Towards a virtual research environment for paediatric endocrinology across Europe

Paediatric endocrinology is a medical specialty dealing with variations of physical growth and sexual development in childhood. Genetic anomalies that can cause disorders of sexual development in children are rare. Given this, sharing and collaboration on the small number of cases that occur is needed by clinical experts in the field. The EU-funded EuroDSD project (www.eurodsd.eu) is one such collaboration involving clinical centres and clinical and genetic experts across Europe. Through the establishment of a virtual research environment (VRE) supporting sharing of data and a variety of clinical and bioinformatics analysis tools, EuroDSD aims to provide a research infrastructure for research into disorders of sex development. Security, ethics and information governance are at the heart of this infrastructure. This paper describes the infrastructure that is being built and the inherent challenges in security, availability and dependability that must be overcome for the enterprise to succeed

Intermediate QoS Prototype for the EDGI Infrastructure

This document provides the first deliverable of EDGI JRA2. It is produced by the INRIA team, the SZTAKI team, the LAL/IN2P3 team and the University of Coimbra team. This document aims at describing achievements and results of JRA2 tasks "Advanced QoS Scheduler and Oracle" and "Support In Science Gateway". Hybrid Distributed Computing Infrastructures (DCIs) allow users to combine Grids, Desktop Grids, Clouds, etc. to obtain for their users large computing capabilities. The EDGI infrastructure belongs to this kind of DCIs. The document presents the SpeQuloS framework to provide quality of service (QoS) for application executed on the EDGI infrastructure. It also introduces EDGI QoS portal, an user-friendly and integrated access to QoS features for users of EDGI infrastructure. In this document, we first introduce new results from JRA2.1 task, which collected and analyzed batch execution on Desktop Grid. Then, we present the advanced Cloud Scheduling and Oracle strategies designed inside the SpeQuloS framework (task JRA2.2). We demonstrate efficiency of these strategies using performance evaluation carried out with simulations. Next, we introduce Credit System architecture and QoS user portal as part of the JRA2 Support In Science Gateway (task JRA2.3). Finally, we conclude and provide references to JRA2 production.Ce document fournit le premier livrable pour la tâche JRA2 du projet européen European Desktop Grid Initiative (FP7 EDGI). Il est produit par les équipes de l'INRIA, de SZTAKI, du LAL/IN2P3 et de l'Université de Coimbra. Ce document vise à décrire les réalisations et les résultats qui concernent la qualité de service pour l'infrastructure de grilles de PCs européenne EDGI

On Evaluating Commercial Cloud Services: A Systematic Review

Background: Cloud Computing is increasingly booming in industry with many competing providers and services. Accordingly, evaluation of commercial Cloud services is necessary. However, the existing evaluation studies are relatively chaotic. There exists tremendous confusion and gap between practices and theory about Cloud services evaluation. Aim: To facilitate relieving the aforementioned chaos, this work aims to synthesize the existing evaluation implementations to outline the state-of-the-practice and also identify research opportunities in Cloud services evaluation. Method: Based on a conceptual evaluation model comprising six steps, the Systematic Literature Review (SLR) method was employed to collect relevant evidence to investigate the Cloud services evaluation step by step. Results: This SLR identified 82 relevant evaluation studies. The overall data collected from these studies essentially represent the current practical landscape of implementing Cloud services evaluation, and in turn can be reused to facilitate future evaluation work. Conclusions: Evaluation of commercial Cloud services has become a world-wide research topic. Some of the findings of this SLR identify several research gaps in the area of Cloud services evaluation (e.g., the Elasticity and Security evaluation of commercial Cloud services could be a long-term challenge), while some other findings suggest the trend of applying commercial Cloud services (e.g., compared with PaaS, IaaS seems more suitable for customers and is particularly important in industry). This SLR study itself also confirms some previous experiences and reveals new Evidence-Based Software Engineering (EBSE) lessons

Supporting security-oriented, collaborative nanoCMOS electronics research

Grid technologies support collaborative e-Research typified by multiple institutions and resources seamlessly shared to tackle common research problems. The rules for collaboration and resource sharing are commonly achieved through establishment and management of virtual organizations (VOs) where policies on access and usage of resources by collaborators are defined and enforced by sites involved in the collaboration. The expression and enforcement of these rules is made through access control systems where roles/privileges are defined and associated with individuals as digitally signed attribute certificates which collaborating sites then use to authorize access to resources. Key to this approach is that the roles are assigned to the right individuals in the VO; the attribute certificates are only presented to the appropriate resources in the VO; it is transparent to the end user researchers, and finally that it is manageable for resource providers and administrators in the collaboration. In this paper, we present a security model and implementation improving the overall usability and security of resources used in Grid-based e-Research collaborations through exploitation of the Internet2 Shibboleth technology. This is explored in the context of a major new security focused project at the National e-Science Centre (NeSC) at the University of Glasgow in the nanoCMOS electronics domain

Analyzing the EGEE production grid workload: application to jobs submission optimization

International audienceGrids reliability remains an order of magnitude below clusters on production infrastructures. This work is aims at improving grid application performances by improving the job submission system. A stochastic model, capturing the behavior of a complex grid workload management system is proposed. To instantiate the model, detailed statistics are extracted from dense grid activity traces. The model is exploited in a simple job resubmission strategy. It provides quantitative inputs to improve job submission performance and it enables quantifying the impact of faults and outliers on grid operations

Performance Modeling to Support Multi-Tier Application Deployment to Infrastructure-As-A-Service Clouds

