[Beowulf] Re: [Bioclusters] FW: cluster newbie (fwd from dag at sonsorol.org)

Eugen Leitl eugen at leitl.org
Wed Jan 5 12:12:27 PST 2005

----- Forwarded message from Chris Dagdigian <dag at sonsorol.org> -----

From: Chris Dagdigian <dag at sonsorol.org>
Date: Wed, 05 Jan 2005 14:43:55 -0500
To: "Clustering,  compute farming & distributed computing in life science informatics" <bioclusters at bioinformatics.org>
Subject: Re: [Bioclusters] FW: cluster newbie
Organization: Bioteam Inc. 
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Reply-To: "Clustering,  compute farming & distributed computing in life science informatics" <bioclusters at bioinformatics.org>

Hi Nick,

I've written about this in the past; you can find stuff in the list 

Some of the articles and presentations I've done on "bioclusters"  are 
linked off this URL: http://bioteam.net/dag/ - something there may be of 

In general I'd go with BioBrew or the ROCKS cluster kit ("roll") that 
comes with Grid Engine as the scheduler if you are starting out.

If you want to roll your own cluster to have maximum flexibility and 
really learn the behind the scenes stuff just pick the "best" (or your 
favorite) componants to match the following requirements:

1. A Linux distribution

2. A Resource manager & scheduler software (Grid Engine, etc.)

3. Software for doing unattended "bare metal" installs and incremental 
updates (SystemImager, etc.)

4. Management & monitoring packages (ganglia, nagios, bigbrother, etc.)

Take what you chose for #1-4 and put all the compute nodes on a private 
gigabit ethernet switch. There should be a common NFS share for user 
home directories and maybe for the scheduler system. Pick one node to be 
the "master" node and connect one of its NICs to the "private" cluster 
network and the 2nd NIC to the company/department network. This way you 
and your users only have to login to and deal with the one single 
"master" node.


Nick D'Angelo wrote:

>I am sure this has been asked many times before, but what is the preferred
>method or perhaps 'best' method of clustering a few 3-5 RedHat or other
>Linux flavours to best suit our Bioinfo R and D group?
>I have come across biobrew with their own cd distribution install and also
>this group.
>I was going to originally look at Fedora core 2, but that appeared to be
>painful due to the kernel re-compile and to be honest, the documentation
>appeared to be quite poor, at least what I found.
> Any suggestions?
> Thanks,

Chris Dagdigian, <dag at sonsorol.org>
BioTeam  - Independent life science IT & informatics consulting
Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E iChat/AIM: bioteamdag  Web: http://bioteam.net
Bioclusters maillist  -  Bioclusters at bioinformatics.org

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