Re: AMBER: Myrinet or Gigabit ethernet?

From: Robert Duke <>
Date: Thu, 20 Jul 2006 10:45:45 -0400

In my opinion, if you have more than about 8 to 16 cpu's, and you are
running large long simulations, money spent on good interconnects is money
well spent. You simply cannot efficiently run 16+ processor jobs on GB
ethernet, and honestly I don't much like going above about 4 processor jobs
on GB ethernet. I would recomment an infiniband implementation these days;
I don't know what the costs are vs. myrinet (which is also ok but I believe
I am seeing better numbers and stability in some of the infiniband
installations I use (honestly, I no longer have access to any myrinet
systems)). These comments are all predicated on the assumption you
primarily run pme simulations; generalized Born is less demanding on the
interconnect so using GB ethernet is less of a problem.
Regards - Bob Duke

----- Original Message -----
From: "Mingfeng Yang" <>
To: <>
Sent: Thursday, July 20, 2006 9:35 AM
Subject: AMBER: Myrinet or Gigabit ethernet?

> I am planning to build a dual-core opteron based linux cluster. Mostly, we
> will run amber9 on this cluster for MD simulation. Due to limited budget,
> I don't like to spend several thousand dollars on interconnector like
> myrinet and infiniband. But I am afraid gigabit ethernet will give poor
> parallel efficiencity. If any of you have experience on these
> interconnectors, can you tell me how much difference they can give?
> Thanks,
> Mingfeng
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Received on Sun Jul 23 2006 - 06:07:07 PDT
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