AMBER Archive (2004)

Subject: AMBER: Gigabit Ethernet Switch/Opteron 246

From: jianhui wu (jhuiwu_at_yahoo.com)
Date: Tue Dec 07 2004 - 11:09:11 CST

Dear Amber users,
 
I am shoping for a 64-bit AMD opteron cluster for MD simulations using Amber. This cluster will be around 14 nodes, plus a server. I would like to have your advice/experience before I spend the money.
 
1) Which brand of Gigabit ethernet switch is better?
 
Currently, I have a 32-bit cluster using NetGear GS516T gigabit swtich (copper). It is fairly stable. To do a very simple test, I ping node1 from the server. The time is around 0.08ms if the job load in the cluster is zero. Is the NetGear GS516T a good choice for the 64-bit opteron cluster? If you are using an AMD opteron cluster, what kind of ethernet swtich do you use?
 
2) To run amber, do you expect significant performance gain of Opteron 248 ($690, AMD homepage) over Opteron 246 ($455)? I was told Opteron 246 is a good choice in term of price/performance ratio. If you have experience with various opteron models, would you share your experience?
 
Thanks a lot for your help,
 
 
Jian Hui Wu, Ph.D.
McGill University
Montreal, Canada
  

                
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