A batch scheduler with high level components

In this article we present the design choices and the evaluation of a batch scheduler for large clusters, named OAR. This batch scheduler is based upon an original design that emphasizes on low software complexity by using high level tools. The global architecture is built upon the scripting language Perl and the relational database engine Mysql. The goal of the project OAR is to prove that it is possible today to build a complex system for ressource management using such tools without sacrificing efficiency and scalability. Currently, our system offers most of the important features implemented by other batch schedulers such as priority scheduling (by queues), reservations, backfilling and some global computing support. Despite the use of high level tools, our experiments show that our system has performances close to other systems. Furthermore, OAR is currently exploited for the management of 700 nodes (a metropolitan GRID) and has shown good efficiency and robustness

Expériences autour d'une nouvelle approche de conception d'un gestionnaire de travaux pour grappe

Dans cet article nous présentons les choix de conception et l'évaluation d'un gestionnaire de travaux pour grappe de grande taille, baptisé OAR. Ce gestionnaire repose sur une conception originale qui réduit la complexité logicielle, permet une extension aisée ainsi qu'une bonne réponse au problème du passage à l'échelle. %se distingue sur plusieurs points dont le passage à l'échelle, une faible complexité logicielle etc surtout une capacité d'extension aisée. L'architecture globale repose principalement sur deux composants de haut niveau~: un outil générique d'administration d'application (lancement, déploiement) passant à l'échelle et l'utilisation d'une base de données comme seul médium d'échange d'information entre les modules internes. Dans l'évaluation nous montrons à la fois le bon niveau de performance du système et sa capacité d'extension dans une utilisation de type Global Computing (utilisation des ressources inutilisées)

A batch scheduler with high level components

International audienceIn this article we present the design choices and the evaluation of a batch scheduler for large clusters, named OAR. This batch scheduler is based upon an original design that emphasizes on low software complexity by using high level tools. The global architecture is built upon the scripting language Perl and the relational database engine Mysql. The goal of the project OAR is to prove that it is possible today to build a complex system for ressource management using such tools without sacrificing efficiency and scalability. Currently, our system offers most of the important features implemented by other batch schedulers such as priority scheduling (by queues), reservations, backfilling and some global computing support. Despite the use of high level tools, our experiments show that our system has performances close to other systems. Furthermore, OAR is currently exploited for the management of 700 nodes (a metropolitan GRID) and has shown good efficiency and robustness

Mise au point d’un système peptidique réversible pour l’exploration de chimies hors équilibre

Les êtres vivants sont des systèmes chimiques maintenus en état de hors équilibre en dissipant l’énergie qu’ils prélèvent dans leur milieu. Ceci leur confère des capacités remarquables telles que le mouvement, la capacité de communication, des structures dynamiques et le maintiens de conditions propices à leur fonctionnement. Si l’on souhaite que les matériaux de demain possède de telles capacité alors il convient d’étudier et d’apprendre à élaborer des systèmes dissipatifs hors équilibre. C’est l’objectif que ce fixe le présent travail de thèse. La mise au point d’un système polymérisable de façon réversible qui conduirait à un système hors équilibre en présence d’un gradient de température par phénomènes de réaction diffusion. Le système polymérisable choisi est le système peptidique dont la liaison est rendue dynamique via l’incorporation de N-méthyl-cystéine au sein de la séquence d’acides aminés. Pour ce faire les données thermocinétiques de la réaction de ligation/dissociation sont obtenues et un système dynamique surnommée « polymère vivant » est mis au point. Son évolution dans différentes conditions de températures et concentrations sont évalué ainsi que l’évolution sur la distribution des espèces générées. Une approche théorique est ensuite réalisée afin d’obtenir un modèle cinétique simple du système.Living organisms are chemical systems self-maintained in an out of equilibrium state through the dissipation of energy taken from its environment. This allows for some remarkable properties such as movement, the ability for communication, dynamic structures and the upkeep of conditions vital for the survival of those systems. If the materials of the future are to possess such properties, then the study and creation of out of equilibrium dissipative systems is of the uttermost interest. This is the main goal of this thesis work. The design of a polymerizable reversible system which would to an out of equilibrium system in a temperature gradient by reaction diffusion processes. The chosen polymerizable system is the peptide system and the peptide bond is made reversible through the incorporation of an N-methyl-cysteine in the amino acid sequence. To this end, the thermokinetic data for the ligation/dissociation reaction were obtained and a dynamic system dubbed “living polymer” was designed. The evolution of such system in different temperature and concentration conditions is then monitored to track the evolution of the distribution of species. A theoretical approach of the system then leads to the creation of a simplistic kinetic model to predict its behavior

Mise au point d’un système peptidique réversible pour l’exploration de chimies hors équilibre

