| 1 |
jmc |
1.4 |
#! /usr/bin/env bash |
| 2 |
jmc |
1.1 |
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| 3 |
jmc |
1.6 |
# $Header: /u/gcmpack/MITgcm/verification/cpl_aim+ocn/run_cpl_test,v 1.23 2015/10/26 21:04:35 jmc Exp $ |
| 4 |
jmc |
1.1 |
# $Name: $ |
| 5 |
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| 6 |
jmc |
1.6 |
bdPfx='build'; # build-dir prefix |
| 7 |
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| 8 |
jmc |
1.1 |
#- default: |
| 9 |
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Npr=3 ; NpOc=1 ; |
| 10 |
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#Npr=25; NpOc=12; |
| 11 |
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MTH= |
| 12 |
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MTHo= |
| 13 |
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MTHa= |
| 14 |
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GMKopt='-devel' |
| 15 |
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#GMKopt='-ieee' |
| 16 |
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#GMKopt= |
| 17 |
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rnkO=1 ; rnkA=`expr $rnkO + $NpOc` |
| 18 |
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| 19 |
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#- parse options: |
| 20 |
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if [ $# -ge 1 ] ; then if test $1 = '-mth' ; then |
| 21 |
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MTH='-omp' ; shift |
| 22 |
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if test -f input_ocn/eedata.mth ; then MTHo=$MTH ; fi |
| 23 |
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if test -f input_atm/eedata.mth ; then MTHa=$MTH ; fi |
| 24 |
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fi ; fi |
| 25 |
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#- allows more argument for building step (step=1) |
| 26 |
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chkArg=$# ; if [ $# -gt 1 ]; then chkArg=$1 ; fi |
| 27 |
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if [ $chkArg -ne 1 ]; then |
| 28 |
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echo 'Usage:'`basename $0`' [opt] step [bld-arg]' |
| 29 |
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echo ' => test coupled set-up on linux box (1.cpu)' |
| 30 |
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echo 'opt = -mth : compile and run (if eedata.mth) 2-threads for ocn & atm' |
| 31 |
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echo ' step = 0 : clean all directories' |
| 32 |
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echo ' step = 1 : compile the 3 executables (cpl,ocn,atm); optional arg:' |
| 33 |
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echo ' -of Optfile_Name : using option-file "Optfile_Name"' |
| 34 |
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echo ' step = 2 : copy input files and dir(s)' |
| 35 |
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echo " step = 3 : run with $Npr mpi processes" |
| 36 |
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echo ' step = 4 : check the results' |
| 37 |
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echo ' step = 5 : remove output files in rank_0,1,2 dir.' |
| 38 |
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exit |
| 39 |
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fi |
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kpr=$1 |
| 41 |
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dir=`pwd` |
| 42 |
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| 43 |
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#============================================================================ |
| 44 |
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| 45 |
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if test $kpr = 0 |
| 46 |
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then |
| 47 |
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rm -f pr_group std_outp comp_res.{ocn,atm,land,sice} |
| 48 |
jmc |
1.6 |
rm -f ${bdPfx}_???/TTT.*make.* ${bdPfx}_???/TTT.mkdepend.* |
| 49 |
jmc |
1.1 |
/bin/rm -r -f rank_? rank_1? rank_2? |
| 50 |
jmc |
1.6 |
if test -f ${bdPfx}_cpl/Makefile ; then cd ${bdPfx}_cpl ; make Clean ; cd .. ; fi |
| 51 |
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if test -f ${bdPfx}_ocn/Makefile ; then cd ${bdPfx}_ocn ; make Clean ; cd .. ; fi |
