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

Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara
Tohoku University, Miyagi, Japan
Information Engineering Express, International Institute of Applied Informatics, Vol.3, No.2, P.11 – 23, 2017


   title={OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation},

   author={Waidyasooriya, Hasitha Muthumala},

   journal={Information Engineering Express},






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Molecular dynamics (MD) simulations are very important to studyphysical 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 accelerationusing FPGAs provides promising results, huge design time and hardware design skills are required to implement an accelerator successfully. In this paper, we propose an OpenCL-based 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 anFPGA board with over 50 GBps bandwidth.
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