cmake exported target uses undefined hdf5::hdf5 imported target

[jschueller]

on mingw (win32), compiling netcdf with cmake, with a cmake-compiled hdf5 using its exported target (module mode, not config mode), results in an installed netcdf-targets.cmake that contains the hdf5::hdf5 target (and hdf5::hdf5_hl) in the INTERFACE_LINK_LIBRARIES properties.

But then, when using netcdf in module mode (with find_package(netCDF)) these hdf5 targets are undefined (the hdf5 cmake config is not included), and cmake is not happy:

-- Configuring done
CMake Error at CMake/vtkModule.cmake:2968 (add_library):
  Target "IONetCDF" links to target "hdf5::hdf5_hl-shared" but the target was not found

We first encountered this bug in vtk: https://gitlab.kitware.com/vtk/vtk/issues/17637

A workaround is to provide manually hdf5 paths when configuring netcdf, doing so results in actual library paths being written to the exported targets file instead of hdf5 targets.

[mathstuf]

Well, netCDFConfig.cmake should do a find_package(HDF5) and may provide hints to where it found it at build-time via the HDF5_DIR and/or HDF5_ROOT variables.

[WardF]

The netCDFConfig.cmake file is generated automatically; let me take a look to see if I can find out how it is properly modified/updated.

[jschueller]

@WardF it is configured from https://github.com/Unidata/netcdf-c/blob/master/netCDFConfig.cmake.in

[WardF]

Coming back to revisit 4.7.1 issues in the lead-up to the release. @jschueller thanks for the pointer.

[jsharpe]

Note that a similar issue is with missing a dependency on MPI as well. This commit: https://github.com/Unidata/netcdf-c/commit/bc2a3babf9cbe80fa7ae3dec5d7622594a7ae51e introduces a call to find_package(MPI) on MSVC but surely this should be done for all platforms that use mpi as ncdispatch.h includes mpi.h if HDF5_PARALLEL or USE_PNETCDF is defined.

[jsharpe]

I think the issue here is that cmake's current FIndHDF5.cmake file doesn't define any imported targets (the hdf5::hdf5 target) but hdf5 build with cmake defines a cmake config file that does provide this target. See https://gitlab.kitware.com/cmake/cmake/issues/18560 for the upstream discussions regarding this.

So I suspect the best route to fixing this is to ignore the hdf5 provided config files by passing NO_MODULE to the find_package(HDF5) calls?

[mathstuf]

VTK has a patched FindHDF5 that contains imported targets. It's been working pretty well there, but every time I breathe on it, new bugs crop up :) . I'll resurrect my MR to put it in over the holidays.

[jsharpe]

@mathstuf Its actually in the context of VTK and the superbuild that I was seeing issues with this. I've had to define -DHDF5_NO_FIND_PACKAGE_CONFIG_FILE:BOOL=ON on dependencies of hdf5 to get it to work correctly for the netcdf build but then I have to manually define HDF5_HL_LIBRARIES and HDF5_C_LIBRARY_hdf5_hl to get it to pass the configuration step in paraview / VTK.

[mathstuf]

That's probably with VTK 8.2 / ParaView 5.6 and older (where the build system choked on imported targets). Now with VTK 8.90 / ParaView 5.7 and newer, imported targets are heavily preferred (non-targets are usually warned about if it comes to the attention of the new build system infrastructure).

[jschueller]

hdf5 logic is complicated https://github.com/Unidata/netcdf-c/issues/877

[WardF]

@jschueller Indeed.

[WardF]

Addressing this now before it slips under the radar again.

[jschueller]

hi @WardF with your patch now I get just "hdf5_hl-shared" instead of the previous "hdf5::hdf5_hl-shared", but it's not right yet ;)

[WardF]

Yes, the logic for HDF5 is tricky. Thanks for checking in, I was going to ask, once I had something that looked like a fix. I imagine I'll need to pattern something off of the hdf5 logic found in the netcdf-c top-level CMakeLists.txt file. It's good to have something to do :).

[Chrismarsh]

Is there progress on this? I see that a netcdf-c cmake built library has a pkgconfig file that references libraries that don't exist (Libs.private: -lhdf5_hl-shared -lhdf5-shared)

Name: netCDF
Description: NetCDF Client Library for C
URL: https://www.unidata.ucar.edu/netcdf
Version: 4.9.2
Libs: -L${libdir} -lnetcdf
Libs.private: -lhdf5_hl-shared -lhdf5-shared -lm -lz -lzstd -lbz2 -lcurl -lpnetcdf -lxml2
Cflags: -I${includedir}

[WardF]

Wow this has really lingered. My sincere, embarrassed apologies. @K20shores this feels like something that might fit in with the work we're doing over at #2847?

[K20shores]

@WardF, yes, I think the updates we've added may fix this. I'll have to check