[gmx-users] gigabit scaling, DPPC benchmark
Jason de Joannis
jdejoan at emory.edu
Mon Jun 6 21:07:37 CEST 2005
> Date: Mon, 6 Jun 2005 13:16:46 -0400
> From: Diego Enry <diego.enry at gmail.com>
> Subject: Re: [gmx-users] gigabit scaling, DPPC benchmark
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <eae4cfe705060610167b069fee at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 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.
Diego, I don't think hyperthreading was used on these runs since there
were only two processes running on each node. Is there a way to easily
toggle hyperthreading? I'd rather not go into the BIOS or reboot the
system. To estimate the effect of hyperthreading I usually just make
sure there are 4 processes per node (e.g. for -np 2, run two copies
simultaneously). For example I get 109,209,354 for 1-,2-,4-thread jobs
as compared to 158,404,517 for real cpus.
> 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.
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