Molecular Dynamics Range-Limited Force Evaluation Optimized for FPGAs

FPGA Molecular Dynamics was much studied from 2004-2010. Due to limited chip resources of that era, and the inherent variety and complexity of tasks comprising Molecular Dynamics simulations (MD), those FPGA accelerators relied on host or embedded processors to organize and pre-process input and output data. This introduced long latency for data movement between simulation iterations and, as technology advanced, drastically limited performance. Current generation FPGAs are equipped not only with abundant on-chip resources, but also have hardware support for floating point operations; these advances provide an opportunity for creating self-contained MD simulation systems on a single device. In this paper, we demonstrate such a system based on the range-limited force, which comprises 90% of the flops in a typical MD simulation. It features online particle-pair generation, hundreds of force evaluation pipelines, motion update, and particle data migration. We integrate into OpenMM and find that, for a representative dataset (liquid argon with 20K atoms), we can achieve a simulation throughput of 1.4us/day with a single FPGA, more than twice the performance of a comparable generation GPU. The bulk of the work presented here explores the design of an independent MD range-limited force evaluation system tailored for modern FPGAs without data exchange with any off-chip devices. The primary contributions are the designs of the new features, the methods for coupling those features into an integrated system, and, especially, the analysis of the most likely mappings among particles/cells, on-chip memories (BRAMs), and on-chip compute units (pipelines).