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guide:moab

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guide:moab [2013/07/18 16:40]
ischeepers [BlueGene/P CLUSTER] 		guide:moab [2021/12/09 16:42] (current)
Line 70: Line 70:
  
 Edit the file with, for example,  ''vi mpi.job'' Edit the file with, for example,  ''vi mpi.job''
- +<file bash mpi.job> 
-  #/bin/sh +#/bin/sh 
-  #MSUB -l nodes=1:ppn=8 +#MSUB -l nodes=1:ppn=8 
-  #MSUB -l feature=nehalem|harpertown +#MSUB -l feature=nehalem|harpertown 
-  #MSUB -l walltime=3:00:00 +#MSUB -l walltime=3:00:00 
-  #MSUB -m be +#MSUB -m be 
-  #MSUB -V +#MSUB -V 
-  #MSUB -o /export/home/username/scratch/stdout +#MSUB -o /export/home/username/scratch/stdout 
-  #MSUB -e /export/home/username/scratch/stderr +#MSUB -e /export/home/username/scratch/stderr 
-  #MSUB -d /export/home/username/scratch +#MSUB -d /export/home/username/scratch 
-  #MSUB -mb +#MSUB -mb 
-  ##### Running commands +##### Running commands 
-  exe=/opt/gridware/usersexecutable +exe=/opt/gridware/usersexecutable 
-  nproc=`cat $PBS_NODEFILE | wc -l` +nproc=`cat $PBS_NODEFILE | wc -l` 
-  mpirun -np $nproc -machinefile $PBS_NODEFILE $exe > users.out +mpirun -np $nproc -machinefile $PBS_NODEFILE $exe > users.out 
 +</file>
  
  
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 Edit with ''vi mpi.job'' as before. Edit with ''vi mpi.job'' as before.
- +<file bash mpi.job> 
-  ###These lines are for Moab +###These lines are for Moab 
-  #MSUB -l nodes=2:ppn=16:gpus=4 +#MSUB -l nodes=2:ppn=16:gpus=4 
-  #MSUB -l feature=c2070 +#MSUB -l feature=c2070 
-  #MSUB -l walltime=168:00:00 +#MSUB -l walltime=168:00:00 
-  #MSUB -m be +#MSUB -m be 
-  #MSUB -V +#MSUB -V 
-  #MSUB -o /GPU/home/username/stdout +#MSUB -o /GPU/home/username/stdout 
-  #MSUB -e /GPU/home/username/stderr +#MSUB -e /GPU/home/username/stderr 
-  #MSUB -d /GPU/home/username +#MSUB -d /GPU/home/username 
-  #MSUB -mb +#MSUB -mb 
-  ##### Running commands +##### Running commands 
-  echo "original machine file is:" +echo "original machine file is:" 
-  echo "++++++++++" +echo "++++++++++" 
-  cat $PBS_NODEFILE +cat $PBS_NODEFILE 
-  echo "++++++++++" +echo "++++++++++" 
-  cat $PBS_NODEFILE|sed -e 's/.*/&-ib/'>$PBS_STEP_OUT.hostfile +cat $PBS_NODEFILE|sed -e 's/.*/&-ib/'>$PBS_STEP_OUT.hostfile 
-  echo "modified machine file is:" +echo "modified machine file is:" 
-  echo "++++++++++" +echo "++++++++++" 
-  cat $PBS_STEP_OUT.hostfile +cat $PBS_STEP_OUT.hostfile 
-  exe=location of the executable +exe=location of the executable 
-  nproc=`cat $PBS_NODEFILE | wc -l` +nproc=`cat $PBS_NODEFILE | wc -l` 
-  cd /GPU/home/username/testjob/ +cd /GPU/home/username/testjob/ 
-  mpirun $nproc $exe > /GPU/home/username/testjob/OUTPUT +mpirun $nproc $exe > /GPU/home/username/testjob/OUTPUT 
 +</file>
  
  
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 The ''mpi.job'' file contains: The ''mpi.job'' file contains:
- +<file bash mpi.job> 
-  ###These lines are for Moab +###These lines are for Moab 
-  #MSUB -l ppn=128 +#MSUB -l ppn=128 
-  #MSUB -l walltime=168:00:00 +#MSUB -l walltime=168:00:00 
-  #MSUB -m be +#MSUB -m be 
-  #MSUB -V +#MSUB -V 
-  #MSUB -o /CHPC/work/username/testjob/out +#MSUB -o /CHPC/work/username/testjob/out 
-  #MSUB -e /CHPC/work/username/testjob/err +#MSUB -e /CHPC/work/username/testjob/err 
-  #MSUB -d /CHPC/work/username/testjob/ +#MSUB -d /CHPC/work/username/testjob/ 
-  #MSUB -mb +#MSUB -mb 
-  ##### Running commands +##### Running commands 
-  /bgsys/drivers/ppcfloor/bin/mpirun -np 128 \ +/bgsys/drivers/ppcfloor/bin/mpirun -np 128 \ 
-  -mode VN -exe LOCATIONOFTHEEXECUTABLE +-mode VN -exe LOCATIONOFTHEEXECUTABLE 
- +</file>
- +
 As before, use ''msub mpi.job'' to submit the job. As before, use ''msub mpi.job'' to submit the job.
  
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 To get the definitions, and details of other flags, of the  MSUB statements run the command ''man msub'' [[http://www.adaptivecomputing.com/resources/docs/mwm/commands/msub.php|online version]]. To get the definitions, and details of other flags, of the  MSUB statements run the command ''man msub'' [[http://www.adaptivecomputing.com/resources/docs/mwm/commands/msub.php|online version]].
  
- +<file bash job.msub> 
-  ###These lines are for Moab +###These lines are for Moab 
-  #MSUB -l nodes=4:ppn=8 +#MSUB -l nodes=4:ppn=8 
-  #MSUB -l walltime=2:00:00 +#MSUB -l walltime=2:00:00 
-  #MSUB -m be +#MSUB -m be 
-  #MSUB -o /export/home/nmonama/scratch/test/dlpoly.3.07.out +#MSUB -o /export/home/nmonama/scratch/test/dlpoly.3.07.out 
-  #MSUB -e /export/home/nmonama/scratch/test/dlpoly.3.07.err +#MSUB -e /export/home/nmonama/scratch/test/dlpoly.3.07.err 
-  #MSUB -d /export/home/nmonama/scratch/test +#MSUB -d /export/home/nmonama/scratch/test 
-  #MSUB -mb +#MSUB -mb 
-  #MSUB -M nmonama@csir.co.za+#MSUB -M nmonama@csir.co.za
      
-  ##### Running commands +##### Running commands 
-  NP=`cat $PBS_NODEFILE | wc –l` +NP=`cat $PBS_NODEFILE | wc –l` 
-  mpirun –np $NP –machinefile $PBS_NODEFILE DLPOLY_3.07.SPARC.Y +mpirun –np $NP –machinefile $PBS_NODEFILE DLPOLY_3.07.SPARC.Y 
 +</file>
  
 Details of each line of the job script: Details of each line of the job script:
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 ^ showres | Show existing reservations | ^ showres | Show existing reservations |
 ^ showstart | Show estimate of when job can or will start | ^ showstart | Show estimate of when job can or will start |
-^ Checkjob | Provide report for specified job |+^ checkjob | Provide report for specified job |
      
  
/app/dokuwiki/data/attic/guide/moab.1374158402.txt.gz · Last modified: 2021/12/09 16:42 (external edit)

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