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#!/bin/bash -e |
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# new script for running testreport on ollie.awi.de |
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# - compile and run on compute nodes |
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# - use ssh to call mpack command from the head node ollie0 |
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#$Header: /u/gcmpack/MITgcm_contrib/test_scripts/ollie/mitgcmtestreport_cray,v 1.9 2018/04/16 08:35:39 mlosch Exp $ |
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#$Name: $ |
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|
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# needed for cron-job |
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#source /usr/Modules/current/init/bash |
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source /etc/profile.d/cray_pe.sh |
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# this seems to be enough to make the module cmd work |
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source /etc/profile.d/modules.sh |
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# |
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module purge |
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module load PrgEnv-cray |
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module load netcdf |
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# set the netcdf root directory here, because the definitions always |
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# change with different "default" netcdf modules |
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export NETCDF_ROOT=`nc-config --prefix` |
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# not sure why I have to set these paths here again |
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export MPI_ROOT=$(dirname $(dirname `which mpicc`)) |
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# $(dirname `echo $LD_LIBRARY_PATH | awk -F: '{print $1}'`) |
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export MPI_INC_DIR=${MPI_ROOT}/include |
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|
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# there is no slurm module anymore and this is the current recommendation to |
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# have sbatch in your path (rather than running /etc/profile.d./slurm.sh) |
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export PATH=${PATH}:/global/opt/slurm/default/bin |
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|
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dNam='ollie' |
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TST_DIR="/work/ollie/mlosch/test_$dNam" |
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echo "start from TST_DIR='$TST_DIR' at: "`date` |
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|
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umask 0022 |
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|
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sfx='cray' |
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RUNIT="runit_"$sfx |
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|
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OPTFILE=../tools/build_options/linux_ia64_${sfx}_ollie |
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options="-MPI 6" |
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options="$options -odir ${dNam}-c" |
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options="$options -j 6" |
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#options="$options -t global_ocean.cs32x15" |
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|
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#EXE='srun --mpi=pmi2 -n TR_NPROC ./mitgcmuv' |
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#EXE='srun -n TR_NPROC ./mitgcmuv' |
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EXE='srun -n TR_NPROC --cpu_bind=cores ./mitgcmuv' |
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|
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if [ -e $TST_DIR ]; then |
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echo "$TST_DIR exists" |
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else |
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mkdir $TST_DIR |
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fi |
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cd $TST_DIR |
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HERE=$TST_DIR/output |
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if [ -e $HERE ]; then |
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echo "$HERE" |
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else |
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mkdir $HERE |
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fi |
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OUTFILE=$HERE/slurm_${sfx}.out |
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MYOUTPUT=$HERE/out_$sfx |
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if [ -e $MYOUTPUT ]; then |
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rm -rf $MYOUTPUT |
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fi |
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if [ -e $OUTFILE ]; then |
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rm -r $OUTFILE |
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fi |
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gcmDIR="MITgcm_${sfx}" |
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git_repo='MITgcm' |
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git_code='MITgcm' |
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|
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# checkOut determines how much checking out is being done |
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# checkOut = 3: new clone from GitHub and make a new copy |
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# checkOut = 2: update (git pull) existing repo and make a new copy |
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# checkOut = 1: skip update |
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# checkOut = 0: use existing test code (if available otherwise switch to 1) |
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|
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checkOut=2 |
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tdir=${TST_DIR} |
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today=`date +%Y%m%d` |
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TODAY=`date +%d` |
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#tmpFil="/tmp/"`basename $0`".$$" |
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tmpFil=$TST_DIR/error.out |
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|
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if [ $checkOut -le 1 ] ; then |
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if test -e $TST_DIR/${gcmDIR}/doc ; then |
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echo $TST_DIR/${gcmDIR}/doc 'exist' |
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else |
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echo -n "$TST_DIR/${gcmDIR} missing ; " |
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checkOut=2 |
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echo "will make a new copy ( checkOut=$checkOut )" |
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fi |
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fi |
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|
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if [ $checkOut -ge 2 ] ; then |
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#---- cleaning: |
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cd $TST_DIR |
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|
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#---- Make a new clone or update existing one: |
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if test -e ${gcmDIR}/.git/config ; then |
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echo "${gcmDIR}/.git/config exist" |
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else |
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echo -n "${gcmDIR}/.git/config missing ; " |
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checkOut=3 |
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echo "will get new clone ( checkOut=$checkOut )" |
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fi |
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if [ $checkOut -eq 3 ] ; then |
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echo -n "Removing old clone: $TST_DIR/${gcmDIR} ..." |
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test -e $TST_DIR/${gcmDIR} && rm -rf $TST_DIR/${gcmDIR} |
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echo " done" |
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echo -n "Make a new clone of $git_code from repo: $git_repo ..." |
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git clone https://github.com/$git_repo/${git_code}.git ${gcmDIR} 2> $tmpFil |
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retVal=$? |
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if test $retVal = 0 ; then |
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echo ' --> done!' |
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rm -f $tmpFil |
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else |
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echo " Error: 'git clone' returned: $retVal" |
