Immersed Boundary Method Halo Exchange in a Hemodynamics Application

John Gounley; Erik W. Draeger; Amanda Randles

doi:10.1007/978-3-030-22734-0_32

Immersed Boundary Method Halo Exchange in a Hemodynamics Application

John Gounley, Erik W. Draeger, Amanda Randles

Scalable Biomedical Modeling

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

10 Scopus citations

Abstract

In recent years, highly parallelized simulations of blood flow resolving individual blood cells have been demonstrated. Simulating such dense suspensions of deformable particles in flow often involves a partitioned fluid-structure interaction (FSI) algorithm, with separate solvers for Eulerian fluid and Lagrangian cell grids, plus a solver - e.g., immersed boundary method - for their interaction. Managing data motion in parallel FSI implementations is increasingly important, particularly for inhomogeneous systems like vascular geometries. In this study, we evaluate the influence of Eulerian and Lagrangian halo exchanges on efficiency and scalability of a partitioned FSI algorithm for blood flow. We describe an MPI+OpenMP implementation of the immersed boundary method coupled with lattice Boltzmann and finite element methods. We consider how communication and recomputation costs influence the optimization of halo exchanges with respect to three factors: immersed boundary interaction distance, cell suspension density, and relative fluid/cell solver costs.

Original language	English
Title of host publication	Computational Science – ICCS 2019 - 19th International Conference, Proceedings
Editors	João M.F. Rodrigues, Pedro J.S. Cardoso, Jânio Monteiro, Roberto Lam, Valeria V. Krzhizhanovskaya, Michael H. Lees, Peter M.A. Sloot, Jack J. Dongarra
Publisher	Springer Verlag
Pages	441-455
Number of pages	15
ISBN (Print)	9783030227333
DOIs	https://doi.org/10.1007/978-3-030-22734-0_32
State	Published - 2019
Event	19th International Conference on Computational Science, ICCS 2019 - Faro, Portugal Duration: Jun 12 2019 → Jun 14 2019

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	11536 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	19th International Conference on Computational Science, ICCS 2019
Country/Territory	Portugal
City	Faro
Period	06/12/19 → 06/14/19

Funding

Keywords: Red blood cell · Immersed boundary method · Parallel computing This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).

Funders	Funder number
National Institutes of Health	DP5OD019876
U.S. Department of Energy
Office of the Director
U.S. Department of Veterans Affairs
Lawrence Livermore National Laboratory	DE-AC52-07NA27344
Hartwell Foundation

Keywords

Immersed boundary method
Parallel computing
Red blood cell

Access to Document

10.1007/978-3-030-22734-0_32

Cite this

Gounley, J., Draeger, E. W., & Randles, A. (2019). Immersed Boundary Method Halo Exchange in a Hemodynamics Application. In J. M. F. Rodrigues, P. J. S. Cardoso, J. Monteiro, R. Lam, V. V. Krzhizhanovskaya, M. H. Lees, P. M. A. Sloot, & J. J. Dongarra (Eds.), Computational Science – ICCS 2019 - 19th International Conference, Proceedings (pp. 441-455). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11536 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-030-22734-0_32

Gounley, John ; Draeger, Erik W. ; Randles, Amanda. / Immersed Boundary Method Halo Exchange in a Hemodynamics Application. Computational Science – ICCS 2019 - 19th International Conference, Proceedings. editor / João M.F. Rodrigues ; Pedro J.S. Cardoso ; Jânio Monteiro ; Roberto Lam ; Valeria V. Krzhizhanovskaya ; Michael H. Lees ; Peter M.A. Sloot ; Jack J. Dongarra. Springer Verlag, 2019. pp. 441-455 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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title = "Immersed Boundary Method Halo Exchange in a Hemodynamics Application",

abstract = "In recent years, highly parallelized simulations of blood flow resolving individual blood cells have been demonstrated. Simulating such dense suspensions of deformable particles in flow often involves a partitioned fluid-structure interaction (FSI) algorithm, with separate solvers for Eulerian fluid and Lagrangian cell grids, plus a solver - e.g., immersed boundary method - for their interaction. Managing data motion in parallel FSI implementations is increasingly important, particularly for inhomogeneous systems like vascular geometries. In this study, we evaluate the influence of Eulerian and Lagrangian halo exchanges on efficiency and scalability of a partitioned FSI algorithm for blood flow. We describe an MPI+OpenMP implementation of the immersed boundary method coupled with lattice Boltzmann and finite element methods. We consider how communication and recomputation costs influence the optimization of halo exchanges with respect to three factors: immersed boundary interaction distance, cell suspension density, and relative fluid/cell solver costs.",

keywords = "Immersed boundary method, Parallel computing, Red blood cell",

author = "John Gounley and Draeger, {Erik W.} and Amanda Randles",

note = "Publisher Copyright: {\textcopyright} 2019, Springer Nature Switzerland AG.; 19th International Conference on Computational Science, ICCS 2019 ; Conference date: 12-06-2019 Through 14-06-2019",

