Assessing and Improving Interoperability of Distributed Systems

Interoperabilität von verteilten Systemen ist eine Grundlage für die Entwicklung von neuen und innovativen Geschäftslösungen. Sie erlaubt es existierende Dienste, die auf verschiedenen Systemen angeboten werden, so miteinander zu verknüpfen, dass neue oder erweiterte Dienste zur Verfügung gestellt werden können. Außerdem kann durch diese Integration die Zuverlässigkeit von Diensten erhöht werden. Das Erreichen und Bewerten von Interoperabilität stellt jedoch eine finanzielle und zeitliche Herausforderung dar. Zur Sicherstellung und Bewertung von Interoperabilität werden systematische Methoden benötigt. Um systematisch Interoperabilität von Systemen erreichen und bewerten zu können, wurde im Rahmen der vorliegenden Arbeit ein Prozess zur Verbesserung und Beurteilung von Interoperabilität (IAI) entwickelt. Der IAI-Prozess beinhaltet drei Phasen und kann die Interoperabilität von verteilten, homogenen und auch heterogenen Systemen bewerten und verbessern. Die Bewertung erfolgt dabei durch Interoperabilitätstests, die manuell oder automatisiert ausgeführt werden können. Für die Automatisierung von Interoperabilitätstests wird eine neue Methodik vorgestellt, die einen Entwicklungsprozess für automatisierte Interoperabilitätstestsysteme beinhaltet. Die vorgestellte Methodik erleichtert die formale und systematische Bewertung der Interoperabilität von verteilten Systemen. Im Vergleich zur manuellen Prüfung von Interoperabilität gewährleistet die hier vorgestellte Methodik eine höhere Testabdeckung, eine konsistente Testdurchführung und wiederholbare Interoperabilitätstests. Die praktische Anwendbarkeit des IAI-Prozesses und der Methodik für automatisierte Interoperabilitätstests wird durch drei Fallstudien belegt. In der ersten Fallstudie werden Prozess und Methodik für Internet Protocol Multimedia Subsystem (IMS) Netzwerke instanziiert. Die Interoperabilität von IMS-Netzwerken wurde bisher nur manuell getestet. In der zweiten und dritten Fallstudie wird der IAI-Prozess zur Beurteilung und Verbesserung der Interoperabilität von Grid- und Cloud-Systemen angewendet. Die Bewertung und Verbesserung dieser Interoperabilität ist eine Herausforderung, da Grid- und Cloud-Systeme im Gegensatz zu IMS-Netzwerken heterogen sind. Im Rahmen der Fallstudien werden Möglichkeiten für Integrations- und Interoperabilitätslösungen von Grid- und Infrastructure as a Service (IaaS) Cloud-Systemen sowie von Grid- und Platform as a Service (PaaS) Cloud-Systemen aufgezeigt. Die vorgestellten Lösungen sind in der Literatur bisher nicht dokumentiert worden. Sie ermöglichen die komplementäre Nutzung von Grid- und Cloud-Systemen, eine vereinfachte Migration von Grid-Anwendungen in ein Cloud-System sowie eine effiziente Ressourcennutzung. Die Interoperabilitätslösungen werden mit Hilfe des IAI-Prozesses bewertet. Die Durchführung der Tests für Grid-IaaS-Cloud-Systeme erfolgte manuell. Die Interoperabilität von Grid-PaaS-Cloud-Systemen wird mit Hilfe der Methodik für automatisierte Interoperabilitätstests bewertet. Interoperabilitätstests und deren Beurteilung wurden bisher in der Grid- und Cloud-Community nicht diskutiert, obwohl sie eine Basis für die Entwicklung von standardisierten Schnittstellen zum Erreichen von Interoperabilität zwischen Grid- und Cloud-Systemen bieten.Achieving interoperability of distributed systems offers means for the development of new and innovative business solutions. Interoperability allows the combination of existing services provided on different systems, into new or extended services. Such an integration can also increase the reliability of the provided service. However, achieving and assessing interoperability is a technical challenge that requires high effort regarding time and costs. The reasons are manifold and include differing implementations of standards as well as the provision of proprietary interfaces. The implementations need to be engineered to be interoperable. Techniques that assess and improve interoperability systematically are required. For the assurance of reliable interoperation between systems, interoperability needs to be assessed and improved in a systematic manner. To this aim, we present the Interoperability Assessment and Improvement (IAI) process, which describes in three phases how interoperability of distributed homogeneous and heterogeneous systems can be improved and assessed systematically. The interoperability assessment is achieved by means of interoperability testing, which is typically performed manually. For the automation of interoperability test execution, we present a new methodology including a generic development process for a complete and automated interoperability test system. This methodology provides means for a formalized and systematic assessment of systems' interoperability in an automated manner. Compared to manual interoperability testing, the application of our methodology has the following benefits: wider test coverage, consistent test execution, and test repeatability. We evaluate the IAI process and the methodology for automated interoperability testing in three case studies. Within the first case study, we instantiate the IAI process and the methodology for Internet Protocol Multimedia Subsystem (IMS) networks, which were previously assessed for interoperability only in a manual manner. Within the second and third case study, we apply the IAI process to assess and improve the interoperability of grid and cloud computing systems. Their interoperability assessment and improvement is challenging, since cloud and grid systems are, in contrast to IMS networks, heterogeneous. We develop integration and interoperability solutions for grids and Infrastructure as a Service (IaaS) clouds as well as for grids and Platform as a Service (PaaS) clouds. These solutions are unique and foster complementary usage of grids and clouds, simplified migration of grid applications into the cloud, as well as efficient resource utilization. In addition, we assess the interoperability of the grid-cloud interoperability solutions. While the tests for grid-IaaS clouds are performed manually, we applied our methodology for automated interoperability testing for the assessment of interoperability to grid-PaaS cloud interoperability successfully. These interoperability assessments are unique in the grid-cloud community and provide a basis for the development of standardized interfaces improving the interoperability between grids and clouds

