Mary Thomas

The Open Grid Computing Environments collaboration: Portlets and services for science gateways

We review the efforts of the Open Grid Computing Environments collaboration. By adopting a general three-tiered architecture based on common standards for portlets and Grid Web services, we can deliver numerous capabilities to science gateways from our diverse constituent efforts. In this paper, we discuss our support for standards-based Grid portlets using the Velocity development environment. Our Grid portlets are based on abstraction layers provided by the Java CoG kit, which hide the differences of different Grid toolkits. Sophisticated services are decoupled from the portal container using Web service strategies. We describe advance information, semantic data, collaboration, and science application services developed by our consortium. Copyright

Grid portal architectures for scientific applications

Computational scientists often develop large models and codes intended to be used by larger user communities or for repetitive tasks such as parametric studies. Lowering the barrier of entry for access to these codes is often a technical and sociological challenge. Portals help bridge the gap because they are well known interfaces enabling access to a large variety of resources, services, applications, and tools for private, public, and commercial entities, while hiding the complexities of the underlying software systems to the user. This paper presents an overview of the current state-of-the-art in grid portals, based on a component approach that utilizes portlet frameworks and the most recent Grid standards, the Web Services Resource Framework and a summary of current DOE portal efforts.

The Open Grid Computing Environments collaboration: portlets and services for science gateways: Research Articles

Web portals are one of the possible ways to access the remote computing resources offered by Grid environments. Since the emergence of the first middleware for the Grid, works have been conducted on delivering the functionality of Grid services on the Web. Many interesting Grid portal solutions have been designed help organize remote access to Grid resources and applications from within Web browsers. They are technically advanced and more and more widely used around the world, resulting in feedback from the community. Some of these user comments concern the flexibility and user-friendliness of the developed solutions. In this paper we present how we addressed the need for a flexible and user-friendly Grid portal environment within the PROGRESS project and how our approach facilitates the use of the Grid within Web portals. Copyright

Development of a computational environment for the General Curvilinear Ocean Model

The General Curvilinear Ocean Model (GCOM) differs significantly from the traditional approach, where the use of Cartesian coordinates forces the model to simulate terrain as a series of steps. GCOM utilizes a full three-dimensional curvilinear transformation, which has been shown to have greater accuracy than similar models and to achieve results more efficiently. The GCOM model has been validated for several types of water bodies, different coastlines and bottom shapes, including the Alarcon Seamount, Southern California Coastal Region, the Valencia Lake in Venezuela, and more recently the Monterey Bay. In this paper, enhancements to the GCOM model and an overview of the computational environment (GCOM-CE) are presented. Model improvements include migration from F77 to F90; approach to a component design; and initial steps towards parallelization of the model. Through the use of the component design, new models are being incorporated including biogeochemical, pollution, and sediment transport. The computational environment is designed to allow various client interactions via secure Web applications (portal, Web services, and Web 2.0 gadgets). Features include building jobs, managing and interacting with long running jobs; managing input and output files; quick visualization of results; publishing of Web services to be used by other systems such as larger climate models. The CE is based mainly on Python tools including a grid-enabled Pylons Web application Framework for Web services, pyWSRF (python-Web Services-Resource Framework), pyGlobus based web services, SciPy, and Google code tools.

Using the Pylons Web Framework for Science Gateways

Science portals and gateways are built using a variety of tools ranging from elementary customized tools to existing frameworks that bring both greater capabilities (authentication, account management, interfaces, logging etc) and more complexity (resulting in long learning curves and complex code bases). For gateways, it is important to identify frameworks that can be easily adapted to the specialized environments needed for accessing the required cyberinfrastructure. In this paper we present our experiences in developing a basic gateway portal using the Pylons Web framework, Python tools, the Globus Core Python Toolkit including pyWSRF (Web Services-Resource Framework) and pyGlobus, developing Web service clients to TeraGrid information services, and Google code tools. We have found that the Pylons Web framework, which utilizes WSGI (WS-gateway interface) and AJAX (asynchronous JavaScript and XML), is easy to use and learn, is very flexible and has the ability to dynamically reload services without restarting the server (which dramatically reduces development and testing time). Additionally, Pylons components can be published as services, widgets and gadgets, and desktop applications.

Interfacing an ensemble Data Assimilation system with a 3D nonhydrostatic Coastal Ocean Model, an OSSE experiment

This paper presents the integration of a data assimilation framework and a nonhydrostatic coastal ocean model for the study of turbulent processes and state variables. Interfacing our General Curvilinear Coastal Ocean Model (GCCOM) with NCARs Data Assimilation Research Testbed (DART), enable the integration of very high-resolution observations into the system. These results included observation system simulation experiments (OSSEs) for test cases using a very steep seamount, by using different observation error variances. Our results demonstrated that the DART-GCCOM model can assimilate high-resolution observations using as few as 30 ensemble members.

Nesting nonhydrostatic GCCOM within hydrostatic ROMS for multiscale Coastal Ocean Modeling

The Regional Ocean Modeling System (ROMS) is a hydrostatic free-surface ocean model ideally suited to simulate mesoscale to basin-scale (10 km - 10000 km) ocean processes. The General Curvilinear Coastal Ocean Model (GCCOM) is a nonhydrostatic large eddy simulation (LES) model designed specifically for high-resolution (meters) simulations. In this research, a hybrid model is developed that nests a fine-grid GCCOM model within a coarse-grid ROMS. The nested GCCOM-ROMS model is tested in an idealized flow over a seamount.

Parallelization of the 3D Unified Curvilinear Coastal Ocean Model: Initial Results

The Unified Curvilinear Ocean Atmospheric Model (UCOAM) is a Large Eddie Simulation (LES) CFD model capable of running both ocean and atmospheric simulations. It is the only environmental model in existence today using a full, 3D curvilinear coordinate system, which results in increased accuracy and resolution. UCOAM is a petascale model: it is capable of resolving sub-km scale fluctuations requires large arrays (1010 elements, the curvilinear system requires large number of arrays (~100); communication occurs along all 3 axes, and full simulations will generate TBytes of data. Consequently, this model requires parallelization. To facilitate UCOAM computations and data management, we have developed a new parallel framework capable of distributing the computations across arbitrary 3D processor arrangements, manages the complexity of the staggered grid variables, and performs communications along all axes, including diagonal and tridiagonal neighbors. To facilitate computations, we have developed computational environment (CE) based on the Cyber infrastructure Web Application Framework (Cyber Web) which supports the development of web services and portals. In this paper we discuss the design and architecture of the parallel framework and supporting CE infrastructure, as well as challenges associated with parallelizing this novel model. We include the first initial parallel results for a small (105 nodes) 1 meter resolution seamount test case that shows scaling of the parallel model.

Special Issue: Workshop on Grid Computing Portals (GCE 2005)

This article summarizes the outcome of a workshop held at Supercomputing 2005 that focused on grid computing portals and environments. This workshop is the first in a series of workshops planned in conjunction with the supercomputing meetings for the next few years. The intent of the workshop was to provide a venue for the community to share ideas, exchange experiences, and advance the field. Grid portals are faced with the challenge of providing simplified user interfaces to cyberinfrastructure, which results in the need for the portal developer to program to every layer in the cyberinfrastructure fabric and to develop unique solutions. This article summarizes the papers presented at this workshop. Copyright