89,223 research outputs found
Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems
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.Comment: 33 pages, 19 figures, add references and figures are revise
Parallel Weighted Random Sampling
Data structures for efficient sampling from a set of weighted items are an important building block of many applications. However, few parallel solutions are known. We close many of these gaps both for shared-memory and distributed-memory machines. We give efficient, fast, and practicable algorithms for sampling single items, k items with/without replacement, permutations, subsets, and reservoirs. We also give improved sequential algorithms for alias table construction and for sampling with replacement. Experiments on shared-memory parallel machines with up to 158 threads show near linear speedups both for construction and queries
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