[gmx-users] cluster hardware, gigabit

Marc Lensink marc.lensink at oulu.fi
Tue Sep 17 14:39:51 CEST 2002

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?

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?


Dept of Biochemistry, Lipoprotein Chemistry,
Hospitaalstraat 13, B-9000, Gent.

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