Workflow models for heterogeneous distributed systems

The role of data in modern scientific workflows becomes more and more crucial. The unprecedented amount of data available in the digital era, combined with the recent advancements in Machine Learning and High-Performance Computing (HPC), let computers surpass human performances in a wide range of fields, such as Computer Vision, Natural Language Processing and Bioinformatics. However, a solid data management strategy becomes crucial for key aspects like performance optimisation, privacy preservation and security. Most modern programming paradigms for Big Data analysis adhere to the principle of data locality: moving computation closer to the data to remove transfer-related overheads and risks. Still, there are scenarios in which it is worth, or even unavoidable, to transfer data between different steps of a complex workflow. The contribution of this dissertation is twofold. First, it defines a novel methodology for distributed modular applications, allowing topology-aware scheduling and data management while separating business logic, data dependencies, parallel patterns and execution environments. In addition, it introduces computational notebooks as a high-level and user-friendly interface to this new kind of workflow, aiming to flatten the learning curve and improve the adoption of such methodology. Each of these contributions is accompanied by a full-fledged, Open Source implementation, which has been used for evaluation purposes and allows the interested reader to experience the related methodology first-hand. The validity of the proposed approaches has been demonstrated on a total of five real scientific applications in the domains of Deep Learning, Bioinformatics and Molecular Dynamics Simulation, executing them on large-scale mixed cloud-High-Performance Computing (HPC) infrastructures

Power-Aware Job Dispatching in High Performance Computing Systems

This works deals with the power-aware job dispatching problem in supercomputers; broadly speaking the dispatching consists of assigning finite capacity resources to a set of activities, with a special concern toward power and energy efficient solutions. We introduce novel optimization approaches to address its multiple aspects. The proposed techniques have a broad application range but are aimed at applications in the field of High Performance Computing (HPC) systems. Devising a power-aware HPC job dispatcher is a complex, where contrasting goals must be satisfied. Furthermore, the online nature of the problem request that solutions must be computed in real time respecting stringent limits. This aspect historically discouraged the usage of exact methods and favouring instead the adoption of heuristic techniques. The application of optimization approaches to the dispatching task is still an unexplored area of research and can drastically improve the performance of HPC systems. In this work we tackle the job dispatching problem on a real HPC machine, the Eurora supercomputer hosted at the Cineca research center, Bologna. We propose a Constraint Programming (CP) model that outperforms the dispatching software currently in use. An essential element to take power-aware decisions during the job dispatching phase is the possibility to estimate jobs power consumptions before their execution. To this end, we applied Machine Learning techniques to create a prediction model that was trained and tested on the Euora supercomputer, showing a great prediction accuracy. Then we finally develop a power-aware solution, considering the same target machine, and we devise different approaches to solve the dispatching problem while curtailing the power consumption of the whole system under a given threshold. We proposed a heuristic technique and a CP/heuristic hybrid method, both able to solve practical size instances and outperform the current state-of-the-art techniques

Contribution à la convergence d'infrastructure entre le calcul haute performance et le traitement de données à large échelle

The amount of produced data, either in the scientific community or the commercialworld, is constantly growing. The field of Big Data has emerged to handle largeamounts of data on distributed computing infrastructures. High-Performance Computing (HPC) infrastructures are traditionally used for the execution of computeintensive workloads. However, the HPC community is also facing an increasingneed to process large amounts of data derived from high definition sensors andlarge physics apparati. The convergence of the two fields -HPC and Big Data- iscurrently taking place. In fact, the HPC community already uses Big Data tools,which are not always integrated correctly, especially at the level of the file systemand the Resource and Job Management System (RJMS).In order to understand how we can leverage HPC clusters for Big Data usage, andwhat are the challenges for the HPC infrastructures, we have studied multipleaspects of the convergence: We initially provide a survey on the software provisioning methods, with a focus on data-intensive applications. We contribute a newRJMS collaboration technique called BeBiDa which is based on 50 lines of codewhereas similar solutions use at least 1000 times more. We evaluate this mechanism on real conditions and in simulated environment with our simulator Batsim.Furthermore, we provide extensions to Batsim to support I/O, and showcase thedevelopments of a generic file system model along with a Big Data applicationmodel. This allows us to complement BeBiDa real conditions experiments withsimulations while enabling us to study file system dimensioning and trade-offs.All the experiments and analysis of this work have been done with reproducibilityin mind. Based on this experience, we propose to integrate the developmentworkflow and data analysis in the reproducibility mindset, and give feedback onour experiences with a list of best practices.RésuméLa quantité de données produites, que ce soit dans la communauté scientifiqueou commerciale, est en croissance constante. Le domaine du Big Data a émergéface au traitement de grandes quantités de données sur les infrastructures informatiques distribuées. Les infrastructures de calcul haute performance (HPC) sont traditionnellement utilisées pour l’exécution de charges de travail intensives en calcul. Cependant, la communauté HPC fait également face à un nombre croissant debesoin de traitement de grandes quantités de données dérivées de capteurs hautedéfinition et de grands appareils physique. La convergence des deux domaines-HPC et Big Data- est en cours. En fait, la communauté HPC utilise déjà des outilsBig Data, qui ne sont pas toujours correctement intégrés, en particulier au niveaudu système de fichiers ainsi que du système de gestion des ressources (RJMS).Afin de comprendre comment nous pouvons tirer parti des clusters HPC pourl’utilisation du Big Data, et quels sont les défis pour les infrastructures HPC, nousavons étudié plusieurs aspects de la convergence: nous avons d’abord proposé uneétude sur les méthodes de provisionnement logiciel, en mettant l’accent sur lesapplications utilisant beaucoup de données. Nous contribuons a l’état de l’art avecune nouvelle technique de collaboration entre RJMS appelée BeBiDa basée sur 50lignes de code alors que des solutions similaires en utilisent au moins 1000 fois plus.Nous évaluons ce mécanisme en conditions réelles et en environnement simuléavec notre simulateur Batsim. En outre, nous fournissons des extensions à Batsimpour prendre en charge les entrées/sorties et présentons le développements d’unmodèle de système de fichiers générique accompagné d’un modèle d’applicationBig Data. Cela nous permet de compléter les expériences en conditions réellesde BeBiDa en simulation tout en étudiant le dimensionnement et les différentscompromis autours des systèmes de fichiers.Toutes les expériences et analyses de ce travail ont été effectuées avec la reproductibilité à l’esprit. Sur la base de cette expérience, nous proposons d’intégrerle flux de travail du développement et de l’analyse des données dans l’esprit dela reproductibilité, et de donner un retour sur nos expériences avec une liste debonnes pratiques

