A Smoothing Algorithm for the Dual Marching Tetrahedra Method

abstract: The Dual Marching Tetrahedra algorithm is a generalization of the Dual Marching Cubes algorithm, used to build a boundary surface around points which have been assigned a particular scalar density value, such as the data produced by and Magnetic Resonance Imaging or Computed Tomography scanner. This boundary acts as a skin between points which are determined to be "inside" and "outside" of an object. However, the DMT is vague in regards to exactly where each vertex of the boundary should be placed, which will not necessarily produce smooth results. Mesh smoothing algorithms which ignore the DMT data structures may distort the output mesh so that it could incorrectly include or exclude density points. Thus, an algorithm is presented here which is designed to smooth the output mesh, while obeying the underlying data structures of the DMT algorithm.Dissertation/ThesisM.S. Computer Science 201

One machine, one minute, three billion tetrahedra

This paper presents a new scalable parallelization scheme to generate the 3D Delaunay triangulation of a given set of points. Our first contribution is an efficient serial implementation of the incremental Delaunay insertion algorithm. A simple dedicated data structure, an efficient sorting of the points and the optimization of the insertion algorithm have permitted to accelerate reference implementations by a factor three. Our second contribution is a multi-threaded version of the Delaunay kernel that is able to concurrently insert vertices. Moore curve coordinates are used to partition the point set, avoiding heavy synchronization overheads. Conflicts are managed by modifying the partitions with a simple rescaling of the space-filling curve. The performances of our implementation have been measured on three different processors, an Intel core-i7, an Intel Xeon Phi and an AMD EPYC, on which we have been able to compute 3 billion tetrahedra in 53 seconds. This corresponds to a generation rate of over 55 million tetrahedra per second. We finally show how this very efficient parallel Delaunay triangulation can be integrated in a Delaunay refinement mesh generator which takes as input the triangulated surface boundary of the volume to mesh

Parallel Geometric Algorithms for Multi-Core Computers

International audienceComputers with multiple processor cores using shared memory are now ubiquitous. In this paper, we present several parallel geometric algorithms that specifically target this environment, with the goal of exploiting the additional computing power. The d-dimensional algorithms we describe are (a) spatial sorting of points, as is typically used for preprocessing before using incremental algorithms, (b) kd-tree construction, (c) axis-aligned box intersection computation, and finally (d) bulk insertion of points in Delaunay triangulations for mesh generation algorithms or simply computing Delaunay triangulations. We show experimental results for these algorithms in 3D, using our implementations based on the Computational Geometry Algorithms Library (CGAL, http://www.cgal.org/). This work is a step towards what we hope will become a parallel mode for CGAL, where algorithms automatically use the available parallel resources without requiring significant user intervention

Scalable Parallel Delaunay Image-to-Mesh Conversion for Shared and Distributed Memory Architectures

Mesh generation is an essential component for many engineering applications. The ability to generate meshes in parallel is critical for the scalability of the entire Finite Element Method (FEM) pipeline. However, parallel mesh generation applications belong to the broader class of adaptive and irregular problems, and are among the most complex, challenging, and labor intensive to develop and maintain. In this thesis, we summarize several years of the progress that we made in a novel framework for highly scalable and guaranteed quality mesh generation for finite element analysis in three dimensions. We studied and developed parallel mesh generation algorithms on both shared and distributed memory architectures. In this thesis we present a novel two-level parallel tetrahedral mesh generation framework capable of delivering and sustaining close to 6000 of concurrent work units (cores). We achieve this by leveraging concurrency at two different granularity levels by using a hybrid message passing and multi-threaded execution model which is suitable to the hierarchy of the hardware architecture of the distributed memory clusters. An end-user productivity and scalability study was performed on up to 6000 cores, and indicated very good end-user productivity with about 300 million tets per second and about 3600 weak scaling speedup. Both of these results suggest that: compared to the best previous algorithm, we have seen an improvement of more than 7000 times in performance, measured in terms of speed (elements per second) by using about 180 times more CPUs, for geometries that are by many orders of magnitude more complex

