| 1 |
jmc |
1.1 |
#! /bin/sh |
| 2 |
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| 3 |
jmc |
1.3 |
# $Header: /u/gcmpack/MITgcm_contrib/jmc_script/run_cpl_test.aces,v 1.2 2011/08/01 23:52:33 jmc Exp $ |
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jmc |
1.1 |
# $Name: $ |
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| 6 |
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#- default: |
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Npr=3 ; NpOc=1 ; |
| 8 |
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#Npr=25; NpOc=12; |
| 9 |
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MTH= |
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MTHo= |
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MTHa= |
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GMKopt='-ieee' |
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#GMKopt= |
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rnkO=1 ; rnkA=`expr $rnkO + $NpOc` |
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#- parse options: |
| 17 |
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if [ $# -ge 1 ] ; then if test $1 = '-mth' ; then |
| 18 |
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MTH='-omp' ; shift |
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if test -f input_ocn/eedata.mth ; then MTHo=$MTH ; fi |
| 20 |
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if test -f input_atm/eedata.mth ; then MTHa=$MTH ; fi |
| 21 |
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fi ; fi |
| 22 |
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if [ $# -ne 1 ] |
| 23 |
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then |
| 24 |
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echo 'Usage:'`basename $0`' [opt] step' |
| 25 |
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echo ' => test coupled set-up on ACES cluster' |
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echo 'opt = -mth : compile and run (if eedata.mth) 2-threads for ocn & atm' |
| 27 |
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echo ' step = 0 : clean all directories' |
| 28 |
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echo ' step = 1 : compile the 3 executables (cpl,ocn,atm)' |
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echo ' step = 2 : copy input files and dir(s)' |
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echo " step = 3 : run with $Npr mpi processes" |
| 31 |
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echo ' step = 4 : check the results' |
| 32 |
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echo ' step = 5 : remove output files in rank_0,1,2 dir.' |
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exit |
| 34 |
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fi |
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kpr=$1 |
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dir=`pwd` |
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| 38 |
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#============================================================================ |
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#- only works from a 3 (or more) nodes PBS bach session on ACES cluster |
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# (tested on ao) ( qsub -I -l nodes=3 -or- |
| 42 |
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# qsub -I -l nodes=3:ppn=2 ) |
| 43 |
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# need to be on one computer node, |
| 44 |
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# and with the correct module loaded (i.e, one of the 3): |
| 45 |
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# > module load mpich/gnu |
| 46 |
jmc |
1.3 |
# export MPI_INC_DIR='/usr/local/pkg/mpich/mpich-gcc/include' |
| 47 |
jmc |
1.1 |
# > module load mpich/intel netcdf/3.6.1/icc |
| 48 |
jmc |
1.3 |
# export MPI_INC_DIR='/usr/local/pkg/mpich/mpich-intel/include' |
| 49 |
jmc |
1.1 |
# > module load mpich/pgi |
| 50 |
jmc |
1.3 |
# export MPI_INC_DIR='/usr/local/pkg/mpich/mpich-pgi/include' |
| 51 |
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# export NETCDF_ROOT='/usr/local/pkg/pgi/pgi-5.2/linux86/5.2' |
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| 53 |
jmc |
1.1 |
if test 'dummy'$PBS_NODEFILE = 'dummy' |
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then |
| 55 |
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echo ' $PBS_NODEFILE not defined' |
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echo "for now, works only from a (at least) $Npr nodes PBS bach session" |
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exit 8 |
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else nprc=`wc -l $PBS_NODEFILE | awk '{print $1}'` |
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if [ $nprc -lt $Npr ] ; then |
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echo ' Nb of nodes from $PBS_NODEFILE =' $nprc |
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echo "for now, works only from a (at least) $Npr nodes PBS bach session" |
| 62 |
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exit 8 |
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fi |
| 64 |
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fi |
| 65 |
jmc |
1.2 |
umask 0022 |
| 66 |
jmc |
1.1 |
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#============================================================================ |
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| 69 |
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if test $kpr = 0 |
| 70 |
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then |
| 71 |
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rm -f pr_group std_outp comp_res.{ocn,atm,land,sice} |
| 72 |
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rm -f build_???/TTT.*make.* build_???/TTT.mkdepend.* |
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/bin/rm -r -f rank_? rank_1? rank_2? |
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if test -f build_cpl/Makefile ; then cd build_cpl ; make Clean ; cd .. ; fi |
