Sudhakar Pamidighantam

Community Science Exemplars in SEAGrid Science Gateway

We describe the science discovered by some of the community of researchers using the SEAGrid Science gateway. Specific science projects to be discussed include calcium carbonate and bicarbonate hydrochemistry, mechanistic studies of redox proteins and diffraction modeling of metal and metal-oxide structures and interfaces. The modeling studies involve a variety of ab initio and molecular dynamics computational techniques and coupled execution of a workflows using specific set of applications enabled in the SEAGrid Science Gateway. The integration of applications and resources that enable workflows that couple empirical, semi-empirical, ab initio DFT, and Moller-Plesset perturbative models and combine computational and visualization modules through a single point of access is now possible through the SEAGrid gateway. Integration with the Apache Airavata infrastructure to gain a sustainable and more easily maintainable set of services is described. As part of this integration we also provide a web browser based SEAGrid Portal in addition to the SEAGrid rich client based on the previous GridChem client. We will elaborate the services and their enhancements in this process to exemplify how the new implementation will enhance the maintainability and sustainability. We will also provide exemplar science workflows and contrast how they are supported in the new deployment to showcase the adoptability and user support for services and resources.

Apache Airavata Sharing Service: A Tool for Enabling User Collaboration in Science Gateways

Science Gateways provide user environments and a set of supporting services that help researchers make effective and enhanced use of a diverse set of computing, storage, and related resources. Gateways provide the services and tools users require to enable their scientific exploration, which includes tasks such as running computer simulations or performing data analysis. Historically gateways have been constructed to support the workflow of individual users, but collaboration between users has become an increasingly important part of the discovery process. This trend has created a driving need for gateways to support data sharing between users. For example, a chemistry research group may want to run simulations collaboratively, analyze experimental data or tune parameter studies based on simulation output generated by peers, whether as a default capability, or through explicit creation of sharing privileges. As another example, students in a classroom setting may be required to share their simulation output or data analysis results with the instructor. However most existing gateways (including the popularly used XSEDE gateways SEAGrid, Ultrascan, CIPRES, and NSG), do not support direct data sharing, so users have to handle these collaborations outside the gateway environment. Given the importance of collaboration in current scientific practice, user collaboration should be a prime consideration in building science gateways. In this work, we present design considerations and implementation of a generic model that can be used to describe and handle a diverse set of user collaboration use cases that arise in gateways, based on general requirements gathered from the SEAGrid, CIPRES, and NSG gateways. We then describe the integration of this sharing service into these gateways. Though the model and the system were tested and used in the context of Science Gateways, the concepts are universally applicable to any domain, and the service can support data sharing in a wide variety of use cases.

Publishing and consuming GLUE v2.0 resource information in XSEDE

XSEDE users, science gateways, and services need a variety of accurate information about XSEDE resources so that they can use those resources effectively. They need information to decide which resources to use, to track their usage of resources, and to provide services to their users. To support this, XSEDE is deploying a new system to gather and publish static and dynamic resource information. This paper gives an overview of the resource information available with this new system, describes the design and performance of the software and services that make up this system, and finally provides examples of how to use this new resource information.

Ab Initio Studies of Calcium Carbonate Hydration.

Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance.

Anatomy of the SEAGrid Science Gateway

The SEAGrid science gateway provides scientists and educators with user interfaces and tools for conducting computational chemistry, material science, and engineering experiments online using XSEDE and campus computing resources. This paper describes the architecture of the recently completed technology refresh for the gateway, replacing its desktop user interface, adding a web browser user interface, using Apache Airavata middleware for job management, and providing enhanced data search and feature extraction capabilities. These introduce several challenges, particularly in providing unified authentication and authorization mechanisms to middleware services for the desktop and web clients, and in extending Apache Airavata middleware with new components. Access, authentication, and authorization problems were solved by using standard-based approaches (OAuth2, XACML) that were implemented by incorporating WSO2s Identity Server into both SEAGrid and Apache Airavata. SEAGrid-specific data extraction capabilities were added to Airavata middleware using a message-based component approach. This approach is generalizable to other advanced and gateway-specific capabilities and enables Airavata to add additional data analysis components without modifying its core functionality.

