[gmx-users] mpi performance issues

[Osmany Guirola Cruz]

 I have problems in my cluster with MPI "poooor scalable" 
I think that my problem is in the options --with-tcp-short 
And --with-rpi of my lam/mpi which should be the perfect values for
these options or how ca I found the prefect values for my network
I have a linux cluster Suse 8.2 dual PIII 933 100Mbs

-----Original Message-----
From: David [mailto:spoel at xray.bmc.uu.se] 
Sent: Monday, April 19, 2004 7:01 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] mpi performance issues


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?

http://www.nersc.gov/research/FTG/via/

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


-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.