High-performance parallel systems for data-intensive computing

Thesis (Ph.D.)--University of Washington, 2016-08

Applications of a Collaborative Open Object Oriented Learning Environment to Electronics, Computing and Mathematics Education

A lightweight Java application suite has been developed and deployed allowing collaborative learning between students and tutors at remote locations. Students can engage in group activities online and also collaborate with tutors. A generic Java framework has been developed and applied to electronics, computing and mathematics education. The applications are respectively: (a) a digital circuit simulator, which allows students to collaborate in building simple or complex electronic circuits; (b) a Java programming environment where the paradigm is behavioural-based robotics, and (c) a differential equation solver useful in modelling of any complex and nonlinear dynamic system. Each student sees a common shared window on which may be added text or graphical objects and which can then be shared online. A built-in chat room supports collaborative dialogue. Students can work either in collaborative groups or else in teams as directed by the tutor. This paper summarises the technical architecture of the system as well as the pedagogical implications of the suite. A report of student evaluation is also presented distilled from use over a period of twelve months. We intend this suite to facilitate learning between groups at one or many institutions and to facilitate international collaboration. We also intend to use the suite as a tool to research the establishment and behaviour of collaborative learning groups. We shall make our software freely available to interested researchers.

The stochastic geometric machine model

This paper introduces the stochastic version of the Geometric Machine Model for the modelling of sequential, alternative, parallel (synchronous) and nondeterministic computations with stochastic numbers stored in a (possibly infinite) shared memory. The programming language L(D! 1), induced by the Coherence Space of Processes D! 1, can be applied to sequential and parallel products in order to provide recursive definitions for such processes, together with a domain-theoretic semantics of the Stochastic Arithmetic. We analyze both the spacial (ordinal) recursion, related to spacial modelling of the stochastic memory, and the temporal (structural) recursion, given by the inclusion relation modelling partial objects in the ordered structure of process construction.

Separate compilation of structured documents

This paper draws a parallel between document preparation and the traditional processes of compilation and link editing for computer programs. A block-based document model is described which allows for separate compilation of various portions of a document. These portions are brought together and merged by a linker program, called dlink, whose pilot implementation is based on ditroff and on its underlying intermediate code. In the light of experiences with dlink the requirements for a universal object-module language for documents are discussed. These requirements often resemble the characteristics of the intermediate codes used by programming-language compilers but with interesting extra constraints which arise from the way documents are executed .

Characterizing neural tissues with mass spectrometry imaging via enhanced computational approaches

Neuropeptides affect the activity of the myriad of neuronal circuits in the brain. They are under tight spatial and chemical control and the dynamics of their release and catabolism directly modify neuronal network activity. Understanding neuropeptide functioning requires approaches to determine their chemical and spatial heterogeneity within neural tissue, but most imaging techniques do not provide the complete information desired. To provide chemical information, most imaging techniques used to study the nervous system require preselection and labeling of the peptides of interest; however, mass spectrometry imaging (MSI) detects analytes across a broad mass range without the need to target a specific analyte. When used with matrix-assisted laser desorption/ionization (MALDI), MSI detects analytes in the mass range of neuropeptides. MALDI MSI simultaneously provides spatial and chemical information resulting in images that plot the spatial distributions of neuropeptides over the surface of a thin slice of neural tissue. Here a variety of approaches for neuropeptide characterization are developed. Specifically, several computational approaches are combined with MALDI MSI to create improved approaches that provide spatial distributions and neuropeptide characterizations. After successfully validating these MALDI MSI protocols, the methods are applied to characterize both known and unidentified neuropeptides from neural tissues. The methods are further adapted from tissue analysis to be able to perform tandem MS (MS/MS) imaging on neuronal cultures to enable the study of network formation. In addition, MALDI MSI has been carried out over the timecourse of nervous system regeneration in planarian flatworms resulting in the discovery of two novel neuropeptides that may be involved in planarian regeneration. In addition, several bioinformatic tools are developed to predict final neuropeptide structures and associated masses that can be compared to experimental MSI data in order to make assignments of neuropeptide identities. The integration of computational approaches into the experimental design of MALDI MSI has allowed improved instrument automation and enhanced data acquisition and analysis. These tools also make the methods versatile and adaptable to new sample types.

