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view on githubraw file Latest commit b837625b on 2007-01-11 17:56:31 UTC
b837625b2f Andr*0001 #!/bin/csh
0002 #
0003 # Example PBS script to run a job on the myrinet-3 cluster.
0004 # The lines beginning #PBS set various queuing parameters.
0005 #
0006 # o -N Job Name
0007 #PBS -N fizhi
0008 #
0009 #
0010 # o -l resource lists that control where job goes
0011 # here we ask for 3 nodes, each with the attribute "p4".
0012 #PBS -l nodes=6:p4
0013 #
0014 #PBS -q four-twelve
0015 #
0016 # o Where to write output
0017 # #PBS -e TTT.err.$$
0018 #
0019 # #PBS -o TTT.out.$$
0020 #
0021 #
0022 # o Export all my environment variables to the job
0023 #PBS -V
0024 #
0025
0026 echo 'start'
0027 #----------------------------------------------
0028 set namPBS=fizhi
0029 set runDir=/SCRATCH/s04/molod/fizhi-cs-32x32x40/input
0030 set executable=/SCRATCH/s04/molod/fizhi-cs-32x32x40/build/mitgcmuv
0031 #-------------------
0032 # echo 'run in dir :' $runDir
0033 cd $runDir
0034
0035 set its=`egrep 'nIter0' data | sed 's/ nIter0=//'| sed 's/,$//'`
0036
0037 set numPBS=`echo $PBS_NODEFILE | sed 's/\/usr\/spool\/PBS\/aux\///g'| sed 's/\.cg01//g'`
0038
0039 #-- avoid any output before this point !
0040 #----------------------------------------------
0041 #echo $PBS_NODEFILE
0042 #cat $PBS_NODEFILE
0043 #echo 'The list above shows the nodes this job has exclusive access to.'
0044 #echo 'The list can be found in the file named in the variable $PBS_NODEFILE'
0045
0046 rm -f run_here
0047 date > run_here
0048 cat $PBS_NODEFILE >> run_here
0049 echo 'PBS job Number:' $numPBS >> run_here
0050 echo on `hostname` run $executable 'in dir:' $runDir >> run_here
0051
0052 #-------------------
0053 rm -f IamReady
0054 echo on `hostname` run $executable 'in dir:' `pwd`
0055
0056 #-------------------
0057 cp -p run_here std_outp
0058 echo ' ' >> std_outp
0059
0060 cat $PBS_NODEFILE > mf
0061 set ncpus = ( `wc -l mf | awk '{print $1}'` )
0062 if ( $ncpus == 1 ) then
0063 $executable >>& std_outp
0064 set out=$?
0065 echo 'end with status' $out
0066 else
0067 /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 $executable
0068 set out=$?
0069 echo 'end with status' $out
0070 set out=0
0071 endif
0072
0073 echo 'Copying datetime file to datetime0 - time is: ' `cat datetime`
0074 cp datetime datetime0
0075
0076 set ite=`grep CHECKPOINT STDOUT.0000 | grep ckptA | sed 's/(PID.TID 0000.0001) %CHECKPOINT//' | sed 's/ //g' | sed 's/ckptA//'`
0077 set nitPick = `/home/molod/bin/add0upto10c $ite`
0078 if ( -f pickup.ckptA.001.001.data ) then
0079 echo 'file:' pickup.ckptA.001.001.data 'exist'
0080 if ( $out == 0 ) then
0081 #- prepare new submission :
0082 echo 'Copy pickup ckptA files to pickup ' $nitPick 'files'
0083 mv pickup.ckptA.001.001.data pickup.$nitPick.001.001.data
0084 mv pickup.ckptA.002.001.data pickup.$nitPick.002.001.data
0085 mv pickup.ckptA.003.001.data pickup.$nitPick.003.001.data
0086 mv pickup.ckptA.004.001.data pickup.$nitPick.004.001.data
0087 mv pickup.ckptA.005.001.data pickup.$nitPick.005.001.data
0088 mv pickup.ckptA.006.001.data pickup.$nitPick.006.001.data
0089 mv pickup.ckptA.001.001.meta pickup.$nitPick.001.001.meta
0090 mv pickup.ckptA.002.001.meta pickup.$nitPick.002.001.meta
0091 mv pickup.ckptA.003.001.meta pickup.$nitPick.003.001.meta
0092 mv pickup.ckptA.004.001.meta pickup.$nitPick.004.001.meta
0093 mv pickup.ckptA.005.001.meta pickup.$nitPick.005.001.meta
0094 mv pickup.ckptA.006.001.meta pickup.$nitPick.006.001.meta
0095 mv pickup_fizhi.ckptA.001.001.data pickup_fizhi.$nitPick.001.001.data
0096 mv pickup_fizhi.ckptA.002.001.data pickup_fizhi.$nitPick.002.001.data
0097 mv pickup_fizhi.ckptA.003.001.data pickup_fizhi.$nitPick.003.001.data
0098 mv pickup_fizhi.ckptA.004.001.data pickup_fizhi.$nitPick.004.001.data
0099 mv pickup_fizhi.ckptA.005.001.data pickup_fizhi.$nitPick.005.001.data
0100 mv pickup_fizhi.ckptA.006.001.data pickup_fizhi.$nitPick.006.001.data
0101 mv pickup_fizhi.ckptA.001.001.meta pickup_fizhi.$nitPick.001.001.meta
0102 mv pickup_fizhi.ckptA.002.001.meta pickup_fizhi.$nitPick.002.001.meta
0103 mv pickup_fizhi.ckptA.003.001.meta pickup_fizhi.$nitPick.003.001.meta
0104 mv pickup_fizhi.ckptA.004.001.meta pickup_fizhi.$nitPick.004.001.meta
0105 mv pickup_fizhi.ckptA.005.001.meta pickup_fizhi.$nitPick.005.001.meta
0106 mv pickup_fizhi.ckptA.006.001.meta pickup_fizhi.$nitPick.006.001.meta
0107 mv pickup_vegtiles.ckptA.001.001.data pickup_vegtiles.$nitPick.001.001.data
0108 mv pickup_vegtiles.ckptA.002.001.data pickup_vegtiles.$nitPick.002.001.data
0109 mv pickup_vegtiles.ckptA.003.001.data pickup_vegtiles.$nitPick.003.001.data
0110 mv pickup_vegtiles.ckptA.004.001.data pickup_vegtiles.$nitPick.004.001.data
0111 mv pickup_vegtiles.ckptA.005.001.data pickup_vegtiles.$nitPick.005.001.data
0112 mv pickup_vegtiles.ckptA.006.001.data pickup_vegtiles.$nitPick.006.001.data
0113 echo 'Change start iteration number for next run '
0114 sed "s/ nIter0=$its/ nIter0=$ite/" data > data.tmp.$numPBS
0115 mv data.tmp.$numPBS data
0116 sleep 5
0117 endif
0118 else
0119 echo 'file:' pickup.ckptA.001.001.data 'do not exist !'
0120 set out=9
0121 endif
0122
0123 if ( $out != 0 ) then
0124 echo 'bad return status => STOP here'
0125 exit $out
0126 endif
0127
0128 touch IamReady
0129 qsub runScript
0130
0131 exit
