Durch die parallele Programmierung wird ermöglicht, dass Programme nebenläufig auf mehreren CPU-Kernen oder CPUs ausgeführt werden können. Um das parallele Programmieren zu erleichtern, wurden diverse Sprachen (z.B. Erlang) und Bibliotheken (z.B. OpenMP) aufbauend auf parallele Programmiermodelle (z.B. Parallel Random Access Machine) entwickelt. Möchte z.B. ein Softwarearchitekt sich in einem Projekt für ein Programmiermodell entscheiden, muss er dabei auf mehrere wichtige Kriterien (z.B. Abhängigkeiten zur Hardware) achten. erleichternd für diese Suche sind Übersichten, die die Programmiermodelle in diesen Kriterien unterscheiden und ordnen. Werden existierenden Übersichten jedoch betrachtet, finden sich Unterschiede in der Klassifizierung, den verwendeten Begriffen und den aufgeführten Programmiermodellen. Diese Arbeit begleicht dieses Defizit, indem zuerst durch ein Systematic Literature Review die existierenden Taxonomien gesammelt und analysiert werden. Darauf aufbauend wird eine einheitliche Taxonomie erstellt. Mit dieser Taxonomie kann eine Übersicht über die parallelen Programmiermodelle erstellt werden. Diese Übersicht wird zusätzlich durch Informationen zu den jeweiligen Abhängigkeiten der Programmiermodelle zu der Hardware-Architektur erweitert werden. Der Softwarearchitekt (oder Projektleiter, Softwareentwickler,...) kann damit eine informierte Entscheidung treffen und ist nicht gezwungen alle Programmiermodelle einzeln zu analysieren.

Les systèmes de calcul actuels sont généralement des grappes de machines composés de nombreux processeurs à l'architecture fortement hiérarchique. Leur exploitation constitue le défi majeur des implémentations de modèles de programmation tels MPI ou OpenMP. Une pratique courante consiste à mélanger ces deux modèles pour bénéficier des avantages de chacun. Cependant ces modèles n'ont pas été pensés pour fonctionner conjointement ce qui pose des problèmes de performances. Les travaux de cette thèse visent à assister le développeur dans la programmation d'application de type hybride. Il s'appuient sur une analyse de la hiérarchie architecturale du système de calcul pour dimensionner les ressources d'exécution (processus et threads). Plutôt qu'une approche hybride classique, créant un processus MPI multithreadé par noeud, nous évaluons de façon automatique des solutions alternatives, avec plusieurs processus multithreadés par noeud, mieux adaptées aux machines de calcul modernes. / Modern computing servers usually consist in clusters of computers with several multi-core CPUs featuring a highly hierarchical hardware design. The major challenge of the programming models implementations is to efficiently take benefit from these servers. Combining two type of models, like MPI and OpenMP, is a current trend to reach this point. However these programming models haven't been designed to work together and that leads to performance issues. In this thesis, we propose to assist the programmer who develop hybrid applications. We lean on an analysis of the computing system architecture in order to set the number of processes and threads. Rather than a classical hybrid approach, that is to say creating one multithreaded MPI process per node, we automatically evaluate alternative solutions, with several multithreaded processes per node, better fitted to modern computing systems.

