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NEES Cyberinfrastructure

by Gregory P Rodgers, Rajesh Thyagarajan

NEES Cyberinfrastructure

The NEES cyberinfrastructure is the Information Technology that enables the Network of Earthquake Engineers (NEES) to work as an integrated co-laboratory. It is a collection of tools, servers, and networks to support NEES. The centerpiece of the NEES cyberinfrastructure is the NEEShub website located at http://nees.org.

Some of the NEES cyberinfrastructure exists at the individual facility sites to collect and process data from simulation experiments. The website servers and data servers for the project warehouse exist at Purdue University. In addition to NEES data servers, there are other servers used for simulation including execution servers, Xsede supercomputers, and Open Science Grid servers that form a cloud computing capability for simulation tools.

The NEES Cyberinfrastructure can be organized as follows:

   A. Site Operations Tools
   B. The NEEShub Web Server
   C. Cloud / Simulation Environment
   D. The Project Warehouse
   E. Education, Outreach, and Training (EOT)
   F. Online spreadsheet databases

The following diagram depicts the NEES Cyberinfrastructure. Above the horizontal dotted line represents cyberinfrastructure at NEES equipment sites. Below the dotted line represents cyberinfrastructure at Purdue University. The block arrows crossing the line represent tools used to transfer data between the equipment sites and the NEEScomm servers at Purdue University.

NEESCyberInfrastructure.jpg

A. Site Operations Tools

Site Operations Tools include local web servers, telepresence tools, visualization tools, and local data management tools. These tools are managed in the NEEShub, downloaded, and executed on servers and workstations managed by the local site IT manager.

B. The NEEShub Web Server

The NEEShub website (http://nees.org) is powered by the HUBzero software developed at Purdue University. HUBzero was specifically designed to help a scientific community share resources and work together with one another. Users can upload their own content—including tutorials, courses, publications, and animations—and share them with the rest of the community. But each hub is more than just a repository of information. It is a place where researchers and educators can share data and simulation tools online. Users can launch simulations and post-process results with an ordinary web browser—without having to download, compile, or install any code. The tools they access are not just web forms, but powerful graphical tools that support visualization and comparison of results.

How Does a Hub Differ From a Web Site?

At its core, a hub is a web site built with many familiar open source packages—the Linux operating system, an Apache web server, a mysql database, PHP web scripting, and the Joomla content management system. The HUBzero software builds upon that infrastructure to create an environment in which researchers, educators, and students can access simulation tools and share information. Specifically, we define a “hub” as a web-based collaboration environment with the following features

  • Interactive simulation tools, hosted on the hub cluster and delivered to your browser
  • Simulation tool development area, including source code control and bug tracking
  • Animated presentations delivered in a light-weight, Flash-based format
  • Mechanism for uploading and sharing resources
  • 5-star ratings and user feedback for resources
  • User support area, with question-and-answer forum
  • Statistics about users and usage patterns

The HUB contains collaboration features as well as user-contributed resources

Collaboration Tools:

NEES research is usually done in groups of investigators from multiple research organizations. The NEEShub provides tools that support such collaborations. A group space allows team data to be stored, viewed and manipulated by the members. The teams can also use the NEEShub group space to maintain group web pages, group Wikis, and discussion forums.

Earthquake Engineering Web Resources:

The NEEShub hosts a myriad of web resources that are of use to researchers, students, practicing engineers, and the general public. These resources include teaching tools, earthquake-related presentations, videos, a bibliography of earthquake-related publications, databases containing diverse earthquake engineering information beyond NEES research, and detailed information about the NEES network.

C. Cloud / Simulation Environment

Computational tools exist that perform computer simulations that predict the seismic response of various components of the civil infrastructure. These tools allow researchers to evaluate the seismic performance of infrastructure components and compare them against the physically measured response from an experiment. Computer simulations also allow researchers to modify parameters and investigate what-if scenarios. Because many of the NEES physical experiments are destructive, computer simulations are often the only way to conduct parameter studies.

