| 1 |
jmc |
1.1 |
#!/bin/bash |
| 2 |
jmc |
1.9 |
#SBATCH -J pgiMPI_tst |
| 3 |
jmc |
1.5 |
#SBATCH -p fdr |
| 4 |
jmc |
1.14 |
#SBATCH -t 23:30:00 |
| 5 |
jmc |
1.5 |
#SBATCH --mem-per-cpu 4000 |
| 6 |
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#SBATCH -N 1 |
| 7 |
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#SBATCH --tasks-per-node 6 |
| 8 |
jmc |
1.16 |
#SBATCH -x curly,larry,moe,shemp |
| 9 |
jmc |
1.9 |
#SBATCH -e /home/jm_c/test_svante/output/pgiMPI_tst.stderr |
| 10 |
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#SBATCH -o /home/jm_c/test_svante/output/pgiMPI_tst.stdout |
| 11 |
jmc |
1.7 |
#SBATCH --no-requeue |
| 12 |
jmc |
1.1 |
|
| 13 |
jmc |
1.17 |
# $Header: /u/gcmpack/MITgcm_contrib/test_scripts/svante/test_svante_pgi_mpi,v 1.16 2018/06/12 21:42:22 jmc Exp $ |
| 14 |
jmc |
1.1 |
# $Name: $ |
| 15 |
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| 16 |
jmc |
1.5 |
if test -f /etc/profile.d/modules.sh ; then . /etc/profile.d/modules.sh ; fi |
| 17 |
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if test -f /etc/profile.d/zz_modules.sh ; then . /etc/profile.d/zz_modules.sh ; fi |
| 18 |
jmc |
1.1 |
# Note: added "ulimit -s unlimited" in file "~/.bashrc" |
| 19 |
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# to pass big test (the 2 fizhi-cs-* test & adjoint tests) with MPI |
| 20 |
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| 21 |
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umask 0022 |
| 22 |
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#- to get case insensitive "ls" (and order of tested experiments) |
| 23 |
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export LC_ALL="en_US.UTF-8" |
| 24 |
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echo " running on: "`hostname` |
| 25 |
jmc |
1.6 |
headNode='svante-login' |
| 26 |
jmc |
1.1 |
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| 27 |
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dNam='svante' |
| 28 |
jmc |
1.2 |
HERE="$HOME/test_${dNam}" |
| 29 |
jmc |
1.1 |
OUTP="$HERE/output"; SavD="$HERE/send" |
| 30 |
jmc |
1.6 |
SEND="ssh $headNode $SavD/mpack" |
| 31 |
jmc |
1.15 |
#TST_DISK="/net/fs09/d1/jm_c" |
| 32 |
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TST_DISK="/scratch/jm_c" |
| 33 |
jmc |
1.2 |
TST_DIR="$TST_DISK/test_${dNam}" |
| 34 |
jmc |
1.14 |
#- where local copy of code is (need to be consistent with "test_submit_svante"): |
| 35 |
jmc |
1.15 |
#srcDIR='.' |
| 36 |
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srcDIR=$HERE |
| 37 |
jmc |
1.14 |
srcCode="MITgcm_today" |
| 38 |
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| 39 |
jmc |
1.17 |
#- following lines are not used here: |
| 40 |
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cmdCVS='cvs -d :pserver:cvsanon@mitgcm.org:/u/gcmpack -q' |
| 41 |
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#- which GitHub repository to use and how to access it: |
| 42 |
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git_repo='MITgcm'; git_code='MITgcm' ; git_other='verification_other' |
| 43 |
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#git_repo='altMITgcm'; #git_code='MITgcm66h' |
| 44 |
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#-- |
| 45 |
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git_repo="https://github.com/$git_repo" |
| 46 |
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#git_repo="git://github.com/$git_repo" |
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#git_repo="git@github.com:$git_repo" |
| 48 |
jmc |
1.1 |
|
| 49 |
jmc |
1.10 |
typ='' ; addExp='' ; skipExp='' |
| 50 |
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sfx='pgiMPI' |
| 51 |
jmc |
1.5 |
module add pgi/16.9 |
| 52 |
jmc |
1.1 |
module add openmpi |
| 53 |
jmc |
1.5 |
module add netcdf |
| 54 |
jmc |
1.1 |
OPTFILE="../tools/build_options/linux_amd64_pgf77" |
| 55 |
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#- needed for DIVA with MPI: |
| 56 |
jmc |
1.5 |
#export MPI_INC_DIR="/home/software/pgi/16.9/linux86-64/2016/mpi/openmpi-1.10.2/include" |
| 57 |
jmc |
1.1 |
options="$typ -MPI 6" |
| 58 |
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#- need this to get "staf": |
| 59 |
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#export PATH="$PATH:$HOME/bin" |
| 60 |
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| 61 |
jmc |
1.17 |
gcmDIR="MITgcm_$sfx" |
| 62 |
jmc |
1.1 |
dAlt=`date +%d` ; dAlt=`expr $dAlt % 3` |
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if [ $dAlt -eq 1 ] ; then options="$options -fast" |
| 64 |
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else options="$options -devel" ; fi |
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| 66 |
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checkOut=2 ; #options="$options -do" |
| 67 |
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#options="$options -nc" ; checkOut=1 |
