VisIt Visualization Tool - University of Chicagoflash.uchicago.edu/.../June2009/Visit_9.pdf ·...
Transcript of VisIt Visualization Tool - University of Chicagoflash.uchicago.edu/.../June2009/Visit_9.pdf ·...
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An Advanced Simulation and Computing (ASC) Academic Strategic Alliances Program (ASAP) Center
at The University of Chicago
The Center for Astrophysical Thermonuclear Flashes
VisIt Visualization Tool
Randy Hudson [email protected]
Argonne National Laboratory Flash Center, University of Chicago
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Tutorial
❑ Lecture ❑ Practice
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Lecture
❑ About VisIt ❑ Using VisIt
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
About VisIt
❑ Developed by DOE’s Advanced Simulation & Computing Initiative
❑ Continued by DOE’s Office of Nuclear Energy, ASC and Office of Science
❑ Free, open-source ❑ Built upon VTK (which is built upon OpenGL)
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
About VisIt
❑ Documentation ❑ Features ❑ Platforms ❑ Support
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
VisIt: documentation
❑ Online at https://wci.llnl.gov/codes/visit/manuals.html ❑ Not new ❑ Very useful ❑ “VisIt Getting Started Manual”
❑ Two tutorials ❑ Basics ❑ Running remotely
❑ Appendix of command-line options ❑ “Getting Data into VisIt”
❑ Creating compatible files ❑ Creating a reader plug-in ❑ Instrumenting simulation code
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
VisIt: documentation
❑ Online, cont. ❑ “VisIt User’s Manual”
❑ Using VisIt ❑ “VisIt Python Interface Manual”
❑ Writing Python scripts to control VisIt ❑ More at https://wci.llnl.gov/codes/visit/doc.html ❑ Many tips at https://wci.llnl.gov/codes/visit/FAQ.html
❑ “On board” ❑ Newer ❑ Menu: Help → Help…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
VisIt: features
❑ 1d, 2d, 3d data ❑ Meshes
❑ Structured & unstructured ❑ Regular grids
❑ Parallel, distributed (client-server) ❑ Data and visualization remote ❑ Rendering remote or local
❑ Singular, local ❑ Data, visualization, rendering local
❑ Rendering in software or hardware ❑ Handles files of several GB
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
VisIt: platforms
❑ Executables of current release for ❑ Several Windows ❑ OSX 10.4 (& 10.5): PPC, Intel ❑ Several Linuxen ❑ AIX 5.3
❑ Older releases, other platforms at https://wci.llnl.gov/codes/visit/executables.html
❑ Can build from source
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
VisIt: support
❑ Mailing lists ❑ General community support: [email protected] ❑ Special others: http://visitusers.org/index.php?title=MailingLists ❑ VisIt-development group is very helpful
❑ Wiki ❑ http://visitusers.org
❑ Occasional patches from me, as needed ❑ http://flash.uchicago.edu/website/codesupport/visit/
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Using VisIt
❑ Starting VisIt ❑ Settings ❑ Opening files ❑ Visualizing data (plots & operators) ❑ Colormapping ❑ Quantitative analysis ❑ Writing output ❑ Client-server ❑ Python ❑ Animation
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Starting VisIt (GUI)
❑ Command line examples ❑ visit -debug <n> ❑ visit -assume_format FLASH
❑ OSX, Linux, Unix: recommend ❑ Set PATH to visit directory ❑ cd to data directory ❑ Run visit
❑ OSX 10.4: X11 ❑ Windows
❑ Icon, command line, program menu ❑ Non-GUI alternatives
❑ Python command-line interface (CLI) ❑ Python script
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Settings : adjusting & saving
❑ Make changes in these ❑ Preferences ❑ File menu ❑ Controls menu ❑ Options menu ❑ Plot Attributes menu ❑ Operator Attributes menu
❑ Menu: Options → Save Settings ❑ (Might require repetition)
❑ New settings should be permanent with restart
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Preferences
❑ Mac ❑ Menu: VisIt → Preferences…
❑ XP & Linux ❑ Menu: Options → Preferences…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Preferences
❑ A few global settings:
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
File menu
❑ Saving and printing ❑ Each function requires a
pair of menu items
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Controls menu
❑ Controls ❑ A few of these later
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Options menu
❑ Appearance, rendering, plugins ❑ Save Settings
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Options: rendering
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Opening files - this directory
