title: MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms.
abstract: Our new molecular dynamics (MD) simulation program, MODYLAS, is a general-purpose program appropriate for very large physical, chemical, and biological systems. It is equipped with most standard MD techniques. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT). Several new methods have also been developed for extremely fine-grained parallelism of the MD calculation. The virtually buffering-free methods for communications and arithmetic operations, the minimal communication latency algorithm, and the parallel bucket-relay communication algorithm for the upper-level multipole moments in the FMM realize excellent scalability. The methods for blockwise arithmetic operations avoid data reload, attaining very small cache miss rates. Benchmark tests for MODYLAS using 65 536 nodes of the K-computer showed that the overall calculation time per MD step including communications is as short as about 5 ms for a 10 million-atom system; that is, 35 ns of simulation time can be computed per day. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers.
authors.affiliation: Department of Applied Chemistry, Nagoya University , Nagoya 464-8603, Japan.
authors.forename: Yoshimichi
authors.initials: Y
authors.lastname: Andoh
authors.affiliation: Department of Applied Chemistry, Nagoya University , Nagoya 464-8603, Japan.
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Yoshii
authors.affiliation: Department of Applied Chemistry, Nagoya University , Nagoya 464-8603, Japan.
authors.forename: Kazushi
authors.initials: K
authors.lastname: Fujimoto
authors.affiliation: Department of Applied Chemistry, Nagoya University , Nagoya 464-8603, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Mizutani
authors.affiliation: Department of Applied Chemistry, Nagoya University , Nagoya 464-8603, Japan.
authors.forename: Hidekazu
authors.initials: H
authors.lastname: Kojima
authors.affiliation: Department of Applied Chemistry, Nagoya University , Nagoya 464-8603, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Yamada
authors.affiliation: Department of Applied Chemistry, Nagoya University , Nagoya 464-8603, Japan.
authors.forename: Susumu
authors.initials: S
authors.lastname: Okazaki
authors.affiliation: Graduate School of Natural Science and Technology, Kanazawa University , Kanazawa 920-1192, Japan.
authors.forename: Kazutomo
authors.initials: K
authors.lastname: Kawaguchi
authors.affiliation: Graduate School of Natural Science and Technology, Kanazawa University , Kanazawa 920-1192, Japan.
authors.forename: Hidemi
authors.initials: H
authors.lastname: Nagao
authors.affiliation: Institute for Molecular Science , Okazaki 444-8585, Japan.
authors.forename: Kensuke
authors.initials: K
authors.lastname: Iwahashi
authors.affiliation: Institute for Molecular Science , Okazaki 444-8585, Japan.
authors.forename: Fumiyasu
authors.initials: F
authors.lastname: Mizutani
authors.affiliation: Advanced Institute for Computational Science , Riken, Kobe 650-0047, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Minami
authors.affiliation: Computational Science and Engineering Solution Division, Fujitsu Limited , Chiba 261-8588, Japan.
authors.forename: Shin-Ichi
authors.initials: S
authors.lastname: Ichikawa
authors.affiliation: Computational Science and Engineering Solution Division, Fujitsu Limited , Chiba 261-8588, Japan.
authors.forename: Hidemi
authors.initials: H
authors.lastname: Komatsu
authors.affiliation: Computational Science and Engineering Solution Division, Fujitsu Limited , Chiba 261-8588, Japan.
authors.forename: Shigeru
authors.initials: S
authors.lastname: Ishizuki
authors.affiliation: Computational Science and Engineering Solution Division, Fujitsu Limited , Chiba 261-8588, Japan.
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Takeda
authors.affiliation: Computational Science and Engineering Solution Division, Fujitsu Limited , Chiba 261-8588, Japan.
authors.forename: Masao
authors.initials: M
authors.lastname: Fukushima