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guide:moab

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guide:moab [2013/07/18 16:37]
ischeepers [SUN HYBRID SYSTEM] 		guide:moab [2021/12/09 16:42] (current)
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 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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 In this example we have requested four C2070 GPUs and 32 processors In this example we have requested four C2070 GPUs and 32 processors
  
-====BlueGene/P CLUSTER====+====(Obsolete) BlueGene/P CLUSTER==== 
 + 
 +The BlueGene has been decommissioned and is no longer available.
  
 Users can only use 32, 64, 128, 256 or 512 processors (''ppn''). Users can only use 32, 64, 128, 256 or 512 processors (''ppn'').
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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.1374158244.txt.gz · Last modified: 2021/12/09 16:42 (external edit)

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