Developing a distributed electronic health-record store for India

The DIGHT project is addressing the problem of building a scalable and highly available information store for the Electronic Health Records (EHRs) of the over one billion citizens of India

Contributions to Desktop Grid Computing : From High Throughput Computing to Data-Intensive Sciences on Hybrid Distributed Computing Infrastructures

Since the mid 90’s, Desktop Grid Computing - i.e the idea of using a large number of remote PCs distributed on the Internet to execute large parallel applications - has proved to be an efficient paradigm to provide a large computational power at the fraction of the cost of a dedicated computing infrastructure.This document presents my contributions over the last decade to broaden the scope of Desktop Grid Computing. My research has followed three different directions. The first direction has established new methods to observe and characterize Desktop Grid resources and developed experimental platforms to test and validate our approach in conditions close to reality. The second line of research has focused on integrating Desk- top Grids in e-science Grid infrastructure (e.g. EGI), which requires to address many challenges such as security, scheduling, quality of service, and more. The third direction has investigated how to support large-scale data management and data intensive applica- tions on such infrastructures, including support for the new and emerging data-oriented programming models.This manuscript not only reports on the scientific achievements and the technologies developed to support our objectives, but also on the international collaborations and projects I have been involved in, as well as the scientific mentoring which motivates my candidature for the Habilitation `a Diriger les Recherches

Multi-GPU support on the marrow algorithmic skeleton framework

Dissertação para obtenção do Grau de Mestre em Engenharia InformáticaWith the proliferation of general purpose GPUs, workload parallelization and datatransfer optimization became an increasing concern. The natural evolution from using a single GPU, is multiplying the amount of available processors, presenting new challenges, as tuning the workload decompositions and load balancing, when dealing with heterogeneous systems. Higher-level programming is a very important asset in a multi-GPU environment, due to the complexity inherent to the currently used GPGPU APIs (OpenCL and CUDA), because of their low-level and code overhead. This can be obtained by introducing an abstraction layer, which has the advantage of enabling implicit optimizations and orchestrations such as transparent load balancing mechanism and reduced explicit code overhead. Algorithmic Skeletons, previously used in cluster environments, have recently been adapted to the GPGPU context. Skeletons abstract most sources of code overhead, by defining computation patterns of commonly used algorithms. The Marrow algorithmic skeleton library is one of these, taking advantage of the abstractions to automate the orchestration needed for an efficient GPU execution. This thesis proposes the extension of Marrow to leverage the use of algorithmic skeletons in the modular and efficient programming of multiple heterogeneous GPUs, within a single machine. We were able to achieve a good balance between simplicity of the programming model and performance, obtaining good scalability when using multiple GPUs, with an efficient load distribution, although at the price of some overhead when using a single-GPU.projects PTDC/EIA-EIA/102579/2008 and PTDC/EIA-EIA/111518/200

Contribution au calcul sur GPU: considérations arithmétiques et architecturales

L’optimisation du calcul passe par une gestion conjointe du matériel et du logiciel. Cette règle se trouve renforcée lorsque l’on aborde le domaine des architectures multicoeurs où les paramètres à considérer sont plus nombreux que sur une architecture superscalaire classique. Ces architectures offrent une grande variété d’unité de calcul, de format de représentation, de hiérarchie mémoire et de mécanismes de transfert de donnée.Dans ce mémoire, nous décrivons quelques-uns de nos résultats obtenus entre 2004 et 2013 au sein de l'équipe DALI de l'Université de Perpignan relatifs à l'amélioration de l’efficacité du calcul dans sa globalité, c'est-à-dire dans la suite d’opérations décrite au niveau algorithmique et exécutées par les éléments architecturaux, en nous concentrant sur les processeurs graphiques.Nous commençons par une description du fonctionnement de ce type d'architecture, en nous attardant sur le calcul flottant. Nous présentons ensuite des implémentations efficaces d'opérateurs arithmétiques utilisant des représentations non-conventionnelles comme l'arithmétique multiprécision, par intervalle, floue ou logarithmique. Nous continuerons avec nos contributions relatives aux éléments architecturaux associés au calcul à travers la simulation fonctionnelle, les bancs de registres, la gestion des branchements ou les opérateurs matériels spécialisés. Enfin, nous terminerons avec une analyse du comportement du calcul sur les GPU relatif à la régularité, à la consommation électrique, à la fiabilisation des calculs ainsi qu'à laprédictibilité

