  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.
