A Fault Tolerance protocol for ASP calculus: Design and Proof

This research report first details a communication induced checkpointing fault tolerance protocol adapted to ProActive, a Java library that implements the ASP model. This model is based n a request/reply mechanism. In order to prove the correctness of this protocol, we introduce a local partial order between events occurring on a given process. This order is extended into a global order by the Lamport's happened-before relation. Finally, we prove that from a cut that is ''consistent enough'', a second execution is constrained to go equivalently to the first one until a consistent global state of the first one (the history closure). Thus, the protocol described in this report ensures that, even from a inconsistent recovery line, a reexecution cannot lead to an inconsistent state that could not exist in a normal execution

Dynamically-Fulfilled Application Constraints through Technical Services - Towards Flexible Component Deployments

We propose in this paper, a mechanism for Grid computing frameworks, for specifying environmental requirements that may set and be optimized by deployers. Specified by designers by parameterizing deployment abstractions, the constraints can be dynamically mapped onto the infrastructure. This work is integrated in the ProActive middleware with the concept of technical services. We illustrate this mechanism with a concrete use case: deploying a component-based application with fault-tolerance on an heterogeneous grid provided by the ProActive Peer-to-Peer infrastructure

Dynamically-Fulfilled Application Constraints through Technical Services - Towards Flexible Component Deployments

We propose in this paper, a mechanism for Grid computing frameworks, for specifying environmental requirements that may set and be optimized by deployers. Specified by designers by parameterizing deployment abstractions, the constraints can be dynamically mapped onto the infrastructure. This work is integrated in the ProActive middleware with the concept of technical services. We illustrate this mechanism with a concrete use case: deploying a component-based application with fault-tolerance on an heterogeneous grid provided by the ProActive Peer-to-Peer infrastructure

HPC in Java: Experiences in Implementing the NAS Parallel Benchmarks

International audienceThis paper reports on the design, implementation and benchmarking of a Java version of the Nas Parallel Benchmarks. We first briefly describe the implementation and the performance pitfalls. We then compare the overall performance of the Fortran MPI (PGI) version with a Java implementation using the ProActive middleware for distribution. All Java experiments were conducted on virtual machines with different vendors and versions. We show that the performance varies with the type of computation but also with the Java Virtual Machine, no single one providing the best performance in all experiments. We also show that the performance of the Java version is close to the Fortran one on computational intensive benchmarks. However, on some communications intensive benchmarks, the Java version exhibits scalability issues, even when using a high performance socket implementation (JFS)

HPC in Java: Experiences in Implementing the NAS Parallel Benchmarks

International audienceThis paper reports on the design, implementation and benchmarking of a Java version of the Nas Parallel Benchmarks. We first briefly describe the implementation and the performance pitfalls. We then compare the overall performance of the Fortran MPI (PGI) version with a Java implementation using the ProActive middleware for distribution. All Java experiments were conducted on virtual machines with different vendors and versions. We show that the performance varies with the type of computation but also with the Java Virtual Machine, no single one providing the best performance in all experiments. We also show that the performance of the Java version is close to the Fortran one on computational intensive benchmarks. However, on some communications intensive benchmarks, the Java version exhibits scalability issues, even when using a high performance socket implementation (JFS)

The synthetic peptide P111-136 derived from the C-terminal domain of heparin affin regulatory peptide inhibits tumour growth of prostate cancer PC-3 cells

