FYI: superlinear speedups in GROMACS (fwd)

[Dominic Wu]

Would not a single CPU with a larger L2 cache solve the problem better then?

-----Original Message-----
From: beowulf-admin at beowulf.org [mailto:beowulf-admin at beowulf.org]On
Behalf Of Eugene Leitl
Sent: Friday, March 08, 2002 12:26 PM
To: Beowulf at beowulf.org
Subject: CCL:FYI: superlinear speedups in GROMACS (fwd)




-- Eugen* Leitl <a href="http://leitl.org">leitl</a>
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---------- Forwarded message ----------
Date: Fri, 8 Mar 2002 20:34:03 +0100 (CET)
From: David van der Spoel <spoel at xray.bmc.uu.se>
Cc: chemistry at ccl.net
Subject: CCL:FYI: superlinear speedups in GROMACS

On Fri, 8 Mar 2002, Eugene Leitl wrote:

>Ask David VanDerSpoel, he'll tell you that they see superlinear speedups
>in Gromacs jobs quite often. Has to do with the cache, I'd guess something
>like with one CPU the job cant fit in L2 cache by itself, so lots of
>main memory accesses are required - when the job is split for 2 cpus,
>more of the job is in L2 caches, and despite the shared memory that LAM
>uses for communications for dual nodes, the overhead for that doesnt
outweigh
>the advantage of having the job divided into more cache ram... works
>out well! :)
It works on IBM Sp2 as well, and is very nice indeed on Scali networks:
http://www.gromacs.org/benchmarks/scaling.php

Our memory access pattern is "quite serial", but not entirely, that's
why the cache improves performance so much.

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://zorn.bmc.uu.se/~spoel
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