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R: Beowulf in Bioinformatics

I do not know exactly Palp, but I can tell you that if you try to run a program that was written for sequential machines, on a multicore machine, most likely you will not get any benefit.. The solution is to rewrite program for example to use quad-core CPUs.

If you're thinking of running a program on  beowulf architectures, in this case too the solution is to rewrite the program  in a way that it can run in parallel on the nodes of beowulf cluster.


Antonio Dima 

----Messaggio originale----
Da: guilherme@gf7.com.br
Data: 21/06/2011 20.05
A: <debian-beowulf@lists.debian.org>
Ogg: Beowulf in Bioinformatics

Hello all,

my name is Guilherme Rocha, Biotechnologist and a Debian user since Potato, a stupid older user that think to be an advanced user, no more than this.
Help sometimes to Debian l10n team to localize Debian to PT_BR. 

I'm in charge to plan and build a cluster in our lab.  Our lab is Genev - Laboratory of Genetics of Population and Molecular Evolution,
in the Federal University of Bahia - Brasil.

We already have some tasks being done in a Ubuntu Dell Server Machine, but in a very slow procedure.
In a Dell quadcore running Ubuntu this task (PALP analysis) delay 9 days to be done.

We want to reduce this time drastically.

So we want to listen you, gurus, about the best practices in order to do it,
and also, to understand if we will have a significant time reduction with our hardware, described below.

To use Debian Med in order to make philogenetics analysis, protein modeling, DNA alignment, genetics stuff...
Open Softwares like PALP, GAMGI, GARLIC, GDPC, PyMOL, Perl Primer, etc...
We'll have very few people, 10 I think. Not sure if the tasks need to be scheduled
to be run. We are intended to use Debian Med, (med-bio meta-package) running in
a small size beowulf cluster. Almost 10 to 15 nodes.

Yes, sure, Debian Med.  :)

We have very obsolete hardware, our server-node will be a pentium IV 1,5GHz with 1GB RAM,
with work-nodes from k6-500MHz (5 unities) to pentium III 266MHz (10 unities), Thin Clients ATOM 1GHz


ThinClients with ATOM processor could be used?
The performance will be good enough?

 Then you need to look into networking 
(Infiniband or high performance Ethernet), is the software susceptible to 
latency and/or bandwidth available......

We have a 10/100 Switch. We are looking to the possibility to acquire a 100/100/1000 switch.

So the questions are: 

  1. With this hardware, we will have a significant time reduction on these tasks with our hardware?
  2. Can we use thin clients to build a cluster?
  3. Some "Debian beowulf Way" method to be reviewed before start?
  4. Another type of cluster may be better than Beowulf to do it?
  5. Any Idea will be very welcome
cheers and long life to Debian,
Guilherme Rocha
GF7 Doc & Systems - Soluções Tecnológicas
Home Page: http://www.gf7.com.br
Telefone: + 55 71 4062 9142
Mobile:   + 55 71 9279 0829

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