FYI: superlinear speedups in GROMACS (fwd)

Dominic Wu dwu at
Fri Mar 8 13:15:51 PST 2002

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

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

-- Eugen* Leitl <a href="">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>
Cc: chemistry at
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
>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:

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	spoel at

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