Les êtres vivants sont des systèmes chimiques maintenus en état de hors équilibre en dissipant l’énergie qu’ils prélèvent dans leur milieu. Ceci leur confère des capacités remarquables telles que le mouvement, la capacité de communication, des structures dynamiques et le maintiens de conditions propices à leur fonctionnement. Si l’on souhaite que les matériaux de demain possède de telles capacité alors il convient d’étudier et d’apprendre à élaborer des systèmes dissipatifs hors équilibre. C’est l’objectif que ce fixe le présent travail de thèse. La mise au point d’un système polymérisable de façon réversible qui conduirait à un système hors équilibre en présence d’un gradient de température par phénomènes de réaction diffusion. Le système polymérisable choisi est le système peptidique dont la liaison est rendue dynamique via l’incorporation de N-méthyl-cystéine au sein de la séquence d’acides aminés. Pour ce faire les données thermocinétiques de la réaction de ligation/dissociation sont obtenues et un système dynamique surnommée « polymère vivant » est mis au point. Son évolution dans différentes conditions de températures et concentrations sont évalué ainsi que l’évolution sur la distribution des espèces générées. Une approche théorique est ensuite réalisée afin d’obtenir un modèle cinétique simple du système.Living organisms are chemical systems self-maintained in an out of equilibrium state through the dissipation of energy taken from its environment. This allows for some remarkable properties such as movement, the ability for communication, dynamic structures and the upkeep of conditions vital for the survival of those systems. If the materials of the future are to possess such properties, then the study and creation of out of equilibrium dissipative systems is of the uttermost interest. This is the main goal of this thesis work. The design of a polymerizable reversible system which would to an out of equilibrium system in a temperature gradient by reaction diffusion processes. The chosen polymerizable system is the peptide system and the peptide bond is made reversible through the incorporation of an N-methyl-cysteine in the amino acid sequence. To this end, the thermokinetic data for the ligation/dissociation reaction were obtained and a dynamic system dubbed “living polymer” was designed. The evolution of such system in different temperature and concentration conditions is then monitored to track the evolution of the distribution of species. A theoretical approach of the system then leads to the creation of a simplistic kinetic model to predict its behavior

Evaluations of the Lightweight Grid CIGRI upon the Grid5000 Platform

International audienceA widely used method for large scale experiment execution upon P2P or cluster computing platforms, is the exploitation of idle resources. Specifically in the case of clusters, administrators share their cluster's idle cycles into computational grids, for the execution of the so called bag-of-tasks applications. Fault-tolerance and scheduling are some of the important challenges that have arisen on the specific research field. On this paper, we present a simple, scalable, fault tolerant and user-transparent approach of harnessing idle cluster resources for executing grid bag-of-tasks applications. Our main interest lies on the large-scale deployment and evaluation of our lightweight grid computing approach, under real-life parameters. Under this context, we experiment with CIGRI and a fully transparent system-level checkpointing feature for scheduling and turnaround-time optimisation. We discuss the value of experimentation on computer science, we propose reproducible experiments based on real workload traces and we explain how our experimental methodology contributes on the development and evaluation of our grid platform

IGGI, A computing Framework for large Scale Parametric Simulations, Application to uncertainty analysis with TOUGHREACT

International audienceIGGI stands for infrastructure for grids, cluster and intranet. This research project partially funded by the French government is aiming at developing technologies allowing the access and the gathering of the whole computing resources spread over the intranet of a company. This could include dedicated computing power or personal computers. The project is collaboration between BRGM, INRIA and Mandriva. Scientific computing has evolved for last few years and commodity-based components can run a wide range of applications. In this study, our focus will be on the software environment required to carry out large scale parametric simulations, but we will also report on experience of the deployment of such an infrastructure in the day to day life of an intranet. The IGGI software suite is mainly based on two components: ComputeModeTM which smoothly aggregates idle user machine to a virtual computing cluster. This is done through a transparent switch of the PC to a secondary, protected mode from which it boots from the ComputeMode server taking advantage of the PXE protocol. The second IGGI component is CIGRI which scheduled and executed computing tasks on the idle nodes of clusters. Special attention has been paid on the end-users ability to perform easily parametric simulations. Transparent access to the batch-scheduler, checkpoint and migration of the application will be exposed for the test-case of the analysis of uncertainty with TOUGHREACT : "Uncertainty in predictions of transfer model response to a thermal and alkaline perturbation in clay" . The calculations reported were carried out using idle computing capacity on personal computers inside the BRGM. This new architecture is particularly well suited to explore the wide rang

Expériences autour d'une nouvelle approche de conception d'un gestionnaire de travaux pour grappe

Dans cet article nous présentons les choix de conception et l'évaluation d'un gestionnaire de travaux pour grappe de grande taille, baptisé OAR. Ce gestionnaire repose sur une conception originale qui réduit la complexité logicielle, permet une extension aisée ainsi qu'une bonne réponse au problème du passage à l'échelle. %se distingue sur plusieurs points dont le passage à l'échelle, une faible complexité logicielle etc surtout une capacité d'extension aisée. L'architecture globale repose principalement sur deux composants de haut niveau~: un outil générique d'administration d'application (lancement, déploiement) passant à l'échelle et l'utilisation d'une base de données comme seul médium d'échange d'information entre les modules internes. Dans l'évaluation nous montrons à la fois le bon niveau de performance du système et sa capacité d'extension dans une utilisation de type Global Computing (utilisation des ressources inutilisées)

Poroelasticity of Methane-Loaded Mature and Immature Kerogen from Molecular Simulations

International audienceWhile hydrocarbon expulsion from kerogen is certainly the key step in shale oil/gas recovery, the poromechanical couplings governing this desorption process, taking place under a significant pressure gradient, are still poorly understood. Especially, most molecular simulation investigations of hydrocarbon adsorption and transport in kerogen have so far been performed under the rigid matrix approximation, implying that the pore space is independent of pressure, temperature, and fluid loading, or in other words, neglecting poromechanics. Here, using two hydrogenated porous carbon models as proxies for immature and overmature kerogen, that is, highly aliphatic hydrogen-rich vs highly aromatic hydrogen-poor models, we perform an extensive molecular-dynamics-based investigation of the evolution of the poroelastic properties of those matrices with respect to temperature, external pressure, and methane loading as a prototype alkane molecule. The rigid matrix approximation is shown to hold reasonably well for overmature kerogen even though accounting for flexibility has allowed us to observe the well-known small volume contraction at low fluid loading and temperature. Our results demonstrate that immature kerogen is highly deformable. Within the ranges of conditions considered in this work, its density can double and its accessible porosity (to a methane molecule) can increase from 0 to ∼30%. We also show that these deformations are significantly nonaffine (i.e., nonhomogeneous), especially upon fluid adsorption or desorption