Example PBS Job Script

Audience: Faculty, Postdocs, Researchers, Staff and Students

This KB Article References: High Performance Computing
This Information is Intended for: Faculty, Postdocs, Researchers, Staff, Students
Last Updated: May 31, 2018

This is an example PBS bash script:

#!/bin/bash
#PBS -l nodes=2:ppn=28,walltime=00:05:00
#PBS -N my_example_job
#PBS -q short

module load shared
module load mvapich2/gcc/64/2.2rc1

cd $HOME

mpirun ./myexec > /gpfs/home/<user>/output.txt

In this simple example, I want to run the executable called myexec. The output of myexec is captured in the file output.txt in the user’s home directory – this is decided by the program being run, which takes the first command line argument as the file to write to. The bash comments that begin as "#PBS" are PBS directives giving vital information to the batch scheduler.

The command

#PBS -l nodes=2:ppn=28,walltime=00:05:00

tells the batch scheduler that you are requesting 2 nodes (currently some SeaWulf nodes have 28 cores while others have 24), that you want to execute 28 MPI tasks on each node for 5 minutes. If your job exceeds the specified walltime (which is 5 minutes in this case), then your job will be killed.

The directive

#PBS -N my_example_job

gives the name "my_example_job" to your job.

The directive

#PBS -q short

indicates to the batch scheduler that you want to use the short queue.

You can see a list of other queues on SeaWulf.

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