Abstract

In this work we formally derive and prove the correctness of the algorithms and data structures in a parallel, distributed-memory, generic finite element framework that supports $h$-adaptivity on computational domains represented as forest-of-trees. The framework is grounded on a rich representation of the adaptive mesh suitable for generic finite elements that is built on top of a low-level, light-weight forest-of-trees data structure handled by a specialized, highly parallel adaptive meshing engine, for which we have identified the requirements it must fulfill to be coupled into our framework. Atop this two-layered mesh representation, we build the rest of the data structures required for the numerical integration and assembly of the discrete system of linear equations. We consider algorithms that are suitable for both subassembled and fully assembled distributed data layouts of linear system matrices. The proposed framework has been implemented within the FEMPAR scientific software library, using p4est as a practical forest-of-octrees demonstrator. A strong scaling study of this implementation when applied to Poisson and Maxwell problems reveals remarkable scalability up to 32.2K CPU cores and 482.2M degrees of freedom. Besides, a comparative performance study of FEMPAR and the state-of-the-art deal.II finite element software shows at least comparative performance, and at most a factor of 2--3 improvement in the $h$-adaptive approximation of a Poisson problem with first- and second-order Lagrangian finite elements, respectively.

Keywords

  1. partial differential equations
  2. finite elements
  3. adaptive mesh refinement
  4. forest of trees
  5. parallel algorithms
  6. scientific software