Rotina computacional de obtenção, tratamento e visualização de dados oceanográficos

Atualmente, sensores remotos e computadores de alto desempenho estão sendo utilizados como instrumentos principais na coleta e produção de dados oceanográficos. De posse destes dados, é possível realizar estudos que permitem simular e prever o comportamento do oceano por meio de modelos numéricos regionais. Dentre os fatores importantes no estudo da oceanografia, podem ser destacados àqueles referentes aos impactos ambientais, de contaminação antrópica, utilização de energias renováveis, operações portuárias e etc. Contudo, devido ao grande volume de dados gerados por instituições ambientais, na forma de resultados de modelos globais como o HYCOM (Hybrid Coordinate Ocean Model) e dos programas de Reanalysis da NOAA (National Oceanic and Atmospheric Administration), torna-se necessária a criação de rotinas computacionais para realizar o tratamento de condições iniciais e de contorno, de modo que possam ser aplicadas a modelos regionais como o TELEMAC3D (www.opentelemac.org). Problemas relacionados a baixa resolução, ausência de dados e a necessidade de interpolação para diferentes malhas ou sistemas de coordenadas verticais, tornam necessária a criação de um mecanismo computacional que realize este tratamento adequadamente. Com isto, foram desenvolvidas rotinas na linguagem de programação Python, empregando interpoladores de vizinho mais próximo, de modo que, a partir de dados brutos dos modelos HYCOM e do programa de Reanalysis da NOAA, foram preparadas condições iniciais e de contorno para a realização de uma simulação numérica teste. Estes resultados foram confrontados com outro resultado numérico onde, as condições foram construídas a partir de um método de interpolação mais sofisticado, escrita em outra linguagem, e que já vem sendo utilizada no laboratório. A análise dos resultados permitiu concluir que, a rotina desenvolvida no âmbito deste trabalho, funciona adequadamente para a geração de condições iniciais e de contorno do modelo TELEMAC3D. Entretanto, um interpolador mais sofisticado deve ser desenvolvido de forma a aumentar a qualidade nas interpolações, otimizar o custo computacional, e produzir condições que sejam mais realísticas para a utilização do modelo TELEMAC3D.

Desenvolvimento de plataforma digital para análise da satisfação dos utentes de unidades de saúde

