{MAHEVE}: An Efficient Reliable Mapping of Asynchronous Iterative Applications on volatile and Heterogeneous Environments

International audienceThe asynchronous iteration model, called AIAC, has been proven to be an efficient solution for heterogeneous and distributed architectures. An efficient mapping of application tasks is essential to reduce their execution time. In this paper we present a new mapping algorithm, called MAHEVE (Mapping Algorithm for HEterogeneous and Volatile Environments) which is efficient on such architectures and integrates a fault tolerance mechanism to resist computing node failures. Our experiments show gains on a typical AIAC application execution time up to 65%, executed on distributed clusters architectures containing more than 400 computing cores with the JaceP2P-V2 environment

Adaptation and Evaluation of the Multisplitting-Newton and Waveform Relaxation Methods Over Distributed Volatile Environments

International audienceThis paper presents new adaptations of two methods that solve large differential equations systems, to the grid context. The first method isbased on the Multisplitting concept and the second on the Waveform Relaxation concept. Their adaptations are implemented according to the asynchronous iteration model which is well suited to volatile architectures that suffer from high latency networks. Many experiments were conducted to evaluate and compare the accuracy and performance of both methods while solving the advection-diffusion problem over heterogeneous, distributed and volatile architectures. The JACEP2P-V2 middleware provided the fault tolerant asynchronous environment, required for these experiments

Patterns d'Analyse pour l'Ingénierie de Systèmes d'Information à base d'Agents : Une Application au Domaine du Transport

National audienceIntelligent Transport Information Systems may find benefit of using agent-based solutions. Actually, transport information systems require adaptability to varying changes in offers, and unexpected occurring events. Agents and multiagent systems provide such requirements. Unfortunately, agent-based information systems such as other distributed, asynchronous, loose-coupling applications are difficult to design and implement due to lack of best practices to ease development. This paper describes an approach based on software pattern reuse facilitating engineering of such systems. Patterns are generic solutions to frequently occurring problems. Metamodel represents and structures agent concepts. Fourteen analysis patterns have been specified from this metamodel and describe conceptual entities for the design of an agent-based IS application. Reuse support patterns help designers to reuse former patterns during the information system application engineering

Patterns for Agent-Based Information Systems: A Case Study in Transport

International audienceIntelligent Transport Information Systems may find benefit of using agent-based solutions. Actually, transport information systems require adaptability to varying changes in offers, and unexpected occurring events. Agents and multiagent systems provide such requirements. Unfortunately, agent-based information systems such as other distributed, asynchronous, loose coupling applications are difficult to design and implement due to lack of best practices to ease development. This paper describes an approach based on software pattern reuse that facilitates engineering of these systems. Some patterns have been specified for the analysis and design of such information systems and are described here. Implementation patterns for a specific platform are sketched in perspectives of this research

