CDI-Type I: Accelerating Simulations Using CPU+FPGA Heterogeneous Processing

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The computational modeling of biological and physiological processes is becoming a growing component of any comprehensive research effort aimed at understanding complex systems. A significant limitation to such studies is the computational efficiency used to assess complex data sets that often span multiple time scales. An example of this is the heart which is one of the most important organs in the body, and for which computational modeling is becoming increasingly important to understanding its function. In addition to the large number of cells in the heart, computational modeling and simulation of cardiac function becomes extremely complex when considering both the feedback inherent in many cardiac processes (requiring a fine timescale) and the long-term effects of various stimuli (requiring long simulations). Multi-timescale simulations are therefore required. This project will utilize cardiac function as a model system to develop new and faster computational tools. New processing capabilities will be developed for automatically partitioning intra- and inter-time-step computation among heterogeneous processing units that are now becoming commonplace in commodity computer systems. In particular, computation will be partitioned and mapped to graphics processing units (GPUs) and field programmable gate arrays (FPGAs) in addition to general-purpose central processing units (CPUs), with each processing unit targeting different types of parallelism and computational bottlenecks. These capabilities will dramatically accelerate multi-timescale simulation and other computationally complex algorithms, providing an improved understanding of cardiac function and other complex systems. The project will produce an open-source resource for partitioning computation to heterogeneous computing units that will be broadly useful across a range of disciplines. The research will provide interdisciplinary training for graduate students in systems biology and computer science. In addition to carrying out much of the research on this project, these students will also perform outreach aimed to encourage younger students to pursue careers in science and engineering.