VisIt for M3DC1


1.  Run VisIt

Version 2.4.0 of VisIt is on the PPL file system in /p/vis/visit/new/visit2.4.0.
To run this version, log in to portal, e.g.:

ssh -X portal

1.1 Get the parallel rendering config file
In your home directory, make the directory .visit/hosts if it is not already there.

cd .visit/hosts
cp /u/efeibush/.visit/hosts/host_visit2_4_0.xml .

module purge
module load ppplcluster/1.1
module load pathscale/3.2

/p/vis/visit/new/visit2.4.0/src/bin/visit
    This brings up the graphical user interface and display window.


2.  Load Data File

Large data files stored on the cluster are handled with parallel rendering.
File --> Open file ...

In the File open dialog box:
    Change Host from localhost to visit2.4.0
    Change Open file as type: M3DC1

    Navigate to a directory and select a data file, such as /p/vis/m3d/data2/C1.h5
        Click on OK.

        This will bring up a dialog box for setting the number of processors.  You can increase it to 8 but that could delay the start of the batch rendering job.  Click on OK.
        This will bring up an info box showing compute engine launch progress.  The box will go away when the file reading is complete.  The example file is 60 GB and takes about 3 minutes to read in.
        At the command line it will print the batch job number of the parallel rendering process.  You can check this using qstat to see if the batch job for the parallel rendering is running.


3.  Select Plots

mesh
In the GUI, go to Add-->Mesh
    Mesh - mesh will be shown in the drawing list area.
    Click on Draw.  This may take a while.  Some messages will be shown in the status area at the bottom of the GUI.


view1
Rotate the mesh to a 3-D view by dragging the mouse cursor in the display window.
To move the mesh horizontally and vertically, hold down the Ctrl key while dragging the cursor.


pseudo
Add--->Pseudocolor   for variable P
    (Watch for rendering messages in the status area at the bottom of the UI window.  Takes almost 2 minutes to draw).


timestep
This dataset contains several time steps.  Use the Time slider to display another time step.
Redrawing each time step takes about 2 minutes.


4.  Appearance

yview
Displaying the pseudocolor plot can be time consuming.  Interactive view positioning will be faster when just the mesh is displayed.  Click on Pseudocolor in the plot list and then click on Hide/Show to turn it off.

Go to the Controls--->View... menu.  The 3D view tab will be shown.  Change the Align to axis field to -Y and turn off Perspective.  Click on Apply.  Set the Image zoom to 1.9 and click on Apply.

Go to the Controls--->Annotation... menu.  Click on the 3D tab.  Turn off Show axes, Show triad, and Show bounding box.  Go to the General tab, turn off User information, and click Apply.  This will display just the mesh.

To change the background color go to the Colors tab in the Annotation menu and press down on the rectangle next to Background color.  This will bring up a palette of colors.

4.1 Legend
Click on Pseudocolor in the plot list and then click on Hide/Show to display it.
Click on Mesh in the plot list and then click on Hide/Show to hide it.
Go to the Objects tab in the Annotation menu and click on the Legend Pseudocolor - P to select it.
Go down to the Legend panel in the menu.  There are tabs for Position, Tick Marks, and Appearance.
Use these controls to clarify the presentation of the legend.  For example, for Tick Marks, turn off the checkbox for Let Visit determine tick labels.  Then you can set the number of tick marks and specify the label at each tick mark to simplify the numbering if desired.
Go to the appearance tab and turn off Draw min/max.

Go to Controls--->Color table... to bring up the color map menu.  In the Manager section you can click on the name of each color table to see its colors in the Editor area.   You can also create your own color table in this menu.
To actually use a different color table, go to PlotAtts--->Pseudocolor...
Press down on the menu next to Color table and select a color table, such as "difference".  Then click on Apply in the Pseudocolor menu to see the color change.

4.2 Labels
In the Annotation menu, click on Text to add a new label.  Then use the menu to set the text, font, location, etc.  Click on Apply to display the label.
appearance


5.  Time Step Movie

To create a movie, go to File--->Save movie...   This brings up the movie wizard dialog box.
Select New simple movie and click Next.
Change the Format to JPEG images. 
Click on the -> button in the center to put the JPEG images format into the Output list.  Click Next.
Specify the First frame (time step) and Last frame (time step).  You can ignore Frames per second for now.  Click Next.
Specify the Output directory for the JPEG image files.  You can specify a base name for the files.  Click next.
Ignore email notification, click Next.
Select Now, use currently allocated processors.  Click Finish.
This brings up a progress dialog box and a window that runs a script.

By default, VisIt renders each time step with its min-max data range.  This is usually undesirable for a movie where each frame should be rendered against a consistant scale.  For consistancy over all time steps, go to the Pseudocolor plot attributes window and set the global Minimum and Maximum for your data.  Unfortunately VisIt does not calculate the global range.  You may have to look at a number of the time steps to determine the global min-max.
Then go to the Annotation window and select the Legend Pseudocolor - P.  You may have to change the Labels for the tick mark values.

The JPEG images are used to create a movie file.  One technique for creating the movie file on the PPL cluster is to run this java program:

module load java/v1.6

java -jar /u/efeibush/w3_html/makemovie/jpegtomovie.jar -f 5 -o mymovie.mov -d /u/efeibush/example

In this command line it creates a QuickTime movie file with 5 frames per second.  The output file is named mymovie.mov.  The image files are located in /u/feibush/example.

6.  3-D Torus

Select the mesh in the list of plots.  Go to Operators--->Transforms--->Transform.  This adds a transformation to the mesh.  Double click on Transform in the list to bring up the Transform operator attributes menu.  Go to the Coordinate tab.  Set Input to Cylindrical and Output to Cartesian.  Click on Apply and Draw.

torus


clip
Go to Operators--->Selection--->Clip and click on Draw.
Rotate the view to see the cross sections.
Show the pseudocolor plot and hide the mesh plot.


6.1  Isosurface
Turn off:  Apply operators to all plots and Apply subset selections to all plots.

iso2
Add another pseudocolor plot and then add the same transform operator to it. 
Then go to Operators--->Slicing--->Isosurface. 
Double click on Isosurface in the plot listing to bring up the Isosurface operator attributes menu.
Set Select by to Value(s).  Enter a value, such as .005.  Click Apply and Draw.

An additional legend is normally drawn for the isosurface.  To suppress this legend double click on Pseudocolor listed below Isosurface.  This will bring up the menu window for Pseudocolor plot attributes.  Uncheck the Legend box and click Apply to turn off the additional legend.


6.2 Slice Plane
slice
Select the first pseudocolor plot from the list.  Remove the Clip operator by clicking on the red X.
Then go to Operators--->Slicing--->ThreeSlice.  Click on Draw.  Initially this will display 3 planes intersecting the torus.
Double click on ThreeSlice in the list of plots to bring up the ThreeSlice operator attributes window.  Set Y to -10 and Z to -10 to move those 2 slice planes outside of the torus.  Click Apply and only the 2 cross sections in the X = 0 plane will be displayed as shown.



Use the instructions in section 5 to make a time step movie of the isosurface visualization.