Re: 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
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