| 1 |
jmc |
1.1 |
#!/bin/bash |
| 2 |
jmc |
1.9 |
#SBATCH -J ifcMpi_tst |
| 3 |
jmc |
1.1 |
#SBATCH -p sched_mit_hill |
| 4 |
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#SBATCH --mem-per-cpu 4000 |
| 5 |
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#SBATCH -N 2 |
| 6 |
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#SBATCH --tasks-per-node 4 |
| 7 |
jmc |
1.9 |
#SBATCH -e /home/jm_c/test_engaging/output/ifcMpi_tst.stderr |
| 8 |
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#SBATCH -o /home/jm_c/test_engaging/output/ifcMpi_tst.stdout |
| 9 |
jmc |
1.1 |
#SBATCH --no-requeue --constraint=centos6 |
| 10 |
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| 11 |
jmc |
1.14 |
# $Header: /u/gcmpack/MITgcm_contrib/test_scripts/engaging/test_engag_ifc_mpi,v 1.13 2019/06/27 22:26:36 jmc Exp $ |
| 12 |
jmc |
1.1 |
# $Name: $ |
| 13 |
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| 14 |
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if test -f /etc/profile.d/modules.sh ; then |
| 15 |
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. /etc/profile.d/modules.sh |
| 16 |
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fi |
| 17 |
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# Note: added "ulimit -s unlimited" in file "~/.bashrc" |
| 18 |
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# to pass big test (the 2 fizhi-cs-* test & adjoint tests) with MPI |
| 19 |
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| 20 |
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umask 0022 |
| 21 |
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#- to get case insensitive "ls" (and order of tested experiments) |
| 22 |
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export LC_ALL="en_US.UTF-8" |
| 23 |
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echo " running on: "`hostname` |
| 24 |
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| 25 |
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dNam='engaging' |
| 26 |
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HERE="$HOME/test_$dNam" |
| 27 |
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OUTP="$HERE/output"; SavD="$HERE/send" |
| 28 |
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SEND="ssh eofe4 $SavD/mpack" |
| 29 |
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TST_DIR="/pool001/jm_c/test_$dNam" |
| 30 |
jmc |
1.7 |
tmpFil="/tmp/"`basename $0`".$$" |
| 31 |
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cmdCVS='cvs -d :pserver:cvsanon@mitgcm.org:/u/gcmpack -q' |
| 32 |
jmc |
1.9 |
#- which GitHub repository to use and how to access it: |
| 33 |
jmc |
1.10 |
git_repo='MITgcm'; git_code='MITgcm' ; git_other='verification_other' |
| 34 |
jmc |
1.7 |
#git_repo='altMITgcm'; #git_code='MITgcm66h' |
| 35 |
jmc |
1.9 |
#-- |
| 36 |
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git_repo="https://github.com/$git_repo" |
| 37 |
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#git_repo="git://github.com/$git_repo" |
| 38 |
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#git_repo="git@github.com:$git_repo" |
| 39 |
jmc |
1.1 |
|
| 40 |
jmc |
1.2 |
typ='' ; addExp='' ; skipExp='' |
| 41 |
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sfx='ifcMpi' |
| 42 |
jmc |
1.1 |
addExp='global_oce_cs32 global_oce_llc90' |
| 43 |
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module add slurm |
| 44 |
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module add gcc |
| 45 |
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module add engaging/intel/2013.1.046 |
| 46 |
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#export MPI_INC_DIR="$MPI_HOME/include" |
| 47 |
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OPTFILE="../tools/build_options/linux_amd64_ifort+impi" |
| 48 |
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mpiCMD="mpirun -env I_MPI_DEBUG 2 -n TR_NPROC ./mitgcmuv" #- currently not used |
| 49 |
jmc |
1.4 |
options="$typ -MPI 8" |
| 50 |
jmc |
1.5 |
#options="-j 4 $options" |
| 51 |
jmc |
1.1 |
#export OMP_NUM_THREADS=2 |
| 52 |
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#export KMP_SLAVE_STACK_SIZE=400m |
| 53 |
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#options="$options -gsl" |
| 54 |
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#export GSL_IEEE_MODE=double-precision,mask-underflow,mask-denormalized |
| 55 |
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ulimit -s unlimited |
| 56 |
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#- need this to get "staf" & "do_make_syntax.sh": |
| 57 |
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export PATH="$PATH:$HOME/bin" |
| 58 |
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| 59 |
jmc |
1.7 |
gcmDIR="MITgcm_$sfx" |
| 60 |
jmc |
1.1 |
dAlt=`date +%d` ; dAlt=`expr $dAlt % 3` |
| 61 |
