Raminderjeet Singh

Building the PolarGrid portal using web 2.0 and OpenSocial

Science requires collaboration. In this paper, we investigate the feasibility of coupling current social networking techniques to science gateways to provide a scientific collaboration model. We are particularly interested in the integration of local and third party services, since we believe the latter provide more long-term sustainability than gateway-provided service instances alone. Our prototype use case for this study is the PolarGrid portal, in which we combine typical science portal functionality with widely used collaboration tools. Our goal is to determine the feasibility of rapidly developing a collaborative science gateway that incorporates third-party collaborative services with more typical science gateway capabilities. We specifically investigate Google Gadget, OpenSocial, and related standards.

The apache airavata application programming interface: overview and evaluation with the UltraScan science gateway

We present an overview of the Apache Airavata Application Programming Interface (API), describe the design choices and implementation details, and describe how API methods map to the UltraScan Science Gateway use case. The Airavata API is designed to standardize access to Airavata services that provide gateways with scientific application metadata and execution management. The API also represents an important milestone in the development of Science Gateway Platform as a Service (SciGaP), a hosted, multi-tenanted gateway service based on open source Airavata software. The UltraScan gateway is a production XSEDE gateway that has been using Airavata services for over three years through customized interfaces and represents a stringent test of the API design and implementation.

A high throughput workflow environment for cosmological simulations

The next generation of wide-area sky surveys offer the power to place extremely precise constraints on cosmological parameters and to test the source of cosmic acceleration. These observational programs will employ multiple techniques based on a variety of statistical signatures of galaxies and large-scale structure. These techniques have sources of systematic error that need to be understood at the percent-level in order to fully leverage the power of next-generation catalogs. Simulations of large-scale structure provide the means to characterize these uncertainties. We are using XSEDE resources to produce multiple synthetic sky surveys of galaxies and large-scale structure in support of science analysis for the Dark Energy Survey. In order to scale up our production to the level of fifty 1010-particle simulations, we are working to embed production control within the Apache Airavata workflow environment. We explain our methods and report how the workflow has reduced production time by 40% compared to manual management.

UltraScan gateway enhancements: in collaboration with TeraGrid advanced user support

The Ultrascan gateway provides a user friendly web interface for evaluation of experimental analytical ultracentrifuge data using the UltraScan modeling software. The analysis tasks are executed on the TeraGrid and campus computational resources. The gateway is highly successful in providing the service to end users and consistently listed among the top five gateway community account usage. This continued growth and challenges of sustainability needed additional support to revisit the job management architecture. In this paper we describe the enhancements to the Ultrascan gateway middleware infrastructure provided through the TeraGrid Advanced User Support program. The advanced support efforts primarily focused on a) expanding the TeraGrid resources incorporate new machines; b) upgrading UltraScans job management interfaces to use GRAM5 in place of the deprecated WS-GRAM; c) providing realistic usage scenarios to the GRAM5 and INCA resource testing and monitoring teams; d) creating general-purpose, resource-specific, and UltraScan-specific error handling and fault tolerance strategies; and e) providing forward and backward compatibility for the job management system between UltraScans version 2 (currently in production) and version 3 (expected to be released mid-2011).

Open community development for science gateways with apache rave

Science gateways enable researchers and students to use distributed scientific computing infrastructure (cyberinfrastructure) through Web browsers and Web-enabled desktop clients. This paper describes the use of the open source, open community Apache Rave project as the basis for developing science gateways. Building on Apache Shindig (for OpenSocial Gadgets) and Apache Wookie (for W3C Widgets), Rave provides an out-of-the box deployment that can be used to host reusable social Web components. Rave is based on the Spring MVC framework and so can also be extensively customized or extended with (for example) custom database back-ends and authentication modules. In this paper we consider Rave as a development platform for science gateways and discuss how the source code may be extended through three use cases that focus on gateway security requirements. A major consideration of this paper is how to design Rave as a development environment so that developers can make local customizations and extensions freely on both a rapidly changing code base (during Raves initial development), and (later) between stable code bases during version upgrades. We conclude with a discussion of the implications of developing science gateways and other cyberinfrastructure software within the Apache Software Foundation and present its potential advantages.

