Parallel Optimization of the Crystal-KMC on Tianhe-2

Jianjiang Li; Baixue Ji; Yun Yang; Peng Wei; Jie Wu

doi:10.26599/TST.2019.9010075

Tsinghua Science and Technology 2021, 26(3): 309-321 https://doi.org/10.26599/TST.2019.9010075

Open Access | Issue | Published: 12 October 2020

Parallel Optimization of the Crystal-KMC on Tianhe-2

Show Author's Information Hide Author's Information Jianjiang Li, Baixue Ji, Yun Yang, Peng Wei(

), Jie Wu

Department of Computer Science and Technology, University of Science and Technology Beijing, Beijing 100083, China.

Industrial and Commercial Bank of China Shandong Branch, Jinan 250001, China.

Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA.

Keywords:

Kinetic Monte Carlo (KMC), Tianhe-2, parallel optimization, OpenMP

Cite this article:

Li J, Ji B, Yang Y, et al. Parallel Optimization of the Crystal-KMC on Tianhe-2. Tsinghua Science and Technology, 2021, 26(3): 309-321. https://doi.org/10.26599/TST.2019.9010075

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Abstract

The Kinetic Monte Carlo (KMC) is one of the commonly used methods for simulating radiation damage of materials. Our team develops a parallel KMC software named Crystal-KMC, which supports the Embedded Atom Method (EAM) potential energy and utilizes the Message Passing Interface (MPI) technology to simulate the vacancy transition of the Copper (Cu) element under neutron radiation. To make better use of the computing power of modern supercomputers, we develop the parallel efficiency optimization model for the Crystal-KMC on Tianhe-2, to achieve a larger simulation of the damage process of materials under irradiation environment. Firstly, we analyze the performance bottleneck of the Crystal-KMC software and use the MIC offload statement to implement the operation of key modules of the software on the MIC coprocessor. We use OpenMP to develop parallel optimization for the Crystal-KMC, combined with existing MPI inter-process communication optimization, finally achieving hybrid parallel optimization. The experimental results show that in the single-node CPU and MIC collaborative parallel mode, the speedup of the calculation hotspot reaches 30.1, and the speedup of the overall software reaches 7.43.

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Parallel Optimization of the Crystal-KMC on Tianhe-2

Show Author's information Hide Author's Information Jianjiang Li, Baixue Ji, Yun Yang, Peng Wei(

), Jie Wu

Department of Computer Science and Technology, University of Science and Technology Beijing, Beijing 100083, China.

Industrial and Commercial Bank of China Shandong Branch, Jinan 250001, China.

Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA.

Abstract

Keywords: Kinetic Monte Carlo (KMC), Tianhe-2, parallel optimization, OpenMP

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Publication history

Received: 08 October 2019

Accepted: 05 December 2019

Published: 12 October 2020

Issue date: June 2021

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Acknowledgements

This work was supported by the National Key R&D Program of China (No. 2017YFB0202104).

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The articles published in this open access journal are distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/).