Comparison of Lagrangian Coherent Structures and Relative Dispersion in a Mixing Layer

Thesis (Master's)--University of Washington, 2016-06

Semi-Smooth Newton Methods for the Time Optimal Control of Nonautonomous Ordinary Differential Equations

AMS Subj. Classification: 49J15, 49M15

Multi-threaded parallel numerical modelling of femtosecond pulse propagation in laser machining

Femtosecond laser microfabrication has emerged over the last decade as a 3D flexible technology in photonics. Numerical simulations provide an important insight into spatial and temporal beam and pulse shaping during the course of extremely intricate nonlinear propagation (see e.g. [1,2]). Electromagnetics of such propagation is typically described in the form of the generalized Non-Linear Schrdinger Equation (NLSE) coupled with Drude model for plasma [3]. In this paper we consider a multi-threaded parallel numerical solution for a specific model which describes femtosecond laser pulse propagation in transparent media [4, 5]. However our approach can be extended to similar models. The numerical code is implemented in NVIDIA Graphics Processing Unit (GPU) which provides an effitient hardware platform for multi-threded computing. We compare the performance of the described below parallel code implementated for GPU using CUDA programming interface [3] with a serial CPU version used in our previous papers [4,5]. © 2011 IEEE.

Analisi della propagazione elettrica nel tessuto cardiaco mediante simulazione numerica implementata su GPU

Il segnale elettrico si propaga nel tessuto cardiaco attraverso gap-junctions che si trovano tra i miociti cardiaci e in ciascuno di essi si avvia un processo chiamato potenziale d'azione (PA). In questa tesi prenderò in considerazione il modello Luo-Rudy 1991 e il difetto oggetto di studio sono le Early Afterdepolarizations (EADs). Si analizzerà la propagazione del potenziale d’azione in un cavo di 300 cellule. Dopo alcune simulazioni preliminari è emersa l’utilità di trovare una soluzione che permettesse di ridurre i tempi di calcolo, il modello è stato quindi implementato in CUDA. Il lavoro è stato sviluppato nei seguenti step: 1) l’impiego dell’ambiente di calcolo MATLAB per implementare il modello, descrivendo ogni cellula attraverso il modello Luo-Rudy 1991 e l’interazione elettrica inter-cellulare, considerando un cavo di 300 cellule; 2) individuazione dei parametri che, adeguatamente modificati, sono in grado di indurre EADs a livello single cell; 3) implementazione del modello in CUDA, creando uno strumento che potrà essere utilizzato per aumentare notevolmente il numero delle simulazioni nell’unità di tempo; 4) messa a punto di un criterio per valutare in modo conciso la bontà (safety factor) della relazione source-sink. L’utilità di un simile criterio è quella di valutare, sia nel caso di propagazione di AP che in quello di eventuale propagazione di EADs, la propensione alla propagazione in un tessuto. Il primo capitolo descriverà il potenziale d’azione, il modello usato e la teoria del cavo. Il secondo capitolo discuterà l’implementazione del modello usato, descriverà CUDA e come il modello sia stato implementato. Il terzo capitolo riguarderà i primi risultati ottenuti dalle simulazioni e come la variazione dei parametri influisce sulla forma delle EADs. L’ultimo capitolo approfondirà i requisiti necessari per far avvenire una propagazione in un cavo.

Computação de alto desempenho aplicada a modelagem numérica de fenômenos atmosféricos

