Opening MPAS mesh file with an error

[dkang2]

Describe the bug An MPAS mesh file in netcdf format can't be opened

To Reproduce Steps to reproduce the behavior:

1. verdi -f /work/MOD3DEV/dkj/MPAS/data/x1.2621442.grid.nc
2. The following error window pops up and verdi freezes: Screenshots

Desktop (please complete the following information):

• OS: Linux (on EPA Atmos)

Additional context Add any other context about the problem here.

[dkang2]

This new feature works very well and it has achieved the desired results.

[yadongxuEPA]

Retested VERDI 2.1.4 20230924 builds on Atmos, confirmed that the new feature of displaying MPAS mesh structure works well.

[yadongxuEPA]

Retested VERDI 2.1.4 20231012 builds on Atmos, confirmed that the new feature of displaying MPAS mesh structure works well.

[lizadams]

I added a small mesh file to the github branch but, when I went to visualize it I couldn't see the mesh.

Is there a pull down menu option that I need to set to visualize it, or do I need to zoom into some region to find a mesh definition?

I know that the x1.2621442.nc file is too large to put in the VERDI distribution on github, so the file that Daiwen had shared with me was much smaller, x1.40962.grid.nc.

netcdf x1.40962.grid { dimensions: nCells = 40962 ; nEdges = 122880 ; nVertices = 81920 ; maxEdges = 10 ; maxEdges2 = 20 ; TWO = 2 ; vertexDegree = 3 ; nVertLevels = 1 ; Time = UNLIMITED ; // (0 currently)

x1.40962.grid.nc.tar.gz

File that has been used above for testing x1.2621442.tar

[lizadams]

I figured it out, the user needs to use the pull down menu option Tile Plot > Controls > Show Cell

Borders

I will add this to the documentation.

[dkang2]

Thanks, Liz, for doing all these updates. It is in a very good shape to have the VERDIv2.1.5 release.

[yadongxuEPA]

Checked VERDI_2.1.5_linux64_20231222.tar.gz on Atmos and it worked.

[lizadams]

Using VERDI_2.1.5_mac_20240103.tar.gz

Tried using the CLI option to create a tile plot using the meshStructure variable, and it failed.

This works in the GUI. Using the GUI, after creating the tile plot, I was able to select Controls>Show Cell Borders, and then zoom in to see the mesh structure.

Error message from the command line option:

./verdi.command -f $cwd/data/model/x1.40962.grid.nc -s "meshStructure[1]" -g tile in netcdfdataset.java openDataset 1 arguments in netcdfdataset.java openDataset 3 arguments in netcdfdataset.java ready to return openDataset 5 arguments 2024.01.04 18:34:52.250 [main] ERROR anl.verdi.commandline.ScriptHandler - Error in ScriptHandler.dataMap.put 'G' java.lang.NullPointerException: Cannot invoke "anl.verdi.data.DataFrameAxis.getOrigin()" because the return value of "anl.verdi.data.Axes.getTimeAxis()" is null at anl.verdi.commandline.ScriptHandler$14.run(ScriptHandler.java:579) [core.jar:?] at anl.verdi.commandline.ScriptHandler.handleOptions(ScriptHandler.java:1525) [core.jar:?] at anl.verdi.commandline.ScriptHandler.run(ScriptHandler.java:167) [core.jar:?] at anl.verdi.core.VerdiPlugin.run(VerdiPlugin.java:168) [core.jar:?] at saf.core.runtime.CorePlugin.runApplicationRunnable(CorePlugin.java:93) [saf.core.runtime.jar:?] at saf.core.runtime.CorePlugin.run(CorePlugin.java:48) [saf.core.runtime.jar:?] at jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) ~[?:?] at java.lang.reflect.Method.invoke(Method.java:580) ~[?:?] at saf.core.runtime.Boot.run(Boot.java:178) [saf.core.runtime.jar:?] at saf.core.runtime.Boot.main(Boot.java:388) [saf.core.runtime.jar:?]

[yadongxuEPA]

Checked VERDI_2.1.5_linux64_20240103.tar.gz on Atmos with command line and got the same error:

[yadongxuEPA]

Additional re-test also done on VERDI_2.1.4_linux64_20231013.tar.gz (before Java update) on Atmos with command line and got the same error:

[lizadams]

Testing after Tony's build of VERDI_2.1.5_mac_20240124.tar.gz

cd /Users/lizadams/downloads/VERDI_2.1.5_01_24
./verdi.command -f $cwd/../x1.40962.grid.nc -s "meshStructure[1]" -g tile

Output:

in netcdfdataset.java openDataset 1 arguments
in netcdfdataset.java openDataset 3 arguments
in netcdfdataset.java ready to return openDataset 5 arguments

Then in the GUI selected Control > Show Cell Borders

Saved screenshot showing successful display of the mesh structure.

This test was successful

[yadongxuEPA]

Checked VERDI_2.1.5_linux64_20240124.tar.gz on Atmos with command line and confirmed that this issue has resolved.