AMBER Archive (2000)

Subject: RE: Myrinet + Beowulf for AMBER?

From: Kouji Hayama (hayama_at_osaka.email.ne.jp)
Date: Wed Aug 09 2000 - 00:11:41 CDT

Hi, Smith.

You want to get the benchmark.
In japanese web site, I know the alpha based benchmark with Myrinet.
The url is...
http://www.hpc.co.jp
http://www.hpc.co.jp/Parallel/hpc-PA264LAMBER.htm

But this page is japanese.
 Thank you.

>We are currently considering upgrading our Intel-based Beowulf cluster with
>Myrinet interconnects in an attempt to improve scaling with AMBER jobs.
>Right now we're using standard fast ethernet, and we get the expected
>results. Scaling tails off after about 8 CPUs depending on compiler, job
>size, etc. The conventional wisdom is that the bottleneck is packet
>latency, which leads us to consider Myrinet where latencies are claimed to
>be reduced from 50ms with ethernet to ~20us.
>
>We'd like to get good scaling up to at least 16 processors (32 if
possible).
>We're trying to get Myrinet to lend us some hardware for benchmarking, but
>the best they'll come up with is 4 cards and a 4 port switch, which won't
>tell us much. Considering the fact that this will nearly double the cost
of
>our cluster, we want to see some indication of real-world benefit before
>committing to the hardware. Does anybody have experience running AMBER on
a
>cluster with this technology?
>
>Thanks in advance.
>
>Jarrod A. Smith
>Research Asst. Professor, Biochemistry
>Assistant Director, Center for Structural Biology
>Computation and Molecular Graphics
>Vanderbilt University
>
>jsmith_at_structbio.vanderbilt.edu
>