[Beowulf] Please help to setup Beowulf

Micha Feigin michf at post.tau.ac.il
Tue Feb 17 09:24:06 EST 2009


On Tue, 17 Feb 2009 05:56:18 -0600
Geoff Jacobs <gdjacobs at gmail.com> wrote:

> 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.
> 

Debian has most of the programs needed to run a cluster except as far as I can
tell a queue system. I had to install torcs/maui from source and recompile
openmpi to support them (regrettably the latest version of debian's openmpi
source package doesn't compile properly with torcs support  so I had to go one
back. It doesn't link with the torcs library for some reason).
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