The NEEShub enables all tools to execute online, at nees.org, without the need for installing programs or downloading data on local computers. This functionality is often referred to as cloud-computing. Furthermore, the NEEShub has the capability of sending large simulation jobs to national high-performance computer platforms, including resources of the Open Science Grid and Xsede (formerly Teragrid).

D. NEES Project Warehouse

The NEES project Warehouse contains the data and results of the research projects that made use of the NEES infrastructure. It is a combination of an oracle database, a file system, and access methods to injest and deliver data for analysis.

NEES research projects involve researchers from different universities who collaborate to perform large-scale experiments that investigate the response of the infrastructure during earthquakes. For example, an experiment may involve constructing a building on a shake table at a NEES site, shaking the building with a motion mimicking a recent earthquake, and measuring the resulting forces and deformations in the building. In the Project Warehouse, the researchers store all sensor measurements (e.g., force, deformation), as well as project/experiment descriptions, drawings, material information, sensor types and locations, pictures and videos of the experiments, and publications that document the results of the research. The NEEShub provides for researchers data ingestion tools that support the easy upload of project information into the repository. The end users of the information in the Project Warehouse are other researchers who want to learn from past research projects, students, practicing engineers, and the general public. To facilitate data discovery, the Project Warehouse includes tools for viewing the information in meaningful ways. These tools include the Project Editor, Web Services, the Project Explorer for NEES (PEN), and Synchronees.

Project Editor:

The NEES Project Editor is a component of NEEShub that browses a project and updates a project. The underlying technology behind the Project Editor is propel. Propel is used to query Oracle from PHP. NEESComm IT maintains this PHP code. You can get to the Project Editor from the main page or through this URL https://nees.org/warehouse

Web Services:

Web services provides and API for remote acesss to the warehouse. This allows researchers with minimal experience to retrieve and query the database. The underlying technology behind the implementation of NEES Web Services is hibernate. Hibernate is used to query oracle with Java. NEESComm IT maintains the server side Java code for Web Services. For tool developers who want to use NEES REST Web Services, a set of sample queries can be found at https://nees.org/resources/restws .

Upload/Download Tools:

Different tools are used depending on the source and destination. The Project Explorer for NEES (PEN) is used to bulk copy files from the sites into the project warehouse. The Synchronees tool is used to copy files into an ad-hoc group sharing space. Other utilities allow individual file transfer.

The Project Explorer for NEES (PEN) is a downloadable tool that uses web services for uploading and downloading files to the warehouse. For more information about PEN see the tool page for PEN at https://nees.org/resources/pen .

The Synchronees tool is also downloadable and can be found at https://nees.org/resources/synchronees .

Storage Services:

NEES_site_hardware_v2_20120514.pngNEES_site_hardware_v2_20120514.png

Backup Services:

Neeshub-Backup-diagram_v8_20130212.pngNeeshub-Backup-diagram_v8_20130212.png

Disaster Recovery Plan

Neeshub-Data_Disaster-Recovery-diagram_v2.pngNeeshub-Data_Disaster-Recovery-diagram_v2.png

E. Education, Outreach, and Training

This area of NEEShub is called NEES Academy. The NEES Academy is organized into sections for Students, Teachers, Professionals, and the Public. NEES Academy can be found at https://nees.org/education.

The NEES Academy cyberinfrastructure consists of enhanced resource types, Moodle integration and media services:

Enhanced Resources

The enhanced HUB resource types are Learning Objects, Multimedia, and Series and operate within the normal hub infrastructure. They have been enhanced with new editing capabilities and rich media embedding . Additionally a new resource access API that allows open resource access to mobile devices and web browsers was added to allow rapid content sharing. The NEES Academy enhanced resources can be found at https://nees.org/resources as well as being embedded and used within the NEESacademy pages at http://nees.org/education . The resource system is built on PHP, Java, and Javascript with data residing in a mySQL database.

