Sun Grid Engine

A processing grid / cluster has been set up on the BCNI compute server machines using SGE (Sun Grid Engine) and is now available for general use.

The full SGE user documentation can be found at [1]

Most usage in an imaging context is with FSL, and the queues Ian has set up are in accordance with FSL usage. See: [2] and [3]

BCNI users can check with Cinly Ooi or Roger Tait for advice on using the grid with FSL or Freesurfer.

To use the grid you will need to set up your shell environment.

Add the following to your .bashrc file:

. /opt/sge/default/common/settings.sh

(Note there's a space after the initial dot.)

You'll probably also want to add:

export FSLPARALLEL=1

Recently created user accounts will already have these added to their shell environment.

Cinly Ooi has produced a document which gives fuller details of grid usage.

Some useful commands:

qhost : gives a quick overview of the resources available on grid hosts

qhost -f : as above but with queue status

qstat : see the status of your jobs

qstat -f : lists full queue status

qsub : submit a job to a queue

There are some example jobs in /opt/sge/examples/jobs which are worth looking at.

Grid jobs run at lower priority than conventional direct application usage, so shouldn't have too much impact on general processing.