mAMBER: Accelerating Explicit Solvent Molecular Dynamic with Intel Xeon Phi Many-Integrated Core Coprocessors

Abstract

Molecular dynamics (MD) is a computer simulation of physical movements of atoms and molecules, which is a very important research technique for the study of biological and chemical systems at micro-scale. Assisted Model Building with Energy Refinement (AMBER) is one of the most commonly used software for MD. However, the microsecond MD simulation of large-scale atom system requires a lot of computation power. In this paper, we propose mAMBER: an Intel Xeon Phi Many-Integrated Core (MIC) Coprocessors accelerated implementation of explicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package. We mAMBER also includes new parallel algorithm using CPUs and MIC coprocessors on Tianhe-2 supercomputer. With several optimizing techniques including CPU/MIC collaborated parallelization, factorization and asynchronous data transfer framework, we can accelerate the sander program of AMBER (version 12) in 'offload' mode, and achieves a 4.17-fold overall speedup compared with the CPU-only sander program.