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 <g...@hotmail.com> escribió:
De: Berk Hess <g...@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@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: flormart...@yahoo.com.ar
To: gmx-users@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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