| 75 |
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if test -f build_ocn/Makefile ; then cd build_ocn ; make Clean ; cd .. ; fi |
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if test -f build_atm/Makefile ; then cd build_atm ; make Clean ; cd .. ; fi |
| 77 |
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fi |
| 78 |
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if test $kpr = 5 |
| 79 |
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then |
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echo 'remove output files in rank_0,1,2 dir.' |
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rm -f pr_group std_outp comp_res.{ocn,atm,land,sice} |
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if test -d rank_0 ; then cd rank_0 ; rm -f Coupler.0000.clog ; cd .. ; fi |
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if test -d rank_$rnkO |
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then cd rank_$rnkO ; rm -f *.data *.meta STD???.0000 UV-*.0001.clog ; cd .. ; fi |
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if test -d rank_$rnkA |
| 86 |
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then cd rank_$rnkA ; rm -f *.data *.meta STD???.0000 UV-*.0001.clog ; cd .. ; fi |
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fi |
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if test $kpr = 1 |
| 90 |
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then |
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| 92 |
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#- find the optfile that corresponds to the currently loaded mpich module |
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. /etc/profile.d/modules.sh |
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module list -t >& tmp_compiler |
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compiler=`sed -n 's/mpich.*\///p' tmp_compiler` |
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case $compiler in |
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jmc |
1.3 |
'gnu') OPTFILE="../../tools/build_options/linux_ia32_g77" ;; |
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'intel') OPTFILE="../../tools/build_options/linux_ia32_ifort" ;; |
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'pgi') OPTFILE="../../tools/build_options/linux_ia32_pgf77" ;; |
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jmc |
1.1 |
*) echo 'ERROR: cannot use compiler:' $compiler ; |
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echo ""; cat tmp_compiler ; exit 7 ;; |
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esac |
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rm -f tmp_compiler |
| 104 |
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echo " Using optfile: $OPTFILE (compiler=$compiler) $MTH" |
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zz=`echo $OPTFILE | grep -c '^\/'` |
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if test $zz = 0 ; then OPTFILE="../$OPTFILE" ; fi |
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#--- |
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echo '==== compile coupler:' |
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cd build_cpl |
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echo ' --- genmake2 (cpl):' |
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../../../tools/genmake2 -of $OPTFILE -mpi $GMKopt > TTT.genmake.$$ |
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tail -5 TTT.genmake.$$ |
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echo ' --- make depend (cpl):' |
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make depend > TTT.mkdepend.$$ |
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tail -5 TTT.mkdepend.$$ |
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echo ' --- make (cpl):' |
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make > TTT.make.$$ 2>&1 |
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tail -10 TTT.make.$$ |
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echo ' ' ; cd $dir |
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echo '==== compile OGCM:' |
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cd build_ocn |
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echo ' --- genmake2 (ocn):' |
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../../../tools/genmake2 -of $OPTFILE -mpi $MTHo $GMKopt > TTT.genmake.$$ |
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tail -5 TTT.genmake.$$ |
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echo ' --- make depend (ocn):' |
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make depend > TTT.mkdepend.$$ |
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tail -10 TTT.mkdepend.$$ |
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echo ' --- make (ocn):' |
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make > TTT.make.$$ 2>&1 |
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tail -10 TTT.make.$$ |
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echo ' ' ; cd $dir |
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echo '==== compile AGCM:' |
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cd build_atm |
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echo ' --- genmake2 (atm):' |
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../../../tools/genmake2 -of $OPTFILE -mpi $MTHa $GMKopt > TTT.genmake.$$ |
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tail -5 TTT.genmake.$$ |
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echo ' --- make depend (atm):' |
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make depend > TTT.mkdepend.$$ |
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tail -10 TTT.mkdepend.$$ |
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echo ' --- make (atm):' |
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make > TTT.make.$$ 2>&1 |
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tail -10 TTT.make.$$ |
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echo ' ' ; cd $dir |