MSC codes

  1. 65Y05
  2. 65Y20
  3. 65N30
  4. 65M50

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References

1.
J. Holke, Scalable Algorithms for Parallel Tree-based Adaptive Mesh Refinement with General Element Types, Ph.D. thesis, Bonn University, Bonn, Germany, 2018.
2.
C. Burstedde, L. C. Wilcox, and O. Ghattas, p4est: Scalable algorithms for parallel adaptive mesh refinement on forests of octrees, SIAM J. Sci. Comput., 33 (2011), pp. 1103--1133, https://doi.org/10.1137/100791634.
3.
T. Isaac, C. Burstedde, L. C. Wilcox, and O. Ghattas, Recursive algorithms for distributed forests of octrees, SIAM J. Sci. Comput., 37 (2015), pp. C497--C531, https://doi.org/10.1137/140970963.
4.
H. Sundar, R. S. Sampath, and G. Biros, Bottom-up construction and 2:1 balance refinement of linear octrees in parallel, SIAM J. Sci. Comput., 30 (2008), pp. 2675--2708, https://doi.org/10.1137/070681727.
5.
C. Burstedde and J. Holke, A tetrahedral space-filling curve for nonconforming adaptive meshes, SIAM J. Sci. Comput., 38 (2016), pp. C471--C503, https://doi.org/10.1137/15M1040049.
6.
L. C. Wilcox, G. Stadler, C. Burstedde, and O. Ghattas, A high-order discontinuous Galerkin method for wave propagation through coupled elastic-acoustic media, J. Comput. Phys., 229 (2010), pp. 9373--9396, https://doi.org/10.1016/J.JCP.2010.09.008.
7.
J. Rudi, O. Ghattas, A. C. I. Malossi, T. Isaac, G. Stadler, M. Gurnis, P. W. J. Staar, Y. Ineichen, C. Bekas, and A. Curioni, An extreme-scale implicit solver for complex PDEs: Highly heterogeneous flow in earth's mantle, in Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis - SC '15, ACM, New York, 2015, pp. 1--12, https://doi.org/10.1145/2807591.2807675.
8.
M. Olm, S. Badia, and A. F. Martín, Simulation of high temperature superconductors and experimental validation, Comput. Phys. Commun., 237 (2018), pp. 154--167, https://doi.org/10.1016/J.CPC.2018.11.021.
9.
E. Neiva, S. Badia, A. F. Martín, and M. Chiumenti, A scalable parallel finite element framework for growing geometries. Application to metal additive manufacturing, Internat. J. Numer. Methods Engrg., 119 (2019), pp. 1098--1125.
10.
S. Badia, A. F. Martín, and F. Verdugo, Mixed aggregated finite element methods for the unfitted discretization of the Stokes problem, SIAM J. Sci. Comput., 40 (2018), pp. B1541--B1576, https://doi.org/10.1137/18M1185624.
11.
S. Badia, F. Verdugo, and A. F. Martín, The aggregated unfitted finite element method for elliptic problems, Comput. Methods Appl. Mech. Engrg., 336 (2018), pp. 533--553, https://doi.org/10.1016/j.cma.2018.03.022.
12.
W. C. Rheinboldt and C. K. Mesztenyi, On a data structure for adaptive finite element mesh refinements, ACM Trans. Math. Software, 6 (1980), pp. 166--187, https://doi.org/10.1145/355887.355891.
13.
M. S. Shephard, Linear multipoint constraints applied via transformation as part of a direct stiffness assembly process, Internat. J. Numer. Methods Engrg., 20 (1984), pp. 2107--2112, https://doi.org/10.1002/nme.1620201112.
14.
W. Bangerth, C. Burstedde, T. Heister, and M. Kronbichler, Algorithms and data structures for massively parallel generic adaptive finite element codes, ACM Trans. Math. Software, 38 (2012), 14, https://doi.org/10.1145/2049673.2049678.
15.
W. Bangerth, R. Hartmann, and G. Kanschat, DEAL.$II$---A general-purpose object-oriented finite element library, ACM Trans. Math. Software, 33 (2007), https://doi.org/10.1145/1268776.1268779.
16.
S. Badia, A. F. Martín, and J. Principe, A highly scalable parallel implementation of balancing domain decomposition by constraints, SIAM J. Sci. Comput., 36 (2014), pp. C190--C218, https://doi.org/10.1137/130931989.
17.
S. Badia, A. F. Martín, and J. Principe, Multilevel balancing domain decomposition at extreme scales, SIAM J. Sci. Comput., 38 (2016), pp. C22--C52, https://doi.org/10.1137/15M1013511.
18.
S. Balay, S. Abhyankar, M. F. Adams, J. Brown, P. Brune, K. Buschelman, L. Dalcin, V. Eijkhout, W. D. Gropp, D. Kaushik, M. G. Knepley, L. C. McInnes, K. Rupp, B. F. Smith, S. Zampini, H. Zhang, and H. Zhang, PETSc Users Manual, Technical Report ANL-95/11 - Revision 3.7, Argonne National Laboratory, Argonne, IL, 2016.
19.
M. A. Heroux, R. A. Bartlett, V. E. Howle, R. J. Hoekstra, J. J. Hu, T. G. Kolda, R. B. Lehoucq, K. R. Long, R. P. Pawlowski, E. T. Phipps, A. G. Salinger, H. K. Thornquist, R. S. Tuminaro, J. M. Willenbring, A. Williams, and K. S. Stanley, An Overview of the Trilinos Project, ACM Trans. Math. Software, 31 (2005), pp. 397--423, https://doi.org/10.1145/1089014.1089021.
20.
S. Badia, A. F. Martín, and J. Principe, FEMPAR: An object-oriented parallel finite element framework, Arch. Comput. Methods Eng., 25 (2018), 195--271, https://doi.org/10.1007/s11831-017-9244-1.
21.
T. Isaac, C. Burstedde, and O. Ghattas, Low-cost parallel algorithms for $2{:}1$ octree balance, in Proceedings of the 2012 IEEE 26th International Parallel and Distributed Processing Symposium, IEEE, Piscataway, NJ, 2012, pp. 426--437, https://doi.org/10.1109/IPDPS.2012.47.
22.
M. Olm, S. Badia, and A. F. Martín, On a general implementation of $h$- and $p$-adaptive curl-conforming finite elements, Adv. Eng. Software, 132 (2019), pp. 74--91, https://doi.org/10.1016/J.ADVENGSOFT.2019.03.006.
23.
J. Cervený, V. Dobrev, and T. Kolev, Nonconforming mesh refinement for high-order finite elements, SIAM J. Sci. Comput., 41 (2019), pp. C367--C392, https://doi.org/10.1137/18M1193992.
24.
D. W. Kelly, J. P. De S. R. Gago, O. C. Zienkiewicz, and I. Babuska, A posteriori error analysis and adaptive processes in the finite element method: Part I: Error analysis, Internat. J. Numer. Methods Engrg., 19 (1983), https://doi.org/10.1002/nme.1620191103.

Information & Authors

Information

Published In

cover image SIAM Journal on Scientific Computing
SIAM Journal on Scientific Computing
Pages: C436 - C468
ISSN (online): 1095-7197

History

Submitted: 3 April 2020
Accepted: 19 August 2020
Published online: 18 December 2020

Keywords

  1. partial differential equations
  2. finite elements
  3. adaptive mesh refinement
  4. forest of trees
  5. parallel algorithms
  6. scientific software

MSC codes

  1. 65Y05
  2. 65Y20
  3. 65N30
  4. 65M50

Authors

Affiliations

Funding Information

Barcelona Supercomputing Center https://doi.org/10.13039/501100006433 : FI-2018-2-0009, FI-2018-3-0029, IM-2020-1-0002
Horizon 2020 Framework Programme https://doi.org/10.13039/100010661 : 690725, 800898
Generalitat de Catalunya https://doi.org/10.13039/501100002809
Generalitat de Catalunya https://doi.org/10.13039/501100002809 : 2019 FI-B2-00090, 2018 FI-B1-00095, 2017-FI-B-00219
Generalitat de Catalunya https://doi.org/10.13039/501100002809 : 2016 BP-00145
Ministerio de Economía, Industria y Competitividad, Gobierno de España https://doi.org/10.13039/501100010198 : MTM2014-60713-P

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