Kerrighed: A SSI Cluster OS Running OpenMP

Writing parallel programs for clusters of workstations is still a challenging task. In this paper, we present Kerrighed, a Single System Image (SSI) operating system giving the illusion of an SMP machine, and providing the standard posix thread interface to developers. It is therefore possible to use Kerrighed to run OpenMP programs compiled for SMP-machines using the posix thread interface. In this paper, we explain how we managed to achieve that goal, and present the benefits of providing OpenMP support through the SSI approach as opposed to a dedicated run-time environment

Ghost Process: a Sound Basis to Implement Process Duplication, Migration and Checkpoint/Restart in Linux Clusters

Process management mechanisms (process duplication, migration and checkpoint/restart) are very useful for high performance and high availability in clustering systems. The single system image approach aims at providing a global process management service with mechanisms for process checkpoint, process migration and process duplication. In this context, a common mechanism for process virtualization is highly desirable but traditional operating systems do not provide such a mecahnism. This paper presents a kernel service for process virtualization called ghost process, extending the Linux kernel. The ghost process mechanism has been implemented in the Kerrighed single system image based on Linux. \\ Les mécanismes de gestion de processus (duplication, migration et création de point de reprise/reprise de processus) sont particulièrement intéressants pour les systèmes pour grappes de calculateurs à haute performance et à haute disponibilité. L'un des buts des systèmes à image unique est d'offrir un service de gestion globale des processus fondé sur des mécamismes de création de points de reprise de processus, de migration de processus et de duplication de processus. Dans ce contexte, un mécanisme commun pour la virtualisation de processus est hautement bénéfique mais les systèmes d'exploitation traditionnels n'offrent pas un tel mécanisme. Ce document présente un service noyau pour la virtualisation de processus, appelé processus fantôme, fondé sur une extension du noyau Linux. Le mécanisme de processus fantôme a été mis en oeuvre dans le système à image unique Kerrughed fondé sur Linux

A New Approach to Configurable Dynamic Scheduling in Clusters based on Single System Image Technologies

Clusters are now considered as an alternative to parallel machines to execute workloads made up of sequential and/or parallel applications. For efficient application execution on clusters, dynamic global process scheduling is of prime importance. Different dynamic scheduling policies that have been studied for distributed systems or parallel machines may be used in clusters. The choice of a particular policy depends on the kind of workload to be executed. In a cluster, it is thus highly desirable to implement a configurable global scheduler to be able to adapt the dynamic scheduling policy to the workload characteristics, to take benefit of all cluster resources and tocope with node shutdown and reboot. In this paper, we present the architecture of the global scheduler and the process management mechanisms of Kerrighed, a single system image operating system designed for high performance computing on clusters. Kerrighed provides a development framework allowing to easily implement dynamic scheduling policies without kernel modification. In Kerrighed, the global scheduling policy can be dynamically changed while applications execute on the cluster. Kerrighed's process management mechanisms allow to easily deploy parallelapplications in the cluster and to efficiently migrate or checkpoint processes, including processes sharing memory. Kerrighed has been implemented as a set of modules extending Linux kernel. Preliminary performance results are presented

Five distinct biological processes and 14 differentially expressed genes characterize TEL/AML1-positive leukemia

<p>Abstract</p> <p>Background</p> <p>The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of <it>ETV6 </it>(<it>TEL</it>) and <it>RUNX1 </it>(<it>AML1</it>) genes and defines a relatively uniform category, although only some patients suffer very late relapse. <it>TEL/AML1</it>-positive patients are thus an interesting subgroup to study, and such studies should elucidate the biological processes underlying TEL/AML1 pathogenesis. We report an analysis of gene expression in 60 children with B-lineage ALL using Agilent whole genome oligo-chips (44K-G4112A) and/or real time RT-PCR.</p> <p>Results</p> <p>We compared the leukemia cell gene expression profiles of 16 <it>TEL/AML1</it>-positive ALL patients to those of 44 <it>TEL/AML1</it>-negative patients, whose blast cells did not contain any additional recurrent translocation. Microarray analyses of 26 samples allowed the identification of genes differentially expressed between the TEL/AML1-positive and negative ALL groups. Gene enrichment analysis defined five enriched GO categories: cell differentiation, cell proliferation, apoptosis, cell motility and response to wounding, associated with 14 genes -<it>RUNX1, TCFL5, TNFRSF7, CBFA2T3</it>, <it>CD9</it>, <it>SCARB1, TP53INP1, ACVR1C, PIK3C3, EGFL7</it>, <it>SEMA6A, CTGF, LSP1, TFPI </it>– highlighting the biology of the <it>TEL/AML1 </it>sub-group. These results were first confirmed by the analysis of an additional microarray data-set (7 patient samples) and second by real-time RT-PCR quantification and clustering using an independent set (27 patient samples). Over-expression of <it>RUNX1 (AML1) </it>was further investigated and in one third of the patients correlated with cytogenetic findings.</p> <p>Conclusion</p> <p>Gene expression analyses of leukemia cells from 60 children with <it>TEL/AML1</it>-positive and -negative B-lineage ALL led to the identification of five biological processes, associated with 14 validated genes characterizing and highlighting the biology of the <it>TEL/AML1</it>-positive ALL sub-group.</p

Exome sequencing identifies germline variants in DIS3 in familial multiple myeloma

