Implementingmolecular dynamics simulation on the Sunway TaihuLight system with heterogeneous many-core processors

摘要

In various research of atom and molecule physical movements, molecular dynamics (MD) simulationrnis a common tool to simulate and investigate the real molecular motion. However, it introducesrna significant penalty in performance, power, electricity, and running time. Consequently,rnonce the simulation size scales up and computing demands keep growing, it comes at substantialrncosts in performance and energy usage. In this paper, an optimized MD implementation onrnthe Sunway TaihuLight supercomputerwith heterogeneousmany-core processors is developed tornaddress the abovementioned issues. The Sunway TaihuLight is a totally independently designedrnand developed Chinese supercomputer with a profusely customized integration approach and arnbrand new many-core processor, the SW26010. The computing power mainly supported by thernhomegrown many-core SW26010 processors differs from other existing heterogeneous supercomputers.rnThe SunwayTaihuLight is a heterogeneous supercomputer that ranks first in theworldrnwith its peak performance over 100 PFLOPS. Firstly,we propose a new algorithm based on clusterrnparticles to fit the special architecture of SW26010. Then, three optimization methods of theMDrnsimulation are implemented step by step: parallelized extensions to SW26010, memory-accessrnoptimizations, and vectorization. After these optimization processes, a 14x speedup is achievedrnon a single computing node and yields significant performance and energy improvements. Superiorly,rnalmost 24,000 computing nodes (6,000,000 cores) are applied in our experiments, whichrngain an almost linear speedup.Besides, the proposed methods also can be adapted and fit to otherrnmolecular dynamics codes, even other similar scientific applications.