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

Berk Hess gmx3 at hotmail.com
Thu Sep 24 16:22:58 CEST 2009


You don't mention what kind of benchmark system tou are using for these tests.
A too small system could explain these results.


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


   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
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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