Low-cost parallel algorithms for 2:1 octree balance

Proceedings of the 2012 IEEE 26th International Parallel and Distributed Processing Symposium, IPDPS 2012

Volumn , Issue , 2012, Pages 426-437

  Isaac, Tobin ^a   Burstedde, Carsten ^a,b   Ghattas, Omar ^a,c,d  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b UNIVERSITY OF BONN   (Germany)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^d The University of Texas at Austin   (United States)

Author keywords

Adaptive mesh refinement; High performance computing; Octrees; Parallel algorithms; Scientific computing

Indexed keywords

ADAPTIVE MESH REFINEMENT; BENCH-MARK PROBLEMS; COMMUNICATION PATTERN; CPU CORES; CPU TIME; FAST ALGORITHMS; HIGH PERFORMANCE COMPUTING; LOGICAL STRUCTURE; NONLOCAL; OCTREES; OPEN-SOURCE; PARENT NODE; PETASCALE; RUNTIMES; SCALABLE ALGORITHMS;

COMMUNICATION; DISTRIBUTED PARAMETER NETWORKS; NATURAL SCIENCES COMPUTING; NUMERICAL ANALYSIS; PARALLEL ALGORITHMS; SUPERCOMPUTERS;

PARALLEL ARCHITECTURES;

EID: 84866876701     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPS.2012.47     Document Type: Conference Paper

References (30)

