[gmx-users] AMD cluster
lindahl at stanford.edu
Wed Jul 10 19:33:38 CEST 2002
Dmitry Kovalsky wrote:
> Hi there
> I got a device: 4 nodes of double AMD TYAN Motherboards and 100Mbit Ethernet
> And would like to create a GROMACS cluster on it. I'm not a specialist in
> building clusters and I need a help. In order not to put there a half of year
> to build it what software you advice me to setup(e.g. lam or mpich, using
> your rmp's or compiling from the sourse, what the Linux should I use etc.).
> Now there a ALT Linux (Russian Mandrake) is installed. Is there any cluster
> installation howto?
I'm been configuring a 30-node cluster in Groningen and our 100-node
cluster here in the Netherlands.
In general, if you only have 5-10 nodes it is probably easiest to set
them up manually. (the alternative is to create a netboot server, but
that will take more time than to just install Linux on 10 machines :-)
I would Recommend Redhat (latest release is 7.3, you can download it
from the net and burn a cd) - not because it is better, but because it
is the most common Linux distribution, so it's easier to get help...
Don't install the X server on the nodes. Unless you already have a
firewall, to protect the cluster from hacking I would strongly suggest
that you buy another ethernet card for one of your workstations and use
it as a firewall to have a private
network for your clusternodes:
INTERNET----WORKSTATION-----CLUSTER (with IPs like 168.0.0.*)
Install Redhat with normal options, the LAM rpm from Gromacs.org (or the
lam from Redhat, but then you will need to compile Gromacs and FFTW).
Put all your home directories on NFS so they are the same on all cluster
nodes; We've also found it practical to use an the 'amd' automounter and
export all directories in the cluster so that any node can access files
on the others like
To manage jobs on the cluster it is nice to have a queue system, for
instance PBS - look at www.openpbs.org
You can probably find tons of information by searching for 'beowulf' or
(Scyld might be an alternative - the have a distribution which is almost
100% automatic for cluster installations, but I've never tried it)
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