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Prog. Theor. Phys. Vol. 126 No. 2 (2011) pp. 203-235
Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems
Hiroshi Watanabe,1,2,*
Masaru Suzuki3 and
Nobuyasu Ito4
1Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-8581, Japan
2Information Technology Center, The University of Tokyo, Tokyo 113-8558, Japan
3Department of Applied Quantum Physics and Nuclear Engineering, Kyushu University, Fukuoka 819-0395, Japan
4Department of Applied Physics, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
(Received January 24, 2011; Revised June 24, 2011)
Abstract:
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.
Subject Index :
020
URL :
http://ptp.ipap.jp/link?PTP/126/203/
DOI : 10.1143/PTP.126.203
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