Parallel with job array

Overview

Teaching: 5 min min
Exercises: 0 min

Questions

• How to run parallel with job array in Palmetto

Objectives

Here is a sample of running job array in batch script:

The following example create 8 different directories then go into each directory, creating a new txt file:

#PBS -N Test_Array_Job
#PBS -l select=1:ncpus=1:mem=1gb
#PBS -l walltime=00:02:00
#PBS -j oe
#PBS -J 1-8

cd $PBS_O_WORKDIR

mkdir dir_PBS_${PBS_ARRAY_INDEX}
cd dir_PBS_${PBS_ARRAY_INDEX}
touch file${PBS_ARRAY_INDEX}.txt

Note: -J create an array job that drive the ${PBS_ARRAY_INDEX}

Key Points

• parallel, job array