Aplicações paralelas geralmente são executadas com o máximo número de threads de hardware disponíveis no sistema para maximizar o seu desempenho. Contudo, esta abordagem pode não ser a melhor escolha quando se busca eficiência energética e, em alguns casos, pode até mesmo degradar o desempenho. Desta maneira, o presente trabalho aplica a adaptação dinâmica do número de threads para otimizar o Energy-Delay Product (EDP) de aplicações paralelas OpenMP executadas em sistemas embarcados. Ao contrário de soluções anteriores, que focam em processadores de propósito geral (GPP, do inglês General Purpose Processors), o presente trabalho considera as características intrínsecas de sistemas embarcados, os quais geralmente possuem menos núcleos disponíveis, assim como apresentam diferenças significativas em relação à micro-arquitetura e à hierarquia de memória. Por meio de experimentos realizados em um sistema embarcado real com processador octa-core, este trabalho mostrou que a adaptação dinâmica do número de threads permite, em média, economizar 15,35% no consumo de energia com apenas 3,41% de perda de desempenho, gerando assim 12,47% de otimização de EDP em relação à configuração padrão (uso do máximo número de threads disponíveis no sistema). No melhor caso, a adaptação dinâmica foi capaz de economizar 26,97% em energia enquanto promoveu 25,74% de aumento no desempenho, resultando em 45,77% de melhora no EDP. / Parallel applications usually execute using the maximum number of threads allowed by the available hardware at hand to maximize performance. However, this approach may not be the best when it comes to energy efficiency and may even lead to performance decrease in some particular cases. In this way, the present work proposes a new apporach for the dynamic adaptation of the number of threads to optimize Energy-Delay Product (EDP) of OpenMP applications when running on Embedded Systems. Differently from previous solutions, which focus on General Purpose Processors (GPP), the current one takes into account the intrinsic characteristics of embedded systems, which usually have a lower number of cores and significantly different characteristics concerning the microarchitecture and memory hierarchy when compared to GPPs. Through experiments on a real embedded system with an octa-core processor, this work demonstrates that adapting the number of threads at runtime saves energy, on average, by 15,35% with only 3,41% loss performance, improving the EDP by 12,47% over the default configuration (maximum number of threads available in the system). In the best case, the dynamic adaptation saves 26,97 % in energy while promoting a 25,74 % increase in performance, resulting in a 45,77 % improvement in EDP.

Most systems in HPC make use of hierarchical designs that allow multiple levels of parallelism to be exploited by programmers. The use of multiple multi-core/multi-processor computers to form a computer cluster supports both fine-grain and large-grain parallel computation. Aggregate function communications provide an easy to use and efficient set of mechanisms for communicating and coordinating between processing elements, but the model originally targeted only fine grain parallel hardware. This work shows that a hierarchical implementation of aggregate functions is a viable alternative to MPI (the standard Message Passing Interface library) for programming clusters that provide both fine grain and large grain execution. Performance of a prototype implementation is evaluated and compared to that of MPI.

In order to better understand the behavior of the human brain, it is very important to perform large scale neural network simulation which may reveal the relationship between the whole network activity and the biophysical dynamics of individual neurons. However, considering the complexity of the network and the large amount of variables, researchers choose to either simulate smaller neural networks or use simple spiking neuron models. Recently, supercomputing platforms have been employed to greatly speedup the simulation of large brain models. However, there are still limitations of these works such as the simplicity of the modeled network structures and lack of biophysical details in the neuron models. In this work, we propose a parallel simulator using biophysically realistic neural models for the simulation of large scale neural networks. In order to improve the performance of the simulator, we adopt several techniques such as merging linear synaptic receptors mathematically and using two level time steps, which significantly accelerate the simulation. In addition, we exploit the efficiency of parallel simulation through three parallel implementation strategies: MPI parallelization, MPI parallelization with dynamic load balancing schemes and Hybrid MPI/OpenMP parallelization. Through experimental studies, we illustrate the limitation of MPI implementation due to the imbalanced workload among processors. It is shown that the two developed MPI load balancing schemes are not able to improve the simulation efficiency on the targeted parallel platform. Using 32 processors, the proposed hybrid approach, on the other hand, is more efficient than the MPI implementation and is about 31X faster than a serial implementation of the simulator for a network consisting of more than 100,000 neurons. Finally, it is shown that for large neural networks, the presented approach is able to simulate the transition from the 3Hz delta oscillation to epileptic behaviors due to the alterations of underlying cellular mechanisms.