| 52 |
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if test -f ${bdPfx}_atm/Makefile ; then cd ${bdPfx}_atm ; make Clean ; cd .. ; fi |
| 53 |
jmc |
1.1 |
fi |
| 54 |
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if test $kpr = 5 |
| 55 |
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then |
| 56 |
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echo 'remove output files in rank_0,1,2 dir.' |
| 57 |
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rm -f pr_group std_outp comp_res.{ocn,atm,land,sice} |
| 58 |
jmc |
1.6 |
test -f rank_0/Coupler.0000.clog && rm -f rank_0/Coupler.0000.clog |
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if test -d rank_$rnkO ; then |
| 60 |
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#( cd rank_$rnkO ; rm -f *.data *.meta *.txt *.log STD???.00?? UV-*.00??.clog ) |
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( cd rank_$rnkO ; $HOME/bin/move_res tmp_trash |
| 62 |
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mv STD???.00?? UV-*.00??.clog tmp_trash |
| 63 |
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/bin/rm -rf tmp_trash ) |
| 64 |
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fi |
| 65 |
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if test -d rank_$rnkA ; then |
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#( cd rank_$rnkA ; rm -f *.data *.meta *.txt *.log STD???.00?? UV-*.00??.clog ) |
| 67 |
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( cd rank_$rnkA ; $HOME/bin/move_res tmp_trash |
| 68 |
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mv STD???.00?? UV-*.00??.clog tmp_trash |
| 69 |
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/bin/rm -rf tmp_trash ) |
| 70 |
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fi |
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jmc |
1.1 |
fi |
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if test $kpr = 1 |
| 74 |
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then |
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#- choice of the optfile: |
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# default: take a local one in dir verification with sufix '+mpi' |
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nbOpF=`ls ../linux_* | grep '+mpi' 2> /dev/null | wc -l` |
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# or take the one given as argument: |
| 80 |
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if [ $# -ge 3 ]; then |
| 81 |
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if test $2 = '-of' -a -f $3 ; then nbOpF=-1 ; OPTFILE=$3 ; fi |
| 82 |
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fi |
| 83 |
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if test $nbOpF = 1 ; then |
| 84 |
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OPTFILE=`ls ../linux_* | grep '+mpi'` |
| 85 |
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elif [ $nbOpF -ge 2 ] ; then |
| 86 |
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echo "pick the 1rst of these ( $nbOpF ) optfiles:" |
| 87 |
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ls ../linux_* | grep '+mpi' |
| 88 |
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OPTFILE=`ls ../linux_* | grep '+mpi' | head -1` |
| 89 |
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elif [ $nbOpF -ne -1 ] ; then |
| 90 |
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echo "Pb in finding optfile: found $nbOpF :" |
| 91 |
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ls ../linux_* | grep '+mpi' ; exit |
| 92 |
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fi |
| 93 |
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zz=`grep '^ *FC=' $OPTFILE | tail -1` |
| 94 |
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echo " Using optfile: $OPTFILE (compiler: $zz) $MTH" |
| 95 |
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zz=`echo $OPTFILE | grep -c '^\/'` |
| 96 |
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if test $zz = 0 ; then OPTFILE="../$OPTFILE" ; fi |
| 97 |
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#--- |
| 98 |
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echo '==== compile coupler:' |
| 99 |
jmc |
1.6 |
cd ${bdPfx}_cpl |
| 100 |
jmc |
1.1 |
echo ' --- genmake2 (cpl):' |
| 101 |
jmc |
1.4 |
../../../tools/genmake2 -of $OPTFILE -mpi $GMKopt > TTT.genmake.$$ 2>&1 |
| 102 |
