[phenixbb] den_refine on cluster

Das, Debanu debanu at slac.stanford.edu
Tue Nov 13 16:23:16 PST 2012


Hi Mike,

You can use our scripts for running DEN on a Linux cluster available at the CNS Wiki page for this (http://cns-online.org/wiki/index.php/DEN_Grid_Searches).

If you have a Linux cluster, run the script as is.

If you don't, as in your case, just edit the variable (in the "Edit seven variables below" section of the first script) from:
my $use_cluster      = 'Yes';       ## change it to NO if not using cluster
to "NO".

Thanks,
Debanu.
-------------------------------------
Debanu Das, Ph.D.,
Staff Scientist,
JCSG Structure Determination Core,
SSRL Structural Genomics Division,
SLAC National Accelerator Laboratory,
Menlo Park, CA 94025
-------------------------------------

-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Michael Thompson
Sent: Tuesday, November 13, 2012 3:57 PM
To: phenixbb
Subject: [phenixbb] den_refine on cluster

Hi All,

Apologies if this is a naive question, but I would like to run DEN refinement and I notice the documentation says that it runs optimally on a machine with at least 30 processor cores. Is there any way to run DEN refinement on a SGE cluster as a batch job using something like run_command="qsub" as can be done with autobuild, etc.?

Thanks,

Mike


 
-- 
Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

miket at chem.ucla.edu
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