[gmx-users] gigabit scaling, DPPC benchmark

[Diego Enry]

Jason, I don't know if that's the problem but when I use a P4EE 3Ghz,
Gromacs runs  faster without hyperthreading. I would like to ask you
to repeat this benchmark without hyperthreading.


On 6/6/05, Jason de Joannis <jdejoan at emory.edu> 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?
> 
>   /Jason
> 
> --
> Jason de Joannis, Ph.D.
> Emory University
> 1515 Pierce Dr, Atlanta, GA 30329
> Phone: (404) 712-2983
> Email: jdejoan at emory.edu
> http://userwww.service.emory.edu/~jdejoan
> 
> 
> 
> 
> 
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.