Infrastructure-as-a-service (IaaS) clouds support migration of multi-tier applications through virtualization of diverse application stack(s) of components which may require various operating systems and environments. To maximize performance of applications deployed to IaaS clouds while minimizing deployment costs, it is necessary to create virtual machine images to host application components with consideration for component dependencies that may affect load balancing of physical resources of VM hosts including CPU time, disk and network bandwidth. This paper presents results of an investigation utilizing physical machine (PM) and virtual machine (VM) resource utilization statistics to build performance models to predict application performance and rank performance of application component deployment configurations deployed across VMs. Our objective was to predict which component compositions provide best performance while requiring the fewest number of VMs. Eighteen individual resource utilization statistics were investigated for use as independent variables to predict service execution time using four different modeling approaches. Overall CPU time was the strongest predictor of execution time. The strength of individual predictors varied with respect to the resource utilization profiles of the applications. CPU statistics including idle time and number of context switches were good predictors when the test application was more disk I/O bound, while disk I/O statistics were better predictors when the application was more CPU bound. All performance models built were effective at determining the best performing service composition deployments validating the utility of our approach

Service Isolation vs. Consolidation: Implications for Iaas Cloud Application Deployment

Service isolation, achieved by deploying components of multi -tier applications using separate virtual machines (VMs), is a common \u27best\u27 practice. Various advantages cited include simpler deployment architectures, easier resource scalability for supporting dynamic application throughput requirements, and support for component-level fault tolerance . This paper presents results from an empirical study which investigates the performance implications of component placement for deployments of multi -tier applications to Infrastructure-as-a- Service (IaaS) clouds. Relationship s between performance and resource utilization (CPU, disk, network) are investigated to better understand the implications which result from how applications are deployed. All possible deployments for two variants of a multi -tier application were tested, one computationally bound by the model, the other bound by a geospatial database. The best performing deployments required as few as 2 VMs, half the number required for service isolation, demonstrating potential cost savings with service consolidation. Resource use (CPU time, disk I/O, and network I/O) varied based on component placement and VM memory allocation. Using separate VMs to host each application component resulted in performance overhead of ~1 -2%. Relationships between resource utilization an d performance were harnessed to build a multiple linear regression model to predict performance of component deployments. CPU time, disk sector reads, and disk sector writes are identified as the most powerful performance predictors for component deployments

Adding Storage Simulation Capacities to the SimGrid Toolkit: Concepts, Models, and API

International audienceFor each kind of distributed computing infrastructures, i.e., clusters, grids, clouds, data centers, or supercomputers, storage is a essential component to cope with the tremendous increase in scientific data production and the ever-growing need for data analysis and preservation. Understanding the performance of a storage subsystem or dimensioning it properly is an important concern for which simulation can help by allowing for fast, fully repeatable, and configurable experiments for arbitrary hypothetical scenarios. However, most simulation frameworks tailored for the study of distributed systems offer no or little abstractions or models of storage resources.In this paper, we detail the extension of SimGrid, a versatile toolkit for the simulation of large-scale distributed computing systems, with storage simulation capacities. We first define the required abstractions and propose a new API to handle storage components and their contents in SimGrid-based simulators. Then we characterize the performance of the fundamental storage component that are disks and derive models of these resources. Finally we list several concrete use cases of storage simulations in clusters, grids, clouds, and data centers for which the proposed extension would be beneficial

BIGhybrid: A Simulator for MapReduce Applications in Hybrid Distributed Infrastructures Validated with the Grid5000 Experimental Platform

International audienceSUMMARY Cloud computing has increasingly been used as a platform for running large business and data processing applications. Conversely, Desktop Grids have been successfully employed in a wide range of projects, because they are able to take advantage of a large number of resources provided free of charge by volunteers. A hybrid infrastructure created from the combination of Cloud and Desktop Grids infrastructures can provide a low-cost and scalable solution for Big Data analysis. Although frameworks like MapReduce have been designed to exploit commodity hardware, their ability to take advantage of a hybrid infrastructure poses significant challenges due to their large resource heterogeneity and high churn rate. In this paper is proposed BIGhybrid, a simulator for two existing classes of MapReduce runtime environments: BitDew-MapReduce designed for Desktop Grids and BlobSeer-Hadoop designed for Cloud computing, where the goal is to carry out accurate simulations of MapReduce executions in a hybrid infrastructure composed of Cloud computing and Desktop Grid resources. This work describes the principles of the simulator and describes the validation of BigHybrid with the Grid5000 experimental platform. Owing to BigHybrid, developers can investigate and evaluate new algorithms to enable MapReduce to be executed in hybrid infrastructures. This includes topics such as resource allocation and data splitting. Concurrency and Computation: Practice and Experienc

Monte Carlo Simulation With The GATE Software Using Grid Computing

DémonstrationInternational audienceMonte Carlo simulations needing many replicates to obtain good statistical results can be easily executed in parallel using the "Multiple Replications In Parallel" approach. However, several precautions have to be taken in the generation of the parallel streams of pseudo-random numbers. In this paper, we present the distribution of Monte Carlo simulations performed with the GATE software using local clusters and grid computing. We obtained very convincing results with this large medical application, thanks to the EGEE Grid (Enabling Grid for E-sciencE), achieving in one week computations that could have taken more than 3 years of processing on a single computer. This work has been achieved thanks to a generic object-oriented toolbox called DistMe which we designed to automate this kind of parallelization for Monte Carlo simulations. This toolbox, written in Java is freely available on SourceForge and helped to ensure a rigorous distribution of pseudo-random number streams. It is based on the use of a documented XML format for random numbers generators statuses