On Jun 6, 2009, at 1:20 PM, XAvier Periole wrote:


On Jun 6, 2009, at 1:08 PM, Justin A. Lemkul wrote:



XAvier Periole wrote:
Dears,
I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very
straightforwardly best.
I'd appreciate if some of you could post their experience in that matter. I mean the
number of pme nodes as compared the total number of CPUs used.
I think this info as been discussed recently on the list but the archive is not accessible. It may matter that I have a system containing about 70000 atoms, a protein in a bilayer.

Some advice that I got from Berk long ago has worked beautifully for me. You want a 3:1 PP:PME balance for a regular triclinic cell (grompp will report the relative PME load as 25% if your parameters create such a balance), 2:1 for an octahedron. My scaling has been great using this information, without having to alter -rdd, -rcon, etc.

Thanks for the info. I got more or less to that ratio. Although a 2:1 PP:PME sometimes is better.

However my problem now is to get 256 CPUs more efficient (ns/day) than 128 CPUs. The communications become a limiting factor ... can't get it to go faster! The system might be small, but not sure.

I'll take a look at the CVS tool.
There is also a version for gromacs 4.0.x available for download at
www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/

Regards,
   Carsten



--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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