Email this article Domain-Decomposition Parallelization for Molecular Dynamics Algorithm with Short-Ranged Potentials on Epiphany Architecture
- Authors: Nikolskii V.1,2, Stegailov V.1,2
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Affiliations:
- National Research University Higher School of Economics
- Joint Institute for High Temperatures
- Issue: Vol 39, No 9 (2018)
- Pages: 1228-1238
- Section: Part 1. Special issue “High Performance Data Intensive Computing” Editors: V. V. Voevodin, A. S. Simonov, and A. V. Lapin
- URL: https://journals.rcsi.science/1995-0802/article/view/203129
- DOI: https://doi.org/10.1134/S1995080218090159
- ID: 203129
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Abstract
Many-core processor architecture is a promising paradigm for the development of modern supercomputers. In this paper, we consider the parallel implementation of the generic molecular dynamics algorithm for the many-core Epiphany architecture. This architecture implements a new type of many-core processor composed of 16 simple cores connected by a network on chip with mesh topology. New approaches to parallel programming are required to deploy this processor. We use LAMMPS running on one 64-bit ARMv8 Cortex-A53 CPU core for comparing the accuracy of the results of the presented variant of the molecular dynamics algorithm for Epiphany and its computational efficiency.
About the authors
V. Nikolskii
National Research University Higher School of Economics; Joint Institute for High Temperatures
Author for correspondence.
Email: vnikolskiy@hse.ru
Russian Federation, ul. Myasnitskaya 20, Moscow, 101000; ul. Izhorskaya 13, str. 2, Moscow, 125412
V. Stegailov
National Research University Higher School of Economics; Joint Institute for High Temperatures
Email: vnikolskiy@hse.ru
Russian Federation, ul. Myasnitskaya 20, Moscow, 101000; ul. Izhorskaya 13, str. 2, Moscow, 125412
