Cell-List based Molecular Dynamics on Many-Core Processors: A Case Study on Sunway TaihuLight Supercomputer

XH Duan and P Gao and M Zhang and TJ Zhang and HS Meng and YX Li and B Schmidt and HH Fu and L Gan and W Xue and WG Liu and GW Yang, PROCEEDINGS OF SC20: THE INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS (SC20) (2020).

Molecular dynamics (MD) simulations are playing an increasingly important role in several research areas. The most frequently used potentials in MI) simulations are pair-wise potentials. Due to the memory wall, computing pair-wise potentials on many-core processors are usually memory bounded. In this paper, we take the SW26010 processor as an exemplary platform to explore the possibility to break the memory bottleneck by improving data reusage via cell-list-based methods. We use cell lists instead of neighbor-lists in the potential computation, and apply a number of novel optimization methods. Theses methods include: an adaptive replica arrangement strategy, a parameter profile data structure, and a particle-cell cutoff checking filter. An incremental cell-list building method is also realized to accelerate the construction of cell-lists. Furthermore, we have established an open source standalone framework, ESMD, featuring the techniques above. Experiments show that ESMD is 50,-170% faster than previous ports on a single node, and can scale to 1,024 nodes with a weak scalibility of 95%.

Return to Publications page