Automating Fault Tolerance in High-Performance Computational Biological Jobs Using Multi-Agent Approaches

Background: Large-scale biological jobs on high-performance computing systems require manual intervention if one or more computing cores on which they execute fail. This places not only a cost on the maintenance of the job, but also a cost on the time taken for reinstating the job and the risk of losing data and execution accomplished by the job before it failed. Approaches which can proactively detect computing core failures and take action to relocate the computing core's job onto reliable cores can make a significant step towards automating fault tolerance. Method: This paper describes an experimental investigation into the use of multi-agent approaches for fault tolerance. Two approaches are studied, the first at the job level and the second at the core level. The approaches are investigated for single core failure scenarios that can occur in the execution of parallel reduction algorithms on computer clusters. A third approach is proposed that incorporates multi-agent technology both at the job and core level. Experiments are pursued in the context of genome searching, a popular computational biology application. Result: The key conclusion is that the approaches proposed are feasible for automating fault tolerance in high-performance computing systems with minimal human intervention. In a typical experiment in which the fault tolerance is studied, centralised and decentralised checkpointing approaches on an average add 90% to the actual time for executing the job. On the other hand, in the same experiment the multi-agent approaches add only 10% to the overall execution time.Comment: Computers in Biology and Medicin

Découverte et allocation des ressources pour le traitement de requêtes dans les systèmes grilles

De nos jours, les systèmes Grille, grâce à leur importante capacité de calcul et de stockage ainsi que leur disponibilité, constituent l'un des plus intéressants environnements informatiques. Dans beaucoup de différents domaines, on constate l'utilisation fréquente des facilités que les environnements Grille procurent. Le traitement des requêtes distribuées est l'un de ces domaines où il existe de grandes activités de recherche en cours, pour transférer l'environnement sous-jacent des systèmes distribués et parallèles à l'environnement Grille. Dans le cadre de cette thèse, nous nous concentrons sur la découverte des ressources et des algorithmes d'allocation de ressources pour le traitement des requêtes dans les environnements Grille. Pour ce faire, nous proposons un algorithme de découverte des ressources pour le traitement des requêtes dans les systèmes Grille en introduisant le contrôle de topologie auto-stabilisant et l'algorithme de découverte des ressources dirigé par l'élection convergente. Ensuite, nous présentons un algorithme d'allocation des ressources, qui réalise l'allocation des ressources pour les requêtes d'opérateur de jointure simple par la génération d'un espace de recherche réduit pour les nœuds candidats et en tenant compte des proximités des candidats aux sources de données. Nous présentons également un autre algorithme d'allocation des ressources pour les requêtes d'opérateurs de jointure multiple. Enfin, on propose un algorithme d'allocation de ressources, qui apporte une tolérance aux pannes lors de l'exécution de la requête par l'utilisation de la réplication passive d'opérateurs à état. La contribution générale de cette thèse est double. Premièrement, nous proposons un nouvel algorithme de découverte de ressource en tenant compte des caractéristiques des environnements Grille. Nous nous adressons également aux problèmes d'extensibilité et de dynamicité en construisant une topologie efficace sur l'environnement Grille et en utilisant le concept d'auto-stabilisation, et par la suite nous adressons le problème de l'hétérogénéité en proposant l'algorithme de découverte de ressources dirigé par l'élection convergente. La deuxième contribution de cette thèse est la proposition d'un nouvel algorithme d'allocation des ressources en tenant compte des caractéristiques de l'environnement Grille. Nous abordons les problèmes causés par la grande échelle caractéristique en réduisant l'espace de recherche pour les ressources candidats. De ce fait nous réduisons les coûts de communication au cours de l'exécution de la requête en allouant des nœuds au plus près des sources de données. Et enfin nous traitons la dynamicité des nœuds, du point de vue de leur existence dans le système, en proposant un algorithme d'affectation des ressources avec une tolérance aux pannes.Grid systems are today's one of the most interesting computing environments because of their large computing and storage capabilities and their availability. Many different domains profit the facilities of grid environments. Distributed query processing is one of these domains in which there exists large amounts of ongoing research to port the underlying environment from distributed and parallel systems to the grid environment. In this thesis, we focus on resource discovery and resource allocation algorithms for query processing in grid environments. For this, we propose resource discovery algorithm for query processing in grid systems by introducing self-stabilizing topology control and converge-cast based resource discovery algorithms. Then, we propose a resource allocation algorithm, which realizes allocation of resources for single join operator queries by generating a reduced search space for the candidate nodes and by considering proximities of candidates to the data sources. We also propose another resource allocation algorithm for queries with multiple join operators. Lastly, we propose a fault-tolerant resource allocation algorithm, which provides fault-tolerance during the execution of the query by the use of passive replication of stateful operators. The general contribution of this thesis is twofold. First, we propose a new resource discovery algorithm by considering the characteristics of the grid environments. We address scalability and dynamicity problems by constructing an efficient topology over the grid environment using the self-stabilization concept; and we deal with the heterogeneity problem by proposing the converge-cast based resource discovery algorithm. The second main contribution of this thesis is the proposition of a new resource allocation algorithm considering the characteristics of the grid environment. We tackle the scalability problem by reducing the search space for candidate resources. We decrease the communication costs during the query execution by allocating nodes closer to the data sources. And finally we deal with the dynamicity of nodes, in terms of their existence in the system, by proposing the fault-tolerant resource allocation algorithm

Rendezvous in Networks in Spite of Delay Faults

Two mobile agents, starting from different nodes of an unknown network, have to meet at the same node. Agents move in synchronous rounds using a deterministic algorithm. Each agent has a different label, which it can use in the execution of the algorithm, but it does not know the label of the other agent. Agents do not know any bound on the size of the network. In each round an agent decides if it remains idle or if it wants to move to one of the adjacent nodes. Agents are subject to delay faults: if an agent incurs a fault in a given round, it remains in the current node, regardless of its decision. If it planned to move and the fault happened, the agent is aware of it. We consider three scenarios of fault distribution: random (independently in each round and for each agent with constant probability 0 < p < 1), unbounded adver- sarial (the adversary can delay an agent for an arbitrary finite number of consecutive rounds) and bounded adversarial (the adversary can delay an agent for at most c consecutive rounds, where c is unknown to the agents). The quality measure of a rendezvous algorithm is its cost, which is the total number of edge traversals. For random faults, we show an algorithm with cost polynomial in the size n of the network and polylogarithmic in the larger label L, which achieves rendezvous with very high probability in arbitrary networks. By contrast, for unbounded adversarial faults we show that rendezvous is not feasible, even in the class of rings. Under this scenario we give a rendezvous algorithm with cost O(nl), where l is the smaller label, working in arbitrary trees, and we show that \Omega(l) is the lower bound on rendezvous cost, even for the two-node tree. For bounded adversarial faults, we give a rendezvous algorithm working for arbitrary networks, with cost polynomial in n, and logarithmic in the bound c and in the larger label L