Communication patterns abstractions for programming SDN to optimize high-performance computing applications

Orientador : Luis Carlos Erpen de BonaCoorientadores : Magnos Martinello; Marcos Didonet Del FabroTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa: Curitiba, 04/09/2017Inclui referências : f. 95-113Resumo: A evolução da computação e das redes permitiu que múltiplos computadores fossem interconectados, agregando seus poderes de processamento para formar uma computação de alto desempenho (HPC). As aplicações que são executadas nesses ambientes processam enormes quantidades de informação, podendo levar várias horas ou até dias para completar suas execuções, motivando pesquisadores de varias áreas computacionais a estudar diferentes maneiras para acelerá-las. Durante o processamento, essas aplicações trocam grandes quantidades de dados entre os computadores, fazendo que a rede se torne um gargalo. A rede era considerada um recurso estático, não permitindo modificações dinâmicas para otimizar seus links ou dispositivos. Porém, as redes definidas por software (SDN) emergiram como um novo paradigma, permitindoa ser reprogramada de acordo com os requisitos dos usuários. SDN já foi usado para otimizar a rede para aplicações HPC específicas mas nenhum trabalho tira proveito dos padrões de comunicação expressos por elas. Então, o principal objetivo desta tese é pesquisar como esses padrões podem ser usados para ajustar a rede, criando novas abstrações para programá-la, visando acelerar as aplicações HPC. Para atingir esse objetivo, nós primeiramente pesquisamos todos os níveis de programabilidade do SDN. Este estudo resultou na nossa primeira contribuição, a criação de uma taxonomia para agrupar as abstrações de alto nível oferecidas pelas linguagens de programação SDN. Em seguida, nós investigamos os padrões de comunicação das aplicações HPC, observando seus comportamentos espaciais e temporais através da análise de suas matrizes de tráfego (TMs). Concluímos que as TMs podem representar as comunicações, além disso, percebemos que as aplicações tendem a transmitir as mesmas quantidades de dados entre os mesmos nós computacionais. A segunda contribuição desta tese é o desenvolvimento de um framework que permite evitar os fatores da rede que podem degradar o desempenho das aplicações, tais como, sobrecarga imposta pela topologia, o desbalanceamento na utilização dos links e problemas introduzidos pela programabilidade do SDN. O framework disponibiliza uma API e mantém uma base de dados de TMs, uma para cada padrão de comunicação, anotadas com restrições de largura de banda e latência. Essas informações são usadas para reprogramar os dispositivos da rede, alocando uniformemente as comunicações nos caminhos da rede. Essa abordagem reduziu o tempo de execução de benchmarks e aplicações reais em até 26.5%. Para evitar que o código da aplicação fosse modificado, como terceira contribuição, desenvolvemos um método para identificar automaticamente os padrões de comunicação. Esse método gera texturas visuais di_erentes para cada TM e, através de técnicas de aprendizagem de máquina (ML), identifica as aplicações que estão usando a rede. Em nossos experimentos, o método conseguiu uma taxa de acerto superior a 98%. Finalmente, nós incorporamos esse método ao framework, criando uma abstração que permite programar a rede sem a necessidade de alterar as aplicações HPC, diminuindo em média 15.8% seus tempos de execução. Palavras-chave: Redes Definidas por Software, Padrões de Comunicação, Aplicações HPC.Abstract: The evolution of computing and networking allowed multiple computers to be interconnected, aggregating their processing powers to form a high-performance computing (HPC). Applications that run in these computational environments process huge amounts of information, taking several hours or even days to complete their executions, motivating researchers from various computational fields to study different ways for accelerating them. During the processing, these applications exchange large amounts of data among the computers, causing the network to become a bottleneck. The network was considered a static resource, not allowing dynamic adjustments for optimizing its links or devices. However, Software-Defined Networking (SDN) emerged as a new paradigm, allowing the network to be reprogrammed according to users' requirements. SDN has already been used to optimize the network for specific HPC applications, but no existing work takes advantage of the communication patterns expressed by those applications. So, the main objective of this thesis is to research how these patterns can be used for tuning the network, creating new abstractions for programming it, aiming to speed up HPC applications. To achieve this goal, we first surveyed all SDN programmability levels. This study resulted in our first contribution, the creation of a taxonomy for grouping the high-level abstractions offered by SDN programming languages. Next, we investigated the communication patterns of HPC applications, observing their spatial and temporal behaviors by analyzing their traffic matrices (TMs). We conclude that TMs can represent the communications, furthermore, we realize that the applications tend to transmit the same amount of data among the same computational nodes. The second contribution of this thesis is the development of a framework for avoiding the network factors that can degrade the performance of applications, such as topology overhead, unbalanced links, and issues introduced by the SDN programmability. The framework provides an API and maintains a database of TMs, one for each communication pattern, annotated with bandwidth and latency constraints. This information is used to reprogram network devices, evenly placing the communications on the network paths. This approach reduced the execution time of benchmarks and real applications up to 26.5%. To prevent the application's source code to be modified, as a third contribution of our work, we developed a method to automatically identify the communication patterns. This method generates different visual textures for each TM and, through machine learning (ML) techniques, identifies the applications using the network. In our experiments the method succeeded with an accuracy rate over 98%. Finally, we incorporate this method into the framework, creating an abstraction that allows programming the network without changing the HPC applications, reducing on average 15.8% their execution times. Keywords: Software-Defined Networking, Communication Patterns, HPC Applications

