An efficiently extendable and fine-grain parallelised molecular dynamics simulation program: Mid |
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Authors: | Takahiro Koishi Hironori Takeichi |
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Affiliation: | 1. Department of Applied Physics, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japankoishi@u-fukui.ac.jp;3. Department of Applied Physics, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan |
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Abstract: | A new implementation of molecular dynamics simulation is presented. We employed policy-based design to achieve static polymorphism within our simulation programs. This technique provides flexibility and extensibility without additional if-statement branching in the simulation program development. It is shown that policy-based implementation prevents computational performance degradation. We used a fine-grained domain decomposition scheme to parallelise the simulation program. The smaller size decomposition reduces the total amount of inter-processing-core communication and affords good scalability for parallel calculation of short-range forces. The calculation of long-range interactions limits the total scalability. For enhanced performance at high levels of parallelism, the calculation methods for long-range interactions should be improved. |
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Keywords: | molecular dynamics simulation fine-grained parallelisation static polymorphism |
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