Enabling dark energy survey science analysis with simulations on XSEDE resources

Upcoming wide-area sky surveys offer the power to test the source of cosmic acceleration by placing extremely precise constraints on existing cosmological model parameters. These observational surveys will employ multiple tests based on statistical signatures of galaxies and larger-scale structures such as clusters of galaxies. Simulations of large-scale structure provide the means to maximize the power of sky survey tests by characterizing key sources of systematic uncertainties. We describe an XSEDE program to produce multiple synthetic sky surveys of galaxies and large-scale cosmic structure in support of science analysis for the Dark Energy Survey. We explain our Airavata-enabled methods and report extensions to our workflow processing over the last year. We highlight science analysis focused on counts of clusters of galaxies.

US-SOMO cluster methods: year one perspective

UltraScan Solution Modeler (US-SOMO) computes hydrodynamic parameters and small-angle scattering data from biological macromolecular structural representations and compares them with experimental data for structural determination and validation. At XSEDE 12, a GUI integrated gateway was introduced to offload large computations to various HPC resources. The gateway was directly integrated into the Qt/GUI based software to allow the users a seamless experience. The software is available as source code or precompiled for Apple Mac OSX, MS-Windows and Linux. Current cluster resources include TACC Lonestar and Stampede, SDSC Trestles and a 256 CPU cluster local to the University of Texas Health Science Center at San Antonio. The simplicity of design allowed the implementation of a new method of modeling small angle scattering data that provided new scientific insights and was presented at the 2012 international small-angle scattering conference. Since introduction, multiple workshops have been taught and users are beginning to utilize the gateway in their biological research.

Enabling HPC simulation workflows for complex industrial flow problems

The use of simulation based engineering taking advantage of massively parallel computing methods by industry is limited due to the costs associated with developing and using high performance computing software and systems. To address industries ability to effectively include large-scale parallel simulations in daily production use, two key areas need to be addressed. The first is access to large-scale parallel computing systems that are cost effective to use. The second is support for complete simulation workflow execution on these systems by industrial users. This paper presents an approach, and set of associated software components, that can support industrial users on large-scale parallel computing systems available at various national laboratories, universities, or on clouds.

Investigating the Use of Gadgets, Widgets, and OpenSocial to Build Science Gateways

Many science applications require more and more computing power as the amount of input data keeps increasing. To simplify using large-scale clusters and complicated application codes, and to facilitate cross-disciplinary collaboration, there has been substantial research and development work on Web-based science gateways. With numerous gateways needing to be developed for many different scientific domains, there has also been a long-standing need for reusable codes and extensible component models. During the previous decade, the component model for many gateways was the Java port let. To overcome some of the port let models limitations, new gateways take a different approach that utilizes modern Web technologies. In this paper, we examine the use of new standards such as Open Social, Gadgets, and W3C Widgets to build science gateway user interfaces. These standards overcome many shortcomings of the older port let development model. As general-purpose Web standards, however, they lack support for specialized science gateway requirements and so must be extended. We propose a generic architecture in which Open Social is integrated with backend services and grid infrastructures. We implement and evaluate these concepts in the Gadget Container, software developed by the authors.

US-SOMO cluster methods

UltraScan Solution Modeler (US-SOMO) computes hydrodynamic parameters and small-angle scattering data from biological macromolecular structural representations and compares them with experimental data for structural determination and validation. At XSEDE 12, a GUI integrated gateway was introduced to offload large computations to various HPC resources. The gateway was directly integrated into the Qt/GUI based software to allow the users a seamless experience. The software is available as source code or precompiled for Apple Mac OSX, MS-Windows and Linux. Current cluster resources include TACC Lonestar and Stampede, SDSC Trestles and a 256 CPU cluster local to the University of Texas Health Science Center at San Antonio. The simplicity of design allowed the implementation of a new method of modeling small angle scattering data that provided new scientific insights and was presented at the 2012 international small-angle scattering conference. Since introduction, multiple workshops have been taught and users are beginning to utilize the gateway in their biological research.