Volumetric Medical Images Visualization on Mobile Devices

Volumetric medical images visualization is an important tool in the diagnosis and treatment of diseases. Through history, one of the most dificult tasks for Medicine Specialists has been the accurate location of broken bones and of the damaged tissues during Chemotherapy treatment, among other applications; like techniques used in Neurological Studies. Thus these situations enhance the need of visualization in Medicine. New technologies, the improvement and development of new hardware as well as software and the updating of old ones for graphic applications have resulted in specialized systems for medical visualization. However the use of these techniques in mobile devices has been poor due to its low performance. In our work, we propose a client-server scheme, where the model is compressed in the server side and is reconstructed in a nal thin-client device. The technique restricts the natural density values to achieve good bone visualization in medical models, transforming the rest of the data to zero. Our proposal uses a tridimensional Haar Wavelet Function locally applied inside units blocks of 16x16x16, similar to the Wavelet Based 3D Compression Scheme for Interactive Visualization of Very Large Volume Data approach. We also implement a quantization algorithm which handles error coeficients according to the frequency distributions of these coe cients. Finally, we made an evaluation of the volume visualization; on current mobile devices .We present the speci cations for the implementation of our technique in the Nokia n900 Mobile Phone

ICASE/LaRC Symposium on Visualizing Time-Varying Data

Time-varying datasets present difficult problems for both analysis and visualization. For example, the data may be terabytes in size, distributed across mass storage systems at several sites, with time scales ranging from femtoseconds to eons. In response to these challenges, ICASE and NASA Langley Research Center, in cooperation with ACM SIGGRAPH, organized the first symposium on visualizing time-varying data. The purpose was to bring the producers of time-varying data together with visualization specialists to assess open issues in the field, present new solutions, and encourage collaborative problem-solving. These proceedings contain the peer-reviewed papers which were presented at the symposium. They cover a broad range of topics, from methods for modeling and compressing data to systems for visualizing CFD simulations and World Wide Web traffic. Because the subject matter is inherently dynamic, a paper proceedings cannot adequately convey all aspects of the work. The accompanying video proceedings provide additional context for several of the papers

