Article ID: 88 - Last Modified: April 30, 2012
Can I run a ligand preparation on multiple processors ?
Yes. You can do this when you start the LigPrep job from Maestro, in the Start panel, or you can specify multiple processors from the command line. Prior to Suite 2011, the utility to use was para_ligprep; from Suite 2011 on, distributing a ligand preparation is done with the ligprep command.
For multi-processor submission, there are two choices to be made: the number of processors to use simultaneously (CPUs), and the number of subjobs to divide the ligands into (NJOBS). For load balancing, we suggest to choose approximately three subjobs per processor. If the queue controlling the subjob submission is very full, perhaps one subjob per requested processor could be more appropriate. By default, para_ligprep divides the preparation into subjobs of 10,000 structures each.
Here is an example of both a command-line ligprep (Suite 2011 on) and para_ligprep submission.
$SCHRODINGER/ligprep -NJOBS 20 -HOST big_host:5 etc
$SCHRODINGER/utilities/para_ligprep -NJOBS 20 -HOST big_host:5 etc
The etc are the normal LigPrep options. This multi-processor preparation would be divided into 20 subjobs, and 5 processors will be used simultaneously on the host "big_host" until all 20 subjobs are completed. See the section "Distributing LigPrep Jobs" in the LigPrep User Manual for more information.
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