Non-Cooperative Scheduling of Multiple Bag-of-Task Applications

Multiple applications that execute concurrently on heterogeneous platforms compete for CPU and network resources. In this paper we analyze the behavior of $K$ non-cooperative schedulers using the optimal strategy that maximize their efficiency while fairness is ensured at a system level ignoring applications characteristics. We limit our study to simple single-level master-worker platforms and to the case where each scheduler is in charge of a single application consisting of a large number of independent tasks. The tasks of a given application all have the same computation and communication requirements, but these requirements can vary from one application to another. In this context, we assume that each scheduler aims at maximizing its throughput. We give closed-form formula of the equilibrium reached by such a system and study its performance. We characterize the situations where this Nash equilibrium is optimal (in the Pareto sense) and show that even though no catastrophic situation (Braess-like paradox) can occur, such an equilibrium can be arbitrarily bad for any classical performance measure

SimGrid: a Sustained Effort for the Versatile Simulation of Large Scale Distributed Systems

In this paper we present Simgrid, a toolkit for the versatile simulation of large scale distributed systems, whose development effort has been sustained for the last fifteen years. Over this time period SimGrid has evolved from a one-laboratory project in the U.S. into a scientific instrument developed by an international collaboration. The keys to making this evolution possible have been securing of funding, improving the quality of the software, and increasing the user base. In this paper we describe how we have been able to make advances on all three fronts, on which we plan to intensify our efforts over the upcoming years.Comment: 4 pages, submission to WSSSPE'1

Effective Reproducible Research with Org-Mode and Git

International audienceIn this article we address the question of developing a lightweight and effective workflow for conducting experimental research on modern parallel computer systems in a reproducible way. Our workflowsimply builds on two well-known tools (Org-mode and Git) and enablesto address issues such as provenance tracking, experimental setup reconstruction, replicable analysis. Although this workflow is perfectible and cannot be seen as a final solution, we have been usingit for two years now and we have recently published a fully reproduciblearticle, which demonstrates the effectiveness of our proposal

How to measure efficiency?

In the context of applied game theory in networking environments, a number of concepts have been proposed to measure both efficiency and optimality of resource allocations, the most famous certainly being the price of anarchy and the Jain index. Yet, very few have tried to question these measures and compare them one to another, in a general framework, which is the aim of the present article

Versatile, Scalable, and Accurate Simulation of Distributed Applications and Platforms

International audienceThe study of parallel and distributed applications and platforms, whether in the cluster, grid, peer-to-peer, volunteer, or cloud computing domain, often mandates empirical evaluation of proposed algorithmic and system solutions via simulation. Unlike direct experimentation via an application deployment on a real-world testbed, simulation enables fully repeatable and configurable experiments for arbitrary hypothetical scenarios. Two key concerns are accuracy (so that simulation results are scientifically sound) and scalability (so that simulation experiments can be fast and memory-efficient). While the scalability of a simulator is easily measured, the accuracy of many state-of-the-art simulators is largely unknown because they have not been sufficiently validated. In this work we describe recent accuracy and scalability advances made in the context of the SimGrid simulation framework. A design goal of SimGrid is that it should be versatile, i.e., applicable across all aforementioned domains. We present quantitative results that show that SimGrid compares favorably to state-of-the-art domain-specific simulators in terms of scalability, accuracy, or the trade-off between the two. An important implication is that, contrary to popular wisdom, striving for versatility in a simulator is not an impediment but instead is conducive to improving both accuracy and scalability

Static Scheduling Strategies for Heterogeneous Systems

In this paper, we consider static scheduling techniques for heterogeneous systems, such as clusters and grids. We successively deal with minimum makespan scheduling, divisible load scheduling and steady-state scheduling. Finally, we discuss the limitations of static scheduling approaches

Identification de nouveaux partenaires protéiques de l'oncoprotéine Ets-1 et étude de sa régulation par l'enzyme de réparation de l'ADN PARP-1 au sein des cellules tumorales

