Visualization at Visualization at SDSCSDSC

Dr. Steve CutchinDr. Steve Cutchin

The Earth’s MantleThe Earth’s Mantle

140Km

The Earth’s MantleThe Earth’s Mantle

Volume VisualizationsVolume Visualizations

Molecular VisualizationsMolecular Visualizations

Work for Discovery Science Channel

Sample VisualizationsSample Visualizations

UCSD Cancer Center Universe Simulations

Crystal PalaceCrystal Palace

Monuments and Dust:The Culture of Victorian London

Visualization ToolsVisualization Tools VISTA Volume RendererVISTA Volume Renderer MeshViewer Volume Viewer for the MeshViewer Volume Viewer for the

desktopdesktop Maya animation packageMaya animation package Imagemagick – Standard Image PackageImagemagick – Standard Image Package Visit – LLNL visualization tool.Visit – LLNL visualization tool. Adobe Content Creation SuiteAdobe Content Creation Suite GIMPGIMP VTKVTK RasMOLRasMOL

Web SitesWeb Sites

http://visservices.sdsc.eduhttp://visservices.sdsc.edu http://www.sdsc.eduhttp://www.sdsc.edu http://www.syncenter.orghttp://www.syncenter.org

TerashakeTerashake

Puente Hills FaultPuente Hills Fault

Domefest Early Universe Domefest Early Universe RenderRender

www.domefest.com

Medical VisualizationMedical Visualization

Cancer Center Cancer Center VisualizationVisualization

Visualization Expertise

Supercomputers

Software Development

Visualization Tools

Shared Staff

SDSC

UCSD Cancer Center

Cancer Expertise

Medical Expertise

Latest Microscopy Tools

Cancer Research Scientists

Computational ScientistsResearch Intern

1 Research Scientist

ImagesAnimationsMovies

Volume Visualization of the Orion NebulaVolume Visualization of the Orion Nebula

The San Diego Supercomputer Center andThe San Diego Supercomputer Center andThe American Museum of Natural History Hayden PlanetariumThe American Museum of Natural History Hayden Planetarium

Hubble Space Telescope images of the Orion Nebula and the HST-10 proplyd.

Astronomical Astronomical VisualizationVisualization

Visualization ofAn Emission Nebulae from 3 Terabytes of Simulation DataCredits:American Museum of Natural HistoryDave Nadeau SDSCErik Engquist SDSC

Hands On VisHands On Vis

Repeat list of tools - 5 minutes tops.Repeat list of tools - 5 minutes tops. Gnuplot - 5 minutes.Gnuplot - 5 minutes. Image Magick – 5 minutes.Image Magick – 5 minutes. VISTA - 10 minutes.VISTA - 10 minutes. Mpeg Encoding – 5 minutes.Mpeg Encoding – 5 minutes. Tecplot - 10 minutes. Tecplot - 10 minutes. Paraview - 10 minutes.Paraview - 10 minutes. Q&A Session - 15 minutes.Q&A Session - 15 minutes.

Visualization Tools on Visualization Tools on HPCHPC

VISTA Volume RendererVISTA Volume Renderer Maya animation package – broken at Maya animation package – broken at

moment.moment. Image Magick – Standard Image PackageImage Magick – Standard Image Package Visit – LLNL visualization tool.Visit – LLNL visualization tool. TecplotTecplot GIMPGIMP VTK – Visualization Toolkit.VTK – Visualization Toolkit. ParaviewParaview NCL – NCAR Command Language.NCL – NCAR Command Language.

Configure X-WindowsConfigure X-Windows

Set up X-Windows on your desktopSet up X-Windows on your desktop Then ssh to dslogin with X-Then ssh to dslogin with X-

Forwarding enabled.Forwarding enabled. Source Source

/gpfs/projecsts/vis/cutchin/paths/gpfs/projecsts/vis/cutchin/paths

Image MagickImage Magick

Great command Great command line image tools.line image tools.

Well documented, Well documented, well supported.well supported.

Great for piping, Great for piping, scripting, easily scripting, easily extensible.extensible.

Image MagickImage Magick

Current version in: Current version in: /usr/local/apps32/imagemagick-6.2.8/bin/usr/local/apps32/imagemagick-6.2.8/bin

Add to your path.Add to your path. Type %convert to testType %convert to test Web site: www.imagemagick.orgWeb site: www.imagemagick.org Formats: Formats:

www.imagemagick.org/script/formats.phpwww.imagemagick.org/script/formats.php Bug: /opt/freeware/bin/display,animateBug: /opt/freeware/bin/display,animate

ImageMagick CommandsImageMagick Commands

Ex: convert magick:rose rose.jpgEx: convert magick:rose rose.jpg Convert: change formats, change various Convert: change formats, change various

params.params. Composite: combine images together.Composite: combine images together. Animate: animate series*.jpgAnimate: animate series*.jpg Display: display images*.jpg…Display: display images*.jpg… Montage: creates a thumbnail sheet.Montage: creates a thumbnail sheet. conjure: …..script engine . Magic scripting conjure: …..script engine . Magic scripting

language.language. Others: compare, identify, import, mogrify…Others: compare, identify, import, mogrify…

GnuPlotGnuPlot

www.gnuplot.infowww.gnuplot.info A free GNU tool.A free GNU tool. Supports 2D & 3D Supports 2D & 3D

Plotting.Plotting. Very feature rich.Very feature rich. Command line Command line

usage.usage. Great for quick and Great for quick and

dirty plots and text.dirty plots and text.