Este documento descreve o trabalho realizado em conjunto com a empresa MedSUPPORT[1] no desenvolvimento de uma plataforma digital para análise da satisfação dos utentes de unidades de saúde. Atualmente a avaliação de satisfação junto dos seus clientes é um procedimento importante e que deve ser utilizado pelas empresas como mais uma ferramenta de avaliação dos seus produtos ou serviços. Para as unidades de saúde a avaliação da satisfação do utente é atualmente considerada como um objetivo fundamental dos serviços de saúde e tem vindo a ocupar um lugar progressivamente mais importante na avaliação da qualidade dos mesmos. Neste âmbito idealizou-se desenvolver uma plataforma digital para análise da satisfação dos utentes de unidades de saúde. O estudo inicial sobre o conceito da satisfação de consumidores e utentes permitiu consolidar os conceitos associados à temática em estudo. Conhecer as oito dimensões que, de acordo com os investigadores englobam a satisfação do utente é um dos pontos relevantes do estudo inicial. Para avaliar junto do utente a sua satisfação é necessário questiona-lo diretamente. Para efeito desenvolveu-se um inquérito de satisfação estudando cuidadosamente cada um dos elementos que deste fazem parte. No desenvolvimento do inquérito de satisfação foram seguidas as seguintes etapas: Planeamento do questionário, partindo das oito dimensões da satisfação do utente até às métricas que serão avaliadas junto do utente; Análise dos dados a recolher, definindo-se, para cada métrica, se os dados serão nominais, ordinais ou provenientes de escalas balanceadas; Por último a formulação das perguntas do inquérito de satisfação foi alvo de estudo cuidado para garantir que o utente percecione da melhor forma o objetivo da questão. A definição das especificações da plataforma e do questionário passou por diferentes estudos, entre eles uma análise de benchmarking[2], que permitiram definir que o inquérito iv estará localizado numa zona acessível da unidade de saúde, será respondido com recurso a um ecrã táctil (tablet) e que estará alojado na web. As aplicações web desenvolvidas atualmente apresentam um design apelativo e intuitivo. Foi fundamental levar a cabo um estudo do design da aplicação web, como garantia que as cores utilizadas, o tipo de letra, e o local onde a informação são os mais adequados. Para desenvolver a aplicação web foi utilizada a linguagem de programação Ruby, com recurso à framework Ruby on Rails. Para a implementação da aplicação foram estudadas as diferentes tecnologias disponíveis, com enfoque no estudo do sistema de gestão de base de dados a utilizar. O desenvolvimento da aplicação web teve também como objetivo melhorar a gestão da informação gerada pelas respostas ao inquérito de satisfação. O colaborador da MedSUPPORT é o responsável pela gestão da informação pelo que as suas necessidades foram atendidas. Um menu para a gestão da informação é disponibilizado ao administrador da aplicação, colaborador MedSUPPORT. O menu de gestão da informação permitirá uma análise simplificada do estado atual com recurso a um painel do tipo dashboard e, a fim de melhorar a análise interna dos dados terá uma função de exportação dos dados para folha de cálculo. Para validação do estudo efetuado foram realizados os testes de funcionamento à plataforma, tanto à sua funcionalidade como à sua utilização em contexto real pelos utentes inquiridos nas unidades de saúde. Os testes em contexto real objetivaram validar o conceito junto dos utentes inquiridos.

Adaptação do paradigma orientado a notificações para desenvolvimento de sistemas fuzzy

This work proposes to adjust the Notification Oriented Paradigm (NOP) so that it provides support to fuzzy concepts. NOP is inspired by elements of imperative and declarative paradigms, seeking to solve some of the drawbacks of both. By decomposing an application into a network of smaller computational entities that are executed only when necessary, NOP eliminates the need to perform unnecessary computations and helps to achieve better logical-causal uncoupling, facilitating code reuse and application distribution over multiple processors or machines. In addition, NOP allows to express the logical-causal knowledge at a high level of abstraction, through rules in IF-THEN format. Fuzzy systems, in turn, perform logical inferences on causal knowledge bases (IF-THEN rules) that can deal with problems involving uncertainty. Since PON uses IF-THEN rules in an alternative way, reducing redundant evaluations and providing better decoupling, this research has been carried out to identify, propose and evaluate the necessary changes to be made on NOP allowing to be used in the development of fuzzy systems. After that, two fully usable materializations were created: a C++ framework, and a complete programming language (LingPONFuzzy) that provide support to fuzzy inference systems. From there study cases have been created and several tests cases were conducted, in order to validate the proposed solution. The test results have shown a significant reduction in the number of rules evaluated in comparison to a fuzzy system developed using conventional tools (frameworks), which could represent an improvement in performance of the applications.

