Re: Building cluster

From: Jimmy Tang (
Date: Sun Mar 19 2006 - 05:01:17 CST

Hi Cesar,

Funnily, we just got a dual opteron 265 (4cores in total) IBM machien
for our geneticists (so i cant comment on performace for namd) and I
also own my own amd64 3800+ x2 machine at home with similar specs to
what you're suggesting (8gigs of ram on the 265 system and 2gigs of ram
on my own 3800+)

I ran HPL on the two quite briefly to see what sort of performance
difference there was, the opteron system clocked in around 7giga flops
per core and the amd64 system was around 6.5gigaflops. but on the dual
core system there are 4cores (both physical chips) so you should get
around 28gigaflops at best. these tests were done with out much tuning to
HPL (i just took our settings from a HPL from our opteron 250 based
cluster 8.4gigaflops per core)


On Sat, Mar 18, 2006 at 03:54:38PM -0300, Cesar Luis Avila wrote:
> Dear all,
> I am a biochemist and I am conducting my PhD studies at Universidad
> Nacional de Tucuman in Argentina. Most part of my research will require
> MD simulations so I am willing to build a little cluster for running
> NAMD. I wish I could attend the Cluster Workshop but I am too far away.
> The following setup is what I had in mind:
> Each Node
> 2 x AMD Opteron Dual Core Model 265 (1.8 GHz - 1024 kB L2 Cache)
> 1 x Tyan Thunder K8SD Pro
> 2 x 1 Gb ECC PC-3200 RAM operating at 400MHz
> 1 x HD 80 Gb SATA2
> And all nodes ( 3 or 4 in the first stages) connected through Gigabit
> Ethernet.
> The main problem I face right now is that I cannot find any supplier in
> Argentina for this specific equipment. The only processor available on
> the market is AMD Atlhon X2 (also Dual Core). Do you know of any
> benchmark comparing Atlhon to Opteron performance for NAMD? And how
> would the scalability of the cluster be affected? I think I could buy
> above twice as much nodes for Atlhon than for Opteron setup but I am
> afraid the performance won't be compensated.
> I would be very gratefull with any piece of advice you could give me.
> Best Regards
> Cesar Avila
> Universidad Nacional de Tucuman
> Alternative Node Setup
> 1 x AMD Atlhon 64 X2 Dual-Core Processor 3800+ (2.0 GHz - 512 kB L2 Cache)
> 1 x MSI RS482M4-FD
> 2 x 512 Mb PC-3200 RAM operating at 400MHz
> 1 x HD 80 Gb SATA
---end quoted text---

Jimmy Tang
Trinity Centre for High Performance Computing,
Lloyd Building, Trinity College Dublin.

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