Immersed Boundary Method Halo Exchange in a Hemodynamics Application

Gounley, John; Draeger, Erik; Randles, Amanda

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

Immersed Boundary Method Halo Exchange in a Hemodynamics Application

Conference · 01 June 2019

DOI:https://doi.org/10.1007/978-3-030-22734-0_32· OSTI ID:1526390

Gounley, John ^[1]; Draeger, Erik ^[2]; Randles, Amanda ^[3]

ORNL
Lawrence Livermore National Laboratory (LLNL)
Duke university Duhram, NC

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.

View Conference

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-00OR22725;

OSTI ID:: 1526390

Conference Information:: International Conference on Computational Science (ICCS 2019) - Faro, , Portugal - 6/12/2019 12:00:00 PM-6/14/2019 12:00:00 PM

Country of Publication:: United States

Language:: English

References (28)

Subdivision surfaces: a new paradigm for thin-shell finite-element analysis Cirak, Fehmi; Ortiz, Michael; Schr�der, Peter International Journal for Numerical Methods in Engineering, Vol. 47, Issue 12 https://doi.org/10.1002/(SICI)1097-0207(20000430)47:12<2039::AID-NME872>3.0.CO;2-1	journal	April 2000
Computer Simulation Study of Collective Phenomena in Dense Suspensions of Red Blood Cells under Shear Krüger, Timm https://doi.org/10.1007/978-3-8348-2376-2	book	January 2012
A nonlinear programming model with implicit variables for packing ellipsoids Birgin, E. G.; Lobato, R. D.; Martínez, J. M. Journal of Global Optimization, Vol. 68, Issue 3 https://doi.org/10.1007/s10898-016-0483-8	journal	December 2016
Efficient and accurate simulations of deformable particles immersed in a fluid using a combined immersed boundary lattice Boltzmann finite element method Krüger, T.; Varnik, F.; Raabe, D. Computers & Mathematics with Applications, Vol. 61, Issue 12 https://doi.org/10.1016/j.camwa.2010.03.057	journal	June 2011
Numerical simulation of stirred tanks using a hybrid immersed-boundary method Di, Shengbin; Xu, Ji; Chang, Qi Chinese Journal of Chemical Engineering, Vol. 24, Issue 9 https://doi.org/10.1016/j.cjche.2016.05.031	journal	September 2016
Parallel computing strategy for a flow solver based on immersed boundary method and discrete stream-function formulation Wang, Shizhao; He, Guowei; Zhang, Xing Computers & Fluids, Vol. 88 https://doi.org/10.1016/j.compfluid.2013.09.001	journal	December 2013
Scalability of an Eulerian-Lagrangian large-eddy simulation solver with hybrid MPI/OpenMP parallelisation Ouro, Pablo; Fraga, Bruño; Lopez-Novoa, Unai Computers & Fluids, Vol. 179 https://doi.org/10.1016/j.compfluid.2018.10.013	journal	January 2019
Numerical methods for simulating blood flow at macro, micro, and multi scales Imai, Yohsuke; Omori, Toshihiro; Shimogonya, Yuji Journal of Biomechanics, Vol. 49, Issue 11 https://doi.org/10.1016/j.jbiomech.2015.11.047	journal	July 2016
An efficient parallel immersed boundary algorithm using a pseudo-compressible fluid solver Wiens, Jeffrey K.; Stockie, John M. Journal of Computational Physics, Vol. 281 https://doi.org/10.1016/j.jcp.2014.10.058	journal	January 2015
Isogeometric FEM-BEM simulations of drop, capsule and vesicle dynamics in Stokes flow Boedec, Gwenn; Leonetti, Marc; Jaeger, Marc Journal of Computational Physics, Vol. 342 https://doi.org/10.1016/j.jcp.2017.04.024	journal	August 2017
A parallel interaction potential approach coupled with the immersed boundary method for fully resolved simulations of deformable interfaces and membranes Spandan, Vamsi; Meschini, Valentina; Ostilla-Mónico, Rodolfo Journal of Computational Physics, Vol. 348 https://doi.org/10.1016/j.jcp.2017.07.036	journal	November 2017
Parallel performance of an IB-LBM suspension simulation framework Mountrakis, Lampros; Lorenz, Eric; Malaspinas, Orestis Journal of Computational Science, Vol. 9 https://doi.org/10.1016/j.jocs.2015.04.006	journal	July 2015
Hemocell: a high-performance microscopic cellular library Zavodszky, Gábor; van Rooij, Britt; Azizi, Victor Procedia Computer Science, Vol. 108 https://doi.org/10.1016/j.procs.2017.05.084	journal	January 2017