Nous assistons à une explosion du nombre d’appareils mobiles équipés de capteurs optiques : smartphones, tablettes, drones... préfigurent un Internet des objets imminent. De nouvelles applications de traitement d’images (filtres, compression, réalité augmentée) exploitent ces capteurs mais doivent répondre à des contraintes fortes de vitesse et d’efficacité énergétique. Les architectures modernes — processeurs manycore, GPUs,... — offrent un potentiel de performance, avec cependant une hausse sensible de la complexité de programmation.L’ambition de cette thèse est de vérifier l’adéquation entre le domaine du traitement d’images et ces architectures modernes : concilier programmabilité, portabilité et performance reste encore aujourd’hui un défi. Le domaine du traitement d’images présente un fort parallélisme intrinsèque, qui peut potentiellement être exploité par les différents niveaux de parallélisme offerts par les architectures actuelles. Nous nous focalisons ici sur le domaine du traitement d’images par morphologie mathématique, et validons notre approche avec l’architecture manycore du processeur MPPA de la société Kalray.Nous prouvons d’abord la faisabilité de chaînes de compilation intégrées, composées de compilateurs, bibliothèques et d’environnements d’exécution, qui à partir de langages de haut niveau tirent parti de différents accélérateurs matériels. Nous nous concentrons plus particulièrement sur les processeurs manycore, suivant les différents modèles de programmation : OpenMP ; langage flot de données ; OpenCL ; passage de messages. Trois chaînes de compilation sur quatre ont été réalisées, et sont accessibles à des applications écrites dans des langages spécifiques au domaine du traitement d’images intégrés à Python ou C. Elles améliorent grandement la portabilité de ces applications, désormais exécutables sur un plus large panel d’architectures cibles.Ces chaînes de compilation nous ont ensuite permis de réaliser des expériences comparatives sur un jeu de sept applications de traitement d’images. Nous montrons que le processeur MPPA est en moyenne plus efficace énergétiquement qu’un ensemble d’accélérateurs matériels concurrents, et ceci particulièrement avec le modèle de programmation flot de données. Nous montrons que la compilation d’un langage spécifique intégré à Python vers un langage spécifique intégré à C permet d’augmenter la portabilité et d’améliorer les performances des applications écrites en Python.Nos chaînes de compilation forment enfin un environnement logiciel complet dédié au développement d’applications de traitement d’images par morphologie mathématique, capable de cibler efficacement différentes architectures matérielles, dont le processeur MPPA, et proposant des interfaces dans des langages de haut niveau. / Many mobile devices now integrate optic sensors; smartphones, tablets, drones... are foreshadowing an impending Internet of Things (IoT). New image processing applications (filters, compression, augmented reality) are taking advantage of these sensors under strong constraints of speed and energy efficiency. Modern architectures, such as manycore processors or GPUs, offer good performance, but are hard to program.This thesis aims at checking the adequacy between the image processing domain and these modern architectures: conciliating programmability, portability and performance is still a challenge today. Typical image processing applications feature strong, inherent parallelism, which can potentially be exploited by the various levels of hardware parallelism inside current architectures. We focus here on image processing based on mathematical morphology, and validate our approach using the manycore architecture of the Kalray MPPA processor.We first prove that integrated compilation chains, composed of compilers, libraries and run-time systems, allow to take advantage of various hardware accelerators from high-level languages. We especially focus on manycore processors, through various programming models: OpenMP, data-flow language, OpenCL, and message passing. Three out of four compilation chains have been developed, and are available to applications written in domain-specific languages (DSL) embedded in C or Python. They greatly improve the portability of applications, which can now be executed on a large panel of target architectures.Then, these compilation chains have allowed us to perform comparative experiments on a set of seven image processing applications. We show that the MPPA processor is on average more energy-efficient than competing hardware accelerators, especially with the data-flow programming model. We show that compiling a DSL embedded in Python to a DSL embedded in C increases both the portability and the performance of Python-written applications.Thus, our compilation chains form a complete software environment dedicated to image processing application development. This environment is able to efficiently target several hardware architectures, among them the MPPA processor, and offers interfaces in high-level languages.

La thèse porte sur la résolution des problèmes de satisfaisabilité booléenne (SAT) dans un cadre massivement parallèle. Le problème SAT est largement utilisé pour résoudre des problèmes combinatoires de première importance comme la vérification formelle de matériels et de logiciels, la bio-informatique, la cryptographie, la planification et l’ordonnancement de tâches. Plusieurs contributions sont apportées dans cette thèse. Elles vont de la conception d’algorithmes basés sur les approches « portfolio » et « diviser pour mieux régner », à l’adaptation de modèles de programmation parallèle, notamment hybride (destinés à des architectures à mémoire partagée et distribuée), à SAT, en passant par l’amélioration des stratégies de résolution. Ce travail de thèse a donné lieu à plusieurs contributions dans des conférences internationales du domaine ainsi qu’à plusieurs outils (open sources) de résolution des problèmes SAT, compétitifs au niveau international. / This thesis deals with propositional satisfiability (SAT) in a massively parallel setting. The SAT problem is widely used for solving several combinatorial problems (e.g. formal verification of hardware and software, bioinformatics, cryptography, planning, scheduling, etc.). The first contribution of this thesis concerns the design of efficient algorithms based on the approaches « portfolio » and « divide and conquer ». Secondly, an adaptation of several parallel programming models including hybrid (parallel and distributed computing) to SAT is proposed. This work has led to several contributions to international conferences and highly competitive distributed SAT solvers.

