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  • 1. VLab ( Virtual Laboratory for Earth and Planetary Materials ) A Grid Facility for Computational Mineral Physics
  • 2. Principal IT Investigators
    • University of Minnesota
      • Prof. David A. Yuen : Dept. of Geology and Geophysics
        • Evan F. Bollig
        • Martin F. Lyness
        • Paul Jensen
      • Prof. Renata Wentzocvitch : Dept. of Chemical Engineering and Materials Science
        • Dr. Cesar da Silva
        • Pedro da Silveira
    • Florida State University
      • Prof. Gordon Erlebacher : School of Computational Science
    • Indiana University
      • Dr. Marlon Pierce : IU Community Grids Lab
  • 3. Photographs David A. Yuen Renata Wentzcovitch Gordon Erlebacher Martin F. Lyness Evan F. Bollig Pedro da Silveira Cesar da Silva Paul Jensen Marlon Pierce
  • 4. VLab : An Overview On the web: http://vlab.msi.umn.edu/
    • The VLab Portal - Middleware to integrate software across grid computing environments
    • WATT – Automating visualization Web Service generation
    • Sphynx – Simplifying Web Application testing
    • AJAX – Re-thinking the web interface experience.
    • Porky Portal – Real-time workflow monitoring system.
    • Connecting Researchers – Software and technologies that enhance collaboration.
  • 5. Questions Answered
    • What is VLab?
      • An interdisciplinary consortium dedicated to the development and promotion of the theory of planetary materials.
    • What will VLab accomplish?
      • Address materials physics and physical chemistry issues of importance to planetary sciences.
      • Develop and improve first principles simulations methodologies, integrating highly tested first principles software with utility programs, and creating novel human/software interfaces to facilitate and automate time-consuming human tasks.
      • Develop an educational program to provide training and bridge the gap between mineral physicists and materials theorists.
  • 6. VLab Activities On the web: http://vlab.msi.umn.edu/events/
    • Workshops & Seminars
      • More to be announced in the Fall
    • Tutorials
      • Latest Event: First annual VLab Tutorial (5/21-6/3)
    • Summer Research Internship (Univ. of Minnesota)
      • 8 undergraduate students, each from unique educational disciplines actively participate in research and development of novel technologies for VLab.
    • Nuggets: Short Research Bulletins
      • Straight to the point updates as we accomplish new goals
      • http://vlab.msi.umn.edu/reports/nuggets/
  • 7. The VLab Portal http://dasilveira.msi.umn.edu:8080/vlab/ Large scale molecular dynamics simulations through a simplified grid middleware
  • 8. Molecular Dynamics with PWscf On the web: http://www.pwscf.org/
    • Using Plane-Wave self-consistent field (PWscf)
      • http://www.pwscf.org/
    • First Principles Molecular Dynamics (FP-MD)
    • - Use of quantum mechanics to calculate forces - Electronic structures are calculated with-in Density Functional Theory (DFT) framework
    • - Nuclei positions + electronic structure  forces (accurate) - Nuclei motion follow Newton’s laws of motion
    Number of atoms, total energy, and volume (N,E,V) are constant. Only atoms can move
  • 9. Molecular Dynamics with PWscf
    • Variable Cell Shape FP-MD - Cell shape is allowed to change in response to stresses and external pressure - Elastic Strains (Cij) are dynamic variables - In dumped mode PWscf produces configurations (Cell T Atomic Position) at arbitrary external pressure - Stresses and forces are calculated within DFT framework
    VCS-MD: Cell shapes allowed to change
  • 10. Job Submission Middleware On the Web : http://dasilveira.msi.umn.edu:8080/vlab/ Workflows involve iterations through the following steps: 1) Prepare inputs for applications like PWscf or Phonon, and generate a submission bundle complete with input parameters plus required files. 2) Distribute (via web services) the submission bundles to back-end computation nodes (incl. TeraGrid { http://www.teragrid.org/ } ) for execution. 3) Gather results for analysis and refine parameters to reiterate steps 1-3.
  • 11. Equation Of State, Elasticity (Cij) and Phonon Calculations Example of workflow complexity
  • 12. Monitoring Submissions Job submissions to various nodes are monitored by a web interface.
  • 13. ElasVis : Visualization of Elasticity Output On the Web: http://webis.msi.umn.edu/elasticity.php
    • Integrated into VLab portal to visualize simulation results at end of Cij phase.
    • Uses Java WebStart and JOGL for high performance graphics on distributed clients
    • Web-based reposition scheme for datasets allows results to be committed to permanent storage and retrieved anywhere, anytime.
    • Compare previous simulations with current results and tweak simulations to run again.
  • 14. Novel Technologies Emerging technologies being integrated into VLab
  • 15. WATT: An Overview On the Web : http://www.gorerle.com/vlab-wiki/index.php?title=WATT
    • The W eb A utomation and T ranslation T oolkit ( WATT )
    • Automates the conversion of software, specifically for the internet.
