FPGA-based communication protocols for high performance computing: molecular dynamics simulation application

Abstract

Molecular Dynamics (MD) simulation for computing Interatomic Potential (IAP) is a very important High-Performance Computing (HPC) application. MD simulation on particles of experimental relevance takes huge computation time despite using an expensive high-end server. Heterogeneous computing, a combination of FPGA and a computer, is proposed as a solution to compute MD simulation efficiently. In such heterogeneous computation, communication between FPGA and Computer is necessary. One such MD simulation, explained in the paper, is the ANN-based IAP computation of gold (Au147 & Au309) nanoparticles. MD simulation calculates the forces between atoms and the total energy of the chemical system. This work proposes the novel design and implementation of an ANN IAP-based MD simulation for Au147 & Au309 using communication protocols, such as UART and Ethernet, for communication between the FPGA and the host computer. To improve the latency of MD simulation through heterogeneous computing, UART and Ethernet communication protocols were explored to conduct MD simulation of 50,000 cycles. In this study, computation times of 17.54 hours and 18.70 hours were achieved with UART and Ethernet, respectively, compared to the conventional server time of 29 hours for the Au147 atomic cluster. The results pave the way for the development of a Lab-on-a-chip application.