Made available in DSpace on 2015-03-05T14:01:49Z (GMT). No. of bitstreams: 0 Previous issue date: 22 / Bolsa para curso e programa de Pós Graduação / O presente trabalho propõe o Ubiquitous Oriented Programming (abreviadamente UOP), um modelo de programação orientado ao desenvolvimento de sistemas ubíquos. UOP utiliza os conceitos de Serviços e Orientação a Objetos, integrando-os com os requisitos de aplicações ubíquas como contexto, sensibilidade ao contexto, adaptação ao contexto, mobilidade de código e concorrência. Uma linguagem de programação (UbiLanguage) implementa os conceitos deste novo modelo de programação, provendo assim suporte ao desenvolvimento de sistemas ubíquos. O ambiente de desenvolvimento é composto por um compilador (UbiCompiler) que traduz código escrito em UbiLanguage para bytecode. A plataforma de execução é composta por uma máquina virtual ubíqua (UbiVM) que suporta a execução deste bytecode. / This work presents the Ubiquitous Oriented Programming (UOP in short), a programming model oriented to development of ubiquitous systems. UOP uses Services concepts and Object Oriented Programming, integrating them with the requirements of ubiquitous applications as context, context awareness, context adaptation, code mobility and concurrent. A programming language (UbiLanguage) implements the concepts of this new programming model, thus providing the development of ubiquitous systems. The development environment is composed by a compiler (UbiCompiler) which translates code written in UbiLanguage to bytecode. The execution platform is composed by a virtual machine (UbiVM) which supports the execution of this bytecode.

The scope of this thesis is modelling and solving large-scale planning problems in the supply chain within the forest industry. Five research papers are included, the first three of which focus on the modelling, and the last two on the solution methods. All problems included are tactical multi-commodity problems expressed as mixed integer programming (MIP) models. The work has been done in collaboration with two Swedish companies within the forest industry. In Paper I, a problem concerning the supply chain of forest fuel for Sydved Energileveranser AB is modelled and solved. We study the problem of deciding when and where forest residues are to be converted into wood chips, and how the residues and chips are to be transported and stored in order to satisfy energy demand at heating plants. The company has long-term contracts with forest owners and saw mills. Decisions in the model include whether or not additional harvest areas and saw mills are to be contracted and which terminals to use. The planning horizon is one year and monthly time periods are used. Papers II--V are based on planning problems at Södra Cell AB. The planning horizon is normally one year. Papers II--III consider only one time period. In Paper II the supply chain from pulp mills to customers is modelled and the combined problem of deciding terminal locations and which ship routes to use is studied. Shipping vessels chartered on short or long term are used to transport products to terminals in Europe. From each terminal, the products are transported to customers by truck, train, or a combination of both. In addition, trains and trucks can be used for transports directly to customers from mills. In Paper III the entire supply chain, from harvest areas to customers, is considered. Decisions included are transportation of raw materials, production mix, the distribution of pulp products, and the selection of potential orders and their quantities at customers. The ship routes are considered as flow links. In Papers IV--V the problems in Papers II--III are combined into one model and several time periods are used. Lagrangian heuristics based on Lagrangian decomposition are used as solution methods in both papers. In Paper IV, the approach leads to subproblems for each time period, whereas in Paper V, another approach that results in subproblems for different parts of the supply chain is developed. All models are based on real data from the companies. The models are detailed and describe the problems accurately. The solution methods are developed such that the solution time is kept within practical limits. Results from Papers II--III have been used by Södra Cell AB to support the change of the terminal structure as well as in budget planning. / Denna avhandling presenterar matematiska