Native structure-based modeling and simulation of biomolecular systems per mouse click

Background Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions. At the same time, scalability to a large number of cores is limited mostly due to long-range interactions. An appealing alternative to atomic-level simulations is coarse-graining the resolution of the system or reducing the complexity of the Hamiltonian to improve sampling while decreasing computational costs. Native structure-based models, also called Gō-type models, are based on energy landscape theory and the principle of minimal frustration. They have been tremendously successful in explaining fundamental questions of, e.g., protein folding, RNA folding or protein function. At the same time, they are computationally sufficiently inexpensive to run complex simulations on smaller computing systems or even commodity hardware. Still, their setup and evaluation is quite complex even though sophisticated software packages support their realization. Results Here, we establish an efficient infrastructure for native structure-based models to support the community and enable high-throughput simulations on remote computing resources via GridBeans and UNICORE middleware. This infrastructure organizes the setup of such simulations resulting in increased comparability of simulation results. At the same time, complete workflows for advanced simulation protocols can be established and managed on remote resources by a graphical interface which increases reusability of protocols and additionally lowers the entry barrier into such simulations for, e.g., experimental scientists who want to compare their results against simulations. We demonstrate the power of this approach by illustrating it for protein folding simulations for a range of proteins. Conclusions We present software enhancing the entire workflow for native structure-based simulations including exception-handling and evaluations. Extending the capability and improving the accessibility of existing simulation packages the software goes beyond the state of the art in the domain of biomolecular simulations. Thus we expect that it will stimulate more individuals from the community to employ more confidently modeling in their research

