Parallel programming paradigms and frameworks in big data era

With Cloud Computing emerging as a promising new approach for ad-hoc parallel data processing, major companies have started to integrate frameworks for parallel data processing in their product portfolio, making it easy for customers to access these services and to deploy their programs. We have entered the Era of Big Data. The explosion and profusion of available data in a wide range of application domains rise up new challenges and opportunities in a plethora of disciplines-ranging from science and engineering to biology and business. One major challenge is how to take advantage of the unprecedented scale of data-typically of heterogeneous nature-in order to acquire further insights and knowledge for improving the quality of the offered services. To exploit this new resource, we need to scale up and scale out both our infrastructures and standard techniques. Our society is already data-rich, but the question remains whether or not we have the conceptual tools to handle it. In this paper we discuss and analyze opportunities and challenges for efficient parallel data processing. Big Data is the next frontier for innovation, competition, and productivity, and many solutions continue to appear, partly supported by the considerable enthusiasm around the MapReduce paradigm for large-scale data analysis. We review various parallel and distributed programming paradigms, analyzing how they fit into the Big Data era, and present modern emerging paradigms and frameworks. To better support practitioners interesting in this domain, we end with an analysis of on-going research challenges towards the truly fourth generation data-intensive science.Peer ReviewedPostprint (author's final draft

Where are we at with Cloud Computing?: A Descriptive Literature Review

Cloud computing is an exciting area for research, because of its relative novelty and exploding growth. In this paper, we present a descriptive literature review and classification scheme for cloud computing research. The former consists of 58 articles published since the recent inception of cloud computing. Clearly, there is an explosively increasing amount of cloud computing research has been conducted this year. The articles are classified and results are presented, based on a scheme that consists of four main categories: technological issues, business issues, applications, and general. The results show that although current cloud computing research is still skewed towards technological issues, such as performance, network, and data management, new research theme regarding the social and organisational implications of cloud computing is emerging. We hope this review will provide a snapshot and reference source of the current state of cloud computing research and stimulate further research interest

Exascale machines require new programming paradigms and runtimes

Extreme scale parallel computing systems will have tens of thousands of optionally accelerator-equiped nodes with hundreds of cores each, as well as deep memory hierarchies and complex interconnect topologies. Such Exascale systems will provide hardware parallelism at multiple levels and will be energy constrained. Their extreme scale and the rapidly deteriorating reliablity of their hardware components means that Exascale systems will exhibit low mean-time-between-failure values. Furthermore, existing programming models already require heroic programming and optimisation efforts to achieve high efficiency on current supercomputers. Invariably, these efforts are platform-specific and non-portable. In this paper we will explore the shortcomings of existing programming models and runtime systems for large scale computing systems. We then propose and discuss important features of programming paradigms and runtime system to deal with large scale computing systems with a special focus on data-intensive applications and resilience. Finally, we also discuss code sustainability issues and propose several software metrics that are of paramount importance for code development for large scale computing systems

Energy Management of Distributed Generation Systems

The book contains 10 chapters, and it is divided into four sections. The first section includes three chapters, providing an overview of Energy Management of Distributed Systems. It outlines typical concepts, such as Demand-Side Management, Demand Response, Distributed, and Hierarchical Control for Smart Micro-Grids. The second section contains three chapters and presents different control algorithms, software architectures, and simulation tools dedicated to Energy Management Systems. In the third section, the importance and the role of energy storage technology in a Distribution System, describing and comparing different types of energy storage systems, is shown. The fourth section shows how to identify and address potential threats for a Home Energy Management System. Finally, the fifth section discusses about Economical Optimization of Operational Cost for Micro-Grids, pointing out the effect of renewable energy sources, active loads, and energy storage systems on economic operation