Moodle – Course Management

Moodle is a course management system that is installed on the same server as NEEShub, but operates on a separate database. Plugins control communication between NEEShub and Moodle, such that NEEShub is the authoritative system controlling authentication and Moodle accepts that authority to determine course access control. Moodle courses are able to embed NEEShub enhanced resources to further enrich the online curriculum. The Moodle courses can be found in sections of NEESacademy like the Wood Education Institute http://nees.org/education/wood-education-institute. Moodle is a PHP powered web system running on a mySQL database.

Media Services

Media services that supply live video and audio to classroom actives are run on a separate server to NEEShub. These services include VOIP, screen sharing and virtual poster session capabilities. These often high-bandwidth applications are separated from the NEEShub web server to ensure optimal latency for all users. The media services run on a Java server interacting with a red5 flash media server.

F. Online Spreadsheet Databases

A dedicated group of programmers can turn a spreadsheet with input from multiple sources into custom Online Spreadsheet Databases. These Online Spreadsheet Databases can be manipulated with simple filtering criteria and then downloaded in multiple formats for further analysis. Certain tools in the hub can execute on data or data references stored in the cells of these Online Spreadsheet Databases. NEEShub currently has 9 spreadsheets. Several more are in development. The cyberinfrastructure to support these spreadsheets consists of a data server, a mysql database, PHP, xml, and javascript. All these databases can be found at this URL https://nees.org/resources/databases

One of these spreadsheets indexes articles found in the Journal of Earthquake Engineering. The Journal of Earthquake Engineering and NEEScomm are partnering to share experimental data from journal articles that would be of interest to other researchers. Availability of these important data sets will accelerate progress in achieving earthquake-resilient communities around the world. From the spreadsheet main page you will find the data associated with a specific journal manuscript and the figures therein, read the abstract, plot the data in an interactive mode, and download the data files provided by the authors. A link to the journal paper itself is also provided.

References:

  1. M.Mclennan, and R. Kennell, “HUBzero: A Platform for Dissemination and Collaboration in Computational Science and Engineering,” Computing in Science & Engineering, vol. 12, no. 2, pp. 48-53, 2010.
  2. I. Park, N. Kapadia, R. Figueiredo, Eigenmann, R. and Fortes, J. A. B., “Towards an integrated, web-executable parallel programming tool environment,” High-Performance Networking and Computing Conference, November 2000.
  3. Nirav H. Kapadia, Jose A. B. Fortes and Mark S. Lundstrom, “The Purdue University Network-Computing Hubs: Running Unmodified Simulation Tools via the WWW“, ACM Transactions on Modeling and Computer Simulation (TOMACS), January 2000.
  4. Gregory P Rodgers; Ian Mathew (2011), “PEN 1.4.6,” https://nees.org/resources/pen.
  5. Ruth Pordes, NEES Cyberinfratructure Community Forum, “Workshop on Data Curation And Sharing Cyberinfrastructure for Earthquake Science”, https://nees.org/groups/nccf/wiki

Further information:

  • Explore the NEEShub at nees.org
  • T.J. Hacker, R. Eigenmann, S. Bagchi, A. Irfanoglu, S. Pujol, A. Catlin and E. Rathje, E., “The NEEShub Cyberinfrastructure for Earthquake Engineering,” IEEE Computing in Science & Engineering, 2011, vol. 13, no. 4., pp 67-78.
  • R. Eigenmann and T. Hacker and E. Rathje, “NEES Cyberinfrastructure: a Foundation for Innovative Research and Education,” U.S./Canadian Conference on Earthquake Engineering, Toronto, Canada, 2010.
  • Julio Ramirez, Thalia Anagnos and Rudolf Eigenmann, “The George E. Brown, Jr. Network for Earthquake Engineering Simulation (NEES): A Resource for Structural Engineers,” Structural Engineers of California Convention, Indian Wells, California,2010.

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