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Visualization at SDSC

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Title: Visualization at SDSC


1
Visualization at SDSC
  • AAP Workshop
  • March 6th 2007
  • Dr. Steve Cutchin

2
Tutorial Outline
  • 930 to 1000 Introduction
  •  What does Visualization Services Do?
  • 1010 to 1045 Successful examples
  • Terashake 5 minutes.
  • Puente Hills 5 minutes.
  • ENZO 5 minutes.
  • Pk Yeung Visualization. 3 minutes.
  • Cancer Center Imagery 4 minutes.
  • Development of Imaging Portal 5 minutes.
  • Hayden Emission Nebula Visualization 5 minutes.
  • 1045 to 1050 Problems we need help with 5
    minutes.
  • Point clouds
  • Unstructured Meshes
  • Other tools to install.
  • 1100 to 1200 Using visualization tools
  • Repeat list of tools - 5 minutes tops.
  • Gnuplot - 5 minutes.
  • Image Magick 5 minutes.
  • VISTA - 10 minutes.

3
(No Transcript)
4
Mission Statement
  • Advance Science through the creation and
    dissemination of high-quality explanatory
    visualizations.
  • Advance Visualization through creation of
    improved production tools and processes.

5
Strengths
  • Significant Rendering Resources
  • Significant storage resources.
  • Data management and distributed pipelines.
  • Very large renders IMAX or higher.
  • Excellent volume rendering tools.
  • Significant computer graphics expertise.
  • Significant Scientific Expertise
  • Access to a wide variety of scientific data and
    scientists.

6
The Earths Mantle
140Km
7
The Earths Mantle
8
Volume Visualizations
9




10
Molecular Visualizations
Work for Discovery Science Channel
11
Sample Visualizations
Universe Simulations
UCSD Cancer Center
12
Crystal Palace
13
Monuments and Dust The Culture of Victorian
London
14
Partners
15
Visualization Software
16
Development Environment
Trademark Microsoft Corp
17
Visualization Tools
  • VISTA Volume Renderer
  • MeshViewer Volume Viewer for the desktop
  • Maya animation package
  • Imagemagick Standard Image Package
  • Visit LLNL visualization tool.
  • Adobe Content Creation Suite
  • GIMP
  • VTK
  • RasMOL

18
Web Sites
  • http//visservices.sdsc.edu
  • http//www.sdsc.edu
  • http//www.syncenter.org

19
Terashake
20
Puente Hills Fault
21
Domefest Early Universe Render
www.domefest.com
22
Medical Visualization
23
Cancer Center Visualization
Images Animations Movies
Visualization Expertise
UCSD Cancer Center
Software Development
Research Intern
Computational Scientists
Medical Expertise
Visualization Tools
1 Research Scientist
Supercomputers
Latest Microscopy Tools
Shared Staff
Cancer Research Scientists
SDSC
Cancer Expertise
24
Hubble Space Telescope images of the Orion Nebula
and the HST-10 proplyd.
  • Volume Visualization of the Orion Nebula
  • The San Diego Supercomputer Center and The
    American Museum of Natural History Hayden
    Planetarium

25
Astronomical Visualization
Visualization of An Emission Nebulae from 3
Terabytes of Simulation Data Credits American
Museum of Natural History Dave Nadeau SDSC Erik
Engquist SDSC
26
We Need Some Help
  • Support for your data formats.
  • Point clouds.
  • Unstructured meshes.
  • ?????

27
Hands On Vis
  • Repeat list of tools - 5 minutes tops.
  • Gnuplot - 5 minutes.
  • Image Magick 5 minutes.
  • VISTA - 10 minutes.
  • Mpeg Encoding 5 minutes.
  • Tecplot - 10 minutes.
  • Paraview - 10 minutes.
  • QA Session - 15 minutes.

28
Visualization Tools on HPC
  • VISTA Volume Renderer
  • Maya animation package broken at moment.
  • Image Magick Standard Image Package
  • Visit LLNL visualization tool.
  • Tecplot
  • GIMP
  • VTK Visualization Toolkit.
  • Paraview
  • NCL NCAR Command Language.

29
Configure X-Windows
  • Set up X-Windows on your desktop
  • Then ssh to dslogin with X-Forwarding enabled.

30
Image Magick
  • Great command line image tools.
  • Well documented, well supported.
  • Great for piping, scripting, easily extensible.

