Toward interoperable mesh, geometry and field components for PDE simulation development

Chand, Kyle; Diachin, Lori Freitag; Li, Xin; Ollivier‐Gooch, Carl; Seol, E. Seegyoung; Shephard, Mark S.; Tautges, Timothy J.; Trease, Harold E.

doi:10.1007/s00366-007-0080-z

Cited by 23 publications

(19 citation statements)

References 33 publications

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“…For example, Burri et al [2005], Tu et al [2005], Chand et al [2008], Sundar et al [2008], and Knepley and Karpeev [2009] discuss related data structures and algorithms. In the current contribution, we base our work on the open source software library p4est, which realizes the oracle functionality in the sense outlined above, and has been shown to scale to hundreds of thousands of processors [Burstedde et al 2011b].…”

Section: Parallel Construction Of Distributed Meshesmentioning

confidence: 99%

Algorithms and data structures for massively parallel generic adaptive finite element codes

Bangerth

Burstedde

Heister

et al. 2011

ACM Trans. Math. Softw.

164

154

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Today's largest supercomputers have 100,000s of processor cores and offer the potential to solve partial differential equations discretized by billions of unknowns. However, the complexity of scaling to such large machines and problem sizes has so far prevented the emergence of generic software libraries that support such computations, although these would lower the threshold of entry and enable many more applications to benefit from large-scale computing.We are concerned with providing this functionality for mesh-adaptive finite element computations. We assume the existence of an "oracle" that implements the generation and modification of an adaptive mesh distributed across many processors, and that responds to queries about its structure. Based on querying the oracle, we develop scalable algorithms and data structures for generic finite element methods. Specifically, we consider the parallel distribution of mesh data, global enumeration of degrees of freedom, constraints, and postprocessing. Our algorithms remove the bottlenecks that typically limit large-scale adaptive finite element analyses.We demonstrate scalability of complete finite element workflows on up to 16,384 processors. An implementation of the proposed algorithms, based on the open source software p4est as mesh oracle, is provided under an open source license through the widely used deal.II finite element software library.

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Section: Parallel Construction Of Distributed Meshesmentioning

confidence: 99%

Algorithms and data structures for massively parallel generic adaptive finite element codes

Bangerth

Burstedde

Heister

et al. 2011

ACM Trans. Math. Softw.

164

154

View full text Add to dashboard Cite

show abstract

“…The various ITAPS iMesh implementations (Devine et al, 2009;Chand et al, 2008;Ollivier-Gooch et al, 2010), and others, are based on such a topological abstraction of the mesh. Although it is possible to base the representations used on only the specific mesh entities and adjacencies used in the linkage of specific components, many implementations employ a complete representation in the sense that any of the desired 12 mesh adjacencies can be determined in O(1) time (i.e., are not a function of the number of mesh entities) (Beall and Shephard, 1997;Remacle and Shephard, 2003;Seol and Shephard, 2006).…”

Section: Relating Multiphysics Spatial Discretizationsmentioning

confidence: 99%

Multiphysics simulations: challenges and opportunities.

Keyes¹,

McInnes²,

Woodward³

et al. 2012

149

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We consider multiphysics applications from algorithmic and architectural perspectives, where "algorithmic" includes both mathematical analysis and computational complexity and "architectural" includes both software and hardware environments. Many diverse multiphysics applications can be reduced, en route to their computational simulation, to a common algebraic coupling paradigm. Mathematical analysis of multiphysics coupling in this form is not always practical for realistic applications, but model problems representative of applications discussed herein can provide insight. A variety of software frameworks for multiphysics applications have been constructed and refined within disciplinary communities and executed on leading-edge computer systems. We examine several of these, expose some commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities.

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“…One common approach for the distribution of the mesh is to partition it into a set of parts where each part is a set of mesh entities, with the goal of having reasonably continuously connected mesh entities within a single part such that the number of mesh entities on the inter-part boundaries, those mesh entities shared between two or more parts, is minimized in some reasonable fashion. Following somewhat standard practices, and more specifically those being developed by the DOE Sci-DAC for Interoperable Technologies for Advanced Petascale Simulations [11,12], the following are key requirements placed on the definition of mesh parts in a partition:…”

Section: Partitioning Of Unstructured Meshesmentioning

confidence: 99%

Tools to support mesh adaptation on massively parallel computers

Zhou

Xie

Seol

et al. 2011

Engineering with Computers

Self Cite

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The scalable execution of parallel adaptive analyses requires the application of dynamic load balancing to repartition the mesh into a set of parts with balanced work load and minimal communication. As the adaptive meshes being generated reach billions of elements and the analyses are performed on massively parallel computers with 100,000's of computing cores, a number of complexities arise that need to be addressed. This paper presents procedures developed to deal with two of them. The first is a procedure to support multiple parts per processor which is used as the mesh increases in size and it is desirable to partition the mesh to a larger number of computing cores than are currently being used. The second is a predictive load balancing method that sets entity weights before dynamic load balancing steps so that the mesh is well balanced after the mesh adaptation step thus avoiding excessive memory spikes that would otherwise occur during mesh adaptation.

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Toward interoperable mesh, geometry and field components for PDE simulation development

Cited by 23 publications

References 33 publications

Algorithms and data structures for massively parallel generic adaptive finite element codes

Algorithms and data structures for massively parallel generic adaptive finite element codes

Multiphysics simulations: challenges and opportunities.

Tools to support mesh adaptation on massively parallel computers

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