From Quantity to Quality: Massive Molecular Dynamics Simulation of Nanostructures under Plastic Deformation in Desktop and Service Grid Distributed Computing Infrastructure

TL;DR

This paper demonstrates the high efficiency and scientific value of massive molecular dynamics simulations of nanostructures under plastic deformation using distributed computing infrastructure, enabling extensive analysis of defect densities.

Contribution

It introduces a parallel MD simulation approach on distributed grids, analyzes defect density distributions, and highlights the scientific benefits of large-scale simulations in materials science.

Findings

High efficiency and speedup of MD simulations on distributed infrastructure

Change in deformation mode leads to qualitative change in defect density distribution

Distributed computing enables extensive parameter exploration in shorter time

Abstract

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 DCI with 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 other 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 ($\sim10^2$-$10^3$). Statistical analysis (Kolmogorov-Smirnov test, moment analysis, and bootstrapping analysis) of the defect density distribution over the ensemble of nanocrystals had shown 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 $\it{quality}$ from the simulated $\it{quantity}$ 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.