This file allows GRChombo examples to be built with Catalyst. Also add
some more work on the CatalystAdaptor code.

This can be handled by the updated mkdep script in GRTLCollaboration/Chombo#32.

paraview-config is extremely slow and we only want to call it once and
use the cached output otherwise.

Also add compile_commands.json database.

This currently passes ghosted boxes to Catalyst.

In theory only the variables requested in the script should be sent to
Catalyst.

* Change constructor for each vtkAMRBox.
* Generate ghost array for each vtkUniformGrid.
* Audit grid at the end of construction.

This one includes resampling to an image and no raytracing.

Note that now the vtkAMRBox indices are (0,0,0) where the lower
corner of the ghosted domain on the coarsest level is e.g. (-3,-3,-3)
in Chombo indices.
In theory this might make it annoying to calculate coordinates, but
these should be calculated from the associated vtkUniformGrid objects
anyway which have their origin at the correct place (i.e. Chombo's
(0,0,0)).
This is necessary as VTK expects the "origin" of the vtkAMRBoxes to be
the lower bound.

Also change back to the old construction of vtkUniformGrids. I think the
one that used the vtkAMRBoxes assumed node centering leading to the
wrong dimensions.

These have been generated from more representative data of the current
parameter file.

Add some recent new ones and remove some old ones.

This includes "Insitu" in the filename. Note that the default example
executable will be built and linked with ParaView Catalyst if
PARAVIEW_DIR is set correctly but will not be named accordingly.

This allows the user to restrict which variables are passed to Catalyst.
In theory this could be determined from the Catalyst script but the
functions to determine this don't seem to work well with newer Catalyst
scripts (i.e. those generated by v5.9 or later) and always request all
variables.

In order to do this, parameter names have been changed.

This reduces VTK log output to stderr and instead sends it to a
catalyst_pout (this name can be changed with the catalyst_pout_prefix
parameter) file (for each rank) under the usual pout_subpath like the
normal Chombo output (in the case MPI=TRUE). There is also a
catalyst_verbosity parameter which controls both the verbosity of the
VTK log output and the messages from CatalystAdaptor in the normal pout
file.

The -rdynamic flag will also be passed to the linker for the insitu
build target so that the VTK log stack trace (which is output in the
case of some termination signal) has more information for the [GR]Chombo
part of the stack.

This provides instructions on building and using ParaView Catalyst
in-situ visualization with a GRChombo example.

Also refactor error/warning in CatalystAdaptor

These can be specified with the XTRA_VTK_COMPONENT_FLAGS and
XTRA_PARAVIEW_COMPONENT_FLAGS variables in the makefile which will be
passed to paraview-config.

This uses a script generated by ParaView 5.9.1 to extract an image of a
slice and compares this image to a known valid one.

This bug is not apparent in the case OPT=HIGH (so NDEBUG is defined) as
the Chombo asserts are skipped but appears otherwise.

* vtkPVVersion.h not present in all builds so replace with vtkPVConfig.h
* Need to add the ParaView::RemotingCore component for the above header
* Replace error from vtkImageDifference with thresholded error otherwise
the test is way too sensitive

Unfortunately it still won't work in some cases but I don't think
there's an easy way to do so.

This means that any outputs for visualization pipelines will be created
under this path.

This allows copying Chombo arrays to Catalyst without ghost cells (for
debugging purposes).

These should be the same as that of the corresponding vtkUniformGrids.
Thanks to Dave Demarle (@demarle) for finding this.

Switch to using a Catalyst v1.0 script for the test so that it will work
with ParaView v5.8. Also add a header file to determine the ParaView
version (not currently used but possibly useful in future).

If the VTK_SMP_MAX_THREADS environment variable is not set, the number of
VTK SMP threads is set to the same as the number of OpenMP threads.

Also add some small comments to CatalystAdaptor.hpp.

The ghosts are filled for variables requested at the previous CoProcess.
One can also pass a non-positive interval of variables to fillAllGhosts
which will just make it return without doing any ghost filling.

This would occur if Catalyst was used but the extraction parameters were
not set (so minimum extraction_level parameter doesn't exist).

Cells that are marked as ghosts will no longer be visible in ParaView
(e.g. those in the outer boundary).

This writes the created vtkOverlappingAMR object to a file. It's mainly
for debugging but I guess in theory it allows a user to save the state
of the grid at any timestep on any level rather than just a whole
coarsest level timestep.

This shifts the set `origin` of the `vtkUniformGrid`s from the
`global_origin` at (0,0,0) (in Chombo coordinates) to that of the low
corner of the box. This seems to disagree with what is done in the
ParaView Catalyst CxxOverlappingAMRExample but makes the outputted VTK
XML files appear more sensible when loaded in ParaView.

Now, all of the Catalyst parameters used in `CatalystAdaptor` are in a
`CatalystAdaptor::m_p`, a struct of type `CatalystAdaptor::params_t`.
This will make it easier to add/modify parameters. Previously multiple
functions across the `CatalystAdaptor` and `GRAMR` classes as well as a
Setup function needed to be modified every time a Catalyst parameter was
changed. Note that some parameters are used elsewhere (e.g.
`catalyst_coprocess_level` in `GRAMRLevel` and are therefore not part of
`CatalystAdaptor::params_t`.

Some parameters have been renamed in order to make them more consistent
(all Catalyst parameters are now prefixed with `catalyst_`). The Insitu
README has been updated accordingly.

This allows the user to make Catalyst write VTK XML files for the 3D AMR
data that is passed to Catalyst at each Catalyst coprocess and specify
the filename prefix of these files.

The test should not pass with a PNG from a previous run if Catalyst
fails to run for whatever reason.

This was probably obvious but the `tv_nsec` member of a `timespec`
struct is only the number of nanoseconds since the last full second so
it is necessary to compare the `tv_sec` member first.

Remove all the code that checks the modified timestamps and simply just
delete the old file at the start. This way, if nothing is generated, the
test will definitely fail.

The key step is to apply vtkParallelAMRUtilities::StripGhostLayers
(which removes layers of fine ghost cells that only partially cover
coarse cells) and vtkParallelAMRUtilties::BlankCells (which blanks out
coarser cells that are covered by finer cells on a different rank -- I
thought this was automatic previously) to the vtkOverlappingAMR object
(this is done in the [VisIt Chombo
Reader](https://gitlab.kitware.com/paraview/visitbridge/-/blob/df098f4148a96d62c388861c1d476039e02224ae/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx#L511-L514)).
Since the former might require deep copying (in case stripping happens),
a temporary vtkOverlappingAMR object is instantiated in
CatalystAdaptor::coprocess which is used to create the grid and add the
fields. This is then copied (either shallow or deep as necessary) to the
m_vtk_grid_ptr member which is passed to Catalyst. Note that now, no
cells are manually marked as ghosts in CatalystAdaptor::build_vtk_grid
as I observed gaps when doing so. The only marking of ghosts now comes
from BlankCells.

Previously the paraview-config command could fail and the build would
continue going which made it difficult for the user to see where the
problem is. Also commands that exit with non-zero exit codes are no
longer cached by the cache.sh script so that the paraview-config error
always appears.

These don't have the .SHELLSTATUS variable.

Also update CMake version to 3.22.6.

These are set as environment variables which can be recovered in the
Catalyst Python script. Also update slice_chi.py.

The vtkPythonInterpreter::SetRedirectOutput() function was introduced
with VTK version 9.1.0.