| DOI | Author | Title | Journal/Proceedings/Book | Year | |
|---|---|---|---|---|---|
| DOI | Verma, A., Ramyaa, R. and Marru, S. | Validating distance decay through agent based modeling | Security Informatics Vol. 2(1), pp. 3 |
2013 | |
| Abstract: The objectives of this research are to display the utility of using agent based model and simulated experiments in understanding criminal behavior. In particular, this research focuses upon the distance decay function that has wide applicability in understanding ways in which offenders move about their awareness space and select their targets for committing crime. The basis for distance decay is an assumption that the offender apprehends recognition by his neighbors and so tends to commit his crime a little away but not too far from his home location. But this is an untested assumption and based upon another assumption that recognition comes from frequent interactions. There is no simple way to test these assumptions in real life. This paper argues that simulated experiments using agent based modeling are appropriate methods for difficult to test criminological concepts. In this research, two types of agents are created- one representing the offender and the other- the victim. They are assigned specific characteristics that control their action such as moving in a neighborhood, making rational choice to maximize their gain while minimizing the risk of apprehension from interaction with other residents of the neighborhood. The simulation result displays that beginning with these small principles the final model emerges as a pattern of target selection similar to the distance decay function. The importance of this technique lies in the fact that such experiments provide the means to apply agent based modeling to validate a variety of criminological concepts. While the technique has limitations of validation it can help in understanding the behavior of offenders as they commit their crimes individually as well as in groups. | |||||
BibTeX:
@article{verma2013validating,
author = {Verma, A. and Ramyaa, R. and Marru, S.},
title = {Validating distance decay through agent based modeling},
journal = {Security Informatics},
publisher = {Springer},
year = {2013},
volume = {2},
number = {1},
pages = {3},
doi = {http://dx.doi.org/10.1186/2190-8532-2-3}
}
|
|||||
| DOI | Erickson, B.M.S., Singh, R., Evrard, A.E., Becker, M.R., Busha, M.T., Kravtsov, A.V., Marru, S., Pierce, M. and Wechsler, R.H. | A high throughput workflow environment for cosmological simulations [BibTeX] |
XSEDE '12: Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment, pp. 1-8 | 2012 | |
BibTeX:
@inproceedings{2335830,
author = {Erickson, Brandon M. S. and Singh, Raminderjeet and Evrard, August E. and Becker, Matthew R. and Busha, Michael T. and Kravtsov, Andrey V. and Marru, Suresh and Pierce, Marlon and Wechsler, Risa H.},
title = {A high throughput workflow environment for cosmological simulations},
booktitle = {XSEDE '12: Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment},
publisher = {ACM},
year = {2012},
pages = {1--8},
doi = {http://doi.acm.org/10.1145/2335755.2335830}
}
|
|||||
| DOI | Brookes, E., Singh, R., Pierce, M., Marru, S., Demeler, B. and Rocco, M. | Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting tools [BibTeX] |
XSEDE '12: Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment, pp. 1-8 | 2012 | |
BibTeX:
@inproceedings{2335839,
author = {Brookes, Emre and Singh, Raminderjeet and Pierce, Marlon and Marru, Suresh and Demeler, Borries and Rocco, Mattia},
title = {Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting tools},
booktitle = {XSEDE '12: Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment},
publisher = {ACM},
year = {2012},
pages = {1--8},
doi = {http://doi.acm.org/10.1145/2335755.2335839}
}
|
|||||
| DOI | Basney, J., Butler, R., Fraser, D., Marru, S. and Stewart, C. | Security for science gateways and campus bridging: XSEDE12 panel [BibTeX] |
XSEDE '12: Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment, pp. 1-1 | 2012 | |
BibTeX:
@inproceedings{2335863,
author = {Basney, Jim and Butler, Randy and Fraser, Dan and Marru, Suresh and Stewart, Craig},
title = {Security for science gateways and campus bridging: XSEDE12 panel},
booktitle = {XSEDE '12: Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment},
publisher = {ACM},
year = {2012},
pages = {1--1},
doi = {http://doi.acm.org/10.1145/2335755.2335863}
}
|
|||||
| DOI | Herath, C., Liu, F., Marru, S., Gunathilake, L., Sosonkina, M., Vary, J., Maris, P. and Pierce, M. | Web Service andWorkflow Abstractions to Large Scale Nuclear Physics Calculations | Services Computing (SCC), 2012 IEEE Ninth International Conference on, pp. 703 -710 | 2012 | |
| Abstract: This paper discusses the web service and scientific workflow abstractions to next generation ab initio computational nuclear physics resources as part of the Leadership Class Configuration Interaction (LCCI) Environment. These abstractions will rapidly and efficiently involve new collaborators and graduate students in productive research. The workflow infrastructure democratizes the access to the nuclear physics simulations executing on remote supercomputing resources. The paper focuses on employing an open community based workflow system in developing and deploying LCCI infrastructures. The paper also emphasizes on the enhancements made to infrastructure to add advanced workflow capabilities providing greater flexibility in handling parametric sweeps and provenance aware workflows. The paper discusses on how the provenance integration will not only capture execution trace but dynamically modify the workflow graph at run time to re-use retrospective execution results. | |||||
BibTeX:
@inproceedings{6274220,
author = {Herath, C. and Fang Liu and Marru, S. and Gunathilake, L. and Sosonkina, M. and Vary, J.P. and Maris, P. and Pierce, M.},
title = {Web Service andWorkflow Abstractions to Large Scale Nuclear Physics Calculations},
booktitle = {Services Computing (SCC), 2012 IEEE Ninth International Conference on},
year = {2012},
pages = {703 -710},
doi = {http://dx.doi.org/10.1109/SCC.2012.112}
}
|
|||||
| DOI | Duffy, C., Gil, Y., Deelman, E., Marru, S., Pierce, M., Demir, I. and Wiener, G. | Designing a road map for geoscience workflows | Eos, Transactions American Geophysical Union Vol. 93(24), pp. 225-226 |
2012 | |
| Abstract: Advances in geoscience research and discovery are fundamentally tied to data and computation, but formal strategies for managing the diversity of models and data resources in the Earth sciences have not yet been resolved or fully appreciated. The U.S. National Science Foundation (NSF) EarthCube initiative (http://earthcube.ning.com), which aims to support community-guided cyberinfrastructure to integrate data and information across the geosciences, recently funded four community development activities: Geoscience Workflows; Semantics and Ontologies; Data Discovery, Mining, and Integration; and Governance. The Geoscience Workflows working group, with broad participation from the geosciences, cyberinfrastructure, and other relevant communities, is formulating a workflows road map (http://sites.google.com/site/earthcubeworkflow/). The Geoscience Workflows team coordinates with each of the other community development groups given their direct relevance to workflows. Semantics and ontologies are mechanisms for describing workflows and the data they process. | |||||
BibTeX:
@article{ecWorfkflowsDuffy2012,
author = {Duffy, Christopher and Gil, Yolanda and Deelman, Ewa and Marru, Suresh and Pierce, Marlon and Demir, Ibrahim and Wiener, Gerry},
title = {Designing a road map for geoscience workflows},
journal = {Eos, Transactions American Geophysical Union},
year = {2012},
volume = {93},
number = {24},
pages = {225--226},
url = {http://dx.doi.org/10.1029/2012EO240002},
doi = {http://dx.doi.org/10.1029/2012EO240002}
}
|
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| DOI | Lee, H., Yang, Y., Chae, H., Nam, S., Choi, D., Tangchaisin, P., Herath, C., Marru, S., Nephew, K. and Kim, S. | BioVLAB-MMIA: A Cloud Environment for microRNA and mRNA Integrated Analysis (MMIA) on Amazon EC2 | NanoBioscience, IEEE Transactions on Vol. 11(3), pp. 266 -272 |
2012 | |
