2010/12/31 by H. Watanabe, Hiroshi Watanabe, M. Suzuki +3 · 17 citations
Chemistry · Physics and Astronomy · #Advanced Chemical Physics Studies #Advanced Physical and Chemical Molecular Interactions #Classical mechanics #Computer science #Dynamics (music) #Implementation #Molecular dynamics #Physics #Programming language #Quantum mechanics #Spectroscopy and Quantum Chemical Studies #Statistical physics #Theoretical physics #cond-mat.stat-mech #physics.comp-ph
paper · pdf · doi:10.1143/ptp.126.203
published in Progress of Theoretical Physics 126(2), 203-235 (Oxford University Press) · 33 pages, 19 figures, add references and figures are revised
arxiv created 2011/06/24 · openalex publication_date 2011/08/01 · arxiv updated 2015/03/17 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/08
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatial-decomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93 GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo. The parallelization efficiency of the largest run, consisting of 4.1 billion particles with 8192 MPI processes, is about 73% relative to that of the smallest run with 128 MPI processes at NIFS, and it is about 66% relative to that of the smallest run with 4 MPI processes at ISSP. The factors causing the parallel overhead are investigated. It is found that fluctuations of the execution time of each process degrade the parallel efficiency. These fluctuations may be due to the interference of the operating system, which is known as OS Jitter.