[gmx-users] gigabit scaling, DPPC benchmark
Jason de Joannis
jdejoan at emory.edu
Mon Jun 6 18:48:26 CEST 2005
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
o Linux 2.4.20-64GB-SMP
o LAM 6.5.9/MPI 2 C++/ROMIO
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.
1515 Pierce Dr, Atlanta, GA 30329
Phone: (404) 712-2983
Email: jdejoan at emory.edu
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