Energy-aware service provisioning in P2P-assisted cloud ecosystems

Cotutela Universitat Politècnica de Catalunya i Instituto Tecnico de LisboaEnergy has been emerged as a first-class computing resource in modern systems. The trend has primarily led to the strong focus on reducing the energy consumption of data centers, coupled with the growing awareness of the adverse impact on the environment due to data centers. This has led to a strong focus on energy management for server class systems. In this work, we intend to address the energy-aware service provisioning in P2P-assisted cloud ecosystems, leveraging economics-inspired mechanisms. Toward this goal, we addressed a number of challenges. To frame an energy aware service provisioning mechanism in the P2P-assisted cloud, first, we need to compare the energy consumption of each individual service in P2P-cloud and data centers. However, in the procedure of decreasing the energy consumption of cloud services, we may be trapped with the performance violation. Therefore, we need to formulate a performance aware energy analysis metric, conceptualized across the service provisioning stack. We leverage this metric to derive energy analysis framework. Then, we sketch a framework to analyze the energy effectiveness in P2P-cloud and data center platforms to choose the right service platform, according to the performance and energy characteristics. This framework maps energy from the hardware oblivious, top level to the particular hardware setting in the bottom layer of the stack. Afterwards, we introduce an economics-inspired mechanism to increase the energy effectiveness in the P2P-assisted cloud platform as well as moving toward a greener ICT for ICT for a greener ecosystem.La energía se ha convertido en un recurso de computación de primera clase en los sistemas modernos. La tendencia ha dado lugar principalmente a un fuerte enfoque hacia la reducción del consumo de energía de los centros de datos, así como una creciente conciencia sobre los efectos ambientales negativos, producidos por los centros de datos. Esto ha llevado a un fuerte enfoque en la gestión de energía de los sistemas de tipo servidor. En este trabajo, se pretende hacer frente a la provisión de servicios de bajo consumo energético en los ecosistemas de la nube asistida por P2P, haciendo uso de mecanismos basados en economía. Con este objetivo, hemos abordado una serie de desafíos. Para instrumentar un mecanismo de servicio de aprovisionamiento de energía consciente en la nube asistida por P2P, en primer lugar, tenemos que comparar el consumo energético de cada servicio en la nube P2P y en los centros de datos. Sin embargo, en el procedimiento de disminuir el consumo de energía de los servicios en la nube, podemos quedar atrapados en el incumplimiento del rendimiento. Por lo tanto, tenemos que formular una métrica, sobre el rendimiento energético, a través de la pila de servicio de aprovisionamiento. Nos aprovechamos de esta métrica para derivar un marco de análisis de energía. Luego, se esboza un marco para analizar la eficacia energética en la nube asistida por P2P y en la plataforma de centros de datos para elegir la plataforma de servicios adecuada, de acuerdo con las características de rendimiento y energía. Este marco mapea la energía desde el alto nivel independiente del hardware a la configuración de hardware particular en la capa inferior de la pila. Posteriormente, se introduce un mecanismo basado en economía para aumentar la eficacia energética en la plataforma en la nube asistida por P2P, así como avanzar hacia unas TIC más verdes, para las TIC en un ecosistema más verde.Postprint (published version

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Un framework pour l'exécution efficace d'applications sur GPU et CPU+GPU

Technological limitations faced by the semi-conductor manufacturers in the early 2000's restricted the increase in performance of the sequential computation units. Nowadays, the trend is to increase the number of processor cores per socket and to progressively use the GPU cards for highly parallel computations. Complexity of the recent architectures makes it difficult to statically predict the performance of a program. We describe a reliable and accurate parallel loop nests execution time prediction method on GPUs based on three stages: static code generation, offline profiling, and online prediction. In addition, we present two techniques to fully exploit the computing resources at disposal on a system. The first technique consists in jointly using CPU and GPU for executing a code. In order to achieve higher performance, it is mandatory to consider load balance, in particular by predicting execution time. The runtime uses the profiling results and the scheduler computes the execution times and adjusts the load distributed to the processors. The second technique, puts CPU and GPU in a competition: instances of the considered code are simultaneously executed on CPU and GPU. The winner of the competition notifies its completion to the other instance, implying the termination of the latter.Les verrous technologiques rencontrés par les fabricants de semi-conducteurs au début des années deux-mille ont abrogé la flambée des performances des unités de calculs séquentielles. La tendance actuelle est à la multiplication du nombre de cœurs de processeur par socket et à l'utilisation progressive des cartes GPU pour des calculs hautement parallèles. La complexité des architectures récentes rend difficile l'estimation statique des performances d'un programme. Nous décrivons une méthode fiable et précise de prédiction du temps d'exécution de nids de boucles parallèles sur GPU basée sur trois étapes : la génération de code, le profilage offline et la prédiction online. En outre, nous présentons deux techniques pour exploiter l'ensemble des ressources disponibles d'un système pour la performance. La première consiste en l'utilisation conjointe des CPUs et GPUs pour l'exécution d'un code. Afin de préserver les performances il est nécessaire de considérer la répartition de charge, notamment en prédisant les temps d'exécution. Le runtime utilise les résultats du profilage et un ordonnanceur calcule des temps d'exécution et ajuste la charge distribuée aux processeurs. La seconde technique présentée met le CPU et le GPU en compétition : des instances du code cible sont exécutées simultanément sur CPU et GPU. Le vainqueur de la compétition notifie sa complétion à l'autre instance, impliquant son arrêt

