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Publication details

  • MaMiCo: Software design for parallel molecular-continuum flow simulations (Philipp Neumann, Hanno Flohr, Rahul Arora, Piet Jarmatz, Nikola Tchipev, Hans-Joachim Bungartz), In Computer Physics Communications, Series: 200, pp. 324–335, (Editors: N. Stanley Scott), Elsevier, ISSN: 0010-4655, 2016
    Publication detailsDOI

Abstract

The macro–micro-coupling tool (MaMiCo) was developed to ease the development of and modularize molecular-continuum simulations, retaining sequential and parallel performance. We demonstrate the functionality and performance of MaMiCo by coupling the spatially adaptive Lattice Boltzmann framework waLBerla with four molecular dynamics (MD) codes: the light-weight Lennard-Jones-based implementation SimpleMD, the node-level optimized software ls1 mardyn, and the community codes ESPResSo and LAMMPS. We detail interface implementations to connect each solver with MaMiCo. The coupling for each waLBerla-MD setup is validated in three-dimensional channel flow simulations which are solved by means of a state-based coupling method. We provide sequential and strong scaling measurements for the four molecular-continuum simulations. The overhead of MaMiCo is found to come at 10%-20% of the total (MD) runtime. The measurements further show that scalability of the hybrid simulations is reached on up to 500 Intel SandyBridge, and more than 1000 AMD Bulldozer compute cores.

BibTeX

@article{MSDFPMFSNF16,
	author	 = {Philipp Neumann and Hanno Flohr and Rahul Arora and Piet Jarmatz and Nikola Tchipev and Hans-Joachim Bungartz},
	title	 = {{MaMiCo: Software design for parallel molecular-continuum flow simulations}},
	year	 = {2016},
	editor	 = {N. Stanley Scott},
	publisher	 = {Elsevier},
	journal	 = {Computer Physics Communications},
	series	 = {200},
	pages	 = {324--335},
	issn	 = {0010-4655},
	doi	 = {http://dx.doi.org/10.1016/j.cpc.2015.10.029},
	abstract	 = {The macro–micro-coupling tool (MaMiCo) was developed to ease the development of and modularize molecular-continuum simulations, retaining sequential and parallel performance. We demonstrate the functionality and performance of MaMiCo by coupling the spatially adaptive Lattice Boltzmann framework waLBerla with four molecular dynamics (MD) codes: the light-weight Lennard-Jones-based implementation SimpleMD, the node-level optimized software ls1 mardyn, and the community codes ESPResSo and LAMMPS. We detail interface implementations to connect each solver with MaMiCo. The coupling for each waLBerla-MD setup is validated in three-dimensional channel flow simulations which are solved by means of a state-based coupling method. We provide sequential and strong scaling measurements for the four molecular-continuum simulations. The overhead of MaMiCo is found to come at 10\%-20\% of the total (MD) runtime. The measurements further show that scalability of the hybrid simulations is reached on up to 500 Intel SandyBridge, and more than 1000 AMD Bulldozer compute cores.},
}

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