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    Latest News

    BioBrew-3.1 for x86 is here
    Friday February 25 2005 @ 04:08PM EST

    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 Rocks-3.1 include:

    -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 /opt/BioBrew
    upgraded NCBI BLAST with ncbitoools 6.1.0-2 and ncbi.tar.gz from 10/20/04)
    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

    New applications:

    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


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    Golden Eggs
    (HP Visual Diagram and Config Guides)
    Integrity:
    » rx2620 1600MHz 2P IA64
    » rx2620 Cluster MSA1000 IA64
    » rx2600 1500MHz 2P IA64
    » rx2600 Cluster MSA1000 IA64
    ProLiant:
    » DL140 3060MHz 2P IA32
    » DL140 G2 3600MHz 2P EM64T
    » DL145 2600MHz 2P Opteron
    » DL360 G4 3400MHz 2P EM64T
    » DL360 G4p 3800MHz 2P EM64T
    » DL380 G4 3800MHz 2P EM64T
    » DL385 2800MHz 2P Opteron
    » DL560 3000MHz 4P IA32
    » DL585 2600MHz 4P Opteron
    » DL580 G3 3330MHz 4P EM64T
    Clusters:
    » CP3000 32x DL145G2 & DL360G4p GigE EM64T
    » CP4000 32x DL145 GigE Opteron
    » CP4000 64x DL145 GigE Opteron
    » CP4000 102x DL145 GigE Opteron
    » CP4000 32x DL145 Myri Opteron
    » Rocks Cluster 16-22 DL145 Opteron
    » Rocks Cluster 30-46 DL145 Opteron
    » Rocks Cluster 64-84 DL145 Opteron
    » LC3000 GigaE 24-36 DL145 Opteron
    » LC3000 Myri 16-32x DL145 Opteron
    » LC3000 GigaE 16-22x DL145 Opteron
    » LC2000 GigaE 16-22x DL360G3 Xeon
    Storage:
    » MSA500 G2, SCSI
    » MSA1500 24TB, SCSI and SATA
    Misc:
    » AMD64 and EM64T systems with MSA1500






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