❑ In Selected files panel of main window ❑ Double-click file name ❑ Or…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Opening files - other directory
❑ Open File open dialog with one of ❑ Key: O ❑ Menu: File → Open file …
❑ In File open dialog, go to directory here or here
❑ Double-click file name ❑ Can group files
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Opening files - by format
❑ In File open dialog ❑ Select FLASH before
opening
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Visualizing data
❑ Plots and operators ❑ Plots are chosen first ❑ Operators operate first
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Visualizing data
❑ Plots ❑ Data or meshes, mapped
to shapes or colors ❑ Read data from file ❑ Displayed in
“visualization” windows (also “the viewer”) on the local machine
❑ Which plots appear on the menu is under user control
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Visualizing data
❑ Operators ❑ Subsets of data or
meshes, selected for plotting
❑ Which operators appear on the menu is under user control
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Visualizing data
❑ Scalar data: examples ❑ 1d data
❑ Curve plot ❑ Cut Plane ❑ Isosurface
❑ Colored by same variable ❑ Colored by other variable
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Scalar data - 1d data
❑ Menu: Plots → Curve → <varname> ❑ Optional settings change
❑ Menu: Plot Attributes → Curve…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Scalar data - cut plane
❑ Menu: Plots → Pseudocolor → <varname> ❑ Menu: Operators → Slice ❑ Optional settings change
❑ Menu: Plot Attributes → Pseudocolor… ❑ Menu: Operator Attributes → Slice…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Isosurface - same variable
❑ Menu: Plots → Contour → <varname> ❑ Optional settings change
❑ Menu: Plot Attributes → Contour…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Isosurface - other variable
❑ Menu: Plots → Pseudocolor → <varname>
❑ Menu: Operators → Isosurface ❑ Required settings change
❑ Menu: Operator Attributes → Isosurface…
❑ Change Variable
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Isosurface - other variable
❑ Optional settings change ❑ Menu: Operator Attributes →
Isosurface…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Visualizing data
❑ Vector data: examples ❑ (Read vector data set) ❑ (Define vector from input scalars) ❑ Glyphs ❑ Streamlines
❑ As tubes ❑ As lines
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Vector data - define vector
❑ Menu: Controls → Expressions…
❑ Define <vectorvarname> as Vector Mesh Variable with {<xname>,<yname>,<zname>}
❑ Check Show variable in plot menus
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Vector data - glyphs
❑ Menu: Plots → Vector → <vectorvarname>
❑ Optional settings change ❑ Menu: Plot Attributes →
Vector…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Vector data - streamlines
❑ Add Streamline plugin to Plot menu ❑ Menu: Options → Plugin
Manager … ❑ Plots tab: click Streamline ❑ Menu: Options → Save
Settings ❑ Restart VisIt
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Streamlines - as tubes
❑ Menu: Plots → Streamline → <vectorvarname>
❑ Required settings change ❑ Menu: Plot Attributes → Streamline… ❑ On Appearance tab, select Tubes
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Streamlines - as tubes
❑ Optional settings change ❑ Menu: Plot Attributes →
Streamline…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Streamlines - as lines
❑ Menu: Plots → Streamline → <vectorvarname> ❑ Required settings change
❑ Menu: Plot Attributes → Streamline… ❑ On Appearance tab, select Lines
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Streamlines - as lines
❑ Optional settings change ❑ Menu: Plot Attributes →
Streamline…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Visualizing data
❑ Particle data: examples ❑ Pseudocolor ❑ Cut Plane ❑ Isosurface ❑ Volume rendering ❑ Particle tracks
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Particle data - pseudocolor
❑ Menu: Plots → Pseudocolor → <varname> ❑ Optional settings change
❑ Menu: Plot Attributes → Pseudocolor…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Particle data - cut plane
❑ Menu: Plots → Pseudocolor → <varname> ❑ Menu: Operators → Resample ❑ Menu: Operators → Slice ❑ Optional settings change
❑ Menu: Plot Attributes → Pseudocolor… ❑ Menu: Operator Attributes → Resample… ❑ Menu: Operator Attributes → Slice…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Particle data - isosurface
❑ Menu: Plots → Pseudocolor → <varname> ❑ Menu: Operators → Resample ❑ Menu: Operators → Isosurface ❑ Optional settings change