modeller och lösningsmetoder för optimering av olika logistikproblem inom skogsindustrin. Vi studerar försörjningskedjor för skogsbränsle och massaproduker, och beaktar den årliga planeringen i syfte att optimera flödet. Det första problemet behandlar skogsbränsle och är ett samarbete med Sydved Energileveranser AB. Råmaterial i form av grenar och toppar från avverkningsplatser ska flisas och transporteras till värmeverk, eventuellt via terminaler. Det finns möjlighet att flisa både i skogen och på terminaler. Biprodukter från sågverk kan också användas som råmaterial. Vid behov kan utbudet av råmaterial utökas genom att fler avverkningsplatser och sågverk kontrakteras. Värmeverken har en efterfrågan, angiven i kWh per månad, som ska uppfyllas. Exempel på beslut som ska tas är var flisning ska ske, om nya avverkningsplatser ska kontrakteras, var lagring ska ske, samt hur och när skogsbränslet ska transporteras. Nästföljande problem behandlar massaprodukter och är ett samarbete med Södra Cell AB. Olika sorters massaved från skogen och biprodukter från sågverk utgör råmaterial för produktion av massaprodukter. Råmaterialet transporteras till massabruk för tillverkning enligt specificerade recept. De färdiga produkterna transporteras sedan med fartyg till terminaler i Europa. Från terminalerna transporteras produkterna vidare till pappersbruk, vilka är företagets slutkunder. Massaprodukterna transporteras i vissa fall med lastbil eller tåg direkt från massabruken till kunderna. Efterfrågan är angiven inom vissa gränser i olika order. Vissa order är fasta, vilket innebär att dess efterfrågan måste uppfyllas, medan andra order är fria. Exempel på beslut som ska tas är vilka bruk olika produkter ska produceras på, hur många och vilka terminaler som ska användas, samt hur transporterna ska utföras för att ge bästa resultat. Utifrån ovanstående beskrivningar har matematiska modeller formulerats. Ge-nom att lösa dessa kan vi få svar på logistik- och transportfrågorna och ett optimalt flöde kan hittas. För att lösa modellerna har kommersiell programvara använts. Heuristiker och mer avancerade optimeringsmetoder har också utvecklats i syfte att producera bra lösningar snabbare. / Article 4 was a manuscript entitled "Solving a multi-period supply chain problem for a pulp industry using Lagrangian heuristics based on time periods" at the time of the thesis defence.

Les applications de gestion de flux sont responsables de la majorité des calculs des systèmes embarqués (vidéo conférence, vision par ordinateur). Leurs exigences de haute performance rendent leur mise en œuvre parallèle nécessaire. Par conséquent, il est de plus en plus courant que les systèmes embarqués modernes incluent des processeurs multi-cœurs qui permettent un parallélisme massif. La mise en œuvre des applications de gestion de flux sur des multi-cœurs est difficile à cause de leur complexité, qui tend à augmenter, et de leurs exigences strictes à la fois qualitatives (robustesse, fiabilité) et quantitatives (débit, consommation d'énergie). Ceci est observé dans l'évolution de codecs vidéo qui ne cessent d'augmenter en complexité, tandis que leurs exigences de performance demeurent les mêmes. Les modèles de calcul (MdC) flot de données ont été développés pour faciliter la conception de ces applications qui sont typiquement composées de filtres qui échangent des flux de données via des liens de communication. Ces modèles fournissent une représentation intuitive des applications de gestion de flux, tout en exposant le parallélisme de tâches de l'application. En outre, ils fournissent des analyses statiques pour la vivacité et l'exécution en mémoire bornée. Cependant, les applications de gestion de flux modernes comportent des filtres qui échangent des quantités de données variables, et des liens de communication qui peuvent être activés / désactivés. Dans cette thèse, nous présentons un nouveau MdC flot de données, le Boolean Parametric Data Flow (BPDF), qui permet le paramétrage de la quantité de données échangées entre les filtres en utilisant des paramètres entiers et l'activation et la désactivation de liens de communication en utilisant des paramètres booléens. De cette manière, BPDF est capable de exprimer des applications plus complexes, comme les décodeurs vidéo modernes. Malgré l'augmentation de l'expressivité, les applications BPDF restent statiquement analysables pour la vivacité et l'exécution en mémoire