[gmx-users] cluster hardware, gigabit

Bert de Groot bgroot at gwdg.de
Wed Sep 18 09:19:57 CEST 2002


we just ordered a new cluster. We chose dual athlons because they still offer
the best price-performance ratio. And the cooling issue seems to be just as 
severe with the dual P4 boards that require even more power than the AMD boxes.

we ordered them with gigabit network, as we saw that it gives about 40% better
performance compared to fast ethernet on 2x2 processors (161 vs 225 seconds 
in a gmx3.1 benchmark). (test system: protein/lipids/water ~100.000 atoms,PME). 
If you go for Gigabit cards, make sure you get the 64 bit ones (~130 euro).

Either using fast ethernet or gigabit ehternet, you might get your latency down
with M-via:


If anyone would like to try it out and provide the list with some benchmark 
numbers, that would be highly appreciated!

BTW a modern IDE should be fast enough for most purposes (if you combine two or
more in a RAID device it will be even faster).


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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