jmc |
1.5 |
RetVal=$? ; tail -5 TTT.genmake.$$ |
| 103 |
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if test "x$RetVal" != x0 ; then |
| 104 |
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echo "Error in genmake2 (cpl)" ; exit 11 |
| 105 |
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fi |
| 106 |
jmc |
1.1 |
echo ' --- make depend (cpl):' |
| 107 |
jmc |
1.4 |
make depend > TTT.mkdepend.$$ 2>&1 |
| 108 |
jmc |
1.5 |
RetVal=$? ; tail -5 TTT.mkdepend.$$ |
| 109 |
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if test "x$RetVal" != x0 ; then |
| 110 |
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echo "Error in mkdepend (cpl)" ; exit 12 |
| 111 |
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fi |
| 112 |
jmc |
1.2 |
echo ' --- make (cpl):' ; touch TTT.make.$$ |
| 113 |
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#do_make_syntax.sh obj > TTT.make.$$ 2>&1 |
| 114 |
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make >> TTT.make.$$ 2>&1 |
| 115 |
jmc |
1.5 |
RetVal=$? ; tail -10 TTT.make.$$ |
| 116 |
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if test "x$RetVal" != x0 ; then |
| 117 |
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echo "Error in make (cpl)" ; exit 13 |
| 118 |
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fi |
| 119 |
jmc |
1.1 |
echo ' ' ; cd $dir |
| 120 |
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| 121 |
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echo '==== compile OGCM:' |
| 122 |
jmc |
1.6 |
cd ${bdPfx}_ocn |
| 123 |
jmc |
1.1 |
echo ' --- genmake2 (ocn):' |
| 124 |
jmc |
1.4 |
../../../tools/genmake2 -of $OPTFILE -mpi $MTHo $GMKopt > TTT.genmake.$$ 2>&1 |
| 125 |
jmc |
1.5 |
RetVal=$? ; tail -5 TTT.genmake.$$ |
| 126 |
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if test "x$RetVal" != x0 ; then |
| 127 |
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echo "Error in genmake2 (ocn)" ; exit 21 |
| 128 |
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fi |
| 129 |
jmc |
1.1 |
echo ' --- make depend (ocn):' |
| 130 |
jmc |
1.4 |
make depend > TTT.mkdepend.$$ 2>&1 |
| 131 |
jmc |
1.5 |
RetVal=$? ; tail -10 TTT.mkdepend.$$ |
| 132 |
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if test "x$RetVal" != x0 ; then |
| 133 |
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echo "Error in mkdepend (ocn)" ; exit 22 |
| 134 |
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fi |
| 135 |
jmc |
1.2 |
echo ' --- make (ocn):' ; touch TTT.make.$$ |
| 136 |
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#do_make_syntax.sh obj > TTT.make.$$ 2>&1 |
| 137 |
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make >> TTT.make.$$ 2>&1 |
| 138 |
jmc |
1.5 |
RetVal=$? ; tail -10 TTT.make.$$ |
| 139 |
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if test "x$RetVal" != x0 ; then |
| 140 |
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echo "Error in make (ocn)" ; exit 23 |
| 141 |
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fi |
| 142 |
jmc |
1.1 |
echo ' ' ; cd $dir |
| 143 |
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| 144 |
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echo '==== compile AGCM:' |
| 145 |
jmc |
1.6 |
cd ${bdPfx}_atm |
| 146 |
jmc |
1.1 |
echo ' --- genmake2 (atm):' |
| 147 |
jmc |
1.4 |
../../../tools/genmake2 -of $OPTFILE -mpi $MTHa $GMKopt > TTT.genmake.$$ 2>&1 |
| 148 |
jmc |
1.5 |
RetVal=$? ; tail -5 TTT.genmake.$$ |
| 149 |
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if test "x$RetVal" != x0 ; then |
| 150 |
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echo "Error in genmake2 (atm)" ; exit 31 |
| 151 |
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fi |
| 152 |
jmc |
1.1 |
echo ' --- make depend (atm):' |
| 153 |
jmc |
1.4 |
make depend > TTT.mkdepend.$$ 2>&1 |
| 154 |
jmc |
1.5 |
RetVal=$? ; tail -10 TTT.mkdepend.$$ |
| 155 |
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if test "x$RetVal" != x0 ; then |
| 156 |
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echo "Error in mkdepend (atm)" ; exit 32 |
| 157 |
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fi |
| 158 |
jmc |
1.2 |
echo ' --- make (atm):' ; touch TTT.make.$$ |
| 159 |
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#do_make_syntax.sh obj > TTT.make.$$ 2>&1 |
| 160 |
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make >> TTT.make.$$ 2>&1 |