A constante evolução da tecnologia disponibilizou, atualmente, ferramentas computacionais que eram apenas expectativas há 10 anos atrás. O aumento do potencial computacional aplicado a modelos numéricos que simulam a atmosfera permitiu ampliar o estudo de fenômenos atmosféricos, através do uso de ferramentas de computação de alto desempenho. O trabalho propôs o desenvolvimento de algoritmos com base em arquiteturas SIMT e aplicação de técnicas de paralelismo com uso da ferramenta OpenACC para processamento de dados de previsão numérica do modelo Weather Research and Forecast. Esta proposta tem forte conotação interdisciplinar, buscando a interação entre as áreas de modelagem atmosférica e computação científica. Foram testadas a influência da computação do cálculo de microfísica de nuvens na degradação temporal do modelo. Como a entrada de dados para execução na GPU não era suficientemente grande, o tempo necessário para transferir dados da CPU para a GPU foi maior do que a execução da computação na CPU. Outro fator determinante foi a adição de código CUDA dentro de um contexto MPI, causando assim condições de disputa de recursos entre os processadores, mais uma vez degradando o tempo de execução. A proposta do uso de diretivas para aplicar computação de alto desempenho em uma estrutura CUDA parece muito promissora, mas ainda precisa ser utilizada com muita cautela a fim de produzir bons resultados. A construção de um híbrido MPI + CUDA foi testada, mas os resultados não foram conclusivos.

Random path sampling applied to vector models of magnetism

The recently reported Monte Carlo Random Path Sampling method (RPS) is here improved and its application is expanded to the study of the 2D and 3D Ising and discrete Heisenberg models. The methodology was implemented to allow use in both CPU-based high-performance computing infrastructures (C/MPI) and GPU-based (CUDA) parallel computation, with significant computational performance gains. Convergence is discussed, both in terms of free energy and magnetization dependence on field/temperature. From the calculated magnetization-energy joint density of states, fast calculations of field and temperature dependent thermodynamic properties are performed, including the effects of anisotropy on coercivity, and the magnetocaloric effect. The emergence of first-order magneto-volume transitions in the compressible Ising model is interpreted using the Landau theory of phase transitions. Using metallic Gadolinium as a real-world example, the possibility of using RPS as a tool for computational magnetic materials design is discussed. Experimental magnetic and structural properties of a Gadolinium single crystal are compared to RPS-based calculations using microscopic parameters obtained from Density Functional Theory.

Supercomputación gráfica aplicada al análisis de imágenes cerebrales con niftyreg

Abstract: Medical image processing in general and brain image processing in particular are computationally intensive tasks. Luckily, their use can be liberalized by means of techniques such as GPU programming. In this article we study NiftyReg, a brain image processing library with a GPU implementation using CUDA, and analyse different possible ways of further optimising the existing codes. We will focus on fully using the memory hierarchy and on exploiting the computational power of the CPU. The ideas that lead us towards the different attempts to change and optimize the code will be shown as hypotheses, which we will then test empirically using the results obtained from running the application. Finally, for each set of related optimizations we will study the validity of the obtained results in terms of both performance and the accuracy of the resulting images.

Procesamiento de imágenes cerebrales en GPU

Abstract: As time has passed, the general purpose programming paradigm has evolved, producing different hardware architectures whose characteristics differ widely. In this work, we are going to demonstrate, through different applications belonging to the field of Image Processing, the existing difference between three Nvidia hardware platforms: two of them belong to the GeForce graphics cards series, the GTX 480 and the GTX 980 and one of the low consumption platforms which purpose is to allow the execution of embedded applications as well as providing an extreme efficiency: the Jetson TK1. With respect to the test applications we will use five examples from Nvidia CUDA Samples. These applications are directly related to Image Processing, as the algorithms they use are similar to those from the field of medical image registration. After the tests, it will be proven that GTX 980 is both the device with the highest computational power and the one that has greater consumption, it will be seen that Jetson TK1 is the most efficient platform, it will be shown that GTX 480 produces more heat than the others and we will learn other effects produced by the existing difference between the architecture of the devices.

A three-dimensional representation method for noisy point clouds based on growing self-organizing maps accelerated on GPUs

The research described in this thesis was motivated by the need of a robust model capable of representing 3D data obtained with 3D sensors, which are inherently noisy. In addition, time constraints have to be considered as these sensors are capable of providing a 3D data stream in real time. This thesis proposed the use of Self-Organizing Maps (SOMs) as a 3D representation model. In particular, we proposed the use of the Growing Neural Gas (GNG) network, which has been successfully used for clustering, pattern recognition and topology representation of multi-dimensional data. Until now, Self-Organizing Maps have been primarily computed offline and their application in 3D data has mainly focused on free noise models, without considering time constraints. It is proposed a hardware implementation leveraging the computing power of modern GPUs, which takes advantage of a new paradigm coined as General-Purpose Computing on Graphics Processing Units (GPGPU). The proposed methods were applied to different problem and applications in the area of computer vision such as the recognition and localization of objects, visual surveillance or 3D reconstruction.

