Library not loaded: @rpath/libhdf5.310.dylib

[windemut]

I can't get tables to work at all on Mac M1 Ventura 13.4. It can't find the hdf5 dynamic library, it seems. I installed like this:

brew install hdf5 c-blosc lzo bzip2
export HDF5_DIR="$(brew --prefix hdf5)"
pip3 install tables

% python3 -m tables.tests.test_all
Traceback (most recent call last):
  File "<frozen runpy>", line 189, in _run_module_as_main
  File "<frozen runpy>", line 112, in _get_module_details
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/__init__.py", line 32, in <module>
    from .utilsextension import get_hdf5_version as _get_hdf5_version
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/utilsextension.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libhdf5.310.dylib
  Referenced from: <97D08AE0-CC5C-35AA-AC56-C45460DE5186> /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/utilsextension.cpython-311-darwin.so
  Reason: tried: '/usr/lib/libhdf5.310.dylib' (no such file, not in dyld cache)

Any ideas?

[avalentino]

Dear @windemut
It would be nice to understand that is $(brew --prefix hdf5) to have a better picture of what is happening.
Moreover, could you please clarify if you are using a native PyTables build or if you are working with x86 emulation?

As a general comment I can say that many users reported strange behaviours related with brew used on M1 HW. Maybe you could try to give a look to some of the old tickets (many of them already closed) to understand is a solution to your problem has been already found.
We try to label these issues with osx or osx-arm64. Maybe it will help you in the search.

[windemut]

Thank you for your response, @avalentino! The hdf5 path expands to ‘/opt/homebrew/opt/hdf5’, and libhdf5.310.dylib is found in the ‘lib’ subdirectory thereof. I don’t know about emulation, I just used ‘pip3 install tables’. I will search some more, but I have already done a lot. The problem seems to be related with @rpath, and I have little understanding of that.

[avalentino]

hmm, I don't think that the rpath link flag is used in the PyTables build process, but I could be wrong.
Unfortunately I do not have access to a Mac M1 to reproduce the issue.
Is it possible for you to attach the full build log of PyTables?

You could also try to set DYLD_LIBRARY_PATH to point to the installation path of HDF5.
I'm not sure that it will work if rpath is set, but this is something easy to try.

[avalentino]

Dear @windemut , did you manage to solve the issue?

[windemut]

No, I had to move on to other things. If I try again and get results I’ll come back here. Thanks for your help!