gaussian} < ${job}.${ExtIn} > ${HDir}/${job}.${ExtOut}"
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|
| 88 |
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|
| 89 |
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|
| 90 |
/usr/bin/time ${Gaussian} < ${job}.${ExtIn} > ${HDir}/${job}.${ExtOut}
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|
| 91 |
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|
| 92 |
sleep 120 |
|
| 93 |
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|
| 94 |
cp *.wfn $HDir/. |
|
| 95 |
|
|
| 96 |
if [ -s $NChk ]; then |
|
| 97 |
gzip -9 $NChk |
|
| 98 |
cp $NChk.gz $HDir/. |
|
| 99 |
fi |
|
| 100 |
|
|
| 101 |
rm -r $GAUSS_SCRDIR # not usefull |
|
| 102 |
rm -r $CalcDir |
|
| 103 |
rm $HDir/${job}_${Machine}.${ExtOut}
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| 0 | 104 | |
| submit/gaussian/old/run_g09d-TLB.sh (revision 9) | ||
|---|---|---|
| 1 |
#!/bin/bash |
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| 2 |
# PSMN: $Id$ |
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| 3 |
#$ -S /bin/bash |
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| 4 |
#$ -N c0a-a0scan.com |
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| 5 |
#$ -cwd |
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| 6 |
#$ -j y |
|
| 7 |
#$ -o c0a-a0.batch-log |
|
| 8 |
#$ -q r815lin128ib |
|
| 9 |
#$ -pe gaussian8 8 |
|
| 10 |
|
|
| 11 |
set -x |
|
| 12 |
job1=c0a-a0 |
|
| 13 |
ExtIn=com |
|
| 14 |
ExtOut=log |
|
| 15 |
|
|
| 16 |
HOMEDIR=$SGE_O_WORKDIR |
|
| 17 |
echo $HOMEDIR |
|
| 18 |
export g09root=/softs/gaussian/g09d01 |
|
| 19 |
export GAUSS_SCRDIR=/scratch/$SGE_O_LOGNAME |
|
| 20 |
source $g09root/g09/bsd/g09.profile |
|
| 21 |
export Gaussian=$g09root/g09/g09 |
|
| 22 |
|
|
| 23 |
#mettre en commentaire la ligne suivante sur le nouveau cluster, la laisser sur l'ancien |
|
| 24 |
#export LD_ASSUME_KERNEL=2.4.1 |
|
| 25 |
#export Gaussian=$g03root/g03a02/g09 |
|
| 26 |
|
|
| 27 |
cd $SGE_O_WORKDIR |
|
| 28 |
|
|
| 29 |
export RSHCOMMAND=ssh |
|
| 30 |
export P4_RSHCOMMAND=ssh |
|
| 31 |
|
|
| 32 |
export LD_LIBRARY_PATH=/softs/acml/acml2.7.0/pathscale64/lib:/softs/fftw/2.1.5/ps-ib/lib:$LD_LIBRARY_PATH:/usr/lib |
|
| 33 |
|
|
| 34 |
echo "########## debut env##################" |
|
| 35 |
env |
|
| 36 |
echo "########## fin env ##################" |
|
| 37 |
|
|
| 38 |
echo "########## Hostname ##################" |
|
| 39 |
hostname |
|
| 40 |
|
|
| 41 |
WKDIR=/scratch |
|
| 42 |
|
|
| 43 |
DirT=$PWD |
|
| 44 |
CalcDir="" |
|
| 45 |