| 161 |
jmc |
1.5 |
RetVal=$? ; tail -10 TTT.make.$$ |
| 162 |
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if test "x$RetVal" != x0 ; then |
| 163 |
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echo "Error in make (atm)" ; exit 33 |
| 164 |
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fi |
| 165 |
jmc |
1.1 |
echo ' ' ; cd $dir |
| 166 |
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| 167 |
jmc |
1.6 |
ls -l ${bdPfx}_???/mitgcmuv |
| 168 |
jmc |
1.1 |
|
| 169 |
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fi |
| 170 |
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| 171 |
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if test $kpr = 2 |
| 172 |
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then |
| 173 |
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echo 'rm dir:' rank_? rank_1? rank_2? |
| 174 |
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/bin/rm -r -f rank_? rank_1? rank_2? |
| 175 |
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echo 'Link files from dir:' input_cpl '->' rank_0 |
| 176 |
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mkdir rank_0 |
| 177 |
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( cd rank_0 ; ln -s ../input_cpl/* . ) |
| 178 |
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| 179 |
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n=$rnkO |
| 180 |
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echo 'Link files from dir:' input_ocn '->' rank_$n |
| 181 |
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mkdir rank_$n |
| 182 |
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cd rank_$n |
| 183 |
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ln -s ../input_ocn/* . |
| 184 |
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if test -x prepare_run ; then ./prepare_run ; fi |
| 185 |
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if test "x$MTHo" != x ; then |
| 186 |
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echo " MTH run: mv -f eedata.mth eedata" |
| 187 |
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if test -h eedata ; then rm -f eedata ; fi |
| 188 |
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mv -f eedata.mth eedata |
| 189 |
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fi |
| 190 |
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cd $dir |
| 191 |
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n=`expr $n + 1` |
| 192 |
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while [ $n -le $NpOc ] ; do |
| 193 |
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ln -s rank_$rnkO rank_$n |
| 194 |
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n=`expr $n + 1` |
| 195 |
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done |
| 196 |
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| 197 |
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n=$rnkA |
| 198 |
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echo 'Link files from dir:' input_atm '->' rank_$n |
| 199 |
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mkdir rank_$n |
| 200 |
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cd rank_$n |
| 201 |
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ln -s ../input_atm/* . |
| 202 |
|
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if test -x prepare_run ; then ./prepare_run ; fi |
| 203 |
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if test "x$MTHa" != x ; then |
| 204 |
|
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echo " MTH run: mv -f eedata.mth eedata" |
| 205 |
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if test -h eedata ; then rm -f eedata ; fi |
| 206 |
|
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mv -f eedata.mth eedata |
| 207 |
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fi |
| 208 |
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cd $dir |
| 209 |
|
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n=`expr $n + 1` |
| 210 |
|
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while [ $n -lt $Npr ] ; do |
| 211 |
|
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ln -s rank_$rnkA rank_$n |
| 212 |
|
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n=`expr $n + 1` |
| 213 |
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done |
| 214 |
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| 215 |
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fi |
