Shared memory multi-core processor technology has seen a drastic developmentwith faster and increasing number of processors per chip. This newarchitecture challenges computer programmers to write code that scales overthese many cores to exploit full computational power of these machines.Shared-memory parallel programming paradigms such as OpenMP and IntelThreading Building Blocks (TBB) are two recognized models that offerhigher level of abstraction, shields programmers from low level detailsof thread management and scales computation over all available resources.At the same time, need for high performance power-ecient computing iscompelling developers to exploit GPGPU computing due to GPU's massivecomputational power and comparatively faster multi-core growth. Thistrend leads to systems with heterogeneous architectures containing multicoreCPUs and one or more programmable accelerators such as programmableGPUs. There exist dierent programming models to program these architecturesand code written for one architecture is often not portable to anotherarchitecture. OpenCL is a relatively new industry standard framework, de-ned by Khronos group, which addresses the portability issue. It oers aportable interface to exploit the computational power of a heterogeneous setof processors such as CPUs, GPUs, DSP processors and other accelerators. In this work, we evaluate the eectiveness of OpenCL for programmingmulti-core CPUs in a comparative case study with two CPU specic stableframeworks, OpenMP and Intel TBB, for ve benchmark applicationsnamely matrix multiply, LU decomposition, image convolution, Pi value approximationand image histogram generation. The evaluation includes aperformance comparison of the three frameworks and a study of the relativeeects of applying compiler optimizations on performance numbers.OpenCL performance on two vendor-dependent platforms Intel and AMD,is also evaluated. Then the same OpenCL code is ported to a modern GPUand its code correctness and performance portability is investigated. Finally,usability experience of coding using the three multi-core frameworksis presented.

O gênero Leishmania apresenta espécies capazes de desenvolver doenças de grande importância para a saúde pública, as leishmanioses, que apresentam prevalência mundial de 12 milhões de pessoas. Quando os parasitos entram em contato com o hospedeiro humano passam por um processo de metaciclogênese adquirindo capacidade de interagir com os macrófagos. Inúmeras atividades biológicas são desencadeadas pela ativação de sistemas de transdução de sinais, onde as proteínas cinases e fosfatases desempenham papel fundamental. A proteína cinase CK2 parece estar presente em todas as células eucarióticas (núcleo, citoplasma e superfície). É caracterizada como enzima serina/treonina cinase, embora também seja capaz de fosforilar resíduos de tirosina em suas proteínas-alvo. No presente trabalho, demonstramos que o principal inibidor da CK2, TBB, foi capaz de inibir o crescimento de formas promastigotas de L. donovani e mostrou um mecanismo de ação irreversível, entretanto não foi capaz de induzir apoptose nas formas promastigotas de L. donovani. O pré-tratamento dos parasitos e macrófagos, assim como a adição do TBB durante o processo de infecção induziram uma redução significativa no número de amastigotas por macrófagos possivelmente pelo mecanismo de morte celular programada demosntrada pela técnica do TUNEL. O tratamento de macrófagos com TBB não induziram o aumento de óxido nítrico. Ensaios de imunofluorescência demonstraram a presença de CK2α em promastigotas. Macrófagos não infectados demonstraram pouca marcação para CK2α. Após a interação, a enzima mostrou-se distribuída preferencialmente na periferia dos macrófagos. Os dados do trabalho sugerem que a CK2 é uma importante enzima para a atividade biológica da Leishmania donovani, tendo seu estudo importante relevância para a descoberta de novos alvos terapêuticos. / The genus Leishmania contains multiple species that are responsible for a group of diseases, leishmaniasis. Current estimates suggest that 12 million people are infected. When parasites enter a human host, they undergo metacyclogenesis and acquire the ability to interact with macrophages. This interaction activites signal transduction pathways inducing numerous biological activities, including protein kinase CK2. CK2 has been observed in all eukaryotic cells residing in the nucleus, the cytoplasm and on the cell surface. It appears to have an essential function and recognizes serine/threonine or tyrosine residues in target proteins for phosphorylation. In the present study, we demonstrate that the treatment of L. donovani promastigotes with TBB resulted in inhibition of cell growth and showed an irreversible mechanism of action, however was not able to induce apoptosis in L. donovani promastigotes. The pre-treatment of promastigotes and macrophages, as well as the addition of TBB during infection induced a significant reduction in the number of amastigotes per macrophages, possibly via the mechanism of programmed cell death showed by TUNEL technique. Treatment of macrophages with TBB did not induce the increase of nitric oxide. Immunofluorescence assays demonstrated the presence of CK2α distributed throughout the surface the promastigotes. Uninfected macrophages showed little to no CK2α. After initiating the interaction of parasites with macrophages, CK2α was observed distributed preferentially in the nucleus of macrophages. Job data suggest that CK2 is an important enzyme for the biological activity of Leishmania donovani, and its study important relevance to the discovery of new therapeutic targets.

