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jmc |
1.1 |
#! /usr/bin/env bash |
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jmc |
1.4 |
# $Header: /u/gcmpack/MITgcm_contrib/test_scripts/nasa_ames/test_submit_pleiades,v 1.3 2018/11/07 23:10:02 jmc Exp $ |
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jmc |
1.1 |
# $Name: $ |
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today=`date +%Y%m%d` |
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dInWeek=`date +%a` |
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if test $# = 0 |
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then |
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TEST_LIST='ieee fast' |
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else |
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TEST_LIST=$* |
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fi |
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headNode=`hostname -s` |
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QSUB="/PBS/bin/qsub" |
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QSTAT="/PBS/bin/qstat -u $USER" |
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#dNam=$headNode |
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#QSUB="/usr/bin/sbatch" |
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#QLIST="/usr/bin/squeue -u $USER" |
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dNam='pleiades' |
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HERE="$HOME/test_${dNam}" |
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jmc |
1.4 |
TST_DISK="/nobackupp17/$USER" |
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jmc |
1.1 |
TST_DIR="$TST_DISK/test_${dNam}" |
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jmc |
1.2 |
tmpFil="/tmp/"`basename $0`".$$" |
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#- where local copy of code is (need to be consistent with run-job scripts): |
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srcDIR=$TST_DIR |
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srcCode="MITgcm_today" |
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jmc |
1.1 |
logPfix='test_submit' |
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SUB_DIR="$HERE/nasa_ames" |
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OUT_DIR="$HERE/output" |
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LOG_FIL="$OUT_DIR/$logPfix."`date +%m%d`".log" |
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#SUB_DIR="$HERE/temp" |
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#-- clean up old log files and start a new one: |
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cd $OUT_DIR |
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rm -f $logPfix.*.log_bak |
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if test -f $LOG_FIL ; then mv -f $LOG_FIL ${LOG_FIL}_bak ; fi |
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echo -n '-- Starting: ' | tee -a $LOG_FIL |
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date | tee -a $LOG_FIL |
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n=$(( `ls $logPfix.*.log | wc -l` - 10 )) |
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if test $n -gt 0 ; then |
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echo ' remove old log files:' | tee -a $LOG_FIL |
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ls -lt $logPfix.*.log | tail -"$n" | tee -a $LOG_FIL |
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ls -t $logPfix.*.log | tail -"$n" | xargs rm -f |
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fi |
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#------------------------------------------------------------- |
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# defaults |
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#export PATH="$PATH:/usr/local/bin" |
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if [ -d ~/bin ]; then export PATH=$PATH:~/bin ; fi |
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#- to get case insensitive "ls" (and order of tested experiments) |
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export LC_ALL="en_US.UTF-8" |
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# Turn off stack limit for FIZHI & AD-tests |
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#ulimit -s unlimited |
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if test -f /etc/profile.d/modules.sh ; then . /etc/profile.d/modules.sh ; fi |
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#- load standard modules: |
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#module add fedora slurm maui svante |
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#module add slurm |
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module list >> $LOG_FIL 2>&1 |
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#- method to acces CVS: |
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cmdCVS='cvs -d :pserver:cvsanon@mitgcm.org:/u/gcmpack -q' |
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jmc |
1.2 |
#- and which GitHub repository to use: |
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git_repo='MITgcm'; git_code='MITgcm' |
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#git_repo='altMITgcm'; #git_code='MITgcm66h' |
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jmc |
1.1 |
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checkOut=1 |
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jmc |
1.2 |
addExp='' |
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jmc |
1.1 |
updFile='updated_code' |
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jmc |
1.2 |
#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----| |
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if [ $checkOut -ge 1 ] ; then |
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#-- Download/Update reference version of MITgcm code: |
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jmc |
1.1 |
|
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jmc |
1.2 |
if test $srcDIR = $TST_DIR ; then |
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echo "cd $TST_DISK ; pwd (x2)" | tee -a $LOG_FIL |
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cd $TST_DISK | tee -a $LOG_FIL 2>&1 |
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pwd | tee -a $LOG_FIL |
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fi |
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if test ! -d $srcDIR ; then |
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echo -n "Creating a working dir: $srcDIR ..." | tee -a $LOG_FIL |
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#/bin/rm -rf $srcDIR |
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mkdir $srcDIR |
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retVal=$? |
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if test "x$retVal" != x0 ; then |
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echo "Error: unable to make dir: $srcDIR (err=$retVal ) --> Exit" | tee -a $LOG_FIL |
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exit 1 |
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fi |
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fi |
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cd $srcDIR |
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pwd | tee -a $LOG_FIL |
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jmc |
1.1 |
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jmc |
1.2 |
#- remove date/lock-file and old copy: |
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if test -f $updFile ; then rm -f $updFile ; sleep 2 ; fi |
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test -e $srcCode && rm -rf $srcCode |
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if [ $checkOut -eq 1 ] ; then |
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if test -e $git_code/.git/config ; then |
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echo -n "Updating current clone ( $git_code ) ..." | tee -a $LOG_FIL |
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echo '' >> $LOG_FIL |
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( cd $git_code ; git pull ) >> $LOG_FIL 2>&1 |
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retVal=$? |
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if test "x$retVal" != x0 ; then echo '' |
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echo "'git pull' on '"`hostname`"' fail (return val=$retVal) => exit" | tee -a $LOG_FIL |
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exit |
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else echo " done" | tee -a $LOG_FIL |
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fi |
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jmc |
1.3 |
echo " and checkout master:" | tee -a $LOG_FIL |
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( cd $git_code ; git checkout master -- . ) | tee -a $LOG_FIL |
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jmc |
