Wilke:Using lab cluster

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Revision as of 15:53, 20 September 2012

THE WILKE LAB

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Using the lab cluster

The lab cluster is phylocluster.ccbb.utexas.edu. You will need an account on the cluster to be able to use it.

The operating system on the cluster is Linux. If you have no experience with the Linux shell and command line, you will have to learn about that first. This is a good tutorial for beginners: [1]

The cluster uses the Sun Grid Engine (SGE) to distribute computing tasks over the various compute nodes that are available. You will have to start all jobs that you want to run using SGE. This is different from how you run jobs on your computer at home, so even if you have plenty of experience with Linux on your own computer you may not know your way around SGE.

A brief introduction to using SGE is given here: https://wikis.utexas.edu/display/CCBB/sge-tutorial

There's a lot of material in this document. The most important part is that every job on the cluster should use the provided bare-bones script as a starting point: https://wikis.utexas.edu/display/CCBB/sge-tutorial#sge-tutorial-BareBonesScript

If you have many independent runs that can run in parallel and don't need to talk to each other, you should also read this page: https://wikis.utexas.edu/display/CCBB/sge-task-array

Finally, it is good practice to copy your jobs to /state/partition1 before running them. /state/partition1 refers to the local hard drive on the compute node. We will soon provide a tutorial on how to do this exactly.

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