A Parallel Mesh-Adaptive Framework for Hyperbolic Conservation Laws

We report on the development of a computational framework for the parallel, mesh-adaptive solution of systems of hyperbolic conservation laws like the time-dependent Euler equations in compressible gas dynamics or Magneto-Hydrodynamics (MHD) and similar models in plasma physics. Local mesh refinement is realized by the recursive bisection of grid blocks along each spatial dimension, implemented numerical schemes include standard finite-differences as well as shock-capturing central schemes, both in connection with Runge-Kutta type integrators. Parallel execution is achieved through a configurable hybrid of POSIX-multi-threading and MPI-distribution with dynamic load balancing. One- two- and three-dimensional test computations for the Euler equations have been carried out and show good parallel scaling behavior. The Racoon framework is currently used to study the formation of singularities in plasmas and fluids.Comment: late submissio

Parallel Query Processing on 2D Mesh and Linear Array Architectures

As the size of the web grows, it is necessary to parallelize the process of retrieving information from the web. Incorporating parallelism in search engines is one of the approaches towards achieving this aim. This paper presents an algorithm for query processing on the 2D mesh architecture and two algorithms for linear array architectures. We attempt to exploit the arrangement of processors and the communication pattern in both 2D mesh and linear array architectures to attain high speedup and efficiency for queries-keywords comparisons. A cost model is presented for each algorithm based on both processing and communication cost. Proposed algorithms are evaluated using speedup and efficiency performance metrics. For the same number of processors, 2D Mesh_QP outperforms both linear array algorithms (LA_QPAKP and LA_QPKE). Keywords: 2D Mesh, Linear Arrays, Parallel computing, Query processin

Management, design and developement of a mesh generation environment using open source software

In this paper we present an object oriented implementation of a general-purpose mesh generation environment for geometry-based simulations. The aim of this application is to unify available legacy code and new research algorithms in only one mesh generation suite. We focus in two aspects that can be of the general interest for managers, designers and developers of similar projects. On the one hand, we analyze the software engineering practices that we have followed in the management and development process. In addition, we detail and discuss the Open Source tools and libraries that we have used. On the other hand, we discuss the design and the data structure of the environment. In particular, we first summarize the topological and geometrical representation. Second, we detail our implementation of the hierarchical mesh generation structure. Third we present our design to mediate collaboration between classes. Finally, we present some of the mesh generation features to show the capabilities of the environment

Evaluation of Single-Chip, Real-Time Tomographic Data Processing on FPGA - SoC Devices

A novel approach to tomographic data processing has been developed and evaluated using the Jagiellonian PET (J-PET) scanner as an example. We propose a system in which there is no need for powerful, local to the scanner processing facility, capable to reconstruct images on the fly. Instead we introduce a Field Programmable Gate Array (FPGA) System-on-Chip (SoC) platform connected directly to data streams coming from the scanner, which can perform event building, filtering, coincidence search and Region-Of-Response (ROR) reconstruction by the programmable logic and visualization by the integrated processors. The platform significantly reduces data volume converting raw data to a list-mode representation, while generating visualization on the fly.Comment: IEEE Transactions on Medical Imaging, 17 May 201

A framework for local terrain deformation based on diffusion theory

Terrains have a key role in making outdoor virtual scenes believable and immersive as they form the support for every other natural element in the scene. Although important, terrains are often given limited interactivity in real-time applications. However, in nature, terrains are dynamic and interact with the rest of the environment changing shape on different levels, from tracks left by a person running on a gravel soil (micro-scale), to avalanches on the side of a mountain (macro-scale). The challenge in representing dynamic terrains correctly is that the soil that forms them is vastly heterogeneous and behaves differently depending on its composition. This heterogeneity introduces difficulties at different levels in dynamic terrains simulations, from modelling the large amount of different elements that compose the oil to simulating their dynamic behaviour. This work presents a novel framework to simulate multi-material dynamic terrains by taking into account the soil composition and its heterogeneity. In the proposed framework soil information is obtained from a material description map applied to the terrain mesh. This information is used to compute deformations in the area of interaction using a novel mathematical model based on diffusion theory. The deformations are applied to the terrain mesh in different ways depending on the distance of the area of interaction from the camera and the soil material. Deformations away from the camera are simulated by dynamically displacing normals. While deformations in a neighbourhood of the camera are represented by displacing the terrain mesh, which is locally tessellated to better fit the displacement. For gravel based soils the terrain details are added near the camera by reconstructing the meshes of the small rocks from the texture image, thus simulating both micro and macro-structure of the terrain. The outcome of the framework is a realistic interactive dynamic terrain animation in real-time

A distributed multi-threaded data partitioner with space-filling curve orders

The problem discussed in this thesis is distributed data partitioning and data re-ordering on many-core architectures. We present extensive literature survey, with examples from various application domains - scientific computing, databases and large-scale graph processing. We propose a low-overhead partitioning framework based on geometry, that can be used to partition multi-dimensional data where the number of dimensions is >=2. The partitioner linearly orders items with good spatial locality. Partial output is stored on each process in the communication group. Space-filling curves are used to permute data - Morton order is the default curve. For dimensions <=3, we have options to generate Hilbert-like curves. Two metrics used to determine partitioning overheads are memory consumption and execution time, although these two factors are dependent on each other. The focus of this thesis is to reduce partitioning overheads as much as possible. We have described several optimizations to this end - incremental adjustments to partitions, careful dynamic memory management and using multi-threading and multi-processing to advantage. The quality of partitions is an important criteria for evaluating a partitioner. We have used graph partitioners as base-implementations against which our partitions are compared. The degree and edge-cuts of our partitions are comparable to graph partitions for regular grids. For irregular meshes, there is still room for improvement. No comparisons have been made for evaluating partitions of datasets without edges. We have deployed these partitions on two large applications - atmosphere simulation in 2D and adaptive mesh refinement in 3D. An adaptive mesh refinement benchmark was built to be part of the framework, which later became a testcase for evaluating partitions and load-balancing schemes. The performance of this benchmark is discussed in detail in the last chapter