Appraisal of open software for finite element simulation of 2D metal sheet laser cut.

FEA simulation of thermal metal cutting is central to interactive design and manufacturing. It is therefore relevant to assess the applicability of FEA open software to simulate 2D heat transfer in metal sheet laser cuts. Application of open source code (e.g. FreeFem++, FEniCS, MOOSE) makes possible additional scenarios (e.g. parallel, CUDA, etc.), with lower costs. However, a precise assessment is required on the scenarios in which open software can be a sound alternative to a commercial one. This article contributes in this regard, by presenting a comparison of the aforementioned freeware FEM software for the simulation of heat transfer in thin (i.e. 2D) sheets, subject to a gliding laser point source. We use the commercial ABAQUS software as the reference to compare such open software. A convective linear thin sheet heat transfer model, with and without material removal is used. This article does not intend a full design of computer experiments. Our partial assessment shows that the thin sheet approximation turns to be adequate in terms of the relative error for linear alumina sheets. Under mesh resolutions better than 10e−5 m , the open and reference software temperature differ in at most 1 % of the temperature prediction. Ongoing work includes adaptive re-meshing, nonlinearities, sheet stress analysis and Mach (also called ‘relativistic’) effects.

Contributions to 3D Data Registration and Representation

Nowadays, new computers generation provides a high performance that enables to build computationally expensive computer vision applications applied to mobile robotics. Building a map of the environment is a common task of a robot and is an essential part to allow the robots to move through these environments. Traditionally, mobile robots used a combination of several sensors from different technologies. Lasers, sonars and contact sensors have been typically used in any mobile robotic architecture, however color cameras are an important sensor due to we want the robots to use the same information that humans to sense and move through the different environments. Color cameras are cheap and flexible but a lot of work need to be done to give robots enough visual understanding of the scenes. Computer vision algorithms are computational complex problems but nowadays robots have access to different and powerful architectures that can be used for mobile robotics purposes. The advent of low-cost RGB-D sensors like Microsoft Kinect which provide 3D colored point clouds at high frame rates made the computer vision even more relevant in the mobile robotics field. The combination of visual and 3D data allows the systems to use both computer vision and 3D processing and therefore to be aware of more details of the surrounding environment. The research described in this thesis was motivated by the need of scene mapping. Being aware of the surrounding environment is a key feature in many mobile robotics applications from simple robotic navigation to complex surveillance applications. In addition, the acquisition of a 3D model of the scenes is useful in many areas as video games scene modeling where well-known places are reconstructed and added to game systems or advertising where once you get the 3D model of one room the system can add furniture pieces using augmented reality techniques. In this thesis we perform an experimental study of the state-of-the-art registration methods to find which one fits better to our scene mapping purposes. Different methods are tested and analyzed on different scene distributions of visual and geometry appearance. In addition, this thesis proposes two methods for 3d data compression and representation of 3D maps. Our 3D representation proposal is based on the use of Growing Neural Gas (GNG) method. This Self-Organizing Maps (SOMs) has been successfully used for clustering, pattern recognition and topology representation of various kind of data. Until now, Self-Organizing Maps have been primarily computed offline and their application in 3D data has mainly focused on free noise models without considering time constraints. Self-organising neural models have the ability to provide a good representation of the input space. In particular, the Growing Neural Gas (GNG) is a suitable model because of its flexibility, rapid adaptation and excellent quality of representation. However, this type of learning is time consuming, specially for high-dimensional input data. Since real applications often work under time constraints, it is necessary to adapt the learning process in order to complete it in a predefined time. This thesis proposes a hardware implementation leveraging the computing power of modern GPUs which takes advantage of a new paradigm coined as General-Purpose Computing on Graphics Processing Units (GPGPU). Our proposed geometrical 3D compression method seeks to reduce the 3D information using plane detection as basic structure to compress the data. This is due to our target environments are man-made and therefore there are a lot of points that belong to a plane surface. Our proposed method is able to get good compression results in those man-made scenarios. The detected and compressed planes can be also used in other applications as surface reconstruction or plane-based registration algorithms. Finally, we have also demonstrated the goodness of the GPU technologies getting a high performance implementation of a CAD/CAM common technique called Virtual Digitizing.

