Efficient particle-pair filtering for acceleration of molecular dynamics simulation

The acceleration of molecular dynamics (MD) simulations using high performance reconfigurable computing (HPRC) has been much studied. Given the intense competition from multicore and GPUs, there has been a question whether MD on HPRC can be competitive. We concentrate here on the MD kernel computation: determining the short-range force between particle pairs. In particular, we present the first FPGA study on the filtering of particle pairs with nearly zero mutual force, a standard optimization in MD codes. There are several innovations, including a novel partitioning of the particle space, and new methods for filtering and mapping work onto the pipelines. As a consequence, highly efficient filtering can be implemented with only a small fraction of the FPGA´s resources. Overall, we find that, for an Altera Stratix-III EP3ES260, 8 force pipelines running at 200MHz can fit on the FPGA, and that they can perform at 95% efficiency. This results in a 80-fold per core speed-up for the short-range force, which is likely to make FPGAs highly competitive for MD.