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Visualization at SDSC

Visualization at SDSC. AAP Workshop March 6 th 2007 Dr. Steve Cutchin. Tutorial Outline. 9:30 to 10:00 Introduction  What does Visualization Services Do? 10:10 to 10:45 Successful examples Terashake – 5 minutes. Puente Hills – 5 minutes. ENZO – 5 minutes.

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Visualization at SDSC

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

  2. Tutorial Outline • 9:30 to 10:00 Introduction •  What does Visualization Services Do? • 10:10 to 10:45 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. • 10:45 to 10:50 Problems we need help with: 5 minutes. • Point clouds • Unstructured Meshes • Other tools to install. • 11:00 to 12:00 Using visualization tools • 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. • Q&A Session - 15 minutes.

  3. Mission Statement • Advance Science through the creation and dissemination of high-quality explanatory visualizations. • Advance Visualization through creation of improved production tools and processes.

  4. 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.

  5. The Earth’s Mantle 140Km

  6. The Earth’s Mantle

  7. Volume Visualizations

  8. Molecular Visualizations Work for Discovery Science Channel

  9. Sample Visualizations Universe Simulations UCSD Cancer Center

  10. Crystal Palace

  11. Monuments and Dust:The Culture of Victorian London

  12. Partners

  13. Visualization Software

  14. Development Environment Trademark Microsoft Corp

  15. 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

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

  17. Terashake

  18. Puente Hills Fault

  19. www.domefest.com Domefest Early Universe Render

  20. Medical Visualization

  21. 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

  22. Volume Visualization of the Orion Nebula The San Diego Supercomputer Center andThe American Museum of Natural History Hayden Planetarium Hubble Space Telescope images of the Orion Nebula and the HST-10 proplyd.

  23. 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

  24. We Need Some Help • Support for your data formats. • Point clouds. • Unstructured meshes. • ?????

  25. 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. • Q&A Session - 15 minutes.

  26. 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.

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

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

  29. 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

  30. ImageMagick Commands • Ex: convert magick:rose 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…

  31. 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.

  32. 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 • gnuplot> set terminal postscript color solid • gnuplot> set output “outfile.ps“ • gnuplot> load ‘simple.gpl’ • gnuplot> set output • gnuplot> set terminal pop

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

  34. 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

  35. 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

  36. 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…

  37. 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.

  38. 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.

  39. 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.

  40. 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.

  41. 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?

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

  43. 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/paraview.html

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