Parallel Programming with Global Asynchronous Memory: Models, C++ APIs and Implementations

In the realm of High Performance Computing (HPC), message passing has been the programming paradigm of choice for over twenty years. The durable MPI (Message Passing Interface) standard, with send/receive communication, broadcast, gather/scatter, and reduction collectives is still used to construct parallel programs where each communication is orchestrated by the developer-based precise knowledge of data distribution and overheads; collective communications simplify the orchestration but might induce excessive synchronization. Early attempts to bring shared-memory programming model—with its programming advantages—to distributed computing, referred as the Distributed Shared Memory (DSM) model, faded away; one of the main issue was to combine performance and programmability with the memory consistency model. The recently proposed Partitioned Global Address Space (PGAS) model is a modern revamp of DSM that exposes data placement to enable optimizations based on locality, but it still addresses (simple) data- parallelism only and it relies on expensive sharing protocols. We advocate an alternative programming model for distributed computing based on a Global Asynchronous Memory (GAM), aiming to avoid coherency and consistency problems rather than solving them. We materialize GAM by designing and implementing a distributed smart pointers library, inspired by C++ smart pointers. In this model, public and pri- vate pointers (resembling C++ shared and unique pointers, respectively) are moved around instead of messages (i.e., data), thus alleviating the user from the burden of minimizing transfers. On top of smart pointers, we propose a high-level C++ template library for writing applications in terms of dataflow-like networks, namely GAM nets, consisting of stateful processors exchanging pointers in fully asynchronous fashion. We demonstrate the validity of the proposed approach, from the expressiveness perspective, by showing how GAM nets can be exploited to implement both standalone applications and higher-level parallel program- ming models, such as data and task parallelism. As for the performance perspective, preliminary experiments show both close-to-ideal scalability and negligible overhead with respect to state-of-the-art benchmark implementations. For instance, the GAM implementation of a high-quality video restoration filter sustains a 100 fps throughput over 70%-noisy high-quality video streams on a 4-node cluster of Graphics Processing Units (GPUs), with minimal programming effort

Twenty years of rewriting logic

AbstractRewriting logic is a simple computational logic that can naturally express both concurrent computation and logical deduction with great generality. This paper provides a gentle, intuitive introduction to its main ideas, as well as a survey of the work that many researchers have carried out over the last twenty years in advancing: (i) its foundations; (ii) its semantic framework and logical framework uses; (iii) its language implementations and its formal tools; and (iv) its many applications to automated deduction, software and hardware specification and verification, security, real-time and cyber-physical systems, probabilistic systems, bioinformatics and chemical systems

Interim research assessment 2003-2005 - Computer Science

This report primarily serves as a source of information for the 2007 Interim Research Assessment Committee for Computer Science at the three technical universities in the Netherlands. The report also provides information for others interested in our research activities

