Learn to Use HPC Systems and Supercomputers/

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PBS `qsub`

PBS `qsub`

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When you are new to PBS, the place to start is the qsub command, which submits jobs to your HPC systems. The only jobs that the qsubaccepts are scripts, so you’ll need to package your tasks appropriately. Here is a simple example script (myjob.pbs):

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#!/bin/bash
#PBS -N demo // job name
#PBS -o demo.txt // output file
#PBS -e demo.txt // error output file
#PBS -q workq // queue name
#PBS -l mem=100mb // requested memory size
mpiexec -machinefile /etc/myhosts -np 4 /home/user/area

The first line specified the shell to use in interpreting the script, while the next few lines starting with #PBS are directives that are passed to PBS. The first names the job, the next two specify where output and error output go, the next to last identifies the queue that is used, and the last lists a resource that will be needed, in this case 100 MB of memory. The blank line signals the end of PBS directives. Lines that follow the blank line indicate the actual job (details on the mpi commands are discussed later). Once you have created the batch script for your job, the qsub command is used to submit the job:

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qsub job.pbs

Some of the more commonly used qsub options are:

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