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Linux Cluster Installation and VLS.

ICM can be configured to run on a linux cluster. You need the following components:

  • A linux cluster each node of which mounts the ICM home directory, your chemical database directory, and the project data.
  • Floating FLEXLM licenses to start the needed number of simultaneous ICM processes, or, alternatively, nodelocked licenses for each node in the cluster you are going to use.
  • The PBS queuing system to submit VLS jobs to the cluster. If you use another queuing system, convert the PBS scrippts to a different queuing program.

To run a PBS docking job do the following:

  • customize your rundock shell script (it should work as is if the connectivity and mounting is OK)
  • customize and test your pbsrun script that queues a single rundock process to PBS and passes parameters to rundock . Example: qsub $ICMHOME/pbsrun -vJOBARGS="-f 1 -t 10000 DOCK1"
  • customize and test your pbsscan script that queues multiple rundock processes to PBS by dividing the compounds into chunks. Example: pbsscan DOCK1 1 1000000 10000 # queues 100 rundock processes each working on 10000 compounds

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