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doi = "10.1007/978-3-030-22734-0_32",

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Gounley, J, Draeger, EW & Randles, A 2019, Immersed Boundary Method Halo Exchange in a Hemodynamics Application. in JMF Rodrigues, PJS Cardoso, J Monteiro, R Lam, VV Krzhizhanovskaya, MH Lees, PMA Sloot & JJ Dongarra (eds), Computational Science – ICCS 2019 - 19th International Conference, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 11536 LNCS, Springer Verlag, pp. 441-455, 19th International Conference on Computational Science, ICCS 2019, Faro, Portugal, 06/12/19. https://doi.org/10.1007/978-3-030-22734-0_32

Immersed Boundary Method Halo Exchange in a Hemodynamics Application. / Gounley, John; Draeger, Erik W.; Randles, Amanda.
Computational Science – ICCS 2019 - 19th International Conference, Proceedings. ed. / João M.F. Rodrigues; Pedro J.S. Cardoso; Jânio Monteiro; Roberto Lam; Valeria V. Krzhizhanovskaya; Michael H. Lees; Peter M.A. Sloot; Jack J. Dongarra. Springer Verlag, 2019. p. 441-455 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11536 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Immersed Boundary Method Halo Exchange in a Hemodynamics Application

AU - Gounley, John

AU - Draeger, Erik W.

AU - Randles, Amanda

PY - 2019

Y1 - 2019

N2 - In recent years, highly parallelized simulations of blood flow resolving individual blood cells have been demonstrated. Simulating such dense suspensions of deformable particles in flow often involves a partitioned fluid-structure interaction (FSI) algorithm, with separate solvers for Eulerian fluid and Lagrangian cell grids, plus a solver - e.g., immersed boundary method - for their interaction. Managing data motion in parallel FSI implementations is increasingly important, particularly for inhomogeneous systems like vascular geometries. In this study, we evaluate the influence of Eulerian and Lagrangian halo exchanges on efficiency and scalability of a partitioned FSI algorithm for blood flow. We describe an MPI+OpenMP implementation of the immersed boundary method coupled with lattice Boltzmann and finite element methods. We consider how communication and recomputation costs influence the optimization of halo exchanges with respect to three factors: immersed boundary interaction distance, cell suspension density, and relative fluid/cell solver costs.

AB - In recent years, highly parallelized simulations of blood flow resolving individual blood cells have been demonstrated. Simulating such dense suspensions of deformable particles in flow often involves a partitioned fluid-structure interaction (FSI) algorithm, with separate solvers for Eulerian fluid and Lagrangian cell grids, plus a solver - e.g., immersed boundary method - for their interaction. Managing data motion in parallel FSI implementations is increasingly important, particularly for inhomogeneous systems like vascular geometries. In this study, we evaluate the influence of Eulerian and Lagrangian halo exchanges on efficiency and scalability of a partitioned FSI algorithm for blood flow. We describe an MPI+OpenMP implementation of the immersed boundary method coupled with lattice Boltzmann and finite element methods. We consider how communication and recomputation costs influence the optimization of halo exchanges with respect to three factors: immersed boundary interaction distance, cell suspension density, and relative fluid/cell solver costs.

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SN - 9783030227333

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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BT - Computational Science – ICCS 2019 - 19th International Conference, Proceedings

A2 - Rodrigues, João M.F.

A2 - Cardoso, Pedro J.S.

A2 - Monteiro, Jânio

A2 - Lam, Roberto

A2 - Krzhizhanovskaya, Valeria V.

A2 - Lees, Michael H.

A2 - Sloot, Peter M.A.

A2 - Dongarra, Jack J.

PB - Springer Verlag

T2 - 19th International Conference on Computational Science, ICCS 2019

Y2 - 12 June 2019 through 14 June 2019

ER -

Gounley J, Draeger EW, Randles A. Immersed Boundary Method Halo Exchange in a Hemodynamics Application. In Rodrigues JMF, Cardoso PJS, Monteiro J, Lam R, Krzhizhanovskaya VV, Lees MH, Sloot PMA, Dongarra JJ, editors, Computational Science – ICCS 2019 - 19th International Conference, Proceedings. Springer Verlag. 2019. p. 441-455. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-030-22734-0_32

Immersed Boundary Method Halo Exchange in a Hemodynamics Application

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