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

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

Hypercube technology

The JPL designed MARKIII hypercube supercomputer has been in application service since June 1988 and has had successful application to a broad problem set including electromagnetic scattering, discrete event simulation, plasma transport, matrix algorithms, neural network simulation, image processing, and graphics. Currently, problems that are not homogeneous are being attempted, and, through this involvement with real world applications, the software is evolving to handle the heterogeneous class problems efficiently

Towards a theory of automated elliptic mesh generation

The theory of elliptic mesh generation is reviewed and the fundamental problem of constructing computational space is discussed. It is argued that the construction of computational space is an NP-Complete problem and therefore requires a nonstandard approach for its solution. This leads to the development of graph-theoretic, combinatorial optimization and integer programming algorithms. Methods for the construction of two dimensional computational space are presented

A practical and robust method to compute the boundary of three-dimensional axis-aligned boxes

The union of axis-aligned boxes results in a constrained structure that is advantageous for solving certain geometrical problems. A widely used scheme for solid modelling systems is the boundary representation (Brep). We present a method to obtain the B-rep of a union of axis-aligned boxes. Our method computes all boundary vertices, and additional information for each vertex that allows us to apply already existing methods to extract the B-rep. It is based on dividing the three-dimensional problem into two-dimensional boundary computations and combining their results. The method can deal with all geometrical degeneracies that may arise. Experimental results prove that our approach outperforms existing general methods, both in efficiency and robustness.)Peer ReviewedPostprint (author’s final draft

Using a multifrontal sparse solver in a high performance, finite element code

We consider the performance of the finite element method on a vector supercomputer. The computationally intensive parts of the finite element method are typically the individual element forms and the solution of the global stiffness matrix both of which are vectorized in high performance codes. To further increase throughput, new algorithms are needed. We compare a multifrontal sparse solver to a traditional skyline solver in a finite element code on a vector supercomputer. The multifrontal solver uses the Multiple-Minimum Degree reordering heuristic to reduce the number of operations required to factor a sparse matrix and full matrix computational kernels (e.g., BLAS3) to enhance vector performance. The net result in an order-of-magnitude reduction in run time for a finite element application on one processor of a Cray X-MP

Probabilistic structural mechanics research for parallel processing computers

Aerospace structures and spacecraft are a complex assemblage of structural components that are subjected to a variety of complex, cyclic, and transient loading conditions. Significant modeling uncertainties are present in these structures, in addition to the inherent randomness of material properties and loads. To properly account for these uncertainties in evaluating and assessing the reliability of these components and structures, probabilistic structural mechanics (PSM) procedures must be used. Much research has focused on basic theory development and the development of approximate analytic solution methods in random vibrations and structural reliability. Practical application of PSM methods was hampered by their computationally intense nature. Solution of PSM problems requires repeated analyses of structures that are often large, and exhibit nonlinear and/or dynamic response behavior. These methods are all inherently parallel and ideally suited to implementation on parallel processing computers. New hardware architectures and innovative control software and solution methodologies are needed to make solution of large scale PSM problems practical

Multi-Dimensional Astrophysical Structural and Dynamical Analysis I. Development of a Nonlinear Finite Element Approach

A new field of numerical astrophysics is introduced which addresses the solution of large, multidimensional structural or slowly-evolving problems (rotating stars, interacting binaries, thick advective accretion disks, four dimensional spacetimes, etc.). The technique employed is the Finite Element Method (FEM), commonly used to solve engineering structural problems. The approach developed herein has the following key features: 1. The computational mesh can extend into the time dimension, as well as space, perhaps only a few cells, or throughout spacetime. 2. Virtually all equations describing the astrophysics of continuous media, including the field equations, can be written in a compact form similar to that routinely solved by most engineering finite element codes. 3. The transformations that occur naturally in the four-dimensional FEM possess both coordinate and boost features, such that (a) although the computational mesh may have a complex, non-analytic, curvilinear structure, the physical equations still can be written in a simple coordinate system independent of the mesh geometry. (b) if the mesh has a complex flow velocity with respect to coordinate space, the transformations will form the proper arbitrary Lagrangian- Eulerian advective derivatives automatically. 4. The complex difference equations on the arbitrary curvilinear grid are generated automatically from encoded differential equations. This first paper concentrates on developing a robust and widely-applicable set of techniques using the nonlinear FEM and presents some examples.Comment: 28 pages, 9 figures; added integral boundary conditions, allowing very rapidly-rotating stars; accepted for publication in Ap.