for i in `echo $PWD | sed 's/\// /g'` |
|
| 46 |
do |
|
| 47 |
Rep=$i |
|
| 48 |
if [ $Rep = "home" -o $Rep = "maestro" ]; then |
|
| 49 |
Rep=$WKDIR |
|
| 50 |
fi |
|
| 51 |
# echo $Rep " --- " $i " ---- " $CalcDir |
|
| 52 |
CalcDir=$CalcDir"/"$Rep |
|
| 53 |
# echo $Rep " --- " $i " ---- " $CalcDir |
|
| 54 |
if [ ! \( -s $CalcDir \) ]; then |
|
| 55 |
echo "Creating $CalcDir" |
|
| 56 |
mkdir $CalcDir |
|
| 57 |
fi |
|
| 58 |
done |
|
| 59 |
|
|
| 60 |
#### On rajoute le nom du calcul a la fin de CalcDir (Paul -> Mika) |
|
| 61 |
CalcDir=$CalcDir"/"${job1}_`date +%s`
|
|
| 62 |
# echo $Rep " --- " $i " ---- " $CalcDir |
|
| 63 |
if [ ! \( -s $CalcDir \) ]; then |
|
| 64 |
echo "Creating $CalcDir" |
|
| 65 |
mkdir $CalcDir |
|
| 66 |
fi |
|
| 67 |
#### Fin de l'ajout |
|
| 68 |
|
|
| 69 |
echo "CalcDir="$CalcDir |
|
| 70 |
|
|
| 71 |
#### We add GScratch as the Gaussian Scratch Dir (Paul -> Mika) |
|
| 72 |
export GAUSS_SCRDIR=$CalcDir"/GScratchDir" |
|
| 73 |
if [ ! \( -s $GAUSS_SCRDIR \) ]; then |
|
| 74 |
echo "Creating $GAUSS_SCRDIR" |
|
| 75 |
mkdir $GAUSS_SCRDIR |
|
| 76 |
fi |
|
| 77 |
#### Fin de l'ajout |
|
| 78 |
|
|
| 79 |
Machine=`hostname` |
|
| 80 |
HDir=$PWD |
|
| 81 |
|
|
| 82 |
#### We check if there is a chk |
|
| 83 |
NChk=` grep -i "chk" ${job1}.${ExtIn} | head -1 | sed 's/=/ /g' | \awk '{print $2}' `
|
|
| 84 |
NChk=` basename $NChk .chk`.chk |
|
| 85 |
if [ -s $HDir/$NChk ]; then |
|
| 86 |
cp $HDir/$NChk $CalcDir/$NChk |
|
| 87 |
fi |
|
| 88 |
#### Eventuellement on ajoute avant fi: gunzip $HDir/$NChk.gz |
|
| 89 |
|
|
| 90 |
#### We check if there is a cube file |
|
| 91 |
NCube=` grep -i "cube" ${job1}.${ExtIn} | head -1 | sed 's/=/ /g' | \awk '{print $2}' `
|
|
| 92 |
NCube=` basename $NChk .cube`.cube |
|
| 93 |
if [ -s $HDir/$NCube ]; then |
|
| 94 |
cp $HDir/$NCube $CalcDir/$NCube |
|
| 95 |
fi |
|
| 96 |
#### Eventuellement on ajoute avant fi: gunzip $HDir/$NChk.gz |
|
| 97 |
|
|
| 98 |
#### Si le calcul plante, regarde ce qu'il y a dans le scratch, recupere et vide |
|
| 99 |
echo "ssh ${SGE_O_LOGNAME}@${Machine} gzip $CalcDir/*.chk " > $HDir/${job1}_${Machine}.${ExtOut}
|
|
| 100 |
echo "scp ${SGE_O_LOGNAME}@${Machine}:$CalcDir/* ." >> $HDir/${job1}_${Machine}.${ExtOut}
|
|
| 101 |
echo "ssh ${SGE_O_LOGNAME}@${Machine} rm -r $CalcDir" >> $HDir/${job1}_${Machine}.${ExtOut}
|
|
| 102 |
echo "rm ${job1}_${Machine}.${ExtOut}" >> $HDir/${job1}_${Machine}.${ExtOut}
|
|
| 103 |
chmod u+x $HDir/${job1}_${Machine}.${ExtOut}
|
|
| 104 |
|
|
| 105 |
cp $HDir/${job1}.${ExtIn} $CalcDir/.