❑ Menu: Plot Attributes → Pseudocolor… ❑ Menu: Operator Attributes → Resample … ❑ Menu: Operator Attributes → Isosurface…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Particle data - volume rendering
❑ Menu: Plots → Pseudocolor → <varname> ❑ Menu: Operators → Volume ❑ (Implicit resampling) ❑ Optional settings change
❑ Menu: Plot Attributes → Pseudocolor… ❑ Menu: Operator Attributes → Volume…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Particle data - particle tracks
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Colormapping
❑ Pseudocolor (seen earlier) ❑ Custom color table ❑ (Truecolor takes color from color vector in dataset)
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Custom color table
❑ Menu: Controls → Color table…
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Quantitative Analysis
❑ Of data ❑ Samples at points ❑ Samples in cells ❑ Samples along lines
❑ Of meshes ❑ Size (area, volume) ❑ Number elements
❑ Via expressions: derived data
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Quantitative Analysis
❑ Zone Pick: cell the pick point falls in ❑ Node Pick: nearest node of data set
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Data analysis - points & cells
❑ Create isosurface ❑ Select visualization window ❑ Click on “zone pick” or “node pick”
button: ❑ Click somewhere on plot
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Data analysis - points & cells
❑ Picked points are displayed in visualization window
❑ Pick panel displays data at picked points
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Data analysis - along line
❑ Create, e.g., Pseudocolor plot ❑ Menu: Controls → Query… ❑ In Queries list of Query panel
❑ Select Lineout ❑ Select visualization window ❑ Click on “line tool” button:
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Data analysis - along line
❑ A “widget” ❑ Line tool controls
sampling line ❑ Change the line tool via
its red control points to change the sampling line
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Data analysis - along line
❑ Curve is displayed in a visualization window
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Mesh analysis
❑ Menu: Controls → Query…
❑ Select a query ❑ Click query button
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Data analysis and synthesis
❑ Expressions: function
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Data analysis and synthesis
❑ Expressions: output variable
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Data analysis and synthesis
❑ Expressions: input variable
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Writing output
❑ Hardcopy ❑ Image ❑ Geometry ❑ Export database ❑ Animation
❑ (Animations can be saved, but I don’t cover that in these slides)
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Output - hardcopy
❑ Hardcopy of visualization window ❑ Menu: File → Set Print options…
❑ Menu: File → Print window
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Output - image file
❑ Image of visualization window ❑ Menu: File → Set Save options… ❑ Select an image format ❑ Click apply ❑ Menu: File → Save window
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Output - geometry file
❑ (Outer, viewable) geometry of visualization window ❑ Menu: File → Set Save options… ❑ Select a geometry format ❑ Click apply ❑ Menu: File → Save window
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Output - data base
❑ Entire data base (all (changed) geometry and data) ❑ Menu: File → Export database… ❑ Select variables ❑ Select format ❑ Click Apply ❑ Click Export
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Client-server
Client
Server
Main Window
Visualization Window
Database Server
Compute Engine Compute
Engine Compute Engine
Other Windows
Data
VisIt Component Launcher (VCL)
Local
Remote
❑ Local GUI ❑ Local viewer
❑ Remote database server ❑ Remote compute engines
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Client-server
❑ Rendering can be remote or local, depending on the need
❑ There are user-controlled parameters that can affect this
❑ Data remains remote ❑ Visualization (graphical
primitives from simulation data) is remote
Main Window
Visualization Window
Database Server
Compute Engine Compute
Engine Compute Engine
Other Windows
Data
VisIt Component Launcher (VCL)
Local
Remote
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Client-server
❑ Rendering remotely ⇒ image pieces sent to client ❑ Rendering locally ⇒ graphical primitives sent to client (cut plane
pieces, isosurface pieces, e.g.)
