GPU Acceleration of Top Genomics Application With OpenACC Promises to Help Speed Delivery of Life-Saving Drugs

Monday, August 6, 2012

Easy 16x Speed-Up of "DNADist" Software to Help Roche and Other Pharmaceutical Companies Accelerate Drug Research

SHANGHAI, CHINA -- NVIDIA today announced that the OpenACC programming standard has enabled Chinese researchers to dramatically accelerate the DNADist genomics application,1 which is used in the early stages of development of treatments for genetic conditions, such as Down syndrome, hemophilia, cystic fibrosis, and sickle-cell disease.

Using the CAPS enterprise OpenACC compiler, Shanghai Jia Tong University researchers accelerated the DNADist application by 16 times on an NVIDIA® Tesla® GPU-based system by adding just four simple hints -- known as "directives" -- to the application code.

DNADist, a distance-matrix application for studying the genetic relationships between various species over evolutionary history, enables researchers to extract information from sequenced DNA data by reading nucleotide sequences, which may potentially lead to a greater understanding of the causes of and treatments for pervasive genetic diseases. Accelerating the DNADist application allows researchers to study a significantly larger range of input data and obtain actionable information earlier in the disease treatment research process.

A programming standard for parallel computing using directives, OpenACC is designed to enable millions of researchers around the world to easily take advantage of the transformative power of GPU computing. It provides the easiest way for users, with or without extensive parallel programming expertise, to accelerate their research in a matter of hours using familiar programming models.

Roche Impressed with OpenACC, Power of GPU Acceleration
By quickly delivering game-changing application acceleration with minimal effort, OpenACC provides world-leading pharmaceutical companies like Roche with the ability to research, identify and develop more effective drugs faster and more cost-effectively.

"I am astonished at how quickly and easily OpenACC unlocked the power of GPU acceleration for DNADist, which is one of our most critical applications," said Steve Pan, project director, Roche Pharma Global Informatics. "The potential impact of GPUs is priceless because getting our products to market faster, even one day earlier, will save more lives."

"Extracting meaningful information from the vast collection of available DNA sequencing data requires ever-increasing amounts of computational power," said Sumit Gupta, senior director of the Tesla business at NVIDIA. "OpenACC enables researchers to quickly and easily leverage the enormous performance of GPU accelerators to analyze mountains of genomics data. This dramatically reduces the time to study biological systems, and potentially leads to the development of more effective next-generation medicines."

A large and growing number of researchers and engineers are using OpenACC-supported compilers and hybrid CPU/GPU computing systems to accelerate all types of applications, including CAD/CAM, image processing, materials science, molecular dynamics, quantum chemistry, and many other applications. In many cases, users are reporting that they have achieved as much as 5-10X or faster levels of acceleration in as little as a few hours of work.

Webinar to Showcase OpenACC, DNADist - Sept. 6, 2012
CAPS enterprise will deliver a free public webinar on Thursday, Sept. 6, 2012, to educate participants about OpenACC use cases and best practices, and provide more detail on the acceleration of the DNADist application. To learn more or to register, visit

About NVIDIA Tesla GPUs
NVIDIA Tesla GPUs are massively parallel accelerators based on the NVIDIA CUDA® parallel computing platform and programming model. Tesla GPUs are designed from the ground up for power-efficient, high performance computing, computational science and supercomputing, delivering dramatically higher application acceleration for a range of scientific and commercial applications than a CPU-only approach.

More information about NVIDIA Tesla GPUs is available at the Tesla website. To learn more about CUDA or download the latest version, visit the CUDA website. More NVIDIA news, company and product information, videos, images and other information is available at the NVIDIA newsroom. You can also follow us on Twitter (@NVIDIATesla).

NVIDIA (NASDAQ: NVDA) awakened the world to computer graphics when it invented the GPU in 1999. Today, its processors power a broad range of products from smartphones to supercomputers. NVIDIA's mobile processors are used in cell phones, tablets and auto infotainment systems. PC gamers rely on GPUs to enjoy spectacularly immersive worlds. Professionals use them to create 3D graphics and visual effects in movies and to design everything from golf clubs to jumbo jets. And researchers utilize GPUs to advance the frontiers of science with high performance computing. The company has more than 5,000 patents issued, allowed or filed, including ones covering ideas essential to modern computing. For more information, see

1) DNADist is part of the Phylip (PHYLogeny Inference Package) open source package of programs used by academicians in the field of biosciences, primarily in phylogeny. Source:

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NVIDIA (NASDAQ: NVDA) is the AI computing company. Its invention of the GPU in 1999 sparked the growth of the PC gaming market, redefined modern computer graphics and revolutionized parallel computing. More recently, GPU deep learning ignited modern AI — the next era of computing — with the GPU acting as the brain of computers, robots and self-driving cars that can perceive and understand the world. More information at 
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