AstroGrid-D: Grid Technology for Astronomical Science

We present status and results of AstroGrid-D, a joint effort of astrophysicists and computer scientists to employ grid technology for scientific applications. AstroGrid-D provides access to a network of distributed machines with a set of commands as well as software interfaces. It allows simple use of computer and storage facilities and to schedule or monitor compute tasks and data management. It is based on the Globus Toolkit middleware (GT4). Chapter 1 describes the context which led to the demand for advanced software solutions in Astrophysics, and we state the goals of the project. We then present characteristic astrophysical applications that have been implemented on AstroGrid-D in chapter 2. We describe simulations of different complexity, compute-intensive calculations running on multiple sites, and advanced applications for specific scientific purposes, such as a connection to robotic telescopes. We can show from these examples how grid execution improves e.g. the scientific workflow. Chapter 3 explains the software tools and services that we adapted or newly developed. Section 3.1 is focused on the administrative aspects of the infrastructure, to manage users and monitor activity. Section 3.2 characterises the central components of our architecture: The AstroGrid-D information service to collect and store metadata, a file management system, the data management system, and a job manager for automatic submission of compute tasks. We summarise the successfully established infrastructure in chapter 4, concluding with our future plans to establish AstroGrid-D as a platform of modern e-Astronomy.Comment: 14 pages, 12 figures Subjects: data analysis, image processing, robotic telescopes, simulations, grid. Accepted for publication in New Astronom

A Taxonomy of Workflow Management Systems for Grid Computing

With the advent of Grid and application technologies, scientists and engineers are building more and more complex applications to manage and process large data sets, and execute scientific experiments on distributed resources. Such application scenarios require means for composing and executing complex workflows. Therefore, many efforts have been made towards the development of workflow management systems for Grid computing. In this paper, we propose a taxonomy that characterizes and classifies various approaches for building and executing workflows on Grids. We also survey several representative Grid workflow systems developed by various projects world-wide to demonstrate the comprehensiveness of the taxonomy. The taxonomy not only highlights the design and engineering similarities and differences of state-of-the-art in Grid workflow systems, but also identifies the areas that need further research.Comment: 29 pages, 15 figure

DRIVER Technology Watch Report

This report is part of the Discovery Workpackage (WP4) and is the third report out of four deliverables. The objective of this report is to give an overview of the latest technical developments in the world of digital repositories, digital libraries and beyond, in order to serve as theoretical and practical input for the technical DRIVER developments, especially those focused on enhanced publications. This report consists of two main parts, one part focuses on interoperability standards for enhanced publications, the other part consists of three subchapters, which give a landscape picture of current and surfacing technologies and communities crucial to DRIVER. These three subchapters contain the GRID, CRIS and LTP communities and technologies. Every chapter contains a theoretical explanation, followed by case studies and the outcomes and opportunities for DRIVER in this field

Research and development of accounting system in grid environment

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.The Grid has been recognised as the next-generation distributed computing paradigm by seamlessly integrating heterogeneous resources across administrative domains as a single virtual system. There are an increasing number of scientific and business projects that employ Grid computing technologies for large-scale resource sharing and collaborations. Early adoptions of Grid computing technologies have custom middleware implemented to bridge gaps between heterogeneous computing backbones. These custom solutions form the basis to the emerging Open Grid Service Architecture (OGSA), which aims at addressing common concerns of Grid systems by defining a set of interoperable and reusable Grid services. One of common concerns as defined in OGSA is the Grid accounting service. The main objective of the Grid accounting service is to ensure resources to be shared within a Grid environment in an accountable manner by metering and logging accurate resource usage information. This thesis discusses the origins and fundamentals of Grid computing and accounting service in the context of OGSA profile. A prototype was developed and evaluated based on OGSA accounting-related standards enabling sharing accounting data in a multi-Grid environment, the World-wide Large Hadron Collider Grid (WLCG). Based on this prototype and lessons learned, a generic middleware solution was also implemented as a toolkit that eases migration of existing accounting system to be standard compatible.Engineering and Physical Sciences Research Council (EPSRC), Stanford Universit

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