AuthorsF. V. Lionetti, A. D. McCulloch and S. Baden
TitleGPU Accelerated Electrophysiology Simulations
AfilliationCenter for Biomedical Computing (SFF), Scientific Computing
Project(s)Center for Biomedical Computing (SFF)
StatusPublished
Publication TypeProceedings, non-refereed
Year of Publication2009
Conference NameProceedings of the 2009 ACM/IEEE Conference on supercomputing (SC 2009)
Abstract

Numerical simulations of cellular membranes are useful for basic science and increasingly for clinical diagnostic and therapeutic applications. A common bottleneck arises from solving large stiff systems of ODEs at thousands of integration points in a three-dimensional whole organ model. When performing a modern electrophysiogy simulation on a single conventional core, the ODE bottleneck consumed 99.4% of the running time. Using an nVidia GTX 295 GPU, we reduced the time to 2%, eliminating the bottleneck. This speedup comes at a small loss in accuracy, due to the use of single precision. By comparison, a multithreaded implementation running on the CPU yielded a speedup of 3.3 only. We are currently investigating the new bottleneck-a PDE solver. We plan to present results at the conference demonstrating the benefits of hybrid execution, whereby the PDE solver runs as multiple threads on the front end CPU. This choice balances development costs against performance.