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

FLOR MARTINI flormartini at yahoo.com.ar
Thu Sep 24 16:01:04 CEST 2009


   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)

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