[Fmeub]

Hi!

I have been given a project to link a few PC's and build a Linux cluster so that Gaussian (GaussView) could be run on it. It seems that my supervisor wants to use it to speed up calculations, and not necessarily to handle many little jobs at once.

I came across an article "Commodity Cluster Computing for Computational Chemistry" by Hawick,Grove,Coddington and Buntine from the University of Adelaide which was extremely helpful, but since that was written in 2000, I was wondering what some of the newer trends and tricks in software are in this regard.

I have a little computer science background, but I don't feel confident about doing something like this, and I don't actually know where possible pitfalls would be, or where the best place would be to start.

Do you know of any good websites or books that could help me?

[pjaj]

I don't know if it will help, but there is a UK magazine "PCPlus" http://www.pcplus.co.uk/ that has an article in the February issue (Issue 278) entitled "Build the Ultimate PC" which describes how to combine all your spare PCs into a Linux cluster. It uses a cheap 1Gb ethernet switch and runs Ubuntu Linux on all the boxes. There is far too much to go into here, but you can find the back issues at

http://www.myfavouritemagazines.co.uk/store/displayitem.asp?sid=464&id=9004&custid=23@02@200984979@788002283

It's the article featured on the cover.

[Fmeub]

Hi !

Hm, a few months later...
I managed to build the cluster and get Gaussian 03 to run on it. However, I used a cluster installation toolkit program suite named OSCAR which makes life much easier for chemists who aren't highly knowledgeable in Linux.

In the process of setting up the cluster, I found the following resources very helpful:

Cluster Resources Incorporated, 2009 Torque Resource Manager [Online] Available from
http://www.clusterresources.com/products/torque/docs/a.ltorquequickstart.shtml

Hekman J.P., 1997 Linux in a Nutshell Sebastopol, CA, O'Reilly & Associates

Sloan J.D., 2005 High Performance Linux Clusters with OSCAR, Rocks, openMosix & MPI Sebastopol, CA, O'Reilly Media.

Van Eck A., 2009a Welcome to the Computational Chemistry SIG – Software Web [Online] South Africa, University of the Free State, Available from http://sig.sagrid.ac.za/bin/view/CompChem/Software/OscarInstall

If you want to do something similar I would suggest that you do thorough (and I mean thorough) reading before you start loading any operating systems or application software on your hardware. Even the hardware needs special attention actually.

I want to encourage anyone who needs computational chemistry results in less time without sacrificing accuracy, and who doesn't have a big budget, to consider this option. I think any chemist would be able to do this, however, the time it would take to build a cluster is directly proportional to your computer background knowledge.

;-)

[saras.ganapathy]

Sir,

You have said that you have successfully built a Linux Cluster for Gaussian 03. Could you kindly the hardware details of the same. Will it be very expensive?

Thanking you,

Sincerely,

Saras Ganapathy

[daveyboy]

There is a program called "Hadoop" which might also be of some interest to you.

[JoshW]

yes,"Hadoop".  Useful program