Le domaine applicatif de la simulation numérique requiert toujours plus de puissance de calcul. La technologie multicœur aide à satisfaire ces besoins mais impose toutefois de nouvelles contraintes aux programmeurs d'applications scientifiques qu'ils devront respecter s'ils souhaitent en tirer la quintessence. En particulier, il devient plus que jamais nécessaire de structurer le parallélisme des applications pour s'adapter au relief imposé par la hiérarchie mémoire des architectures multicœurs. Les approches existantes pour les programmer ne tiennent pas compte de cette caractéristique, et le respect de la structure du parallélisme reste à la charge du programmeur. Il reste de ce fait très difficile de développer une application qui soit à la fois performante et portable.La contribution de cette thèse s'articule en trois axes. Il s'agit dans un premier temps de s'appuyer sur le langage OpenMP pour générer du parallélisme structuré, et de permettre au programmeur de transmettre cette structure au support exécutif ForestGOMP. L'exécution structurée de ces flots de calcul est ensuite laissée aux ordonnanceurs Cacheet Memory développés au cours de cette thèse, permettant respectivement de maximiser la réutilisation des caches partagés et de maximiser la bande passante mémoire accessible par les programmes OpenMP. Enfin, nous avons étudié la composition de ces ordonnanceurs, et plus généralement de bibliothèques parallèles, en considérant cette voie comme une piste sérieuse pour exploiter efficacement les multiples unités de calcul des architectures multicœurs.Les gains obtenus sur des applications scientifiques montrent l'intérêt d'une communication forte entre l'application et le support exécutif, permettant l'ordonnancement dynamique et portable de parallélisme structuré sur les architectures hiérarchiques.

Nowadays clusters are one of the most used platforms in High Performance Computing and most programmers use the Message Passing Interface (MPI) library to program their applications in these distributed platforms getting their maximum performance, although it is a complex task. On the other side, OpenMP has been established as the de facto standard to program applications on shared memory platforms because it is easy to use and obtains good performance without too much effort. So, could it be possible to join both worlds? Could programmers use the easiness of OpenMP in distributed platforms? A lot of researchers think so. And one of the developed ideas is the distributed shared memory (DSM), a software layer on top of a distributed platform giving an abstract shared memory view to the applications. Even though it seems a good solution it also has some inconveniences. The memory coherence between the nodes in the platform is difficult to maintain (complex management, scalability issues, high overhead and others) and the latency of the remote-memory accesses which can be orders of magnitude greater than on a shared bus due to the interconnection network. Therefore this research improves the performance of OpenMP applications being executed on distributed memory platforms using a DSM with sequential consistency evaluating thoroughly the results from the NAS parallel benchmarks. The vast majority of designed DSMs use a relaxed consistency model because it avoids some major problems in the area. In contrast, we use a sequential consistency model because we think that showing these potential problems that otherwise are hidden may allow the finding of some solutions and, therefore, apply them to both models. The main idea behind this work is that both runtimes, the OpenMP and the DSM layer, should cooperate to achieve good performance, otherwise they interfere one each other trashing the final performance of applications. We develop three different contributions to improve the performance of these applications: (a) a technique to avoid false sharing at runtime, (b) a technique to mimic the MPI behaviour, where produced data is forwarded to their consumers and, finally, (c) a mechanism to avoid the network congestion due to the DSM coherence messages. The NAS Parallel Benchmarks are used to test the contributions. The results of this work shows that the false-sharing problem is a relative problem depending on each application. Another result is the importance to move the data flow outside of the critical path and to use techniques that forwards data as early as possible, similar to MPI, benefits the final application performance. Additionally, this data movement is usually concentrated at single points and affects the application performance due to the limited bandwidth of the network. Therefore it is necessary to provide mechanisms that allows the distribution of this data through the computation time using an otherwise idle network. Finally, results shows that the proposed contributions improve the performance of OpenMP applications on this kind of environments.

