RE: Myrinet + Beowulf for AMBER?

From: Kouji Hayama <>
Date: Wed 9 Aug 2000 14:11:41 +0900

Hi, Smith.

You want to get the benchmark.
In japanese web site, I know the alpha based benchmark with Myrinet.
The url is...

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
>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
>our cluster, we want to see some indication of real-world benefit before
>committing to the hardware. Does anybody have experience running AMBER on
>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
Received on Tue Aug 08 2000 - 22:11:41 PDT
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