[Bioclusters] Details On A Local Blast Cluster

Lai Loong Fong bioclusters@bioinformatics.org
Sun, 06 Oct 2002 13:17:17 +0800

Hi Steve,
> We wanted to be able to house database splits locally on
> each node since I did not want to rely on NFS to supply
> the databases.  This has worked well despite the
> hassle ( a minimal one) of pushing out data to each node
> after a new version of a database comes out. That's
> soon to be automated - for example download the latest
> version of nr, split it , formatdb each split, and push out
> the splits to each cluster node. The script is easily written.
> We purchased Platform LSF 5.0 licenses to manage the
> cluster and as a side benefit they had example Perl scripts
> that provided working examples on how to split up target
> databases and associated queries to take advantage of the
> cluster thus economizing search time. There is nothing
> particularly magic about these programs though they do work
> well. You could certainly write your own or easily modify
> theirs to suit your specific needs. Its also possible to
> adapt the scripts for use with  GridEngine or PBS.
Where can I find the example Perl scripts that you mentioned above? I cannot
seems to find any under my LSF 5.0 installation.

> Relative to software I also have tested out TurboGenomic's
> TurboBlast and have recently been evaluating Paracel's
> Blast product. Both of these have their strengths and
> understand they are packages designed to do high throughput
> blasting so there isn't really load management built in
> to them. They are meant to benefit from a cluster environment
> so you can quite easily use either with , for more about my
> experiences with either of these products then drop me a line.
Are you able to share with me your experiences with both TurboGenomic's
TurboBlast and Paracel's Blast? TIA.

Lai Loong-Fong
Bioinformatics Institute
Agency for Science, Technology And Research