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Title: Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique

Abstract

Here, we discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within 10%–15% accuracy, is given by the Amdahl’s Law adapted to the specific quantities involved in the problem. The derivation of the predictive formula is general enough that it may be applied to the general case of molecular dynamics approaches where a reduction of degrees of freedom in a multi scale fashion occurs.

Authors:
ORCiD logo; ;
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1343720
Report Number(s):
LA-UR-17-20430
Journal ID: ISSN 0010-4655; TRN: US1700518
Grant/Contract Number:
AC52-06NA25396; LA-UR-17-20430
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Computer Physics Communications
Additional Journal Information:
Journal Volume: 215; Journal Issue: C; Journal ID: ISSN 0010-4655
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; adaptive resolution simulation; Amdahl’s law; computational performance

Citation Formats

Junghans, Christoph, Agarwal, Animesh, and Delle Site, Luigi. Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique. United States: N. p., 2017. Web. doi:10.1016/j.cpc.2017.01.030.
Junghans, Christoph, Agarwal, Animesh, & Delle Site, Luigi. Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique. United States. doi:10.1016/j.cpc.2017.01.030.
Junghans, Christoph, Agarwal, Animesh, and Delle Site, Luigi. 2017. "Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique". United States. doi:10.1016/j.cpc.2017.01.030.
@article{osti_1343720,
title = {Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique},
author = {Junghans, Christoph and Agarwal, Animesh and Delle Site, Luigi},
abstractNote = {Here, we discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within 10%–15% accuracy, is given by the Amdahl’s Law adapted to the specific quantities involved in the problem. The derivation of the predictive formula is general enough that it may be applied to the general case of molecular dynamics approaches where a reduction of degrees of freedom in a multi scale fashion occurs.},
doi = {10.1016/j.cpc.2017.01.030},
journal = {Computer Physics Communications},
number = C,
volume = 215,
place = {United States},
year = 2017,
month = 6
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on June 1, 2018
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