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Parallel Computing (Beowulf) and CNS

Alan Grossfield alan at hammer.med.jhmi.edu
Mon Dec 13 22:21:55 EST 1999

:> Our lab is strongly considering purchasing a cluster of ~12 PC with dual PII
-: 450 MHz processors and 256 MB RAM each to configure in a Beowulf cluster run
-:ning Linux.  Does anyone have experience running this type of system?  Readin
-:g over past postings, I have come across people mentioning "possible" configu
-:rations, but I have never read where anyone has actually successfully ran CNS
-: over a cluster.  I know that some software, such as Shelx, is made to run on
-: only one CPU.  What about CNS?  I would be very interested in hearing either
-: positive or negative comments from people who have experience running CNS on
-: a Beowulf cluster.

    Depending on what you're interested in, you could use CHARMM instead
    of CNS.  Since I installed Josip Loncharic's TCP patches, I've seen 
    good scaling to 8 processors using dynamics with cutoffs, and good
    scaling to 4 processors using Ewald sums.  As I understand
    it, CHARMM isn't nearly as easy to use for refinement, but the core
    functionality (simulated annealing and NMR restraints) is present.

Alan Grossfield
|"In theory, there is no difference between theory and practice.  In     |
|practice, there is."   Jan L.A. van de Snepscheut                       |

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