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Additional Info
GPU Computing gives us a 100-fold increase in some of our programs, and this is on desktop machines where previously we would have had to run these calculations on a cluster.

—John Stone, Senior Research Programmer, University of Illinois Urbana-Champaign

 
Science & Education
UIUC University of Illinois,
Urbana-Champaign

The Challenge

Simulation of complex molecular system.

The University of Illinois at Urbana-Champaign’s (UIUC) Nanoscale Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD) are powerful and widely used tools for simulating and visualizing biomolecular processes. Simulating complex molecular systems is time consuming and requires large, sophisticated clusters of computers.

The Solution

To boost performance, the UIUC researchers ported the "cionize" ion placement tool to an NVIDIA GPU Computing solution. The goal was to accelerate the computationally intensive kernels for calculating the interaction of biological molecules and ions. In doing so, UIUC researchers achieved speedups on ion simulations over 100 times that of an 18-CPU cluster (based on total CPU time vs total GPU time).

With a three-GPU workstation, a similar calculation for time-averaged electrostatics in the VMD tool reaches 705 gigaflops of realized performance. This remarkable performance allows any bioscience researcher to have the equivalent of a computing cluster on their workstation.

The Impact

UIUC calculates the interaction of biological molecules and ions with computationally intensive kernels.

With GPU Computing, these molecular simulations are no longer restricted to clusters in server rooms.

The combination of NAMD and NVIDIA GPU Computing solutions is a marriage of cutting-edge research and software development, aimed at harnessing the nation’s fastest supercomputers to decipher the tiniest components of living cells. These new computing tools are quickening the pace of drug discovery and other vital research in unraveling biological processes.

For more information, visit: http://www.ks.uiuc.edu/

For more information about NVIDIA GPU Computing solutions, visit: www.nvidia.com/tesla