1. I. Babuška, J. Chandra, and J. E. Flaherty, Eds., Adaptive Computational Methods for Partial Differential Equations. SIAM, 1983.
2. M. J. Berger and J. Oliger, "Adaptive mesh refinement for hyperbolic partial differential equations," Journal of Computational Physics, vol. 53, no. 3, pp. 484-512, 1984.
3. W. Dahmen, "Wavelets and multiscale methods for operator equations," in Acta Numerica 1997, A. Iserles, Ed. Cambridge, London, New York: Cambridge University Press, 1997, pp. 55-228.
4. I. Babuška, U. Banerjee, and J. E. Osborn, "Survey of meshless and generalized finite element methods," in Acta Numerica 2003, A. Iserles, Ed. Cambridge, London, New York: Cambridge University Press, 2003, pp. 1-126.
5. M. J. Berger and R. J. LeVeque, "Adaptive mesh refinement using wave-propagation algorithms for hyperbolic systems," SIAM Journal on Numerical Analysis, vol. 35, no. 6, pp. 2298-2316, 1998.
6. J. E. Flaherty, R. M. Loy, M. S. Shephard, B. K. Szymanski, J. D. Teresco, and L. H. Ziantz, "Adaptive local refinement with octree load balancing for the parallel solution of three-dimensional conservation laws," Journal of Parallel and Distributed Computing, vol. 47, no. 2, pp. 139-152, 1997.
7. A. C. Calder, B. C. Curtis, L. J. Dursi, B. Fryxell, G. Henry, P. MacNeice, K. Olson, P. Ricker, R. Rosner, F. X. Timmes, H. M. Tufo, J. W. Truran, and M. Zingale, "High-performance reactive fluid flow simulations using adaptive mesh refinement on thousands of processors," in SC '00: Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis. ACM/IEEE, 2000, pp. 56-56.
8. G. L. Bryan, T. Abel, and M. L. Norman, "Achieving extreme resolution in numerical cosmology using adaptive mesh refinement: Resolving primordial star formation," in SC '01: Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis. ACM/IEEE, 2001.
9. T. Goodale, G. Allen, G. Lanfermann, J. Masso, T. Radke, E. Seidel, and J. Shalf, "The Cactus framework and toolkit: Design and applications," in Vector and Parallel Processing - VECPAR '2002, 5th International Conference. Springer, 2003.
10. B. W. O'Shea, G. Bryan, J. Bordner, M. L. Norman, T. Abel, R. Harkness, and A. Kritsuk, "Introducing Enzo, an AMR cosmology application," in Lecture Notes in Computational Science and Engineering, T. Plewa, T. Linde, and V. G. Weirs, Eds. Springer, 2004.
11. J. Luitjens, B. Worthen, M. Berzins, and T. C. Henderson, "Scalable parallel AMR for the Uintah multiphysics code," in Petascale Computing Algorithms and Applications, D. A. Bader, Ed. Chapman and Hall/CRC, 2007.
12. P. Colella, D. T. Graves, N. Keen, T. J. Ligocki, D. F. Martin, P. W. McCorquodale, D. Modiano, P. O. Schwartz, T. D. Sternberg, and B. Van Straalen, Chombo Software Package for AMR Applications. Design Document., Applied Numerical Algoirthms Group, NERSC Division, Lawrence Berkeley National Laboratory, Berkeley, CA, May 2007.
13. C. D. Norton, J. Z. Lou, and T. A. Cwik, "Status and directions for the PYRAMID parallel unstructured AMR library," in Proceedings of the 15th IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2001, p. 120.
14. O. S. Lawlor, S. Chakravorty, T. L. Wilmarth, N. Choudhury, I. Dooley, G. Zheng, and L. V. Kalé, "ParFUM: a parallel framework for unstructured meshes for scalable dynamic physics applications," Engineering with Computers, vol. 22, no. 3, pp. 215-235, 2006.
15. J. Luitjens and M. Berzins, "Improving the performance of Uintah: A large-scale adaptive meshing computational framework," in Proceedings of the 24th International Parallel and Distributed Processing Symposium. IEEE, 2010.
16. M. Zhou, O. Sahni, K. D. Devine, M. S. Shephard, and K. E. Jansen, "Controlling unstructured mesh partitions for massively parallel simulations," SIAM Journal on Scientific Computing, vol. 32, no. 6, pp. 3201-3227, 2010.
17. S. Popinet, "Gerris: a tree-based adaptive solver for the incompressible Euler equations in complex geometries," Journal of Computational Physics, vol. 190, no. 2, pp. 572-600, 2003.
18. J. R. Stewart and H. C. Edwards, "A framework approach for developing parallel adaptive multiphysics applications," Finite Elements in Analysis and Design, vol. 40, no. 12, pp. 1599-1617, 2004.
19. T. Tu, D. R. O'Hallaron, and O. Ghattas, "Scalable parallel octree meshing for terascale applications," in SC '05: Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis. ACM/IEEE, 2005.
20. D. Rosenberg, A. Fournier, P. Fischer, and A. Pouquet, "Geophysical-astrophysical spectral-element adaptive refinement (GASpAR): Object-oriented h-adaptive fluid dynamics simulation," Journal of Computational Physics, vol. 215, no. 1, pp. 59-80, 2006.
21. W. Bangerth, R. Hartmann, and G. Kanschat, "deal.II - a general-purpose object-oriented finite element library," ACM Transactions on Mathematical Software, vol. 33, no. 4, p. 24, 2007.
22. H. Sundar, R. Sampath, and G. Biros, "Bottom-up construction and 2:1 balance refinement of linear octrees in parallel," SIAM Journal on Scientific Computing, vol. 30, no. 5, pp. 2675-2708, 2008.
23. J. J. Camata and A. L. G. A. Coutinho, "Parallel linear octree meshing with immersed surfaces," in 22nd International Symposium on Computer Architecture and High Performance Computing. IEEE, 2010.
24. W. Bangerth, C. Burstedde, T. Heister, and M. Kronbichler, "Algorithms and data structures for massively parallel generic adaptive finite element codes," ACM Transactions on Mathematical Software, vol. 38, no. 2, 2011.
25. C. Burstedde, O. Ghattas, M. Gurnis, T. Isaac, G. Stadler, T. Warburton, and L. C. Wilcox, "Extreme-scale AMR," in SC10: Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis. ACM/IEEE, 2010.
26. C. Burstedde, M. Burtscher, O. Ghattas, G. Stadler, T. Tu, and L. C. Wilcox, "ALPS: A framework for parallel adaptive PDE solution," Journal of Physics: Conference Series, vol. 180, p. 012009, 2009.
27. G. Stadler, M. Gurnis, C. Burstedde, L. C. Wilcox, L. Alisic, and O. Ghattas, "The dynamics of plate tectonics and mantle flow: From local to global scales," Science, vol. 329, no. 5995, pp. 1033-1038, 2010.
28. C. Burstedde, L. C. Wilcox, and O. Ghattas, "p4est: Scalable algorithms for parallel adaptive mesh refinement on forests of octrees," SIAM Journal on Scientific Computing, vol. 33, no. 3, pp. 1103-1133, 2011.
29. M. P. I. Forum, "MPI: A message-passing interface standard," May 1994.
30. C. Burstedde, "p4est: Parallel AMR on forests of octrees," 2010, http://www.p4est.org/.