Technical Papers Archive

FASDA: An FPGA-Aided, Scalable, and Distributed Accelerator for Range-Limited Molecular Dynamics

Authors: Chunshu Wu (Boston University); Tong Geng (University of Rochester); Anqi Guo, Sahan Bandara, and Pouya Haghi (Boston University); Chuan Liu (University of Rochester); Ang Li (Pacific Northwest National Laboratory (PNNL)); and Martin Herbordt (Boston University)

Abstract: Conducting long-timescale simulations of small molecules using Molecular Dynamics (MD) is crucial in drug design. However, traditional methods to accelerate the process, including ASICs or GPUs, have limitations. ASIC solutions are not always generally available, while GPU solutions may not scale when processing small molecules. FPGAs are both communication processors and accelerators, with tight coupling between these capabilities, and so could be used to address strong scaling in this domain.

We present FASDA, the first FPGA-based MD accelerator available for community development. FASDA enables the use of FPGA enhanced clusters and clouds to execute range-limited MD, which is the most resource-intensive and computation-demanding component in MD. FASDA is built with a series of plugable components that are adjustable based on user requirements and demonstrates nearly linear scaling on an eight FPGA cluster. It outperforms the state-of-the-art GPU solution by 4.67x, with the resulting prospect of significantly reducing lead evaluation time.




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