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The replace_ugrid_metadata.py script fails to detect netCDF time variables named time and misinterprets netCDF dimension names such as surface_tiles as UGRID dimensions.

The following mesh handling issues were found with recent LFRic output:

• Mesh files (as produced by the mesh generator) are not accepted by the reader plugin as valid UGRID files
• Periodicity of some global (cubed-sphere) meshes is not correctly resolved
• Wrap-around cells in biperiodic planar meshes are invisible

The package does not currently build with the MS Visual C++ compiler on Windows, which is a prerequisite for including a conda-forge package for Windows.

The LFRic Reader package no longer builds with recent ParaView release v5.10.0 due to an issue in the CMake configuration, where versions numbers are not handled correctly.

Hi,

I built paraview from source on Mac OS X (latest from github) and I'm getting

(base) niwa-1019500~/lfric_reader/src/cxx/build$ cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local/paraview/
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found OpenGL: /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework found components: OpenGL
CMake Deprecation Warning at /usr/local/paraview/lib/cmake/paraview-5.8/paraview-use-file-deprecated.cmake:1 (message):
The PARAVIEW_USE_FILE is no longer used starting with 5.7.
Call Stack (most recent call first):
CMakeLists.txt:18 (INCLUDE)

CMake Error at CMakeLists.txt:26 (ADD_PARAVIEW_PLUGIN):
Unknown CMake command "ADD_PARAVIEW_PLUGIN".

-- Configuring incomplete, errors occurred!

It should be possible to install the replace_ugrid_metadata script using Python's setuptools, to make it more easily available to users.

UGRID metadata (in particular mesh connectivity and units) can be inconsistent in LFRic output files. Add a Python script to fix these issues as a post-processing step, until a permanent fix is available in LFRic IO.

Having built an image from Singularity-headless the example script src/python/paraview_script.py fails to find the shared object file for the plugin:

$ singularity exec paraview_headless.sif pvpython src/python/paraview_script.py
(   1.136s) [main thread     ]  vtkPVPluginLoader.cxx:519    ERR| vtkPVPluginLoader (0x55c22149af90): libnetCDFLFRicReader.so: cannot open shared object file: No such file or directory

Traceback (most recent call last):
  File "src/python/paraview_script.py", line 7, in <module>
    pvs.LoadPlugin(pluginPath+'libnetCDFLFRicReader.so', remote=False)
  File "/usr/local/lib/python3.6/site-packages/paraview/simple.py", line 1880, in LoadPlugin
    servermanager.LoadPlugin(filename, remote)
  File "/usr/local/lib/python3.6/site-packages/paraview/servermanager.py", line 2381, in LoadPlugin
    raise RuntimeError ("Problem loading plugin %s" % (filename))
RuntimeError: Problem loading plugin libnetCDFLFRicReader.so

Checking the image contents shows a different filename:

$ singularity shell paraview_headless.sif.root
Singularity> ls /usr/local/lib/netCDFLFRicReader/
libvtkNetCDFLFRicReader.so  netCDFLFRicReader.so  vtk

Modifying the example script to use the filename in the image fixes the problem:

pvs.LoadPlugin(pluginPath+'netCDFLFRicReader.so', remote=False)

Presumably the filename currently in the example script works on some systems when not built within a Singularity container? It would be nice to have the example script work in both circumstances. I'm not familiar with ParaView builds, configuration, etc. but one simple option would be to define an environment variable in the Singularity image that is picked up by the example script when present.

So in the Singularity definition files we could add:

%environment
    ... <existing variable definitions >
    export PV_NC_PLUGIN_PATH=netCDFLFRicReader.so

And the start of the example script would become:

import os

import paraview.simple as pvs


# Load the LFRic reader plugin - it may be necessary to provide the full path to
# libnetCDFLFRicReader.so, depending on the installation. Set remote=True if you
# connect ParaView with a separate server.
pluginPath = os.environ.get('PV_NC_PLUGIN_PATH', 'libnetCDFLFRicReader.so')
pvs.LoadPlugin(pluginPath, remote=False)