| Abstract: MicroRNAs, by regulating the expression of hundreds of target genes, play critical roles in developmental biology and the etiology of numerous diseases, including cancer. As a vast amount of microRNA expression profile data are now publicly available, the integration of microRNA expression data sets with gene expression profiles is a key research problem in life science research. However, the ability to conduct genome-wide microRNA-mRNA (gene) integration currently requires sophisticated, high-end informatics tools, significant expertise in bioinformatics and computer science to carry out the complex integration analysis. In addition, increased computing infrastructure capabilities are essential in order to accommodate large data sets. In this study, we have extended the BioVLAB cloud workbench to develop an environment for the integrated analysis of microRNA and mRNA expression data, named BioVLAB-MMIA. The workbench facilitates computations on the Amazon EC2 and S3 resources orchestrated by the XBaya Workflow Suite. The advantages of BioVLAB-MMIA over the web-based MMIA system include: 1) readily expanded as new computational tools become available; 2) easily modifiable by re-configuring graphic icons in the workflow; 3) on-demand cloud computing resources can be used on an #x201C;as needed #x201D; basis; 4) distributed orchestration supports complex and long running workflows asynchronously. We believe that BioVLAB-MMIA will be an easy-to-use computing environment for researchers who plan to perform genome-wide microRNA-mRNA (gene) integrated analysis tasks. | |||||
BibTeX:
@article{leeBioVlab2012,
author = {Hyungro Lee and Youngik Yang and Heejoon Chae and Seungyoon Nam and Donghoon Choi and Tangchaisin, P. and Herath, C. and Marru, S. and Nephew, K.P. and Sun Kim},
title = {BioVLAB-MMIA: A Cloud Environment for microRNA and mRNA Integrated Analysis (MMIA) on Amazon EC2},
journal = {NanoBioscience, IEEE Transactions on},
year = {2012},
volume = {11},
number = {3},
pages = {266 -272},
doi = {http://dx.doi.org/10.1109/TNB.2012.2212030}
}
|
|||||
| DOI | Marru, S., Gunathilake, L., Herath, C., Tangchaisin, P., Pierce, M., Mattmann, C., Singh, R., Gunarathne, T., Chinthaka, E., Gardler, R., Slominski, A., Douma, A., Perera, S. and Weerawarana, S. | Apache airavata: a framework for distributed applications and computational workflows | Proceedings of the 2011 ACM workshop on Gateway computing environments, pp. 21-28 | 2011 | |
| Abstract: In this paper, we introduce Apache Airavata, a software framework to compose, manage, execute, and monitor distributed applications and workflows on computational resources ranging from local resources to computational grids and clouds. Airavata builds on general concepts of service-oriented computing, distributed messaging, and workflow composition and orchestration. This paper discusses the architecture of Airavata and its modules, and illustrates how the software can be used as individual components or as an integrated solution to build science gateways or general-purpose distributed application and workflow management systems. | |||||
BibTeX:
@inproceedings{airavataMarruGCE2011,
author = {Marru, Suresh and Gunathilake, Lahiru and Herath, Chathura and Tangchaisin, Patanachai and Pierce, Marlon and Mattmann, Chris and Singh, Raminder and Gunarathne, Thilina and Chinthaka, Eran and Gardler, Ross and Slominski, Aleksander and Douma, Ate and Perera, Srinath and Weerawarana, Sanjiva},
title = {Apache airavata: a framework for distributed applications and computational workflows},
booktitle = {Proceedings of the 2011 ACM workshop on Gateway computing environments},
publisher = {ACM},
year = {2011},
pages = {21--28},
url = {http://doi.acm.org/10.1145/2110486.2110490},
doi = {http://dx.doi.org/10.1145/2110486.2110490}
}
|
|||||
| DOI | Marru, S., Chae, H., Tangchaisin, P., Kim, S., Pierce, M. and Nephew, K. | Transitioning BioVLab cloud workbench to a science gateway | Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, pp. 40:1-40:2 | 2011 | |
| Abstract: BioVLab gateway is built upon Open Gateway Computing Environments and is currently used as reconfigurable cloud computing workbench. In this talk, we will discuss the new directions towards a TeraGrid Science Gateway and experiences and technical challenges in migrating a Cloud workbench Grid based science gateway. | |||||
BibTeX:
@inproceedings{bioVLABMarruTG11,
author = {Marru, Suresh and Chae, Heejoon and Tangchaisin, Patanachai and Kim, Sun and Pierce, Marlon and Nephew, Kenneth},
title = {Transitioning BioVLab cloud workbench to a science gateway},
booktitle = {Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery},
publisher = {ACM},
year = {2011},
pages = {40:1--40:2},
url = {http://doi.acm.org/10.1145/2016741.2016784},
doi = {http://doi.acm.org/10.1145/2016741.2016784}
}
|
|||||
| DOI | Basney, J., Dooley, R., Gaynor, J., Marru, S. and Pierce, M. | Distributed web security for science gateways | Proceedings of the 2011 ACM workshop on Gateway computing environments, pp. 13-20 | 2011 | |
| Abstract: Science gateways broaden and simplify access to cyberinfrastructure (CI) by providing advanced interfaces to collaboration, analysis, data management, and other tools for students and researchers. As these science gateway interfaces to cyberinfrastructure grow in popularity, web portal developers adopt ad hoc approaches to the security challenges of authentication, authorization, and delegation. Science gateways integrate cyberinfrastructure resources on the researcher's behalf, i.e., accessing data, compute cycles, instruments, and other valuable resources. Resource access often requires use of the researcher's security credentials, in some cases exposing the researcher's long-lived password to potential compromise at the science gateway. There is no standard approach for a researcher to control and limit a science gateway's access to his or her resources. Thus, researchers are required to accept unnecessary risks when using science gateways. The "Distributed Web Security for Science Gateways" project is addressing these risks by providing authorization and delegation software for science gateways that complies with the Internet Engineering Task Force's standard OAuth protocol. The project is developing an OAuth server implementation and a set of client libraries and authentication modules to enable out of the box integration with common Web platforms, in coordination with gateways and cyberinfrastructure providers. In this paper, we introduce the project, including our planned software architecture. |
|||||
BibTeX:
@inproceedings{DWSBasneyGCE2011,
author = {Basney, Jim and Dooley, Rion and Gaynor, Jeff and Marru, Suresh and Pierce, Marlon},
title = {Distributed web security for science gateways},
booktitle = {Proceedings of the 2011 ACM workshop on Gateway computing environments},
publisher = {ACM},
year = {2011},
pages = {13--20},
url = {http://doi.acm.org/10.1145/2110486.2110489},
doi = {http://dx.doi.org/10.1145/2110486.2110489}
}
|
|||||
| DOI | Lee, H., Yang, Y., Chae, H., Nam, S., Choi, D., Tangchaisin, P., Herath, C., Marru, S., Nephew, K. and Kim, S. | BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis | Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference on, pp. 494 -499 | 2011 | |
| Abstract: MicroRNAs, by regulating the expression of hundreds of target genes, play critical roles in developmental biology and the etiology of numerous diseases, including cancer. As vast amounts of microRNA expression profile data are now publicly available, the integration of those data sets with gene expression profiles represents an extremely active area of life science research. However, the ability to conduct genome wide microRNA-mRNA (gene) integration currently requires sophisticated, high-end informatics tools, significant expertise in bioinformatics and computer science to carry out the complex integration analysis. In addition, increased computing infrastructure capabilities are essential in order to accommodate large data sets. In this study, we have extending BioVLAB cloud workbench to develop an environment for the integrated analysis of microRNA and mRNA expression data, named BioVLAB-MMIA. The workbench facilitates computations on the Amazon EC2 and S3 resources orchestrated by XBaya Workflow Suite. The advantages of BioVLAB-MMIA over the web-based MMIA system include: 1) readily expanded as new computational tools become available; 2) easily modifiable by re-configuring graphic icons in the workflow; 3) on-demand cloud computing resources can be used on an as needed basis; 4) distributed orchestration supports complex and long running workflows asynchronously. | |||||
BibTeX:
@inproceedings{leeBibm2011,
author = {Hyungro Lee and Youngik Yang and Heejoon Chae and Seungyoon Nam and Donghoon Choi and Tangchaisin, P. and Herath, C. and Marru, S. and Nephew, K.P. and Sun Kim},
title = {BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis},
