Eryk Ciepiela

The Collage Authoring Environment

Abstract The Collage Authoring Environment is a software infrastructure which enables domain scientists to collaboratively develop and publish their work in the form of executable papers. It corresponds to the recent developments in both e-Science and computational technologies which call for a novel publishing paradigm. As part of this paradigm, static content (such as traditional scientific publications) should be supplemented with elements of interactivity, enabling reviewers and readers to reexamine the reported results by executing parts of the software on which such results are based as well as access primary scientific data. Taking into account the presented rationale we propose an environment which enables authors to seamlessly embed chunks of executable code (called assets) into scientific publications and allow repeated execution of such assets on underlying computing and data storage resources, as required by scientists who wish to build upon the presented results. The Collage Authoring Environment can be deployed on arbitrary resources, including those belonging to high performance computing centers, scientific e-Infrastructures and resources contributed by the scientists themselves. The environment provides access to static content, primary datasets (where exposed by authors) and executable assets. Execution features are provided by a dedicated engine (called the Collage Server) and embedded into an interactive view delivered to readers, resembling a traditional research publication but interactive and collaborative in its scope. Along with a textual description of the Collage environment the authors also present a prototype implementation, which supports the features described in this paper. The functionality of this prototype is discussed along with theoretical assumptions underpinning the proposed system.

Exploratory programming in the virtual laboratory

GridSpace 2 is a novel virtual laboratory framework enabling researchers to conduct virtual experiments on Grid-based resources and other HPC infrastructures. GridSpace 2 facilitates exploratory development of experiments by means of scripts which can be written in a number of popular languages, including Ruby, Python and Perl. The framework supplies a repository of gems enabling scripts to interface low-level resources such as PBS queues, EGEE computing elements, scientific applications and other types of Grid resources. Moreover, GridSpace 2 provides a Web 2.0-based Experiment Workbench supporting development and execution of virtual experiments by groups of collaborating scientists. We present an overview of the most important features of the Experiment Workbench, which is the main user interface of the Virtual laboratory, and discuss a sample experiment from the computational chemistry domain.

Managing entire lifecycles of e-science applications in the gridspace2 virtual laboratory --- from motivation through idea to operable web-accessible environment built on top of PL-Grid e-infrastructure

The GridSpace2 environment, developed in the scope of the PL-Grid Polish National Grid Initiative, constitutes a comprehensive platform which supports e-science applications throughout their entire lifecycle. Application development may involve multiple phases, including writing, prototyping, testing and composing the application. Once the application attains maturity it becomes operable and capable of being executed, although it may still be subject to further development --- including actions such as sharing with collaborating researchers or making results publicly available with the use of dedicated publishing interfaces. This paper describes each of these phases in detail, showing how the GridSpace2 platform can assist the developers and publishers of computational experiments.

Virtual Laboratory for Development and Execution of Biomedical Collaborative Applications

The ViroLab Virtual Laboratory is a collaborative platform for scientists representing multiple fields of expertise while working together on common scientific goals. This environment makes it possible to combine efforts of computer scientists, virology and epidemiology experts and experienced physicians to support future advances in HIV-related research and treatment. The paper explains the challenges involved in building a modern, inter-organizational platform to support science and gives an overview of solutions to these challenges. Examples of real-world problems applied in the presented environment are also described to prove the feasibility of the solution.

A distributed multiscale computation of a tightly coupled model using the Multiscale Modeling Language

Abstract Nature is observed at all scales; with multiscale modeling, scientists bring together several scales for a holistic analysis of a phenomenon. The models on these different scales may require significant but also heterogeneous computational resources, creating the need for distributed multiscale computing. A particularly demanding type of multiscale models, tightly coupled, brings with it a number of theoretical and practical issues. In this contribution, a tightly coupled model of in-stent restenosis is first theoretically examined for its multiscale merits using the Multiscale Modeling Language (MML); this is aided by a toolchain consisting of MAPPER Memory (MaMe), the Multiscale Application Designer (MAD), and Gridspace Experiment Workbench. It is implemented and executed with the general Multiscale Coupling Library and Environment (MUSCLE). Finally, it is scheduled amongst heterogeneous infrastructures using the QCG-Broker. This marks the first occasion that a tightly coupled application uses distributed multiscale computing in such a general way.