bornée. Cependant, l'expressivité accrue complique grandement la mise en œuvre. Les paramètres entiers entraînent des dépendances de données de type paramétrique et les paramètres booléens peuvent désactiver des liens de communication et ainsi éliminer des dépendances de données. Pour cette raison, nous proposons un cadre d'ordonnancement qui produit des ordonnancements de type ``aussi tôt que possible'' (ASAP) pour un placement statique donné. Il utilise des contraintes d'ordonnancement, soit issues de l'application (dépendance de données) ou de l'utilisateur (optimisations d'ordonnancement). Les contraintes sont analysées pour la vivacité et, si possible, simplifiées. De cette façon, notre cadre permet une grande variété de politiques d'ordonnancement, tout en garantissant la vivacité de l'application. Enfin, le calcul du débit d'une application est important tant avant que pendant l'exécution. Il permet de vérifier que l'application satisfait ses exigences de performance et il permet de prendre des décisions d'ordonnancement à l'exécution qui peuvent améliorer la performance ou la consommation d'énergie. Nous traitons ce problème en trouvant des expressions paramétriques pour le débit maximum d'un sous-ensemble de BPDF. Enfin, nous proposons un algorithme qui calcule une taille des buffers suffisante pour que l'application BPDF ait un débit maximum. / Streaming applications are responsible for the majority of the computation load in many embedded systems (video conferencing, computer vision etc). Their high performance requirements make parallel implementations a necessity. Hence, more and more modern embedded systems include many-core processors that allow massive parallelism. Parallel implementation of streaming applications on many-core platforms is challenging because of their complexity, which tends to increase, and their strict requirements both qualitative (e.g., robustness, reliability) and quantitative (e.g., throughput, power consumption). This is observed in the evolution of video codecs that keep increasing in complexity, while their performance requirements remain the same or even increase. Data flow models of computation (MoCs) have been developed to facilitate the design process of such applications, which are typically composed of filters exchanging streams of data via communication links. Data flow MoCs provide an intuitive representation of streaming applications, while exposing the available parallelism of the application. Moreover, they provide static analyses for liveness and boundedness. However, modern streaming applications feature filters that exchange variable amounts of data, and communication links that are not always active. In this thesis, we present a new data flow MoC, the Boolean Parametric Data Flow (BPDF), that allows parametrization of the amount of data exchanged between the filters using integer parameters and the enabling and disabling of communication links using boolean parameters. In this way, BPDF is able to capture more complex streaming applications, like video decoders. Despite the increase in expressiveness, BPDF applications remain statically analyzable for liveness and boundedness. However, increased expressiveness greatly complicates implementation. Integer parameters result in parametric data dependencies and the boolean parameters disable communication links, effectively removing data dependencies. We propose a scheduling framework that facilitates the scheduling of BPDF applications. Our scheduling framework produces as soon as possible schedules for a given static mapping. It takes us input scheduling constraints that derive either from the application (data dependencies) or from the user (schedule optimizations). The constraints are analyzed for liveness and, if possible, simplified. In this way, our framework provides flexibility, while guaranteeing the liveness of the application. Finally, calculation of the throughput of an application is important both at compile-time and at run-time. It allows to verify at compile-time that the application meets its performance requirements and it allows to take scheduling decisions at run-time that can improve performance or power consumption. We approach this problem by finding parametric throughput expressions for the maximum throughput of a subset of BPDF graphs. Finally, we provide an algorithm that calculates sufficient buffer sizes for the BPDF graph to operate at maximum throughput.

