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jmc |
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#!/bin/csh |
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# |
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# Example PBS script to run a job on the myrinet-3 cluster. |
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# The lines beginning #PBS set various queuing parameters. |
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# |
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# o -N Job Name |
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#PBS -N oce_1 |
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# |
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# |
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# o -l resource lists that control where job goes |
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# here we ask for 3 nodes, each with the attribute "p4". |
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#PBS -l nodes=4:p4 |
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# |
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# o Where to write output |
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# #PBS -e TTT.err |
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# #PBS -o TTT.out |
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# |
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# o Export all my environment variables to the job |
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#PBS -V |
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# |
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echo 'start' |
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#------------------- |
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set namPBS=oce_1 |
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set runDir=$SC6/oce_glob/run_1 |
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set r2nDir=$SC6/oce_glob/run00 |
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set executable=mitgcmuv.ifc+mpi |
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set nit1mn=1800 |
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set endRun=100 |
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set partmn=25 |
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#------------------- |
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# echo 'run in dir :' $runDir |
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set prc2='N' |
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cd $runDir |
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set its=`egrep 'nIter0' data | sed 's/ nIter0=//'| sed 's/,$//'` |
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set nms=`expr $its / $nit1mn` |
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jmc |
1.2 |
set nMs = `printf "%3.3i\n" $nms` |
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jmc |
1.1 |
set nme=`expr $nms + $partmn` |
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jmc |
1.2 |
set nMe = `printf "%3.3i\n" $nme` |
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jmc |
1.1 |
set ite=`expr $nme \* $nit1mn` |
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set numPBS=`echo $PBS_NODEFILE | sed 's/\/usr\/spool\/PBS\/aux\///g'| sed 's/\.cg01//g'` |
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touch move_TTT_files |
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echo mv $namPBS.o$numPBS TTT.out.$nMe >> move_TTT_files |
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echo mv $namPBS.e$numPBS TTT.err.$nMe >> move_TTT_files |
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#---------------------------------------------- |
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echo $PBS_NODEFILE |
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cat $PBS_NODEFILE |
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echo 'The list above shows the nodes this job has exclusive access to.' |
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echo 'The list can be found in the file named in the variable $PBS_NODEFILE' |
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rm -f run_here |
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date > run_here |
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cat $PBS_NODEFILE >> run_here |
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echo 'PBS job Number:' $numPBS >> run_here |
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echo on `hostname` run $executable 'in dir:' $runDir >> run_here |
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if ( $nms >= $endRun ) then |
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echo 'Run already finished : month' $nms |
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exit 9 |
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endif |
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echo on `hostname` run $executable 'in dir:' `pwd` |
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echo 'start at month=' $nMs '(it=' $its '), run until mn=' $nMe '(it=' $ite ')' |
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echo 'start at month=' $nms '(it=' $its '), run until mn=' $nme '(it=' $ite ')'>> run_here |
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#------------------- |
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if ( -f $r2nDir/IamReady ) then |
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set prc2=`sed -n '2 p' $PBS_NODEFILE` |
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echo send 2nd job on $prc2 |
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rsh $prc2 $r2nDir/runscript >& $r2nDir/TTT.out2.$nMe & |
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else |
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echo 'no file dir_run_2/IamReady => no 2nd run.' |
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endif |
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#------------------- |
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#cp -p run_here std_outp |
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#echo ' ' >> std_outp |
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# ./$executable >>& std_outp |
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cat $PBS_NODEFILE > mf |
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set ncpus = ( `wc -l mf | awk '{print $1}'` ) |
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/usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/intel/bin/mpirun.ch_gm -machinefile mf --gm-kill 5 -v -np $ncpus ./$executable |
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set out=$? |
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echo 'end with status' $out |
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jmc |
1.2 |
set iTe = `printf "%10.10i\n" $ite` |
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jmc |
1.1 |
if ( -f pickup.$iTe.001.001.data ) then |
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set out=0 |
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else |
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set out=1 |
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endif |
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echo 'end with status' $out |
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if ( $out != 0 ) then |
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echo 'bad return status => STOP here' |
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else |
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#mv std_outp std_outp.$nMe |
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cp -p run_here std_outp.$nMe |
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echo ' ' >> std_outp.$nMe |
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cat STDOUT.0000 >> std_outp.$nMe |
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mv -f STDOUT.000? STDERR.000? temp |
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#- prepare new submission : |
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sed "s/ nIter0=$its/ nIter0=$ite/" data > TTT.tmp |
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mv TTT.tmp data |
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endif |
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if ( $out == 0 ) then |
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if ( $nme >= $endRun ) then |
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echo 'Run finished : month' $nme 'done !' |
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else |
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qsub runScript |
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endif |
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endif |
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exit $out |
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