Re: Beowulf in Bioinformatics

Hy Guilherme,

I'm graduating in Computer Science at UFBA and work with a cluster at  
Institute of Physics. Maybe we could meet and talk about your cluster.

Citando Guilherme Rocha <[email protected]>:

>
> 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.
>
>
>
>    * We first need to identify what we want/need. what is the (typical)
>      problem you want to solve?
>
> 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...
>
>    * what software do you need for that, do you need a batch scheduler
>      or do you
>      have very few users which work at the same place and share the
>      cluster without technical measures?
>
> 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.
>
>
>    * think about the OS (Debian is a good choice here ;))
>
> Yes, sure, Debian Med.  :)
>
>
>    *   Think about the compute hardware, you probably need a login
>      node, execute nodes and a file server, do you need many local
>      cores or are the problems too large to fit into a few nodes?
>
> 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
>
>
> Question:
>
> 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
>
>
>
>
>
>



-- 

Rogerio de Carvalho Bastos

http://wiki.dcc.ufba.br/Main/RogerioBastos