FPGA-Accelerated Particle-Grid Mapping

摘要

Computing the forces derived from long-range electrostatics is a critical application and also a central part of Molecular Dynamics. Part of that computation, the transformation of a charge grid to a potential grid via a 3D FFT, has received some attention recently and has been found to work extremely well on FPGAs. Here we report on the rest of the computation, which consists of two mappings: charges onto a grid and a potential grid onto the particles. These mappings are interesting in their own right as they are far more compute intensive than the FFTs; each is typically done using tricubic interpolation. We believe that these mappings have been studied only once previously for FPGAs and then found to be exorbitantly expensive; i.e., only bicubic would lit on the chip. In the current work we lind that, when using the Altera Arria 10, not only do both mappings lit, but also an appropriately sized 3D FFT. This enables the building of a balanced accelerator for the entire long-range electrostatics computation on a single FPGA. This design scales directly to FPGA clusters. Other contributions include a new mapping scheme based on table lookup and a measure of the utility of the floating point support of the Arria-10.