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jmc |
1.1 |
#! /usr/bin/env bash |
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jmc |
1.5 |
# $Header: /u/gcmpack/MITgcm_contrib/test_scripts/svante/test_comp_pgiAdm.sh,v 1.4 2017/01/16 14:20:00 jmc Exp $ |
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jmc |
1.1 |
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# Test script for MITgcm to run on head-node of svante cluster (svante-login.mit.edu) |
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# to just generate source code (*.f) including TAF output src code. |
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headNode=`hostname -s` |
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#QSUB="qsub" |
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jmc |
1.2 |
#QSTAT="qstat -u $USER" |
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jmc |
1.1 |
#dNam=$headNode |
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QSUB="/usr/bin/sbatch" |
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jmc |
1.3 |
#QSTAT="/usr/bin/qstat -u $USER" |
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jmc |
1.4 |
QLIST="/usr/bin/squeue -u $USER" |
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jmc |
1.1 |
dNam='svante' |
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HERE="$HOME/test_${dNam}" |
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SUB_DIR="$HERE/$dNam" |
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OUT_DIR="$HERE/output" |
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TST_DISK="/net/fs09/d0/jm_c" |
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TST_DIR="$TST_DISK/test_${dNam}" |
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#SUB_DIR="$HERE/temp" |
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dInWeek=`date +%a` |
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TODAY=`date +%d` |
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#- main options |
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sfx='pgiAdm'; typ='-adm' |
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addExp='' |
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logPfix="test_comp_$sfx" |
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jmc |
1.3 |
BATCH_SCRIPT="run_tst_${sfx}.slurm" |
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#- job name ($JOB) & output-file name ( $JOB.std??? ) must match |
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# definition within $BATCH_SCRIPT slurm script |
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JOB="tst_$sfx" |
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sJob=`printf "%8.8s" $JOB` #- squeue truncate name to only 1rst 8c |
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jmc |
1.1 |
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#------------------------------- |
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# checkOut=2 : download new code ; |
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# =1 : update code (if no existing code -> swith to 2) |
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# =0 : use existing code (if no existing code -> swith to 2) |
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checkOut=1 |
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option= |
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#option="-nc" ; checkOut=1 |
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#option="-q" ; checkOut=0 |
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dAlt=`date +%d` ; dAlt=`expr $dAlt % 3` |
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if [ $dAlt -eq 1 ] ; then options="$options -fast" |
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else options="$options -devel" ; fi |
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#- defaults |
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umask 0022 |
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if [ -d ~/bin ]; then export PATH=$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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if test -f /etc/profile.d/zz_modules.sh ; then . /etc/profile.d/zz_modules.sh ; fi |
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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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#-- clean up old log files and start a new one: |
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LOG_FIL="$OUT_DIR/$logPfix."`date +%m%d`".log" |
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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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#- load standard modules: |
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module add slurm |
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#- load specific modules & set ENV variables: |
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module add pgi/16.9 |
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module add openmpi |
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module add netcdf |
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OPTFILE="../tools/build_options/linux_amd64_pgf77" |
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MPI=6 |
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#- needed for DIVA with MPI: |
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export MPI_INC_DIR="/home/software/pgi/16.9/linux86-64/2016/mpi/openmpi-1.10.2/include" |
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echo '======= modules =======================================' | tee -a $LOG_FIL |
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module list 2>&1 | tee -a $LOG_FIL |
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echo '=======================================================' | tee -a $LOG_FIL |
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dInWeek=`date +%a` |
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TODAY=`date +%d` |
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#tst_list='gads gadm gfo+rs gmpi gmth gmp2+rs ifc pgi' |
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#if test "x$dInWeek" = xSun ; then tst_list="$tst_list tlm oad" ; fi |
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tst_list='pgiAdm' |
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echo "cd $TST_DISK ; pwd (x2)" | tee -a $LOG_FIL |
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cd $TST_DISK 2>&1 | tee -a $LOG_FIL |
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pwd | tee -a $LOG_FIL |
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if test ! -d $TST_DIR ; then |
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echo -n "Creating a working dir: $TST_DIR ..." | tee -a $LOG_FIL |
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#/bin/rm -rf $TST_DIR |
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mkdir $TST_DIR |
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retVal=$? |
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if test "x$retVal" != x0 ; then |
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echo "Error: unable to make dir: $TST_DIR (err=$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 $TST_DIR |
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pwd | tee -a $LOG_FIL |
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#------------------------------------------------------------------------ |
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echo "================================================================" |
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gcmDIR="MITgcm_$sfx" |
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#- check day and time: |
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curDay=`date +%d` ; curHour=`date +%H` |
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if [ $curDay -ne $TODAY ] ; then |
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date ; echo "day is over => skip test $sfx" | tee -a $LOG_FIL |
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exit 2 |
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fi |
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if [ $curHour -ge 18 ] ; then |
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date ; echo "too late to run test $sfx" | tee -a $LOG_FIL |
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exit 2 |
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fi |
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#- check for unfinished jobs |
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jmc |
1.3 |
#job_exist=`$QSTAT | grep $JOB | wc -l` |
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job_exist=`$QLIST | grep $sJob | wc -l` |
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jmc |
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if test "x$job_exist" != x0 ; then |
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jmc |
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echo $BATCH_SCRIPT | tee -a $LOG_FIL |
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jmc |
