Efficient parallelization of molecular dynamics simulations with short- ranged forces
R Meyer, HIGH PERFORMANCE COMPUTING SYMPOSIUM 2013 (HPCS 2013), 540, UNSP 012006 (2014).
Recently, an alternative strategy for the parallelization of molecular dynamics simulations with short-ranged forces has been proposed. In this work, this algorithm is tested on a variety of multi-core systems using three types of benchmark simulations. The results show that the new algorithm gives consistent speedups which are depending on the properties of the simulated system either comparable or superior to those obtained with spatial decomposition. Comparisons of the parallel speedup on different systems indicates that on multi-core machines the parallel efficiency of the method is mainly limited by memory access speed.
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