MD-HM: memoization-based molecular dynamics simulations on big memory system

Abstract

Molecular dynamics (MD) simulation is a fundamental method for modeling ensembles of particles. In this paper, we introduce a new method to improve the performance of MD by leveraging the emerging TB-scale big memory system. In particular, we trade memory capacity for computation capability to improve MD performance by the lookup table-based memoization technique. The traditional memoization technique for the MD simulation uses relatively small DRAM, bases on a suboptimal data structure, and replaces pair-wise computation, which leads to limited performance benefit in the big memory system. We introduce MD-HM, a memoization-based MD simulation framework customized for the big memory system. MD-HM partitions the simulation field into subgrids, and replaces computation in each subgrid as a whole based on a lightweight pattern-match algorithm to recognize computation in the subgrid. MD-HM uses a new two-phase LSM-tree to optimize read/write performance. Evaluating with nine MD simulations, we show that MD-HM outperforms the state-of-the-art LAMMPS simulation framework with an average speedup of 7.6x based on the Intel Optane-based big memory system.