Blog post edited by Anonymous - "Migration of unmigrated content due to installation of a new plugin"

I write a lot of submissions scripts for a lot of users on the HPCC. I find myself using the same tricks over and over again. Recently I came up with the following script as a quick way to cover most of my job submission needs.

What is nice for me is I don't have to rewrite the script for every job. All of the job options can be overwritten on the command line and the script uses the PBS_JOBNAME to determine an executable to run in the current directory. It also replaces any dashes in the name with spaces as a crude method to include input arguments. Since PBS_ARRAYID is automatically appended to the end of the PBS_JOBNAME this also allows job arrays to be used as an input variable.

I hope you find this useful,

• Dirk

  !/bin/bash

  PBS -l nodes=1:ppn=1,walltime=08:00:00,mem=2gb,feature=gbe

  PBS -j oe

  PBS -m ae

  PBS -N a.out

  I personally use openmpi as my default mpi library and not mvapich

  module unload mvapich module load openmpi

  Change to the original working directory where the qsub command is executed

  cd ${PBS_O_WORKDIR}

  set OMP thread is appropriate for MPI jobs

  export OMP_NUM_THREADS=cat ${PBS_NODEFILE} | wc -l

  Run the jobname as a command in the local directory and

  use the ARRAYID as the first input variable if avaliable

  Uses '-' in the jobname to designate spaces

  Example:

  Run a simple single thread program

  qsub -N myprogram quick.qsub

  Run a simple program with three different input numbers

  qsub -N myprogram -t 100,200,300 quick.qsub

  Run a basic openmp program

  qsub -N myprogram -l nodes=1:ppn=8 quick.qsub

  Run a basic openmpi program

  qsub -N mpirun-myprogram -l nodes=64:ppn=1,feature=ib quick.qsub

  Display the execution command for debugging

  echo ./${PBS_JOBNAME} | sed "s/-/ /g"

  Run the command using the PBS_JOBNAME to determine the executable name and input variables

  echo ./${PBS_JOBNAME} | sed "s/-/ /g"

  Display the runtime and resources used for the job

  qstat -f ${PBS_JOBID}

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Blogpost migrated from ICER Wiki using custom python script. Comment on errors below.