|
|
| 106 |
touch $HDir/${job1}_${Machine}.${ExtOut}
|
|
| 107 |
cd $CalcDir |
|
| 108 |
ls -al |
|
| 109 |
|
|
| 110 |
#### S'il y a deja un .log, le copie en .log._X+1 pour sauvegarde s'il y avait deja .log_X |
|
| 111 |
if [ -s $HDir/${job1}.${ExtOut} ]; then
|
|
| 112 |
Ext=1 |
|
| 113 |
while [ -s $HDir/${job1}.${ExtOut}_${Ext} ]
|
|
| 114 |
do |
|
| 115 |
let Ext=Ext+1 |
|
| 116 |
done |
|
| 117 |
mv $HDir/${job1}.${ExtOut} $HDir/${job1}.${ExtOut}_${Ext}
|
|
| 118 |
fi |
|
| 119 |
|
|
| 120 |
echo "time ${Gaussian} < ${job1}.${ExtIn} > ${HDir}/${job1}.${ExtOut}"
|
|
| 121 |
|
|
| 122 |
/usr/bin/time ${Gaussian} < ${job1}.${ExtIn} > ${HDir}/${job1}.${ExtOut}
|
|
| 123 |
|
|
| 124 |
cp ${job1}.${ExtOut} $HDir/${job1}.${ExtOut}
|
|
| 125 |
|
|
| 126 |
rm -r $GAUSS_SCRDIR |
|
| 127 |
if [ -s $NChk ]; then |
|
| 128 |
cp $NChk $HDir/$NChk |
|
| 129 |
fi |
|
| 130 |
|
|
| 131 |
cp $CalcDir/*.cube $HDir/. |
|
| 132 |
|
|
| 133 |
rm -r $CalcDir |
|
| 134 |
rm $HDir/${job1}_${Machine}.${ExtOut}
|
|
| 0 | 135 | |
| submit/gaussian/run_g09d01.sh (revision 9) | ||
|---|---|---|
| 1 |
#!/bin/bash |
|
| 2 |
#$ -S /bin/bash |
|
| 3 |
#$ -N TO_CHANGE |
|
| 4 |
#$ -o $JOB_NAME.batch-log |
|
| 5 |
#$ -j y |
|
| 6 |
#$ -cwd |
|
| 7 |
#$ -V |
|
| 8 |
#$ -q x5570deb24* |
|
| 9 |
#$ -pe gaussian8 8 |
|
| 10 |
|
|
| 11 |
# Version: $Id$ |
|
| 12 |
|
|
| 13 |
# trace script (debug purpose, not mandatory) |
|
| 14 |
set -x |
|
| 15 |
# set globals |
|
| 16 |
job=${JOB_NAME}
|
|
| 17 |
ExtIn=com |
|
| 18 |
ExtOut=log |
|
| 19 |
|
|
| 20 |
## Environment (to find VASP, Ifort, MPI...) |
|
| 21 |
source /usr/share/modules/init/bash |
|
| 22 |
module use /applis/PSMN/Modules |
|
| 23 |
module load Base/psmn |
|
| 24 |
module load Gaussian/g09d01-chimie |
|
| 25 |
# g09root is set by the modulefile |
|
| 26 |
source $g09root/g09/bsd/g09.profile |
|
| 27 |
export Gaussian=$g09root/g09/g09 |
|
| 28 |
|
|
| 29 |
cd ${SGE_O_WORKDIR}
|
|
| 30 |
|
|
| 31 |
echo "########## debut env##################" |
|
| 32 |
env |
|
| 33 |
echo "########## fin env ##################" |
|
| 34 |
|
|
| 35 |
echo "########## Hostname ##################" |
|
| 36 |
hostname |
|
| 37 |
|
|
| 38 |
HOMEDIR=${SGE_O_WORKDIR}
|
|
| 39 |
cd ${HOMEDIR}
|
|
| 40 |
|
|
| 41 |
# Replace 'home' by 'scratch', from SGE_O_WORKDIR, store to SCRATCHDIR |
|
| 42 |
SCRATCHDIR=${SGE_O_WORKDIR/home/scratch}
|
|
| 43 |
# check if scratch exist, create or complain |
|