31
Image Magick
  • Current version in /usr/local/apps32/imagemagick-
    6.2.8/bin
  • Add to your path.
  • Type convert to test
  • Web site www.imagemagick.org
  • Formats www.imagemagick.org/script/formats.php

32
ImageMagick Commands
  • Ex convert magickrose rose.jpg
  • Convert change formats, change various params.
  • Composite combine images together.
  • Animate animate series.jpg
  • Display display images.jpg…
  • Montage creates a thumbnail sheet.
  • conjure …..script engine . Magic scripting
    language.
  • Others compare, identify, import, mogrify…

33
GnuPlot
  • www.gnuplot.info
  • A free GNU tool.
  • Supports 2D 3D Plotting.
  • Very feature rich.
  • Command line usage.
  • Great for quick and dirty plots and text.

34
GnuPlot
  • Path /usr/local/apps/gnuplot-4.0.0/
  • Interactive visualization
  • Ex gnuplot simple.gpl
  • Write image to a file
  • Change the terminal set terminal postscript
  • gnuplotgt set terminal postscript color solid
  • gnuplotgt set output outfile.ps
  • gnuplotgt load simple.gpl
  • gnuplotgt set output
  • gnuplotgt set terminal pop

35
GnuPlot
  • Simple 2D Plot
  • Basic 3D Plot
  • Adding Text
  • Formatting Text
  • Parsing data files
  • More web help www……org

36
VISTA
  • SDSC Built
  • Volume Renderer
  • Command line driven.
  • Lots of options.
  • visservices.sdsc.edu/software/vista/
  • Supports HDR output.

http//visservices.sdsc.edu/software/vista
37
VISTA
  • /gpfs/projects/vis/vistools/bin
  • vista help for list of options.
  • vista raw 512 512 512 monkey_512by3.raw
  • vista raw 512 512 512 minmax -33553920.0
    33554688.0 monkey_512by3.raw
  • display img_00000.ppm

38
VISTA Terashake Example
  • vista lsb raw 40 150 300 rawtype float
    minmax -0.1 0.1 tshake/tshake.05800.raw
  • Recolor vista … --bigspect…
  • Cameras vista … -left right front cam
    camfile…
  • Sizing vista … -r 0.2 0.45 0.8 ….
  • Custom cam vista cam tshake/tshake.cam
  • Colormaps vista …. tmapfile …
  • Format types vista rawtype float int short
    byte…

39
MPEG Creation
  • /usr/local/apps32/mpeg2vidcodec/
  • Take a series of images and generate a simple
    mpeg 1 stream.
  • Good for images at 640x480 resolution.
  • Command line driven.
  • Useful but poor encoding.
  • Best solution offload.
  • http//www.mpeg.org/MPEG/MSSG/
  • Docs are in install directory on datastar.

40
MPEG Creation
  • Path /usr/local/apps32/mpeg2vidcodec/bin
  • Example mpeg2vidcodec …..
  • Uses a .par file.
  • Input format .ppm
  • Set file names, file formats, number of frames.
  • Best used for rough quick and dirty.
  • Not particularly good.
  • No gold standard solutions exist on HPC systems.

41
Tecplot
  • Commercial product.
  • Our users can use it.
  • Excellent tool.
  • GUI based.
  • Very popular and effective.
  • Takes a bit to get started.
  • Supports command line processing.

42
Tecplot
  • In path /usr/local/apps/tecplot/bin
  • setenv TECHOME /usr/local/apps/tecplot
  • setenv TLMHOST dmv.sdsc.edu
  • tecplot
  • Run simple example in tecplot.
  • Batch mode
  • Tecplot batchscript….
  • Display output image
  • www.tecplot.com for lots and lots of support.

43
Tecplot
  • How to output image to a file.
  • How do I get my own data into the tool?
  • What formats does it handle?
  • What are its biggest features?

44
Paraview
  • OpenSource tool.
  • Well supported.
  • Common in HPC
  • Uses VTK
  • Mostly designed for programmers by programmers.
  • www.paraview.org

45
Paraview
  • Path /usr/local/apps32/paraview-2.2.1/
  • Interactive paraview
  • Can load a variety of data formats including
    unstructured and point clouds.
  • Supports client/server mode pserver
  • Run client locally.

http//visservices.sdsc.edu/tools/paraview/paravie
w.html
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