Raspberry Pi-pohjainen dataloggeri

Dataloggerit ovat tärkeitä mittaustekniikassa käytettäviä mittalaitteita, joiden tarkoituksena on kerätä talteen mittausdataa pitkiltä aikaväleiltä. Dataloggereita voidaan käyttää esimerkiksi teollista prosessia osana olevien toimilaitteiden tai kotitalouden energiajärjestelmän seurannassa. Teollisen luokan dataloggerit ovat yleensä hinnaltaan satojen tai tuhansien eurojen luokkaa. Työssä pyrittiin löytämään teollisen luokan laitteille halpa ja helppokäyttöinen vaihtoehto, joka on kuitenkin riittävän tehokas ja toimiva. Työssä suunniteltiin ja toteutettiin dataloggeri Raspberry Pi-alustalle ja testattiin sitä oikeaa teollista ympäristöä vastaavissa olosuhteissa. Kirjallisuudesta ja internet artikkeleista etsittiin samankaltaisia laite- ja ohjelmistoratkaisuja ja niitä käytettiin dataloggausjärjestelmän pohjana. Raspberry Pi-alustalle koodattiin yksinkertainen Python-kielinen data-loggausohjelma, joka käyttää Modbus-tiedonsiirtoprotokollaa. Testien perusteella voidaan todeta, että toteutettu dataloggeri on toimiva ja kykenee kaupallisten dataloggereiden tasoiseen mittaukseen ainakin pienillä näytteistystaajuuksilla. Toteutettu dataloggeri on myös huomattavasti kaupallisia dataloggereita halvempi. Helppokäyttöisyyden näkökulmasta dataloggerissa havaittiin puutteita, joita käydään läpi jatkokehitysideoiden muodossa.

Estudo comparativo de métodos de regionalização hidrológica e desenvolvimento de um aplicativo para o gerenciamento de outorga de águas superficiais

Dissertação (mestrado)—Universidade de Brasília, Instituto de Geociências, 2016.

Trace Oblivious Program Execution

The big data era has dramatically transformed our lives; however, security incidents such as data breaches can put sensitive data (e.g. photos, identities, genomes) at risk. To protect users' data privacy, there is a growing interest in building secure cloud computing systems, which keep sensitive data inputs hidden, even from computation providers. Conceptually, secure cloud computing systems leverage cryptographic techniques (e.g., secure multiparty computation) and trusted hardware (e.g. secure processors) to instantiate a “secure” abstract machine consisting of a CPU and encrypted memory, so that an adversary cannot learn information through either the computation within the CPU or the data in the memory. Unfortunately, evidence has shown that side channels (e.g. memory accesses, timing, and termination) in such a “secure” abstract machine may potentially leak highly sensitive information, including cryptographic keys that form the root of trust for the secure systems. This thesis broadly expands the investigation of a research direction called trace oblivious computation, where programming language techniques are employed to prevent side channel information leakage. We demonstrate the feasibility of trace oblivious computation, by formalizing and building several systems, including GhostRider, which is a hardware-software co-design to provide a hardware-based trace oblivious computing solution, SCVM, which is an automatic RAM-model secure computation system, and ObliVM, which is a programming framework to facilitate programmers to develop applications. All of these systems enjoy formal security guarantees while demonstrating a better performance than prior systems, by one to several orders of magnitude.

Análise gráfica de estruturas porosas sobre a ótica da estereologia

In this work we developed a computer simulation program for physics porous structures based on programming language C + + using a Geforce 9600 GT with the PhysX chip, originally developed for video games. With this tool, the ability of physical interaction between simulated objects is enlarged, allowing to simulate a porous structure, for example, reservoir rocks and structures with high density. The initial procedure for developing the simulation is the construction of porous cubic structure consisting of spheres with a single size and with varying sizes. In addition, structures can also be simulated with various volume fractions. The results presented are divided into two parts: first, the ball shall be deemed as solid grains, ie the matrix phase represents the porosity, the second, the spheres are considered as pores. In this case the matrix phase represents the solid phase. The simulations in both cases are the same, but the simulated structures are intrinsically different. To validate the results presented by the program, simulations were performed by varying the amount of grain, the grain size distribution and void fraction in the structure. All results showed statistically reliable and consistent with those presented in the literature. The mean values and distributions of stereological parameters measured, such as intercept linear section of perimeter area, sectional area and mean free path are in agreement with the results obtained in the literature for the structures simulated. The results may help the understanding of real structures.

