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

[FLOR MARTINI]

Hi, yeah, we have a clearly better performance with 2 nodes (8 CPU)! if
we try the same on 1 node (4 CPU) we have a day of difference. Yes, we
have a Gigabit ethernet network, so it is clear what you say about
congestion problems. We were thinking about to by pass the switch,
using another ethernet between two nodes each. Do you think that it
could be better for our performance??
Thank you in advance.
Flor

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 vie 25-sep-09, Carsten Kutzner <ckutzne at gwdg.de> escribió:

De: Carsten Kutzner <ckutzne at gwdg.de>
Asunto: Re: [gmx-users] trying to get better performance in a Rocks cluster running GROMACS 4.0.4
Para: flormartini at yahoo.com.ar, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Fecha: viernes, 25 de septiembre de 2009, 9:19 am

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 thispaper I assume that your network is gigabit ethernet. If you run on recentprocessors then I would say that for a 10000 atom system on 8 cores theethernet is clearly the limiting factor, even if it runs optimal (the chance forcongestion problems on two nodes only is also very limited - these arelikely 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 networkimpact.
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 KutznerMax Planck Institute for Biophysical ChemistryTheoretical and Computational BiophysicsAm Fassberg 11, 37077 Goettingen, GermanyTel. +49-551-2012313, Fax: +49-551-2012302http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne


 



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