Delaunay Tessellations and Voronoi Diagrams in CGAL

The Cgal library provides a rich variety of Voronoi diagrams and Delaunay triangulations. This variety covers several aspects: generators, dimensions and metrics, which we describe in Section 2. One aim of this paper is to present the main paradigms used in CGAL: Generic programming, separation between predicates/constructions and combinatorics, and exact geometric computation (not to be confused with exact arithmetic!). The first two paradigms translate into software design choices, described in Section 4, while the last covers both robustness and efficiency issues, respectively described in Sec- tion 6 and 7. Other important aspects of the Cgal library are the interface issues, be they for traversing a tessellation, or for interoperability with other libraries or languages, see Section 5. We present in Section 8 some tessellations at work in the context of surface reconstruction and mesh generation. Section 9 is devoted to some on-going and future work on periodic triangulations (triangulations in periodic spaces), and on high-quality mesh generation with optimized tessellations. Section 10 provides typical numbers in terms of efficiency and scalability for constructing tessellations, and lists the remaining weaknesses. We conclude by listing some of our directions for the future

Efficient Generating And Processing Of Large-Scale Unstructured Meshes

Unstructured meshes are used in a variety of disciplines to represent simulations and experimental data. Scientists who want to increase accuracy of simulations by increasing resolution must also increase the size of the resulting dataset. However, generating and processing a extremely large unstructured meshes remains a barrier. Researchers have published many parallel Delaunay triangulation (DT) algorithms, often focusing on partitioning the initial mesh domain, so that each rectangular partition can be triangulated in parallel. However, the comproblems for this method is how to merge all triangulated partitions into a single domain-wide mesh or the significant cost for communication the sub-region borders. We devised a novel algorithm --Triangulation of Independent Partitions in Parallel (TIPP) to deal with very large DT problems without requiring inter-processor communication while still guaranteeing the Delaunay criteria. The core of the algorithm is to find a set of independent} partitions such that the circumcircles of triangles in one partition do not enclose any vertex in other partitions. For this reason, this set of independent partitions can be triangulated in parallel without affecting each other. The results of mesh generation is the large unstructured meshes including vertex index and vertex coordinate files which introduce a new challenge \-- locality. Partitioning unstructured meshes to improve locality is a key part of our own approach. Elements that were widely scattered in the original dataset are grouped together, speeding data access. For further improve unstructured mesh partitioning, we also described our new approach. Direct Load which mitigates the challenges of unstructured meshes by maximizing the proportion of useful data retrieved during each read from disk, which in turn reduces the total number of read operations, boosting performance

Real-Time High-Quality Image to Mesh Conversion for Finite Element Simulations

Technological Advances in Medical Imaging have enabled the acquisition of images accurately describing biological tissues. Finite Element (FE) methods on these images provide the means to simulate biological phenomena such as brain shift registration, respiratory organ motion, blood flow pressure in vessels, etc. FE methods require the domain of tissues be discretized by simpler geometric elements, such as triangles in two dimensions, tetrahedra in three, and pentatopes in four. This exact discretization is called a mesh . The accuracy and speed of FE methods depend on the quality and fidelity of the mesh used to describe the biological object. Elements with bad quality introduce numerical errors and slower solver convergence. Also, analysis based on poor fidelity meshes do not yield accurate results specially near the surface. In this dissertation, we present the theory and the implementation of both a sequential and a parallel Delaunay meshing technique for 3D and ---for the first time--- 4D space-time domains. Our method provably guarantees that the mesh is a faithful representation of the multi-tissue domain in topological and geometric sense. Moreover, we show that our method generates graded elements of bounded radius-edge and aspect ratio, which renders our technique suitable for Finite Element analysis. A notable feature of our implementation is speed and scalability. The single-threaded performance of our 3D code is faster than the state of the art open source meshing tools. Experimental evaluation shows a more than 82% weak scaling efficiency for up to 144 cores, reaching a rate of more than 14.3 million elements per second. This is the first 3D parallel Delaunay refinement method to achieve such a performance, on either distributed or shared-memory architectures. Lastly, this dissertation is the first to develop and examine the sequential and parallel high-quality and fidelity meshing of general space-time 4D multi-tissue domains

Engineering a compact parallel delaunay algorithm in 3d

We describe an implementation of a compact parallel algorithm for 3D Delaunay tetrahedralization on a 64-processor shared-memory machine. Our algorithm uses a concurrent version of the Bowyer-Watson incremental insertion, and a thread-safe space-efficient structure for representing the mesh. Using the implementation we are able to generate significantly larger Delaunay meshes than have previously been generated—10 billion tetrahedra on a 64 processor SMP using 200GB of RAM. The implementation makes use of a locality based relabeling of the vertices that serves three purposes—it is used as part of the space efficient representation, it improves the memory locality, and it reduces the overhead necessary for locks. The implementation also makes use of a caching technique to avoid excessive decoding of vertex information, a technique for backing out of insertions that collide, and a shared work queue for maintaining points that have yet to be inserted