TeraGrid Visualization Tutorial

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TeraGrid Visualization Tutorial

• TeraGrid 2007
• June 4, 2007

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Tutorial Schedule (Morning)

• 830 900 Introduction and Open Discussion
• What is the purpose of the tutorial?
• What are attendees hoping to gain from the
  tutorial?
• Have you tried using TG vis resources
  previously?
• What is good about TG vis resources and what is
  missing?
• 900 1000 Overview of TG Visualization
  Resources
• Mission and Vision
• Hardware Resources
• General Visualization Applications that Users
  Can Expect
• Custom Applications Being Built
• TeraGrid Visualization Gateway
• 1000 1030 Break
• 1030 1115 TeraGrid Visualization Gateway
  Hands-On
• 1115 1200 Discussion Session about Users
  Data
• Discuss What Attendees Data Looks Like
• Discuss and Evaluate Potential Applications

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Tutorial Schedule (Afternoon)

• 1200 - 130 Lunch
• 130 300 Interactive Visualization Examples
• EnVision
• Hand On Visualization Examples
• 300 - 330 Break
• 330 - 430 Hands On Session
• 430 - 500 Wrap Up and Discussion

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Introduction and Open Discussion

• What is the purpose of the tutorial?
• What are attendees hoping to gain from the
  tutorial?
• Have you tried using TG vis resources
  previously?
• What is good about TG vis resources and what is
  missing?

5
Overview of TeraGrid Visualization Resources
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TeraGrid Vision

• TeraGrid is a national production
  cyberinfrastructure facility whose vision is to
  create integrated, persistent, and pioneering
  computational resources that will significantly
  improve our nations ability and capacity to gain
  new insights into our most challenging research
  questions and societal problems.
• This vision requires an integrated approach to
  the entire scientific workflow including
  obtaining access, application development and
  execution, data analysis, collaboration and data
  management.

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TeraGrid Objectives

• DEEP Science Enabling Petascale Science
• Make Science More Productive through an
  integrated set of very-high capability resources
• Address key challenges prioritized by users
• WIDE Impact Empowering Communities
• Bring TeraGrid capabilities to the broad science
  community
• Partner with science community leaders - Science
  Gateways
• OPEN Infrastructure, OPEN Partnership
• Provide a coordinated, general purpose, reliable
  set of services and resources
• Partner with campuses and facilities

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What Role Does Visualization and Data Analysis
Play in the TeraGrid?

• We focus explicitly on data movement, data
  management, data collections and visualization as
  value added services that enhance and compliment
  the core capabilities of the TeraGrid.
• Visualization is managed through the
  Visualization Working Group and provides
  resources and services to the user community.
• Data Movement and data management are managed
  through the Data Working Group that deploys
  services and tools through the Common TeraGrid
  Software Stack (CTSS)
• Data Collections are relatively new to the
  TeraGrid and are managed through a newly formed
  Data Collections Working Group that define the
  provision, growth and expansion of data
  collections as resources provided by the TeraGrid.

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TeraGrid Visualization Strategy and Mission

• Combine existing resources and current
  technology
• Commodity clusters and commodity graphics
• Terascale visualization clusters
• Grid technology
• Efforts, expertise, and tools from each of the TG
  sites
• to enable new and novel ways of visually
  interacting with and gaining insight into science
  through the analysis of simulations and data.
• TeraGrid deploys 2 visualization resources, but
  has 9 resource provider sites that do active
  visualization for the TeraGrid user community.
• TeraGrid also deploys visualization resources for
  batch, interactive, and collaborative
  visualization.

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TeraGrid Visualization Software Stack (VTSS)
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TeraGrid Areas of Interest and Expertise

• Purdue University (Purdue)
• Remote batch rendering
• Remote interactive visualization
• Hardware-assisted remote rendering
• San Diego Supercomputer Center (SDSC)
• Visualization web services
• Volume rendering
• Remote rendering
• High definition resolution visualization
• Texas Advanced Computing Center (TACC)
• Remote and collaborative visualization
• Large data visualization
• Feature detection
• The University of Chicago / Argonne National
  Laboratory (UC/ANL)
• Visualization, analysis, and collaboration
  services
• Remote rendering
• Hardware-assisted volume rendering

• Indiana University (IU)
• Distributed software rendering
• Data repository and visualization integration
• National Center for Atmospheric Research (NCAR)
• Analysis tools
• Multiresolution rendering of large data
• Volume rendering
• Domain specific tools
• National Center for Supercomputing Applications
  (NCSA)
• High definition resolution visualization
• Volume rendering
• Visualization web services
• Oak Ridge National Laboratory (ORNL)
• Visualization of experimental data collected from
  spallation neutron source
• Pittsburgh Supercomputing Center (PSC)
• Simulation-time Visualization with hardware
  rendering directly tied in to the supercomputer

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TeraGrid Visualization Hardware Resources

• University of Texas at Austin/Texas Advanced
  Computing Center (TACC) Visualization Resource
• Large, shared memory machine with 512 GB of
  shared memory and 16 dual out commodity graphics
  cards
• Uses VNC as a means for remote/collaborative
  visualization
• Enables any third party visualization package
  that uses OpenGL such as
• Paraview
• EnSight
• Amira
• VMD
• University of Chicago/Argonne National Lab
  Visualization Resource
• Cluster configuration, 96 visualization nodes, 62
  compute nodes
• Focused on a solution that provides a
  client-server visualization mechanism through the
  use of Paraview