Modélisation à haut niveau d'abstraction pour les systèmes embarqués

Modern embedded systems have reached a level of complexity such that it is no longer possible to wait for the first physical prototypes to validate choices on the integration of hardware and software components. It is necessary to use models, early in the design flow. The work presented in this document contribute to the state of the art in several domains. First, we present some verification techniques based on abstract interpretation and SMT-solving for programs written in general-purpose languages like C, C++ or Java. Then, we use verification tools on models written in SystemC at the transaction level (TLM). Several approaches are presented, most of them using compilation techniques specific to SystemC to turn the models into a format usable by existing tools. The second part of the document deal with non-functional properties of models: timing performances, power consumption and temperature. In the context of TLM, we show how functional models can be enriched with non-functional information. Finally, we present contributions to the modular performance analysis (MPA) with real-time calculus (RTC) framework. We describe several ways to connect RTC to more expressive formalisms like timed automata and the synchronous language Lustre. These connections raise the problem of causality, which is defined formally and solved with the new causality closure algorithm.Les systèmes embarqués modernes ont atteint un niveau de complexité qui fait qu'il n'est plus possible d'attendre les premiers prototypes physiques pour valider les décisions sur l'intégration des composants matériels et logiciels. Il est donc nécessaire d'utiliser des modèles, tôt dans le flot de conception. Les travaux présentés dans ce document contribuent à l'état de l'art dans plusieurs domaines. Nous présentons dans un premier temps de nouvelles techniques de vérification de programmes écrits dans des langages généralistes comme C, C++ ou Java. Dans un second temps, nous utilisons des outils de vérification formelle sur des modèles écrits en SystemC au niveau transaction (TLM). Plusieurs approches sont présentées, la plupart d'entre elles utilisent des techniques de compilations spécifiques à SystemC pour transformer le programme SystemC en un format utilisable par les outils. La seconde partie du document s'intéresse aux propriétés non-fonctionnelles des modèles~: performances temporelles, consommation électrique et température. Dans le contexte de la modélisation TLM, nous proposons plusieurs techniques pour enrichir des modèles fonctionnels avec des informations non-fonctionnelles. Enfin, nous présentons les contributions faites à l'analyse de performance modulaire (MPA) avec le calcul temps-réel (RTC). Nous proposons plusieurs connections entre ces modèles analytiques et des formalismes plus expressifs comme les automates temporisés et le langage de programmation Lustre. Ces connexion posent le problème théorique de la causalité, qui est formellement défini et résolu avec un algorithme nouveau dit de " fermeture causale "

Finite horizon analysis of Markov automata

Markov automata constitute an expressive continuous-time compositional modelling formalism, featuring stochastic timing and nondeterministic as well as probabilistic branching, all supported in one model. They span as special cases, the models of discrete and continuous-time Markov chains, as well as interactive Markov chains and probabilistic automata. Moreover, they might be equipped with reward and resource structures in order to be used for analysing quantitative aspects of systems, like performance metrics, energy consumption, repair and maintenance costs. Due to their expressive nature, they serve as semantic backbones of engineering frameworks, control applications and safety critical systems. The Architecture Analysis and Design Language (AADL), Dynamic Fault Trees (DFT) and Generalised Stochastic Petri Nets (GSPN) are just some examples. Their expressiveness thus far prevents them from efficient analysis by stochastic solvers and probabilistic model checkers. A major problem context of this thesis lies in their analysis under some budget constraints, i.e. when only a finite budget of resources can be spent by the model. We study mathematical foundations of Markov automata since these are essential for the analysis addressed in this thesis. This includes, in particular, understanding their measurability and establishing their probability measure. Furthermore, we address the analysis of Markov automata in the presence of both reward acquisition and resource consumption within a finite budget of resources. More specifically, we put the problem of computing the optimal expected resource-bounded reward in our focus. In our general setting, we support transient, instantaneous and final reward collection as well as transient resource consumption. Our general formulation of the problem encompasses in particular the optimal time-bound reward and reachability as well as resource-bounded reachability. We develop a sound theory together with a stable approximation scheme with a strict error bound to solve the problem in an efficient way. We report on an implementation of our approach in a supporting tool and also demonstrate its effectiveness and usability over an extensive collection of industrial and academic case studies.Markov-Automaten bilden einen mächtigen Formalismus zur kompositionellen Modellierung mit kontinuierlicher stochastischer Zeit und nichtdeterministischer sowie probabilistischer Verzweigung, welche alle in einem Modell unterstützt werden. Sie enthalten als Spezialfälle die Modelle diskreter und kontinuierlicher Markov-Ketten sowie interaktive Markov-Ketten und probabilistischer Automaten. Darüber hinaus können sie mit Belohnungs- und Ressourcenstrukturen ausgestattet werden, um quantitative Aspekte von Systemen wie Leistungsfähigkeit, Energieverbrauch, Reparatur- und Wartungskosten zu analysieren. Sie dienen aufgrund ihrer Ausdruckskraft als semantisches Rückgrat von Engineering Frameworks, Steuerungsanwendungen und sicherheitskritischen Systemen. Die Architekturanalyse und Designsprache (AADL), Dynamic Fault Trees (DFT) und Generalized Stochastic Petri Nets (GSPN) sind nur einige Beispiele dafür. Ihre Aussagekraft verhindert jedoch bisher eine effiziente Analyse durch stochastische Löser und probabilistische Modellprüfer. Ein wichtiger Problemzusammenhang dieser Arbeit liegt in ihrer Analyse unter Budgetbeschränkungen, das heisst wenn nur ein begrenztes Budget an Ressourcen vom Modell aufgewendet werden kann. Wir studieren mathematische Grundlagen von Markov-Automaten, da diese für die in dieser Arbeit angesprochene Analyse von wesentlicher Bedeutung sind. Dazu gehört insbesondere das Verständnis ihrer Messbarkeit und die Festlegung ihrer Wahrscheinlichkeitsmaßes. Darüber hinaus befassen wir uns mit der Analyse von Markov-Automaten in Bezug auf Belohnungserwerb sowie Ressourcenverbrauch innerhalb eines begrenzten Ressourcenbudgets. Genauer gesagt stellen wir das Problem der Berechnung der optimalen erwarteten Ressourcen-begrenzte Belohnung in unserem Fokus. Dieser Fokus umfasst transiente, sofortige und endgültige Belohnungssammlung sowie transienten Ressourcenverbrauch. Unsere allgemeine Formulierung des Problems beinhalet insbesondere die optimale zeitgebundene Belohnung und Erreichbarkeit sowie ressourcenbeschränkte Erreichbarkeit. Wir entwickeln die grundlegende Theorie dazu. Zur effizienten Lösung des Problems entwerfen wir ein stabilen Approximationsschema mit einer strikten Fehlerschranke. Wir berichten über eine Umsetzung unseres Ansatzes in einem Software-Werkzeug und zeigen seine Wirksamkeit und Verwendbarkeit anhand einer umfangreichen Sammlung von industriellen und akademischen Fallstudien

