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1 2013

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From quantity to quality: massive molecular dynamics simulation of nanostructures under plastic deformation in desktop and service grid distributed computing infrastructure

Gatsenko O., Bekenev L., Pavlov E., Gordienko Y. G.

Computer Science

2013

Vol. 14 (1)

27--44

The distributed computing infrastructure (DCI) on the basis of BOINC and EDGeS-bridge technologies for high-performance distributed computing is used for porting the sequential molecular dynamics (MD) application to its parallel version for DCIwith Desktop Grids (DGs) and Service Grids (SGs). The actual metrics of the working DG-SG DCI were measured, and the normal distribution of host performances, and signs of log-normal distributions of Rother characteristics (CPUs, RAM, and HDD per host) were found. The practical feasibility and high efficiency of the MD simulations on the basis of DG-SG DCI were demonstrated during the experiment with the massive MD simulations for the large quantity of aluminum nanocrystals (Statistical analysis (Kolmogorov-Smirnov test, moment analysis, and bootstrapping analysis) of the defect density distribution over the ensemble of nanocrystals had show that change of plastic deformation mode is followed by the qualitative change of defect density distribution type over ensemble of nanocrystals. Some limitations (fluctuating performance, unpredictable availability of resources, etc.) of the typical DG-SG DCI were outlined, and some advantages (high efficiency, high speedup, and low cost) were demonstrated. Deploying on DG DCI allows to get new scientific quality from the simulated quantity of numerous configurations by harnessing sufficient computational power to undertake MD simulations in a wider range of physical parameters (configurations) in a much shorter timeframe.