[gmx-users] Scaling on IBM/SP2 Power3

[David van der Spoel]

On Wed, 2002-11-06 at 12:01, Anton Feenstra wrote:
> Hi All,
> 
> 
> I'm examining the scaling properties on our IBM/SP2 Power3 AIX4.3
> 16/32 cpus/node machine here. Problem is, at 10 cpu's (all on one
> node) scaling is down to 50-55% (for a 40000 atoms system). Looking
> at the scaling benchmarks on the Gromacs page, I'd expect something
> well above 70-80% at least! Worse, for the 2 cpu job scaling is
> already only 94% while that should be close(r) to 100%. 
> 
> I am now trying to convince the loadleveler to run a new job with
> MP_EAGER_LIMIT=65536, which should reduce message sending latency
> for MPI. I've already set '#@network.mpi = csss,shared,us' and
> MP_SHARED_MEMORY=yes, which should convince MPI to use shared
> memory communication. 
> 
> I'd appreciate any comments and/or other suggestions!
You are omitting the most important information: is this with PME or
with a cut-off? With cut-off you should be able to reproduce the gmx
benchmarks, with PME it won't be as nice... Erik (and me) are working on
this though...

> 
> 
> -- 
> Groetjes,
> 
> Anton
>  ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "It's Bicycle Repair Man !" (Monty Python)                |
> |________|___________________________________________________________|
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 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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