Building cluster

From: Cesar Luis Avila (
Date: Sat Mar 18 2006 - 12:54:38 CST

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

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

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