O gênero Leishmania apresenta espécies capazes de desenvolver doenças de grande importância para a saúde pública, as leishmanioses, que apresentam prevalência mundial de 12 milhões de pessoas. Quando os parasitos entram em contato com o hospedeiro humano passam por um processo de metaciclogênese adquirindo capacidade de interagir com os macrófagos. Inúmeras atividades biológicas são desencadeadas pela ativação de sistemas de transdução de sinais, onde as proteínas cinases e fosfatases desempenham papel fundamental. A proteína cinase CK2 parece estar presente em todas as células eucarióticas (núcleo, citoplasma e superfície). É caracterizada como enzima serina/treonina cinase, embora também seja capaz de fosforilar resíduos de tirosina em suas proteínas-alvo. No presente trabalho, demonstramos que o principal inibidor da CK2, TBB, foi capaz de inibir o crescimento de formas promastigotas de L. donovani e mostrou um mecanismo de ação irreversível, entretanto não foi capaz de induzir apoptose nas formas promastigotas de L. donovani. O pré-tratamento dos parasitos e macrófagos, assim como a adição do TBB durante o processo de infecção induziram uma redução significativa no número de amastigotas por macrófagos possivelmente pelo mecanismo de morte celular programada demosntrada pela técnica do TUNEL. O tratamento de macrófagos com TBB não induziram o aumento de óxido nítrico. Ensaios de imunofluorescência demonstraram a presença de CK2α em promastigotas. Macrófagos não infectados demonstraram pouca marcação para CK2α. Após a interação, a enzima mostrou-se distribuída preferencialmente na periferia dos macrófagos. Os dados do trabalho sugerem que a CK2 é uma importante enzima para a atividade biológica da Leishmania donovani, tendo seu estudo importante relevância para a descoberta de novos alvos terapêuticos. / The genus Leishmania contains multiple species that are responsible for a group of diseases, leishmaniasis. Current estimates suggest that 12 million people are infected. When parasites enter a human host, they undergo metacyclogenesis and acquire the ability to interact with macrophages. This interaction activites signal transduction pathways inducing numerous biological activities, including protein kinase CK2. CK2 has been observed in all eukaryotic cells residing in the nucleus, the cytoplasm and on the cell surface. It appears to have an essential function and recognizes serine/threonine or tyrosine residues in target proteins for phosphorylation. In the present study, we demonstrate that the treatment of L. donovani promastigotes with TBB resulted in inhibition of cell growth and showed an irreversible mechanism of action, however was not able to induce apoptosis in L. donovani promastigotes. The pre-treatment of promastigotes and macrophages, as well as the addition of TBB during infection induced a significant reduction in the number of amastigotes per macrophages, possibly via the mechanism of programmed cell death showed by TUNEL technique. Treatment of macrophages with TBB did not induce the increase of nitric oxide. Immunofluorescence assays demonstrated the presence of CK2α distributed throughout the surface the promastigotes. Uninfected macrophages showed little to no CK2α. After initiating the interaction of parasites with macrophages, CK2α was observed distributed preferentially in the nucleus of macrophages. Job data suggest that CK2 is an important enzyme for the biological activity of Leishmania donovani, and its study important relevance to the discovery of new therapeutic targets.