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if [ $dAlt -eq 1 ] ; then options="$options -ur4 -match 5" ; fi |
| 62 |
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options="$options -devel" |
| 63 |
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| 64 |
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checkOut=1 ; #options="$options -do" |
| 65 |
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#options="$options -nc" ; checkOut=1 |
| 66 |
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#options="$options -q" ; checkOut=0 |
| 67 |
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| 68 |
jmc |
1.7 |
if test -d $TST_DIR ; then |
| 69 |
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echo "start from TST_DIR='$TST_DIR' at: "`date` |
| 70 |
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else |
| 71 |
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#if test ! -d $TST_DIR ; then mkdir $TST_DIR ; fi |
| 72 |
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#if test ! -d $TST_DIR ; then |
| 73 |
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# echo "ERROR: Can't create directory \"$TST_DIR\"" |
| 74 |
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# exit 1 |
| 75 |
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#fi |
| 76 |
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#echo "start in new dir TST_DIR='$TST_DIR' at: "`date` |
| 77 |
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echo "ERROR: missing directory \"$TST_DIR\"" |
| 78 |
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exit 1 |
| 79 |
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fi |
| 80 |
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cd $TST_DIR |
| 81 |
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pwd |
| 82 |
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| 83 |
jmc |
1.1 |
NSLOTS=$SLURM_NTASKS |
| 84 |
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THEDATE=`date` |
| 85 |
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echo '********************************************************************************' |
| 86 |
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echo 'Start job '$THEDATE |
| 87 |
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echo 'NSLOTS = '$NSLOTS |
| 88 |
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echo '======= NODELIST ===============================================================' |
| 89 |
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echo $SLURM_NODELIST |
| 90 |
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cat /etc/redhat-release |
| 91 |
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echo '======= env ====================================================================' |
| 92 |
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env | grep SLURM |
| 93 |
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echo '======= modules ================================================================' |
| 94 |
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module list 2>&1 |
| 95 |
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echo '================================================================================' |
| 96 |
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| 97 |
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#- |
| 98 |
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MPI_MFile="${OUTP}/mf_${sfx}" #- currently not used |
| 99 |
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#mpiCMD="mpirun -hostfile TR_MFILE -n TR_NPROC ./mitgcmuv" |
| 100 |
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#- make the testreport MPI_MFILE: |
| 101 |
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listNODES=`echo $SLURM_NODELIST | sed -e 's/\[/ /' -e 's/\]//' -e 's/,/ /' -e 's/-/ /'` |
| 102 |
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# duplicate the 2 listed nodes into a 6 list file: |
| 103 |
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/bin/rm -f $MPI_MFile ; touch $MPI_MFile |
| 104 |
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for nc in `seq 1 4` ; do pfx='' |
| 105 |
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for nd in $listNODES ; do |
| 106 |
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if test "x$pfx" = x ; then pfx=$nd ; else |
| 107 |
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echo "${pfx}${nd}" >> $MPI_MFile |
| 108 |
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fi |
| 109 |
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done |
| 110 |
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done |
| 111 |
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| 112 |
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#- check for disk space: relative space (99%) or absolute (10.G): |
| 113 |
