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quick:pbspro [2015/09/17 12:28]
andyr [Example 6 : job array]
quick:pbspro [2020/05/26 12:03] (current)
kevin
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 ====== Job submission using PBSPro ====== ====== Job submission using PBSPro ======
  
-As of January 2014, CHPC has a new scheduler - PBSPro.+The CHPC system uses the PBSPro ​scheduler.
  
-Main user documentation can be found at http://resources.altair.com/​pbs/documentation/​support/​PBSProUserGuide12.1.pdf+Main user documentation can be found at [[https://www.altair.com/​pbs-works-documentation/​|Altair]]
  
 But here is a summary of how to submit jobs at CHPC. But here is a summary of how to submit jobs at CHPC.
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 ... ...
 </​code>​ </​code>​
- 
-===== Example 6 : job array ===== 
-See [[howto:​pbs-pro_job_submission_examples#​job_arrays|here]] for a longer explanation. 
-<file bash simple_job_array.pbs>​ 
-#! /bin/bash 
-#PBS -l select=1:​ncpus=1 
-#PBS -l walltime=00:​01:​00 
-#PBS -o /​lustre/​SCRATCH5/​users/​username/​simple_jobarray.stderr 
-#PBS -e /​lustre/​SCRATCH5/​users/​username/​simple_jobarray.stderr 
-#PBS -M youremail@address.com 
-#PBS -m abe 
-#PBS -N J_example 
-#PBS -J 1-24 
- 
- 
-# Make sure we're in the right working directory 
-cd /​export/​home/​username/​scratch5/​ 
- 
-#sleep a random number of seconds (<10) 
-sleep $[ ( $RANDOM % 10 )  + 1 ]s 
- 
-#see what happens when we write to a file... 
-echo "​Wawaweewaa! This is sub-job ${PBS_ARRAY_INDEX} of job ${PBS_JOBID} running on ${HOSTNAME} run by ${USER} writing to stdout!"​ 
-echo "​Wawaweewaa! This is sub-job ${PBS_ARRAY_INDEX} of job ${PBS_JOBID} running on ${HOSTNAME} run by ${USER} writing to stderr!"​ 1>&2 
-echo "​Wawaweewaa! This is sub-job ${PBS_ARRAY_INDEX} of job ${PBS_JOBID} running on ${HOSTNAME} run by ${USER} appending to simple_jobarray.txt"​ >> simple_jobarray.txt 
-</​file>​ 
- 
-Thing to note: the stdout and stderr outputs do not all get joined together as they might with an mpi job. 
- 
 ===== Further examples ===== ===== Further examples =====
   * Various [[howto:​bioinformatics?&#​basic_examples|bioinformatics examples]] illustrate some further possibilities. Specifically the blast examples illustrate job arrays and job dependencies.   * Various [[howto:​bioinformatics?&#​basic_examples|bioinformatics examples]] illustrate some further possibilities. Specifically the blast examples illustrate job arrays and job dependencies.
   * This [[howto:​gpu_gromacs#​pbs_job_script|gromacs example]] shows an interesting case where mpi, openmp and the gpus are used in a single job.   * This [[howto:​gpu_gromacs#​pbs_job_script|gromacs example]] shows an interesting case where mpi, openmp and the gpus are used in a single job.
/var/www/wiki/data/attic/quick/pbspro.1442485701.txt.gz · Last modified: 2015/09/17 12:28 by andyr