booktitle = {Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference on},
year = {2011},
pages = {494 -499},
doi = {http://dx.doi.org/10.1109/BIBM.2011.93}
}
|
|||||
| DOI | Ghosh, J., Marru, S., Singh, N., Vanomesslaeghe, K., Fan, Y. and Pamidighantam, S. | Molecular parameter optimization gateway (ParamChem): workflow management through TeraGrid ASTA | Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, pp. 35:1-35:8 | 2011 | |
| Abstract: Parameter optimization for chemical systems requires generation of initial guesses. These parameters should be generated using systematic sampling of parameter space, minimizing differences between output data and the corresponding reference data. In this paper we discuss the ParamChem project, which is creating reusable and extensible infrastructure for the computational chemistry community that will reduce unnecessary and eliminate redundancies in parametrized computations using modern software engineering tools. The paper particularly focuses on constructing and executing coupled molecular chemistry models as complicated workflow graphs. These workflow management capabilities have been integrated with the GridChem Science Gateway infrastructure through the TeraGrid advanced user support program. Further, we describe how the project is enabling a sustainable growth for science gateway infrastructure by building upon tools provided by the Open Gateway Computing Environments. The paper also discusses plans for integrating TeraGrid information, monitoring and prediction services to provide automated job scheduling with resource maintenance and fault aware services. | |||||
BibTeX:
@inproceedings{paramChemTG11,
author = {Ghosh, Jayeeta and Marru, Suresh and Singh, Nikhil and Vanomesslaeghe, Kenno and Fan, Ye and Pamidighantam, Sudhakar},
title = {Molecular parameter optimization gateway (ParamChem): workflow management through TeraGrid ASTA},
booktitle = {Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery},
publisher = {ACM},
year = {2011},
pages = {35:1--35:8},
url = {http://doi.acm.org/10.1145/2016741.2016779},
doi = {http://doi.acm.org/10.1145/2016741.2016779}
}
|
|||||
| DOI | Pierce, M.E., Singh, R., Guo, Z., Marru, S., Rattadilok, P. and Goyal, A. | Open community development for science gateways with apache rave | Proceedings of the 2011 ACM workshop on Gateway computing environments, pp. 29-36 | 2011 | |
| Abstract: 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 Rave's 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. | |||||
BibTeX:
@inproceedings{ravePierceGCE2011,
author = {Pierce, Marlon E. and Singh, Raminderjeet and Guo, Zhenhua and Marru, Suresh and Rattadilok, Pairoj and Goyal, Ankur},
title = {Open community development for science gateways with apache rave},
booktitle = {Proceedings of the 2011 ACM workshop on Gateway computing environments},
publisher = {ACM},
year = {2011},
pages = {29--36},
url = {http://doi.acm.org/10.1145/2110486.2110491},
doi = {http://dx.doi.org/10.1145/2110486.2110491}
}
|
|||||
| DOI | Demeler, B., Singh, R., Pierce, M., Brookes, E.H., Marru, S. and Dubbs, B. | UltraScan gateway enhancements: in collaboration with TeraGrid advanced user support | Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, pp. 34:1-34:8 | 2011 | |
| Abstract: 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 UltraScan's 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 UltraScan's version 2 (currently in production) and version 3 (expected to be released mid-2011). | |||||
BibTeX:
@inproceedings{ultrascanDemelerTG11,
author = {Demeler, Borries and Singh, Raminderjeet and Pierce, Marlon and Brookes, Emre H. and Marru, Suresh and Dubbs, Bruce},
title = {UltraScan gateway enhancements: in collaboration with TeraGrid advanced user support},
booktitle = {Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery},
publisher = {ACM},
year = {2011},
pages = {34:1--34:8},
url = {http://doi.acm.org/10.1145/2016741.2016778},
doi = {http://doi.acm.org/10.1145/2016741.2016778}
}
|
|||||
| DOI | Verma, A., Ramyaa, R., Marru, S., Fan, Y. and Singh, R. | Rationalizing police patrol beats using Voronoi Tessellations | Intelligence and Security Informatics (ISI), 2010 IEEE International Conference on, pp. 165 -167 | 2010 | |
| Abstract: Computational criminology is an emerging interdisciplinary field that applies computer science and mathematical methods to the study of criminological problems. In order to understand the nature of crime one has to comprehend not only its spatio-temporal dimensions, but also the victim-offender relationship, role of guardians and history of similar incidents. In this position paper we explore a problem in rationalizing police patrolling beats using Voronoi Tessellations which provide a powerful technique to explore variety of criminological perspectives and understand the geography of crime and its control mechanism. The paper presents a method to rationally design an equitable workload amongst the police patrol beats in order to better handle the challenge of crime. | |||||
BibTeX:
@inproceedings{5484750,
author = {Verma, Arvind and Ramyaa, Ramyaa and Marru, Suresh and Ye Fan and Singh, Raminder},
title = {Rationalizing police patrol beats using Voronoi Tessellations},
booktitle = {Intelligence and Security Informatics (ISI), 2010 IEEE International Conference on},
year = {2010},
pages = {165 -167},
doi = {http://dx.doi.org/10.1109/ISI.2010.5484750}
}
|
|||||
| Knezek, P., Stobie, B., Michael, S., Valdes, F., Marru, S., Henschel, R. and Pierce, M. | A Concept for the One Degree Imager (ODI) Data Reduction Pipeline and Archiving System | Vol. 41Bulletin of the American Astronomical Society, pp. 824 |
2010 | ||
| Abstract: The One Degree Imager (ODI), currently being built by the WIYN Observatory, will provide tremendous possibilities for conducting diverse scientific programs. ODI will be a complex instrument, using non-conventional Orthogonal Transfer Array (OTA) detectors. Due to its large field of view, small pixel size, use of OTA technology, and expected frequent use, ODI will produce vast amounts of astronomical data. If ODI is to achieve its full potential, a data reduction pipeline must be developed. Long-term archiving must also be incorporated into the pipeline system to ensure the continued value of ODI data. This paper presents a concept for an ODI data reduction pipeline and archiving system. To limit costs and development time, our plan leverages existing software and hardware, including existing pipeline software, Science Gateways, Computational Grid & Cloud Technology, Indiana University's Data Capacitor and Massive Data Storage System, and TeraGrid compute resources. Existing pipeline software will be augmented to add functionality required to meet challenges specific to ODI, enhance end-user control, and enable the execution of the pipeline on grid resources including national grid resources such as the TeraGrid and Open Science Grid. The planned system offers consistent standard reductions and end-user flexibility when working with images beyond the initial instrument signature removal. It also gives end-users access to computational and storage resources far beyond what are typically available at most institutions. Overall, the proposed system provides a wide array of software tools and the necessary hardware resources to use them effectively. |
|||||
BibTeX:
@inproceedings{ODIknezekAAS10,
author = {Knezek, P. and Stobie, B. and Michael, S. and Valdes, F. and Marru, S. and Henschel, R. and Pierce, M.},
title = {A Concept for the One Degree Imager (ODI) Data Reduction Pipeline and Archiving System},
booktitle = {Bulletin of the American Astronomical Society},
year = {2010},
volume = {41},
pages = {824}
}
|
|||||
| DOI | Challa, S., Pierce, M. and Marru, S. | Integrating chemistry scholarship with web architectures, grid computing and semantic web | Gateway Computing Environments Workshop (GCE), 2010, pp. 1 -8 | 2010 | |
| Abstract: A chemist given a compound would be interested in knowing the experiments performed using the compound, journals containing the compound and also molecular properties of the compound. If there is a way to integrate this data, it would enhance the chemist's knowledge about a given compound. The Object Reuse and Exchange (ORE) specification may provide a solution to this problem. ORE is a model proposed by the digital libraries community to aggregate resources on the web. OREChem is a research project funded by Microsoft External Research that aims to apply and extend ORE to enable the integration of experimental, bibliographical and molecular properties data. OREChem targets crystallography as its primary application domain. This effort will design a prototypical, semantic-based eScience infrastructure for chemistry and chemical informatics. In this paper we describe how we have used REST as well as SOAP web services, TeraGrid cyberinfrastructure and Semantic Web technologies, such as RDF and triple stores, to facilitate the metadata integration. | |||||