Algoritmo paralelo para determinação de autovalores de matrizes hermitianas

Dissertação (mestrado)–Universidade de Brasília, Universidade UnB de Planaltina, Programa de Pós-Graduação em Ciência de Materiais, 2015.

Visualization of flow fields in the web platform

Visualization of vector fields plays an important role in research activities nowadays -- Web applications allow a fast, multi-platform and multi-device access to data, which results in the need of optimized applications to be implemented in both high-performance and low-performance devices -- Point trajectory calculation procedures usually perform repeated calculations due to the fact that several points might lie over the same trajectory -- This paper presents a new methodology to calculate point trajectories over highly-dense and uniformly-distributed grid of points in which the trajectories are forced to lie over the points in the grid -- Its advantages rely on a highly parallel computing architecture implementation and in the reduction of the computational effort to calculate the stream paths since unnecessary calculations are avoided, reusing data through iterations -- As case study, the visualization of oceanic currents through in the web platform is presented and analyzed, using WebGL as the parallel computing architecture and the rendering Application Programming Interface

Sistema integrado de generación de mapas de profundidad para videoconferencia 3D en tiempo real

This paper presents the implementation of a high quality real-time 3D video system intended for 3D videoconferencing -- Basically, the system is able to extract depth information from a pair of images coming from a short-baseline camera setup -- The system is based on the use of a variant of the adaptive support-weight algorithm to be applied on GPU-based architectures -- The reason to do it is to get real-time results without compromising accuracy and also to reduce costs by using commodity hardware -- The complete system runs over the GStreamer multimedia software platform to make it even more flexible -- Moreover, an autoestereoscopic display has been used as the end-up terminal for 3D content visualization

Esquemas de volúmenes finitos de alto orden: implementación en GPUs y aplicación a la simulación de flujos geofísicos

En esta tesis doctoral se exponen los fundamentos teóricos necesarios en el diseño de esquemas numéricos de volúmenes finitos para sistemas hiperbólicos no conservativos de una y dos dimensiones. Para el caso unidimensional se repasan los conceptos de esquema camino-conservativo y esquema bien equilibrado, así como la extensión de los esquemas numéricos a alto orden, basados en la reconstrucción de estados. En particular, se presentan los esquemas de tipo PVM (Polynomial Viscosity Matrix), así como diversos esquemas de limitadores de flujo que resultan de la extensión natural del método WAF, utilizando como base algunos esquemas de tipo PVM. Para el caso bidimensional se aborda el diseño de esquemas numéricos camino-conservativos y bien equilibrados de volúmenes finitos para sistemas hiperbólicos no conservativos y su extensión a alto orden, en particular se presenta una reconstrucción de estados de tercer orden compacta y que resulta de la combinación WENO de paraboloides y planos. 
 Se presenta además el desarrollo de métodos numéricos para el sistema de aguas someras bidimensional de una capa. En particular se definen esquemas de primer orden de tipo HLL y FORCE y su extensión a alto orden, un método de limitadores de flujo basado en el esquema HLL-WAF, así como su implementación en arquitecturas de tipo GPU, usando el entorno de programación CUDA. A continuación, se presenta un esquema numérico de orden uno para el sistema de aguas someras de una capa bidimensional en coordenadas esféricas (longitud/latitud), así como la extensión natural del método de limitadores de flujo presentado en el Capítulo 3 a este sistema. Finalmente, se presenta la validación del esquema de limitadores de flujo mediante la simulación de tsunamis reales, y la comparación con datos de campo.