An FPGA implementation of the smooth particle mesh Ewald Reciprocal Sum Compute Engine (RSCE).

摘要

Currently, molecular dynamics simulations are mostly accelerated either by a cluster of microprocessors or by a custom ASIC system. However, the power dissipation of the microprocessors and the non-recurring engineering cost of the custom ASICs could make these systems not very cost-efficient. With the increasing performance and density of the Field Programmable Gate Array (FPGA), an FPGA system is now capable of accelerating molecular dynamics simulations in a cost-effective way.; This thesis describes the design, the implementation, and the verification effort of an FPGA compute engine, named the Reciprocal Sum Compute Engine (RSCE), that calculates the reciprocal space contribution to the electrostatic energy and forces using the Smooth Particle Mesh Ewald (SPME) algorithm. Furthermore, this thesis also investigates the fixed pointed precision requirement, the speedup capability, and the parallelization strategy of the RSCE. This RSCE is intended to be used with other compute engines in a multi-FPGA system to speedup molecular dynamics simulations.