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cat $tmpFil |
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rm -f $tmpFil |
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exit 2 |
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fi |
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else |
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# echo "clean tst_2+2 + testreport output" |
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( cd $gcmDIR/verification ; ../tools/do_tst_2+2 -clean ) |
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( cd $gcmDIR/verification ; ./testreport -clean ) |
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echo "Updating current clone ( $git_code ) ..." |
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( cd ${gcmDIR}; git checkout master ; git pull ; git ls-files -d | xargs git checkout -- ) |
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echo ' --> done!' |
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fi |
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else |
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cd $TST_DIR |
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fi |
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|
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cd ${TST_DIR}/${gcmDIR}/verification |
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|
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cwd=\`pwd\` |
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SENDCMD="ssh ollie0 ${TST_DIR}/${gcmDIR}/tools/mpack-1.6/mpack" |
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runtestreport="./testreport $options -of $OPTFILE -command \"${EXE}\" -send \"${SENDCMD}\" -sd ${cwd}" |
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emailaddress="-a jm_c@mitgcm.org" |
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testrestart="../tools/do_tst_2+2 -mpi -exe \"${EXE}\" -o ${dNam}-c -send \"${SENDCMD}\" -sd ${cwd}" |
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|
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if [ ! -e $MYOUTPUT ] |
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then |
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touch $MYOUTPUT |
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fi |
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|
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# echo "running testreport like this:" |
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# echo ${runtestreport} -norun |
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# eval "${runtestreport} -norun >> $MYOUTPUT 2>&1" |
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|
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# create batch script |
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# |
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JOBNAME=tst$sfx |
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echo "creating batch script $HERE/$RUNIT" |
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cat << EOF >| $HERE/$RUNIT |
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#!/bin/bash |
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#SBATCH --job-name=${JOBNAME} |
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#SBATCH -o ${OUTFILE} |
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#SBATCH --time=12:00:00 |
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#SBATCH --ntasks=6 |
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|
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# still need this to be able to run a few experiments: |
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# cfc_example, fizhi, tutorial_deep_convection |
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ulimit -s unlimited |
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|
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# binds OpenMP task to given cores |
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export OMP_PROC_BIND=TRUE |
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|
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# for debugging |
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# export FLEXLM_DIAGNOSTICS=2 |
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# export FNP_IP_ENV=1 |
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# export LM_A_CONN_TIMEOUT=99 |
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|
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cd \${SLURM_SUBMIT_DIR} |
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|
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cwd=`pwd` |
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echo "running testreport like this in \${cwd}:" |
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echo "${runtestreport} -devel -match 10" |
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${runtestreport} -devel -match 10 ${emailaddress} >> $MYOUTPUT 2>&1 |
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|
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echo "running testreport like this in \${cwd}:" |
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echo "./testreport -clean" |
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./testreport -clean |
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|
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# Hack,hack,hack to avoid running dome: |
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rm -f dome/results/output.txt |
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echo "running testreport like this in \${cwd}:" |
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echo "${runtestreport} -fast -match 10" |
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${runtestreport} -fast -match 10 ${emailaddress} >> $MYOUTPUT 2>&1 |
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|
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echo "running restart test like this in \${cwd}:" |
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echo "${testrestart}" |
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${testrestart} ${emailaddress} >> $MYOUTPUT 2>&1 |
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|
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EOF |
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|
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chmod a+x $HERE/$RUNIT |
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|
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echo " " >> $MYOUTPUT |
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echo "***********************************************************" >> $MYOUTPUT |
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echo "Submitting this job script:" >> $MYOUTPUT |
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echo "***********************************************************" >> $MYOUTPUT |
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cat $HERE/$RUNIT >> $MYOUTPUT |
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echo "***********************************************************" >> $MYOUTPUT |
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echo "end of job script" >> $MYOUTPUT |
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echo "***********************************************************" >> $MYOUTPUT |
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echo " " >> $MYOUTPUT |
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|
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echo "sbatch $HERE/$RUNIT" |
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sbatch $HERE/$RUNIT |
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|
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# # keep looking for the job in the job queues and wait until it has disappeared |
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# jobruns=somedummy |
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# while [ "${jobruns}"x != x ] |
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# do |
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# sleep 200 |
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# jobruns=`squeue --noheader -u mlosch | grep "$JOBNAME" | awk '{print $1}'` |
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# echo "waiting for job ${jobruns%% *} ($JOBNAME) to complete" |
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# currentexp=`grep Experiment $MYOUTPUT | tail -1` |
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# echo "currently running $currentexp" |
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# done |
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|
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# # workaround for mailing the stuff |
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# echo "mail the stuff" |
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|
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# MPACKCMD=../tools/mpack-1.6/mpack |
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# fn=`ls -dtr tr_$dNam* | grep -v tar.gz | tail -1` |
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# echo "fname ${fn}" |
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# tar cf - $fn | gzip > "${fn}.tar.gz" |
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# $MPACKCMD -s MITgcm-test -m 3555000 ${fn}.tar.gz jm_c@mitgcm.org |
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# sleep 2 |
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# rm -rf "${fn}.tar.gz" |
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|
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echo "end of mitgcmtestreport" |
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