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Apresentamos um problema de dinâmica molecular e quatro algoritmos seqüenciais para a implementação do mesmo. Em seguida esses algoritmos são estudados quanto ao tempo de execução e possibilidades de paralelização. É escolhido então dentre os quatro o algoritmo que apresenta melhores características para a paralelização. Introduzimos a seguir uma proposta de implementação do mesmo em um rede de transputers, com a. definição das interligações entre os processadores e da. programação dos mesmos. A seguir é realizado um estudo da eficiência da estrutura proposta quanto a. tempo de execução e características de expansibilidade do número de processadores. Os resultados mostram que conseguem-se velocidades de execução próximas às de supercomputadores para redes com baixos números de elementos. / In the present work, we describe four sequential algorithms for simulating molecular dynamics. The parallelism and execution times of these algorithms are assessed. Using the best suited algorithm for parallelism exploitation a transputer based architecture is suggested including needed link and software. The evaluation of the eficiency regarding execution time and number of processors is analyzed. The results show that speeds dose to those of supercomputers can be achieved with a low number of processors.

Neste trabalho, propomos um método de paralelização de simulações de dinâmica molecular para execução em máquinas de memória distribuída, trabalhando sob passagem de mensagens. Nos limitamos à análise de implementação de sistemas com ensemble microcanônico de partículas de Lennard-Jones, desenvolvendo no entanto um sistema que pode ser expandido para incluir outras características. Mostramos que o sistema apresenta bom desempenho com relação à paralelização, representando uma alternativa viável para a simulação de sistemas com muitas partículas. / A method for parallelization of molecular dynamics simulations in distributed memory machines operating under the message-passing paradigm is proposed. Even though the analysis and implementation presented in this work were primarily restricted to the system model known as microcanonical emsemble of Lennard--Jones particles. the obtained system can easily be adapted for inclusion of other characteristics. It is shown t,hat. the developed system is well suited for parallelization, resulting in a feasible a1ternative for simulation of many-particle systems.

Apresentamos um problema de dinâmica molecular e quatro algoritmos seqüenciais para a implementação do mesmo. Em seguida esses algoritmos são estudados quanto ao tempo de execução e possibilidades de paralelização. É escolhido então dentre os quatro o algoritmo que apresenta melhores características para a paralelização. Introduzimos a seguir uma proposta de implementação do mesmo em um rede de transputers, com a. definição das interligações entre os processadores e da. programação dos mesmos. A seguir é realizado um estudo da eficiência da estrutura proposta quanto a. tempo de execução e características de expansibilidade do número de processadores. Os resultados mostram que conseguem-se velocidades de execução próximas às de supercomputadores para redes com baixos números de elementos. / In the present work, we describe four sequential algorithms for simulating molecular dynamics. The parallelism and execution times of these algorithms are assessed. Using the best suited algorithm for parallelism exploitation a transputer based architecture is suggested including needed link and software. The evaluation of the eficiency regarding execution time and number of processors is analyzed. The results show that speeds dose to those of supercomputers can be achieved with a low number of processors.

Neste trabalho, propomos um método de paralelização de simulações de dinâmica molecular para execução em máquinas de memória distribuída, trabalhando sob passagem de mensagens. Nos limitamos à análise de implementação de sistemas com ensemble microcanônico de partículas de Lennard-Jones, desenvolvendo no entanto um sistema que pode ser expandido para incluir outras características. Mostramos que o sistema apresenta bom desempenho com relação à paralelização, representando uma alternativa viável para a simulação de sistemas com muitas partículas. / A method for parallelization of molecular dynamics simulations in distributed memory machines operating under the message-passing paradigm is proposed. Even though the analysis and implementation presented in this work were primarily restricted to the system model known as microcanonical emsemble of Lennard--Jones particles. the obtained system can easily be adapted for inclusion of other characteristics. It is shown t,hat. the developed system is well suited for parallelization, resulting in a feasible a1ternative for simulation of many-particle systems.