Traçage de logiciels bénéficiant d'accélération graphique

RÉSUMÉ En programmation, les récents changements d'architecture comme les processeurs à plusieurs cœurs de calcul rendirent la synchronisation des tâches qui y sont exécuté plus complexe à analyser. Pour y remédier, des outils de traçage comme LTTng furent implémentés dans l'optique de fournir des outils d'analyse de processus tout en gardant en tête les défis qu'implique les systèmes multi-cœur. Une seconde révolution dans le monde de l'informatique, les accélérateurs graphiques, créa alors un autre besoin de traçage. Les manufacturiers d'accélérateurs graphiques fournirent alors des outils d'analyse pour accélérateurs graphiques. Ces derniers permettent d'analyser l'exécution de commandes sur les accélérateurs graphiques. Ce mémoire apporte une solution au manque d'outil de traçage unifié entre le système hôte (le processeur central (CPU)) et l'exécution de noyaux de calcul OpenCL sur le périphérique (l'accélérateur graphique (GPU)). Par unifié, nous référons à la capacité d'un outil de prise de traces à collecter une trace du noyau de l'hôte sur lequel un périphérique d'accélération graphique est présent en plus de la trace d'exécution du périphérique d'accélération graphique. L'objectif initial principal de ce mémoire avait été défini comme suit: fournir un outil de traçage et les méthodes d’analyse qui permettent d'acquérir simultanément les traces de l’accélérateur graphique et du processeur central. En plus de l'objectif principal, les objectifs secondaires ajoutaient des critères de performance et de visualisation des traces enregistrés par la solution que ce mémoire présente. Les différentes notions de recherche explorés ont permis d'établir de hypothèses de départ. Ces dernières mentionnaient que le format de trace Common Trace Format (CTF) semblait permettre l'enregistrent de traces à faible surcoût et que des travaux précédents permettront d'effectuer la synchronisation entre les différents espaces temporels du CPU et du GPU. La solution présentée, OpenCL User Space Tracepoint (CLUST) consiste en une librairie qui remplace les symboles de la librairie de calcul GPGPU OpenCL. Pour l'utiliser, elle doit être chargée dynamiquement avant de lancer le programme à tracer. Elle instrumente ensuite toutes les fonctions d'OpenCL grâce aux points de trace LTTng-UST, permettant alors d'enregistrer les appels et de gérer les événements asynchrones communs aux GPUs. La performance de la librairie faisant partie des objectifs de départ, une analyse de la performance des différents cas d'utilisation de cette dernière démontre son faible surcoût : pour les charges de travail d'une taille raisonnable, un surcoût variant entre 0.5 % et 2 % fut mesuré. Cet accomplissement ouvre la porte à plusieurs cas d'utilisation. Effectivement, considérant le faible surcoût d'utilisation, CLUST ne représente pas seulement un outil qui permet l'acquisition de traces pour aider au développement de programmes mais peut aussi servir en tant qu'enregistreur permanent dans les systèmes critiques. La fonction "d'enregistreur de vol" de LTTng permet d'enregistrer une trace au disque seulement lorsque requis : l'ajout de données concernant l'état du GPU peut se révéler être un précieux avantage pour diagnostiquer un problème sur un serveur de production. Le tout sans ralentir le système de façon significative.----------ABSTRACT In the world of computing, programmers now have to face the complex challenges that multi-core processors have brought. To address this problem, tracing frameworks such as LTTng were implemented to provide tools to analyze multi-core systems without adding a major overhead on the system. Recently, Graphical Processing Units (GPUs) started a new revolution: General Purpose Graphical Processing Unit (GPGPU) computing. This allows programs to offload their parallel computation sections to the ultra parallel architecture that GPUs offer. Unfortunately, the tracing tools that were provided by the GPU manufacturers did not interoperate with CPU tracing. We propose a solution, OpenCL User Space Tracepoint (CLUST), that enables OpenCL GPGPU computing tracing as an extension to the LTTng kernel tracer. This allows unifying the CPU trace and the GPU trace in one efficient format that enables advanced trace viewing and analysis, to include both models in the analysis and therefore provide more information to the programmer. The objectives of this thesis are to provide a low overhead unified CPU-GPU tracing extension of LTTng, the required algorithms to perform trace domain synchronization between the CPU and the GPU time source domain, and provide a visualization model for the unified traces. As foundation work, we determined that already existing GPU tracing techniques could incorporate well with LTTng, and that trace synchronization algorithms already presented could be used to synchronize the CPU trace with the GPU trace. Therefore, we demonstrate the low overhead characteristics of the CLUST tracing library for typical applications under different use cases. The unified CPU-GPU tracing overhead is also measured to be insignificant (less than 2%) for a typical GPGPU application. Moreover, we use synchronization methods to determine the trace domain synchronization value between both traces. This solution is a more complete and robust implementation that provides the programmer with the required tools, never before implemented, in the hope of helping programmers develop more efficient OpenCL applications

Distinctive Mechanisms and Patterns of Exudative Versus Tractional Intraretinal Cystoid Spaces as Seen With Multimodal Imaging.

PurposeTo determine clear-cut distinctions between tractional and exudative intraretinal cystoid spaces subtypes.DesignRetrospective, multicenter, observational case series.MethodsA cohort of patients diagnosed with intraretinal cystoid spaces and imaged with optical coherence tomography (OCT), fluorescein angiography (FA), blue fundus autofluorescence (BFAF), en face OCT, and OCT angiography (OCT-A) was included in the study. All images were qualitatively and quantitatively evaluated.ResultsIn this study were included 72 eyes of 69 patients. Exudative intraretinal cystoid spaces (36/72 eyes, 50%) displayed a "petaloid" morphology as seen with en face OCT, FA, and BFAF. Tractional intraretinal cystoid spaces (24/72 eyes, 33.3%), displayed a radial "spoke-wheel" en face OCT pattern. There was no leakage with FA and BFAF did not reveal specific patterns. Eyes with full-thickness macular hole (FTMH, 12/72 eyes, 16.7%) displayed a "sunflower" en face OCT appearance. FTMH showed OCT, OCT-A, and BFAF features of both exudative and tractional cystoid spaces, but without any FA leakage. Inner nuclear layer (INL) thickness was significantly lower in tractional cystoid spaces (P < .001). There were a greater number of INL cystoid spaces in both the exudative and FTMH subgroups (P = .001). The surface area of INL cystoid spaces was significantly lower in the tractional subgroup (P < .001). There was a significant reduction of the microvascular density in eyes with exudative vs tractional (P = .002) and FTMH (P < .001) subgroups.ConclusionsExudative and tractional intraretinal cystoid spaces displayed characteristic multimodal imaging features and they may represent 2 different pathologic conditions with equally different clinical implications

LTTng CLUST: A System-Wide Unified CPU and GPU Tracing Tool for OpenCL Applications

