Genomics MATLAB® applications on the GPU

by vishy on September 26, 2012

in Benchmarks,Case Studies,CUDA,Jacket,Webinar

Recently, AccelerEyes held a free webinar that dealt with accelerating genomics MATLAB applications on the GPU. We recently added new genomics examples to Jacket, and wanted to use this webinar to showcase these examples and run through some code.

This was part of the free series of AccelerEyes webinars that provide a great opportunity for you to interact with AccelerEyes engineers, see demos executing live on GPUs, and learn about AccelerEyes products and services.

Over the course of the last decade, GPUs have continued to advance at a large pace, and are leaving CPUs behind in some ways, specifically in terms of their ability to perform massively parallel computations. Jacket is proven to be very efficient at harnessing this ability of GPUs, and has given scientists and engineers many-fold increases in productivity.

The webinar, like all AccelerEyes webinars, introduced basic Jacket concepts as well as important cornerstones of GPU computing. With respect to Genomics, many different examples and case studies were illustrated.

At the Centers for Disease Control and Prevention, a US Government organization tasked with the onerous responsibility of protecting public health, researchers used Jacket to explore random genetic mutations in the Hepatitis C virus. On a CPU, this would have taken months to compute! Wisely, however, they exploited parallelism through Jacket and were able to reduce this to less than half a day. The importance of this kind of boost to productivity in preserving public health cannot be understated.

The hands-on section of the webinar focused on various Genomics applications that have been ported to the GPU to achieve tremendous successes.

One example, which also happens to be included with every version of Jacket, was the Multi-dimensional scaling example from the Leibniz Institute, that gave about 15x speedup on Jacket.

We recently added two more examples to Jacket:

  • The Mantel-Haenzel Test example gives a 25x performance improvement over the CPU.
  • The Log-Fisher Test example gives an immense 400x performance improvement over the CPU!

Many more case studies were discussed, and many intelligent questions were asked during the webinar. We thank you for your attendance and interest, and gladly welcome feedback on these case studies and questions on whether your specific applications can be accelerated with Jacket!

Please view the webinar video here:

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