| 44 |
if [[ -d "/scratch" ]] |
|
| 45 |
then |
|
| 46 |
mkdir -p ${SCRATCHDIR}
|
|
| 47 |
else |
|
| 48 |
echo "/scratch not found, cannot create ${SCRATCHDIR}"
|
|
| 49 |
fi |
|
| 50 |
|
|
| 51 |
# check if scratchdir is OK |
|
| 52 |
echo "ok" > ${SCRATCHDIR}/toto
|
|
| 53 |
Ok=$(cat ${SCRATCHDIR}/toto)
|
|
| 54 |
if [[ "${Ok}" != "ok" ]]
|
|
| 55 |
then |
|
| 56 |
# if scratch is unavailable, fallback to home |
|
| 57 |
CalcDir="${SGE_O_WORKDIR}/scratch"_${job}
|
|
| 58 |
else |
|
| 59 |
CalcDir=${SCRATCHDIR}_${job}
|
|
| 60 |
fi |
|
| 61 |
mkdir -p ${CalcDir}
|
|
| 62 |
|
|
| 63 |
# Gaussian specific ScratchDir |
|
| 64 |
export GAUSS_SCRDIR=${CalcDir}"/"${job}_$(date +%s)
|
|
| 65 |
mkdir -p ${GAUSS_SCRDIR}
|
|
| 66 |
|
|
| 67 |
Machine=$(hostname) |
|
| 68 |
|
|
| 69 |
# check if there is a chk or chk.gz |
|
| 70 |
# TODO/FIXME there's a problem here, watching the trace: if no chk, it create a .chk.chk |
|
| 71 |
NChk=$(grep -i "chk" ${job}.${ExtIn} | head -1 | sed 's/=/ /g' | awk '{print $2}')
|
|
| 72 |
NChk=$(basename ${NChk:-none} .chk).chk
|
|
| 73 |
if [[ -s ${HOMEDIR}/${NChk} ]]
|
|
| 74 |
then |
|
| 75 |
cp ${HOMEDIR}/${NChk} ${CalcDir}/${NChk}
|
|
| 76 |
fi |
|
| 77 |
if [[ -s ${HOMEDIR}/${NChk}.gz ]]
|
|
| 78 |
then |
|
| 79 |
cp ${HOMEDIR}/${NChk}.gz ${CalcDir}/${NChk}.gz
|
|
| 80 |
gunzip ${CalcDir}/${NChk}.gz
|
|
| 81 |
fi |
|
| 82 |
|
|
| 83 |
cp ${HOMEDIR}/${job}.${ExtIn} ${CalcDir}/
|
|
| 84 |
|
|
| 85 |
# prepare postprocess script |
|
| 86 |
# TODO/FIXME is this still usefull ? |
|
| 87 |
# - compress .chk |
|
| 88 |
# - copy chk from $SCRATCHDIR to $HOMEDIR |
|
| 89 |
# - cleanup $SCRATCHDIR |
|
| 90 |
# add exec mode on script |
|
| 91 |
echo "ssh ${SGE_O_LOGNAME}@${Machine} gzip ${CalcDir}/*.chk " > ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 92 |
echo "scp ${SGE_O_LOGNAME}@${Machine}:${CalcDir}/* ." > ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 93 |
echo "ssh ${SGE_O_LOGNAME}@${Machine} rm -fr ${CalcDir}" >> ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 94 |
echo "rm ${job}_${Machine}_CLEAN.${ExtOut}" >> ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 95 |
chmod u+x ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 96 |
|
|
| 97 |
# logrotate old logs |
|
| 98 |
if [[ -s ${HOMEDIR}/${job}.${ExtOut} ]]
|
|
| 99 |
then |
|
| 100 |
Ext=1 |
|
| 101 |
while [[ -s ${HOMEDIR}/${job}.${ExtOut}_${Ext} ]]
|
|
