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GPU Enabled Bioinformatics Applications



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  • GPU Enabled Bioinformatics Applications

    In a bit of a debate with a colleague about how many (or, as I put it, how FEW) application codes are currently GPU-enabled in the wide application case considered "Bioinformatics". Of course, it probably depends on how broad one defines "Bioinformatics"...but when you look at the list of very commonly used applications that get regular coverage on SeqAnswers....I think VERY few are GPU capable.

    So, how many broadly used Bio apps do YOU know of out there? Please feel free to name as well as comment on if the GPU "enhancement" is significant or not...

  • #2
    So, last time this was discussed on SeqAnswers appears to have been mid-2016, and the answers were as I would expect:

    After a lot of digging, I'm still not seeing any mainstream software tools designed for Bioinformatics workloads that utilize GPU's, though there is some work to improve distributed parallel computing functionality as in the case of "HipMer: An Extreme-Scale De Novo Genome Assembler" for example.

    Just seems like the GPU architecture doesn't readily lend itself to the current algorithms and data sets perhaps?


    • #3
      Reviving an old thread. With the advent of the RTX nVIDIA GPU units, and the considerable efforts of nVIDIA to get people into GPU computing; we're very seriously considering buying a workstation with GPU capacity. Here are the current "Official" list of bioinformatics apps (https://www.nvidia.com/en-us/data-ce...tions/catalog/).

      What are people's thought's on this new approach to GPU computing?