VLab (Virtual Laboratory for

Earth and Planetary Materials)

A Grid Facility for Computational Mineral Physics

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

Photographs

David A. YuenRenata

WentzcovitchGordon

Erlebacher

Martin F. Lyness

Evan F. Bollig

Pedro da Silveira Cesar

da Silva

Paul Jensen

Marlon Pierce

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.

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.

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/

The VLab Portalhttp://dasilveira.msi.umn.edu:8080/vlab/

Large scale molecular dynamics simulations through a simplified grid middleware

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

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

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.

Equation Of State, Elasticity (Cij) and Phonon Calculations

Example of workflow complexity

Monitoring Submissions

Job submissions to various nodes are monitored by a web interface.

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.

Novel Technologies

Emerging technologies being integrated into VLab

WATT: An Overview On the Web: http://www.gorerle.com/vlab-wiki/index.php?title=WATT

The Web Automation and Translation Toolkit (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.

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;”)

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

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

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.

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.

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

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)

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.

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

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.

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/