BibTeX:
@inproceedings{orechemGCE10,
author = {Challa, S.K. and Pierce, M. and Marru, S.},
title = {Integrating chemistry scholarship with web architectures, grid computing and semantic web},
booktitle = {Gateway Computing Environments Workshop (GCE), 2010},
year = {2010},
pages = {1 -8},
doi = {http://dx.doi.org/10.1109/GCE.2010.5676123}
}
|
|||||
| DOI | Pierce, M., Marru, S., Singh, R., Kulshrestha, A. and Muthuraman, K. | Open grid computing environments: advanced gateway support activities | Proceedings of the 2010 TeraGrid Conference, pp. 16:1-16:9 | 2010 | |
| Abstract: We describe three case studies for providing advanced support for TeraGrid Science Gateways as part of our participation in the Advanced User Support (AUS) team. These case studies include providing workflow support, robust job management, and mass job submission to existing gateways targeting computational chemistry, biophysics, and bioinformatics, respectively. Selected tools from the Open Grid Computing Environments and other projects were used, demonstrating the need for flexibility when integrating tools from multiple software providers into specific gateways' software stacks. | |||||
BibTeX:
@inproceedings{Pierce:2010:OGC:1838574.1838590,
author = {Pierce, Marlon and Marru, Suresh and Singh, Raminder and Kulshrestha, Archit and Muthuraman, Karthik},
title = {Open grid computing environments: advanced gateway support activities},
booktitle = {Proceedings of the 2010 TeraGrid Conference},
publisher = {ACM},
year = {2010},
pages = {16:1--16:9},
url = {http://doi.acm.org/10.1145/1838574.1838590},
doi = {http://doi.acm.org/10.1145/1838574.1838590}
}
|
|||||
| Valdes, F. and Marru, S. | The Marriage of Mario (NHPPS) and Luigi (OGCE) [BibTeX] |
Vol. 442Astronomical Society of the Pacific Conference Series, pp. 211 |
2010 | ||
BibTeX:
@inproceedings{valdes2010OGCENHPPS,
author = {Valdes, F. and Marru, S.},
title = {The Marriage of Mario (NHPPS) and Luigi (OGCE)},
booktitle = {Astronomical Society of the Pacific Conference Series},
year = {2010},
volume = {442},
pages = {211}
}
|
|||||
| Yang, Y., Choi, J., Herath, C., Marru, S. and Kim, S. | BioVLAB: Bioinformatics Data Analysis Using Cloud Computing and Graphical Workflow Composers [BibTeX] |
Cloud Computing and Software Services: Theory and Techniques, pp. 309 | 2009 | ||
BibTeX:
@article{biovlabBook,
author = {Yang, Y. and Choi, J.Y. and Herath, C. and Marru, S. and Kim, S.},
title = {BioVLAB: Bioinformatics Data Analysis Using Cloud Computing and Graphical Workflow Composers},
journal = {Cloud Computing and Software Services: Theory and Techniques},
publisher = {CRC},
year = {2009},
pages = {309}
}
|
|||||
| Chinthaka, E., Marru, S. and Plale, B. | Sigiri: Towards A Light-Weight Job Management System for Large Scale Systems [BibTeX] |
School of Informatics and Computing, Indiana University, Bloomington, Indiana, Tech. Rep. TR681 | 2009 | ||
BibTeX:
@article{chinthaka2009sigiri,
author = {Chinthaka, E. and Marru, S. and Plale, B.},
title = {Sigiri: Towards A Light-Weight Job Management System for Large Scale Systems},
journal = {School of Informatics and Computing, Indiana University, Bloomington, Indiana, Tech. Rep. TR681},
publisher = {Citeseer},
year = {2009}
}
|
|||||
| DOI | Perera, S., Marru, S., Gunarathne, T., Gannon, D. and Plale, B. | Application of Management Frameworks to Manage Workflow-Based Systems: A Case Study on a Large Scale E-science Project | Web Services, 2009. ICWS 2009. IEEE International Conference on, pp. 519 -526 | 2009 | |
| Abstract: Management architectures are well discussed in the literature, but their application in real life settings has not been as well covered. Automatic management of a system involves many more complexities than closing the control-loop by reacting to sensor data and executing corrective actions. In this paper, we discuss those complexities and propose solutions to those problems on top of Hasthi management framework, where Hasthi is a robust, scalable, and distributed management framework that enables users to manage a system by enforcing management logic authored by users themselves. Furthermore, we present in detail a real life case study, which uses Hasthi to manage a large, SOA based, e-science cyberinfrastructure. | |||||
BibTeX:
@conference{hashiICWS,
author = {Srinath Perera and Suresh Marru and Thilina Gunarathne and Dennis Gannon and Beth Plale},
title = {Application of Management Frameworks to Manage Workflow-Based Systems: A Case Study on a Large Scale E-science Project},
booktitle = {Web Services, 2009. ICWS 2009. IEEE International Conference on},
year = {2009},
pages = {519 -526},
doi = {http://dx.doi.org/10.1109/ICWS.2009.52}
}
|
|||||
| DOI | Gunarathne, T., Herath, C., Chinthaka, E. and Marru, S. | Experience with adapting a WS-BPEL runtime for eScience workflows [BibTeX] |
Proceedings of the 5th Grid Computing Environments Workshop, pp. 7:1-7:10 | 2009 | |
BibTeX:
@conference{odeLeadGCE09,
author = {Gunarathne, Thilina and Herath, Chathura and Chinthaka, Eran and Marru, Suresh},
title = {Experience with adapting a WS-BPEL runtime for eScience workflows},
booktitle = {Proceedings of the 5th Grid Computing Environments Workshop},
publisher = {ACM},
year = {2009},
pages = {7:1--7:10},
url = {http://doi.acm.org/10.1145/1658260.1658270},
doi = {http://doi.acm.org/10.1145/1658260.1658270}
}
|
|||||
| Pierce, M., Marru, S., Wu, W., Kandaswami, G., von Laszewski, G., Dooley, R., Dahan, M., Wilkins-Diehr, N., Thomas, M., Center, T. and others | Open grid computing environments [BibTeX] |
Proceedings of the Fourth Annual TeraGrid Conference | 2009 | ||
BibTeX:
@conference{ogceTG09,
author = {Pierce, M. and Marru, S. and Wu, W. and Kandaswami, G. and von Laszewski, G. and Dooley, R. and Dahan, M. and Wilkins-Diehr, N. and Thomas, M. and Center, T.A.C. and others},
title = {Open grid computing environments},
booktitle = {Proceedings of the Fourth Annual TeraGrid Conference},
year = {2009}
}
|
|||||
| Marru, S., Perera, S., Feller, M. and Martin, S. | Reliable and Scalable Job Submission: LEAD Science Gateway?s Testing and Experiences with WS GRAM on TeraGrid Resources | Proceedings of the Third Annual TeraGrid Conference | 2008 | ||
| Abstract: Linked Environments for Atmospheric Discovery (LEAD) is a TeraGrid Science Gateway based on Service Oriented Architecture. As a typical SOA Gateway with web portal front-end, hundreds of users login to LEAD Portal and submit workflows to perform computations on TeraGrid Resources. WS GRAM, a required grid service component for many TeraGrid users and Science Gateways, facilitates LEAD Workflow computational job submissions, monitoring, accounting and auditing. WS GRAM provides a single common interface to access the compute resources at the various TeraGrid sites. Many different users can access WS GRAM services simultaneously. Thus, the WS GRAM service’s ability to reliably handle many simultaneous requests is a must. The LEAD science gateway uses the CoG kit and WS GRAM to effi- ciently use TG compute resources at multiple sites. This paper describes the LEAD Gateways recent experiences in managing 100s of simultaneous job submissions to TeraGrid resources. To help current and future gateways deal with similar large-scale job submission requirements, LEAD has conducted a set of comprehensive tests to simulate the consolidated load on WS GRAM under various usage conditions. This paper discusses the methodology used to test scalability and reliability and then concludes with results from the testing. This methodology can be used as a benchmark for WS GRAM service scalability and reliability on TeraGrid as well as others grids. |
|||||
BibTeX:
@article{gramTestingTG08,
author = {Suresh Marru and Srinath Perera and Martin Feller and Stuart Martin},
title = {Reliable and Scalable Job Submission: LEAD Science Gateway?s Testing and Experiences with WS GRAM on TeraGrid Resources},
journal = {Proceedings of the Third Annual TeraGrid Conference},
year = {2008}
}
|
|||||
| DOI | Perera, S., Marru, S. and Gannon, D. | Monitoring and Managing E-Science Cyber-Infrastructures: A Case Study | eScience, 2008. eScience '08. IEEE Fourth International Conference on, pp. 402 -403 | 2008 | |
