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

被引：75

作者：

Andoh, Yoshimichi ^{[1
]}

Yoshii, Noriyuki ^{[1
]}

Fujimoto, Kazushi ^{[1
]}

Mizutani, Keisuke ^{[1
]}

Kojima, Hidekazu ^{[1
]}

Yamada, Atsushi ^{[1
]}

Okazaki, Susumu ^{[1
]}

Kawaguchi, Kazutomo ^{[2
]}

Nagao, Hidemi ^{[2
]}

Iwahashi, Kensuke ^{[3
]}

Mizutani, Fumiyasu ^{[3
]}

Minami, Kazuo ^{[4
]}

Ichikawa, Shin-ichi ^{[5
]}

Komatsu, Hidemi ^{[5
]}

Ishizuki, Shigeru ^{[5
]}

Takeda, Yasuhiro ^{[5
]}

Fukushima, Masao ^{[5
]}

机构：

[1] Nagoya Univ, Dept Appl Chem, Nagoya, Aichi 4648603, Japan

[2] Kanazawa Univ, Grad Sch Nat Sci & Technol, Kanazawa, Ishikawa 9201192, Japan

[3] Natl Inst Nat Sci, Inst Mol Sci, Okazaki, Aichi 4448585, Japan

[4] RIKEN, Adv Inst Computat Sci, Kobe, Hyogo 6500047, Japan

[5] Fujitsu Ltd, Computat Sci & Engn Solut Div, Chiba 2618588, Japan

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2013年 / 9卷 / 07期

关键词：

FIELD; INTEGRATORS; EQUATIONS; MOTION;

D O I：

10.1021/ct400203a

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

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 ins 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.

引用

页码：3201 / 3209

页数：9