    • Translates source code to incorporate new technologies.
    • Currently supports direct compilation of VTK ( http://www.vtk.org ) Tcl scripts into remote visualization web services.
    • Three components: the WATT compiler, fcon , and sixpak .
  • 16. Component 1: The WATT Compiler
    • Uses type-inference to convert type-less Tcl to strictly-typed C++
    • Compiler is language independent; configuration modules define input and output syntax.
    • Register and Interrupt systems allow the compiler to reconfigure itself as it runs.
      • Parser for input configuration files registers new types or translations that are immediately available for use.
      • Interrupts are invoked by registered inputs and result in unique output (i.e. Tcl “set a 1” --> C++ “int a = 1;”)
  • 17. WATT : Design
    • Tcl scripts written for VTK are sent to our Watt Compiler
    • WATT generates C++ calls for VTK and adds template calls to gSOAP ( http://www.cs.fsu.edu/~engelen/soap.html )
    • gSOAP headers autogenerated by WATT are compiled by the soapcpp2 compiler to produce SOAP enabled C++ objects
    • WATT output plus additional gSOAP output are compiled together to produce a single binary visualization web service
  • 18. Component 2: FCON
    • FCON is an extensible file conversion utility.
    • The user provides a pattern describing the input and desired output, and FCON generates a program (written in C) to do the conversion.
    • Designed to be system independent, allowing the user to convert files of different endian-ness.
    • FCON module will write file converters as WATT compiles source into web services
  • 19. Component 3: SIXPAK
    • SIXPAK is the “Simple XML Parsing Kit”.
    • Generates XML parsers and verifiers for the Watt compiler and FCON during runtime.
      • Reconfigures system without re-running processes
    • SIXPAK goes beyond standard XML to verify the logical correctness of input files.
      • SIXPAK ’s parsers are used while the compiler and FCON run, so correctness is essential.
  • 20. The WATT Client On the web: http://webis.msi.umn.edu:8080/WattClientWebApp
    • A generic client for any VTK ( http://www.vtk.org ) services generated by WATT
    • Uses JOGL and Java WebStart for fast feedback on client machines.
    • Remote service performs complex visualization, releasing clients from memory and processor requirements imposed by VTK.
    • Shown here with output produced by a charge density simulation in the VLab portal.
  • 21. Sphynx : Overview On the Web: http://www.gorerle.com/vlab-wiki/index.php?title=Sphynx
    • Automated Unit Testing for web interfaces
      • Pluggable design for extensions and test classes detected at runtime
      • Cross platform design based on XML -- Tests are XML descriptions, not blocks of code
      • Generates reusable test structures to reduce time consumed by unit testing in the past
    • Useful as both a development tool and an end-user feature
    • Anything accessible via http/https streams can be tested
  • 22. Sphynx: Workflow Diagram
    • Will allow developers
    • to take locally tested
    • copies of their
    • software and generate test
    • suites to verify
    • proper installations
    • on client machines.
    • Extensions allow developers to place code executions at various points in the life cycle.
    • A visual dashboard to report status of individual tests (in development)
  • 23. Porky Portlet :: Real-time job status monitoring On the Web: http://webis.msi.umn.edu/porky.php
    • Extend current workflow monitoring to add graphical representation of workflow status
    • Retrieve job status from databases or standardized workflow (XML) documents
    • Applications not just for job monitoring in grid applications, but any other field that utilizes workflows (i.e. Sphynx Unit Testing status).
    Example workflows monitored by Porky Portlet. Green indicates completed-, while Red represents services that have not finished executing.
  • 24. Yuen Collab On the Web: http://webis.msi.umn.edu/yuen_collab
    • Intuitive interface allowing easy multi-tasking
    • Use any software you like, modules are loaded in their own environment so virtually any software servable on the web will work!
    • Built in packages with research collaboration in mind.
    • Complete module management system to make administration a cinch
  • 25. Yuen Collab: Lightning Fast
    • Nobody wants to wait for slow pages to load
    • Ajax and preload technology allow pages to be served like they would on desktop applications by preloading them one on top of another.
  • 26. VLab: Conclusion
    • The VLab Portal – integrates the a simple web interface with powerful grid computing services
      • On the Web: http://dasilveira.msi.umn.edu:8080/vlab/
    • WATT – Automates the conversion of software, specifically for the internet.
      • On the Web: http://www.gorerle.com/vlab-wiki/index.php?title=WATT
    • Sphynx – Fast Web Interface test suites
      • On the Web: http://www.gorerle.com/vlab-wiki/index.php?title=Sphynx
    • AJAX – Bringing the Desktop experience to the Web
      • On the Web: http://www.gorerle.com/vlab-wiki/index.php?title=Ajax
    • Porky Portal – Real-time workflow monitoring system.
      • On the Web: http://www.gorerle.com/vlab-wiki/index.php?title=Porky_Portlet
    • Connecting Researchers – Emphasizing collaboration
      • On the Web: http://webis.msi.umn.edu/yuen_collab/