[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".

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.?



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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