Raster Time Series: Learning and Processing

As the amount of remote sensing data is increasing at a high rate, due to great improvements in sensor technology, efficient processing capabilities are of utmost importance. Remote sensing data from satellites is crucial in many scientific domains, like biodiversity and climate research. Because weather and climate are of particular interest for almost all living organisms on earth, the efficient classification of clouds is one of the most important problems. Geostationary satellites such as Meteosat Second Generation (MSG) offer the only possibility to generate long-term cloud data sets with high spatial and temporal resolution. This work, therefore, addresses research problems on efficient and parallel processing of MSG data to enable new applications and insights. First, we address the lack of a suitable processing chain to generate a long-term Fog and Low Stratus (FLS) time series. We present an efficient MSG data processing chain that processes multiple tasks simultaneously, and raster data in parallel using the Open Computing Language (OpenCL). The processing chain delivers a uniform FLS classification that combines day and night approaches in a single method. As a result, it is possible to calculate a year of FLS rasters quite easy. The second topic presents the application of Convolutional Neural Networks (CNN) for cloud classification. Conventional approaches to cloud detection often only classify single pixels and ignore the fact that clouds are highly dynamic and spatially continuous entities. Therefore, we propose a new method based on deep learning. Using a CNN image segmentation architecture, the presented Cloud Segmentation CNN (CS-CNN) classifies all pixels of a scene simultaneously. We show that CS-CNN is capable of processing multispectral satellite data to identify continuous phenomena such as highly dynamic clouds. The proposed approach provides excellent results on MSG satellite data in terms of quality, robustness, and runtime, in comparison to Random Forest (RF), another widely used machine learning method. Finally, we present the processing of raster time series with a system for Visualization, Transformation, and Analysis (VAT) of spatio-temporal data. It enables data-driven research with explorative workflows and uses time as an integral dimension. The combination of various raster and vector data time series enables new applications and insights. We present an application that combines weather information and aircraft trajectories to identify patterns in bad weather situations

Enabling Cyber-Physical Communication in 5G Cellular Networks: Challenges, Solutions and Applications

Cyber-physical systems (CPS) are expected to revolutionize the world through a myriad of applications in health-care, disaster event applications, environmental management, vehicular networks, industrial automation, and so on. The continuous explosive increase in wireless data traffic, driven by the global rise of smartphones, tablets, video streaming, and online social networking applications along with the anticipated wide massive sensors deployments, will create a set of challenges to network providers, especially that future fifth generation (5G) cellular networks will help facilitate the enabling of CPS communications over current network infrastructure. In this dissertation, we first provide an overview of CPS taxonomy along with its challenges from energy efficiency, security, and reliability. Then we present different tractable analytical solutions through different 5G technologies, such as device-to-device (D2D) communications, cell shrinking and offloading, in order to enable CPS traffic over cellular networks. These technologies also provide CPS with several benefits such as ubiquitous coverage, global connectivity, reliability and security. By tuning specific network parameters, the proposed solutions allow the achievement of balance and fairness in spectral efficiency and minimum achievable throughout among cellular users and CPS devices. To conclude, we present a CPS mobile-health application as a case study where security of the medical health cyber-physical space is discussed in details