[gmx-users] cluster hardware, gigabit

David van der Spoel spoel at xray.bmc.uu.se
Tue Sep 17 15:35:21 CEST 2002

On Tue, 2002-09-17 at 14:39, Marc Lensink wrote:
> For our department we're going to buy a small cluster, that will
> mainly be used for running MD simulations. It'll only be a small
> cluster, and we were thinking about four dual processor nodes, with
> one acting as the server and equipped with a lot of memory. That one
> would also be used for applications demanding a lot of memory (eg,
> certain sequence alignments). Echo additional node (3) would be
> something like dual Athlon, 512MB, 80GB, connected through a gigabit
> switch. All machines would run debian, and have LAM with OpenPBS.
> What is the Current Opinion about suitable hardware?
Get dual Xeons instead. Faster, and more reliable. Even if yo uonly can
get three for the same money it's worth it. Gbit doesn't buy you much
right now, since linux is limited by latency... Check my dual xeon
numbers at www.gromacs.org

Scsi is not necessary unless you do a lot of quantum mechanics that is
disk bound.
> Although superior, Myrinet is obciously too expensive for such a small
> system. Is there any advantage of gigabit over fast ethernet
> (100Mbit), for MD? Or are there other alternatives?
> Is it wise to have the server equipped with a SCSI disk that is
> exported to the nodes, or would IDE suffice?
> Cheers,
> Marc
> -- 
> Dept of Biochemistry, Lipoprotein Chemistry,
> Hospitaalstraat 13, B-9000, Gent.
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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