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dsp=`df -P . | tail -1 | awk '{print $5}' | sed 's/%$//'` |
| 114 |
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if [ $dsp -gt 99 ] ; then |
| 115 |
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#dsp=`df -P . | tail -1 | awk '{print $4}'` |
| 116 |
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#if [ $dsp -le 100000000 ] ; then |
| 117 |
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echo 'Not enough space on this disk => do not run testreport.' |
| 118 |
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df . |
| 119 |
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exit |
| 120 |
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fi |
| 121 |
jmc |
1.10 |
|
| 122 |
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if [ $checkOut -eq 1 ] ; then |
| 123 |
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if test ! -e $gcmDIR/.git/config ; then |
| 124 |
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echo "no file: $gcmDIR/.git/config => try to download a fresh clone" |
| 125 |
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checkOut=2 |
| 126 |
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fi |
| 127 |
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if test "x$addExp" != x ; then |
| 128 |
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if test ! -e $gcmDIR/$git_other/.git/config ; then |
| 129 |
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echo "no file: $gcmDIR/$git_other/.git/config => try a fresh clone" |
| 130 |
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checkOut=2 |
| 131 |
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fi |
| 132 |
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fi |
| 133 |
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fi |
| 134 |
jmc |
1.1 |
if [ $checkOut -eq 1 ] ; then |
| 135 |
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echo "cleaning output from $gcmDIR/verification :" |
| 136 |
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#- remove previous output tar files and tar & remove previous output-dir |
| 137 |
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/bin/rm -f $gcmDIR/verification/??_${dNam}-${sfx}_????????_?.tar.gz |
| 138 |
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( cd $gcmDIR/verification |
| 139 |
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listD=`ls -1 -d ??_${dNam}-${sfx}_????????_? 2> /dev/null` |
| 140 |
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for dd in $listD |
| 141 |
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do |
| 142 |
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if test -d $dd ; then |
| 143 |
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tar -cf ${dd}".tar" $dd > /dev/null 2>&1 && gzip ${dd}".tar" && /bin/rm -rf $dd |
| 144 |
jmc |
1.7 |
retVal=$? |
| 145 |
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if test "x$retVal" != x0 ; then |
| 146 |
jmc |
1.1 |
echo "ERROR in tar+gzip prev outp-dir: $dd" |
| 147 |
jmc |
1.7 |
echo " on '"`hostname`"' (return val=$retVal) but continue" |
| 148 |
jmc |
1.1 |
fi |
| 149 |
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fi |
| 150 |
|
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done ) |
| 151 |
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echo "clean tst_2+2 + testreport output (+ Makefile_syntax files)" |
| 152 |
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( cd $gcmDIR/verification ; ../tools/do_tst_2+2 -clean ) |
| 153 |
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( cd $gcmDIR/verification ; ./testreport $typ -clean ) |
| 154 |
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( cd $gcmDIR/verification ; rm -f */build/Makefile_syntax ) |
| 155 |
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( cd $gcmDIR/verification ; rm -f */build/port_rand.i */build/ptracers_set_iolabel.i ) |
| 156 |
jmc |
1.10 |
if test "x$addExp" != x ; then |
| 157 |
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( cd $gcmDIR/verification |
| 158 |
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listD=`ls -o | grep '^l' | awk '{print $8}' 2> /dev/null` |
| 159 |
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echo " + remove local links: $listD" |
| 160 |
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/bin/rm -f $listD |
| 161 |
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) |
| 162 |
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fi |
| 163 |
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echo "Update $git_code code in dir $gcmDIR :" |
| 164 |
jmc |
1.12 |
( cd $gcmDIR ; git pull ) 2>&1 |
| 165 |
jmc |
1.7 |
retVal=$? |
| 166 |
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if test "x$retVal" != x0 ; then |
| 167 |
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echo "git pull on '"`hostname`"' fail (return val=$retVal) => exit" |
