RE: questions regarding new single node box for NAMD: re components, CUDA, Fermi

From: Richard Owczarzy (
Date: Fri Oct 02 2009 - 10:42:12 CDT

I would watch for power supplies and power requirements. The latest Xeon
W5590 is using more power than Xeon X5570 and some motherboards and
systems cannot handle it.

We plan to buy a small computer cluster (32-cores) for 10-40K atoms NAMD
simulations. We are considering 4 nodes of 2 x quad Xeon X5570 with
InfiniBand versus single Linux system, SGI Altix 450 with 16 dual
Itanium 2 processors, 1.6 GHz. Some older benchmarks for SGI ALTIX
Itanium look impressive, so we are wondering about the best
price/performance option. I have not seen any recent benchmarks. Does
anybody have any experience comparing SGI Altix Itanium versus Xeon
systems? Any thoughts, suggestions?



-----Original Message-----
From: [] On
Behalf Of Biff Forbush
Sent: Thursday, October 01, 2009 5:27 PM
Subject: namd-l: questions regarding new single node box for NAMD: re
components, CUDA, Fermi

Hi All,

    In the coming weeks I plan to assemble a single node NAMD machine
for short pre-production runs, equilibrations, VMD, etc., for membrane
proteins (100k-200k atoms). The aim is to optimize performance in a
single node system, without a strict limit on cost. I have followed the

NAMD/VMD CUDA discussions with great interest, and it seems clear that
given the not-quite-mature state of GPU utilization and stability, it is

prudent to optimize CPU power, at the same time as providing for GPU
capability, am I right?

  For about $7K or so I am planning:
 Dual Xeon W5590 (3.3 GHz, calculating that the the incremental system
cost/Hz is actually nearly a constant, so you linearly get what you pay
 Tyan s7205 mobo. As far as I have been able to find after reading a
lot of specs, this is the only mobo with (4x) PCI-E.2x16 and dual Xeons
-- please advise if there is other/better.
 Up to 4x GTX-295s, see below.

    I assume that with this weeks' announcement of Fermi, now is not the

time to rush out and buy GTX-295s. Is it reasonable to guess that when
the Fermi devices become available (guesses are 2-4 months?), they will
be plug compatable with current CUDA software? It sounds as though
they may give rather dramatic improvement right out of the box? Is it
also possible that the improved architecture will allow additional
utilization in NAMD...?


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