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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