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UT/TACC Visualization Resource
Sun Microsystems E25K Server 64 Dual Core
UltraSparc IV Processors 512GB Shared Memory
High Performance Fiber Channel Interconnect
High Performance Gigabit Ethernet
Sun Microsystems V890 Login 8 Dual Core
UltraSparc IV Processors 32GB of Shared Memory
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UC/ANL Visualization Resource
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Last Years Future

• Development and deployment of community access
  environment to the TeraGrid Visualization
  Gateway. (Paper Presentation Tomorrow)
• Integration of visualization gateway efforts
  into a single unified solution. (Will be
  viz.teragrid.org)
• Development and deployment of hardware-based
  volume rendering service.
• Integration of Access Grid client into TeraGrid
  Visualization Gateway for collaborative viewing
  and interaction.
• Recruit visualization community to contribute to
  and use the TeraGrid Visualization Gateway. (See
  Purdues TeraDRE)

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Next Years Future

• Continued development and deployment of
  community access environment to the TeraGrid
  Visualization Gateway. (Will be viz.teragrid.org)
• Continued development and deployment of
  hardware-based volume rendering service.
• Continued integration of Access Grid client into
  TeraGrid Visualization Gateway for collaborative
  viewing and interaction. (Dependent on funding)
• Recruit visualization community to contribute to
  and use the TeraGrid Visualization Gateway.
• Renewed focus and effort of the TeraGrid
  visualization working group.
• Investigation of visualization resources for
  Petascale datasets.

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More TeraGrid Visualization Content

• Tuesday, June 5
• Paper - 330 - 400PM
• Chris Gilpin - Visualizing Electron Microscope
  Reconstructions Using TeraGrid Resources
• Paper - 400 - 430PM
• Enabling Science Through The TeraGrid
  Visualization Gateway
• Posters - Tuesday Night 630 - 830
• TeraGrid Visualization Overview
• TACC RP Pylon ? Tuesday Evening
• The University of Chicago RP Pylon ? Posters

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Types of Accounts on TeraGrid Resources
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Getting an Account on TeraGrid Resources

• Goto https//pops-submit.ci-partnership.org
• Fill out an application for a DAC allocation
• You will be given 10K SUs on TG machines.

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BreakBack at 1030
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TeraGrid Visualization Gateway
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Discussion Session about Users Data

• Attendees Data
• Discuss and Evaluate Potential Applications

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LUNCHWe will resume at 130
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Interactive Visualization Session
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EnVision

• Google Maps for general purpose scientific
  visualizations
• Goal drastically simplify the visualization
  process via semi-automation of data importation,
  rendering algorithm selection
• Make visualization accessible to non-experts and
  casual users while offering compelling new
  capability for expert users
• Use remote visualization model to enable new
  capability versus repackaging existing
  visualization software

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Starting Visualization Jobs on Maverick
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Example Scripts in /usr/local/qsub
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Qsub script to start an xterm
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Turbo VNC http//virtualgl.sourceforge.net
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Before running any job set up your vnc password
by typing vncpasswd at the command line prompt
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Visualizing Electron Microscopy Data
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Electron Microscopy Data Dr. Christopher Gilpin

• Data in raw binary format. Use a script to
  create .case file
• Create isosurface using Isosurface button (7th
  from left)
• Data is at fine granularity, so use Reduce
  Polygons option before launching isosurface
  creation (see next slide)This makes surface more
  manageable.

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Electron Microscopy Data Dr. Christopher Gilpin
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Electron Microscopy Data Dr. Christopher Gilpin

• ParaView can open .case file directly
• Create isosurface with Contour button (on top,
  9th from left)
• Apply a Decimate filter to reduce the amount of
  geometry in the isosurface
• Apply a Smooth filter to reduce surface
  artifacts

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Electron Microscopy Data Dr. Christopher Gilpin
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Visualizing Computational Fluid Dynamics (CFD)
Data
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Running EnSight on maverick

• By default, EnSight runs 8 client and 8 server
  threads
• To change the default, load module then
• export ENSIGHT8_MAX_THREADS 1..128 (server)
• export ENSIGHT8_MAX_CTHREADS 1..128 (client)
• Executable command vglrun ensight8
  (vglrun maps OpenGL to X-windows)
• Separate client-server commands
• ensight80.server ltserver optsgt
• ensight80.client ltclient optsgt

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CFD Data Dr. George Karniadakis

• Data originally in many small ParaView files
• Wrote script to aggregate filesLoad time shrank
  from hours to seconds (!!!)
• Left shows single color (change with Actor
  Color button)
• Right shows color by Pressure variable(select in
  Color by menu)

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CFD Data Dr. George Karniadakis

• Data originally not visible when loaded
• Use View-gt3D View Properties from main menu
• Select Camera tab, click a standard view
  button(Left shows X view) (Right shows Y
  view)
• Select General tab and Use Light Kit for
  advanced lighting features
• Use File-gtSave Data to save data as EnSight
  Case

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CFD Data Dr. George Karniadakis

• Load .case file in EnSight loaded as wireframe
• To create shaded surface
• select part in case menu(upper left corner)
• select shading by pressure(paint can icon on
  left)
• select full geometry representation(Rubiks cube
  icon on left)
• use shaded surfaces(sun icon on top)

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CFD Data Dr. George Karniadakis
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CFD Data Dr. George Karniadakis

• Export from ParaView saves only single timestep
• Must save individual timesteps and integrate into
  case file for animation support
• See EnSight user guide for details