OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation

Keywords: OpenCL for FPGA, molecular dynamics simulation, hardware acceleration, scientific computing


Molecular dynamics (MD) simulations are very important to study physical properties of the atoms and molecules. However, a huge amount of processing time is required to simulate a few nano-seconds of an actual experiment. Although the hardware acceleration using FPGAs provides promising results, huge design time and hardware design skills are required to implement an accelerator successfully. In this paper, we propose an OpenCLbased heterogeneous computing system with an FPGA accelerator. OpenCL is a c-like programming environment to design FPGA accelerators. We achieved over 4.9 times speed-up compared to CPU-based processing, by using only 16% of the Arria 10 FPGA resources. The speed-up is limited by the memory access bandwidth. It is possible to achieve 24 times speed-up by using an FPGA board with over 50 GBps bandwidth.

Author Biography

Hasitha Muthumala Waidyasooriya, Tohoku University

Hasitha Muthumala Waidyasooriya received the B.E degree in Information Engineering, M.S degree in Information Sciences and Ph.D. in Information Sciences from Tohoku University, Japan, in 2006, 2008 and 2010 respectively. He is currently an Assistant Professor with the Graduate School of In- formation Sciences, Tohoku University. His research interests include heterogeneous multicore processor architectures and high-level design methodology for VLSIs. 


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Technical Papers (Information and Communication Technology)