| 68 |
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#options="$options -q" ; checkOut=0 |
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| 70 |
jmc |
1.17 |
echo "cd $TST_DISK ; pwd (x2)" |
| 71 |
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cd $TST_DISK |
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pwd |
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if test ! -d $TST_DIR ; then |
| 74 |
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echo -n "Creating a working dir: $TST_DIR ..." |
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#/bin/rm -rf $TST_DIR |
| 76 |
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mkdir $TST_DIR |
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retVal=$? |
| 78 |
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if test "x$retVal" != x0 ; then |
| 79 |
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echo "Error: unable to make dir: $TST_DIR (err=$retVal ) --> Exit" |
| 80 |
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exit 1 |
| 81 |
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fi |
| 82 |
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fi |
| 83 |
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echo "start from TST_DIR='$TST_DIR' at: "`date` |
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cd $TST_DIR |
| 85 |
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pwd |
| 86 |
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| 87 |
jmc |
1.5 |
NSLOTS=$SLURM_NTASKS |
| 88 |
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THEDATE=`date` |
| 89 |
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echo '********************************************************************************' |
| 90 |
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echo 'Start job '$THEDATE |
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echo 'NSLOTS = '$NSLOTS |
| 92 |
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echo '======= NODELIST ===============================================================' |
| 93 |
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echo $SLURM_NODELIST |
| 94 |
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cat /etc/redhat-release |
| 95 |
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echo '======= env ====================================================================' |
| 96 |
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env | grep SLURM |
| 97 |
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echo '======= modules ================================================================' |
| 98 |
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module list 2>&1 |
| 99 |
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echo '================================================================================' |
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jmc |
1.1 |
|
| 101 |
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#- check for disk space: relative space (99%) or absolute (10.G): |
| 102 |
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dsp=`df -P . | tail -1 | awk '{print $5}' | sed 's/%$//'` |
| 103 |
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if [ $dsp -gt 99 ] ; then |
| 104 |
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#dsp=`df -P . | tail -1 | awk '{print $4}'` |
| 105 |
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#if [ $dsp -le 100000000 ] ; then |
| 106 |
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echo 'Not enough space on this disk => do not run testreport.' |
| 107 |
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df . |
| 108 |
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exit |
| 109 |
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fi |
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jmc |
1.17 |
|
| 111 |
jmc |
1.1 |
if [ $checkOut -eq 1 ] ; then |
| 112 |
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echo "cleaning output from $gcmDIR/verification :" |
| 113 |
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#- remove previous output tar files and tar & remove previous output-dir |
| 114 |
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/bin/rm -f $gcmDIR/verification/??_${dNam}-${sfx}_????????_?.tar.gz |
| 115 |
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( cd $gcmDIR/verification |
| 116 |
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listD=`ls -1 -d ??_${dNam}-${sfx}_????????_? 2> /dev/null` |
| 117 |
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for dd in $listD |
| 118 |
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do |
| 119 |
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if test -d $dd ; then |
| 120 |
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tar -cf ${dd}".tar" $dd > /dev/null 2>&1 && gzip ${dd}".tar" && /bin/rm -rf $dd |
| 121 |
jmc |
1.14 |
retVal=$? |