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Client-server: conditions
❑ visit installed on all machines ❑ visit in search path on all machines ❑ Compatible VisIt releases (not patches) on all machines ❑ (Passwordless ssh)
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Client-server: open remote file
❑ Single-process, local VisIt is running ❑ Open File selection window with one of…
❑ Key: F ❑ Menu: File → Select file …
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Client-server: open remote file
❑ Enter name of computer where data is
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Client-server: open remote file
❑ VisIt starts VisIt Component Launcher (VCL) on remote machine ❑ VCL launches database server, compute engines, etc. and runs
until you quit VisIt ❑ Remote files appear in File selection window
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Client-server: open remote file
❑ Add files to Selected files list ❑ Can group files
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Client-server: open remote file
❑ Dismiss File selection window ❑ Visualize the files’ data
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation
❑ Flipbook ❑ Simple ❑ Steps of a time-variant database ❑ Only time changes
❑ Script ❑ If many frames ❑ Python or Java
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation
❑ Keyframe ❑ Complex behavior ❑ Time + multiple other parameters change
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - flipbook
❑ If file format has each time step in separate file ❑ Create .visit
❑ Or ❑ Let visit determine (might not be right)
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ These 11 slides show how to animate the viewpoint (camera location) of a contour plot over 3 time steps
❑ Open file ❑ Create plot ❑ View panel
❑ Menu: Controls → View… ❑ Select Advanced tab
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ Keyframe Editor panel ❑ Menu: Controls → Keyframing… ❑ Set Number of frames to 3 ❑ Click Keyframing enabled
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ Suggestion: resize & move VisIt windows so they’re accessible
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ About the Keyframe editor panel ❑ Attributes area
❑ A horizontal entry for each parameter that can change across frames ❑ Grey Keyframes area
❑ A vertical line for each keyframe ❑ Green bar for Contour attribute means contour will be drawn in
visualization window for all keyframes ❑ Current keyframe is first keyframe, indicated by blue vertical line and
black triangle
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ Make View window active and click on Make camera keyframe from view
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ Current view of plot, in visualization window, becomes first animation frame, as indicated by black diamond
❑ Click below second keyframe’s vertical ine to move black triangle and make that keyframe current
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ Make visualization window (where plot Is drawn) active, and rotate plot a significant amount (e.g., 45 degrees)
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ Make View window active and click on Make camera keyframe from view
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ Current view of plot, in visualization window, becomes second animation frame, as indicated by black diamond
❑ Click below third keyframe’s vertical line to move black triangle and make that keyframe current
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ Rotate plot ❑ Click on Make camera keyframe from view button of View window ❑ This is the resultant Keyframe Editor panel
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animation - keyframe
❑ Click Copy view from camera to enable the Time slider of the main window to animate the viewpoint
❑ A rough, 3-frame animation of the viewpoint can now be run in the visualization window by clicking the play button
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animate - keyframe
❑ These 4 slides show how to refine the 3-step animation to one of 25 steps, thus smoothing it
❑ Change Number of frames to 25 ❑ New (empty)
frames are added to Keyframes area
❑ Green bar reaches keyframe 25
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animate - keyframe
❑ With the mouse, drag the black diamond for keyframe 3 to keyframe 25
❑ Likewise, drag the diamond for keyframe 2 to some keyframe close to the middle (result is on next slide)
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animate - keyframe
❑ Click the play button of the main window’s time slider ❑ Hmm… Result not as expected:
❑ Only the first 3 frames show the plot ❑ Reason: the green bar for the contour plot, which had been extended
to keyframe 25 when the number of frames was changed, has reverted to keyframe 3
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Animate - keyframe
❑ Use the mouse to drag the end of the green bar back to keyframe 25
❑ Run the animation ❑ Good:
❑ Other frames now show views interpolated between original 3
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Python CLI
❑ Run visit -cli ❑ Starts interactive Python session ❑ Loads Python visit module
❑ To visualize a Pseudocolor plot of variable var from data file dfile ❑ At Python prompt, enter
OpenDatabase(“<path_to_file>/dfile”) AddPlot(“Pseudocolor”, “var”) DrawPlots()
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Python script
❑ Run visit -cli -s <pythonscript_name> ❑ Loads Python visit module ❑ Script calls VisIt commands
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The ASCI/Alliances Center for Astrophysical Thermonuclear Flashes The University of Chicago
Python + GUI
❑ Menu: Controls → Command… ❑ Record widget clicks
and see Python ❑ Write Python ❑ Execute written or
recorded Python