Re: CCL:Cluster for AMBER/GAMESS/GAUSSIAN



 FyD wrote:
 
 Dear All,
 We are going to buy a cluster of dual athlon MP 2000+ to work with AMBER6/7,
 GAMESS and GAUSSIAN.
 
We hesitate between - a Myrinet 2GB or a 1GB Ethernet network and - SCSI HDs 15000 rpm/SCSI 10000 rpm or IDE 7200 rpm
 Both Myrinet 2GB and SCSI HD 15000 rpm are really more expensive but might
 or might not be crucial...
 Moreover, GAMESS, GAUSSIAN and AMBER might not need the same network or HDs
 for optimizing calculations...
 What is crucial for AMBER (MM) and for GAMESS/GAUSSIAN (QM) ?
 Thanks to all, Kind regards, Francois
 
 
My 16-Nodes linux cluster (http://www/departments/ChemInf/edda.html) runs on 100 MBit Ethernet. The Gaussian 98 calculations scale nicely (http://www/departments/ChemInf/g98scaling.html) for up to 8 nodes. Please note, that this might be true only for the B3LYP geometry optimization that we do.
 
Due to this behaviour, I have logically splitted the cluster into two, using the PBS batch system, because we run a lot of jobs and two simultaneous jobs on 8 nodes each are much more sensible then one on 16, if you have hundreds of jobs in the queue.
 
For us, the 100 MBit Ethernet seems to be ok. We have been convinved by others that ab-initio calculations of the type that we run always show that scaling behaviour that we see and that thus a faster network would be a waste of money. I understand that today GBit Ethernet costs as must as did the 100 MBit stuff at the time we bought our cluster, so this would be my choice.
 I have nothing to contribute with respect to HD speed and MM calcs :-)
 Cheers,
 Chris
 --
 Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf)
 
MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 Jena, Germany
 Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202
 What is man but that lofty spirit - that sense of enterprise.
 ... Kirk, "I, Mudd," stardate 4513.3..