xdmf I/O HDF5 linking error on MacOS: libhdf5.101.dylib not found

[Ryan Schmidt]

On Nov 14, 2018, at 20:28, Ruben Di Battista wrote:

> Hello, 
> 
> Recently on Macports hdf5 (4.3.0) and netcdf packages were updated. Recompiling vtk with xdmf support  (and python27 bindings) returns me this error: 
> 
> :info:build [ 78%] Python Wrapping - generating vtkFillHolesFilterPython.cxx
> :info:build cd /opt/local/var/macports/build/_Users_***_git_macports-ports_graphics_vtk/vtk/work/build/Wrapping/Python && ../../bin/vtkWrapPython-8.1 @/opt/local/var/macports/build/_Users_***_git_macports-ports_graphics_vtk/vtk/work/build/Wrapping/Python/vtkFiltersModelingPython.Release.args -o /opt/local/var/macports/build/_Users_***_git_macports-ports_graphics_vtk/vtk/work/build/Wrapping/Python/vtkFillHolesFilterPython.cxx /opt/local/var/macports/build/_Users_***_git_macports-ports_graphics_vtk/vtk/work/VTK-8.1.1/Filters/Modeling/vtkFillHolesFilter.h
> :info:build ld: file not found: /opt/local/lib/libhdf5.101.dylib for architecture x86_64
> 
> Checking in the library folder (/opt/local/lib) I have not `libhdf5.101.dylib`, but `libhdf5.103.dylib`. Where in the VTK’s CMakeFiles.txt the actual HDF5 library version gets computed? 
> 
> Can you give me an hint on how I can try to fix this linking error? Seems to be related to some “leftover” of the previous installation maybe… I tried a port clean on vtk and hdf5 but I keep getting this error… 

Make sure you have run "sudo port selfupdate" and "sudo port upgrade outdated" first.

When I tried to reproduce this problem on my system, I did get the same "file not found: /opt/local/lib/libhdf5.101.dylib" error, but when building netcdf-cxx. The problem was that MacPorts did not automatically upgrade netcdf first; the solution was upgrading netcdf manually. I don't know why MacPorts didn't do that; it should have, since it is listed as a dependency of netcdf-cxx.