Numerical simulation of a compound capsule in a constricted microchannel Gounley, John; Draeger, Erik W.; Randles, Amanda Procedia Computer Science, Vol. 108 https://doi.org/10.1016/j.procs.2017.05.209	journal	January 2017
The immersed boundary method Peskin, Charles S. Acta Numerica, Vol. 11 https://doi.org/10.1017/S0962492902000077	journal	January 2002
Quantifying the biophysical characteristics of Plasmodium-falciparum -parasitized red blood cells in microcirculation Fedosov, D. A.; Caswell, B.; Suresh, S. Proceedings of the National Academy of Sciences, Vol. 108, Issue 1 https://doi.org/10.1073/pnas.1009492108	journal	December 2010
Patient-specific blood rheology in sickle-cell anaemia Li, Xuejin; Du, E.; Lei, Huan Interface Focus, Vol. 6, Issue 1 https://doi.org/10.1098/rsfs.2015.0065	journal	February 2016
Three-dimensional multi-scale model of deformable platelets adhesion to vessel wall in blood flow Wu, Ziheng; Xu, Zhiliang; Kim, Oleg Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 372, Issue 2021 https://doi.org/10.1098/rsta.2013.0380	journal	August 2014
Discrete lattice effects on the forcing term in the lattice Boltzmann method Guo, Zhaoli; Zheng, Chuguang; Shi, Baochang Physical Review E, Vol. 65, Issue 4 https://doi.org/10.1103/PhysRevE.65.046308	journal	April 2002
Effect of bending stiffness on the deformation of liquid capsules enclosed by thin shells in shear flow Le, Duc Vinh Physical Review E, Vol. 82, Issue 1 https://doi.org/10.1103/PhysRevE.82.016318	journal	July 2010
Accelerating Lattice Boltzmann Fluid Flow Simulations Using Graphics Processors Bailey, P.; Myre, J.; Walsh, S. D. C. 2009 International Conference on Parallel Processing (ICPP 2009) https://doi.org/10.1109/ICPP.2009.38	conference	September 2009
Performance Analysis of the Lattice Boltzmann Model Beyond Navier-Stokes Randles, Amanda Peters; Kale, Vivek; Hammond, Jeff 2013 IEEE International Symposium on Parallel & Distributed Processing (IPDPS), 2013 IEEE 27th International Symposium on Parallel and Distributed Processing https://doi.org/10.1109/IPDPS.2013.109	conference	May 2013
Distributed Immersed Boundary Simulation in Titanium Givelberg, E.; Yelick, K. SIAM Journal on Scientific Computing, Vol. 28, Issue 4 https://doi.org/10.1137/040618734	journal	January 2006
Massively parallel models of the human circulatory system Randles, Amanda; Draeger, Erik W.; Oppelstrup, Tomas SC15: The International Conference for High Performance Computing, Networking, Storage and Analysis, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis https://doi.org/10.1145/2807591.2807676	conference	November 2015
Lattice Boltzmann Method for Fluid Flows Chen, Shiyi; Doolen, Gary D. Annual Review of Fluid Mechanics, Vol. 30, Issue 1 https://doi.org/10.1146/annurev.fluid.30.1.329	journal	January 1998
Immersed Boundary Methods Mittal, Rajat; Iaccarino, Gianluca Annual Review of Fluid Mechanics, Vol. 37, Issue 1 https://doi.org/10.1146/annurev.fluid.37.061903.175743	journal	January 2005
Erythrocyte Membrane Elasticity and Viscosity Hochmuth, R. M.; Waugh, R. E. Annual Review of Physiology, Vol. 49, Issue 1 https://doi.org/10.1146/annurev.ph.49.030187.001233	journal	March 1987
Large deformation finite element analysis of non-linear viscoelastic membranes with reference to thermoforming Shrivastava, S.; Tang, J. The Journal of Strain Analysis for Engineering Design, Vol. 28, Issue 1 https://doi.org/10.1243/03093247V281031	journal	January 1993

Similar Records

Multi-GPU immersed boundary method hemodynamics simulations

Journal Article · 2020 · Journal of Computational Science · OSTI ID:1649415

Geometric multigrid for an implicit-time immersed boundary method

Journal Article · 2014 · Advances in Computational Mathematics · OSTI ID:1163152

A sharp interface Lagrangian-Eulerian method for flexible-body fluid-structure interaction

Journal Article · 2023 · Journal of Computational Physics · OSTI ID:2425571

Immersed Boundary Method Halo Exchange in a Hemodynamics Application

Citation Formats

References (28)

Similar Records

Related Subjects