| 102 |
do |
|
| 103 |
let Ext=Ext+1 |
|
| 104 |
done |
|
| 105 |
mv ${HOMEDIR}/${job}.${ExtOut} ${HOMEDIR}/${job}.${ExtOut}_${Ext}
|
|
| 106 |
fi |
|
| 107 |
|
|
| 108 |
cd ${CalcDir}
|
|
| 109 |
ls -al |
|
| 110 |
|
|
| 111 |
echo "time ${Gaussian} < ${job}.${ExtIn} > ${HOMEDIR}/${job}.${ExtOut}"
|
|
| 112 |
|
|
| 113 |
/usr/bin/time ${Gaussian} < ${job}.${ExtIn} > ${HOMEDIR}/${job}.${ExtOut}
|
|
| 114 |
|
|
| 115 |
cp *.wfn ${HOMEDIR}/
|
|
| 116 |
|
|
| 117 |
if [[ -s ${NChk} ]]
|
|
| 118 |
then |
|
| 119 |
gzip -9 ${NChk}
|
|
| 120 |
cp ${NChk}.gz ${HOMEDIR}/
|
|
| 121 |
fi |
|
| 122 |
|
|
| 123 |
# final cleanup (commented during debug) |
|
| 124 |
#rm -r ${GAUSS_SCRDIR}
|
|
| 125 |
#rm -r ${CalcDir}
|
|
| 0 | 126 | |
| submit/crystal/sub_prop14.csh (revision 9) | ||
|---|---|---|
| 1 |
#!/bin/tcsh |
|
| 2 |
|
|
| 3 |
#$ -S /bin/tcsh |
|
| 4 |
#$ -N LTaBND11 |
|
| 5 |
#$ -pe openmp12 12 |
|
| 6 |
#$ -q x5650lin24ibA,x5650lin24ibB,x5650lin24ibC |
|
| 7 |
|
|
| 8 |
# version: $Id$ |
|
| 9 |
|
|
| 10 |
source /usr/share/modules/init/tcsh |
|
| 11 |
module use /applis/PSMN/Modules |
|
| 12 |
module load Base/psmn |
|
| 13 |
module load openmpi/1.6.4-intel-14.0.1 |
|
| 14 |
|
|
| 15 |
setenv HOMEDIR $SGE_O_WORKDIR |
|
| 16 |
cd $HOMEDIR |
|
| 17 |
|
|
| 18 |
set INPUT=MgO.d12 |
|
| 19 |
setenv CRY14_SCRDIR `echo $HOMEDIR | awk -F "/" '{$2="scratch"; for(j=2;j<=NF;j++) {printf("/%s",$j);} print ""} ' `/`basename $INPUT .d12`
|
|
| 20 |
/bin/mkdir -p $CRY14_SCRDIR |
|
| 21 |
|
|
| 22 |
setenv PREFIX /softs/openmpi-1.6.4-intel-14.0.1-debian7 |
|
| 23 |
setenv MPIRUN mpirun |
|
| 24 |
setenv HOSTFILE $TMPDIR/machines |
|
| 25 |
/bin/cat $TMPDIR/machines > $HOMEDIR/tmp |
|
| 26 |
|
|
| 27 |
#setenv OMP_NUM_THREADS 1 |
|
| 28 |
#setenv MKL_NUM_THREADS 1 |
|
| 29 |
/home/ssteinma/softs/crystal14/bin/runmpi14 $NSLOTS $INPUT |
|
| 30 |
/home/ssteinma/softs/crystal14/bin/runprop14 MgO MgO |
|
| 31 |
|
|
| 32 |
rm -fr $CRY14_SCRDIR |
|
| 0 | 33 | |
| submit/crystal/README.txt (revision 9) | ||
|---|---|---|
| 1 |
# README.txt |
|
| 2 |
# version: $Id$ |
|
| 3 |
|
|
| 4 |
According to Sigi (Sigismund MELISSEN) : |
|
| 5 |
TODO/FIXME: when translation OK, erase french version ? |
|
| 6 |
|
|
| 7 |
CRYSTAL14: je nomme mes fichiers input "input.d12" (instructions") et "input.gui" |
|
| 8 |
(la structure chimique dans les cas particuliers ou je interroge une structure déjà étudiée avec Crystal) |
|