| 216 |
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| 217 |
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if test $kpr = 3 |
| 218 |
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then |
| 219 |
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ROOTDIR=$dir |
| 220 |
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# rm -f rank_?/pickup*.ckptA.00?.00?.??ta |
| 221 |
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echo $ROOTDIR |
| 222 |
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tmpfil=TTT.$$ |
| 223 |
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| 224 |
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#--- running on the same node: |
| 225 |
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list='' ; nc=0; xx=`hostname` |
| 226 |
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while [ $nc -lt $Npr ] ; do list="$list $xx" ; nc=`expr $nc + 1` ; done |
| 227 |
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#-- On darwin cluster node (from qrsh session): |
| 228 |
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# JOB_ID=`qstat | sed -n '3,$ p' | grep " $USER " | awk '{print $1}'` |
| 229 |
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# NODEFILE="/tmp/$JOB_ID.1.darwin/machines" |
| 230 |
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# echo " JOB_ID = '$JOB_ID' ; NODEFILE = '$NODEFILE'" |
| 231 |
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#-- On ACES cluster (in PBS batch job): |
| 232 |
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# NODEFILE=$PBS_NODEFILE |
| 233 |
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#--- running on different nodes: |
| 234 |
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# ls -l $NODEFILE |
| 235 |
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# nprc=`cat $NODEFILE | uniq | wc -l` |
| 236 |
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# if [ $nprc -ge $Npr ] ; then |
| 237 |
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# list=`cat $NODEFILE | uniq | head -$Npr` |
| 238 |
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# else |
| 239 |
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# list=`cat $NODEFILE | head -$Npr` |
| 240 |
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# fi |
| 241 |
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| 242 |
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nc=0; nn=0; dd1=cpl ; |
| 243 |
|
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rm -f pr_group ; touch pr_group |
| 244 |
|
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for xx in $list |
| 245 |
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do |
| 246 |
jmc |
1.6 |
echo $xx $nn $dir/${bdPfx}_$dd1/mitgcmuv >> pr_group |
| 247 |
jmc |
1.1 |
nc=`expr $nc + 1` |
| 248 |
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if [ $nc -le $NpOc ] ; then dd1=ocn ; else dd1=atm ; fi |
| 249 |
|
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nn=1 |
| 250 |
|
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done |
| 251 |
|
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NpAt=`expr $Npr - 1 - $NpOc` |
| 252 |
jmc |
1.6 |
RunOpt="-np 1 ./${bdPfx}_cpl/mitgcmuv" |
| 253 |
|
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RunOpt="$RunOpt : -np $NpOc ./${bdPfx}_ocn/mitgcmuv" |
| 254 |
|
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RunOpt="$RunOpt : -np $NpAt ./${bdPfx}_atm/mitgcmuv" |
| 255 |
jmc |
1.1 |
|
| 256 |
|
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cd $ROOTDIR |
| 257 |
|
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if test "x$MTH" != x ; then |
| 258 |
|
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export OMP_NUM_THREADS=2 ; export KMP_STACKSIZE=400m |
| 259 |
|
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if test "x$MTHo" != x ; then |
| 260 |
|
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echo -n " run OCN ($MTHo) with $OMP_NUM_THREADS threads ;" |
| 261 |
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fi |
| 262 |
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if test "x$MTHa" != x ; then |
| 263 |
|
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echo -n " run ATM ($MTHa) with $OMP_NUM_THREADS threads ;" |
| 264 |
|
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fi |
| 265 |
|
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echo "" |