The accurate determination of gender of biological samples has valuable applications in medical and forensic investigations. Gender determination based on length variations in the X-Y homologous amelogenin gene, is part of most commercial multiplex DNA profiling kits. The first report of a failure of the amelogenin sex test was in 1998 when two normal males were typed as female. Subsequently, several amelogenin Y (AMELY) negative males have been reported. This study represents the first report of this phenomenon in the black South African population. This study determined the size of the Y-chromosome deletion that resulted in the failure of the amelogenin sex test in two black South African AMELY-negative males by typing specific DNA markers surrounding the amelogenin locus. Through deletion size and Y-chromosome microsatellite haplotypes, the relationship between the samples was investigated. The samples were sequenced at the amelogenin gene and typed for thirteen sites on the short arm of the Y-chromosome. In order to determine the Y-chromosome haplotypes, eleven Y-chromosome microsatellite markers were typed. These samples had the same size deletion of approximately 3 Mb. The Y-chromosome haplotypes indicated that these were probably independent events. The frequency of AMELY-negative males is rare in this population sample of 8,344 individuals, with a frequency of 0.065% in the black South African sample population. Notwithstanding, tests performed for detecting the presence of male DNA based on the presence of the amelogenin gene alone should be reconsidered, as this study confirms that these deletions do occur in the African population. The impact of the results generated in this study on the medical and forensic practise of DNA testing is significant. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2011.

There are many practical decision problems that fall into the category of network flow problems: numerous examples of applications can be found in areas such as telecommunications, logistics, distributions, engineering, computer science and so on. One of the most popular and valuable tools to solve network flow problems of a topological nature is the use of linear programming models. An important extension of these models is that of integer programming models that deal with problems where some, or all, of the variables are required to assume integer variables. A significant application in this class of problems is the knapsack problem that arises in different contexts such as loading containers in aircraft or satisfying the demand for various lengths of cloth which must be cut from fixed length bolts of fabric. In this study, the feasibility of representing a network flow model in a tree network model and subsequently solving it using a tree knapsack approach is investigated. To compare and validate the proposed technique, a specific case study was chosen from the literature that can be used as a basis for the research project. The said study was an oil pipeline design problem, addressed by Brimberg et al. (2003). This focuses on the optimal design of an oil pipeline network for the South Gabon oil field in Africa. The objective was to reduce oil transportation costs to a major port. Following an overview of different network flow and knapsack models, an overview of the said matter is presented. A description of the proposed tree knapsack approach and the application of this approach to the given problem is given. Results have indicated that it is feasible to apply a tree knapsack approach to solve network flow problems. / Thesis (M.Sc. (Computer Science))--North-West University, Potchefstroom Campus, 2011.

The accurate determination of gender of biological samples has valuable applications in medical and forensic investigations. Gender determination based on length variations in the X-Y homologous amelogenin gene, is part of most commercial multiplex DNA profiling kits. The first report of a failure of the amelogenin sex test was in 1998 when two normal males were typed as female. Subsequently, several amelogenin Y (AMELY) negative males have been reported. This study represents the first report of this phenomenon in the black South African population. This study determined the size of the Y-chromosome deletion that resulted in the failure of the amelogenin sex test in two black South African AMELY-negative males by typing specific DNA markers surrounding the amelogenin locus. Through deletion size and Y-chromosome microsatellite haplotypes, the relationship between the samples was investigated. The samples were sequenced at the amelogenin gene and typed for thirteen sites on the short arm of the Y-chromosome. In order to determine the Y-chromosome haplotypes, eleven Y-chromosome microsatellite markers were typed. These samples had the same size deletion of approximately 3 Mb. The Y-chromosome haplotypes indicated that these were probably independent events. The frequency of AMELY-negative males is rare in this population sample of 8,344 individuals, with a frequency of 0.065% in the black South African sample population. Notwithstanding, tests performed for detecting the presence of male DNA based on the presence of the amelogenin gene alone should be reconsidered, as this study confirms that these deletions do occur in the African population. The impact of the results generated in this study on the medical and forensic practise of DNA testing is significant. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2011.