An effective tool used by planners and policy makers in public health, such as Center for Disease Control (CDC), to curtail spread of infectious diseases over a given population is contagion diffusion simulations. These simulations model the relevant characteristics of the population (age, gender, income etc.) and the disease (attack rate, etc.) and compute the spread under various configuration and plausible intervention strategies (such as vaccinations, school closure, etc.). Hence, the model and the computation form a complex agent based system and are highly compute and resource intensive. In this work, we design a benchmark consisting of several kernels which capture the essential compute, communication, and data access patterns for such applications. For each kernel, the benchmark provides different evaluation strategies. The goal is to (a) derive alternative implementations for computing the contagion by combining different implementation of the kernels, and (b) evaluate which combination of implementation, runtime, and hardware is most effective in running large scale contagion diffusion simulations. Our proposed benchmark is designed using C++ generic programming primitives and lifting sequential strategies for parallel computations. Together, these lead to a succinct description of the benchmark and significant code reuse when deriving strategies for new hardware. For the benchmark to be effective, this aspect is crucial, because the potential combination of hardware and runtime are growing rapidly thereby making infeasible to write optimized strategy for the complete contagion diffusion from ground up for each compute system. / Master of Science

No description available.

Dans la course vers l’exascale, les architectures des supercalculateurs évoluent vers des nœuds massivement multicœurs, sur lesquels les accès mémoire sont non-uniformes et les registres de vectorisation toujours plus grands. Ces évolutions entraînent une baisse de l’efficacité des applications homogènes (MPI simple), et imposent aux développeurs l’utilisation de fonctionnalités de bas-niveau afin d’obtenir de bonnes performances.Dans le contexte de la dynamique moléculaire (DM) appliqué à la physique de la matière condensée, les études du comportement des matériaux dans des conditions extrêmes requièrent la simulation de systèmes toujours plus grands avec une physique de plus en plus complexe. L’adaptation des codes de DM aux architectures exaflopiques est donc un enjeu essentiel.Cette thèse propose la conception et l’implémentation d’une plateforme dédiée à la simulation de très grands systèmes de DM sur les futurs supercalculateurs. Notre architecture s’organise autour de trois niveaux de parallélisme: décomposition de domaine avec MPI, du multithreading massif sur chaque domaine et un système de vectorisation explicite. Nous avons également inclus une capacité d’équilibrage dynamique de charge de calcul. La conception orienté objet a été particulièrement étudiée afin de préserver un niveau de programmation utilisable par des physiciens sans altérer les performances.Les premiers résultats montrent d’excellentes performances séquentielles, ainsi qu’une accélération quasi-linéaire sur plusieurs dizaines de milliers de cœurs. En production, nous constatons une accélération jusqu’à un facteur 30 par rapport au code utilisé actuellement par les chercheurs du CEA. / In the exascale race, supercomputer architectures are evolving towards massively multicore nodes with hierarchical memory structures and equipped with larger vectorization registers. These trends tend to make MPI-only applications less effective, and now require programmers to explicitly manage low-level elements to get decent performance.In the context of Molecular Dynamics (MD) applied to condensed matter physics, the need for a better understanding of materials behaviour under extreme conditions involves simulations of ever larger systems, on tens of thousands of cores. This will put molecular dynamics codes among software that are very likely to meet serious difficulties when it comes to fully exploit the performance of next generation processors.This thesis proposes the design and implementation of a high-performance, flexible and scalable framework dedicated to the simulation of large scale MD systems on future supercomputers. We managed to separate numerical modules from different expressions of parallelism, allowing developers not to care about optimizations and still obtain high levels of performance. Our architecture is organized in three levels of parallelism: domain decomposition using MPI, thread parallelization within each domain, and explicit vectorization. We also included a dynamic load balancing capability in order to equally share the workload among domains.Results on simple tests show excellent sequential performance and a quasi linear speedup on several thousands of cores on various architectures. When applied to production simulations, we report an acceleration up to a factor 30 compared to the code previously used by CEA’s researchers.

No description available.