Redesign NAMD Molecular Dynamics Non-Bonded Force-Field on Sunway Manycore Processor

摘要

NAnoscale Molecular Dynamics (NAMD) is a parallel molecular dynamics application used to study the structure and dynamics of large biomolecular complexes, such as various types of viruses. In a biomolecular system, billions of time steps are required to understand the biological phenomena of interest. It requires enormous computing power to have a long-timescale observation of the molecule behavior of a large simulation system. NAMD meets this demand with thousands of state-of-the-art manycore processors. The Sunway Taihulight supercomputer is the number one computing system in the top 500 list of supercomputers in November 2017, with a peak performance of 125 PFlops and equipped with 40,960 SW26010 manycore processors. In this paper, we present various optimization techniques that enable the non-bonded force calculation, which is the most computation intensive and time-consuming part of NAMD, to achieve high performance on the SW26010 manycore processor. The optimizations include software cache design on local data memory, separated computing and storage cores, fine-grained inter-core data communication for fast force updating, and vectorization.