Cluster Usage

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Information on how to use the Shoichet Lab Cluster. Note this information is only relevant if you have ssh access to the cluster.

To request a shell on a cluster node, type


Or for a shell on a specific set of nodes (say any from the node-5-* or node-6-* sets):

qrsh -q all.q -l hostname="node-[56]*" -now no

The -now no parameter is necessary if the cluster is otherwise full and you'll have to wait to get a job.

If you're interested in writing your own cluster scripts, the nice way of doing this is to use the following lines:

#$ -q all.q

The first line uses the correct queue, all.q for basically any job.

#$ -t 1-500

This line (modify the 500 to mean the max) should be used in concert with $SGE_TASK_ID to write array job scripts, instead of scripts that only run single jobs.

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