[Beowulf] Please help to setup Beowulf

Geoff Jacobs gdjacobs at gmail.com
Tue Feb 17 13:46:48 EST 2009


Micha Feigin wrote:
> 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).

Slurm and SGE. Alas no Torque or PBS.

-- 
Geoffrey D. Jacobs
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