STUDYING THE H1N1 VIRUS USING NVIDIA GPUS

by Linda Barney

In the NVIDIA booth yesterday, we had a chance to hear from Klaus Schulten and John Stone from the University of Illinois. They demonstrated how they use NVIDIA GPUs with NAMD and VMD research software to simulate and visualize cell structures.

Their research focuses on a variety of health issues but one important aspect of their research is centered on cell disruption and viruses, including the H1N1 virus. Their H1N1 research focuses on the structure of the that virus, how it reacts to drug treatment, and what may be happening in relation to drug resistance.

Schulten went on to say that the swine flu epidemic provided a chance for theoretical scientists to apply ‘emergency computing’ to help a real world problem.

Schulten and Stone use supercomputers but also use PCs running NVIDIA GPUs in their research. Schulten indicates that a problem in traditional computing where processing is done on the CPU is that processing speeds are too slow to adequately see the living cell.

“When we use systems with GPUs running NAMD and VMD software, this speed is accelerated and we can do simulations of cells. Important biomedical cellular research problems can be solved by the acceleration offered by GPU chips. With NVIDIA GPUs, our calculations can be done between 200 – 400 times faster on the GPU,” states Schulten.

In his presentation, Stone also described how desktop or laptops with NVIDIA GPUs are used in post-processing analysis of gas molecules.  “Calculations that would run for a month can now be done in a day.  In addition, our researchers can do calculations on a laptop in a few minutes.  This allows us to perform calculations and research that previously would have been too time consuming to do,” states Stone.