Shape based classification and functional forecast of traffic flow profiles

This dissertation proposes a methodology for traffic flow pattern analysis, its validation, and forecasting. The shape of the daily traffic flows are directly related to the commuter’s traffic behavior which merit analysis based on their shape characteristics. As a departure from the traditional approaches, this research proposed a methodology based on shape for traffic flow analysis. Specifically, Granulometric Size Distributions (GSDs) were used to achieve classification of daily traffic flow patterns. A mathematical morphology method was used that allows the clustering of shapes. The proposed methodology leads to discovery of interesting daily traffic phenomena such as five normal daily traffic shapes beside abnormal shapes representing accidents, congestion behavior, peak time fluctuations, and malfunctioning sensors. To ascertain the significance of shape in traffic analysis, the proposed methodology was validated through a comparative classification analysis of the original data and GSD transformed data using the Back Prorogation Neural Network (BPNN). Results demonstrated that through shape based clustering more appropriate grouping can be accomplished that can result in better estimates of model parameters. Lastly, a functional time series approach was proposed to forecast traffic flow for short and medium-term horizons. It is based on functional principal components decomposition to forecast three different traffic scenarios. Real-time forecast scenarios of partially observed traffic profiles through Penalized Least squares (PLS) technique were also demonstrated. Functional methods outperform the conventional ARIMA model in both short and medium-term forecast horizons. In addition, performance of functional methods in forecasting beyond one hour was also found to be robust and consistent. --Abstract, page iii

Object Recognition

Vision-based object recognition tasks are very familiar in our everyday activities, such as driving our car in the correct lane. We do these tasks effortlessly in real-time. In the last decades, with the advancement of computer technology, researchers and application developers are trying to mimic the human's capability of visually recognising. Such capability will allow machine to free human from boring or dangerous jobs

Análise de multidões usando coerência de vizinhança local

Large numbers of crowd analysis methods using computer vision have been developed in the past years. This dissertation presents an approach to explore characteristics inherent to human crowds – proxemics, and neighborhood relationship – with the purpose of extracting crowd features and using them for crowd flow estimation and anomaly detection and localization. Given the optical flow produced by any method, the proposed approach compares the similarity of each flow vector and its neighborhood using the Mahalanobis distance, which can be obtained in an efficient manner using integral images. This similarity value is then used either to filter the original optical flow or to extract features that describe the crowd behavior in different resolutions, depending on the radius of the personal space selected in the analysis. To show that the extracted features are indeed relevant, we tested several classifiers in the context of abnormality detection. More precisely, we used Recurrent Neural Networks, Dense Neural Networks, Support Vector Machines, Random Forest and Extremely Random Trees. The two developed approaches (crowd flow estimation and abnormality detection) were tested on publicly available datasets involving human crowded scenarios and compared with state-of-the-art methods.Métodos para análise de ambientes de multidões são amplamente desenvolvidos na área de visão computacional. Esta tese apresenta uma abordagem para explorar características inerentes às multidões humanas - comunicação proxêmica e relações de vizinhança - para extrair características de multidões e usá-las para estimativa de fluxo de multidões e detecção e localização de anomalias. Dado o fluxo óptico produzido por qualquer método, a abordagem proposta compara a similaridade de cada vetor de fluxo e sua vizinhança usando a distância de Mahalanobis, que pode ser obtida de maneira eficiente usando imagens integrais. Esse valor de similaridade é então utilizado para filtrar o fluxo óptico original ou para extrair informações que descrevem o comportamento da multidão em diferentes resoluções, dependendo do raio do espaço pessoal selecionado na análise. Para mostrar que as características são realmente relevantes, testamos vários classificadores no contexto da detecção de anormalidades. Mais precisamente, usamos redes neurais recorrentes, redes neurais densas, máquinas de vetores de suporte, floresta aleatória e árvores extremamente aleatórias. As duas abordagens desenvolvidas (estimativa do fluxo de multidões e detecção de anormalidades) foram testadas em conjuntos de dados públicos, envolvendo cenários de multidões humanas e comparados com métodos estado-da-arte