[Bioclusters] blast server on OpenMosix cluster

[Joe Landman]

On Mon, 2004-01-05 at 10:37, Hong Zhang wrote:
> Thanks for your information. I read the article before.
> I'd like to know 
> 1. whether it is possible to set up a wwwblast server on 
> cluster. 

Hi Hong:

  Yes this is possible.  A number of folks have done this to date.  Some
of the tools are open source (see bioinformatics.org), some are not.  I
have a background project to integrate my query segmenting tool
(http://scalableinformatics.com/downloads/segment.pl) with some other
tools I am developing to do blast submissions from the original NCBI web
pages.

There are a number of side items that you have to worry about when you
do this, such as data transport to the compute nodes and so forth.  If
you wish to try the mpiBLAST tool (http://mpiblast.lanl.gov), I have a
nice/simple interface for using it under SGE
(http://scalableinformatics.com/sge_mpiblast.html), and it "solves" some
of the data migration issues for you.  It is not hard to interface into
a web client (the sge_mpiblast tool).

> Our goal is allow users to access blast database through web page 
> instead of command line. I am not sure whether query from web page can be 
> migrated. 
> 
> 2. whether SGE can be used in Debian.

Should not be a problem, though you might need to compile from source.

Joe

> 
> 
>  On Fri, 2 Jan 2004, Ron Chen wrote:
> 
> > It takes time to let openmosix to migrate your jobs.
> > SGE is more suitable in the compute farm environment.
> > 
> > "Integrating BLAST with Sun ONE Grid Engine Software"
> > available at:
> > http://developers.sun.com/solaris/articles/integrating_blast.html
> > 
> >  -Ron
> > 
> > --- Hong Zhang <hzhang@research.dfci.harvard.edu>
> > wrote:
> > > But I have trouble make blast command line execute
> > > in every node.
> > > 
> > > And don't you think openmosix is suitable for blast
> > > cluster? You suggested 
> > > SGE?
> > > 
> > > 
> > > 
> > >  On Thu, 11 Dec 2003, Farul Mohd. Ghazali wrote:
> > > 
> > > > On Wed, 10 Dec 2003
> > > hong.zhang@research.dfci.harvard.edu wrote:
> > > > 
> > > > > I am working on set up a blast server on
> > > Debian/OpenMosix cluster with 4
> > > > > nodes. Actually it is totally new to me. So is
> > > there anyone can give me
> > > > > some advice? Thanks.
> > > > 
> > > > I've used OpenMosix in the form of ClusterKnoppix
> > > some months back to test
> > > > it out. The setup was very easy, boot off the CD,
> > > configure some settings
> > > > and the rest of the nodes boot off the network.
> > > Applications are
> > > > automatically load balanced across nodes.
> > > > 
> > > > While configuration and actual use was very easy,
> > > performance wasn't too
> > > > great. I think the main reason was that OpenMosix
> > > dynamically migrates
> > > > applications to the different nodes to
> > > automatically load balance the
> > > > system thus the overhead of migration for long
> > > running jobs suddenly
> > > > became apparent.
> > > > 
> > > > To be honest, we didn't try to optimize it much
> > > and went to implement our
> > > > blast cluster with SGE and hopefully soon
> > > mpiblast.
> > > > 
> > > > 
> > > > 
> > > > _______________________________________________
> > > > Bioclusters maillist  - 
> > > Bioclusters@bioinformatics.org
> > > >
> > >
> > https://bioinformatics.org/mailman/listinfo/bioclusters
> > > > 
> > > 
> > > -- 
> > > Hong Zhang, MIS
> > > Bioinformatics Analyst
> > > Dana Farber Cancer Institute
> > > Harvard Medical School
> > > 44 Binney St, D1510A
> > > Boston MA 02115
> > > Email: hong.zhang@research.dfci.harvard.edu
> > > Phone: 617-632-3824
> > > Fax: 617-632-3351
> > > 
> > > _______________________________________________
> > > Bioclusters maillist  - 
> > > Bioclusters@bioinformatics.org
> > >
> > https://bioinformatics.org/mailman/listinfo/bioclusters
> > 
> > 
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-- 
Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman@scalableinformatics.com
  web: http://scalableinformatics.com
phone: +1 734 612 4615