Importing custom python module fails
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I am using Matlab2014b and try to import python packages. I am on a linux computer and executing the command py.numpy.* works and py.importlib.import_module('numpy') gives me the correct output. However, numpy lives in my /usr/lib/pymodules/python2.7/ directory, which according to the output of py.sys.path is in the search directory, so the import should work.
However, I have another package that I would like to include, which is in /usr/lib/python2.7/dist-packages/. Again, according to py.sys.path, this directory is included in the search path, however, importing the package fails ("Import argument 'py.fabio' cannot be found or cannot be imported."). I hope someone has an advice how to solve this problem.
PS: pyversion returns my current installation (2.7) and shows isloaded: 1
PPS: Adding the directory to the search path, as outlined in http://www.mathworks.com/help/matlab/matlab_external/call-python-from-matlab.html has failed.
PPPS: When I try to get feedback from py.importlib.import_module, Matlab crashes.
4 Comments
Robert Snoeberger
on 26 Jan 2016
To clarify, what do you mean by "Matlab crashes" and what was the full command given? I'm using Python 3.4 and it works for me:
>> py.importlib.import_module('fabio')
ans =
Python module with properties:
version: [1x5 py.str]
HiPiCimage: [1x1 py.module]
COMPRESSORS: [1x1 py.dict]
openheader: [1x1 py.function]
pilatusimage: [1x1 py.module]
edfimage: [1x1 py.module]
...
Note: I truncated the display of ans because it is quite long.
Fernando Bechtelar
on 26 Jan 2016
Robert Snoeberger
on 27 Jan 2016
/usr/bin/python2.7.so is the shared library for Python. It might be helpful to attach the stack trace.
Fernando Bechtelar
on 27 Jan 2016
Accepted Answer
Robert Snoeberger
on 28 Jan 2016
Edited: Robert Snoeberger
on 28 Jan 2016
Based on the stack trace, your issue looks like a library conflict with libhdf5.so. It seems like the libhdf5 that is in the stack trace is a library that is installed with MATLAB; I am assuming this based on the '/matlab_2015b/bin/glnxa64/' in the path to the library. I would guess that the appropriate version of libhdf5.so for Python should be located at /usr/lib/libhdf5.so. Try the following command to look for the correct libhdf5.so.
ldd /usr/lib/python2.7/dist-packages/h5py/h5f.so | grep libhdf5
My hunch about the library conflict is further confirmed by the fact that the libhdf5.so function that is executing is called H5check_version (line [2] of the stack trace). The documentation I found for that function says, "If this check fails, H5check_version causes the application to abort (by means of a standard C abort() call)..." [1].
Assuming you aren't using MATLAB's interface to HDF5, you should be able to use LD_PRELOAD to load the correct version of libhdf5.so [2,3].
References
- https://www.hdfgroup.org/HDF5/doc1.6/RM_H5.html#Library-VersCheck
- http://man7.org/linux/man-pages/man8/ld.so.8.html -- Search for "LD_PRELOAD". It should say, "A list of additional, user-specified, ELF shared objects to be loaded before all others..."
- http://stackoverflow.com/questions/426230/what-is-the-ld-preload-trick
6 Comments
Fernando Bechtelar
on 28 Jan 2016
Robert Snoeberger
on 28 Jan 2016
Another workaround to try is to set the dlopen flag to RTLD_NOW | RTLD_DEEPBIND [1], which can be done with Python's sys.setdlopenflags [2].
Example
>> RTLD_NOW = 2;
>> RTLD_DEEPBIND = 8;
>> flag = bitor(RTLD_NOW, RTLD_DEEPBIND); % RTLD_NOW | RTLD_DEEPBIND
>> py.sys.setdlopenflags(int32(flag));
>> py.importlib.import_module('fabio');
References
- http://linux.die.net/man/3/dlopen -- Search for "RTLD_DEEPBIND".
- https://docs.python.org/2/library/sys.html#sys.setdlopenflags
Fernando Bechtelar
on 29 Jan 2016
Bingzhao Shan
on 17 Oct 2018
Hi, I'm having Similar issue on Windows10. I tried the previous method but it seems that they don't work on Windows. Is there any suggestion? Thanks!
Michael Thieme
on 18 Oct 2018
I'm also having this issue on Windows 10, it would be great if someone is able to find a workaround!
Michael Thieme
on 18 Oct 2018
Edited: Michael Thieme
on 18 Oct 2018
All,
I found a solution to this problem. My problem was related to tensorflow/keras rather than fabio. This thread (https://github.com/NeurodataWithoutBorders/api-python/issues/28) led me to the solution. Basically my order of operations was:
- conda uninstall hdf5
- conda uninstall h5py
- pip uninstall hdf5
- pip uninstall h5py
- conda install hdf5=1.8.12 h5py=2.7.0 -c jonc
- pip install keras
- pip install tensorflow-gpu
More Answers (1)
Rafael Rebouças
on 19 Jan 2021
Edited: Rafael Rebouças
on 19 Jan 2021
My solution:
% Simple way to load your library
copyfile(my_library_file_path, pwd, 'f');
% It's necessary to load library
py.my_library.any_method_or_function();
delete 'my_library.py';
Now, your Python library is loaded to use in any directory.
1 Comment
Ronan Fleming
on 12 Apr 2021
https://nl.mathworks.com/help/releases/R2021a/matlab/matlab_external/out-of-process-execution-of-python-functionality.html
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