[gmx-users] AMD cluster

[Erik Lindahl]

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?
> 

Hi Dima,

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

cd /net/node3/export/home/mydir/


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'.

(Scyld might be an alternative - the have a distribution which is almost
100% automatic for cluster installations, but I've never tried it)

Cheers,

Erik