| Abstract: Due to their scale, complexity, and dynamic nature, e-science cyber-infrastructures have raised major system management challenges. It has been argued that employing system management frameworks to monitor and control large scale systems is a possible solution to address these challenges. This paper presents an application of a management framework, known as Hasthi (Sanskrit name of Elephant which represents robustness), to manage an e-science project called linked environments for atmospheric discovery (LEAD). Hasthi is a generic framework that manages a system according to rules written by administrators, where rules define how Hasthi should respond to changes and failures. Using LEAD as an example, we demonstrate how such extensible management framework can be utilized to manage a complex system, while describing common problems and solutions. | |||||
BibTeX:
@conference{hasthiEScience,
author = {Perera, S. and Marru, S. and Gannon, D.},
title = {Monitoring and Managing E-Science Cyber-Infrastructures: A Case Study},
booktitle = {eScience, 2008. eScience '08. IEEE Fourth International Conference on},
publisher = {IEEE Computer Society},
year = {2008},
pages = {402 -403},
doi = {http://doi.ieeecomputersociety.org/10.1109/eScience.2008.90}
}
|
|||||
| Droegemeier, K.K., Alameda, J., Burge, L., Brewster, K., V., C., Christie, M., Clark, R., Domenico, B., Gannon, D., Graves, S., Joseph, E., Marru, S., Plale, B., Ramachandran, R., Ramamurthy, M., Reed, D., Rushing, J., Rossi, A., Tanner, S., Thomas, K.W., Weber, D., Wilhelmson, R., Wilson, A., Xue, M. and Yalda, S. | Linked Environments for Atmospheric Discovery (LEAD): Web services for meteorological research and education | 24th Conference on IIPS | 2008 | ||
| Abstract: Linked Environments for Atmospheric Discovery (LEAD) is a 5-year NSF Large Information Technology Research grant that has created an integrated web service architecture to support mesoscale meteorological data acquisition, analysis, assimilation, simulation modeling, prediction, mining and visualization. A unique component of LEAD is the operation of meteorological resources, and associated cyberinfrastructure, as dynamically adaptive, on-demand systems that can a) change configuration rapidly and automatically in response to weather; b) respond to decision-driven inputs from users; c) initiate other processes automatically; d) steer remote observing technologies, such as Doppler radars, to optimize data collection for the problem at hand; and e) provide the fault tolerance necessary to achieve required levels of performance. The overarching objectives of LEAD are to: •Lower the entry barrier for using, and make broadly available, several sophisticated meteorological tools and data services for graduate and undergraduate research and education; •Improve our understanding of and ability to detect, analyze and predict mesoscale atmospheric phenomena by interacting with weather in a dynamically adaptive manner. The LEAD web services framework – not unlike familiar resources such as Amazon.com, Travelocity.com – provides users with an almost endless set of capabilities, ranging from simply accessing real time or historical data and perhaps visualizing it, to running highly complex and linked data ingest, assimilation and forecast processes in real time and in a manner that adjusts dynamically to inputs as well as outputs. As part of the IIPS special session on LEAD, we describe in this overview paper the latest capabilities of and application experiences with LEAD, the latter from the NOAA Hazardous Weather Test Bed Spring 2007 Experiment as well as Weather Challenge 2007. We also describe plans to deploy LEAD as a community facility as well as its extensibility for problems such as Earth system prediction and regional climate modeling. |
|||||
BibTeX:
@article{lead-ams08,
author = {Kelvin K. Droegemeier and Jay Alameda and Legand Burge and Keith Brewster and Chandrasekar V. and Marcus Christie and Richard Clark and Ben Domenico and Dennis Gannon and Sara Graves and Everette Joseph and Suresh Marru and Beth Plale and Rahul Ramachandran and Mohan Ramamurthy and Daniel Reed and John Rushing and Al Rossi and Steve Tanner and Kevin W. Thomas and Daniel Weber and Robert Wilhelmson and Anne Wilson and Ming Xue and Sepideh Yalda},
title = {Linked Environments for Atmospheric Discovery (LEAD): Web services for meteorological research and education},
journal = {24th Conference on IIPS},
year = {2008},
url = {http://ams.confex.com/ams/88Annual/techprogram/paper_127719.htm}
}
|
|||||
| Marru, S., Gannon, D., Nadella, S., Beckman, P., Weber, D., Brewster, K. and Droegemeier, K. | LEAD Cyberinfrastructure to Track Real-Time Storms Using SPRUCE Urgent Computing [BibTeX] |
CTWatch Quarterly Vol. Volume 4, pp. 5 - 16 |
2008 | ||
BibTeX:
@article{leadCTWatch,
author = {Suresh Marru and Dennis Gannon and Suman Nadella and Pete Beckman and Daniel Weber and Keith Brewster and Kelvin Droegemeier},
title = {LEAD Cyberinfrastructure to Track Real-Time Storms Using SPRUCE Urgent Computing},
journal = {CTWatch Quarterly},
year = {2008},
volume = {Volume 4},
pages = {5 - 16},
url = {http://www.ctwatch.org/quarterly/articles/2008/03/lead-cyberinfrastructure-to-track-real-time-storms-using-spruce-urgent-computing.html}
}
|
|||||
| Fraser, D., Marru, S., Martin, S., Diehr, N.W., Foster, I., Perera, S. and Team, G.D. | Engaging with the LEAD Science Gateway Project: Lessons Learned in Successfully Deploying Complex System Solutions on TeraGrid | Proceedings of the Third Annual TeraGrid Conference | 2008 | ||
| Abstract: As the LEAD Science Gateway Development and Globus software development teams stepped up their engagements together in late ‘07, it became apparent that LEAD was hitting capability limits and needed to dramatically improve system performance if they were to meet their goals. Successfully deploying complex systems depends on each of the system components, but even more so on how these components are assembled. The probability of failure increases with the complexity of the overall system, and the failures that occur are not often easily traceable to the root causes. Tackling the issues for LEAD required assembling a team of over 20 experts, not just from LEAD and Globus, but also from TeraGrid just to incorporate the expertise needed to understand and improve the system. Having a large team available to oversee the problems that were occurring at any moment in time was crucial to the success of the project. In this paper, we explore some of the problems that were encountered, in categories including component analysis and testing; component deployment; and system integration. We also summarize key lessons learned along the way. Our experiences highlight the interdependence among the teams and the need for cross-domain expertise in attempting to understand and attack science problems using TeraGrid. |
|||||
BibTeX:
@article{lead-gatewaydebug-tg08,
author = {Dan Fraser and Suresh Marru and Stuart Martin and Nancy Wilkins Diehr and Ian Foster and Srinath Perera and Gateway Debug Team},
title = {Engaging with the LEAD Science Gateway Project: Lessons Learned in Successfully Deploying Complex System Solutions on TeraGrid},
journal = {Proceedings of the Third Annual TeraGrid Conference},
year = {2008}
}
|
|||||
| Sun, Y., Marru, S. and Plale, B. | Experience with Bursty Workflow-driven Workloads in LEAD Science Gateway | Proceedings of the Third Annual TeraGrid Conference | 2008 | ||
| Abstract: Workloads created from typical meteorology forecast workflows in LEAD are bursty in nature. As the number of simultaneous workflows increases, the burstiness aggravates and we start to encounter a problem in file transfer failure that can cause the file transfer servers to crash. Our solution addresses the problem by smoothing bursts in file transfer workloads and control for limited resources at the file transfer servers. With this new solution in place, we achieved 0% failure rate whereas it used to be as high as 20 | |||||
BibTeX:
@article{myleadWorkloadTG08,
author = {Yiming Sun and Suresh Marru and Beth Plale},
title = {Experience with Bursty Workflow-driven Workloads in LEAD Science Gateway},
journal = {Proceedings of the Third Annual TeraGrid Conference},
year = {2008}
}
|
|||||
| Brewster, K.A., Weber, D.B., Marru, S., Thomas, K.W., Gannon, D., Droegemeier, K., Alameda, J. and Weiss, S.J. | On-Demand Severe Weather Forecasts Using TeraGrid via the LEAD Portal [BibTeX] |
Proceedings of the Third Annual TeraGrid Conference | 2008 | ||
