Segmentation fault in executable, but not in source

[James Loy]

Hi Folks-

I have a situation that I'm having a tough time debugging.  I'm new to PyInstaller, and I'm also dealing with a very hacked together code base with A LOT of dependencies.

I am able to freeze my code on MacOS mojave, and run with no problem.  However, when I freeze the code on CentOS 7.7 I encounter a seg fault.  When I run the code straight from source (i.e., python myscript.py), the seg fault doesn't pop up and everything runs as expected (on both MacOS and CentOS 7.7).

So my question is: what sort of things would cause an executable to seg fault, but not the python script?  My first hunch is some binary compatibility issue with external libraries and the CentOS, but how does that explain that the python script works perfectly fine?  I say this because, when I change some of the dependencies, I get errors about not being able to find the right version of GLIBCXX.

Anyone have any thoughts?  Thanks in advance.

-James

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[James Loy]

Just a little more context.  I'm working on a machine learning project that makes use of a lot of open source libraries for computation such as tensorflow, sklearn, pandas, and xgboost.  The versioning of each of the libraries hasn't been closely tracked, unfortunately.

I've attached the output of the build procedure in this comment.  In particular, I'm also curious about these few lines:

ldd: warning: you do not have execution permission for `/root/miniconda3/envs/rte/lib/python3.6/site-packages/cryptography-2.5-py3.6-linux-x86_64.egg/cryptography/hazmat/bindings/_constant_time.abi3.so'

ldd: warning: you do not have execution permission for `/root/miniconda3/envs/rte/lib/python3.6/site-packages/cryptography-2.5-py3.6-linux-x86_64.egg/cryptography/hazmat/bindings/_openssl.abi3.so'

ldd: warning: you do not have execution permission for `/root/miniconda3/envs/rte/lib/python3.6/site-packages/cryptography-2.5-py3.6-linux-x86_64.egg/cryptography/hazmat/bindings/_padding.abi3.so'

ldd: warning: you do not have execution permission for `/root/miniconda3/envs/rte/lib/python3.6/site-packages/coverage-5.0a8-py3.6-linux-x86_64.egg/coverage/tracer.cpython-36m-x86_64-linux-gnu.so'

/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/tbbpool.cpython-36m-x86_64-linux-gnu.so: /lib64/libstdc++.so.6: version `CXXABI_1.3.11' not found (required by /root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)

/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/tbbpool.cpython-36m-x86_64-linux-gnu.so: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)

/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/tbbpool.cpython-36m-x86_64-linux-gnu.so: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)

ldd: warning: you do not have execution permission for `/root/miniconda3/envs/rte/plugins/imageformats/../../lib/libgcc_s.so.1'

/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2: /lib64/libstdc++.so.6: version `CXXABI_1.3.11' not found (required by /root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)

/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)

/root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /root/miniconda3/envs/rte/lib/python3.6/site-packages/numba/npyufunc/../.libs/libtbb-52872150.so.2)

I don't see any of these errors when building on MacOS.