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This area is for users to share tips and tricks about using the local Grid Engine setup.

Local official documentation for Grid Engine can be found at http://www.inf.ed.ac.uk/systems/beowulf/doc/gridengine.html For cluster specific info see hermes, lion, lutzow or townhill.

The basics

  • What clusters are available

  • GridEngine is configured so that the cluster cores each have the same amount of memory (1Gb per core on all the above clusters). Other configurations would be possible - add this to the wish list if you want it.

You can monitor the load on the above Informatics compute resources at http://bwganglia.inf.ed.ac.uk/ganglia/

Misc Tips and tricks

  • A sample script calling qsub is /group/project/ami3/amiasr_shef/asrcore/tools/submitjob.hermes a not so nice one /home/vstrom/software/cstr/scripts/multisyn_build/bin/do_alignment_parallel Both do not make use of "submit scripts" since changing the file name for stderr and stdout does not work then, i.e. "qsub -o fname" works, "qsub submit_script" with "#$ -o fname" in submit_script does not. -- VolkerStrom - 13 Dec 2005

  • Some generic jobs submission advice
    • Sanity check your environment before you start to run your job. If the output is going to a file in ~/longrunning_jobs/results/temp then check that the directory exists and is writable before starting any computation.
    • Write intermediate and results files to /disk/scratch on the local filesystem then copy them back to your home directory, if the copy fails you'll still have a set of results that could be retrieved. -- IainRae - 18 Apr 2006
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Topic revision: r9 - 19 Jun 2006 - 09:43:23 - Main.s0565860
 
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