Made available in DSpace on 2014-06-12T15:51:19Z (GMT). No. of bitstreams: 1 license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2008 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Message Sequence Charts (MSC) é uma linguagem gráfica, usada na academia e na indústria, cujo objetivo é descrever o comportamento de componentes de sistemas e seus ambientes. A sintaxe e a semântica de um diagrama MSC padrão são definidos pelo International Telecommunication Union. A motivação para esse trabalho foi originada a partir de esforços para modelar cenários de aplicações de aparelhos móveis com o objetivo de automatizar a geração de testes, no contexto de uma colaboração entre Centro de Informática da Universidade Federal de Pernambuco (CIn- UFPE) e a Motorola, no contexto do projeto Brasil Test Center (BTC). Ao modelar algumas destas aplicações que envolvem múltipla sincronização utilizando como linguagem de modelagem, MSC padrão, constatou-se que os diagramas são de difícil entendimento ou com um comportamento diferente do desejado. É proposta neste trabalho uma extensão de MSC com o objetivo de permitir a descrição de mensagens síncronas, que permitem descrever eventos instantâneos (abstraindo-se a duração do tempo real para que a conexão seja estabelecida) e podendo envolver várias instâncias de MSC. Essa extensão é conservativa, no sentido que o comportamento das construções existentes não é afetado pela mesma; além disso, em um mesmo diagrama é possível conter mensagens síncronas e mensagens assíncronas. Foi desenvolvido um algoritmo de transformação, que a partir de um diagrama escrito na notação MSC estendido, gera um diagrama correspondente na notação de MSC padrão. Este algoritmo tem por objetivo permitir a transitividade entre as notações e demonstrar suas equivalências. Este algoritmo de transformação implementa mensagens síncronas como uma seqüência de mensagens assíncronas seguindo um algoritmo particular de handshake. A segunda contribuição desse trabalho é a definição de uma semântica para a notação padrão e estendida de MSC. Essa definição é dada em termos da álgebra de processos CSP (Communicating Sequential Processes). O formalismo introduzido na notação de Message Sequence Charts com CSP permite mostrar a equivalência entre um diagrama na notação de MSC estendido e seu correspondente descrito em MSC padrão, gerado a partir do algoritmo de transformação. Além disso, modelar MSC como um processo descrito na notação CSP permite uma análise sobre seus diagramas, usando um rico conjunto de leis algébricas de CSP, bem como o uso de ferramentas, como FDR2 e o Probe. Finalmente, para validar a estratégia proposta, desenvolveu-se um exemplo que ilustra a utilização da notação estendida de MSC, notação síncrona; a conversão desta notação para a notação padrão e a equivalência entre o MSC estendido e o padrão. Mostramos, ainda, o uso da ferramenta Power Tool Kit(PTK) para geração de casos de teste a partir de diagramas MSC

The ever-growing competition in current electronics industry has resulted in stringent time-to-market goals and reduced design time available to engineers. Lesser design time has subsequently raised a need for high-level synthesis design methodologies that raise the design to a higher level of abstraction. Higher level of abstraction helps in increasing the predictability and productivity of the design and reduce the number of bugs due to human-error. It also enables the designer to try out dierent optimization strategies early in the design stage. In-spite of all these advantages, high-level synthesis design methodologies have not gained much popularity in the mainstream design flow mainly because of the reasons like lack of readability and reliability of the generated register transfer level (RTL) code. The compiler framework presented in this thesis allows the user to draw high-level graphical models of the system. The compiler translates these models into synthesizeable RTL Verilog designs that exhibit their desired functionality following communicating sequential processes (CSP) model of computation. CSP model of computation introduces a good handshaking mechanism between different components in the design that makes designs less prone to timing violations during implementation and bottlenecks while in actual operation. / Master of Science