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ls -l build_???/mitgcmuv |
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fi |
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if test $kpr = 2 |
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then |
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echo 'rm dir:' rank_? rank_1? rank_2? |
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/bin/rm -r -f rank_? rank_1? rank_2? |
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echo 'Link files from dir:' input_cpl '->' rank_0 |
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mkdir rank_0 |
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( cd rank_0 ; ln -s ../input_cpl/* . ) |
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n=$rnkO |
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echo 'Link files from dir:' input_ocn '->' rank_$n |
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mkdir rank_$n |
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cd rank_$n |
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ln -s ../input_ocn/* . |
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if test -x prepare_run ; then ./prepare_run ; fi |
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if test "x$MTHo" != x ; then |
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echo " MTH run: mv -f eedata.mth eedata" |
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if test -h eedata ; then rm -f eedata ; fi |
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mv -f eedata.mth eedata |
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fi |
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cd $dir |
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n=`expr $n + 1` |
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while [ $n -le $NpOc ] ; do |
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ln -s rank_$rnkO rank_$n |
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n=`expr $n + 1` |
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done |
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n=$rnkA |
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echo 'Link files from dir:' input_atm '->' rank_$n |
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mkdir rank_$n |
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cd rank_$n |
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ln -s ../input_atm/* . |
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if test -x prepare_run ; then ./prepare_run ; fi |
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if test "x$MTHa" != x ; then |
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echo " MTH run: mv -f eedata.mth eedata" |
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if test -h eedata ; then rm -f eedata ; fi |
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mv -f eedata.mth eedata |
| 188 |
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fi |
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cd $dir |
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n=`expr $n + 1` |
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while [ $n -lt $Npr ] ; do |
| 192 |
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ln -s rank_$rnkA rank_$n |
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n=`expr $n + 1` |
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done |
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fi |
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if test $kpr = 3 |
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then |
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ROOTDIR=$dir |
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# rm -f rank_?/pickup*.ckptA.00?.00?.??ta |
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echo $ROOTDIR |
| 203 |
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tmpfil=TTT.$$ |
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#--- running on the same node: |
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list='' ; nc=0; xx=`hostname` |
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while [ $nc -lt $Npr ] ; do list="$list $xx" ; nc=`expr $nc + 1` ; done |
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#-- On darwin cluster node (from qrsh session): |
| 209 |
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#JOB_ID=`qstat | sed -n '3,$ p' | grep " $USER " | awk '{print $1}'` |
| 210 |
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#NODEFILE="/tmp/$JOB_ID.1.darwin/machines" |
| 211 |
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#echo " JOB_ID = '$JOB_ID' ; NODEFILE = '$NODEFILE'" |
| 212 |
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#-- On ACES cluster (in PBS batch job): |
| 213 |
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NODEFILE=$PBS_NODEFILE |
| 214 |
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#--- running on different nodes: |
| 215 |
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ls -l $NODEFILE |
| 216 |
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nprc=`cat $NODEFILE | uniq | wc -l` |
| 217 |
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if [ $nprc -ge $Npr ] ; then |
| 218 |
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list=`cat $NODEFILE | uniq | head -$Npr` |
| 219 |
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else |
| 220 |
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list=`cat $NODEFILE | head -$Npr` |
| 221 |
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fi |
| 222 |
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| 223 |
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nc=0; nn=0; dd1=cpl ; |
| 224 |
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rm -f pr_group ; touch pr_group |
| 225 |
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for xx in $list |
| 226 |
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do |
| 227 |
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echo $xx $nn $dir/build_$dd1/mitgcmuv >> pr_group |
| 228 |
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nc=`expr $nc + 1` |
| 229 |
