SpyderByte.com ;Technical Portals 
 News & Information Related to Linux High Performance Computing, Linux Clustering and Cloud Computing
Home About News Archives Contribute News, Articles, Press Releases Mobile Edition Contact Advertising/Sponsorship Search Privacy
More Links
  • Cluster Monkey
  • BioBrew package
  • bioinformatics.org
  • Ghemical
  • mpiBL! AST
  • Douglas Eadline
  • Cluster Monkey
  • Creative Commons Attribution-NonCommercial-ShareAlike 2.5 License

  • HPC Vendors
    Cluster Quoter (HPC Cluster RFQ)
    Hardware Vendors
    Software Vendors
    HPC Consultants
    Training Vendors
    HPC Resources
    Featured Articles
    Cluster Builder
    User Groups & Organizations
    HP Server Diagrams
    HPC News
    Latest News
    News Archives
    Search Archives
    HPC Links

    HPC Tech Forum (was BW-BUG)
    The Aggregate
    Cluster Computing Info Centre
    Coyote Gultch
    Dr. Robert Brown's Beowulf Page
    FreshMeat.net: HPC Software
    HPC User Forum
    HPC Newsletters
    Stay current on Linux HPC news, events and information.
    LinuxHPC.org Newsletter

    Other Mailing Lists:
    Linux High Availability
    Beowulf Mailing List
    Gelato.org (Linux Itanium)

    Mobile Edition

    Latest News

    Monkey Talk: The Perfect Match
    Posted by Kenneth Farmer, Monday October 03 2005 @ 12:22PM EDT

    Monkey Talk: Cluster Opinions and Insights from Cluster Monkey.

    By Douglas Eadline

    The Perfect Match

    In case you did not know, Biologists have spent a great deal of time putting together a text file that is three billion characters long (The Human Genome). And, next on the list is to figure out what it all means. Not an easy problem. Insights often come from searching the genome with the hope it will yield some biological sentence or paragraphs that helps us understand the mystery of life. This searching it turns out has an insatiable appetite for compute cycles.

    The workhorse program used to examine the genome (human or otherwise) is called BLAST, which stands for Basic Local Alignment Search Tool. BLAST is used to answer a fairly straightforward question: I. In a biological sense, this question is not a simple I or . Results produced by BLAST are a statistical measure of how well two strings match in a biological sense. Even though BLAST was designed to be as efficient as possible, it can seriously strain any computing resource due to the shear size of the data. Clusters have become the platform of choice for BLAST searches.

    Here is an interesting thought, What would the bioinformatics community do if there was no cluster market/community today? I suggest that clusters and cluster technology most certainly would have been developed by the bioinformatics community. Surely the necessity for large amounts of high performance computing would have fostered the invention of a commodity solution. How fortuitous then is the rise of cluster computing for bioinformatics.

    The biology/cluster synergy continues today. Biologists can now take advantage of existing technologies that are ready and waiting for their problem. Indeed, there is the BioBrew package that provides a turnkey bioinformatics software distribution based on the popular ROCKS cluster distribution. The BioBrew package is freely available and is hosted at the bioinformatics.org site where you will find other interesting projects like Ghemical. As the name implies, Ghemical, is an open source application for studying the quantum and molecular mechanics of both small and large molecules. It also has a GUI interface for viewing results. In addition, if fast BLAST processing is what you need, then you may want to check out a parallel version of BLAST called mpiBL! AST.

    So what is so special about these projects? First, they are all freely available. Like much of the software needed for clusters, the user if able to freely modify and possibly re-distribute this type of software. Second, because modifying software to fit your needs is critically to your success, open software is a necessity. (One could certainly argue that science should always use open software, so that there are no "black boxes" involved.) The end result, is that you control your destiny and can help achieve a common goal. I would be willing to guess that, like open commodity clusters, had the there been no open application platform, the bioinformatics community would have developed their own. Sharing is just too powerful a mechanism. The adage "share a little get a lot" is true here as well.

    And, there is money is made by supporting, configuring, designing, and modifying all these open applications and clusters. Because assembling the pieces correctly is just as important as have the pieces in the first place.

    Douglas Eadline can be found swing around the binary trees at Cluster Monkey

    This work licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 2.5 License

    < High Performance on Wall Street 2005 | Coraid EtherDrive Storage Reduces Total System Cost for SAN >



    Cluster Monkey

    HPC Community

    Supercomputing 2010

    - Supercomputing 2010 website...

    - 2010 Beowulf Bash

    - SC10 hits YouTube!

    - Louisiana Governor Jindal Proclaims the week of November 14th "Supercomputing Week" in honor of SC10!

    Appro: High Performance Computing Resources
    IDC: Appro Xtreme-X Supercomputer Blade Solution
    Analysis of the Xtreme-X architecture and management system while assessing challenges and opportunities in the technical computing market for blade servers.

    Video - The Road to PetaFlop Computing
    Explore the Scalable Unit concept where multiple clusters of various sizes can be rapidly built and deployed into production. This new architectural approach yields many subtle benefits to dramatically lower total cost of ownership.
    White Paper - Optimized HPC Performance
    Multi-core processors provide a unique set of challenges and opportunities for the HPC market. Discover MPI strategies for the Next-Generation Quad-Core Processors.

    Appro and the Three National Laboratories
    [Appro delivers a new breed of highly scalable, dynamic, reliable and effective Linux clusters to create the next generation of supercomputers for the National Laboratories.

    AMD Opteron-based products | Intel Xeon-based products

    Home About News Archives Contribute News, Articles, Press Releases Mobile Edition Contact Advertising/Sponsorship Search Privacy
         Copyright © 2001-2011 LinuxHPC.org
    Linux is a trademark of Linus Torvalds
    All other trademarks are those of their owners.
      SpyderByte.com ;Technical Portals