BibTeX:
@article{spc_tg08,
author = {Keith A. Brewster and Daniel B. Weber and Suresh Marru and Kevin W. Thomas and Dennis Gannon and Kelvin Droegemeier and Jay Alameda and Steven J. Weiss},
title = {On-Demand Severe Weather Forecasts Using TeraGrid via the LEAD Portal},
journal = {Proceedings of the Third Annual TeraGrid Conference},
year = {2008}
}
|
|||||
| Brewster, K.A., Weber, D.B., Thomas, K.W., Droegemeier, K.K., Wang, Y., Xue, M., Marru, S., Gannon, D., Alameda, J., Jewett, B.F., Kain, J.S., Weiss, S.J. and Christie, M. | Use of the LEAD Portal for On-Demand Severe Weather Prediction | 24th Conference on IIPS | 2008 | ||
| Abstract: The LEAD Portal was used in real time for on-demand forecasting of severe weather during the 2007 Hazardous Weather Testbed (HWT) Spring Experiment. The Portal is web-based and uses service oriented architecture to provide users with capabilities to access and analyze meteorological data and to prepare, conduct, and monitor WRF forecasts as well as archive, analyze, and verify WRF forecast data. Two 9-hour WRF forecasts, initialized at 15Z over re-locatable regional domains, were submitted once a day during a portion of the two month HWT experiment. The forecast domains were centered on areas of elevated chances for severe weather occurrence as determined by a LEAD project meteorologist using information supplied from Mesoscale Discussions issued by the NOAA/Storm Prediction Center and/or daily HWT weather briefings. The initial conditions for the two forecasts were either interpolated from the LEAD ARPS Data Analysis System (ADAS) 10km CONUS 15Z analysis or from the 3-hour NAM 12Z forecast. The lateral boundary conditions were extracted from the 12Z NAM forecasts using the ARPS EXT2ARPS software package. Due to resource limitations, the WRF forecast data were not available for comparison with other model guidance prior to afternoon convective activity, but the forecast data such as temperature, dew point temperature, winds and precipitation were available for comparison with observations and other model forecasts in near-realtime. This test validated the use of the LEAD Portal for on-demand forecasting of severe weather. Preliminary assessments of forecast skill and recommendations for future on-demand testing will be discussed at the conference. | |||||
BibTeX:
@article{spc07_ams,
author = {Keith A. Brewster and Daniel B. Weber and Kevin W. Thomas and Kelvin K. Droegemeier and Yunheng Wang and Ming Xue and Suresh Marru and Dennis Gannon and Jay Alameda and Brian F. Jewett and Jack S. Kain and Steven J. Weiss and Marcus Christie},
title = {Use of the LEAD Portal for On-Demand Severe Weather Prediction},
journal = {24th Conference on IIPS},
year = {2008},
url = {http://ams.confex.com/ams/88Annual/techprogram/paper_132434.htm}
}
|
|||||
| DOI | Marru, S., Pierce, M., Herath, C. and Perera, S. | Open Grid Computing Environment's Workflow Suite for E-Science Projects | eScience, 2008. eScience '08. IEEE Fourth International Conference on, pp. 332 -333 | 2008 | |
| Abstract: E-Science users will want to construct, share, execute and monitor sequence of tasks. These tasks may execute on machines ranging from their local workstations to high-end, grid-enabled compute resources. Often, these tasks are legacy applications written in various programming and scripting languages and are designed to be run in a single user environment rather than as a Web application. These tasks often need to be tied together into composite applications that need to span multiple computing resources. The majority of the scientific experiments in E-Science involve orchestrating multiple tasks in the correct fashion to produce scientific computational experiments. Scientific workflows have proven to be a coherent and abstract framework that is capable of capturing such scientific experiments and hence have gained popularity among the scientific community. Many of the current E-Science projects have adopted different workflow systems and consequently have adopted custom workflow execution and description standards. We argue that the core of the execution semantics used by most scientific workflows can be expressed as a small common set, and we further investigate the possibility of having a higher level workflow description language that is capable of capturing and possibly bridging these different workflow systems. In this demonstration we present a set of E-Science development tools for managing these problems: a high level workflow composition monitoring and enactment tool, a toolkit that is capable of providing Web service interfaces for command line scientific applications, and a service registry that is used as a repository for sharing. This domain independent workflow suite will allow users from wide verity of environments to selectively and securely share their applications as Web services and construct workflows with these services. The suite also features on-demand service creation, workflow orchestration and monitoring. Furthermore, these components ca- - n be used individually or collectively to build a small to large-scale E-Science infrastructures. | |||||
BibTeX:
@conference{workflowEScience08,
author = {Marru, S. and Pierce, M. and Herath, C. and Perera, S.},
title = {Open Grid Computing Environment's Workflow Suite for E-Science Projects},
booktitle = {eScience, 2008. eScience '08. IEEE Fourth International Conference on},
publisher = {IEEE Computer Society},
year = {2008},
pages = {332 -333},
doi = {http://doi.ieeecomputersociety.org/10.1109/eScience.2008.149}
}
|
|||||
| Perera, S., Marru, S. and Herath, C. | Workflow Infrastructure for Multi-scale Science Gateways [BibTeX] |
Proceedings of the Third Annual TeraGrid Conference | 2008 | ||
BibTeX:
@article{workflowSuiteTG08,
author = {Srinath Perera and Suresh Marru and Chathura Herath},
title = {Workflow Infrastructure for Multi-scale Science Gateways},
journal = {Proceedings of the Third Annual TeraGrid Conference},
year = {2008}
}
|
|||||
| Clark, R.D., Marru, S., Christie, M., Gannon, D., Illston, B., Baltzer, T. and Droegemeier, K.K. | The LEAD-WxChallenge pilot project: enabling the community | 24th Conference on IIPS | 2008 | ||
| Abstract: During the past few decades, the academic meteorology enterprise has supported a national collegiate forecast contest that seeks to engage mostly undergraduate students with some graduate students and faculty in practical forecasting under a variety of geographical and phenomenological circumstances. Known today as Weather Challenge (WxChallenge) and sponsored by the University of Oklahoma, each individual participant forecasts the maximum and minimum temperature, precipitation amount, and maximum sustained wind speed for select North American cities. WxChallenge provides students an opportunity to compete against their peers and faculty mentors at other institutions (64 nationwide in 2006-2007) for honors as the top weather forecaster in the nation. In spring 2007 the NSF-funded ITR project, Linked Environments for Atmospheric Discovery (LEAD) engaged a manageable subset of the WxChallenge community and provided access to the LEAD Gateway portal and its underlying services. The goal of this so-called “LEAD-WxChallenge Pilot Project” was to provide students with the ability to generate, run, analyze, and visualize their own WRF forecasts using the web-enabled services developed by LEAD researchers. For seven weeks, 75 students and faculty from 10 institutions were invited to join the pilot project. For the participants it provided an unprecedented opportunity for enhancing their understanding of numerical modeling, high performance computing, physical parameterization schemes, data assimilation, and workflow orchestration. It also demonstrated a key motivation for LEAD: to democratize and empower students by lowering the barrier for access to complex, integrated services, thereby allowing users the freedom to select inputs such as initialization fields, set model domains, and run WRF at a time and location determined by the user, and not constrained as in static, fixed and prescribed operational environments. In return, LEAD developers benefited from user feedback that exposed strengths and weaknesses, and provided a better sense of the challenges and resource requirements associated with maintaining a reliable and persistent system aimed at enabling a larger community. Participants were given authorization to the LEAD Gateway portal to access data, build experiments, and compose workflows with sufficient computing resources to run WRF and save the WRF output in myLEAD workspace. LEAD also provided tools for visualizing the output and user support. Upon completion of a 42-hour, high-resolution WRF run, students integrated user-generated output products into their personal schema for preparing a forecast for stations previously selected by WxChallenge. Over the seven week pilot project participants launched a total of 279 forecast workflows and generated 0.6 TBytes of data. Over 160 processors were reserved on a multi-processor server five days each week from 10am to 8pm EDT. For the NAM initialized WRF forecast, 78 percent of the workflows submitted were successful, 22 percent failed. The ADAS initialed WRF forecast was less successful with 36 percent successful and 64 percent failing. When the WxChallenge ended and the pilot project concluded, the participants were asked to complete a survey, the results of which will be used to refine the production release and prepare for an expanded release to a much larger population of WxChallenge participants in fall 2007. This paper will present an overview of the LEAD-WxChallenge pilot project along with a more detailed description of the emergent problems and challenges. In addition, preliminary results of the fall 2007 LEAD-WxChallenge project will be reported. |
