[Bioclusters] blast server on OpenMosix cluster

[Chris Dagdigian]

Hong Zhang,

There are several clusters doing Blast and Blast over WWW at Harvard. 
Contact me in private if you want contact information for the people 
running them.

The Bauer Center for Genomics Research has a big cluster system running 
Platform LSF. (http://cgr.harvard.edu)

The Harvard Stats department over in the Science Center is running Grid 
Engine on a small Linux cluster.

The Flybase project people are using Grid Engine on Mac OS X (apple 
Xserves) for some lightweight web bioinformatics portal stuff 
(http://inquiry.flybase.harvard.edu)

There are several more systems I've heard about or visited over at the 
Medical school etc.

Regarding your questions:

1. wwwblast servers are easy to set up on clusters. For a lightweight 
system you can just take the LSF 'lsrun' or Grid Engine 'qrsh' commands 
and use them to wrap the call to the blastall executable. This will not 
work in a large setting as qrsh/lsrun will fail silently if there are no 
resources available; in that case you need to go asynchronous and get 
used to the batch system.

2. SGE easily runs on Debian linux

Regards,
Chris




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. 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.
> 
> 
>  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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>>_______________________________________________
>>Bioclusters maillist  -  Bioclusters@bioinformatics.org
>>https://bioinformatics.org/mailman/listinfo/bioclusters
>>
> 
> 

-- 
Chris Dagdigian, <dag@sonsorol.org>
Independent life science IT & informatics consulting
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