Ets-1 is a transcription factor, member of the Ets family, having a well-conserved DNA binding domain which recognizes a core consensus sequence, GGAA/T, present in the promoter of target genes. This factor regulates genes involved in various physiological processes such as development, haematopoiesis, and angiogenesis and in pathological processes notably cancer progression and invasion. Despite the efforts of the scientific community during these past 10 years, few strategies for Ets-1 therapeutic targeting can be apply to clinical medicine. Considering the fact that this transcription factor is a poor prognostic marker for numerous carcinomas, such as breast, lung or colorectal cancers, the finding of a new strategy for targeting its activity in tumours could be a new advance in the fight against cancer. Ets-1 does not act alone on its target promoters but with a wide range of transcriptional co-regulators. Moreover, this factor is a target for many signal transduction pathways. Identifying novel proteins that interact with Ets-1 should permit a better understanding of its regulation networks to develop a strategy for targeting its activity. For this purpose, we used a purification system to identify interacting partners based on the strong affinity between biotin and streptavidin, called streptavidin pull-down. We thereby identified new potentials interaction partners. Among those, we could confirm as Ets-1 partners, DNA repair proteins, such as the DNA-PK complex and PARP-1. The poly(ADP-ribose) polymerase-1 (PARP-1) is an enzyme with various roles that catalyses poly(ADP-ribosyl)ation or PARylation. Originally, it was identified as a DNA repair protein. Nevertheless, these past few years, many studies have highlighted its role as a co-regulator in transcription processes. We demonstrated that Ets-1 directly interact with PARP-1 and is PARylated in return. In Ets-1-expressing cancer cells, the catalytic inhibition of PARP-1 caused massive accumulation of this factor and enhanced its transcriptional activity. These results suggest that PARylation is involved in Ets-1 protein stability linked to its proteasomal degradation. Nevertheless, under PARP-1 inhibition, accumulation of Ets-1 is toxic for cancer cells. Indeed, we observed a strong increase in DNA damage that leads to cancer cells death. We assume that an unregulated activity of Ets-1 is harmful to the cellular outcome even more when a DNA repair protein such as PARP-1 is inhibited.These results give new insight into Ets-1 regulation in cancer cells linked to DNA repair proteins. Furthermore, our findings suggest that PARP-1 inhibitors would be useful in a new therapeutic strategy that specifically targets Ets-1-expressing tumours.Ets-1 est un facteur de transcription, membre de la famille Ets, possédant un domaine de liaison à l’ADN hautement conservé, qui permet de reconnaître un cœur consensus GGAA/T présent dans le promoteur de ses gènes cibles. Ce facteur régule des gènes impliqués dans divers processus physiologiques tels que le développement, l’hématopoïèse et l’angiogenèse ou pathologiques notamment dans la progression et l’invasion tumorale. Malgré les efforts engagés par la communauté scientifique ces dix dernières années, il y a peu de stratégies de ciblage thérapeutique d’Ets-1 qui peuvent être transposées dans un cadre clinique. Compte tenu du fait que ce facteur de transcription est un marqueur de mauvais pronostic pour de nombreux carcinomes, dont entre autres, ceux du sein, des poumons ou encore du colon, la mise en évidence d’une stratégie de ciblage de son activité pro-tumorale pourrait constituer une avancée majeure dans la lutte contre le cancer. Ets-1 n’agit pas seule au niveau de ses promoteurs cibles mais en coopération avec une variété de co-régulateurs transcriptionnels. De plus, ce facteur est ciblé par de nombreuses voies de transduction des signaux cellulaires. L’identification de nouveaux partenaires interagissant avec Ets-1 devrait donc nous permettre de mieux appréhender ses réseaux de régulation afin de mettre au point une stratégie de ciblage de son activité. Dans ce but, nous avons mis en œuvre un système de purification de partenaires basé sur la forte affinité entre la biotine et la streptavidine, appelé « streptavidin pull-down ». Nous avons ainsi identifié de nouveaux partenaires protéiques potentiels. Parmi ceux-ci, nous avons pu confirmer comme partenaires interagissant avec Ets-1, des protéines de réparation de l’ADN tels que le complexe DNA-PK et la PARP-1. La poly(ADP-ribose) polymérase -1 (PARP-1) est une enzyme aux rôles multiples qui catalyse la poly(ADP-ribosyl)ation ou PARylation. Si elle fut identifiée à l’origine comme une protéine de réparation de l’ADN, de nombreux travaux ont montré ces dernières années qu’elle est un co-régulateur majeur des mécanismes de transcription. Nous avons démontré qu’Ets-1 interagit directement avec la PARP-1 et est PARylée par celle-ci. L’utilisation d’inhibiteurs catalytiques de la PARP-1 sur des cellules de lignées cancéreuses, exprimant Ets-1, a pour conséquences l’accumulation massive de ce facteur et une augmentation de son activité transcriptionnelle. Ceci suggère une implication de la PARylation dans la stabilité d’Ets-1 en lien avec sa dégradation par le protéasome. Cependant, sous inhibition de la PARP-1, l’accumulation d’Ets-1 est toxique pour la cellule cancéreuse. En effet, nous avons observé une forte augmentation des dommages à l’ADN qui corrèle avec la mort des cellules tumorales. Nous supposons qu’une activité non régulée d’Ets-1 est néfaste pour le devenir cellulaire d’autant plus quand une enzyme de réparation de l’ADN comme la PARP-1 est inhibée.Ces résultats mettent en évidence un nouveau mécanisme de régulation d’Ets-1 au sein des cellules cancéreuses en liaison avec les protéines de réparation de l’ADN. De plus, l’utilisation d’inhibiteurs de la PARP-1 pourrait constituer une nouvelle stratégie afin de cibler spécifiquement les tumeurs exprimant Ets-1