|||||
BibTeX:
@article{wxc_ams08,
author = {Richard D. Clark and Suresh Marru and Marcus Christie and Dennis Gannon and Brad Illston and Thomas Baltzer and Kelvin K. Droegemeier},
title = {The LEAD-WxChallenge pilot project: enabling the community},
journal = {24th Conference on IIPS},
year = {2008},
url = {http://ams.confex.com/ams/88Annual/techprogram/paper_134261.htm}
}
|
|||||
| Clark, R.D., Marru, S., Christie, M., Baltzer, T., Droegemeier, K., Joseph, E. and Illston, B. | The LEAD-WxChallenge Pilot Project: The Potential of Grid-Enabled Learning | Proceedings of the Third Annual TeraGrid Conference | 2008 | ||
| Abstract: This paper discusses the need and potential benefit that could be realized with access to a stable, reliable, and persistent allocation of distributed TeraGrid infrastructure and software technologies for the atmospheric science education community. During the past few decades, the academic meteorology enterprise has supported a national collegiate forecast contest that seeks to engage mostly undergraduate students with some graduate students and faculty in practical forecasting under a variety of geographical and phenomenological circumstances. Known today as The Weather Challenge (WxChallenge), each participant forecasts the maximum and minimum temperature, precipitation amount, and maximum sustained wind speed for select North American cities. WxChallenge provides students an opportunity to compete against their peers and faculty mentors at other institutions (64 nationwide in 2006-2007) for honors as the top weather forecaster in the nation. In spring 2007 the NSF-funded ITR project, Linked Environments for Atmospheric Discovery (LEAD) engaged a manageable subset of the WxChallenge community and provided access to the LEAD Gateway portal and its underlying services. The goal of the so- called “LEAD-WxChallenge Pilot Project” was to begin ushering in a fundamental paradigm shift in how experiments are conceived and performed, in the structure of user application tools and middleware, and in methodologies used to observe and model the atmosphere. Students were provided with the ability to generate, run, analyze, and visualize their own WRF forecasts using the web-enabled service oriented architecture developed by LEAD IT researchers. For seven weeks, the 75 students and faculty from 10 institutions were given an unprecedented opportunity for enhancing their understanding of numerical modeling, high performance computing, physical parameterization schemes, data assimilation, and workflow orchestration. Participants were given sufficient compute cycles on TeraGrid servers to build their own experiments and run the WRF numerical modeling system. The project participants launched a total of 279 forecast workflows and generated 0.6 TB of data. Over 160 processors were reserved five days each week from 10am to 8pm EDT. For the NAM initialized WRF forecast, 78 percent of the workflows submitted were successful, 22 percent failed. The ADAS initialed WRF forecast was less successful with 36 percent completing and 64 percent failing. Moreover, significant intervention was necessary on the part of developers to achieve these moderate success rates. Since its inception LEAD has espoused the motivation to empower a community of users, and to provide the necessary grid-enabled infrastructure and tools to facilitate research and education. In return, LEAD developers benefited from user feedback that exposed strengths and weaknesses, and provided a better sense of the challenges and resource requirements associated with maintaining a reliable and persistent system. While this pilot project revealed an overall satisfaction with LEAD capability, the fragility of the infrastructure was a serious limitation and one that has the potential to thwart the efforts of LEAD developers and the TeraGrid leadership even with the best intentions, and may prevent a larger user community from ever realizing the benefits of grid computing. | |||||
BibTeX:
@article{wxc-tg08,
author = {Richard D Clark and Suresh Marru and Marcus Christie and Thomas Baltzer and Kelvin Droegemeier and Everette Joseph and Brad Illston},
title = {The LEAD-WxChallenge Pilot Project: The Potential of Grid-Enabled Learning},
journal = {Proceedings of the Third Annual TeraGrid Conference},
year = {2008}
}
|
|||||
| Gannon, D., Plale, B., Christie, M., Huang, Y., Jensen, S., Liu, N., Marru, S., Pallickara, S., Perera, S. and Shirasuna, S. | Building Grid Portals for e-Science: A Service Oriented Architecture [BibTeX] |
High Performance Computing and Grids in Action, IOS Press, Amsterdam | 2007 | ||
BibTeX:
@article{escience-book,
author = {Dennis Gannon and Beth Plale and Marcus Christie and Yi Huang and Scott Jensen and Ning Liu and Suresh Marru and Sangmi Pallickara and Srinath Perera and Satoshi Shirasuna},
title = {Building Grid Portals for e-Science: A Service Oriented Architecture},
journal = {High Performance Computing and Grids in Action, IOS Press, Amsterdam},
year = {2007}
}
|
|||||
| Gannon, D., Christie, M., Marru, S., Shirasuna, S. and Slominski, A. | Programming Paradigms for Scientific Problem Solving Environments [BibTeX] |
IFIP International Federation for Information Processing Vol. 239, pp. 3-15 |
2007 | ||
BibTeX:
@article{gannon2007pps,
author = {Dennis Gannon and Marcus Christie and Suresh Marru and Satoshi Shirasuna and Aleksander Slominski},
title = {Programming Paradigms for Scientific Problem Solving Environments},
journal = {IFIP International Federation for Information Processing},
publisher = {Springer},
year = {2007},
volume = {239},
pages = {3-15}
}
|
|||||
| DOI | Christie, M. and Marru, S. | The LEAD Portal: a TeraGrid gateway and application service architecture | Concurrency and Computation: Practice and Experience Vol. 19(6), pp. 767-781 |
2007 | |
| Abstract: The Linked Environments for Atmospheric Discovery (LEAD) Portal is a science application portal designed to enable effective use of Grid resources in exploring mesoscale meteorological phenomena. The aim of the LEAD Portal is to provide a more productive interface for doing experimental work by the meteorological research community, as well as bringing weather research to a wider class of users, meaning pre-college students in grades 6–12 and undergraduate college students. In this paper, we give an overview of the LEAD project and the role that LEAD portal is playing in reaching its goals. We then describe the various technologies we are using to bring powerful and complex scientific tools to educational and research users. These technologies—a fine-grained capability based authorization framework, an application service factory toolkit, and a Web services-based workflow execution engine and supporting tools—enable our team to deploy these once inaccessible, stovepipe scientific codes onto a Grid where they can be collectively utilized. | |||||
BibTeX:
@article{leadPortal,
author = {Marcus Christie and Suresh Marru},
title = {The LEAD Portal: a TeraGrid gateway and application service architecture},
journal = {Concurrency and Computation: Practice and Experience},
publisher = {John Wiley and Sons Ltd.},
year = {2007},
volume = {19},
number = {6},
pages = {767--781},
url = {http://portal.acm.org/citation.cfm?id=1232515.1232525},
doi = {http://dx.doi.org/10.1002/cpe.v19:6}
}
|
|||||