| 266 |
|
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fi |
| 267 |
|
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mpich=`which mpirun` |
| 268 |
|
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echo $mpich | grep 'mpich-mx' > /dev/null 2>&1 |
| 269 |
|
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mpichmx=$? |
| 270 |
jmc |
1.2 |
echo $mpich | grep 'mpich-1' > /dev/null 2>&1 |
| 271 |
|
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mpich1=$? |
| 272 |
jmc |
1.1 |
echo $mpich | grep 'mpich2' > /dev/null 2>&1 |
| 273 |
|
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mpich2=$? |
| 274 |
|
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echo $mpich | grep 'openmpi' > /dev/null 2>&1 |
| 275 |
|
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opnmpi=$? |
| 276 |
jmc |
1.2 |
if test $mpich1 == 0 ; then |
| 277 |
jmc |
1.6 |
# /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/pgi/bin/mpirun.ch_gm -pg pr_group -wd $ROOTDIR --gm-kill 5 -v ./${bdPfx}_cpl/mitgcmuv > std_outp 2>&1 |
| 278 |
jmc |
1.2 |
#- with mpich-1 (on danton, old aces: ao, geo, itrda): |
| 279 |
jmc |
1.6 |
echo "execute 'mpirun -p4pg pr_group -v ./${bdPfx}_cpl/mitgcmuv' :" |
| 280 |
|
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mpirun -p4pg pr_group -v ./${bdPfx}_cpl/mitgcmuv > std_outp 2>&1 |
| 281 |
jmc |
1.1 |
elif test $mpichmx == 0 ; then |
| 282 |
|
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#- with mpich-mx (on beagle): |
| 283 |
jmc |
1.6 |
echo "execute 'mpirun -pg pr_group -v ./${bdPfx}_cpl/mitgcmuv' :" |
| 284 |
|
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mpirun -pg pr_group -v ./${bdPfx}_cpl/mitgcmuv > std_outp 2>&1 |
| 285 |
jmc |
1.2 |
elif test $mpich2 == 0 -o $opnmpi == 0 ; then |
| 286 |
|
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#- with Hydra mpich2 (on baudelaire) or with openmpi: |
| 287 |
|
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echo "execute 'mpirun $RunOpt' :" |
| 288 |
|
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mpirun $RunOpt > std_outp 2>&1 |
| 289 |
jmc |
1.1 |
else |
| 290 |
jmc |
1.2 |
#- new mpich (mpich2) installation often just put in "mpich" dir |
| 291 |
|
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echo "execute 'mpirun $RunOpt' :" |
| 292 |
|
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mpirun $RunOpt > std_outp 2>&1 |
| 293 |
jmc |
1.1 |
fi |
| 294 |
|
|
tail -20 std_outp |
| 295 |
jmc |
1.6 |
#ls -l rank_$rnkO/pickup*.ckptA.001.001.data |
| 296 |
|
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#ls -l rank_$rnkA/pickup*.ckptA.001.001.data |
| 297 |
|
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ls -l rank_$rnkO/pickup.ckptA.*data | tail -1 |
| 298 |
|
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ls -l rank_$rnkA/pickup.ckptA.*data | tail -1 |
| 299 |
jmc |
1.1 |
|
| 300 |
|
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fi |
| 301 |
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| 302 |
|
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if test $kpr = 4 |
| 303 |
|
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then |
| 304 |
|
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CompRes="$HOME/bin/comp_res" |
| 305 |
|
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|
| 306 |
|
|
if test -f rank_$rnkO/STDOUT.0000 |
| 307 |
|
|
then echo '==> check Ocean output:' |
| 308 |
|
|
$CompRes rank_$rnkO/STDOUT.0000 results/ocnSTDOUT.0000 |
| 309 |
|
|
mv -f comp_res.log comp_res.ocn |
| 310 |
|
|
echo ' ' |
| 311 |
|
|
else echo "No Ocean output file in rank_$rnkO" ; fi |
| 312 |
|
|
|
| 313 |
|
|
if test -f rank_$rnkA/STDOUT.0000 |
| 314 |
|
|
then |
| 315 |
|
|
echo '==> check Atmos output:' |
| 316 |
|
|
$CompRes rank_$rnkA/STDOUT.0000 results/atmSTDOUT.0000 |
| 317 |
|
|
mv -f comp_res.log comp_res.atm |
| 318 |
jmc |
1.3 |
#echo '==> check Land output:' |
| 319 |
|
|
#$CompRes rank_$rnkA/STDOUT.0000 results/atmSTDOUT.0000 L |
| 320 |
|
|
#mv -f comp_res.log comp_res.land |
| 321 |
|
|
#echo '==> check thSIce output:' |
| 322 |
|
|
#$CompRes rank_$rnkA/STDOUT.0000 results/atmSTDOUT.0000 I |
| 323 |
|
|
#mv -f comp_res.log comp_res.sice |
| 324 |
jmc |
1.1 |
echo ' ' |
| 325 |
|
|
else echo "No Atmos output file in rank_$rnkA" ; fi |
| 326 |
|
|
|
| 327 |
|
|
fi |
| 328 |
|
|
|
| 329 |
|
|
exit 0 |
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