Abstract:

Nanoscale molecular dynamics (NAMD) is an open source free molecular dynamics simulation software based on the Charm++ parallel programming model, which can quickly simulate millions of atomic-level macromolecules in large-scale parallel computer system. SunwayTaihuLight System is a supercomputer developed independently by China, which has a theoretical peak performance of 125.4 Pflop/s with 10 million cores，and the LINPACK efficiency is no less than 70%. The NAMD partitions the atoms in the space, divides the force in the calculation, fully exposes the parallelism of the single-step simulation, and controls the load balance through the CHARM++. In response to the characteristics of NAMD simulation calculation, we port and optimize NAMD calculation code, allowing it to run better on the supercomputer SunwayTaihuLight System. After optimization, the performance is improved by nearly 20 times, and the performance of the single core group is 3 times higher than Intel XeonE5-2650V2. Scalability at present parallel degree reaches about 3.25 millions of cores, which makes a breakthrough of a million of cores.

Key words: molecular dynamics (MD), Sunway supercomputer, heterogeneous many-core processor