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-G
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- 作者：Yoshimichi Andoh ; Noriyuki Yoshii ; Kazushi Fujimoto ; Keisuke Mizutani ; Hidekazu Kojima ; Atsushi Yamada ; Susumu Okazaki ; Kazutomo Kawaguchi ; Hidemi Nagao ; Kensuke Iwahashi ; Fumiyasu Mizutani ; Kazuo Minami ; Shin-ichi Ichikawa ; Hidemi Komatsu ; Shigeru Ishizuki ; Yasuhiro Takeda ; Masao Fukushima
- 刊名：Journal of Chemical Theory and Computation
- 出版年：2013
- 出版时间：July 9, 2013
- 年：2013
- 卷：9
- 期：7
- 页码：3201-3209
- 全文大小：376K
- 年卷期：v.9,no.7(July 9, 2013)
- ISSN：1549-9626
文摘
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鈥?36 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.