Jogo para aprender a programar

Neste documento foi feita a apresentação do conceito de Programação Visual, estudados alguns exemplos de Linguagens de Programação Visual e investigado vantagens e desvantagens sobre o seu uso comparativamente à programação tradicional (por texto) e, adicionalmente, foram estudados três jogos para aprender a programar com fortes características visuais. A partir desta investigação, foi criada uma nova Linguagem de Programação Visual(LPV) sendo a base de um prototipo de um jogo para aprender a programar. Este jogo é representado pela deslocação e execução de tarefas feitas por um robô dentro de uma casa, sendo o objetivo do programador colocar objetos nesta casa que manipulam a deslocação do robô dentro desta de forma a resolver um problema; Abstract: A game to learn programming Aplication of concepts of visual programming to create a game to learn how to program In this document we will explain the concept of Visual Programming, study some examples of Visual Programming Languages, analyze some arguments in favor and against its use in comparison to traditional programming (by text) and, additionally, study three games to learn programming with strong visual features. Using this research, a new Visual Programming Language(VPL) was created, being the basis of a prototype of a game to learn programming. This game is represented by the movement and execution of tasks done by a robot inside a house, being the goal of the programmer to place objects in this house that manipulate the movement of the robot inside of it in order to solve a problem.

Interoperability Challenges in Internet of Things Systems: a Service-Oriented Computing Approach

Internet of Things systems are pervasive systems evolved from cyber-physical to large-scale systems. Due to the number of technologies involved, software development involves several integration challenges. Among them, the ones preventing proper integration are those related to the system heterogeneity, and thus addressing interoperability issues. From a software engineering perspective, developers mostly experience the lack of interoperability in the two phases of software development: programming and deployment. On the one hand, modern software tends to be distributed in several components, each adopting its most-appropriate technology stack, pushing programmers to code in a protocol- and data-agnostic way. On the other hand, each software component should run in the most appropriate execution environment and, as a result, system architects strive to automate the deployment in distributed infrastructures. This dissertation aims to improve the development process by introducing proper tools to handle certain aspects of the system heterogeneity. Our effort focuses on three of these aspects and, for each one of those, we propose a tool addressing the underlying challenge. The first tool aims to handle heterogeneity at the transport and application protocol level, the second to manage different data formats, while the third to obtain optimal deployment. To realize the tools, we adopted a linguistic approach, i.e.\ we provided specific linguistic abstractions that help developers to increase the expressive power of the programming language they use, writing better solutions in more straightforward ways. To validate the approach, we implemented use cases to show that the tools can be used in practice and that they help to achieve the expected level of interoperability. In conclusion, to move a step towards the realization of an integrated Internet of Things ecosystem, we target programmers and architects and propose them to use the presented tools to ease the software development process.

Big Code Applications and Approaches

The availability of a huge amount of source code from code archives and open-source projects opens up the possibility to merge machine learning, programming languages, and software engineering research fields. This area is often referred to as Big Code where programming languages are treated instead of natural languages while different features and patterns of code can be exploited to perform many useful tasks and build supportive tools. Among all the possible applications which can be developed within the area of Big Code, the work presented in this research thesis mainly focuses on two particular tasks: the Programming Language Identification (PLI) and the Software Defect Prediction (SDP) for source codes. Programming language identification is commonly needed in program comprehension and it is usually performed directly by developers. However, when it comes at big scales, such as in widely used archives (GitHub, Software Heritage), automation of this task is desirable. To accomplish this aim, the problem is analyzed from different points of view (text and image-based learning approaches) and different models are created paying particular attention to their scalability. Software defect prediction is a fundamental step in software development for improving quality and assuring the reliability of software products. In the past, defects were searched by manual inspection or using automatic static and dynamic analyzers. Now, the automation of this task can be tackled using learning approaches that can speed up and improve related procedures. Here, two models have been built and analyzed to detect some of the commonest bugs and errors at different code granularity levels (file and method levels). Exploited data and models’ architectures are analyzed and described in detail. Quantitative and qualitative results are reported for both PLI and SDP tasks while differences and similarities concerning other related works are discussed.