1.2 |
else |
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echo "missing file: $git_code/.git/config => try a new clone" | tee -a $LOG_FIL |
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checkOut=2 |
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jmc |
1.1 |
fi |
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fi |
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jmc |
1.2 |
if [ $checkOut -eq 2 ] ; then |
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if test -e $git_code ; then |
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echo -n " removing dir: $git_code ..." | tee -a $LOG_FIL |
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rm -rf $git_code |
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echo " done" | tee -a $LOG_FIL |
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jmc |
1.1 |
fi |
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jmc |
1.2 |
echo -n "Make a clone of $git_code from repo: $git_repo ..." | tee -a $LOG_FIL |
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git clone https://github.com/$git_repo/${git_code}.git 2> $tmpFil |
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retVal=$? |
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if test $retVal = 0 ; then |
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echo ' --> done!' | tee -a $LOG_FIL |
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rm -f $tmpFil |
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else echo '' | tee -a $LOG_FIL |
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echo " Error: 'git clone' returned: $retVal" | tee -a $LOG_FIL |
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cat $tmpFil ; rm -f $tmpFil |
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exit 2 |
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jmc |
1.1 |
fi |
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jmc |
1.2 |
fi |
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#---- making a new working copy: MITgcm_today |
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rsync -a $git_code/ $srcCode --exclude '.git' |
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ls -ld $srcCode | tee -a $LOG_FIL |
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if test -d $srcCode/verification ; then |
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for exp2add in $addExp ; do |
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echo " add dir: $exp2add (from Contrib:verification_other)" | tee -a $LOG_FIL |
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( cd $srcCode/verification ; $cmdCVS co -P -d $exp2add \ |
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MITgcm_contrib/verification_other/$exp2add > /dev/null ) |
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done |
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fi |
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/usr/bin/find $srcCode -type d | xargs chmod g+rxs |
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/usr/bin/find $srcCode -type f | xargs chmod g+r |
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#- update date/lock-file: |
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if test -d $srcCode/verification ; then |
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echo $today > $updFile ; sleep 2 |
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ls -l $updFile | tee -a $LOG_FIL |
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echo '' | tee -a $LOG_FIL |
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fi |
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jmc |
1.1 |
|
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jmc |
1.2 |
#-- Done with Download/Update of MITgcm code |
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jmc |
1.1 |
fi |
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jmc |
1.2 |
#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----| |
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jmc |
1.1 |
|
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jmc |
1.2 |
#-- leave srcDIR and go back to output dir |
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jmc |
1.1 |
cd $OUT_DIR |
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#-- now really do something: |
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JOB_LIST=$TEST_LIST |
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NB_SUB_JOBS=0 |
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for i in $JOB_LIST |
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do |
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case $i in |
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'pgiAdm') sfx='pgi_adm' ;; |
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'pgiMth') sfx='pgi_mth' ;; |
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*) sfx=`echo ${i} | sed 's/MPI$/_mpi/'` ;; |
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esac |
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BATCH_SCRIPT="test_${dNam}_$sfx" |
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if test -f $SUB_DIR/$BATCH_SCRIPT ; then |
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#- job name ( $JOB ) & output-file name ( $JOB.std??? ) must match |
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# definition within $BATCH_SCRIPT slurm script |
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JOB="tst_${i}" |
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job_exist=`$QSTAT | grep $JOB | wc -l` |
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#sJob=`printf "%8.8s" $JOB` #- squeue truncate name to only 1rst 8c |
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#job_exist=`$QLIST | grep $sJob | wc -l` |
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if test "x_$job_exist" = x_0 ; then |
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#-- move previous output file |
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outList=`ls $JOB.std??? 2> /dev/null` |
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if test "x$outList" != x ; then |
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echo -n " moving job $JOB old output files:" | tee -a $LOG_FIL |
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if test -d $OUT_DIR/prev ; then |
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for xx in $outList ; do |
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pp=$OUT_DIR/prev/$xx ; echo -n " $xx" | tee -a $LOG_FIL |
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test -f $pp.sav && mv -f $pp.sav $pp.old |
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test -f $pp && mv -f $pp $pp.sav |
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chmod a+r $xx ; mv -f $xx $OUT_DIR/prev |
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done |
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echo " to dir ./prev" | tee -a $LOG_FIL |
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else |
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echo " <-- missing dir $OUT_DIR/prev" | tee -a $LOG_FIL |
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fi |
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else echo " no old output files from job '$JOB'" | tee -a $LOG_FIL |
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fi |
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#-- submit job |
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echo -n "--> $JOB : " | tee -a $LOG_FIL |
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$QSUB $SUB_DIR/$BATCH_SCRIPT | tee -a $LOG_FIL |
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NB_SUB_JOBS=`expr $NB_SUB_JOBS + 1` |
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else |
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echo "--> $JOB :" | tee -a $LOG_FIL |
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$QSTAT | grep $JOB | tee -a $LOG_FIL |
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#$QLIST | grep $sJob | tee -a $LOG_FIL |
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echo ' job already exist => skip this test' | tee -a $LOG_FIL |
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fi |
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else |
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echo 'no file:' $BATCH_SCRIPT 'to submit' | tee -a $LOG_FIL |
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fi |
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done |
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echo "info-sub-list: NB_SUB_JOBS='$NB_SUB_JOBS'" >> $LOG_FIL |
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echo -n '-- Finished at: ' | tee -a $LOG_FIL |
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date | tee -a $LOG_FIL |
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#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----| |
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exit 0 |
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