| 122 |
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if test "x$retVal" != x0 ; then |
| 123 |
jmc |
1.1 |
echo "ERROR in tar+gzip prev outp-dir: $dd" |
| 124 |
jmc |
1.14 |
echo " on '"`hostname`"' (return val=$retVal) but continue" |
| 125 |
jmc |
1.1 |
fi |
| 126 |
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fi |
| 127 |
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done ) |
| 128 |
jmc |
1.17 |
echo "clean tst_2+2 + testreport output" |
| 129 |
jmc |
1.1 |
( cd $gcmDIR/verification ; ../tools/do_tst_2+2 -clean ) |
| 130 |
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( cd $gcmDIR/verification ; ./testreport $typ -clean ) |
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jmc |
1.17 |
if test "x$addExp" != x ; then |
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( cd $gcmDIR/verification |
| 133 |
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listD=`ls -o | grep '^l' | awk '{print $8}' 2> /dev/null` |
| 134 |
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echo " + remove local links: $listD" |
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/bin/rm -f $listD |
| 136 |
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) |
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fi |
| 138 |
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echo "Update $git_code code in dir $gcmDIR :" |
| 139 |
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( cd $gcmDIR ; git pull ) 2>&1 |
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jmc |
1.14 |
retVal=$? |
| 141 |
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if test "x$retVal" != x0 ; then |
| 142 |
jmc |
1.17 |
echo "git pull on '"`hostname`"' fail (return val=$retVal) => exit" |
| 143 |
jmc |
1.1 |
exit |
| 144 |
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fi |
| 145 |
jmc |
1.17 |
echo " and checkout master:" |
| 146 |
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( cd $gcmDIR ; git checkout master -- . ) 2>&1 |
| 147 |
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if test "x$addExp" != x ; then |
| 148 |
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echo "Update $git_other code in dir $gcmDIR/$git_other :" |
| 149 |
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( cd $gcmDIR/$git_other ; git pull ) 2>&1 |
| 150 |
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retVal=$? |
| 151 |
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if test "x$retVal" != x0 ; then |
| 152 |
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echo "git pull on '"`hostname`"' fail (return val=$retVal) => exit" |
| 153 |
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exit |
| 154 |
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fi |
| 155 |
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echo " and checkout master:" |
| 156 |
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( cd $gcmDIR/$git_other ; git checkout master -- . ) 2>&1 |
| 157 |
jmc |
1.1 |
fi |
| 158 |
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fi |
| 159 |
jmc |
1.17 |
|
| 160 |
jmc |
1.1 |
if [ $checkOut -eq 2 ] ; then |
| 161 |
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if test -e $gcmDIR ; then |
| 162 |
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echo -n "Removing working copy: $gcmDIR ..." |
| 163 |
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rm -rf $gcmDIR |
| 164 |
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echo " done" |
| 165 |
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fi |
| 166 |
jmc |
1.17 |
# make a local copy (instead of making a new clone): |
| 167 |
jmc |
1.1 |
today=`date +%Y%m%d` |
| 168 |
jmc |
1.14 |
nCount=0; updFile="${srcDIR}/updated_code" |
| 169 |
jmc |
1.1 |
updDate=0 ; test -f $updFile && updDate=`cat $updFile` |
| 170 |
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while [ $today -gt $updDate ] ; do |
| 171 |
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nCount=`expr $nCount + 1` |
| 172 |
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if [ $nCount -gt 40 ] ; then |
| 173 |
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echo " waiting too long (nCount=$nCount) for updated code" |
| 174 |
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echo " today=$today , updDate=$updDate " |
| 175 |
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ls -l $updFile |
| 176 |
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exit |
| 177 |
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fi |
| 178 |
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sleep 60 |
| 179 |
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updDate=0 ; test -f $updFile && updDate=`cat $updFile` |
| 180 |
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done |
| 181 |
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ls -l $updFile |
| 182 |
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echo " waited nCount=$nCount for updated code ($updDate) to copy" |
