Re: Beowulf in Bioinformatics
Guilherme Rocha <[email protected]>
| Newsgroups | gmane.linux.debian.devel.beowulf |
|---|---|
| Message-ID | <[email protected]> |
Hi all, first of all thanks by your quick answers. :) Thanks a lot by all ideas. Rogério, sure, can I visit your cluster? I can show you all our structure also. Lets discuss it in PVT. I feel lucky by count with help of all of you and Debian. best regards, Guilherme Rocha GF7 Doc& Systems - Soluções Tecnológicas Home Page: http://www.gf7.com.br Telefone: + 55 71 4062 9142 Mobile: + 55 71 9279 0829 Em 22-06-2011 13:09, ROGERIO DE CARVALHO BASTOS escreveu: > 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 >> >> >> >> >> >> > > >