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Re: Gaussian, AMBER, DOCK Xgrid or Pooch development

Noah-

Gaussian in particular works will with Linda, and Linda works well with Mac OS X. So that shouldn't be an issue. Here's a link to more information on that:
http://makeashorterlink.com/?H3176251A

Dock can be operated in an embarrassingly parallel fashion (what they call a "single processor" build) and many people have successfully run it with Xgrid. I would be surprised if someone on this list hasn't already done so. I am aware of some other planned projects to do this, too.. in general, it should be a relatively straightforward task, afaik. Note, too, that Dock includes MPI support (build with what they call the "MPI version" of dock) and information on that is here in the "General Overview" section:
http://dock.compbio.ucsf.edu/DOCK_5/DOCK_v5.1.1.htm

Finally, AMBER.. Depending on how long you want to run AMBER tasks, you can do lots of large ones in an embarrassingly parallel fashion (as they did with folding@home) which produces a longer runtime per task, or you can parallelize the jobs themselves, which allows you to complete individual tasks more quickly. Here's some info on doing an MPI-based AMBER cluster:
http://amber.ch.ic.ac.uk/cluster_info/index.html

I hope this helps.

-matt
--
Matt MacInnis
Manager, Research Computing
Worldwide Science and Technology Markets
Apple Computer, Inc.



On Dec 21, 2004, at 5:31 PM, Noah W. Allen III wrote:

Pardon this very naive question, but I am new to this arena, and wondered if anyone has worked with using Gaussian, AMBER or DOCK on XGrid or Pooch, and if so, has written code for usage to run any of these apps under XGrid or Pooch. I know the application 'Linda' is available for Gaussian/Linux, but we are running a G5 XServe cluster running 10.3.

Any help would be certainly appreciated. This message is being cross-posted to the XGrid list, as well as the HPC list. Please feel free to respond to me personally or via the list.

Thanks in advance.

Noah Allen

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Noah W. Allen, III, Ph.D.
Assistant Professor of Chemistry
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University of North Carolina at Asheville
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Asheville, NC 28804-8511
Phone 828.232.5174
Fax 828.232.5179
Homepage: http://www.theallenlab.org
Instant Messenger or mac.com messenger: theallenlab
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 >Gaussian, AMBER, DOCK Xgrid or Pooch development (From: "Noah W. Allen III" <email@hidden>)



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