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
  • hermes 24 dual-processor-equivalent Dell PE1425 3.2GHz nodes with 2Gb RAM per node (48 cores) HermesBenchmarks
  • lion 64 single-processor Dell gx240 1.8GHz nodes with 1Gb RAM per node (64 cores) LionBenchmarks
  • lutzow 16 single-processor Dell 1.7GHz nodes with 1Gb RAM per node (16 cores) LutzowBenchmarks
  • townhill 34 quad-processor-equivalent Dell PE1425 3.2GHz nodes with 4Gb RAM per node (136 cores) for CSTR/ICCS use. TownhillBenchmarks

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

• ssh -L 8000:bwganglia.inf.ed.ac.uk:80 username@sshREMOVE_THIS.inf.ed.ac.uk
• now point your browser at localhost:8000/ganglia

• LocalWishList - list improvements you would like to see
• UnansweredQuestions - post a question, or see if you can help someone by answering their questions
• AnsweredQuestions - when a question from above is answered, move it here
• UsingGMTKUnderGridEngine - documentation for the genetic algorithm based triangulation script

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