Towards a lightweight generic computational grid framework for biological research

Background: An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology. Results: In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: http://igrid-ext.cryst.bbk.ac.uk/portal_guide/. Conclusion: This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project

Survey and Analysis of Production Distributed Computing Infrastructures

This report has two objectives. First, we describe a set of the production distributed infrastructures currently available, so that the reader has a basic understanding of them. This includes explaining why each infrastructure was created and made available and how it has succeeded and failed. The set is not complete, but we believe it is representative. Second, we describe the infrastructures in terms of their use, which is a combination of how they were designed to be used and how users have found ways to use them. Applications are often designed and created with specific infrastructures in mind, with both an appreciation of the existing capabilities provided by those infrastructures and an anticipation of their future capabilities. Here, the infrastructures we discuss were often designed and created with specific applications in mind, or at least specific types of applications. The reader should understand how the interplay between the infrastructure providers and the users leads to such usages, which we call usage modalities. These usage modalities are really abstractions that exist between the infrastructures and the applications; they influence the infrastructures by representing the applications, and they influence the ap- plications by representing the infrastructures

Global Grids and Software Toolkits: A Study of Four Grid Middleware Technologies

Grid is an infrastructure that involves the integrated and collaborative use of computers, networks, databases and scientific instruments owned and managed by multiple organizations. Grid applications often involve large amounts of data and/or computing resources that require secure resource sharing across organizational boundaries. This makes Grid application management and deployment a complex undertaking. Grid middlewares provide users with seamless computing ability and uniform access to resources in the heterogeneous Grid environment. Several software toolkits and systems have been developed, most of which are results of academic research projects, all over the world. This chapter will focus on four of these middlewares--UNICORE, Globus, Legion and Gridbus. It also presents our implementation of a resource broker for UNICORE as this functionality was not supported in it. A comparison of these systems on the basis of the architecture, implementation model and several other features is included.Comment: 19 pages, 10 figure

Technical support for Life Sciences communities on a production grid infrastructure

Production operation of large distributed computing infrastructures (DCI) still requires a lot of human intervention to reach acceptable quality of service. This may be achievable for scientific communities with solid IT support, but it remains a show-stopper for others. Some application execution environments are used to hide runtime technical issues from end users. But they mostly aim at fault-tolerance rather than incident resolution, and their operation still requires substantial manpower. A longer-term support activity is thus needed to ensure sustained quality of service for Virtual Organisations (VO). This paper describes how the biomed VO has addressed this challenge by setting up a technical support team. Its organisation, tooling, daily tasks, and procedures are described. Results are shown in terms of resource usage by end users, amount of reported incidents, and developed software tools. Based on our experience, we suggest ways to measure the impact of the technical support, perspectives to decrease its human cost and make it more community-specific.Comment: HealthGrid'12, Amsterdam : Netherlands (2012

Shibboleth-based access to and usage of grid resources

Security underpins grids and e-research. Without a robust, reliable and simple grid security infrastructure combined with commonly accepted security practices, large portions of the research community and wider industry will not engage. The predominant way in which security is currently addressed in the grid community is through public key infrastructures (PKI) based upon X.509 certificates to support authentication. Whilst PKIs address user identity issues, authentication does not provide fine grained control over what users are allowed to do on remote resources (authorization). In this paper we outline how we have successfully combined Shibboleth and advanced authorization technologies to provide simplified (from the user perspective) but fine grained security for access to and usage of grid resources. We demonstrate this approach through different security focused e-science projects being conducted at the National e-Science Centre (NeSC) at the University of Glasgow. We believe that this model is widely applicable and encourage the further uptake of e-science by non-IT specialists in the research communitie

A Mediated Definite Delegation Model allowing for Certified Grid Job Submission

Grid computing infrastructures need to provide traceability and accounting of their users" activity and protection against misuse and privilege escalation. A central aspect of multi-user Grid job environments is the necessary delegation of privileges in the course of a job submission. With respect to these generic requirements this document describes an improved handling of multi-user Grid jobs in the ALICE ("A Large Ion Collider Experiment") Grid Services. A security analysis of the ALICE Grid job model is presented with derived security objectives, followed by a discussion of existing approaches of unrestricted delegation based on X.509 proxy certificates and the Grid middleware gLExec. Unrestricted delegation has severe security consequences and limitations, most importantly allowing for identity theft and forgery of delegated assignments. These limitations are discussed and formulated, both in general and with respect to an adoption in line with multi-user Grid jobs. Based on the architecture of the ALICE Grid Services, a new general model of mediated definite delegation is developed and formulated, allowing a broker to assign context-sensitive user privileges to agents. The model provides strong accountability and long- term traceability. A prototype implementation allowing for certified Grid jobs is presented including a potential interaction with gLExec. The achieved improvements regarding system security, malicious job exploitation, identity protection, and accountability are emphasized, followed by a discussion of non- repudiation in the face of malicious Grid jobs

EU DataGRID testbed management and support at CERN

In this paper we report on the first two years of running the CERN testbed site for the EU DataGRID project. The site consists of about 120 dual-processor PCs distributed over several testbeds used for different purposes: software development, system integration, and application tests. Activities at the site included test productions of MonteCarlo data for LHC experiments, tutorials and demonstrations of GRID technologies, and support for individual users analysis. This paper focuses on node installation and configuration techniques, service management, user support in a gridified environment, and includes considerations on scalability and security issues and comparisons with "traditional" production systems, as seen from the administrator point of view.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 7 pages, LaTeX. PSN THCT00

Grid-enabled Workflows for Industrial Product Design

This paper presents a generic approach for developing and using Grid-based workflow technology for enabling cross-organizational engineering applications. Using industrial product design examples from the automotive and aerospace industries we highlight the main requirements and challenges addressed by our approach and describe how it can be used for enabling interoperability between heterogeneous workflow engines