New script for parallel compuoting on SOLEIL Cluster

tracy/tools/lance_tracy3_parallel.sh

+#!/bin/sh
+# 04 February 2012, Laurent S. Nadolski, Synchrotron SOLEIL
+#Option pour voir les details
+#set -x
+
+if [ $# -ne 1 ]         # si le nombre de parametres n'est pas 1
+then                    # affiche l'usage
+    echo Tracy3 not valid
+    echo Missing paremeter file
+    echo Use: $0 parameterfile 
+    exit 1
+fi
+
+## create unique name for executable file
+NUM=`date '+%d%m%y%H%M%s'`
+DIR=$HOME/resultat_tracy/exe
+
+# take file name and remove .prm extension if exists
+INPUT_DIR=$PWD
+INPUT_FILE=$(basename $1 .prm).prm
+EXEC_DIR=/usr/local/applications/physmach/tracy3
+NOM=$EXEC_DIR/psoltracy3
+
+echo executable filename: $NOM
+echo input parameter filename: $INPUT_FILE
+
+JOB=psoltracy_script.$NUM
+
+#########################
+## creation du script PBS
+echo "#!/bin/bash
+#PBS -S /bin/bash
+#PBS -N ParallelTracy
+#PBS -j eo
+#PBS -l nodes=2:ppn=8
+#PBS -l mem=2000mb
+#PBS -l walltime=1000:00:00
+
+
+if [[ \$PBS_ENVIRONMENT = \"PBS_BATCH\" ]]; then 
+ echo PBS_BATCH
+ N=\`cat \$PBS_NODEFILE |wc -l\`
+ echo \" ============================\"
+ echo \"Execution on:\"
+ cat \$PBS_NODEFILE
+ echo \" ============================\"
+else 
+ echo \"Not a batch job !\"
+ exit
+fi
+
+# IMPORTANT : put here the absolute name of the executable 
+set -x
+
+## execute command
+
+echo executable filename: $NOM
+echo input parameter filename: $INPUT_DIR/$INPUT_FILE
+
+### va dans /tmpdir/PBS du noeud ou le job est execute
+cd \$TMPDIR
+cp $INPUT_DIR/$INPUT_FILE  .
+
+### Excecute job soltracy parallel version
+ulimit -s unlimited
+time mpirun -n \$N -f \$PBS_NODEFILE -r ssh $NOM $INPUT_FILE
+
+### SAVE THE RESULTS
+DIRSAVE=\$HOME/resultat_tracy
+mkdir -p \$DIRSAVE/result.\$PBS_JOBID
+mv *.prm \$DIRSAVE/result.\$PBS_JOBID
+mv [^0-9]*.out \$DIRSAVE/result.\$PBS_JOBID  #not save the individual file
+mv [^0-9]*.dat \$DIRSAVE/result.\$PBS_JOBID  #not save the individual file
+
+
+### email pour dire ou sont les resultats du job
+CMD=\"mail -s \\\"Job \$PBS_JOBID\\\" \"\`cat $HOME/.forward\`
+ssh isei \"\$CMD\" <<EOF
+Hello $USER,
+
+Work is done!
+
+Please check results in \$DIRSAVE/result.\$PBS_JOBID
+
+Hoping to see you again in our computation universe
+
+Your friend ISEI
+EOF
+" > $JOB
+
+## creation du script PBS
+#########################
+
+### launch PBS command
+qsub -v INPUT_FILE=$1  $JOB
+
+### clean up
+rm $JOB