[gmx-users] PME scaling

[Robert Bjornson]

Hi David,

Sure, thanks for your interest, here is a bit more info:

I'm running gromacs 3.3, with patch to pme.c (using 1.61.2.5 to fix
pme-order bug)
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
might have.

Sincerely,

Rob Bjornson


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.
> ________________________________________________________________________
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>