| Gannon, D., Plale, B., Christie, M., Marru, S., Kandaswamy, G., Fang, L., Huang, Y., Pallickara, S., Jensen, S., Liu, N., Shirasuna, S., Simmhan, Y., Slominski, A., Ramachandran, R., Clark, R., Lawrence, K. and Kim, I.-H. | The LEAD Science Portal Problem Solving Environment [BibTeX] |
23rd Conference on IIPS | 2007 | ||
BibTeX:
@conference{leadPscAMS07,
author = {Dennis Gannon and Beth Plale and Marcus Christie and Suresh Marru and Gopi Kandaswamy and Liang Fang and Yi Huang and Sangmi Pallickara and Scott Jensen and Ning Liu and Satoshi Shirasuna and Yogesh Simmhan and Aleksander Slominski and Rahul Ramachandran and Rich Clark and Katherine Lawrence and Il-Hwan Kim},
title = {The LEAD Science Portal Problem Solving Environment},
journal = {23rd Conference on IIPS},
year = {2007}
}
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| Baltzer, T., Wilson, A., Ramamurthy, M., Marru, S., Christie, M., Gannon, D., Rossi, A., Hampton, S., Alameda, J. and Droegemeier, K. | LEAD at the Unidata workshop: demonstrating democratization of NWP capabilities | 23rd Int. Conf. on Interactive Information Processing Systems for Meteorology | 2007 | ||
| Abstract: During the week of July 10, 2006 Unidata held its triannual User's Workshop. The theme of this year's workshop was "Expanding the Use of Models as Educational Tools in the Atmospheric & Related Sciences" (See http://www.unidata.ucar.edu/community/2006 workshop/ for more information.) Workshop organizers and LEAD team members saw this as an opportunity to unveil LEAD to and receive feedback from a self-selected group of Unidata community members that are particularly interested in being able to run forecast models. Thus on July 13th 2006,the LEAD lab day, members of the Unidata community got their first experience with capabilities being developed under the Linked Environments for Atmospheric Discovery (LEAD) project. The key LEAD goal demonstrated during the workshop was that of “Democratization,” that is, providing capabilities to the larger meteorological community. | |||||
BibTeX:
@conference{uniWorkshopAMS,
author = {Tom Baltzer and Anne Wilson and Mohan Ramamurthy and Suresh Marru and Marcus Christie and Dennis Gannon and Al Rossi and Shawn Hampton and Jay Alameda and Kelvin Droegemeier},
title = {LEAD at the Unidata workshop: demonstrating democratization of NWP capabilities},
journal = {23rd Int. Conf. on Interactive Information Processing Systems for Meteorology},
year = {2007}
}
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| DOI | Kandaswamy, G., Fang, L., Huang, Y., Shirasuna, S., Marru, S. and Gannon, D. | Building web services for scientific grid applications | IBM Journal of Research and Development Vol. 50(2.3), pp. 249 -260 |
2006 | |
| Abstract: Web service architectures have gained popularity in recent years within the scientific grid research community. One reason for this is that web services allow software and services from various organizations to be combined easily to provide integrated and distributed applications. However, most applications developed and used by scientific communities are not web-service-oriented, and there is a growing need to integrate them into grid applications based on service-oriented architectures. In this paper, we describe a framework that allows scientists to provide a web service interface to their existing applications as web services without having to write extra code or modify their applications in any way. In addition, application providers do not need to be experts in web services standards, such as Web Services Description Language, Web Services Addressing, Web Services Security, or secure authorization, because the framework automatically generates these details. The framework also enables users to discover these application services, interact with them, and compose scientific workflows from the convenience of a grid portal. | |||||
BibTeX:
@article{5388731,
author = {Kandaswamy, G. and Fang, L. and Huang, Y. and Shirasuna, S. and Marru, S. and Gannon, D.},
title = {Building web services for scientific grid applications},
journal = {IBM Journal of Research and Development},
year = {2006},
volume = {50},
number = {2.3},
pages = {249 -260},
doi = {http://dx.doi.org/10.1147/rd.502.0249}
}
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| Simmhan, Y., Plale, B., Gannon, D. and Marru, S. | Performance evaluation of the karma provenance framework for scientific workflows | International Provenance and Annotation Workshop (IPAW) Vol. 4145, pp. 222-236 |
2006 | ||
| Abstract: Provenance about workflow executions and data derivations in scientific applications help estimate data quality, track resources, and validate in silico experiments. The Karma provenance framework provides a means to collect workflow, process, and data provenance from data-driven scientific workflows and is used in the Linked Environments for Atmospheric Discovery (LEAD) project. This article presents a performance analysis of the Karma service as compared against the contemporary PReServ provenance service. Our study finds that Karma scales exceedingly well for collecting and querying provenance records, showing linear or sub-linear scaling with increasing number of provenance records and clients when tested against workloads in the order of 10,000 application-service invocations and over 36 concurrent clients. | |||||
BibTeX:
@article{karmaPerf,
author = {Simmhan, Y. and Plale, B. and Gannon, D. and Marru, S.},
title = {Performance evaluation of the karma provenance framework for scientific workflows},
journal = {International Provenance and Annotation Workshop (IPAW)},
publisher = {Springer},
year = {2006},
volume = {4145},
pages = {222--236}
}
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| Gannon, D., Plale, B., Marru, S., Kandaswamy, G., Simmhan, Y. and Shirasuna, S. | Dynamic, adaptive workflows for mesoscale meteorology [BibTeX] |
Workflows for E-Science: Scientific Workflows for Grids, pp. 97-114 | 2006 | ||
BibTeX:
@article{leadWorkflowBook,
author = {Dennis Gannon and Beth Plale and Suresh Marru and Gopi Kandaswamy and Yogesh Simmhan and Satoshi Shirasuna},
title = {Dynamic, adaptive workflows for mesoscale meteorology},
journal = {Workflows for E-Science: Scientific Workflows for Grids},
publisher = {Springer-Verlag New York Inc},
year = {2006},
pages = {97-114}
}
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| Gannon, D., Plale, B., Christie, M., Fang, L., Huang, Y., Jensen, S., Kandaswamy, G., Marru, S., Pallickara, S.L., Shirasuna, S., Simmhan, Y., Slominski, A. and Sun, Y. | Service Oriented Architectures for Science Gateways on Grid Systems | International Conference on Service Oriented Computing (ICSOC), pp. 21-32 | 2005 | ||
| Abstract: Grid computing is about allocating distributed collections of resources including computers, storage systems, networks and instruments to form a coher- ent system devoted to a “virtual organization” of users who share a common in- terest in solving a complex problem or building an efficient agile enterprise. Ser- vice oriented architectures have emerged as the standard way to build Grids. This paper provides a brief look at the Open Grid Service Architecture, a standard be- ing proposed by the Global Grid Forum, which provides the foundational con- ceptsofmostGridsystems. AbovethisGridfoundationisalayerofapplication- oriented services that are managed by workflow tools and “science gateway” por- tals that provide users transparent access to the applications that use the resources of a Grid. In this paper we will also describe these Gateway framework services and discuss how they relate to and use Grid services. | |||||
BibTeX:
@book{soa-sci-gateways,
author = {Dennis Gannon and Beth Plale and Marcus Christie and Liang Fang and Yi Huang and Scott Jensen and Gopi Kandaswamy and Suresh Marru and Sangmi L. Pallickara and Satoshi Shirasuna and Yogesh Simmhan and Aleksander Slominski and Yiming Sun},
title = {Service Oriented Architectures for Science Gateways on Grid Systems},
booktitle = {International Conference on Service Oriented Computing (ICSOC)},
year = {2005},
pages = {21-32}
}
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| Marru, S. | A Grid-enabled Scientific Workbench for Integrated Predictive Earth System Simulation [BibTeX] |
School: University of Oklahoma | 2004 | ||
BibTeX:
@phdthesis{marru2004grid,
author = {Marru, S.},
title = {A Grid-enabled Scientific Workbench for Integrated Predictive Earth System Simulation},
school = {University of Oklahoma},
year = {2004}
}
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