The Design And Optimization Of High-performance Molecular Dynamics Algorithms On The Sunway TaihuLight Supercomputer

Molecular dynamics simulation means using computers to simulate the motion of molecules and atomic systems.It has been developed for many years and used in many scientific research fields.The basic principle of molecular dynamics is to use computers to simulate the movement of atomic nuclei to calculate the structure and properties of the system.Each of these nuclei is considered to move according to Newton's law under the action of the empirical potential field provided by all other nuclei and electrons.Although MD simulation cannot completely replace the experiment,it makes it possible to obtain the experimental result information under ideal experimental conditions.Molecular dynamics simulation not only occupies an important position in computational chemistry,but also an important research direction in high-performance scientific computing,which is widely used in many fields of research.LAMMPS,GROMACS,and AMBER are several simulation software commonly used in molecular dynamics simulations.They have important positions in the fields of materials,biology,and chemical industry,respectively.However,they are serialized programs,and as the molecular dynamics calculation process is complex,it has a large amount of calculations and many iterative steps,and it often consumes a lot of time when running.Therefore,it is necessary to improve its operating efficiency through high-performance parallel optimization,and it is also of great significance to many related scientific research fileds.The three softwares optimized in parallel are all running on the "Sunway Taihu Light" supercomputer.Sunway is currently the third-ranked supercomputer in the world in terms of computing power and is the top one in China.It is equipped with "SW 26010" domestic heterogeneous many-core processors.The whole machine has 40,960 nodes and has excellent computing power.With the architectural properties of Sunway,it is suitable to accelerate these molecular dynamics applications.In this paper,the optimization of molecular dynamics software mainly focuses on the three aspects,including calculation,communication&IO,and memory access.Combined with the specific application and Sunway's own architectural characteristics,we make specific optimization.Experimental analysis proves that the optimization schemes that we use have certain acceleration effects and are also in line with the theoretical reality,and can be extended to other applications of Sunway or at least provide certain optimization ideas.