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echo "job '$JOB' still in queue:" | tee -a $LOG_FIL |
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jmc |
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#$QSTAT | grep $JOB | tee -a $LOG_FIL |
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$QLIST | grep $sJob | tee -a $LOG_FIL |
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jmc |
1.1 |
echo " => skip this test" | tee -a $LOG_FIL |
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exit 2 |
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fi |
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jmc |
1.3 |
#-- move previous output file |
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outList=`( cd $OUT_DIR ; 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 $OUT_DIR/$xx ; mv -f $OUT_DIR/$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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jmc |
1.1 |
if test -d prev ; then |
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#-- save previous summary: tr_out.txt* tst_2+2_out.txt |
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oldS=`( cd ${gcmDIR}/verification ; ls t*_out.txt* ) 2> /dev/null` |
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for xx in $oldS ; do |
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#ss=`/bin/ls -l ${gcmDIR}/verification/$xx | awk '{print $6 $7}'` |
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ss=`/bin/ls -l --time-style=iso ${gcmDIR}/verification/$xx | awk '{print $6}'` |
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yy=`echo $xx | sed -e "s/\.txt.old/.$sfx.c/" \ |
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-e "s/2_out.txt/2.$sfx./" -e "s/\.txt/.$sfx.r/"` |
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cp -p ${gcmDIR}/verification/$xx prev/${yy}$ss |
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done |
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fi |
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#- clean and update code |
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if [ $checkOut -eq 1 ] ; then |
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if test -d $gcmDIR/CVS ; then |
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echo "cleaning output from $gcmDIR/verification :" | tee -a $LOG_FIL |
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#- remove previous output tar files and tar & remove previous output-dir |
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/bin/rm -f $gcmDIR/verification/??_${dNam}*_????????_?.tar.gz |
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( cd $gcmDIR/verification |
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listD=`ls -1 -d tr_${headNode}_????????_? ??_${dNam}-${sfx}_????????_? 2> /dev/null` |
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for dd in $listD |
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do |
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if test -d $dd ; then |
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tar -cf ${dd}".tar" $dd > /dev/null 2>&1 && gzip ${dd}".tar" && /bin/rm -rf $dd |
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retVal=$? |
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if test "x$retVal" != x0 ; then |
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echo "ERROR in tar+gzip prev outp-dir: $dd" |
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echo " on '"`hostname`"' (return val=$retVal) but continue" |
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fi |
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fi |
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done ) |
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# ( cd $gcmDIR/verification ; ../tools/do_tst_2+2 -clean ) >> $LOG_FIL 2>&1 |
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( cd $gcmDIR/verification ; ./testreport $typ -clean ) >> $LOG_FIL 2>&1 |
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echo "cvs update of dir $gcmDIR :" | tee -a $LOG_FIL |
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( cd $gcmDIR ; $cmdCVS update -P -d ) >> $LOG_FIL 2>&1 |
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retVal=$? |
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if test "x$retVal" != x0 ; then |
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echo "cvs update on '"`hostname`"' fail (return val=$retVal) => exit" |
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exit 3 |
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fi |
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else |
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echo "no dir: $gcmDIR/CVS => try a fresh check-out" | tee -a $LOG_FIL |
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checkOut=2 |
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fi |
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fi |
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#- download new code |
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if [ $checkOut -eq 2 ] ; then |
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test -e $gcmDIR && rm -rf $gcmDIR |
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echo -n "Downloading the MITgcm code using: $cmdCVS ..." | tee -a $LOG_FIL |
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$cmdCVS co -P -d $gcmDIR MITgcm > /dev/null |
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echo " done" | tee -a $LOG_FIL |
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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 $gcmDIR/verification ; $cmdCVS co -P -d $exp2add \ |
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MITgcm_contrib/verification_other/$exp2add > /dev/null 2>&1 ) |
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done |
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/usr/bin/find $gcmDIR -type d | xargs chmod g+rxs |
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/usr/bin/find $gcmDIR -type f | xargs chmod g+r |
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fi |
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#--------------------------------------------------- |
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#-- set the testreport command: |
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comm="./testreport $typ" |
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#-- run the testreport command: |
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echo -n "Running testreport using" | tee -a $LOG_FIL |
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if test $MPI != 0 ; then comm="$comm -MPI $MPI" ; fi |
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if test "x$options" != x ; then comm="$comm $options" ; fi |
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if test "x$OPTFILE" != x ; then |
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comm="$comm -of=$OPTFILE" |
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fi |
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jmc |
1.2 |
echo " option '-src' (only fortran source-files):" | tee -a $LOG_FIL |
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jmc |
1.1 |
comm="$comm -src" |
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echo " \"eval $comm\"" | tee -a $LOG_FIL |
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echo "======================" |
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( cd $gcmDIR/verification |
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eval $comm >> $LOG_FIL 2>&1 |
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) |
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#sed -n "/^An email /,/^======== End of testreport / p" $LOG_FIL |
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sed -n "/^No results email was sent/,/^======== End of testreport / p" $LOG_FIL |
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echo "" | tee -a $LOG_FIL |
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#-- submit SLURM script to run |
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jmc |
1.3 |
if test -e $SUB_DIR/$BATCH_SCRIPT ; then |
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echo " submit SLURM bach script '$SUB_DIR/$BATCH_SCRIPT'" | tee -a $LOG_FIL |
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$QSUB $SUB_DIR/$BATCH_SCRIPT | tee -a $LOG_FIL |
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echo " job '$JOB' in queue:" | tee -a $LOG_FIL |
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#$QSTAT | grep $JOB | tee -a $LOG_FIL |
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$QLIST | grep $sJob | tee -a $LOG_FIL |
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jmc |
1.1 |
else |
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jmc |
1.3 |
echo " no SLURM script '$SUB_DIR/$BATCH_SCRIPT' to submit" | tee -a $LOG_FIL |
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jmc |
1.1 |
continue |
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fi |
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