MATLAB: Update Python module in Matlab

MATLABpython

I'm trying to run a Python script using Matlab's built-in py. It's pretty simple, but I'm running into some difficulty drying to debug an error in my code (which runs fine testing in my Python IDE but crashes when run through Matlab).

The issue is that Matlab seems to be caching the module the first time I call a function, and I can't figure out how to get it to recognize changes to the module without restarting Matlab. Is anyone aware of a way to avoid this issue?

Best Answer

Editing and reloading a Python&reg; module in the same MATLAB session. To use an updated module, restart MATLAB.

Also see: python reload() function matlab 2014b

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MATLAB: Importing custom python module fails

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

MATLAB: How to clean MATLAB cache when MATLAB got corrupted

You could try several of the rehash command options such as

rehash toolboxcache

but it would not surprise me if you ended up needing to reinstall.

Best Answer

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MATLAB: Importing custom python module fails

MATLAB: How to clean MATLAB cache when MATLAB got corrupted

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