FPGA Accelerators for Computing Interatomic Potential-Based Molecular Dynamics Simulation for Gold Nanoparticles:Exploring Different Communication Protocols  

作　　者：Ankitkumar Patel Srivathsan Vasudevan Satya Bulusu 

机构地区：[1]Department of Electrical Engineering,Indian Institute of Technology Indore,Indore,453552,India [2]Department of Chemistry,Indian Institute of Technology Indore,Indore,453552,India

出　　处：《Computers, Materials & Continua》2024年第9期3803-3818,共16页计算机、材料和连续体（英文）

摘　　要：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 the Field Programmable Gate Array(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(Artificial Neural Network)ANN-based IAP computation of gold(Au_(147)&Au_(309))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 Au_(147)&Au_(309) using communication protocols,such as Universal Asynchronous Receiver-Transmitter(UART)and Ethernet,for communication between the FPGA and the host computer.To improve the latency of MD simulation through heterogeneous computing,Universal Asynchronous Receiver-Transmitter(UART)and Ethernet communication protocols were explored to conduct MD simulation of 50,000 cycles.In this study,computation times of 17.54 and 18.70 h were achieved with UART and Ethernet,respectively,compared to the conventional server time of 29 h for Au_(147) nanoparticles.The results pave the way for the development of a Lab-on-a-chip application.

关 键 词：Ethernet hardware accelerator heterogeneous computing interatomic potential(IAP) MDsimulation peripheral component interconnect express(PCIe) UART 

分 类 号：TP39[自动化与计算机技术—计算机应用技术]