| 168 |
jmc |
1.1 |
exit |
| 169 |
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fi |
| 170 |
jmc |
1.12 |
echo " and checkout master:" |
| 171 |
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( cd $gcmDIR ; git checkout master -- . ) 2>&1 |
| 172 |
jmc |
1.10 |
if test "x$addExp" != x ; then |
| 173 |
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echo "Update $git_other code in dir $gcmDIR/$git_other :" |
| 174 |
jmc |
1.12 |
( cd $gcmDIR/$git_other ; git pull ) 2>&1 |
| 175 |
jmc |
1.10 |
retVal=$? |
| 176 |
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if test "x$retVal" != x0 ; then |
| 177 |
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echo "git pull on '"`hostname`"' fail (return val=$retVal) => exit" |
| 178 |
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exit |
| 179 |
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fi |
| 180 |
jmc |
1.12 |
echo " and checkout master:" |
| 181 |
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( cd $gcmDIR/$git_other ; git checkout master -- . ) 2>&1 |
| 182 |
jmc |
1.1 |
fi |
| 183 |
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fi |
| 184 |
jmc |
1.10 |
|
| 185 |
jmc |
1.1 |
if [ $checkOut -eq 2 ] ; then |
| 186 |
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if test -e $gcmDIR ; then |
| 187 |
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echo -n "Removing working copy: $gcmDIR ..." |
| 188 |
|
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rm -rf $gcmDIR |
| 189 |
|
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echo " done" |
| 190 |
|
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fi |
| 191 |
jmc |
1.10 |
echo "Make a clone of $git_code from repo: $git_repo ..." |
| 192 |
jmc |
1.9 |
git clone $git_repo/${git_code}.git $gcmDIR 2> $tmpFil |
| 193 |
jmc |
1.7 |
retVal=$? |
| 194 |
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if test $retVal = 0 ; then |
| 195 |
|
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echo ' done' ; rm -f $tmpFil |
| 196 |
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else |
| 197 |
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echo " Error: 'git clone' returned: $retVal" |
| 198 |
|
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cat $tmpFil ; rm -f $tmpFil |
| 199 |
jmc |
1.1 |
exit |
| 200 |
jmc |
1.7 |
fi |
| 201 |
jmc |
1.10 |
if test "x$addExp" != x ; then |
| 202 |
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echo "Make a clone of $git_other from repo: $git_repo ..." |
| 203 |
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( cd $gcmDIR ; git clone $git_repo/${git_other}.git 2> $tmpFil ) |
| 204 |
|
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retVal=$? |
| 205 |
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if test $retVal = 0 ; then |
| 206 |
|
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echo ' done' ; rm -f $tmpFil |
| 207 |
|
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else |
| 208 |
|
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echo " Error: 'git clone' returned: $retVal" |
| 209 |
|
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cat $tmpFil ; rm -f $tmpFil |
| 210 |
|
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exit |
| 211 |
|
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fi |
| 212 |
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fi |
| 213 |
jmc |
1.1 |
if test -d $gcmDIR/verification ; then |
| 214 |
|
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/usr/bin/find $gcmDIR -type d | xargs chmod g+rxs |
| 215 |
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/usr/bin/find $gcmDIR -type f | xargs chmod g+r |
| 216 |
|
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fi |
| 217 |
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fi |
| 218 |
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| 219 |
jmc |
1.14 |
#- change dir to $gcmDIR/verification + add link for additional experiments: |
| 220 |
jmc |
1.1 |
if test -e $gcmDIR/verification ; then |
| 221 |
|
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if [ $checkOut -lt 2 ] ; then |
| 222 |
|
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echo " dir $gcmDIR/verification exist" ; fi |
| 223 |
|
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cd $gcmDIR/verification |
| 224 |
|
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for exp2add in $addExp ; do |
| 225 |
jmc |
1.10 |
test -r $exp2add && /bin/rm -rf $exp2add |
| 226 |
|
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if test -d ../$git_other/$exp2add ; then |
| 227 |
|
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echo " add $exp2add link from $git_other" |
| 228 |
|
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ln -s ../$git_other/$exp2add . |
| 229 |
jmc |
1.1 |
if test $exp2add = 'global_oce_cs32' ; then |
