On 2012-09-26 16:24, Michael Shirts wrote:
Hi all,
I'd be interested to know about people's experiences with Gromacs on
US national computing centers. Which machines have it set up to scale
the
best? We're putting in an XSEDE request soon, and I'm trying to
figure out which resource to request. Our system is
semi-coarse-grained, using
reaction field electrostatics, so we don't have to worry about PME.
Of course, couldn't hurt to know about PME scaling as well. I'm
interesting
scalings with 100K - 300K atoms.
Of course, best performance will probably change with 4.6 because of
all the setup tweaks, but let's start with 4.5 scaling info!
I guess you're aware of Roland Schulz' paper on cellulose systems on
Jaguar? Over 100 million particles on 100,000 cores. We have done virus
particles (1.2 million particles) on 2000 Cray XE6 cores (in Sweden).
You are probably aware that scaling is different for different systems,
in particular if you don't have waters. Your systems are relatively
small for the big US computers of course, but it is often allowed to do
ensemble calculations.
I would suggest you get a test account for scaling tests for your
particular system.
Best,
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shi...@virginia.edu
(434)-243-1821
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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