[gmx-users] cluster hardware, gigabit

[K.A. Feenstra]

David van der Spoel wrote:
> 
> On Tue, 2002-09-17 at 14:39, Marc Lensink wrote:
> 
> Scsi is not necessary unless you do a lot of quantum mechanics that is
> disk bound.

That also depends a bit on for example if the server will also be used
by a lot of users simultaneously to do (disk-intensive) analysis, and/or
if you will have nfs-mounted systems on all the nodes. In those cases
you need fast multiple disk acces and I think SCSI still beats IDE there.

But, if all the nodes have the system local (the cluster in Groningen
has that for example), and you take a motherboard with 4 IDE channels
and four IDE disks for, say, 20 users, my guess is the disk access 
load will be balanced enough that you won't see a difference with SCSI.

As for your network, Myrinet seems overkill. But I was thinking you
might be able to improve over an ethernet/swith setup, as far as
latency is concerned. Seeing that you will only have a few nodes,
you could give each node several ethernet cards (100M), so it can 
have a direct route to each other node. What I don't know however
is if that will decrease the latency already by itself, or if you
would need some tricks to eliminate some (now superfluous) software
networking layers. Maybe someone has already tried something
similar? The reason I mention it at all, is that when you get
high-end dual boxes, they are really *fast* compared to your network,
especially the latency, so that is were you could gain a lot in
scaling by thinking a bit and trying some...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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