My program has a compiled module that causes the following error when
imported in OSX after freezing with pyinstaller:
Fatal Python error: Interpreter not initialized (version mismatch?)
Abort trap
This only affects OSX. The frozen program works without issue on windows
and linux. I have not tried other versions of OSX besides 10.6.
In OSX it is compiled with the following command lines:
g++ -o pdb2pka/substruct/Algorithms.os -c -fPIC
-I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
-I/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy/core/include
pdb2pka/substruct/Algorithms.cpp
g++ -o pdb2pka/substruct/Algorithms.so -bundle
pdb2pka/substruct/Algorithms.os -lpython2.6
Run normally it works just fine.
Numpy is imported without issue before the problematic module is loaded.
Other potentially useful info:
The problem module is loaded conditionally. (Yay for pyinstaller catching
it!) If I run a case where the module is not imported it works fine.
There are no warnings about Algorithms in warnpdb2pqr.txt
This is in the output of the pyinstaller: 9768 INFO: Using Python library
/System/Library/Frameworks/Python.framework/Versions/2.6/Python
The library "Python" is in the dist/pdb2pqr directory. It is required for
the Algorithms module.
$ otool -L pdb2pka.substruct.Algorithms.so
pdb2pka.substruct.Algorithms.so:
/System/Library/Frameworks/Python.framework/Versions/2.6/Python
(compatibility version 2.6.0, current version 2.6.1)
/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
version 7.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 125.2.11)
$ otool -L pdb2pqr.exe
pdb2pqr.exe:
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 159.1.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
1.2.5)
I'm guessing that the python library is the problem but I'm not sure what
to do about it.
The git repo for this application is
at https://github.com/sobolevnrm/apbs-pdb2pqr and it lives in the pdb2pqr
folder if you want to take a look at the app as a whole.
Any suggestions?
Thanks,
Kyle
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