Recursive Algorithms for Distributed Forests of Octrees

The forest-of-octrees approach to parallel adaptive mesh refinement and coarsening (AMR) has recently been demonstrated in the context of a number of large-scale PDE-based applications. Although linear octrees, which store only leaf octants, have an underlying tree structure by definition, it is not often exploited in previously published mesh-related algorithms. This is because the branches are not explicitly stored, and because the topological relationships in meshes, such as the adjacency between cells, introduce dependencies that do not respect the octree hierarchy. In this work we combine hierarchical and topological relationships between octree branches to design efficient recursive algorithms. We present three important algorithms with recursive implementations. The first is a parallel search for leaves matching any of a set of multiple search criteria. The second is a ghost layer construction algorithm that handles arbitrarily refined octrees that are not covered by previous algorithms, which require a 2:1 condition between neighboring leaves. The third is a universal mesh topology iterator. This iterator visits every cell in a domain partition, as well as every interface (face, edge and corner) between these cells. The iterator calculates the local topological information for every interface that it visits, taking into account the nonconforming interfaces that increase the complexity of describing the local topology. To demonstrate the utility of the topology iterator, we use it to compute the numbering and encoding of higher-order $C^0$ nodal basis functions. We analyze the complexity of the new recursive algorithms theoretically, and assess their performance, both in terms of single-processor efficiency and in terms of parallel scalability, demonstrating good weak and strong scaling up to 458k cores of the JUQUEEN supercomputer.Comment: 35 pages, 15 figures, 3 table

Diamond-based models for scientific visualization

Hierarchical spatial decompositions are a basic modeling tool in a variety of application domains including scientific visualization, finite element analysis and shape modeling and analysis. A popular class of such approaches is based on the regular simplex bisection operator, which bisects simplices (e.g. line segments, triangles, tetrahedra) along the midpoint of a predetermined edge. Regular simplex bisection produces adaptive simplicial meshes of high geometric quality, while simplifying the extraction of crack-free, or conforming, approximations to the original dataset. Efficient multiresolution representations for such models have been achieved in 2D and 3D by clustering sets of simplices sharing the same bisection edge into structures called diamonds. In this thesis, we introduce several diamond-based approaches for scientific visualization. We first formalize the notion of diamonds in arbitrary dimensions in terms of two related simplicial decompositions of hypercubes. This enables us to enumerate the vertices, simplices, parents and children of a diamond. In particular, we identify the number of simplices involved in conforming updates to be factorial in the dimension and group these into a linear number of subclusters of simplices that are generated simultaneously. The latter form the basis for a compact pointerless representation for conforming meshes generated by regular simplex bisection and for efficiently navigating the topological connectivity of these meshes. Secondly, we introduce the supercube as a high-level primitive on such nested meshes based on the atomic units within the underlying triangulation grid. We propose the use of supercubes to associate information with coherent subsets of the full hierarchy and demonstrate the effectiveness of such a representation for modeling multiresolution terrain and volumetric datasets. Next, we introduce Isodiamond Hierarchies, a general framework for spatial access structures on a hierarchy of diamonds that exploits the implicit hierarchical and geometric relationships of the diamond model. We use an isodiamond hierarchy to encode irregular updates to a multiresolution isosurface or interval volume in terms of regular updates to diamonds. Finally, we consider nested hypercubic meshes, such as quadtrees, octrees and their higher dimensional analogues, through the lens of diamond hierarchies. This allows us to determine the relationships involved in generating balanced hypercubic meshes and to propose a compact pointerless representation of such meshes. We also provide a local diamond-based triangulation algorithm to generate high-quality conforming simplicial meshes

Preconditioning for hyperelasticity-based mesh optimisation

A robust mesh optimisation method is presented that directly enforces the resulting deformation to be orientation preserving. Motivated by aspects from mathematical elasticity, the energy functional of the mesh deformation can be related to a stored energy functional of a hyperelastic material. Formulating the functional in the principal invariants of the deformation gradient allows fine grained control over the resulting deformation. Solution techniques for the arising nonconvex and highly nonlinear system are presented. As existing preconditioners are not sufficient, a PDE-based preconditioner is developed

Mapping unstructured grid problems to the connection machine

We present a highly parallel graph mapping technique that enables one to solve unstructured grid problems on massively parallel computers. Many implicit and explicit methods for solving discretizated partial differential equations require each point in the discretization to exchange data with its neighboring points every time step or iteration. The time spent communicating can limit the high performance promised by massively parallel computing. To eliminate this bottleneck, we map the graph of the irregular problem to the graph representing the interconnection topology of the computer such that the sum of the distances that the messages travel is minimized. We show that, in comparison to a naive assignment of processors, our heuristic mapping algorithm significantly reduces the communication time on the Connection Machine, CM-2

A parallel progressive radiosity algorithm based on patch data circulation

Cataloged from PDF version of article.Current research on radiosity has concentrated on increasing the accuracy and the speed of the solution. Although algorithmic and meshing techniques decrease the execution time, still excessive computational power is required for complex scenes. Hence, parallelism can be exploited for speeding up the method further. This paper aims at providing a thorough examination of parallelism in the basic progressive refinement radiosity, and investigates its parallelization on distributed-memory parallel architectures. A synchronous scheme, based on static task assignment, is proposed to achieve better coherence for shooting patch selections. An efficient global circulation scheme is proposed for the parallel light distribution computations, which reduces the total volume of concurrent communication by an asymptotical factor. The proposed parallel algorithm is implemented on an Intel's iPSC/2 hypercube multicomputer. Load balance qualities of the proposed static assignment schemes are evaluated experimentally. The effect of coherence in the parallel light distribution computations on the shooting patch selection sequence is also investigated. Theoretical and experimental evaluation is also presented to verify that the proposed parallelization scheme yields equally good performance on multicomputers implementing the simplest (e.g. ring) as well as the richest (e.g. hypercube) interconnection topologies. This paper also proposes and presents a parallel load re-balancing scheme which enhances our basic parallel radiosity algorithm to be usable in the parallelization of radiosity methods adopting adaptive subdivision and meshing techniques. (C) 1996 Elsevier Science Lt

Rectilinear partitioning of irregular data parallel computations

New mapping algorithms for domain oriented data-parallel computations, where the workload is distributed irregularly throughout the domain, but exhibits localized communication patterns are described. Researchers consider the problem of partitioning the domain for parallel processing in such a way that the workload on the most heavily loaded processor is minimized, subject to the constraint that the partition be perfectly rectilinear. Rectilinear partitions are useful on architectures that have a fast local mesh network. Discussed here is an improved algorithm for finding the optimal partitioning in one dimension, new algorithms for partitioning in two dimensions, and optimal partitioning in three dimensions. The application of these algorithms to real problems are discussed

A tetrahedral space-filling curve for non-conforming adaptive meshes

We introduce a space-filling curve for triangular and tetrahedral red-refinement that can be computed using bitwise interleaving operations similar to the well-known Z-order or Morton curve for cubical meshes. To store sufficient information for random access, we define a low-memory encoding using 10 bytes per triangle and 14 bytes per tetrahedron. We present algorithms that compute the parent, children, and face-neighbors of a mesh element in constant time, as well as the next and previous element in the space-filling curve and whether a given element is on the boundary of the root simplex or not. Our presentation concludes with a scalability demonstration that creates and adapts selected meshes on a large distributed-memory system.Comment: 33 pages, 12 figures, 8 table