AMBER Archive (2002)

Subject: look for benchmark with myrinet vs. 100-BT

From: Jianhui Wu (wujih_at_BRI.NRC.CA)
Date: Fri Aug 02 2002 - 12:15:29 CDT

Dear Amber Users,

Quite some time ago, I asked question about linux cluter vs. Origin 300.
I would like to thank Drs. P. Burger, I. Makino, C. Klein, O. Fossgaard,
S. Patchkovskii, E. Leitl, R. G. Brown, Jon Wright etc. for their very
helpful responses. I am totally convinced that I should go for linux
cluster when I purchase the new system.

I was told that interconnect is important for MD simulation. I wonder if
people did some comparison between the Gigabit (such as Myrinet) vs. 100
Base-T ethernet in term of the benchmark for Sander (such as GB model) and
the parallel scale ratio. As Myrinet is pricy and it will definitely
improve the performance, I would like to know how much it could improve
before I spend 'big buck' on it.

Best wishes,

Jian Hui Wu
Lady Davis Institute for Medical Research
Montreal, QC
Canada