[gmx-users] gigabit scaling, DPPC benchmark

Jordi Camps jcamps at lsi.upc.edu
Mon Jun 6 21:49:02 CEST 2005

Hello Jason,

To check the NIC speed you can use the mii-tool or the ethtool (usually
found in /sbin):
	# /sbin/ethtool eth0
Maybe you shoud be root to get the information you need. I think that with
plain user permissions it doesn't work.

Hope this helps. Regards,

Jordi Camps Puchades
Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
c/. Jordi Girona 1-3              
Modul C6-E201                     Tel.  : 934 011 650
E-08034 Barcelona                 Fax   : 934 017 014
Catalunya (Spain)                 e-mail: jcamps at lsi.upc.edu

-----Mensaje original-----
De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
nombre de Jason de Joannis
Enviado el: lunes, 06 de junio de 2005 18:48
Para: gmx-users at gromacs.org
Asunto: [gmx-users] gigabit scaling, DPPC benchmark

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?


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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