| 183 |
jmc |
1.14 |
if test -d $srcDIR/$srcCode ; then |
| 184 |
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echo -n "Make local copy of dir '$srcDIR/$srcCode' to: $gcmDIR ..." |
| 185 |
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cp -pra $srcDIR/$srcCode $gcmDIR |
| 186 |
jmc |
1.1 |
echo " done" |
| 187 |
jmc |
1.14 |
else echo " dir: $srcDIR/$srcCode missing => exit" ; exit ; fi |
| 188 |
jmc |
1.1 |
fi |
| 189 |
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| 190 |
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#- change dir to $gcmDIR/verification dir: |
| 191 |
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if test -e $gcmDIR/verification ; then |
| 192 |
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if [ $checkOut -lt 2 ] ; then |
| 193 |
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echo " dir $gcmDIR/verification exist" ; fi |
| 194 |
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cd $gcmDIR/verification |
| 195 |
jmc |
1.17 |
for exp2add in $addExp ; do |
| 196 |
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test -r $exp2add && /bin/rm -rf $exp2add |
| 197 |
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if test -d ../$git_other/$exp2add ; then |
| 198 |
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echo " add $exp2add link from $git_other" |
| 199 |
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ln -s ../$git_other/$exp2add . |
| 200 |
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if test $exp2add = 'global_oce_cs32' ; then |
| 201 |
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echo " link dir 'other_input/core2_cnyf' in here" |
| 202 |
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( cd ../${git_other}/${exp2add} |
| 203 |
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test -L core2_cnyf && /bin/rm -f core2_cnyf |
| 204 |
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ln -s ../../../other_input/core2_cnyf . ) |
| 205 |
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fi |
| 206 |
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if test $exp2add = 'global_oce_llc90' ; then |
| 207 |
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echo " link dir 'other_input/gael_oce_llc90_input' to 'input_fields'" |
| 208 |
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( cd ../${git_other}/${exp2add} |
| 209 |
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test -L input_fields && /bin/rm -f input_fields |
| 210 |
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ln -s ../../../other_input/gael_oce_llc90_input input_fields |
| 211 |
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echo " link dirs: 'core2_cnyf' & 'global_oce_input_fields/*' in input_verifs" |
| 212 |
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test ! -e input_verifs && mkdir input_verifs |
| 213 |
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( cd input_verifs ; /bin/rm -f * |
| 214 |
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ln -s ../../../../other_input/core2_cnyf . |
| 215 |
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ln -s ../../../../other_input/global_oce_input_fields/* . ) |
| 216 |
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) |
| 217 |
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fi |
| 218 |
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else |
| 219 |
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echo " missing dir: $git_other/$exp2add" |
| 220 |
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continue |
| 221 |
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fi |
| 222 |
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done |
| 223 |
jmc |
1.1 |
else |
| 224 |
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echo "no dir: $gcmDIR/verification => exit" |
| 225 |
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exit |
| 226 |
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fi |
| 227 |
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| 228 |
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echo '' |
| 229 |
jmc |
1.10 |
echo ./testreport $options -of $OPTFILE -skd \'$skipExp\' \ |
| 230 |
jmc |
1.13 |
-odir ${dNam}-$sfx -send \'$SEND\' -sd $SavD -a jm_c@mitgcm.org |
| 231 |
jmc |
1.10 |
./testreport $options -of $OPTFILE -skd "$skipExp" \ |
| 232 |
jmc |
1.13 |
-odir ${dNam}-$sfx -send "$SEND" -sd $SavD -a jm_c@mitgcm.org |
| 233 |
jmc |
1.1 |
|
| 234 |
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echo '' |
| 235 |
jmc |
1.10 |
echo ../tools/do_tst_2+2 -mpi \ |
| 236 |
jmc |
1.13 |
-o ${dNam}-$sfx -send \'$SEND\' -sd $SavD -a jm_c@mitgcm.org |
| 237 |
jmc |
1.10 |
../tools/do_tst_2+2 -mpi \ |
| 238 |
jmc |
1.13 |
-o ${dNam}-$sfx -send "$SEND" -sd $SavD -a jm_c@mitgcm.org |
| 239 |
jmc |
1.1 |
|
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