As computation schemes evolve and many new tools become available to programmers to enhance the performance of their applications, many programmers started to look towards highly parallel platforms such as Graphical Processing Unit (GPU). Offloading computations that can take advantage of the architecture of the GPU is a technique that has proven fruitful in recent years. This technology enhances the speed and responsiveness of applications. Also, as a side effect, it reduces the power requirements for those applications and therefore extends portable devices battery life and helps computing clusters to run more power efficiently. Many performance analysis tools such as LTTng, strace and SystemTap already allow Central Processing Unit (CPU) tracing and help programmers to use CPU resources more efficiently. On the GPU side, different tools such as Nvidia’s Nsight, AMD’s CodeXL, and third party TAU and VampirTrace allow tracing Application Programming Interface (API) calls and OpenCL kernel execution. These tools are useful but are completely separate, and none of them allow a unified CPU-GPU tracing experience. We propose an extension to the existing scalable and highly efficient LTTng tracing platform to allow unified tracing of GPU along with CPU’s full tracing capabilities

Pigments empoisonnés. Les verts arsenicaux.

Cet article a été réimprimé avec l’autorisation de Bloomsbury Publishing. Il s’agit d’une version légèrement révisée et traduite d’un chapitre intitulé « Poisonous Pigments: Arsenical Greens », in Fashion Victims. The Dangers of Dress Past and Present, Alison MATTHEWS DAVID, Bloomsbury Publishing, 2015, pp. 74-101.International audienc

A thermostable GH45 endoglucanase from yeast: impact of its atypical multimodularity on activity

BACKGROUND: The gene encoding an atypical multi-modular glycoside hydrolase family 45 endoglucanase bearing five different family 1 carbohydrate binding modules (CBM1), designated PpCel45A, was identified in the Pichia pastoris GS115 genome. RESULTS: PpCel45A (full-length open reading frame), and three derived constructs comprising (i) the catalytic module with its proximal CBM1, (ii) the catalytic module only, and (iii) the five CBM1 modules without catalytic module, were successfully expressed to high yields (up to 2 grams per litre of culture) in P. pastoris X33. Although the constructs containing the catalytic module displayed similar activities towards a range of glucans, comparison of their biochemical characteristics revealed striking differences. We observed a high thermostability of PpCel45A (Half life time of 6 h at 80°C), which decreased with the removal of CBMs and glycosylated linkers. However, both binding to crystalline cellulose and hydrolysis of crystalline cellulose and cellohexaose were substantially boosted by the presence of one CBM rather than five. CONCLUSIONS: The present study has revealed the specific features of the first characterized endo β-1,4 glucanase from yeast, whose thermostability is promising for biotechnological applications related to the saccharification of lignocellulosic biomass such as consolidated bioprocessing

Automated assay for screening the enzymatic release of reducing sugars from micronized biomass

<p>Abstract</p> <p>Background</p> <p>To reduce the production cost of bioethanol obtained from fermentation of the sugars provided by degradation of lignocellulosic biomass (<it>i.e</it>., second generation bioethanol), it is necessary to screen for new enzymes endowed with more efficient biomass degrading properties. This demands the set-up of high-throughput screening methods. Several methods have been devised all using microplates in the industrial SBS format. Although this size reduction and standardization has greatly improved the screening process, the published methods comprise one or more manual steps that seriously decrease throughput. Therefore, we worked to devise a screening method devoid of any manual steps.</p> <p>Results</p> <p>We describe a fully automated assay for measuring the amount of reducing sugars released by biomass-degrading enzymes from wheat-straw and spruce. The method comprises two independent and automated steps. The first step is the making of "substrate plates". It consists of filling 96-well microplates with slurry suspensions of micronized substrate which are then stored frozen until use. The second step is an enzymatic activity assay. After thawing, the substrate plates are supplemented by the robot with cell-wall degrading enzymes where necessary, and the whole process from addition of enzymes to quantification of released sugars is autonomously performed by the robot. We describe how critical parameters (amount of substrate, amount of enzyme, incubation duration and temperature) were selected to fit with our specific use. The ability of this automated small-scale assay to discriminate among different enzymatic activities was validated using a set of commercial enzymes.</p> <p>Conclusions</p> <p>Using an automatic microplate sealer solved three main problems generally encountered during the set-up of methods for measuring the sugar-releasing activity of plant cell wall-degrading enzymes: throughput, automation, and evaporation losses. In its present set-up, the robot can autonomously process 120 triplicate wheat-straw samples per day. This throughput can be doubled if the incubation time is reduced from 24 h to 4 h (for initial rates measurements, for instance). This method can potentially be used with any insoluble substrate that is micronizable. A video illustrating the method can be seen at the following URL: <url>http://www.youtube.com/watch?v=NFg6TxjuMWU</url></p