Mathilde Romberg

The UNICORE architecture: seamless access to distributed resources

Seamless access to different systems of different vendors at different sites is an important prerequisite to effective and efficient use of distributed resources. Learning about new systems, new software, and new interfaces is a time-consuming task for users who actually want to run their applications. UNICORE is a project to overcome these difficulties by providing a uniform interface for job preparation and control which gives seamless and secure access to supercomputer resources. It is an ambitious project delivering a production ready prototype within two years. The article focuses on the UNICORE architecture, especially the protocol and the underlying security mechanism.

Unicore — From project results to production grids

The UNICORE Grid-technology provides a seamless, secure and intuitive access to distributed Grid resources. In this paper we present the recent evolution from project results to production Grids. At the beginning UNICORE was developed as a prototype software in two projects funded by the German research ministry (BMBF). Over the following years, in various European-funded projects, UNICORE evolved to a full-grown and well-tested Grid middleware system, which today is used in daily production at many supercomputing centers worldwide. Beyond this production usage, the UNICORE technology serves as a solid basis in many European and International research projects, which use existing UNICORE components to implement advanced features, high level services, and support for applications from a growing range of domains. In order to foster these ongoing developments, UNICORE is available as open source under BSD licence at Source Forge, where new releases are published on a regular basis. This paper is a review of the UNICORE achievements so far and gives a glimpse on the UNICORE roadmap.

Grid-enabled data warehousing for molecular engineering

Molecular engineering is concerned with the design and manufacturing of novel chemical compounds and materials. Molecular engineering for drug development is complex, time-consuming, and expensive. To lower costs and improve the overall drug development process, information technology (IT) is increasingly employed in the molecular engineering phase. Key IT components for molecular engineering include public and proprietary databases containing information on molecular structures and properties and computational models capable of calculating global properties of molecular structures based on structural and other descriptors characterizing the compound. Recently data mining and data warehousing have become critical tools in the molecular engineering process. Increasingly, some of the computational resources--such as data and information bases, computational models, compute power to execute these models, specialized data mining algorithms--required to develop a new compound are not available locally, but accessible via the global computing network infrastructure. This paper describes a Grid-based approach to molecular engineering. Focus of this paper is placed on the data warehousing of the OpenMolGRID system.

OpenMolGRID: using automated workflows in GRID computing environment

Quantitative Structure Activity/Property Relationship (QSAR/QSPR) model development is a complex and time-consuming procedure involving data gathering and preparation. It plays an important role in the drug discovery pipeline, which still is mostly done manually. The current paper describes the automated workflow support of the OpenMolGRID system and provides a case study for the automation of the QSPR model development process in the Grid.

An Interoperable Grid Information System for Integrated Resource Monitoring Based on Virtual Organizations

In many Grid infrastructures different kinds of information services are in use, which utilize different incompatible data structures and interfaces to encode and provide their data. Homogeneous monitoring of these infrastructures with the monitoring data being accessible everywhere independently of the middleware which provided it, is the basis for a consistent status reporting on the Grids’ resources and services. Thus, interoperability or interoperation between the different information services in a heterogeneous Grid infrastructure is required. Monitoring data must contain the identity of the affected Virtual Organization (VO) so that it can be related to the resources and services the VO has allocated to enable VO-specific information provision. This paper describes a distributed architecture for an interoperable information service, which combines data unification and categorization with policies for VO membership, VO resource management and data transformations. This service builds the basis for an integrated and interoperating monitoring of Grids, which provide their data to more than one VO and utilize heterogeneous information services.

Application driven grid developments in the OpenMolGRID project

Within the frame of the OpenMolGRID project, several extensions to the underlying UNICORE Grid infrastructure have been developed. This article gives an overview of these developments, focussing on the support for complex scientific workflows and a newly developed command line client for UNICORE.