On Cluster Resource Allocation for Multiple Parallel Task Graphs

Many scientific applications can be structured as Parallel Task Graphs (PTGs), that is, graphs of data-parallel tasks. Adding data-parallelism to a task-parallel application provides opportunities for higher performance and scalability, but poses additional scheduling challenges. In this paper, we study the off-line scheduling of multiple PTGs on a single, homogeneous cluster. The objective is to optimize performance without compromising fairness among the PTGs. We consider the range of previously proposed scheduling algorithms applicable to this problem, both from the applied and the theoretical literature, and we propose minor improvements when possible. Our main contribution is an extensive evaluation of these algorithms in simulation, using both synthetic and real-world application configurations, using two different metrics for performance and one metric for fairness. We identify a handful of algorithms that provide good trade-offs when considering all these metrics. The best algorithm overall is one that structures the schedule as a sequence of phases of increasing duration based on a makespan guarantee produced by an approximation algorithm

Contracts for Systems Design: Theory

Aircrafts, trains, cars, plants, distributed telecommunication military or health care systems,and more, involve systems design as a critical step. Complexity has caused system design times and coststo go severely over budget so as to threaten the health of entire industrial sectors. Heuristic methods andstandard practices do not seem to scale with complexity so that novel design methods and tools based on astrong theoretical foundation are sorely needed. Model-based design as well as other methodologies suchas layered and compositional design have been used recently but a unified intellectual framework with acomplete design flow supported by formal tools is still lacking.Recently an “orthogonal” approach has been proposed that can be applied to all methodologies introducedthus far to provide a rigorous scaffolding for verification, analysis and abstraction/refinement: contractbaseddesign. Several results have been obtained in this domain but a unified treatment of the topic that canhelp in putting contract-based design in perspective is missing. This paper intends to provide such treatmentwhere contracts are precisely defined and characterized so that they can be used in design methodologiessuch as the ones mentioned above with no ambiguity. In addition, the paper provides an important linkbetween interface and contract theories to show similarities and correspondences.This paper is complemented by a companion paper where contract based design is illustrated throughuse cases

Reliable massively parallel symbolic computing : fault tolerance for a distributed Haskell

As the number of cores in manycore systems grows exponentially, the number of failures is also predicted to grow exponentially. Hence massively parallel computations must be able to tolerate faults. Moreover new approaches to language design and system architecture are needed to address the resilience of massively parallel heterogeneous architectures. Symbolic computation has underpinned key advances in Mathematics and Computer Science, for example in number theory, cryptography, and coding theory. Computer algebra software systems facilitate symbolic mathematics. Developing these at scale has its own distinctive set of challenges, as symbolic algorithms tend to employ complex irregular data and control structures. SymGridParII is a middleware for parallel symbolic computing on massively parallel High Performance Computing platforms. A key element of SymGridParII is a domain specific language (DSL) called Haskell Distributed Parallel Haskell (HdpH). It is explicitly designed for scalable distributed-memory parallelism, and employs work stealing to load balance dynamically generated irregular task sizes. To investigate providing scalable fault tolerant symbolic computation we design, implement and evaluate a reliable version of HdpH, HdpH-RS. Its reliable scheduler detects and handles faults, using task replication as a key recovery strategy. The scheduler supports load balancing with a fault tolerant work stealing protocol. The reliable scheduler is invoked with two fault tolerance primitives for implicit and explicit work placement, and 10 fault tolerant parallel skeletons that encapsulate common parallel programming patterns. The user is oblivious to many failures, they are instead handled by the scheduler. An operational semantics describes small-step reductions on states. A simple abstract machine for scheduling transitions and task evaluation is presented. It defines the semantics of supervised futures, and the transition rules for recovering tasks in the presence of failure. The transition rules are demonstrated with a fault-free execution, and three executions that recover from faults. The fault tolerant work stealing has been abstracted in to a Promela model. The SPIN model checker is used to exhaustively search the intersection of states in this automaton to validate a key resiliency property of the protocol. It asserts that an initially empty supervised future on the supervisor node will eventually be full in the presence of all possible combinations of failures. The performance of HdpH-RS is measured using five benchmarks. Supervised scheduling achieves a speedup of 757 with explicit task placement and 340 with lazy work stealing when executing Summatory Liouville up to 1400 cores of a HPC architecture. Moreover, supervision overheads are consistently low scaling up to 1400 cores. Low recovery overheads are observed in the presence of frequent failure when lazy on-demand work stealing is used. A Chaos Monkey mechanism has been developed for stress testing resiliency with random failure combinations. All unit tests pass in the presence of random failure, terminating with the expected results