Parallel optimization algorithms for high performance computing : application to thermal systems

The need of optimization is present in every field of engineering. Moreover, applications requiring a multidisciplinary approach in order to make a step forward are increasing. This leads to the need of solving complex optimization problems that exceed the capacity of human brain or intuition. A standard way of proceeding is to use evolutionary algorithms, among which genetic algorithms hold a prominent place. These are characterized by their robustness and versatility, as well as their high computational cost and low convergence speed. Many optimization packages are available under free software licenses and are representative of the current state of the art in optimization technology. However, the ability of optimization algorithms to adapt to massively parallel computers reaching satisfactory efficiency levels is still an open issue. Even packages suited for multilevel parallelism encounter difficulties when dealing with objective functions involving long and variable simulation times. This variability is common in Computational Fluid Dynamics and Heat Transfer (CFD & HT), nonlinear mechanics, etc. and is nowadays a dominant concern for large scale applications. Current research in improving the performance of evolutionary algorithms is mainly focused on developing new search algorithms. Nevertheless, there is a vast knowledge of sequential well-performing algorithmic suitable for being implemented in parallel computers. The gap to be covered is efficient parallelization. Moreover, advances in the research of both new search algorithms and efficient parallelization are additive, so that the enhancement of current state of the art optimization software can be accelerated if both fronts are tackled simultaneously. The motivation of this Doctoral Thesis is to make a step forward towards the successful integration of Optimization and High Performance Computing capabilities, which has the potential to boost technological development by providing better designs, shortening product development times and minimizing the required resources. After conducting a thorough state of the art study of the mathematical optimization techniques available to date, a generic mathematical optimization tool has been developed putting a special focus on the application of the library to the field of Computational Fluid Dynamics and Heat Transfer (CFD & HT). Then the main shortcomings of the standard parallelization strategies available for genetic algorithms and similar population-based optimization methods have been analyzed. Computational load imbalance has been identified to be the key point causing the degradation of the optimization algorithm¿s scalability (i.e. parallel efficiency) in case the average makespan of the batch of individuals is greater than the average time required by the optimizer for performing inter-processor communications. It occurs because processors are often unable to finish the evaluation of their queue of individuals simultaneously and need to be synchronized before the next batch of individuals is created. Consequently, the computational load imbalance is translated into idle time in some processors. Several load balancing algorithms have been proposed and exhaustively tested, being extendable to any other population-based optimization method that needs to synchronize all processors after the evaluation of each batch of individuals. Finally, a real-world engineering application that consists on optimizing the refrigeration system of a power electronic device has been presented as an illustrative example in which the use of the proposed load balancing algorithms is able to reduce the simulation time required by the optimization tool.El aumento de las aplicaciones que requieren de una aproximación multidisciplinar para poder avanzar se constata en todos los campos de la ingeniería, lo cual conlleva la necesidad de resolver problemas de optimización complejos que exceden la capacidad del cerebro humano o de la intuición. En estos casos es habitual el uso de algoritmos evolutivos, principalmente de los algoritmos genéticos, caracterizados por su robustez y versatilidad, así como por su gran coste computacional y baja velocidad de convergencia. La multitud de paquetes de optimización disponibles con licencias de software libre representan el estado del arte actual en tecnología de optimización. Sin embargo, la capacidad de adaptación de los algoritmos de optimización a ordenadores masivamente paralelos alcanzando niveles de eficiencia satisfactorios es todavía una tarea pendiente. Incluso los paquetes adaptados al paralelismo multinivel tienen dificultades para gestionar funciones objetivo que requieren de tiempos de simulación largos y variables. Esta variabilidad es común en la Dinámica de Fluidos Computacional y la Transferencia de Calor (CFD & HT), mecánica no lineal, etc. y es una de las principales preocupaciones en aplicaciones a gran escala a día de hoy. La investigación actual que tiene por objetivo la mejora del rendimiento de los algoritmos evolutivos está enfocada principalmente al desarrollo de nuevos algoritmos de búsqueda. Sin embargo, ya se conoce una gran variedad de algoritmos secuenciales apropiados para su implementación en ordenadores paralelos. La tarea pendiente es conseguir una paralelización eficiente. Además, los avances en la investigación de nuevos algoritmos de búsqueda y la paralelización son aditivos, por lo que el proceso de mejora del software de optimización actual se verá incrementada si se atacan ambos frentes simultáneamente. La motivación de esta Tesis Doctoral es avanzar hacia una integración completa de las capacidades de Optimización y Computación de Alto Rendimiento para así impulsar el desarrollo tecnológico proporcionando mejores diseños, acortando los tiempos de desarrollo del producto y minimizando los recursos necesarios. Tras un exhaustivo estudio del estado del arte de las técnicas de optimización matemática disponibles a día de hoy, se ha diseñado una librería de optimización orientada al campo de la Dinámica de Fluidos Computacional y la Transferencia de Calor (CFD & HT). A continuación se han analizado las principales limitaciones de las estrategias de paralelización disponibles para algoritmos genéticos y otros métodos de optimización basados en poblaciones. En el caso en que el tiempo de evaluación medio de la tanda de individuos sea mayor que el tiempo medio que necesita el optimizador para llevar a cabo comunicaciones entre procesadores, se ha detectado que la causa principal de la degradación de la escalabilidad o eficiencia paralela del algoritmo de optimización es el desequilibrio de la carga computacional. El motivo es que a menudo los procesadores no terminan de evaluar su cola de individuos simultáneamente y deben sincronizarse antes de que se cree la siguiente tanda de individuos. Por consiguiente, el desequilibrio de la carga computacional se convierte en tiempo de inactividad en algunos procesadores. Se han propuesto y testado exhaustivamente varios algoritmos de equilibrado de carga aplicables a cualquier método de optimización basado en una población que necesite sincronizar los procesadores tras cada tanda de evaluaciones. Finalmente, se ha presentado como ejemplo ilustrativo un caso real de ingeniería que consiste en optimizar el sistema de refrigeración de un dispositivo de electrónica de potencia. En él queda demostrado que el uso de los algoritmos de equilibrado de carga computacional propuestos es capaz de reducir el tiempo de simulación que necesita la herramienta de optimización

