OpenPBS/Torque Usage

Batch Processing

The Portable Batch System, PBS, is a workload management system for Linux clusters. It supplies command to submit, monitor, and delete jobs. It has the following components.

Below are the steps needed to run production code:
  1. Create a job script containing the following PBS options:

  2. Submit the job script file to PBS.

  3. Monitor the job.

Running serial codes

On the master node no production is allowed and any serial execution program lasting more than 5 minutes is automatically deleted. Execution of serial application on computational nodes can be only done the through the queuing system, even for interactive runs.

Running MPI parallel codes

To run MPI parallel program users have to use the lam environments.

Tips and Tricks

How to specify myri parameter in the job submission if myrinet card is broken down (on Opteron)

if you need myrinet, always ask for it in your qsub statement, e.g.
qsub -l walltime=12:00:00,nodes=2:ppn=2:myri
and the scheduler will avoid non-myrinet nodes. If you don't need myrinet (single- or dual-cpu jobs) please do not append :myri, so you will leave more myrinet nodes free and also if some node has the myrinet card out of order, you can use the node for serial and 2 cpus jobs