<p>Abstract</p> <p>Background</p> <p>Heparin affin regulatory peptide (HARP), also called pleiotrophin, is a heparin-binding, secreted factor that is overexpressed in several tumours and associated to tumour growth, angiogenesis and metastasis. The C-terminus part of HARP composed of amino acids 111 to 136 is particularly involved in its biological activities and we previously established that a synthetic peptide composed of the same amino acids (P111-136) was capable of inhibiting the biological activities of HARP. Here we evaluate the ability of P111-136 to inhibit <it>in vitro </it>and <it>in vivo </it>the growth of a human tumour cell line PC-3 which possess an HARP autocrine loop.</p> <p>Methods</p> <p>A total lysate of PC-3 cells was incubated with biotinylated P111-136 and pulled down for the presence of the HARP receptors in Western blot. <it>In vitro</it>, the P111-136 effect on HARP autocrine loop in PC-3 cells was determined by colony formation in soft agar. <it>In vivo</it>, PC-3 cells were inoculated in the flank of athymic nude mice. Animals were treated with P111-136 (5 mg/kg/day) for 25 days. Tumour volume was evaluated during the treatment. After the animal sacrifice, the tumour apoptosis and associated angiogenesis were evaluated by immunohistochemistry. <it>In vivo </it>anti-angiogenic effect was confirmed using a mouse Matrigel™ plug assay.</p> <p>Results</p> <p>Using pull down experiments, we identified the HARP receptors RPTPβ/ζ, ALK and nucleolin as P111-136 binding proteins. <it>In vitro</it>, P111-136 inhibits dose-dependently PC-3 cell colony formation. Treatment with P111-136 inhibits significantly the PC-3 tumour growth in the xenograft model as well as tumour angiogenesis. The angiostatic effect of P111-136 on HARP was also confirmed using an <it>in vivo </it>Matrigel™ plug assay in mice</p> <p>Conclusions</p> <p>Our results demonstrate that P111-136 strongly inhibits the mitogenic effect of HARP on <it>in vitro </it>and <it>in vivo </it>growth of PC-3 cells. This inhibition could be linked to a direct or indirect binding of this peptide to the HARP receptors (ALK, RPTPβ/ζ, nucleolin). <it>In vivo</it>, the P111-136 treatment significantly inhibits both the PC-3 tumour growth and the associated angiogenesis. Thus, P111-136 may be considered as an interesting pharmacological tool to interfere with tumour growth that has now to be evaluated in other cancer types.</p

Tolérance aux pannes pour objets actifs asynchrones : modèle, protocole et expérimentations

The main goal of this thesis is to define a rollback-recovery fault tolerance protocol for the asynchronous communicating active objects model ASP (Asynchronous Sequential Processes), and its Java implementation ProActive. This work generalises the problem raised by the development of this protocol: we study the recovery of a distributed execution from an inconsistent global state. We then propose a checkpointing protocol and its implementation that does not rely on consistent global states. We demonstrate the model efficiency through realistic experiments using communicating distributed applications that this solution is efficient in practice. Another more general contribution to the problematic of recovering from a inconsistent global state by formally is the definition of the P-consistency, a new recoverability condition based on the concept of promised event. This definition is part of an event-based formalism which can be applied to any system. In particular, by applying this formalism to the ASP model, we are able to prove the correctness of our protocol by showing that every global state created during the execution is a recoverable state. Finally, we propose an extension of our protocol and an implementation adapted to the context of grid computing. This extension relies on the constitution of recovery groups during the deployment of the application. It allows to independently distribute stable storage and to limit the effects of a failure to the concerned group.L'objectif premier de cette thèse est de proposer un protocole de tolérance aux pannes par recouvrement arrière pour le modèle à objets actifs asynchrones communicants ASP (Asynchronous Sequential Processes) et son implémentation en Java ProActive. Cette thèse généralise la problématique soulevée par le développement de ce protocole : nous étudions le recouvrement d'une application répartie depuis un état global non cohérent. Nous proposons donc dans un premier temps un protocole par points de reprise et son implémentation ne supposant pas que les états globaux soient cohérents. Nous montrons à travers des expérimentations réalistes utilisant des applications réparties communicantes que notre solution et son implémentation présentent de bonnes performances. Nous contribuons aussi de manière plus générale à l'étude du recouvrement depuis un état global non cohérent en définissant formellement une nouvelle condition de recouvrabilité, la P-cohérence, basée sur la notion de promesse d'évènement. Cette définition s'intègre dans un formalisme événementiel capable de prendre en compte la sémantique de n'importe quel système ; elle est donc applicable dans un cadre général. En particulier, en appliquant ce formalisme au modèle ASP, nous prouvons la correction de notre protocole en montrant que les états globaux formés durant l'exécution sont toujours recouvrables. Enfin, nous contribuons plus spécifiquement au domaine des grilles de calcul en proposant une extension de notre protocole et son implémentation adaptée à ce contexte. Cette extension se base sur la constitution automatique de groupes de recouvrement au déploiement de l'application. Elle permet une répartition indépendante des mémoires stables et un confinement des effets d'une panne au seul groupe concerné

Promised Consistency for Rollback Recovery

Checkpointing protocols usually rely on the constitution of consistent global states, from which the application can restart upon a failure. This paper proposes a new characterization and technique to build a recoverable state, aiming at relaxing the constraints and overhead. P-consistency, for Promised consistency, is proposed as such a recovery condition on a global state. A key idea is to use promised events: place holders forcing any restart to reach an actual global state of the first execution. A preliminary contribution is a formal treatment of potential causality, studying its impact on recoverability and determinism