CI-P: Collaborative Research: Large-Scale FPGA-Centric Computing with Molecular Dynamics

University Of Florida, Gainesville FL

Investigators

Abstract

Together with theory and experimentation, computer simulation now constitutes the ?third pillar? of scientific inquiry, enabling researchers to build and test models of complex phenomena that cannot be replicated in the laboratory. The method of Molecular Dynamics simulation in particular is critical: applications range from the practical, e.g., drug design, to basic research in understanding disease processes. The overall goal is to give the Molecular Dynamics user community the compute capability to conduct transformative research via scalable, cost-effective, high-performance, general-purpose systems built from off-the-shelf components. The objective of this research is to bridge the many orders-of-magnitude gap between the largest current simulations and the potential physical systems to be studied. Three fundamental issues limiting performance are (i) computational efficiency per chip area, (ii) power density, which is reaching the limit of economical cooling methods, and (iii) the bottleneck between processing and communication devices. All three are addressed by Large-Scale Reconfigurable Computing using Field Programmable Gate Arrays (FPGAs). FPGAs are commodity integrated circuits whose circuitry can be configured, or programmed, in the field. Their reconfigurable architecture gives them the ability to obtain maximum efficiency for a particular application while at the same time drawing less than a quarter the power of a conventional processing device. And because FPGAs are the core components in internet routers, they are built to handle flexible high-throughput communication. This planning award is to investigate the novel system design to use the same FPGAs for communication and for computation. This approach has several advantages. First, it mitigates the critical bottleneck caused by the separation of functions among multiple devices. Second, FPGA-based communication gives the flexibility either to use standard protocols, or to use innovative application-aware routing that enables important patterns, such as the Fast Fourier Transform, to be routed congestion-free. Finally, FPGAs are well-suited for Molecular Dynamics computation allowing the hierarchical data-movement to be addressed through innovative routing, load-balancing, and arithmetic.