[Beowulf] Fwd: Bio-cluster Linux distribution (BioBrew announcement)
andrewxwang at yahoo.com.tw
Thu Jan 22 00:49:12 EST 2004
based on Rocks cluster.
--- Glen Otero <gotero at linuxprophet.com> wrote:
> 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
> http://bioinformatics.org/ftp/biobrew, a
> hosted website.
> BioBrew is an open source Linux cluster distribution
based on the
> Rocks (www.rocksclusters.org) cluster distribution
and enhanced for
> bioinformaticists and life scientists. While BioBrew
> operates like ordinary Red Hat Linux, it includes
popular open source
> clustering and bioinformatics software e.g. the NCBI
> 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
> shortest time possible.
> I used this version of BioBrew to build this
Infiniband cluster for
> and Mellanox for Supercomputing 2003:
> 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
> - 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
> about VMI. I encourage everybody that uses MPICH
> interconnects to read the VMI docs I've posted.
> all interconnects, VMI allows you to compile your
> a standard version of MPICH (mpich-vmi2), and run it
> interconnnect. VMI supports ethernet, myrinet, and
> The README and installation pictorial provide
> instructions. I'll be posting the complete User's
Guide in a week or
> BioBrew 3.0 for x86, ia64, and x86_64 is in early
beta, but will be
> in mid to late February.
> Biobrew-Discuss at bioinformatics.org is an email
discussion list for
> things BioBrew. You can subscribe to the list at
> (Sorry about any double posting)
> Glen Otero, Ph.D.
> Linux Prophet
> Bioclusters maillist -
Bioclusters at bioinformatics.org
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