[Excerpt] Multiple myeloma (MM) is the third most common hematological malignancy, after Non-Hodgkin Lymphoma and Leukemia. MM is generally preceded by Monoclonal Gammopathy of Undetermined Significance (MGUS) [1], and epidemiological studies have identified older age, male gender, family history, and MGUS as risk factors for developing MM [2]. The somatic mutational landscape of sporadic MM has been increasingly investigated, aiming to identify recurrent genetic events involved in myelomagenesis. Whole exome and whole genome sequencing studies have shown that MM is a genetically heterogeneous disease that evolves through accumulation of both clonal and subclonal driver mutations [3] and identified recurrently somatically mutated genes, including KRAS, NRAS, FAM46C, TP53, DIS3, BRAF, TRAF3, CYLD, RB1 and PRDM1 [3,4,5]. Despite the fact that family-based studies have provided data consistent with an inherited genetic susceptibility to MM compatible with Mendelian transmission [6], the molecular basis of inherited MM predisposition is only partly understood. Genome-Wide Association (GWAS) studies have identified and validated 23 loci significantly associated with an increased risk of developing MM that explain ~16% of heritability [7] and only a subset of familial cases are thought to have a polygenic background [8]. Recent studies have identified rare germline variants predisposing to MM in KDM1A [9], ARID1A and USP45 [10], and the implementation of next-generation sequencing technology will allow the characterization of more such rare variants. [...]French National Cancer Institute (INCA) and the Fondation Française pour la Recherche contre le Myélome et les Gammapathies (FFMRG), the Intergroupe Francophone du Myélome (IFM), NCI R01 NCI CA167824 and a generous donation from Matthew Bell. This work was supported in part through the computational resources and staff expertise provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai. Research reported in this paper was supported by the Office of Research Infrastructure of the National Institutes of Health under award number S10OD018522. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The authors thank the Association des Malades du Myélome Multiple (AF3M) for their continued support and participation. Where authors are identified as personnel of the International Agency for Research on Cancer / World Health Organization, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer / World Health Organizatio

Un ordonnanceur de processus pour grappe adaptable : mise en oeuvre dans le système Kerrighed

Aujourd'hui, les grappes de calculateurs sont une alternative économique aux machines parallèle. L'une des approches pour les utiliser est l'approche de système à image unique, comme c'est le cas pour le système d'exploitation Kerrighed. Dans le système Kerrighed, les ressources sont fédérées pour donner la vision d'une machine multi-processeur à mémoire physiquement partagée. La fédération de la ressource processeur est particulièrement importante afin de garantir une exécution efficace des applications, en utilisant un ordonnanceur global.Ce papier présente une architecture modulaire d'ordonnanceur global pour grappe qui permet de fournir un ordonnanceur adaptable à la charge de travail en cours d'exécution, dynamiquement configurable et utilisant efficacement les mécanismes de fédération des ressources du système Kerrighed

SSI-OSCAR: a Cluster Distribution for High Performance Computing Using aSingle System Image

The distributed architecture of clusters implies two ma-jor issues: clusters are difficult to manage (cluster installation and update) and to use (application programmers andusers have to manage cluster resources themselves). Moreover, a large part of clusters run Linux which was becom

OSCAR on Debian: the EDF Experience

Linux clusters are now an interesting solution to execute numerical simulations. But cluster use implies problems of deployment, because of their distributed architecture. In the past, each company developed his own solution based on various tools. Today, software suites like OSCAR are available and can be freely used. But such solutions may not be adapted to the current computing architecture of companies. For example, the current solution deployed inside a company may be based on a Linux distribution not supported by a software suite like OSCAR. Nevertheless, the use of a software suite like OSCAR is very interesting for companies that are not specialized in cluster management. This paper presents the OSCAR port to the Debian distribution in the context of the numerical simulation platform deployed at Électricité de France (Electricity of France). \\ Les grappes de calculateurs Linux sont maintenant une solution intéressante pour exécuter des simulations numériques. Mais les grappes de calculateurs posent des problèmes de déploiement à cause de leur architecture distribuée. Jusque maintenant, chaque entreprise a développé sa propre solution fondée sur divers outils. Aujourd'hui, des suites logicielles telles que OSCAR sont disponibles et peuvent être librement utilisées. Mais de telles solutions peuvent ne pas être adaptées à l'architecture informatique des entreprises. Par exemple, la solution déployée au sein de l'entreprise peut être fondée sur une distribution Linux qui n'est supportée par une suite logicielle telle que OSCAR. Néanmoins, l'utilisation d'une suite logicielle telle que OSCAR est très intéressante pour les entreprises non spécialisée en administration de grappes. Ce document présente le port d'OSCAR sur la distribution Linux Debian dans le cadre de la plate-forme de simulation numérique déployée à Électricité de France

Croissance et survie du homard (Homarus vulgaris) pendant les quinze premiers stades en élevage et sous alimentation composée

Juvenile lobsters were reared for 8 months individually in separate tanks in order to obtain separate estimates of growth. Five batches were studied separately according to the type of diet : deep-frozen krill, paste, ¿try pellets and moist pellets. Growth data were collected over 15 first molt stages for each type of prepared diet. Observations deal with size and weight increments at moult and with weight/length relationships. Regression of total lengths over carapace lengths were fitted in each case.Des homards juvéniles ont été élevés pendant huit mois en logettes individuelles, permettant ainsi de suivre la croissance par individu. Les animaux ont été répartis en 5 lots, chaque. lot recevant une nourriture différente : aliment frais ou aliment composé présenté sous 4 formes différentes. L'expérience a permis de collecter des résultats originaux sur la croissance des juvéniles en élevage pendant les 15 premiers stades, la qualité de l'aliment composé spécialement défini pour cette étude. Les observations portent sur l'accroissement en taille et en poids à chaque mue, la relation taille/poids et la relation longueur totale/ longueur céphalothoracique