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if [ $nc -le $NpOc ] ; then dd1=ocn ; else dd1=atm ; fi |
| 230 |
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nn=1 |
| 231 |
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done |
| 232 |
jmc |
1.3 |
NpAt=`expr $Npr - 1 - $NpOc` |
| 233 |
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RunOpt="-np 1 ./build_cpl/mitgcmuv" |
| 234 |
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RunOpt="$RunOpt : -np $NpOc ./build_ocn/mitgcmuv" |
| 235 |
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RunOpt="$RunOpt : -np $NpAt ./build_atm/mitgcmuv" |
| 236 |
jmc |
1.1 |
|
| 237 |
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cd $ROOTDIR |
| 238 |
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if test "x$MTH" != x ; then |
| 239 |
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export OMP_NUM_THREADS=2 ; export KMP_STACKSIZE=400m |
| 240 |
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if test "x$MTHo" != x ; then |
| 241 |
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echo -n " run OCN ($MTHo) with $OMP_NUM_THREADS threads ;" |
| 242 |
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fi |
| 243 |
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if test "x$MTHa" != x ; then |
| 244 |
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echo -n " run ATM ($MTHa) with $OMP_NUM_THREADS threads ;" |
| 245 |
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fi |
| 246 |
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echo "" |
| 247 |
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fi |
| 248 |
jmc |
1.3 |
mpich=`which mpirun` |
| 249 |
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echo $mpich | grep 'mpich-mx' > /dev/null 2>&1 |
| 250 |
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mpichmx=$? |
| 251 |
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echo $mpich | grep 'mpich2' > /dev/null 2>&1 |
| 252 |
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mpich2=$? |
| 253 |
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if test $mpich2 == 0 ; then |
| 254 |
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#- with Hydra mpich2 (on baudelaire): |
| 255 |
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echo "execute 'mpirun $RunOpt' :" |
| 256 |
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mpirun $RunOpt > std_outp 2>&1 |
| 257 |
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elif test $mpichmx == 0 ; then |
| 258 |
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#- with mpich-mx (on beagle): |
| 259 |
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echo "execute 'mpirun -pg pr_group -v ./build_cpl/mitgcmuv' :" |
| 260 |
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mpirun -pg pr_group -v ./build_cpl/mitgcmuv > std_outp 2>&1 |
| 261 |
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else |
| 262 |
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# /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/pgi/bin/mpirun.ch_gm -pg pr_group -wd $ROOTDIR --gm-kill 5 -v ./build_cpl/mitgcmuv > std_outp 2>&1 |
| 263 |
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#- with mpich-1 (on danton, ACES): |
| 264 |
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echo "execute 'mpirun -p4pg pr_group -v ./build_cpl/mitgcmuv' :" |
| 265 |
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mpirun -p4pg pr_group -v ./build_cpl/mitgcmuv > std_outp 2>&1 |
| 266 |
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fi |
| 267 |
jmc |
1.1 |
tail -20 std_outp |
| 268 |
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ls -l rank_$rnkO/pickup*.ckptA.001.001.data |
| 269 |
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ls -l rank_$rnkA/pickup*.ckptA.001.001.data |
| 270 |
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| 271 |
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fi |
| 272 |
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| 273 |
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if test $kpr = 4 |
| 274 |
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then |
| 275 |
jmc |
1.3 |
CompRes="$HOME/bin/comp_res" |
| 276 |
jmc |
1.1 |
|
| 277 |
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if test -f rank_$rnkO/STDOUT.0000 |
| 278 |
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then echo '==> check Ocean output:' |
| 279 |
jmc |
1.3 |
$CompRes rank_$rnkO/STDOUT.0000 results/ocnSTDOUT.0000 |
| 280 |
jmc |
1.1 |
mv -f comp_res.log comp_res.ocn |
| 281 |
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echo ' ' |
| 282 |
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else echo "No Ocean output file in rank_$rnkO" ; fi |
| 283 |
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| 284 |
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if test -f rank_$rnkA/STDOUT.0000 |
| 285 |
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then |
| 286 |
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echo '==> check Atmos output:' |
| 287 |
jmc |
1.3 |
$CompRes rank_$rnkA/STDOUT.0000 results/atmSTDOUT.0000 |
| 288 |
jmc |
1.1 |
mv -f comp_res.log comp_res.atm |
| 289 |
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echo '==> check Land output:' |
| 290 |
jmc |
1.3 |
$CompRes rank_$rnkA/STDOUT.0000 results/atmSTDOUT.0000 L |
| 291 |
jmc |
1.1 |
mv -f comp_res.log comp_res.land |
| 292 |
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echo '==> check thSIce output:' |
| 293 |
jmc |
1.3 |
$CompRes rank_$rnkA/STDOUT.0000 results/atmSTDOUT.0000 I |
| 294 |
jmc |
1.1 |
mv -f comp_res.log comp_res.sice |
| 295 |
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echo ' ' |
| 296 |
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else echo "No Atmos output file in rank_$rnkA" ; fi |
| 297 |
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| 298 |
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fi |
| 299 |
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| 300 |
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exit 0 |
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