[Beowulf] New BioBrew Release
gotero at linuxprophet.com
Wed Feb 23 00:48:53 PST 2005
BioBrew-3.1 for x86 is here.
BioBrew is an open source Linux cluster distribution based on the
popular Rocks (www.rocksclusters.org) cluster software and enhanced for
bioinformatics. BioBrew includes popular cluster software e.g. MPICH,
PVM, Modules, PVFS, Myrinet GM, Sun Grid Engine, gcc, Ganglia, and
Globus, *and* popular bioinformatics software e.g. the NCBI toolkit,
BLAST, mpiBLAST, HMMER, ClustalW, GROMACS, PHYLIP, WISE, FASTA,
MrBayes, and EMBOSS. A BioBrew DVD iso for x86 is freely available for
download at BioBrew.org, a Bioinformatics.org sponsored and hosted
website. README and INSTALL docs are also available on the website.
Features you'll find in this release that differ slightly from
-Infiniband support from Mellanox (/usr/mellanox)
-Myrinet support with gm-2.0.11
-Virtual Machine Interface (VMI) 2.0. (/opt/vmi-2.0-gcc)
-mpich built for VMI (/opt/mpich-vmi-2.0-gcc)
Application upgrades for 3.1:
added modules back to distro with modulesenv 3.1.6-2
upgraded modulefiles to 1.0.2, including corrections to profile.d
scripts submitted by Humberto Zuazaga
upgraded hmmer to 2.3.2-1
upgraded gromacs to 3.2.1-1
upgraded EMBOSS to 2.9.0-6; EMBOSS now installs to /usr/share and not
upgraded NCBI BLAST with ncbitoools 6.1.0-2 and ncbi.tar.gz from
upgraded mpiBLAST to 1.3; mpiBLAST lives under /opt/NCBI/6.1.0/bin with
the rest of the binaries
upgraded Phylip to 3.61-5 and separated it from EMBOSS
MrBayes 3.0-1 has been added to BioBrew
BioBrew rolls are also here:
BioBrew rolls for Rocks-3.1 and Rocks-3.3 on x86 are also available on
the website, as is a BioBrew roll for Rocks-3.3 on x86_64. The rolls
contain the same bio apps as the full BioBrew release. But know that if
you build a cluster with Rocks + BioBrew roll, you will not have access
to the vmi, mpich-vmi, Infiniband, or Myrinet packages in the full
BioBrew release. You will be relying on Rocks' Infiniband, mpich, and
Myrinet support, which is slightly different than BioBrew's, when using
these rolls. The BioBrew rolls include the SRPMS as well as the RPMS.
This is the first BioBrew release for x86_64:
The BioBrew roll for Rocks-3.3 on x86_64 includes the same apps as the
x86 releases, except for Java and EMBOSS. EMBOSS is not included
because Java for Rocks-3.3-x86_64 was not available at the time this
release was built.
Future BioBrew development is likely to consist of BioBrew rolls only.
I've got more apps planned. I'm also soliciting requests. Hint, hint...
Thanks to Joe Landman of Scalable Informatics and Luc Ducazu of
BioLinux for the SRPMS they make available to the community, and from
which I borrowed liberally. They helped make this release a reality.
Thanks to the beta testers that downloaded the releases over the past
few weeks and pointed out a few problems. Thanks to Aaron Darling and
Humberto Zuazaga for their help with mpiBLAST and Modules,
respectively. Special thanks to the folks running BioBrew mirrors!
Glen Otero Ph.D.
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