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

[Ryan Schmidt]

On Nov 16, 2018, at 18:00, Ruben Di Battista wrote:

> I tested again the build (with also rev-upgrade). No luck, same error. Does anyone here can try to install: vtk +hdf5 +python27 +mpich to see if it’s just a misconfiguration for me or it’s a general problem?

Some file on your system that is being used by the vtk build is linked with /opt/local/lib/libhdf5.101.dylib. We need to identify that file and rebuild it so that it is linked with /opt/local/lib/libhdf5.103.dylib instead.

That's what running "sudo port rev-upgrade" does, so I'm surprised that didn't fix the problem for you.

Maybe rev-upgrade is failing, but isn't printing an error message. You could run it with debug output: "sudo port -d rev-upgrade".

If the output doesn't look like an error is happening, then maybe the problem is that the file that is linked with /opt/local/lib/libhdf5.101.dylib is not in MacPorts, but the vtk build is finding it for some reason. (For example, maybe it is in /usr/local.) If so, you could use trace mode, which tells MacPorts to ignore any files not explicitly listed as dependencies: "sudo port clean vtk && sudo port -t install vtk +hdf5 +python27 +mpich".