GnuPlotGnuPlot Path: /usr/local/apps/gnuplot-4.0.0/ Path: /usr/local/apps/gnuplot-4.0.0/ Interactive visualization:Interactive visualization:

Ex: gnuplot simple.gplEx: gnuplot simple.gpl Write image to a file:Write image to a file:

Change the terminal: set terminal postscriptChange the terminal: set terminal postscript gnuplot> set terminal postscript color solidgnuplot> set terminal postscript color solid gnuplot> set output “outfile.ps“gnuplot> set output “outfile.ps“ gnuplot> load ‘simple.gpl’gnuplot> load ‘simple.gpl’ gnuplot> set outputgnuplot> set output gnuplot> set terminal pop gnuplot> set terminal pop

GnuPlotGnuPlot

Simple 2D Plot:Simple 2D Plot: Basic 3D Plot:Basic 3D Plot: Adding Text:Adding Text: Formatting Text:Formatting Text: Parsing data files:Parsing data files: More web help: www……orgMore web help: www……org

VISTAVISTA

SDSC BuiltSDSC Built Volume RendererVolume Renderer Command line Command line

driven.driven. Lots of options.Lots of options. visservices.sdsc.edvisservices.sdsc.ed

u/software/vista/u/software/vista/ Supports HDR Supports HDR

output.output.http://visservices.sdsc.edu/software/vista

VISTAVISTA

/gpfs/projects/vis/vistools/bin/gpfs/projects/vis/vistools/bin %vista –help for list of options.%vista –help for list of options. %vista –raw 512 512 512 %vista –raw 512 512 512

monkey_512by3.raw monkey_512by3.raw %vista –raw 512 512 512 –minmax -%vista –raw 512 512 512 –minmax -

33553920.0 33554688.0 33553920.0 33554688.0 monkey_512by3.raw monkey_512by3.raw

%display img_00000.ppm%display img_00000.ppm

VISTA Terashake VISTA Terashake ExampleExample

%vista –lsb –raw 40 150 300 –rawtype float –%vista –lsb –raw 40 150 300 –rawtype float –minmax -0.1 0.1 tshake/tshake.05800.rawminmax -0.1 0.1 tshake/tshake.05800.raw

Recolor: vista … --bigspect…Recolor: vista … --bigspect… Cameras: vista … -left –right –front –cam Cameras: vista … -left –right –front –cam

camfile…camfile… Sizing: vista … -r 0.2 0.45 0.8 ….Sizing: vista … -r 0.2 0.45 0.8 …. Custom cam: vista –cam tshake/tshake.camCustom cam: vista –cam tshake/tshake.cam Colormaps: vista …. –tmapfile …Colormaps: vista …. –tmapfile … Format types: %vista –rawtype float | int | Format types: %vista –rawtype float | int |

short | byte…short | byte…

MPEG CreationMPEG Creation /usr/local/apps32/mpeg2vidcodec/ /usr/local/apps32/mpeg2vidcodec/ Take a series of images and generate a Take a series of images and generate a

simple mpeg 1 stream.simple mpeg 1 stream. Good for images at 640x480 resolution.Good for images at 640x480 resolution. Command line driven.Command line driven. Useful but poor encoding.Useful but poor encoding. Best solution: offload.Best solution: offload. http://www.mpeg.org/MPEG/MSSG/http://www.mpeg.org/MPEG/MSSG/ Docs are in install directory on datastar.Docs are in install directory on datastar.

MPEG CreationMPEG Creation

Path: /usr/local/apps32/mpeg2vidcodec/binPath: /usr/local/apps32/mpeg2vidcodec/bin Example: mpeg2vidcodec …..Example: mpeg2vidcodec ….. Uses a .par file.Uses a .par file. Input format .ppmInput format .ppm Set file names, file formats, number of Set file names, file formats, number of

frames.frames. Best used for rough quick and dirty.Best used for rough quick and dirty. Not particularly good.Not particularly good. No gold standard solutions exist on HPC No gold standard solutions exist on HPC

systems.systems.

TecplotTecplot

Commercial product.Commercial product. Our users can use it.Our users can use it. Excellent tool.Excellent tool. GUI based.GUI based. Very popular and Very popular and

effective.effective. Takes a bit to get Takes a bit to get

started.started. Supports command Supports command

line processing.line processing.

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

support.support.

TecplotTecplot

How to output image to a file.How to output image to a file. How do I get my own data into the How do I get my own data into the

tool?tool? What formats does it handle?What formats does it handle? What are its biggest features?What are its biggest features?

ParaviewParaview

OpenSource tool.OpenSource tool. Well supported.Well supported. Common in HPCCommon in HPC Uses VTKUses VTK Mostly designed Mostly designed

for programmers for programmers by programmers.by programmers.

www.paraview.orgwww.paraview.org

ParaviewParaview

Path: /usr/local/apps32/paraview-Path: /usr/local/apps32/paraview-2.2.1/ 2.2.1/

Interactive %paraviewInteractive %paraview Can load a variety of data formats Can load a variety of data formats

including unstructured and point including unstructured and point clouds.clouds.

Supports client/server mode: pserverSupports client/server mode: pserver Run client locally.Run client locally.http://visservices.sdsc.edu/tools/paraview/paraview.html