Issue 931: Old-style restart files

[timspainNERSC]

Read old-style restart files

Fixes #931

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Change Description

Adds the necessary code to allow the old-style restart files with netCDF groups to still be read. This involves making the ParaGridIO code generic so that dimensions and variables can be searched for both in the file root and in the data group. All newly written files are in the flat new style.

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Test Description

The model successfully runs using my old style restart and forcing files.

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Documentation Impact

Since no-one else should be generating the old-style files, this does not really need to be documented. Plus, I should eventually replace my old-style restart files over time.

[jwallwork23]

Nice to have backward compatibility for reading files.

I have a couple of requests:

1. Perhaps add a Logged warning when reading files through the legacy option to say that this is being done? Could even include a deprecation warning, if you think that'd be appropriate.
2. In the ParaGridIO_Xios implementation of getModelState, perhaps we should raise an error if groups are found, with a message saying that the legacy format is not supported in the XIOS implementation? (I'm not sure how readable the XIOS errors would be.) I can then do the same for readForcingTimeStatic in #928.

Also note that some of the other code changes that align the MPI and non-MPI cases will conflict with similar changes in #744.

[jwallwork23]

Note that this will conflict with @TomMelt's changes in #744, although it'll be possible to rectify the two.

[timspainNERSC]

It might be easier to start from scratch.

This branch has conflicts that must be resolved

• core/src/Model.cpp
• core/src/ParaGridIO.cpp
• core/src/RectGridIO.cpp
• core/src/StructureFactory.cpp
• core/src/include/ParaGridIO.hpp
• core/src/include/RectGridIO.hpp
• core/src/include/StructureFactory.hpp
• core/src/modules/StructureModule/include/ParametricGrid.hpp
• core/src/modules/StructureModule/include/RectangularGrid.hpp
• core/src/modules/include/IStructure.hpp
• core/test/ParaGrid_test.cpp
• core/test/RectGrid_test.cpp

[timspainNERSC]

2. In the ParaGridIO_Xios implementation of getModelState, perhaps we should raise an error if groups are found, with a message saying that the legacy format is not supported in the XIOS implementation? (I'm not sure how readable the XIOS errors would be.) I can then do the same for readForcingTimeStatic in XIOS implementation of readForcingTimeStatic #928.

What would be a sensible way of doing this? As far as I can tell, getModelState no longer does anything with the filename parameter, it (presumably) having been passed to the XIOS set up beforehand. It rather seems overkill to re-open the netCDF file from the passed filename, check for groups and then close it again.

[jwallwork23]

What would be a sensible way of doing this? As far as I can tell, getModelState no longer does anything with the filename parameter, it (presumably) having been passed to the XIOS set up beforehand. It rather seems overkill to re-open the netCDF file from the passed filename, check for groups and then close it again.

Ah, good point. There's already an initial read of the NetCDF file in Xios::affixModelMetadata within the conditional that checks if an input file is provided so that would be the best place to add it.

nextsimdg/core/src/Xios.cpp

Lines 673 to 680 in af75f07

	void Xios::affixModelMetadata()
	{
	auto& metadata = ModelMetadata::getInstance();
	// Initial read of the NetCDF file to deduce the dimensions
	if (inputFilename.length() > 0) {
	try {
	auto& modelMPI = ModelMPI::getInstance();
	netCDF::NcFilePar ncFile(inputFilename, netCDF::NcFile::read, modelMPI.getComm());