[Beowulf] getting used to beowulf and building small cluster

Vincent Diepeveen diep at xs4all.nl
Fri Oct 5 08:12:20 PDT 2012

hi Rohit,

First and most important is to analyze very well what you want to  
achieve. So which software programs there are to do your
calculations, or do you need matrixcalculations?

If you need very specific software then the next thing to figure out  
is what sort of software you can use to parallellize your calculations,
or whether you can program this parallellization yourself.

The software will determine then the options you have.

For example suppose there is no MPI software nor that you are capable  
of building MPI software yourself - then getting a cluster is probably
less interesting idea than looking at shared memory solutions.

If your software can use more cores then there is already alternatives.

So figuring out the software aspect of what software you can use at a  
possible cluster is going to determine your hardware options.

Another aspect of computatoinal biology when i worked with someone on  
a project he tried to compute faster,
is commercial software versus open source. In several terrains the  
commercial software is factor million
faster than the open source from 90s.

So the solution then sometimes is to buy this commercial software and  
run it at your core2 duo.

Kind Regards,

On Oct 5, 2012, at 9:26 AM, Rohit Dhamal wrote:

> Hello,
>         My name is Rohit Dhamal and I live in India. I am a medical  
> biotechnologist, now working on computational Biology to generate  
> simulations and sequencing. I am new to linux and have shifted  
> recently from windows. I am in need of a large computational power  
> and want to build a high performance cluster for my simulations.  
> the most simplest simulations require 3 months to complete on  
> core2duo 1.67 ghz at 2 gb ram. I have no idea of cluster computing,  
> I am expert in windows though. can anybody help me building a  
> cluster step by step help on getting and installing packages and  
> setting up the cluster and its configuration?
> I would also need help on how to post on the website, since I am  
> very new to the format, website uses. I am used to GUI. I want to  
> start a new thread for my requirement.
> Thank you.
> Regards,
> Rohit Dhamal
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