Supporting Science Gateways Using Apache Airavata and SciGaP Services

The Science Gateways Platform as a service (SciGaP.org) project provides a rapid development and stable hosting platform for a wide range of science gateways that focus on software as a service. Based on the open source Apache Airavata project, SciGaP services include user management, workflow execution management, computational experiment archiving and access, and sharing services that allow users to share results and other digital artifacts. SciGaP services are multi-tenanted, with clients accessing services through a well-defined, programming language-independent API. SciGaP services can be integrated into web, mobile, and desktop clients. To simplify development for new clients, SciGaP includes the PGA, a generic PHP-based gateway client for SciGaP services that also acts as a reference implementation of the API. Several example gateways using these services are summarized.

Apache Airavata Resource Allocation System: A Tool for Allocating Resources in Science Gateways

Science Gateways provide user environments and a set of supporting services that help researchers make effective and enhanced use of a diverse set of computing, storage, and related resources. In a software framework like Airavata, the distributed computing resources such as local clusters, supercomputers, computational grids, and computing clouds are shared among multiple researchers. Hence it requires an allocations process to track the demand for their resources, understand the scientific objectives of their users, and decide among competing needs when faced with user demand that is greater than the available resources can supply. We describe the design and a prototype implementation in this presentation.

Science Gateway Implementation at the University of South Dakota: Applications in Research and Education

Science Gateways are virtual environments that accelerate scientific discovery by enabling scientific communities to more easily and effectively utilize distributed computing and data resources. Successful Science Gateways provide access to sophisticated and powerful resources, while shielding their users from the underlying complexities. Here we present work completed by the University of South Dakota (USD) Research Computing Group in conjunction with the Science Gateways Community Institute (SGCI) [1] and Indiana University on setting up a Science Gateway to access USDs high-performance computing resources. These resources are now available to both faculty and students and allow ease of access and use of USDs distributed computing and data resources. The implementation of this gateway project has been multifaceted and has included placement of federated user login, user facilitation and outreach, and integration of USDs cyberinfrastructure resources. We present this project as an example for other research computing groups so that they may learn from our successes and the challenges that we have overcome in providing this user resource. Additionally, this project serves to exemplify the importance of creating a broad user base of research computing infrastructure through the development of alternative user interfaces such as Science Gateways.

Simplifying Access to Campus Resources at Southern Illinois University with a Science Gateway

Not all the researchers are comfortable in using High Performance Computing (HPC) Systems. Southern Illinois Universitys Office of Information Technology (OIT) Research Computing assists our researchers to get on these systems and use them for their research activities. One such potential use case at SIU involves the group of researchers from Life Sciences who were trying to use MaSuRCA [3], a genome-sequencing tool for their research. Although the leaders of this research are well versed in using BigDog [4](SIUs HPC Cluster), other fellow researchers did have issues in using the cluster for their work. It was time to look for efficient ways of enabling them to use the cluster. We examined using Science Gateways which can help our researchers to use the computational cluster without logging on to a Linux-based HPC system. OIT is currently collaborating with the Science Gateways Research Center at Indiana University (IU) on the use of Apache Airavata [1] as a Science Gateway framework for the MaSuRCA user community at SIU. The IU team members provide hosting and operations for Apache Airavata middleware as part of the SciGaP.org project. IU collaborators also provide a basic science gateway user interface, the PGA. The SIU gateway, although hosted off campus, is integrated with SIUs BigDog cluster.

A New Science Gateway to Provide Decision Support on Carbon Capture and Storage Technologies

Carbon dioxide capture and storage (CCS) is a promising technology for mitigating climate change, and its implementation is considered critical to meeting threshold targets for global warming in the 21st century. We have developed a new science gateway application for the successful modeling software known as SimCCS that is used for evaluating complex, integrated CCS infrastructure. Using the Apache Airavata middleware and high-performance computing resources made available by the Extreme Science and Engineering Discovery Environment, we built the SimCCS Gateway to expand the tools scalability for decision support and risk assessment. Case studies developed for evaluating a proposed CCS technology at Duke Energys Gibson Station coal-fired power plant in southwest Indiana demonstrate its improved ability in data analysis as well as risk assessment at various uncertainty levels. Further work is continuing to expand the functionality of both web and desktop clients, and to develop an active user group community in research and industry via the SimCCS Gateway interface.