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guide:moab [2013/07/18 16:40]
ischeepers [SUBMITTING A JOB USING MOAB]
guide:moab [2013/11/15 15:12] (current)
dane
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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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 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:
/var/www/wiki/data/pages/guide/moab.txt · Last modified: 2013/11/15 15:12 by dane