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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 fizhi |
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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=6:p4 |
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# |
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#PBS -q four-twelve |
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# |
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# o Where to write output |
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# #PBS -e TTT.err.$$ |
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# |
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# #PBS -o TTT.out.$$ |
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# |
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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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|
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echo 'start' |
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#---------------------------------------------- |
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set namPBS=fizhi |
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set runDir=/SCRATCH/s04/molod/fizhi-cs-32x32x10-newvar/input |
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set executable=/SCRATCH/s04/molod/fizhi-cs-32x32x10-newvar/build/mitgcmuv |
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#------------------- |
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# echo 'run in dir :' $runDir |
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cd $runDir |
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|
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set its=`egrep 'nIter0' data | sed 's/ nIter0=//'| sed 's/,$//'` |
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|
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set numPBS=`echo $PBS_NODEFILE | sed 's/\/usr\/spool\/PBS\/aux\///g'| sed 's/\.cg01//g'` |
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|
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#-- avoid any output before this point ! |
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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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|
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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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|
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#------------------- |
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rm -f IamReady |
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echo on `hostname` run $executable 'in dir:' `pwd` |
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|
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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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|
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cat $PBS_NODEFILE > mf |
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set ncpus = ( `wc -l mf | awk '{print $1}'` ) |
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if ( $ncpus == 1 ) then |
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$executable >>& std_outp |
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set out=$? |
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echo 'end with status' $out |
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else |
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/usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/pgi/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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set out=0 |
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endif |
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|
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echo 'Copying datetime file to datetime0 - time is: ' `cat datetime` |
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cp datetime datetime0 |
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|
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set ite=`grep CHECKPOINT STDOUT.0000 | grep ckptA | sed 's/(PID.TID 0000.0001) %CHECKPOINT//' | sed 's/ //g' | sed 's/ckptA//'` |
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set nitPick = `/home/molod/bin/add0upto10c $ite` |
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if ( -f pickup.ckptA.001.001.data ) then |
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echo 'file:' pickup.ckptA.001.001.data 'exist' |
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if ( $out == 0 ) then |
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#- prepare new submission : |
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echo 'Copy pickup ckptA files to pickup ' $nitPick 'files' |
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mv pickup.ckptA.001.001.data pickup.$nitPick.001.001.data |
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mv pickup.ckptA.002.001.data pickup.$nitPick.002.001.data |
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mv pickup.ckptA.003.001.data pickup.$nitPick.003.001.data |
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mv pickup.ckptA.004.001.data pickup.$nitPick.004.001.data |
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mv pickup.ckptA.005.001.data pickup.$nitPick.005.001.data |
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mv pickup.ckptA.006.001.data pickup.$nitPick.006.001.data |
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mv pickup.ckptA.001.001.meta pickup.$nitPick.001.001.meta |
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mv pickup.ckptA.002.001.meta pickup.$nitPick.002.001.meta |
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mv pickup.ckptA.003.001.meta pickup.$nitPick.003.001.meta |
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mv pickup.ckptA.004.001.meta pickup.$nitPick.004.001.meta |
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mv pickup.ckptA.005.001.meta pickup.$nitPick.005.001.meta |
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mv pickup.ckptA.006.001.meta pickup.$nitPick.006.001.meta |
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mv pickup_fizhi.ckptA.001.001.data pickup_fizhi.$nitPick.001.001.data |
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mv pickup_fizhi.ckptA.002.001.data pickup_fizhi.$nitPick.002.001.data |
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mv pickup_fizhi.ckptA.003.001.data pickup_fizhi.$nitPick.003.001.data |
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mv pickup_fizhi.ckptA.004.001.data pickup_fizhi.$nitPick.004.001.data |
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mv pickup_fizhi.ckptA.005.001.data pickup_fizhi.$nitPick.005.001.data |
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mv pickup_fizhi.ckptA.006.001.data pickup_fizhi.$nitPick.006.001.data |
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mv pickup_fizhi.ckptA.001.001.meta pickup_fizhi.$nitPick.001.001.meta |
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mv pickup_fizhi.ckptA.002.001.meta pickup_fizhi.$nitPick.002.001.meta |
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mv pickup_fizhi.ckptA.003.001.meta pickup_fizhi.$nitPick.003.001.meta |
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mv pickup_fizhi.ckptA.004.001.meta pickup_fizhi.$nitPick.004.001.meta |
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mv pickup_fizhi.ckptA.005.001.meta pickup_fizhi.$nitPick.005.001.meta |
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mv pickup_fizhi.ckptA.006.001.meta pickup_fizhi.$nitPick.006.001.meta |
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mv pickup_vegtiles.ckptA.001.001.data pickup_vegtiles.$nitPick.001.001.data |
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mv pickup_vegtiles.ckptA.002.001.data pickup_vegtiles.$nitPick.002.001.data |
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mv pickup_vegtiles.ckptA.003.001.data pickup_vegtiles.$nitPick.003.001.data |
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mv pickup_vegtiles.ckptA.004.001.data pickup_vegtiles.$nitPick.004.001.data |
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mv pickup_vegtiles.ckptA.005.001.data pickup_vegtiles.$nitPick.005.001.data |
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mv pickup_vegtiles.ckptA.006.001.data pickup_vegtiles.$nitPick.006.001.data |
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echo 'Change start iteration number for next run ' |
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sed "s/ nIter0=$its/ nIter0=$ite/" data > data.tmp.$numPBS |
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mv data.tmp.$numPBS data |
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sleep 5 |
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endif |
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else |
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echo 'file:' pickup.ckptA.001.001.data 'do not exist !' |
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set out=9 |
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endif |
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|
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if ( $out != 0 ) then |
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echo 'bad return status => STOP here' |
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exit $out |
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endif |
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|
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touch IamReady |
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qsub runScript |
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|
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exit |
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