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 For cluster specific info see hermes, lion, lutzow or townhill.

The basics

  • What clusters are available?
    • In preparation for moving to the forum the clusters have been re-organised into two
      • The desktop beowulf machines (GX240/P530) with head nodes lion, lutzow and moselle
      • The rackmount beowulf machines (PE1425) with head nodes hermes, townhill and seville
    • It's expected that the rackmounted machines will be moved to the forum server room within a couple of months of the move to the forum being finished, the older desktop machines will take longer to move.

  • 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 From outside Edinburgh, you can still see this web page, thus:

  • ssh -L
  • now point your browser at localhost:8000/ganglia
  • this has stopped working since the move to FC5 (support ticket 30296)

Misc Tips and tricks

  • A sample script calling qsub is /group/project/ami3/amiasr_shef/asrcore/tools/ 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
Topic revision: r12 - 08 May 2008 - 09:48:43 - IainRae
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