| 9 |
et donc dans ce cas la il s'agit de calcul "LTaCHI1DS" (le "nom" du calcul) |
|
| 10 |
|
|
| 11 |
FIXME: english translation |
|
| 12 |
I name my inputs "input.d12" (instructions") and "input.gui" (chemical |
|
| 13 |
structure in the case of an "already studied with crystal" structure). |
|
| 14 |
Computation named "LTaCHI1DS" (-N sge instruction). |
|
| 15 |
|
|
| 16 |
=> use sub_crystal14.csh |
|
| 17 |
|
|
| 18 |
PROPERTIES: Il faut faire attention a "MgO", moi je nomme mes fichiers input "MgO.d3" |
|
| 19 |
(instructions) et "MgO.f9" (fonction d'onde) pour que ça tourne et donc |
|
| 20 |
"LTaBND11" c'est le nom de calcul particulier. |
|
| 21 |
|
|
| 22 |
FIXME: english translation |
|
| 23 |
Pay attention to "MgO". I name my input file "MgO.d3" (instructions) and |
|
| 24 |
"MgO.f9" (~fonction d'onde~) for properties to compute. |
|
| 25 |
Computation named "LTaBND11" (-N sge instruction). |
|
| 26 |
|
|
| 27 |
|
|
| 28 |
=> use sub_prop14.csh |
|
| 29 |
|
|
| 0 | 30 | |
| submit/crystal/sub_crystal14.csh (revision 9) | ||
|---|---|---|
| 1 |
#!/bin/tcsh |
|
| 2 |
|
|
| 3 |
#$ -S /bin/tcsh |
|
| 4 |
#$ -N LTaCH1DS |
|
| 5 |
#$ -q E5-2670deb64*,E5-2670deb128,E5-2670deb256B |
|
| 6 |
#$ -pe mpi16_debian 16 |
|
| 7 |
|
|
| 8 |
# version: $Id$ |
|
| 9 |
|
|
| 10 |
source /usr/share/modules/init/tcsh |
|
| 11 |
module use /applis/PSMN/Modules |
|
| 12 |
module load Base/psmn |
|
| 13 |
module load openmpi/1.6.4-intel-14.0.1 |
|
| 14 |
|
|
| 15 |
setenv HOMEDIR $SGE_O_WORKDIR |
|
| 16 |
cd $HOMEDIR |
|
| 17 |
|
|
| 18 |
set INPUT=input.d12 |
|
| 19 |
setenv CRY14_SCRDIR `echo $HOMEDIR | awk -F "/" '{$2="scratch"; for(j=2;j<=NF;j++) {printf("/%s",$j);} print ""} ' `/`basename $INPUT .d12`
|
|
| 20 |
/bin/mkdir -p $CRY14_SCRDIR |
|
| 21 |
|
|
| 22 |
setenv PREFIX /softs/openmpi-1.6.4-intel-14.0.1-debian7 |
|
| 23 |
setenv MPIRUN mpirun |
|
| 24 |
setenv HOSTFILE $TMPDIR/machines |
|
| 25 |
setenv hosts $HOMEDIR/hosts_`basename $INPUT .d12` |
|
| 26 |
#Too lazy to do a test, but the file needs to be refreshed! |
|
| 27 |
rm -f $hosts |
|
| 28 |
/bin/cat $TMPDIR/machines > $hosts |
|
| 29 |
setenv OMP_NUM_THREADS 1 |
|
| 30 |
setenv MKL_NUM_THREADS 1 |
|
| 31 |
/home/ssteinma/softs/crystal14/bin/runmpi14.t $NSLOTS $INPUT |
|
| 32 |
rm -fr $CRY14_SCRDIR |
|
| 33 |
rm $HOMEDIR/hosts_`basename $INPUT .d12 |
|
| 34 |
|
|
| 0 | 35 | |
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