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

[Ruben Di Battista]

I reswitched back to the new versions of hdf5. I manually upgraded netcdf and netcdf-cxx and recompiled vtk, but I get the same error at the same point. 

I do not understand if it’s a problem with vtk or with macports… o.O 

I also tried with the new netcdf-cxx4 port, but I get the same error unfortunately. 

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https://rdb.is

On 15 novembre 2018 a 09:14:37, Ruben Di Battista (rubendibattista at gmail.com) scritto:

Hello Ryan, 

Thanks for replying. I think I did my self update (when having a file:// local ports repository on the sources.conf, is there something to take care in addition to standard `sudo port self update`? Because I had the impression that sometimes I was not getting the updates properly…).

Indeed, however, I activated the old versions of hdf5 and netcdf-cxx, and the build proceeds correctly as expected. To me this looks related to hdf5/netcdf-cxx port… :/

I’ll try to investigate a bit more. 

          _    
-.     .´  |∞∞∞∞
  ',  ;    |∞∞∞∞∞∞
    ˜˜     |∞∞∞∞∞∞∞∞∞ RdB
    ,.,    |∞∞∞∞∞∞
  .'   '.  |∞∞∞∞
-'       `’

https://rdb.is

On 15 novembre 2018 a 04:33:19, Ryan Schmidt (ryandesign at macports.org) scritto:



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.

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