[gmx-users] mpi performance issues

David spoel at xray.bmc.uu.se
Mon Apr 19 23:03:01 CEST 2004

On Mon, 2004-04-19 at 22:47, istvan at kolossvary.hu wrote:
> Hi, 
> I see there are a lot of threads on the mailing list on Gromacs mpi scaling. 
> I also tried to do this "out of the box" and got similar, horrible scaling 
> as others. I read through the archive and got some clues, although it seems 
> that scaling is extremely (molecular)system sensitive and I shouldn't expect 
> much with PME. However, looking at the 20-50% CPU usage on dual processor 
> nodes (3.06 GHz Xeons w/ 100Mbit Ethernet and Redhat 9.0) I was wondering if 
> the payload, which is the size of the packets sent between nodes is too 
> small. I believe Erik has mentioned this once on the list. Apparently the 
> payload size is 1000 bytes (plus 40 bytes TCP/IP overhead) on our system. It 
> would be much more efficient having larger payload, say 1400 bytes. My 
> question is whether this is something that can be set in Gromacs, or is this 
> an OS parameter. In either case, how can I change this? 

It is a feature of the MPI library. With LAM-MPI there is an option to
change this. Another option is to try the MPI-VIA implementation. Has
anyone tried that for GROMACS?


This should avoid the Linux TCP/IP stack, and have much lower latency on
cheap hardware. Volunteers please....

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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