[gmx-users] gigabit scaling, DPPC benchmark
spoel at xray.bmc.uu.se
Mon Jun 6 19:12:24 CEST 2005
On Mon, 2005-06-06 at 12:48 -0400, Jason de Joannis wrote:
> Hi, I would like to improve the scaling on my cluster so it is more
> like that published on the Gromacs website.
> Cluster Nodes: Dual Xeon 3.06 GHz (hyperthreaded)
> Network: Gbit ethernet
> System Installion:
> o Linux 2.4.20-64GB-SMP
> o LAM 6.5.9/MPI 2 C++/ROMIO
> o fftw-2.1.5
> o Gromacs 3.2.1
> For the DPPC benchmark with sort/shuffle:
> NP 1 2 4
> ps/day 158 404 517
> scaling 128% 81%
> There is a big drop from 2 to 4 as the Gigabit network comes into play.
> Compare this to the Xeon 2800 benchmark on Gromacs.org where 4 processors
> get 637 ps/day.
> Of course the problem becomes more pronounced when I use PME on this
> NP 1 2 4
> ps/day 115 229 201
> scaling 100% 44%
> I suspect my network may be running a 100 rather than 1000 Mbit as
> suggested by the published 87% scaling for Xeon2800/100Mbit.
> How can a troubleshoot this problem?
I'm afraid this is a GROMACS problem. We are working on resolving this,
but the problem is largely due to the Linux TCP layer which is very
inefficient as regards the start-up time for a communication.
It basically means you can not do much about it (except buy SMP machines
with more than two processors).
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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