Continuous-time temporal logic specification and verification for nonlinear biological systems in uncertain contexts

In this thesis we introduce a complete framework for modelling and verification of biological systems in uncertain contexts based on the bond-calculus process algebra and the LBUC spatio-temporal logic. The bond-calculus is a biological process algebra which captures complex patterns of interaction based on affinity patterns, a novel communication mechanism using pattern matching to express multiway interaction affinities and general kinetic laws, whilst retaining an agent-centric modelling style for biomolecular species. The bond-calculus is equipped with a novel continuous semantics which maps models to systems of Ordinary Differential Equations (ODEs) in a compositional way. We then extend the bond-calculus to handle uncertain models, featuring interval uncertainties in their species concentrations and reaction rate parameters. Our semantics is also extended to handle uncertainty in every aspect of a model, producing non-deterministic continuous systems whose behaviour depends either on time-independent uncertain parameters and initial conditions, corresponding to our partial knowledge of the system at hand, or time-varying uncertain inputs, corresponding to genuine variability in a system’s behaviour based on environmental factors. This language is then coupled with the LBUC spatio-temporal logic which combines Signal Temporal Logic (STL) temporal operators with an uncertain context operator which quantifies over an uncertain context model describing the range of environments over which a property must hold. We develop model-checking procedures for STL and LBUC properties based on verified signal monitoring over flowpipes produced by the Flow* verified integrator, including the technique of masking which directs monitoring for atomic propositions to time regions relevant to the overall verification problem at hand. This allows us to monitor many interesting nested contextual properties and frequently reduces monitoring costs by an order of magnitude. Finally, we explore the technique of contextual signal monitoring which can use a single Flow* flowpipe representing a functional dependency to complete a whole tree of signals corresponding to different uncertain contexts. This allows us to produce refined monitoring results over the whole space and to explore the variation in system behaviour in different contexts