RE: [condor-users] Use of Condor for biological applications

["John J Irwin" <jji@xxxxxxxxxxxx>]

Hi Bruce,

You asked about the use of Condor for biological applications. We are using
Condor to run virtual screening, docking databases of half a million small
molecules against protein targets of biological interest. We do this every
day, around the clock, with about a dozen users, with jobs ranging from 1
minute to 2 days CPU. We've been using Condor for over three years now.

Our condor manages a 50-cpu cluster of dedicated dual CPU linux nodes as
well as a dozen or so dual CPU desktop Window boxes effortlessly. It runs
unattended for weeks at a time with no complaints. We particularly like the
"fair share" feature that lets a dozen investigators launch as many jobs as
they like and leaves the machine to adjudicate the use of the system. The
class ad paradigm is both philosophically compelling and technically very
powerful.

Our colleagues using Sun Grid Engine and PBS have to set rules about what
queue to use or what priority jobs must be run at. The condor_userprio
feature and the class ad mechanism is the fairest general purpose way I have
ever seen to share resources in a competitive environment.

We would like to see the standard universe implemented on Windows, but apart
from that (which few if any other job schedulers have anyway), we're very
happy.

John


John J. Irwin
Pharmaceutical Chemistry, University of California San Francisco
600 16th St, Suite N474E San Francisco CA 94143-2240 USA (94107 for courier)
 mailto:jji@xxxxxxxxxxxx, http://johnirwin.compbio.ucsf.edu
Phone +1 415 514-4127 (Fax 502-1411)
Free 3D screening database: http://zinc.docking.org

If you are interested in Methods in Macromolecular Crystallography or the
Structure and Function of Macromolecular Assemblies, please see the Erice
Crystallography page http://crystalerice.org.

 
-----Original Message-----
From: owner-condor-users@xxxxxxxxxxx [mailto:owner-condor-users@xxxxxxxxxxx]
On Behalf Of Zachary Miller
Sent: Wednesday, May 26, 2004 5:52 AM
To: condor-users@xxxxxxxxxxx
Subject: Re: [condor-users] Use of Condor for biological applications

On Wed, May 26, 2004 at 01:36:06PM +0100, Bruce Beckles wrote:
> 
> Hi all,
> 
> 	Is there anyone out there routinely using Condor for "biological"
> applications?

hi bruce,
i suspect you are looking more for reports from other groups, but i can tell
you that i've run a number of biological applications on a fairly large
scale
using condor.

collaborating with another group here on the UW campus, the BMRB
( http://www.bmrb.wisc.edu/ ), we run BLAST, cns, and cyana and are in the
process of adding several new applications.  let me know if you would like
more details.


cheers,
-zach

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