Ákos Balaskó

WS-PGRADE/gUSE Generic DCI Gateway Framework for a Large Variety of User Communities

The WS-PGRADE/gUSE generic DCI gateway framework has been developed to support a large variety of user communities. It provides a generic purpose, workflow-oriented graphical user interface to create and run workflows on various DCIs including clusters, Grids, desktop Grids and clouds. The framework can be used by NGIs to support small user communities who cannot afford to develop their own customized science gateway. The WS-PGRADE/gUSE framework also provides two API interfaces (Application Specific Module API and Remote API) to create application-specific science gateways according to the needs of different user communities. The paper describes in detail the workflow concept of WS-PGRADE, the DCI Bridge service that enables access to most of the popular European DCIs and the Application Specific Module and Remote API concepts to generate application-specific science gateways.

Enabling scientific workflow sharing through coarse-grained interoperability

E-scientists want to run their scientific experiments on Distributed Computing Infrastructures (DCI) to be able to access large pools of resources and services. To run experiments on these infrastructures requires specific expertise that e-scientists may not have. Workflows can hide resources and services as a virtualization layer providing a user interface that e-scientists can use. There are many workflow systems used by research communities but they are not interoperable. To learn a workflow system and create workflows in this workflow system may require significant efforts from e-scientists. Considering these efforts it is not reasonable to expect that research communities will learn new workflow systems if they want to run workflows developed in other workflow systems. The solution is to create workflow interoperability solutions to allow workflow sharing. The FP7 Sharing Interoperable Workflow for Large-Scale Scientific Simulation on Available DCIs (SHIWA) project developed two interoperability solutions to support workflow sharing: Coarse-Grained Interoperability (CGI) and Fine-Grained Interoperability (FGI). The project created the SHIWA Simulation Platform (SSP) to implement the Coarse-Grained Interoperability approach as a production-level service for research communities. The paper describes the CGI approach and how it enables sharing and combining existing workflows into complex applications and run them on Distributed Computing Infrastructures. The paper also outlines the architecture, components and usage scenarios of the simulation platform.

BUILDING SCIENCE GATEWAYS BY UTILIZING THE GENERIC WS-PGRADE/GUSE WORKFLOW SYSTEM

Enabling scientists to use remote distributed infrastructures, parametrizeand execute common science-domain applications transparently is actual anda highly relevant field of distributed computing. For this purpose a general so-lution is the concept of Science Gateways. WS-PGRADE/gUSE system offersa transparent and web-based interface to access distributed resources (grids,clusters or clouds), extended by a powerful generic purpose workflow editorand enactment system, which can be used to compose scientific applicationsinto data-flow based workflow structures. It’s a generic web-based portal so-lution to organize scientific applications in a workflow structure and executethem on remote computational resources. As the portal defines nodes as black-box applications uploaded by the users, it does not provide any applicationspecific interface by default. In this paper we show what kind of tools, APIsand interfaces are available in WS-PGRADE/gUSE to customize it to have anapplication specific gateway.

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.

Fine-Grain Interoperability of Scientific Workflows in Distributed Computing Infrastructures

Today there exist a wide variety of scientific workflow management systems, each designed to fulfill the needs of a certain scientific community. Unfortunately, once a workflow application has been designed in one particular system it becomes very hard to share it with users working with different systems. Portability of workflows and interoperability between current systems barely exists. In this work, we present the fine-grained interoperability solution proposed in the SHIWA European project that brings together four representative European workflow systems: ASKALON, MOTEUR, WS-PGRADE, and Triana. The proposed interoperability is realised at two levels of abstraction: abstract and concrete. At the abstract level, we propose a generic Interoperable Workflow Intermediate Representation (IWIR) that can be used as a common bridge for translating workflows between different languages independent of the underlying distributed computing infrastructure. At the concrete level, we propose a bundling technique that aggregates the abstract IWIR representation and concrete task representations to enable workflow instantiation, execution and scheduling. We illustrate case studies using two real-workflow applications designed in a native environment and then translated and executed by a foreign workflow system in a foreign distributed computing infrastructure.