Explorer l’hétérogénéité dans la réplication de données décentralisées faiblement cohérentes

Decentralized systems are scalable by design but also difficult to coordinate due to their weak coupling. Replicating data in these geo-distributed systems is therefore a challenge inherent to their structure. The two contributions of this thesis exploit the heterogeneity of user requirements and enable personalizable quality of services for data replication in decentralized systems. Our first contribution Gossip Primary-Secondary enables the consistency criterion Update consistency Primary-Secondary to offer differentiated guarantees in terms of consistency and message delivery latency for large-scale data replication. Our second contribution Dietcoin enriches Bitcoin with diet nodes that can (i) verify the correctness of entire subchains of blocks while avoiding the exorbitant cost of bootstrap verification and (ii) personalize their own security and resource consumption guarantees.Les systèmes décentralisés sont par nature extensibles mais sont également difficiles à coordonner en raison de leur faible couplage. La réplication de données dans ces systèmes géo-répartis est donc un défi inhérent à leur structure. Les deux contributions de cette thèse exploitent l'hétérogénéité des besoins des utilisateurs et permettent une qualité de service personnalisable pour la réplication de données dans les systèmes décentralisés. Notre première contribution Gossip Primary-Secondary étend le critère de cohérence Update consistency Primary-Secondary afin d'offrir des garanties différenciées de cohérence et de latence de messages pour la réplication de données à grande échelle. Notre seconde contribution Dietcoin enrichit Bitcoin avec des nœuds diet qui peuvent (i) vérifier la validité de sous-chaînes de blocs en évitant le coût exorbitant de la vérification initiale et (ii) choisir leur propres garanties de sécurité et de consommation de ressources

RDF Data Indexing and Retrieval: A survey of Peer-to-Peer based solutions

The Semantic Web enables the possibility to model, create and query resources found on the Web. Enabling the full potential of its technologies at the Internet level requires infrastructures that can cope with scalability challenges and support various types of queries. The attractive features of the Peer-to-Peer (P2P) communication model such as decentralization, scalability, fault-tolerance seems to be a natural solution to deal with these challenges. Consequently, the combination of the Semantic Web and the P2P model can be a highly innovative attempt to harness the strengths of both technologies and come up with a scalable infrastructure for RDF data storage and retrieval. In this respect, this survey details the research works that adopt this combination and gives an insight on how to deal with the RDF data at the indexing and querying levels.Le Web Sémantique permet de modéliser, créer et faire des requêtes sur les ressources disponibles sur le Web. Afin de permettre à ses technologies d'exploiter leurs potentiels à l'échelle de l'Internet, il est nécessaire qu'elles reposent sur des infrastructures qui puissent passer à l'échelle ainsi que de répondre aux exigences d'expressivité des types de requêtes qu'elles offrent. Les bonnes propriétés qu'offrent les dernières générations de systèmes pair-à- pair en termes de décentralisation, de tolérance aux pannes ainsi que de passage à l'échelle en font d'eux des candidats prometteurs. La combinaison du modèle pair-à-pair et des technologies du Web Sémantique est une tentative innovante ayant pour but de fournir une infrastructure capable de passer à l'échelle et pouvant stocker et rechercher des données de type RDF. Dans ce contexte, ce rapport présente un état de l'art et discute en détail des travaux autour de systèmes pair-à-pair qui traitent des données de type RDF à large échelle. Nous détaillons leurs mécanismes d'indexation de données ainsi que le traitement des divers types de requêtes offerts