[gmx-users] gigabit scaling, DPPC benchmark

[David]

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
> benchmark:
> 
> 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).
> 
>   /Jason
> 
-- 
David.
________________________________________________________________________
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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