[gmx-users] gigabit scaling, DPPC benchmark

[Jason de Joannis]

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