Nvidia GPUs becomes DNA star

Nvidia GPUs have sped up the number crunching at the world’s largest genome sequencing centre.

Once, the BGI in China needed four days to analyse data describing a human genome. Now it needs just six hours.

That is thanks to the fact that it upgraded the servers to use Nvidia GPUs instead of conventional chips.

Over recent years, the cost of sequencing genomes by mapping out an organism’s entire genetic code has dropped about five-fold each year. But according to Gregg TeHennepe, a senior manager and research liaison in the IT department at The Jackson Laboratory in Bar Harbor, Maine the GPU breakthrough at BGI is shrinking the gap.

This is good news for the medical world. Biological exploration, the study of diseases, and efforts to tailor drugs and other treatments based on an individual’s genetic makeup could be sped up.

According to TeHennepe, the feat BGI and Nvidia pulled off was porting key genome analysis tools to the GPU architecture, an accomplishment that the open source community and others have been working toward.

TeHennepe’s Jackson Laboratory has been conducting high-throughput sequencing for more than a year, and it has been looking into GPU computing to inprove the lab’s ability to look at the data.

The Chinese lab and Nvidia’s accomplishment is an important step forward in the effort to apply the promise of GPU computing to the challenge of scaling the mountain of high-throughput sequencing data, he said.

If BGI had used traditional CPUs, it would have needed 15 times more computer nodes, with an equivalent increase in power and air conditioning.

Another advantage of BGI’s GPU initiative is the likelihood that other institutions will be able to use BGI’s GPU-enabled applications.