These scripts were tested with VisIt 3.1.4. Download VisIt 3.1.4 for Mac and install.
From Terminal, cd to your home directory and clone the repo.
cd
git clone https://github.com/l3-hpc/visit-scripts.git
Change to the visit-scripts directory and check the contents
cd visit-scripts
ls
From Terminal, do:
curl https://renc.osn.xsede.org/ees210015-bucket01/testvisit/mi_0013.nc -o mi_0013.nc
Check size, it should be 383.4M
ls -lh mi_0013.nc
For full instructions on using the 'start' scripts, see the README, but to test, use the commands in the box below.
Make sure you are in the correct directory, and check your path by doing:
cd ~/visit-scripts
pwd
The following commands are meant to be pasted in the VisIt CLI. To open the VisIt CLI, open VisIt and launch the command line interface by doing the following:
- In the top VisIt nav bar, click Controls:Launch CLI
A terminal (CLI command line) will pop up, looking something like (yours will probably be black):
To test, for your convienience, just copy and paste these, after modifying yourusername. (Check the PATH matches what you found above.)
SCRIPT_PATH = "/Users/yourusername/visit-scripts"
FILE_NAME = "/Users/yourusername/visit-scripts/mi_0013.nc"
import sys
sys.path.append(SCRIPT_PATH)
from visit import *
from setup_visit import *
setvars = {"db" : FILE_NAME,"var" : "TP","clim" : 1,"cmin" : 0.002,"cmax" : 0.008,"cmap" : "turbo","scale" : 1000,"percent" : 35,"from_x" : 560998.31,"from_y" : 4767358.50,"to_x" : 539195.69,"to_y" : 4765827.50,"model" : "fvcom"}
open_file(setvars)
create_pseudocolor_3Dplot(setvars)
This should open a 3D plot, similar to the first image on LM. Then you can try:
create_pseudocolor_2Dslice(setvars)
create_pseudocolor_2Dtransect(setvars)
transect_against_3D(setvars)
After confirming the above works, close VisIt, and try again using the instructions in the README.
Use a text editor, like nano, to modify the start_ scripts, e.g.,
cd
cd visit-scripts
nano start_fvcom_lm.py
Then edit the following lines, substituting your actual username for yourusername.
SCRIPT_PATH = "/Users/yourusername/visit-scripts"
FILE_NAME = "/Users/yourusername/visit-scripts/mi_0013.nc"
From nano, to save, do Ctrl X,Y,Enter.
The point of the startup scripts are to minimize your startup time. You should modify the startup script according to your case. To do that, modify setvars.
The file setup_visit.py contains plot 'macros' that make a plot according to setvars parameters. Read the comment lines in startup_fvcom_lm.py for definitions. To illustrate, try the following:
Follow the steps above until
create_pseudocolor_3Dplot(setvars)
Now you should have a 3D plot. Rotate it around and look at it. Click through the timesteps.
The colormap is 'turbo'. Change the colormap to viridis by doing, in the VisIt CLI terminal:
setvars["cmap"] = "viridis"
create_pseudocolor_3Dplot(setvars)
The variable is total phosphorus (TP). Change the variable to temperature (temp) by doing, in the VisIt CLI terminal:
setvars["var"] = "temp"
create_pseudocolor_3Dplot(setvars)
The colormap is defined as the min/max of data at each timestep or by specifying a min and max. The plot looks bad because it is using min/max appropriate for TP. Let VisIt pick the min/max according to data by doing, in the VisIt CLI terminal:
setvars["clim"] = 0
create_pseudocolor_3Dplot(setvars)
Now, change it back to turbo, and pick the limits by doing, in the VisIt CLI terminal:
setvars["cmap"] = "turbo"
setvars["clim"] = 1
setvars["cmin"] = 0
setvars["cmax"] = 7
create_pseudocolor_3Dplot(setvars)
See this video, which shows a demo of what it looks like when you follow the above steps. VisIt Setup Scripts.