An exa-scale high-performance molecular dynamics simulation program: MODYLAS

Yoshimichi Andoh; Shin-Ichi Ichikawa; Tatsuya Sakashita; Kazushi Fujimoto; Noriyuki Yoshii; Tetsuro Nagai; Zhiye Tang; Susumu Okazaki

doi:10.1063/5.0144361

An exa-scale high-performance molecular dynamics simulation program: MODYLAS

J Chem Phys. 2023 May 21;158(19):194803. doi: 10.1063/5.0144361.

Authors

Yoshimichi Andoh¹, Shin-Ichi Ichikawa², Tatsuya Sakashita³, Kazushi Fujimoto⁴, Noriyuki Yoshii⁵, Tetsuro Nagai⁶, Zhiye Tang⁷, Susumu Okazaki⁸

Affiliations

¹ National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan.
² Computational Science Division, Technical Computing Business Unit, Fujitsu Limited, Chiba, Japan.
³ Center for Quantum Information and Quantum Biology, Osaka University, 1-2, Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
⁴ Department of Materials Chemistry, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8603, Japan.
⁵ Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan.
⁶ Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1, Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan.
⁷ Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, 38, Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.
⁸ Department of Advanced Materials Science, The University of Tokyo, 5-1-5, Kashiwa-no-ha, Kashiwa, Chiba 277-0871, Japan.

PMID: 37184018
DOI: 10.1063/5.0144361

Abstract

A new version of the highly parallelized general-purpose molecular dynamics (MD) simulation program MODYLAS with high performance on the Fugaku computer was developed. A benchmark test using Fugaku indicated highly efficient communication, single instruction, multiple data (SIMD) processing, and on-cache arithmetic operations. The system's performance deteriorated only slightly, even under high parallelization. In particular, a newly developed minimum transferred data method, requiring a significantly lower amount of data transfer compared to conventional communications, showed significantly high performance. The coordinates and forces of 101 810 176 atoms and the multipole coefficients of the subcells could be distributed to the 32 768 nodes (1 572 864 cores) in 2.3 ms during one MD step calculation. The SIMD effective instruction rates for floating-point arithmetic operations in direct force and fast multipole method (FMM) calculations measured on Fugaku were 78.7% and 31.5%, respectively. The development of a data reuse algorithm enhanced the on-cache processing; the cache miss rate for direct force and FMM calculations was only 2.74% and 1.43%, respectively, on the L1 cache and 0.08% and 0.60%, respectively, on the L2 cache. The modified MODYLAS could complete one MD single time-step calculation within 8.5 ms for the aforementioned large system. Additionally, the program contains numerous functions for material research that enable free energy calculations, along with the generation of various ensembles and molecular constraints.