AMBER Archive (2006)

Subject: Re: AMBER: Myrinet or Gigabit ethernet?

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Jul 20 2006 - 09:45:45 CDT

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" <mfyang_at_gmail.com>
To: <amber_at_scripps.edu>
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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