[gmx-users] trying to get better performance in a Rocks cluster running GROMACS 4.0.4

[Carsten Kutzner]

Hi,

if you run without PME, there will be no all-to-all communication  
anyway,
so in this sense the paper is (mostly) irrelevant here. Since you  
mention this
paper I assume that your network is gigabit ethernet. If you run on  
recent
processors then I would say that for a 10000 atom system on 8 cores the
ethernet is clearly the limiting factor, even if it runs optimal (the  
chance for
congestion problems on two nodes only is also very limited - these are
likely to appear on 3 or more nodes).

What is your performance on a single node (4 CPUs)? You could compare
that to the performance of 4 CPUs on 2 nodes to determine the network
impact.

Carsten


On Sep 24, 2009, at 5:08 PM, FLOR MARTINI wrote:

> Thanks for your question.
> We are running a lipid bilayer of 128 DPPC and 3655 water molecules  
> and the nstep of the mdp is a total for 10 ns. I don´t think really  
> that our system is a small one...
>
> Dra.M.Florencia Martini
> Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas
> Cátedra de Química General e Inorgánica
> Facultad de Farmacia y Bioquímica
> Universidad de Buenos Aires
> Junín 956 2º (1113)
> TE: 54 011 4964-8249 int 24
>
> --- El jue 24-sep-09, Berk Hess <gmx3 at hotmail.com> escribió:
>
> De: Berk Hess <gmx3 at hotmail.com>
> Asunto: RE: [gmx-users] trying to get better performance in a Rocks  
> cluster running GROMACS 4.0.4
> Para: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Fecha: jueves, 24 de septiembre de 2009, 11:22 am
>
> Hi,
>
> You don't mention what kind of benchmark system tou are using for  
> these tests.
> A too small system could explain these results.
>
> Berk
>
>
> Date: Thu, 24 Sep 2009 07:01:04 -0700
> From: flormartini at yahoo.com.ar
> To: gmx-users at gromacs.org
> Subject: [gmx-users] trying to get better performance in a Rocks  
> cluster	running GROMACS 4.0.4
>
> hi,
>
>    We are about to start running GROMACS 4.0.4 with OpenMPI, in 8
> nodes, quad core Rocks cluster. We made some tests, without PME and
> found two notable things:
>
> * We are getting the best speedup (6) with 2 nodes ( == 8 cores ). I  
> read
> the "Speeding Up Parallel GROMACS in High Latency networks" paper, and
> thought that the culprit was the switch, but ifconfig shows no  
> retransmits
> (neither does ethtool -s or netstat -s). Does version 4 includes the
> alltoall patch? Is the paper irrelevant with GROMACS 4?
>
> * When running with the whole cluster ( 8 nodes, 32 cores ), top  
> reports
> in any node a 50% system CPU usage. Is that normal? Can it be  
> accounted to
> the use of the network? The sys usage gets a bit up when we  
> configured the
> Intel NICs with Interrupt Coalescense Off, so I'm tempted to think  
> it is
> just OpenMPI hammering the tcp stack, polling for packages.
>
> Thanks in advance,
>
> Dra.M.Florencia Martini
> Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas
> Cátedra de Química General e Inorgánica
> Facultad de Farmacia y Bioquímica
> Universidad de Buenos Aires
> Junín 956 2º (1113)
> TE: 54 011 4964-8249 int 24
>
>
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--
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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