View source for Submitting jobs, interactively or to a cluster queue system

This is a brief summary for those who haven't found/read the [http://www-theor.ch.cam.ac.uk/IT/servers/maui/maui-pbs-introduction.html documentation] provided by the COs.

==Interactive==

The basic command for submitting jobs to a queue is qsub.

To submit interactively, using the following syntax:

 qsub -I -q [queue]

When sufficient nodes are available then a session opens and you can execute commands on the assigned nodes until the walltime specified by the queue.  Submitting interactively is handy if you need to keep a close eye on what's going on (though hopefully you might know what your job's meant to be doing anyway...).  Ideally though, it's best to avoid, since if there are no available nodes you can often be waiting around.

==Batch==

Batch jobs are generally executed from scripts.  An example script might be:

 #PBS -q [queue]
 #PBS -lwalltime=[hhh:mm:ss]
 
 cd $PBS_O_WORKDIR
 [commands to execute]

The first line specifies the queue to submit to.  Each queue has a specified walltime (specified by the initial letter) and number of cores (indicated by the number).  The queue configurations can be found here for:
*[http://www-theor.ch.cam.ac.uk/IT/servers/volkhan/volkhan-queues.html Volkhan]
*[http://www-theor.ch.cam.ac.uk/IT/servers/mek-quake/mek-quake-queues.html Mek-quake]
*[http://www-theor.ch.cam.ac.uk/IT/servers/clust/clust-queues.html Clust]

The second line can be used to specify a second (shorter) walltime.  This is handy if your job doesn't fit into a similar timeframe to the available queues (e.g. the shortest walltime is 24 hours on Volkhan).

The third line tells PBS to execute commands from the current working directory from which you submitted the job.

Better example scripts for each cluster are available at /info/pbs on each cluster.