The Parameterised Model Checking Problem asks whether an implementation Impl(t) satisfies a specification Spec(t) for all instantiations of parameter t. In general, t can determine numerous entities: the number of processes used in a network, the type of data, the capacities of buffers, etc. The main theme of this thesis is automation of uniform verification of a subclass of PMCP with the parameter of the first kind, using techniques based on counter abstraction. Counter abstraction works by counting how many, rather than which, node processes are in a given state: for nodes with k local states, an abstract state (c(1), ..., c(k)) models a global state where c(i) processes are in the i-th state. We then use a threshold function z to cap the values of each counter. If for some i, counter c(i) reaches its threshold, z(i) , then this is interpreted as there being z(i) or more nodes in the i-th state. The addition of thresholds makes abstract models independent of the instantiation of the parameter. We adapt standard counter abstraction techniques to concurrent reactive systems modelled using the CSP process algebra. We demonstrate how to produce abstract models of systems that do not use node identifiers (i.e. where all nodes are indistinguishable). Every such abstraction is, by construction, refined by all instantiations of the implementation. If the abstract model satisfies the specification, then a positive answer to the particular uniform verification problem can be deduced. We show that by adding node identifiers we make the uniform verification problem undecidable. We demonstrate a sound abstraction method that extends standard counter abstraction techniques to systems that make full use of node identifiers (in specifications and implementations). However, on its own, the method is not enough to give the answer to verification problems for all parameter instantiations. This issue has led us to the development of a type reduction theory, which, for a given verification problem, establishes a function phi that maps all (sufficiently large) instantiations T of the parameter to some fixed type T and allows us to deduce that if Spec(T) is refined by phi(Impl(T)), then Spec(T) is refined by Impl(T). We can then combine this with our extended counter abstraction techniques and conclude that if the abstract model satisfies Spec(T), then the answer to the uniform verification problem is positive. We develop a symbolic operational semantics for CSP processes that satisfy certain normality requirements and we provide a set of translation rules that allow us to concretise symbolic transition graphs. The type reduction theory relies heavily on these results. One of the main advantages of our symbolic operational semantics and the type reduction theory is their generality, which makes them applicable in other settings and allows the theory to be combined with abstraction methods other than those used in this thesis. Finally, we present TomCAT, a tool that automates the construction of counter abstraction models and we demonstrate how our results apply in practice.

The discipline of component-based modeling and simulation offers promising gains including reduction in development cost, time, and system complexity. This paradigm is very profitable as it promotes the use and reuse of modular components and is auspicious for effective development of complex simulations. It however is confronted by a series of research challenges when it comes to actually practice this methodology. One of such important issue is Composability verification. In modeling and simulation (M&amp;S), composability is the capability to select and assemble components in various combinations to satisfy specific user requirements. Therefore to ensure the correctness of a composed model, it is verified with respect to its requirements specifications.There are different approaches and existing component modeling frameworks that support composability however in our observation most of the component modeling frameworks possess none or weak built-in support for the composability verification. One such framework is Base Object Model (BOM) which fundamentally poses a satisfactory potential for effective model composability and reuse. However it falls short of required semantics, necessary modeling characteristics and built-in evaluation techniques, which are essential for modeling complex system behavior and reasoning about the validity of the composability at different levels.In this thesis a comprehensive verification framework is proposed to contend with some important issues in composability verification and a verification process is suggested to verify composability of different kinds of systems models, such as reactive, real-time and probabilistic systems. With an assumption that all these systems are concurrent in nature in which different composed components interact with each other simultaneously, the requirements for the extensive techniques for the structural and behavioral analysis becomes increasingly challenging. The proposed verification framework provides methods, techniques and tool support for verifying composability at its different levels. These levels are defined as foundations of a consistent model composability. Each level is discussed in detail and an approach is presented to verify composability at that level. In particular we focus on theDynamic-Semantic Composability level due to its significance in the overallcomposability correctness and also due to the level of difficulty it poses in theprocess. In order to verify composability at this level we investigate the application ofthree different approaches namely (i) Petri Nets based Algebraic Analysis (ii) ColoredPetri Nets (CPN) based State-space Analysis and (iii) Communicating SequentialProcesses based Model Checking. All the three approaches attack the problem ofverifying dynamic-semantic composability in different ways however they all sharethe same aim i.e., to confirm the correctness of a composed model with respect to itsrequirement specifications. Beside the operative integration of these approaches inour framework, we also contributed in the improvement of each approach foreffective applicability in the composability verification. Such as applying algorithmsfor automating Petri Net algebraic computations, introducing a state-space reductiontechnique in CPN based state-space analysis, and introducing function libraries toperform verification tasks and help the molder with ease of use during thecomposability verification. We also provide detailed examples of using each approachwith different models to explain the verification process and their functionality.Lastly we provide a comparison of these approaches and suggest guidelines forchoosing the right one based on the nature of the model and the availableinformation. With a right choice of an approach and following the guidelines of ourcomponent-based M&amp;S life-cycle a modeler can easily construct and verify BOMbased composed models with respect to its requirement specifications. / <p>Overseas Scholarship for PHD in selected Studies Phase II Batch I</p><p>Higher Education Commision of Pakistan.</p><p>QC 20130224</p>