Scheduling for Large Scale Distributed Computing Systems: Approaches and Performance Evaluation Issues

Although our everyday life and society now depends heavily oncommunication infrastructures and computation infrastructures,scientists and engineers have always been among the main consumers ofcomputing power. This document provides a coherent overview of theresearch I have conducted in the last 15 years and which targets themanagement and performance evaluation of large scale distributedcomputing infrastructures such as clusters, grids, desktop grids,volunteer computing platforms, ... when used for scientific computing.In the first part of this document, I present how I have addressedscheduling problems arising on distributed platforms (like computinggrids) with a particular emphasis on heterogeneity and multi-userissues, hence in connection with game theory. Most of these problemsare relaxed from a classical combinatorial optimization formulationinto a continuous form, which allows to easily account for keyplatform characteristics such as heterogeneity or complex topologywhile providing efficient practical and distributed solutions.The second part presents my main contributions to the SimGrid project,which is a simulation toolkit for building simulators of distributedapplications (originally designed for scheduling algorithm evaluationpurposes). It comprises a unified presentation of how the questions ofvalidation and scalability have been addressed in SimGrid as well asthoughts on specific challenges related to methodological aspects andto the application of SimGrid to the HPC context

Independent and Divisible Task Scheduling on Heterogeneous Star-shaped Platforms with Limited Memory

In this paper, we consider the problem of allocating and scheduling a collection of independent, equal-sized tasks on heterogeneous star-shaped platforms. We also address the same problem for divisible tasks. For both cases, we take memory constraints into account. We prove strong NP-completeness results for different objective functions, namely makespan minimization and throughput maximization, on simple star-shaped platforms. We propose an approximation algorithm based on the unconstrained version (with unlimited memory) of the problem. We introduce several heuristics, which are evaluated and compared through extensive simulations. An unexpected conclusion drawn from these experiments is that classical scheduling heuristics that try to greedily minimize the completion time of each task are outperformed by the simple heuristic that consists in assigning the task to the available processor that has the smallest communication time, regardless of computation power (hence a "bandwidth-centric" distribution).Dans ce rapport, nous nous intéressons au problème de l’allocation d’un grand nombre de taches indépendantes et de taille identiques sur des plateformes de calcul hétérogènes organisées en étoile. Nous nous intéressons également au modèle des tâches divisibles. Pour ces deux modèles, nous prenons en compte les contraintes mémoires et démontrons des résultats de NP-complétude pour diverses métriques (le «makespakan» et le débit). Nous proposons un algorithme d’approximation basé sur la version non-contrainte (c’est-`a-dire avec une mémoire infinie) du problème. Nous proposons également d’autres heuristiques que nous évaluons à l’aide d’un grand nombre de simulations. Une conclusion inattendue qui ressort de ces expériences est que les heuristiques de listes classiques qui essaient de minimiser gloutonnement la durée de l’ordonnancement sont bien moins performantes que l’heuristique toute simple consistant à envoyer les tâches aux processeurs disponibles ayant le temps de communication le plus faible, sans même tenir compte de leur puissance de calcu