Combining SOA and BPM Technologies for Cross-System Process Automation

This paper summarizes the results of an industry case study that introduced a cross-system business process automation solution based on a combination of SOA and BPM standard technologies (i.e., BPMN, BPEL, WSDL). Besides discussing major weaknesses of the existing, custom-built, solution and comparing them against experiences with the developed prototype, the paper presents a course of action for transforming the current solution into the proposed solution. This includes a general approach, consisting of four distinct steps, as well as specific action items that are to be performed for every step. The discussion also covers language and tool support and challenges arising from the transformation

Empirics-based Line Searches for Deep Learning

This dissertation takes an empirically based perspective on optimization in deep learning. It is motivated by the lack of empirical understanding of the loss landscape's properties for typical deep learning tasks and a lack of understanding of why and how optimization approaches work for such tasks. We solidified the empirical understanding of stochastic loss landscapes to bring color to these white areas on the scientific map with empiric observations. Based on these observations, we introduce understandable line search approaches that compete with and, in many cases outperform, state-of-the-art line search approaches introduced for the deep learning field. This work includes a comprehensive introduction to optimization focusing on line searches in the deep learning field. Based on and guided by this introduction, empirical observations of typical image-classification benchmark tasks' loss landscapes are presented. Further, observations of how optimizers perform and move on such loss landscapes are given. From these observations, the line search approaches Parabolic Approximation Line Search (PAL) and Large Batch Parabolic Approximation Line Search (LABPAL) are derived. In particular, the latter method outperforms all competing line searches in this field in most cases. Furthermore, these observations reveal that well-tuned Stochastic Gradient Descent is already well approximating an almost exact line search, which in parts explains why it is so hard to beat. Given the empirical observations made, it is straightforward to comprehend why and how our optimization approaches work. This contrasts the methodology of many optimization papers in this field which builds upon non-empirically justified theoretical assumptions. Consequently, a general contribution of this work is that it justifies and demonstrates the importance of empirical work in this rather theoretical field