[gmx-users] cluster newbie --> gromacs + openmosix ?

David spoel at xray.bmc.uu.se
Sat May 31 07:45:01 CEST 2003

On Sat, 2003-05-31 at 00:03, Mike Grommet wrote:
> Hi...  
> I've been asked to assist a friend doing medical research in setting
> up a small cluster to run gromacs...  
> I'm trying to set him up something fairly easy to use, and especially
> easy to add new nodes to over time and have recently stumbled upon
> knoppix and Clusterknoppix which appear to have a really nice
> openmosix install and support for diskless clients with no extra
> configuration.
> I guess my question is two fold at this point
> a)  will gromacs benefit from an openmosix environment (some old
> messages in the list archives from a year ago seem to say no, but
> again that was a year ago)
> b)  if not, is there a nice alternative in another free (as in beer)
> package that would fit along these lines?
> I have absolutely no problem digging in up to my armpits, but I'm
> curious if I'm starting off on the right or wrong foot, and a shove in
> the right direction wouldn't hurt.
> I've got a sysadmin background (bsd mostly, but some linux) and am not
> the least bit scared to get in under the hood. 
Sounds good!

What you have to find out is whether the MPI (parallel processing
library) is mosix aware (or whether that's necessary). The normal
communication between nodes is via sockets, and I'm not sure whether
mosix when moving processes accross the cluster takes this into account.
Maybe you want to search the web for MPI + openmosix
If there's evidence that it works, you might try gromacs.

Also if you're a BSD guy: don't the BSD dialects have more efficient TCP
stack than Linux? It could be worthwhile when running in parallel.

Most people (I know of) have vanilla linux installations on their boxes,
maybe trimmed down a bit (no X etc.) and run a queuing system to do the
load balancing.
> Thanks for any suggestions...  they are extrememly appreciated.
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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