Re: AMBER: Benchmarks on Fujitsu PrimePower 2500?

From: Atro Tossavainen <>
Date: Mon, 10 Mar 2008 10:04:20 +0200 (EET)

> Does anyone have absolute benchmarks (that they are willing to share) for
> AMBER 8 or 9 parallel molecular dynamics (PMEMD and/or sander) running on a
> Fujitsu Primepower 2500 (SPARC64) system?

I have experimented with AMBER 8 on a SPARC64 platform (Primepower 200,
single 700 MHz SPARC64 IV) and can run the same tests on another one
(Primepower 250, single 1.1 GHz SPARC64 V). These are single-CPU
machines only, so I can't get you any data on scaling with multiple
CPUs. I've used the same binary I compiled for our Suns with the
Sun Studio compilers; I haven't got anything Fujitsu-specific.

As I see it, the SPARC CPUs are really quite badly suited for this kind
of work. If the interconnect is really spectacular and scaling is good,
it may help balance the CPU shortcomings somewhat in large configurations.
As an initial data point, the SPARC64 IV at 700 MHz takes roughly twice
the time that a Pentium III Xeon at 700 MHz does to do the JAC benchmark
on sander.

Are you aware of


Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
+358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
< URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
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Received on Wed Mar 12 2008 - 06:07:17 PDT
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