Use of the AmgX Library for Solving Problems Related to Cardiac Mechanics

Authors

  • Jonatas Dias Machado Costa Universidade Federal de Juiz de Fora
  • Lucas Silva Santana Universidade Federal de Juiz de Fora
  • Rodrigo Weber dos Santos Universidade Federal de Juiz de Fora https://orcid.org/0000-0002-0633-1391
  • Bernardo Martins Rocha Universidade Federal de Juiz de Fora
  • Joventino de Oliveira Campos Universidade Federal de Juiz de Fora

DOI:

https://doi.org/10.14295/vetor.v33i2.16420

Keywords:

Computational modeling, Linear systems, Multigrid methods, GPU

Abstract

The solution of linear systems plays a fundamental role in computer simulation software based on mathematical models to advance contemporary scientific research. Consequently, there is a growing demand for numerical methods and efficient implementations to face this challenge, particularly in the context of biomedical engineering where it is desired to use these simulators to create digital twins of patients and study certain pathological conditions. This work aims to explore and identify efficient techniques to solve linear systems related to the problem of cardiac biomechanics, thus accelerating simulations related to the intricate human cardiovascular system. To achieve this goal, several multigrid methods available in the AmgX library were selected, which were tested and analyzed in terms of their computational performance. As an initial step, problems based on Poisson's equation were solved considering simplified and complex geometries such as a cube and a human left ventricle. This study revealed distinct advantages associated with each method, depending on the complexity and format of the problems at hand.

Downloads

Download data is not yet available.

References

K. Gillette, M. A. Gsell, A. J. Prassl, E. Karabelas, U. Reiter, G. Reiter, T. Grandits, C. Payer, D. Štern, M. Urschler et al., “A framework for the generation of digital twins of cardiac electrophysiology from clinical 12-leads ECGs,” Medical Image Analysis, vol. 71, p. 102080, 2021. Disponível em: https://doi.org/10.1016/j.media.2021.102080

F. Viola, G. Del Corso, R. De Paulis, e R. Verzicco, “Gpu accelerated digital twins of the human heart open new routes for cardiovascular research,” Scientific Reports, vol. 13, no. 1, p. 8230, 2023. Disponível em: https://doi.org/10.1038/s41598-023-34098-8

J. O. Campos, R. S. Oliveira, R. W. dos Santos, e B. M. Rocha, “Lattice Boltzmann method for parallel simulations of cardiac electrophysiology using GPUs,” Journal of Computational and Applied Mathematics, vol. 295, pp. 70–82, 2016. Disponível em: https://doi.org/10.1016/j.cam.2015.02.008

B. M. Rocha, F. O. Campos, R. M. Amorim, G. Plank, R. d. Santos, M. Liebmann, e G. Haase, “Accelerating cardiac excitation spread simulations using graphics processing units,” Concurrency and Computation: Practice and Experience, vol. 23, no. 7, pp. 708–720, 2011. Disponível em: https://doi.org/10.1002/cpe.1683

M. Pandey, M. Fernandez, F. Gentile, O. Isayev, A. Tropsha, A. C. Stern, e A. Cherkasov, “The transformational role of GPU computing and deep learning in drug discovery,” Nature Machine Intelligence, vol. 4, no. 3, pp. 211–221, 2022. Disponível em: https://doi.org/10.1038/s42256-022-00463-x

W. L. Briggs, V. E. Henson, e S. F. McCormick, A multigrid tutorial, 2a ed. Philadelphia, USA: SIAM, 2000. Disponível em: https://epubs.siam.org/doi/pdf/10.1137/1.9780898719505.fm

M. Naumov, M. Arsaev, P. Castonguay, J. Cohen, J. Demouth, J. Eaton, S. Layton, N. Markovskiy, I. Reguly, N. Sakharnykh, V. Sellappan, e R. Strzodka, “AmgX: A library for GPU accelerated algebraic multigrid and preconditioned iterative methods,” SIAM Journal on Scientific Computing, vol. 37, no. 5, pp. S602–S626, 2015. Disponível em: https://doi.org/10.1137/140980260

J. O. Campos, J. Sundnes, R. W. dos Santos, e B. M. Rocha, “Effects of left ventricle wall thickness uncertainties

on cardiac mechanics,” Biomechanics and Modeling in Mechanobiology, vol. 18, no. 5, pp. 1415–1427, 2019.

Disponível em: https://doi.org/10.1007/s10237-019-01153-1

J. O. Campos, R. W. Dos Santos, J. Sundnes, e B. M. Rocha, “Preconditioned augmented lagrangian

formulation for nearly incompressible cardiac mechanics,” International Journal for Numerical Methods in

Biomedical Engineering, vol. 34, no. 4, p. e2948, 2018. Disponível em: https://doi.org/10.1002/cnm.2948

Published

2023-12-23

How to Cite

Dias Machado Costa, J., Silva Santana, L., Weber dos Santos, R., Martins Rocha, B., & de Oliveira Campos, J. (2023). Use of the AmgX Library for Solving Problems Related to Cardiac Mechanics. VETOR - Journal of Exact Sciences and Engineering, 33(2), 32–40. https://doi.org/10.14295/vetor.v33i2.16420

Issue

Section

Articles

Most read articles by the same author(s)