Compute Cluster

From Ece

How is a job submitted to the compute cluster?

You can submit a job to the cluster using the qsub command from the command line of the host, talus.ece.msstate.edu. The syntax of the qsub command is:

   qsub [options] script_file

The script_file argument is the name of the script file that contains the commands to be run by your job.

For more information, type man qsub at the command prompt.

How are jobs monitored on the compute cluster?

You can monitor jobs that you have submitted to the compute cluster using the qmon command. qmon is a GUI that requires you to have either X-Win32 or X from the Cygwin utilities in the Windows environment in order to view it. If you are running Linux or MacOS, you will not need anything extra.

If you wish to see the status from the command line, use qstat. More information about qstat can be found by running man qstat from the command line.

What should be in the script file that is submitted with qsub?

A sample script is:

#!/bin/bash
# Sample script for Grindengine
# Replace items enclosed by {}
# Remove # to uncomment lines
# man qsub for more options and additional info

#$ -S /usr/bin/csh

#$ -V
#$ -cwd

#$ -M {email address for notification}
#$ -m {condition for notification, e.g. be for beginning and end}

#$ -o {file for standard output}
#$ -e {file for standard error}

{command line(s) to be executed}

How do I submit Matlab jobs to the cluster?

Matlab must be run in a non-interactive mode. You can do that by specifying the following in your batch file:

matbg INFILE.M OUTFILE

infile.m is the script file that has matlab commands.

IMPORTANT: Type "quit" as the last statement in your script. If you forget to do that, the batch job may run forever.

outfile is the file where the output of the Matlab script is saved.