Quantum chemical meta-workflows in MoSGrid

Quantum chemical workflows can be built up within the science gateway Molecular Simulation Grid. Complex workflows required by the end users are dissected into smaller workflows that can be combined freely to larger meta‐workflows. General quantum chemical workflows are described here as well as the real use case of a spectroscopic analysis resulting in an end‐user desired meta‐workflow. All workflow features are implemented via Web Services Parallel Grid Runtime and Developer Environment and submitted to UNICORE. The workflows are stored in the Molecular Simulation Grid repository and ported to the SHIWA repository. Copyright

ENABLING GENERIC DISTRIBUTED COMPUTING INFRASTRUCTURE COMPATIBILITY FOR WORKFLOW MANAGEMENT SYSTEMS

Solving workflow management system’s Distributed Computing Infrastructure (DCI) incompatibility and their workflow interoperability issues are very challenging and complex tasks. Workflow management systems (and therefore their workflows, workflow developers and also their end-users) are bounded tightly to some limited number of supported DCIs, and efforts required to allow additional DCI support. In this paper we are specifying a concept how to enable generic DCI compatibility for grid workflow management systems (such as ASKALON, MOTEUR, gUSE/WS-PGRADE, etc.) on job and indirectly on workflow level. To enable DCI compatibility among the different workflow management systems we have developed the DCI Bridge software solution. In this paper we will describe its internal architecture, provide usage scenarios to show how the developed service resolve the DCI interoperability issues between various middleware types. The generic DCI Bridge service enables the execution of jobs onto the existing major DCI platforms (such as Service Grids (Globus Toolkit 2 and 4, gLite, ARC, UNICORE), Desktop Grids, Web services, or even cloud based DCIs).

Implementation of the ABC Quantum Mechanical Reactive Scattering Program on the EGEE Grid Platform

Computer based simulation of quantum mechanical reactive scattering is a CPU intensive process. Despite the small I/O traffic a single simulation requires several thousand CPU hours. The ABC program provides an impelementation for quantum mechanical reaction simulation in such a way that the code can be efficiently ported to parallel computing platforms. The Computational Chemistry and Application Porting Support groups of the EGEE project worked together to create a grid enabled version of the ABC code. The collaboration resulted a Grid application that is capable of using several clusters and storage servers of the EGEE Grid symultaneously, achieving significant speed-up. The application has been ported to EGEE Grid as a parameter study application with the P-GRADE Grid portal. The paper describes the application porting process, the technical analysis and performance of the local and the Grid enabled ABC application.

Enabling OMNeT++-based simulations on grid systems

Simulations are typically computationally intensive problems, and lend themselves for execution on large-scale PC clusters or grids. Using grid infrastructure for discrete event simulation is currently not prevalent, but making grid technology easily accessible to simulation users can change that picture significantly. In this paper we give a detailed overview how the OMNeT++ simulation framework was ported onto a gLite-based grid infrastructure. The porting of the simulation framework to the grid infrastructure was supported by the GASUC Team of the EGEE III project. Later on in the paper we show an example grid service which is able to execute queuing network simulations, and assess its performance on the grid.

Workflow Concept of WS-PGRADE/gUSE

This chapter introduces the data-driven workflow concept supported by the WS-PGRADE/gUSE system. Workflow management systems were investigated by Workflow Management Coalition, among others in aspects of implemented data flow structures, and several workflow patterns are identified as commonly used and meaningful workflow structures. The workflow concept of gUSE is shown by introducing the supported data patterns and illustrating their creation in the system. Moreover, the possibilities of utilizing parallelization techniques are described, and then the different views of a workflow design and management are described covering the whole lifecycle of a workflow development. Finally, more complex composition of patterns and their creation techniques are shown.