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.
Depends a lot on the interconnect and the ratio atoms/node. You may also
want to play with cut-offs, the tool will help you with this.
I'll take a look at the CVS tool.
XAvier.
-Justin
Best,
XAvier.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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