In this masters’ thesis report we present a graph theoretical method used for automatic bilingual lexicon acquisition with parallel texts. We analyze the concept of graph similarity and give an interpretation, of the parallel texts, connected to the vector space model. We represent the parallel texts by a directed, tripartite graph and from here use the corresponding adjacency matrix, A, to compute the similarity of the graph. By solving the eigenvalue problem ρS = ASAT + ATSA we obtain the self-similarity matrix S and the Perron root ρ. A rank k approximation of the self-similarity matrix is computed by implementations of the singular value decomposition and the non-negative matrix factorization algorithm GD-CLS. We construct an algorithm in order to extract the bilingual lexicon from the self-similarity matrix and apply a statistical model to estimate the precision, the correctness, of the translations in the bilingual lexicon. The best result is achieved with an application of the vector space model with a precision of about 80 %. This is a good result and can be compared with the precision of about 60 % found in the literature.

<p>In this masters’ thesis report we present a graph theoretical method used for automatic bilingual lexicon acquisition with parallel texts. We analyze the concept of graph similarity and give an interpretation, of the parallel texts, connected to the vector space model. We represent the parallel texts by a directed, tripartite graph and from here use the corresponding adjacency matrix, A, to compute the similarity of the graph. By solving the eigenvalue problem ρS = ASAT + ATSA we obtain the self-similarity matrix S and the Perron root ρ. A rank k approximation of the self-similarity matrix is computed by implementations of the singular value decomposition and the non-negative matrix factorization algorithm GD-CLS. We construct an algorithm in order to extract the bilingual lexicon from the self-similarity matrix and apply a statistical model to estimate the precision, the correctness, of the translations in the bilingual lexicon. The best result is achieved with an application of the vector space model with a precision of about 80 %. This is a good result and can be compared with the precision of about 60 % found in the literature.</p>

A hybrid of message passing and shared memory techniques is presented for scalable parallelization of the adaptive integral method (AIM), an FFT based algorithm, on clusters of identical multi-core processors. The proposed hybrid MPI/OpenMP parallelization scheme is based on a nested one-dimensional (1-D) slab decomposition of the 3-D auxiliary uniform grid and the associated AIM calculations: If there are M processors and T cores per processor, the scheme (i) divides the uniform grid into M slabs and MT sub-slabs, (ii) assigns each slab/sub-slab and the associated operations to one of the processors/cores, and (iii) uses MPI for inter-processor data communication and OpenMP for intra-processor data exchange. The MPI/OpenMP parallel AIM is used to accelerate the MOM solution of combined-field integral equations pertinent to the analysis of scattering from perfectly conducting surfaces. The scalability and efficiency of the implementation are investigated theoretically and verified numerically by solving benchmark scattering problems on a (near) petaflop supercomputing cluster of quad-core processors. The timing and speedup results on up to 1024 processors show that the proposed hybrid MPI/OpenMP parallelization exhibits better strong scalability (fixed problem size speedup) compared to pure MPI parallelization when multiple cores are used on each processor. / text

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Modern computers are capable of completing most of the tasks in fairly short time, however there are areas in what calculations can last for months and even years. Parallel algorithms are one of the ways to accelerate long-lasting calculations. In the thesis we analyze parallel computing technologies OpenMP (shared memory) and MPI (distributed memory), cons and pros of their architecture. We identify potential parts of program code of Curonian lagoon model for parallelizing, in which chosen parallel computing technologies OpenMP and MPI is applied. Also we make the runtime speedup analysis.