The unicore grid and its options for performance analysis

UNICORE (Uniform Interface to Computer Resources) is a software infrastructure to support seamless and secure access to distributed resources. It has been developed by the projects UNICORE and UNICORE Plus in 1997 - 2002 (funded by the German Ministry of Education and Research) and is going to be enhanced in the EU-funded projects EUROGRID and GRIP. The UNICORE system allows uniform access to different hardware and software platforms as well as different organizational environments. The core part is the abstract job model. The abstract job specification is translated into a concrete batch job for the target system. Besides others, application specific support is a major feature of the system. By exploiting the plugin mechanism, support for performance analysis of Grid applications can be added. As an example, support of Vampirtrace has been integrated. The UNICORE user interface then gives the option to add a task using Vampirtrace with runtime configuration support into a UNICORE job and retrieve the generated trace files for local visualization. Together with the support for compilation and linkage and for metacomputing, the plugin mechanism may be used to integrate other performance analysis tools in future.

The Chemomentum Data Services --- A Flexible Solution for Data Handling in UNICORE

This paper introduces the Chemomentum data services, a UNICORE-based flexible solution for managing large amounts of data and metadata produced in a Grid. In order to store and manage the increasing amounts of data produced in Grid environments, a highly scalable and distributed Grid storage system is needed. However, the simple storage of data is not enough. To allow a comfortable browsing and retrieving of the data, it is crucial that files are indexed and augmented with metadata. This paper analyses integrated solutions that already provide these functionalities for their features and shortcomings. Incorporating the conclusions drawn from the examination, an architecture for a revised data management solution is presented. This system provides the means to store files with augmenting extensible metadata. It allows also to browse through data using metadata, handle ontologies and transparently access external data sources. In the current stage, most of these functionalities are implemented and running in a distributed environment.

Life science application support in an interoperable e-science environment

In the last decade, life science applications have become more and more integrated into e-Science environments, hence they are typically very demanding, both in terms of computational capabilities and data capacities. Especially the access to life science applications, embedded in such environments via Grid clients still constitutes a major hurdle for scientists that do not have an IT background. Life science applications often comprise a whole set of small programs instead of a single executable. Many of the graphical Grid clients are not perfectly suited for these types of applications, as they often assume that Grid jobs will run a single executable instead of a set of chained executions (i.e. sequences). This means that in order to execute a sequence of multiple programs on a single Grid resource, piping data from one program to the next, the user would have to run a hand-written shell script. Otherwise each program is independently scheduled as a Grid job, which causes unnecessary file transfers between the jobs, even if they are scheduled on the same resource. We present a generic solution to this problem and provide a reference implementation, which seamlessly integrates with the Grid middleware UNICORE. Our approach focuses on a comfortable user interface for the creation of such program sequences, validated in UNICORE-driven HPC-based Grids. Thus, we applied our approach in order to provide support for the usage of the AMBER package (a widely-used collection of programs for molecular dynamics simulations) within Grid workflows. We finally provide a scientific use case of our approach leveraging the interoperability of two different scientific infrastructures that represents an instance of the infrastructure interoperability reference model.

UNICORE – Uniformes Interface für Computer Ressourcen

1 ZUSAMMENFASSUNG Wissenschaftler aus Universitäten und Forschungseinrichtungen nutzen seit langem Rechner an entfernten Standorten, um komplexe Probleme aus Computational Science und Engineering zu lösen. Da Rechner verschiedener Hersteller zum Einsatz kommen, besteht ein erheblicher Lernaufwand, bevor ein neuer Rechner genutzt werden kann. Benutzer, die für ihre Anwendungen Supercomputer benötigen, sind gezwungen, sich mit den system- und rechenzentrums-spezifischen Gegebenheiten vertraut zu machen. Dieses kann sehr zeitaufwendig werden, insbesondere wenn Rechner in verschiedenen Zentren genutzt werden z.B. für heterogenes Rechnen oder Metacomputing. UNICORE (Uniformes Interface für Computer-Ressourcen) wurde entworfen, um den Benutzern einen einfachen und sicheren Zugang zu verteilten Rechner-Ressourcen zu schaffen.