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China Supercomputing Science Hardware

Chinese Lab Speeds Through Genome Processing With GPUs 408

Eric Smalley writes "The world's largest genome sequencing center once needed four days to analyze data describing a human genome. Now it needs just six hours. The trick is servers built with graphics chips — the sort of processors that were originally designed to draw images on your personal computer. They're called graphics processing units, or GPUs — a term coined by chip giant Nvidia. This fall, BGI — a mega lab headquartered in Shenzhen, China — switched to servers that use GPUs built by Nvidia, and this slashed its genome analysis time by more than an order of magnitude."
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Chinese Lab Speeds Through Genome Processing With GPUs

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  • by Anonymous Coward on Sunday January 08, 2012 @05:06PM (#38631808)

    Explaining what a GPU is in a slashdot summary? Come on.

    This is similar to someone telling you a story about something funny happening to them while shopping at the store, pausing mid-story to inform you that a 'store' is a business where goods are displayed and exchanged for a papery substance called 'money'.

  • A reminder (Score:5, Insightful)

    by Mannfred ( 2543170 ) <> on Sunday January 08, 2012 @05:18PM (#38631904)
    It's hardly news that GPUs can be used to speed up parallel tasks/computations, but even so this article is a useful reminder of two things; 1) there are still many important processes that can be sped up by using GPUs, and 2) this can be achieved pretty much anywhere in the world.
  • by MollyB ( 162595 ) on Sunday January 08, 2012 @05:39PM (#38632054) Journal

    If one reads to page 2 of tfa, they only claim the technique works well in this instance. They go on:

    Even for computer-intensive aspects of analysis pipelines, GPUs aren’t necessarily the answer. “Not everything will accelerate well on a GPU, but enough will that this is a technology that cannot be ignored,” says Gollery. “The system of the future will not be some one-size-fits-all type of box, but rather a heterogeneous mix of CPUs, GPUs and FPGAs depending on the applications and the needs of the researcher.”


    GPUs have cranked up the speed of genome sequencing analysis, but in the complicated and fast-moving field of genomics that doesn’t necessarily count as a breakthrough. “The game changing stuff,” says Trunnell, “is still on the horizon for this field.”

    So yes, the article is a bit breathless, but if utilizing GPUs helps cure my potentially impending genetic disorder, I'm all for it.

  • Re:first (Score:5, Insightful)

    by Pieroxy ( 222434 ) on Sunday January 08, 2012 @05:43PM (#38632080) Homepage

    So, a site dedicated to nerds needs to explain what a GPU is? Are we not nerds anymore?

  • by Stormthirst ( 66538 ) on Sunday January 08, 2012 @11:02PM (#38634190)

    Unless you are fortunate to live in a civilised part of the world with a universal healthcare system.

The only function of economic forecasting is to make astrology look respectable. -- John Kenneth Galbraith