Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations

• Published in: Journal of computational chemistry 2021-06, Vol.42 (15), p.1073-1087
• Main Authors: Andoh, Yoshimichi, Ichikawa, Shin‐ichi, Sakashita, Tatsuya, Yoshii, Noriyuki, Okazaki, Susumu
• Format: Article
• Language: English
• Subjects: Algorithms; Boundary conditions; Communication; efficient MPI communication; exascale supercomputers; fast multipole method; Mathematical analysis; Message passing; Molecular dynamics; molecular dynamics calculation; MPI parallelization; Multipoles; Parallel processing; Reduction; Supercomputers
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.26524

In the era of exascale supercomputers, large‐scale, and long‐time molecular dynamics (MD) calculations are expected to make breakthroughs in various fields of science and technology. Here, we propose a new algorithm to improve the parallelization performance of message passing interface (MPI)‐communication in the MPI‐parallelized fast multipole method (FMM) combined with MD calculations under three‐dimensional periodic boundary conditions. Our approach enables a drastic reduction in the amount of communication data, including the atomic coordinates and multipole coefficients, both of which are required to calculate the electrostatic interaction by using the FMM. In communications of multipole coefficients, the reduction rate of communication data in the new algorithm relative to the amount of data in the conventional one increases as both the number of FMM levels and the number of MPI processes increase. The aforementioned rate increase could exceed 50% as the number of MPI processes becomes larger for very large systems. The proposed algorithm, named the minimum‐transferred data (MTD) method, should enable large‐scale and long‐time MD calculations to be calculated efficiently, under the condition of massive MPI‐parallelization on exascale supercomputers. A new algorithm is proposed for message passing interface (MPI)‐communication suitable for the fast multipole method (FMM) combined with molecular dynamics (MD) calculations under three‐dimensional periodic boundary conditions. The method, named the minimum transferred‐data (MTD) method, can reduce the elapsed time of MPI communications in the MPI‐parallelized FMM drastically, enabling efficient large‐scale and long‐time MD calculations on exascale supercomputers.