Bernd Schuller

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.

A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

Structural bioinformatics applies computational methods to analyze and model three-dimensional molecular structures. There is a huge number of applications available to work with structural data on large scale. Using these tools on distributed computing infrastructures (DCIs), however, is often complicated due to a lack of suitable interfaces. The MoSGrid (Molecular Simulation Grid) science gateway provides an intuitive user interface to several widely-used applications for structural bioinformatics, molecular modeling, and quantum chemistry. It ensures the confidentiality, integrity, and availability of data via a granular security concept, which covers all layers of the infrastructure. The security concept applies SAML (Security Assertion Markup Language) and allows trust delegation from the user interface layer across the high-level middleware layer and the Grid middleware layer down to the HPC facilities. SAML assertions had to be integrated into the MoSGrid infrastructure in several places: the workflow-enabled Grid portal WS-PGRADE (Web Services Parallel Grid Runtime and Developer Environment), the gUSE (Grid User Support Environment) DCI services, and the cloud file system XtreemFS. The presented security infrastructure allows a single sign-on process to all involved DCI components and, therefore, lowers the hurdle for users to utilize large HPC infrastructures for structural bioinformatics.

Chemomentum - UNICORE 6 based infrastructure for complex applications in science and technology

Chemomentum, Grid Services based Environment to enable Innovative Research, is an end-user focused approach to exploit Grid computing for diverse application domains. Building on top of UNICORE 6, we are designing and implementing a flexible, user-friendly Grid system focussing on high-performance processing of complex application workflows and management of data, metadata and knowledge. This paper outlines Chemomentum vision, application scenarios, technical challenges, software architecture and design of the system.

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.

The UNICORE Rich Client: Facilitating the Automated Execution of Scientific Workflows

Today, many scientific disciplines heavily rely on computer systems for in-silico experimentation or data management and analysis. The employed computer hard- and software is heterogeneous and complies to different standards, interfaces and protocols for interoperation. Grid middleware systems like UNICORE 6 try to hide some of the complexity of the underlying systems by offering high-level, uniform interfaces for executing computational jobs or storing, moving, and searching through data. Via UNICORE 6 computer resources can be accessed securely with different software clients, e.g. the UNICORE Command line Client (UCC) or the graphical UNICORE Rich Client (URC) which is based on Eclipse. In this paper, we describe the design and features of the URC, and highlight its role as a flexible and extensible Grid client framework using the QSAR field as an example.

Standards-based metadata management for molecular simulations

State‐of‐the‐art research in a variety of natural sciences depends heavily on methods of computational chemistry, for example, the calculation of the properties of materials, proteins, catalysts, and drugs. Applications providing such methods require a lot of expertise to handle their complexity and the usage of high‐performance computing. The MoSGrid (molecular simulation grid) infrastructure relieves this burden from scientists by providing a science gateway, which eases access to and usage of computational chemistry applications. One of its cornerstones is the molecular simulations markup language (MSML), an extension of the chemical markup language. MSML abstracts all chemical as well as computational aspects of simulations. An application and its results can be described with common semantics. Using such application, independent descriptions users can easily switch between different applications or compare them. This paper introduces MSML, its integration into a science gateway, and its usage for molecular dynamics, quantum chemistry, and protein docking. Copyright

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.

Key aspects of the UNICORE 6 security model

This paper presents the security architecture of the sixth version of the UNICORE grid middleware. The sixth iteration of UNICORE introduced a number of new, security-related solutions which make UNICORE distinguishable from the other grid middleware as Globus, gLite or NorduGrid ARC, and these are presented in this paper. The paper discusses the low level security: users authentication, non-repudiation control and trust delegation. The UNICORE unique approach to the challenge of trust delegation is called explicit trust delegation (ETD); discussion of this constitutes the most significant and extensive part of this paper. ETD is compared with the popular grid security infrastructure (GSI). High level security services (such as authorization services) are not described in this paper.

Web Services Interfaces and Open Standards Integration into the European UNICORE 6 Grid Middleware

The UNICORE grid system provides a seamless, secure and intuitive access to distributed grid resources. In recent years, UNICORE 5 is used as a well-tested grid middleware system in production grids (e.g. DEISA, D-Grid) and at many supercomputer centers world-wide. Beyond this production usage, UNICORE serves as a solid basis in many European and International research projects and business scenarios from T-Systems, Philips Research, Intel, Fujitsu and others. To foster ongoing developments in multiple projects, UNICORE is open source under BSD license at SourceForge. More recently, the new Web services-based UNICORE 6 has become available that is based on open standards such as the Web services addressing (WS-A) and the Web services resource framework (WS-RF) and thus conforms to the open grid services architecture (OGSA) of the open grid forum (OGF). In this paper we present the evolution from production UNICORE 5 to the open standards-based UNICORE 6 and its various Web services-based interfaces. It describes the interface integration of emerging open standards such as OGSA-BES and OGSA-RUS and thus provides an overview of UNICORE 6.

Using SAML-based VOMS for authorization within web services-based UNICORE grids

In recent years, the Virtual Organization Membership Service (VOMS) emerged within Grid infrastructures providing dynamic, fine-grained, access control needed to enable resource sharing across Virtual Organization (VOs). VOMS allows to manage authorization information in a VO scope to enforce agreements established between VOs and resource owners. VOMS is used for authorization in the EGEE and OSG infrastructures and is a core component of the respective middleware stacks gLite and VDT. While a module for supporting VOMS is also available as part of the authorization service of the Globus Toolkit, there is currently no support for VO-level authorization within the new Web services-based UNICORE 6. This paper describes the evolution of VOMS towards an open standard compliant service based on the Security Assertion Markup Language (SAML), which in turn provides mechanisms to fill the VO-level authorization service gap within Web service-based UNICORE Grids. In addition, the SAML-based VOMS allows for cross middleware VO management through open standards.