AMBER Archive (2008)

Subject: Re: AMBER: Benchmarks on Fujitsu PrimePower 2500?

From: Atro Tossavainen (
Date: Mon Mar 10 2008 - 08:24:33 CDT

> Well, the scaling looks okay here, but it is only out to 8 cpu, so
> that does not tell you a lot.

No. Of course, we don't even know yet what kind of PRIMEPOWER 2500
configuration the original poster is talking about.

According to product documentation, they go up to 128 CPUs in a single
box and the maximum clock rate is 2.1 GHz these days, FWIW.

> I am peripherally aware of some activity to get pmemd and amber on
> sun machines, but have not had direct access to anything myself (including
> ranger, about which there was another question recently, though I think
> I may get onto that machine before too long).

I had no problem getting pmemd (of the AMBER 8 kind, serial only so far)
built with the Sun Studio compiler. It even appears to work (at least
the results from the JAC benchmark are close enough to qualify to my
untrained eye).

Now here's the interesting deal regarding the relative performance of
sander and pmemd on the SPARC platform. At least on the Sun Ultra
Enterprise 450 that I used to run the tests it took over 3 hours for
the JAC benchmark with sander but only 45 minutes on pmemd (both
serial versions, 400 MHz UltraSPARC II CPU). I'm accustomed to seeing
maybe 20% improvement on pmemd vs sander, so this is rather surprising.

> Here's the deal. First of all, a 700 MHz cpu is pretty darn slow
> these days,

Of course. I wasn't trying to advocate running AMBER on dinosaurs.
The point I was trying to make was that the SPARC64 (and UltraSPARC
even more so) isn't a very efficient processor architecture for running
computationally intensive tasks. Even the 180 MHz R10k's in my quad
Origin 200 do better.

> There is another wrinkle here when one says "Sun". Sun is selling
> high-end hpc systems these days with both ultrasparc chips and
> amd opterons.

Yes, and Intel 64's too. But Fujitsu PRIMEPOWER is all SPARC.

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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