| 230 |
jmc |
1.10 |
echo " link dir 'other_input/core2_cnyf' in here" |
| 231 |
jmc |
1.11 |
( cd ../${git_other}/${exp2add} |
| 232 |
|
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test -L core2_cnyf && /bin/rm -f core2_cnyf |
| 233 |
|
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ln -s ../../../other_input/core2_cnyf . ) |
| 234 |
jmc |
1.1 |
fi |
| 235 |
|
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if test $exp2add = 'global_oce_llc90' ; then |
| 236 |
jmc |
1.10 |
echo " link dir 'other_input/gael_oce_llc90_input' to 'input_fields'" |
| 237 |
|
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( cd ../${git_other}/${exp2add} |
| 238 |
jmc |
1.11 |
test -L input_fields && /bin/rm -f input_fields |
| 239 |
jmc |
1.10 |
ln -s ../../../other_input/gael_oce_llc90_input input_fields |
| 240 |
|
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echo " link dirs: 'core2_cnyf' & 'global_oce_input_fields/*' in input_verifs" |
| 241 |
jmc |
1.12 |
test ! -e input_verifs && mkdir input_verifs |
| 242 |
|
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( cd input_verifs ; /bin/rm -f * |
| 243 |
jmc |
1.10 |
ln -s ../../../../other_input/core2_cnyf . |
| 244 |
|
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ln -s ../../../../other_input/global_oce_input_fields/* . ) |
| 245 |
|
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) |
| 246 |
jmc |
1.1 |
fi |
| 247 |
jmc |
1.10 |
else |
| 248 |
|
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echo " missing dir: $git_other/$exp2add" |
| 249 |
|
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continue |
| 250 |
jmc |
1.1 |
fi |
| 251 |
|
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done |
| 252 |
|
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else |
| 253 |
|
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echo "no dir: $gcmDIR/verification => exit" |
| 254 |
|
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exit |
| 255 |
|
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fi |
| 256 |
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|
| 257 |
jmc |
1.6 |
if [ $checkOut -ge 1 ] ; then |
| 258 |
jmc |
1.1 |
echo '' |
| 259 |
jmc |
1.5 |
#- 0) just make all module header ( *__genmod.mod files) using modified Makefile |
| 260 |
jmc |
1.2 |
echo ./testreport $options -of $OPTFILE \ |
| 261 |
jmc |
1.1 |
-nc -repl_mk do_make_syntax.sh -obj -dd |
| 262 |
jmc |
1.2 |
./testreport $options -of $OPTFILE \ |
| 263 |
jmc |
1.1 |
-nc -repl_mk do_make_syntax.sh -obj -dd |
| 264 |
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| 265 |
|
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echo '' |
| 266 |
jmc |
1.5 |
#- 1) just compile ("-nr"), using "-j 4" to speed up |
| 267 |
|
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echo ./testreport $options -of $OPTFILE \ |
| 268 |
|
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-j 4 -nr -q -odir ${dNam}-$sfx |
| 269 |
|
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./testreport $options -of $OPTFILE \ |
| 270 |
|
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-j 4 -nr -q -odir ${dNam}-$sfx |
| 271 |
|
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nFc=`grep -c '^Y . N N ' tr_out.txt` |
| 272 |
|
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echo " <= fail to compile $nFc experiments" |
| 273 |
jmc |
1.6 |
fi |
| 274 |
jmc |
1.5 |
|
| 275 |
|
|
echo '' |
| 276 |
|
|
#- 2) run and report results ; also finish to compile those who failed with "-j" |
| 277 |
jmc |
1.2 |
#echo ./testreport $options -of $OPTFILE -command \'$mpiCMD\' -mf $MPI_MFile \ |
| 278 |
|
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echo ./testreport $options -of $OPTFILE \ |
| 279 |
jmc |
1.6 |
-q -odir ${dNam}-$sfx -send \'$SEND\' -sd $SavD -a jm_c@mitgcm.org |
| 280 |
jmc |
1.2 |
#./testreport $options -of $OPTFILE -command "$mpiCMD" -mf $MPI_MFile \ |
| 281 |
|
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./testreport $options -of $OPTFILE \ |
| 282 |
jmc |
1.6 |
-q -odir ${dNam}-$sfx -send "$SEND" -sd $SavD -a jm_c@mitgcm.org |
| 283 |
jmc |
1.1 |
|
| 284 |
|
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echo '' |
| 285 |
jmc |
1.5 |
#- 3) test restart and report results |
| 286 |
jmc |
1.2 |
#echo ../tools/do_tst_2+2 -mpi -exe \'$mpiCMD\' -mf $MPI_MFile \ |
| 287 |
|
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echo ../tools/do_tst_2+2 -mpi \ |
| 288 |
jmc |
1.6 |
-o ${dNam}-$sfx -send \'$SEND\' -sd $SavD -a jm_c@mitgcm.org |
| 289 |
jmc |
1.2 |
#../tools/do_tst_2+2 -mpi -exe "$mpiCMD" -mf $MPI_MFile \ |
| 290 |
|
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../tools/do_tst_2+2 -mpi \ |
| 291 |
jmc |
1.6 |
-o ${dNam}-$sfx -send "$SEND" -sd $SavD -a jm_c@mitgcm.org |
| 292 |
jmc |
1.1 |
|
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