GridSpace2 virtual laboratory case study: implementation of algorithms for quantitative analysis of grain morphology in self-assembled hexagonal lattices according to the hillebrand method

This work presents the implementation of a method, originally proposed by Hillebrand et al. [1], of quantitative analysis of the grain morphology in self-assembled hexagonal lattices. This method can be effectively used for investigation of structural features as well as regular hexagonal arrangement of nanoporous alumina layers formed on the metal surface during the self-organized anodization process. The method has been implemented as a virtual experiment in the GridSpace2 Virtual Laboratory [15] which is a scientific computing platform developed in the scope of the PL-Grid [9] project. The experiment is a GridSpace2 pilot and therefore made available to the wider community of PL-Grid users. It is both editable and executable through a web portal offered by the GridSpace2 Experiment Workbench [17], dedicated to PL-Grid users. Moreover, since all GridSpace2 experiments are embeddable on arbitrary web sites owing to the Collage [16] feature, the final version of the experiment has been published as an executable publication [18] with execution rights granted to all PL-Grid users.

Composing, execution and sharing of multiscale applications

This paper presents the research which led to elaboration of an environment for composing, executing and sharing multiscale applications. The resulted environment supports ability to connect software modules to form large-scale, multiscale simulations and directly execute them on distributed e-infrastructures suitable for particular application models chosen by users. It also enables hybrid execution, i.e. different parts of the same application can be executed on various types of e-infrastructures i.e. on a grid (e.g. EGI), HPC (e.g. PRACE) or on a cloud. The environment is web based and gives the user a direct access to the distributed resources from a single browser. It supports a variety of possible realizations of multiscale simulations in a unified and non-invasive way and enables storing model metadata such as scale, inputs and outputs.The presented environment consists of an application composition tool called Multiscale Application Designer (MAD), an application module description registry MAPPER Memory (MaMe) and GridSpace (GS) supporting execution of applications on various infrastructures. We present an architecture of the current implementation along with a detailed description of the tools and their current features. Additionally, we report on validation of our tools by multiscale application developers. We compare the processes of creating and running applications with and without the tools and we present a case study based on a sample multiscale application skeleton. Environment supporting composition and sharing of multiscale applications.Direct execution of multiscale applications on distributed e-infrastructures.Support for hybrid execution on different types of e-infrastructures.Support for a variety of realizations of multiscale simulations in a non-invasive way.Validation by multiscale application developers.

ViroLab Security and Virtual Organization Infrastructure

This paper introduces security requirements and solutions present in the ViroLab Virtual Laboratory. Our approach is to use a federated Single Sign-On mechanism based on the Shibboleth framework that enables multiple partners to authenticate against their local identity systems and use resources provided by all other partners. Since the basic Shibboleth capabilities do not meet our specific requirements related to supporting non-web-based services, we created a set of custom tools that allow us to develop a homogeneous, Shibboleth-based security solution for both Web and non-web-based software components. This paper describes these tools in detail, together with other services of the virtual laboratory which have been integrated with the security infrastructure. A decentralized, attribute-based approach facilitating the creation and management of virtual organizations is the key achievement of our work.

Scripting language extensions offered by the gridspace experiment platform

Many existing problem solving environments provide scientists with convenient methods for building scientific applications over distributed computational and storage resources. In many cases a basic set of features of such environments is sufficient to conduct a complete experiment flow. However, complex cases often require extensions supporting an external piece of software or a communication standard not integrated beforehand. Most environments deal with such cases by providing an extension facility and letting third parties add required features. The GridSpace environment also includes several mechanisms for extending its own functionality and here we describe how this can be accomplished. We focus on extensions already implemented such as local job submission and scripting language repositories, as well as on a GUI extension point which can be used to add custom graphical user interfaces to GridSpace experiments independently of their release process.

Enabling Multiscale Fusion Simulations on Distributed Computing Resources

We describe a way to support the execution of multiphysics simulations on PL-Grid resources. To achieve this, we extended the existing programming and execution framework for multiscale applications to support execution of legacy, computationally intensive applications, which apply various computational patterns. In particular, we focus on a stability simulation involving the plasma edge in a Tokamak device. We also show how to support the parameter sweep pattern of execution used in that application. We combine two approaches for building multiphysics applications: visual composition enabled by the Multiscale Application Designer and a script-based solution supported by the GridSpace platform. The usage and benefits of the PL-Grid e-infrastructure for application execution are outlined.