An extension to VORO++ for multithreaded computation of Voronoi cells

VORO++ is a software library written in C++ for computing the Voronoi tessellation, a technique in computational geometry that is widely used for analyzing systems of particles. VORO++ was released in 2009 and is based on computing the Voronoi cell for each particle individually. Here, we take advantage of modern computer hardware, and extend the original serial version to allow for multithreaded computation of Voronoi cells via the OpenMP application programming interface. We test the performance of the code, and demonstrate that we can achieve parallel efficiencies greater than 95% in many cases. The multithreaded extension follows standard OpenMP programming paradigms, allowing it to be incorporated into other programs. We provide an example of this using the VoroTop software library, performing a multithreaded Voronoi cell topology analysis of up to 102.4 million particles.Comment: Fix typo and section number

Methods and Distributed Software for Visualization of Cracks Propagating in Discrete Particle Systems

Scientific visualization is becoming increasingly important in analyzing and interpreting numerical and experimental data sets. Parallel computations of discrete particle systems lead to large data sets that can be produced, stored and visualized on distributed IT infrastructures. However, this leads to very complicated environments handling complex simulation and interactive visualization on the remote heterogeneous architectures. In micro-structure of continuum, broken connections between neighbouring particles can form complex cracks of unknown geometrical shape. The complex disjoint surfaces of cracks with holes and unavailability of a suitable scalar field defining the crack surfaces limit the application of the common surface extraction methods. The main visualization task is to extract the surfaces of cracks according to the connectivity of the broken connections and the geometry of the neighbouring particles. The research aims at enhancing the visualization methods of discrete particle systems and increasing speed of distributed visualization software. The dissertation consists of introduction, three main chapters and general conclusions. In the first Chapter, a literature review on visualization software, distributed environments, discrete element simulation of particle systems and crack visualization methods is presented. In the second Chapter, novel visualization methods were proposed for extraction of crack surfaces from monodispersed particle systems modelled by the discrete element method. The cell cut-based method, the Voronoi-based method and cell centre-based method explicitly define geometry of propagating cracks in fractured regions. The proposed visualization methods were implemented in the grid visualization e–service VizLitG and the distributed visualization software VisPartDEM. Partial data set transfer from the grid storage element was developed to reduce the data transfer and visualization time. In the third Chapter, the results of experimental research are presented. The performance of e-service VizLitG was evaluated in a geographically distributed grid. Different types of software were employed for data transfer in order to present the quantitative comparison. The performance of the developed visualization methods was investigated. The quantitative comparison of the execution time of local Voronoi-based method and that of global Voronoi diagrams generated by Voro++ library was presented. The accuracy of the developed methods was evaluated by computing the total depth of cuts made in particles by the extracted crack surfaces. The present research confirmed that the proposed visualization methods and the developed distributed software were capable of visualizing crack propagation modelled by the discrete element method in monodispersed particulate media

Hierarchical Graphs as Organisational Principle and Spatial Model Applied to Pedestrian Indoor Navigation

