Re: NAMD on current CPUs

From: Axel Kohlmeyer (
Date: Thu Dec 17 2009 - 09:26:53 CST

hey jerome,

greetings from grey and snowy germany.

just a few notes on the subject. i don't think that the choice of CPU
is that important anymore. particularly for NAMD, since NAMD is
not overly memory bandwidth hungry. thus the old style harpertown
xeon CPUs may be a good deal (large cache and the FPU is
as fast as in the nehalem xeons). recent opterons should be a tiny
bit faster in terms of FP, but they've had reliability issues since the
barcelona generation, primarily due to lack of well tested mainboards.

the biggest question is more how much time do you want to
spend on maintaining the cluster? and thus how much money
are you willing to dedicate to more convenient to set up and
use hardware. this is why the dell nodes are such a good deal
for mike's group. once set up well, they work and the downtime
is little, even if there is next to nobody around to take care of them.

if you go with cheaper hardware, e.g. supermicro nodes assembled
by a reseller. you can save money, but have to deal with more hardware
issue, i.e. need personnel to take care of that.

finally, there is a significant saving potential in the infiniband hardware.
don't get talked into QDR and latest greatest HCAs. for NAMD to
previous generation will do very well, you save a bundle, and don't
have to worry about driver issues. check out the hardware in delta.
node81 to node84 have newer/better q-logic HCAs, but their driver
_sucks_. the older mellanox HCAs in the other nodes have not shown
the tiniest blink since day 1. also the price for the switch goes up
by quite a bit with the size. if you have a large pile of cash, consider
buying two 72 port switches without interconnect instead of one,
very expensive 144 port switch.

if you need more technical help, perhaps you can invite moreno
over from trieste. ;)


On Thu, Dec 17, 2009 at 9:34 AM, Jérôme Hénin <> wrote:
> Hi all,
> Does someone have experience they are willing to share on how well
> various current CPUs (Xeons and Opterons) handle NAMD? We are thinking
> of putting a cluster together here (with IB interconnect), and trying
> to pick CPUs that will give the most bang for our euro-bucks.
> Thanks for any tips,
> Jerome

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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