Re: Is there any point in running NAMD over an ethernet-linked cluster?

From: Nicholas M Glykos (
Date: Sun Sep 21 2014 - 13:21:53 CDT

> Can anyone on this mailing list tell me if they have successfully
> noted a speed increase by running NAMD across an ethernet-linked
> cluster vs. a single node?

Sure. The following page is since the days of NAMD 2.6 using gigabit
ethernet, Q6660 quads and a 60,000 atom system :

We could (back in 2009) go to 8 nodes, but at that point the parallel
efficiency had dropped to only ~45%.

            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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