Parallel and distributed computing in problems of supercomputer simulation of molecular liquids by the Monte Carlo method

AV Teplukhin, JOURNAL OF STRUCTURAL CHEMISTRY, 54, 65-74 (2013).

DOI: 10.1134/S0022476613010095

An effective strategy of molecular Monte Carlo simulation is proposed. The strategy is based on a combination of two key approaches to parallel computing. The advantage of spatial (domain) decomposition is the high scalability of computing algorithms by splitting "big tasks" into several simultaneously solvable subtasks. However, the domain size in this method can be reduced to a certain limit only. Particle decomposition (division of program loops into portions) is, by contrast, very efficient in the study of small and medium size objects, but is poorly scalable and quickly exhausts the computer system memory with increasing size of the model. The combination of the approaches helps neutralize their limitations and create efficient supercomputing programs for the study of molecular models consisting of hundreds of millions of atoms.

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