[gmx-users] PME scaling
rbjornson at gmail.com
Wed Jan 11 00:05:06 CET 2006
Sure, thanks for your interest, here is a bit more info:
I'm running gromacs 3.3, with patch to pme.c (using 18.104.22.168 to fix
I'm using lam 7.1.1 under pbspro, running on a cluster of 3.2 Ghz
EMT-64 xeons. The interconnect is gigE.
The model is 72k atoms, using PME with pme_order=6
Here is the performance I'm seeing (I've rounded numbers):
cpus steps/hour steps/hour/cpu typical node cpu utilization
(remember 2 cpus/node)
8 6200 775 .5-.9
6 8500 1400 .75-1.08
4 25000 6250 2.0
1 8870 8870 1.0
If I run the same model with cutoff instead of PME, I see:
8 82000 10274 1.6-1.8
1 24000 24000 1.0
So, the performance I'm seeing on more than 4 nodes with PME is pretty
bad. How does this compare to what you expected? I can provide you
with more info if you'd like. Thanks very much for any insight you
On 1/10/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Robert Bjornson wrote:
> > Hi,
> > I'm experiencing very poor scaling when using PME on gromacs-3.3, and
> > looking through the list indicates that this is a known issue with
> > that release. However, there was some indication that work has been
> > done on parallelizing PME, and that the top of CVS might contain a
> > version that is worth trying.
> In addition to Erik's answer: can you be more specific? We've seen quite
> decent scaling on up to 16 processors, but depending strongly on the
> size of the system and the interconnect.
> > Has anyone tried this? Did your PME performance improve? If so, did
> > you simply take the top of cvs, or is there a tag that is more likely
> > to work successfully?
> > thanks,
> > Rob Bjornson
> > _______________________________________________
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> 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
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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