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Thread: CD-HIT and multithreading

  1. #1
    Join Date
    Dec 2004
    Beans
    37

    CD-HIT and multithreading

    Hi,
    Has anyone here have CD-HIT running and gotten multithreading to work? Can't seem to get any from the developer and I'm stuck using only one of four cores.

    Rohan

  2. #2
    Join Date
    Oct 2005
    Beans
    100

    Re: CD-HIT and multithreading

    I actually ran into the same problem. cd-hit compiles just fine with the openmp=yes option, but only uses a single thread no matter how I start it. Have you by any chance made any progress with this?

  3. #3
    Join Date
    Nov 2010
    Beans
    6

    Re: CD-HIT and multithreading

    I am suffering the same problem like cd-hit compiles please tel how to solve it.

  4. #4
    Join Date
    Dec 2004
    Beans
    37

    Re: CD-HIT and multithreading

    Hi guys,
    I just noticed you're replies and I have gotten to work under 10.04 using multithreading. There's an updated codebase that should work >> http://code.google.com/p/cdhit/

    Rohan

  5. #5
    Join Date
    Nov 2010
    Beans
    5

    Re: CD-HIT and multithreading

    As far as I know it sounds like the operating system, the passage of the wires is usually cheaper than the transition between jobs. This is because the memory management information is not changed during the thread, only a stack and register set to do, which means less data to copy the context switches.

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