[Beowulf] Please help to setup Beowulf

Geoff Jacobs gdjacobs at gmail.com
Tue Feb 17 06:56:18 EST 2009


Nifty Tom Mitchell wrote:
> On Mon, Feb 16, 2009 at 05:06:17PM +0530, Indrajit Deb wrote:
>>    Hello,
>>    I want to setup beowulf for my eight node cpu to run simulation. Debian
>>    4.0 is installed in each cpu. I am not familiar with beowulf. If any
>>    one help me to setup beowulf for the begining to the end i will be
>>    grateful.
>>    Thanks.
>>    Indrajit Deb
>>    Research Scholar.
>>    Dept. of Biophysics, Molecular Biology & Bioinformatics
>>    Calcutta University
>>    Kolkata
>>    India
>>    Ph. +919239202278
> 
> Hmm Molecular Biology and Bioinformatics....
> Which Molucular modeling code do you plan to run.
> Most but not all are built on MPI libraries does
> Debian have a pre-packaged MPI development and
> run time environment.  Look for things like Open MPI...

Yes, it does. OpenMPI, LAM, MPICH (but only version 1.2.x).

> The simulation codes you plan to run will decide 
> a lot of things.  For example it may cause you to move from
> Debian  to ROCKS/Centos or something else.  Based
> on your question you are a Bio guy more than 
> a computer guy.  If so let your application codes drive
> the cluster decisions.

Why do you say this? Debian (5.0, what I checked just now) includes all
the basic Beowulf elements and even tosses in GROMACS pre-compiled for
OpenMPI. If it's what his people are used to there's no reason to switch.

I would recommend using Debian 5.0 though, just so the latest GNU
compilers are available.

-- 
Geoffrey D. Jacobs
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