[Bioclusters] BioBrew announcement

[Glen Otero]

Hi folks-

I just wanted to announce the release of BioBrew v. 1.0 for the x86
architecture. The three CD iso images are freely available for download 
at
http://bioinformatics.org/ftp/biobrew, a Bioinformatics.org sponsored 
and
hosted website.

BioBrew is an open source Linux cluster distribution based on the NPACI
Rocks (www.rocksclusters.org) cluster distribution and enhanced for
bioinformaticists and life scientists. While BioBrew looks, feels, and
operates like ordinary Red Hat Linux, it includes popular open source
clustering and bioinformatics software e.g. the NCBI toolkit, BLAST,
mpiBLAST, HMMER, ClustalW, GROMACS, PHYLIP, WISE, FASTA, and EMBOSS.
Installing BioBrew is a simple, straightforward procedure that allows
Linux beginners and gurus alike to go from bare metal to cluster in the
shortest time possible.

I used this version of BioBrew to build this Infiniband cluster for 
Intel
and Mellanox for Supercomputing 2003:
http://www.hpcwire.com/hpcwire/hpcwireWWW/03/1114/106388.html.

BioBrew v. 1.0 has the following features:

- GM 1.6 and 2.0 support for Myrinet
- Infiniband support (binary drivers only)
- Automated compute node installation
- RPM software packaging and installation methods
- Cluster management tools
- MySQL database for storing cluster node information
- Cluster status monitoring with Ganglia
- SGE batch processing and job scheduler software
- Message passing interface software (MPICH & LAM)
- Parallel virtual machine (PVM)
- Parallel virtual filesystem support (PVFS)
- Virtual Machine Interface (VMI) 2.0.
- MPICH built for VMI

The big improvement for 1.0 is the inclusion of VMI. I can't say enough
about VMI. I encourage everybody that uses MPICH over multiple
interconnects to read the VMI docs I've posted. Basically, by 
virtualizing
all interconnects, VMI allows you to compile your application once 
against
a standard version of MPICH (mpich-vmi2), and run it over any
interconnnect. VMI supports ethernet, myrinet, and Infiniband.

The README and installation pictorial provide sufficient installation
instructions. I'll be posting the complete User's Guide in a week or so.

BioBrew 3.0 for x86, ia64, and x86_64 is in early beta, but will be 
posted
in mid to late February.

Biobrew-Discuss@bioinformatics.org is an email discussion list for all
things BioBrew. You can subscribe to the list at
http://bioinformatics.org/lists/biobrew-discuss.

Glen

(Sorry about any double posting)


Glen Otero, Ph.D.
Linux Prophet
619.917.1772