In this thesis, hierarchical graphs are investigated from two different angles – as a general modelling principle for (geo)spatial networks and as a practical means to enhance navigation in buildings. The topics addressed are of interest from a multi-disciplinary point of view, ranging from Computer Science in general over Artificial Intelligence and Computational Geometry in particular to other fields such as Geographic Information Science. Some hierarchical graph models have been previously proposed by the research community, e.g. to cope with the massive size of road networks, or as a conceptual model for human wayfinding. However, there has not yet been a comprehensive, systematic approach for modelling spatial networks with hierarchical graphs. One particular problem is the gap between conceptual models and models which can be readily used in practice. Geospatial data is commonly modelled - if at all - only as a flat graph. Therefore, from a practical point of view, it is important to address the automatic construction of a graph hierarchy based on the predominant data models. The work presented deals with this problem: an automated method for construction is introduced and explained. A particular contribution of my thesis is the proposition to use hierarchical graphs as the basis for an extensible, flexible architecture for modelling various (geo)spatial networks. The proposed approach complements classical graph models very well in the sense that their expressiveness is extended: various graphs originating from different sources can be integrated into a comprehensive, multi-level model. This more sophisticated kind of architecture allows for extending navigation services beyond the borders of one single spatial network to a collection of heterogeneous networks, thus establishing a meta-navigation service. Another point of discussion is the impact of the hierarchy and distribution on graph algorithms. They have to be adapted to properly operate on multi-level hierarchies. By investigating indoor navigation problems in particular, the guiding principles are demonstrated for modelling networks at multiple levels of detail. Complex environments like large public buildings are ideally suited to demonstrate the versatile use of hierarchical graphs and thus to highlight the benefits of the hierarchical approach. Starting from a collection of floor plans, I have developed a systematic method for constructing a multi-level graph hierarchy. The nature of indoor environments, especially their inherent diversity, poses an additional challenge: among others, one must deal with complex, irregular, and/or three-dimensional features. The proposed method is also motivated by practical considerations, such as not only finding shortest/fastest paths across rooms and floors, but also by providing descriptions for these paths which are easily understood by people. Beyond this, two novel aspects of using a hierarchy are discussed: one as an informed heuristic exploiting the specific characteristics of indoor environments in order to enhance classical, general-purpose graph search techniques. At the same time, as a convenient by- product of this method, clusters such as sections and wings can be detected. The other reason is to better deal with irregular, complex-shaped regions in a way that instructions can also be provided for these spaces. Previous approaches have not considered this problem. In summary, the main results of this work are: • hierarchical graphs are introduced as a general spatial data infrastructure. In particular, this architecture allows us to integrate different spatial networks originating from different sources. A small but useful set of operations is proposed for integrating these networks. In order to work in a hierarchical model, classical graph algorithms are generalised. This finding also has implications on the possible integration of separate navigation services and systems; • a novel set of core data structures and algorithms have been devised for modelling indoor environments. They cater to the unique characteristics of these environments and can be specifically used to provide enhanced navigation in buildings. Tested on models of several real buildings from our university, some preliminary but promising results were gained from a prototypical implementation and its application on the models

Radial Basis Functions: Biomedical Applications and Parallelization

Radial basis function (RBF) is a real-valued function whose values depend only on the distances between an interpolation point and a set of user-specified points called centers. RBF interpolation is one of the primary methods to reconstruct functions from multi-dimensional scattered data. Its abilities to generalize arbitrary space dimensions and to provide spectral accuracy have made it particularly popular in different application areas, including but not limited to: finding numerical solutions of partial differential equations (PDEs), image processing, computer vision and graphics, deep learning and neural networks, etc. The present thesis discusses three applications of RBF interpolation in biomedical engineering areas: (1) Calcium dynamics modeling, in which we numerically solve a set of PDEs by using meshless numerical methods and RBF-based interpolation techniques; (2) Image restoration and transformation, where an image is restored from its triangular mesh representation or transformed under translation, rotation, and scaling, etc. from its original form; (3) Porous structure design, in which the RBF interpolation used to reconstruct a 3D volume containing porous structures from a set of regularly or randomly placed points inside a user-provided surface shape. All these three applications have been investigated and their effectiveness has been supported with numerous experimental results. In particular, we innovatively utilize anisotropic distance metrics to define the distance in RBF interpolation and apply them to the aforementioned second and third applications, which show significant improvement in preserving image features or capturing connected porous structures over the isotropic distance-based RBF method. Beside the algorithm designs and their applications in biomedical areas, we also explore several common parallelization techniques (including OpenMP and CUDA-based GPU programming) to accelerate the performance of the present algorithms. In particular, we analyze how parallel programming can help RBF interpolation to speed up the meshless PDE solver as well as image processing. While RBF has been widely used in various science and engineering fields, the current thesis is expected to trigger some more interest from computational scientists or students into this fast-growing area and specifically apply these techniques to biomedical problems such as the ones investigated in the present work

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