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I am trying to call a python function from a C program but when trying to run the compiled program I get the error:

Fatal Python error: initfsencoding: unable to load the file system codec
ModuleNotFoundError: No module named 'encodings'

Current thread 0x00007fff94214380 (most recent call first):
Abort trap: 6

I am using python3.7 installed using anaconda3 on macOS High Sierra 10.13.5.

To compile my code called callpy.c, I used

gcc -o callpy callpy.c -I/Users/wernop/anaconda3/include/python3.7m -L/Users/wernop/anaconda3/lib/python3.7/config-3.7m-darwin -lpython3.7m

which runs without errors or warnings.

I saw this question: Fatal Python error: initfsencoding: unable to load the file system codec and therefore made sure to set the environmnent variables

PYTHONPATH='/Users/wernop/anaconda3/bin/python3.7'
PYTHONHOME='/Users/wernop/anaconda3/bin/python3.7'

I would be grateful for any help.

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  • I saw this question: Fatal Python error: initfsencoding: unable to load the file system codec and therefore made sure to set the environmnent variables Are you not using an environment, though? Commented Apr 16, 2020 at 0:12
  • @AMC Yes, I am using the conda base environment, which is located in the directory /Users/wernop/anaconda3. Should my environment variables be set differently? Commented Apr 16, 2020 at 15:20
  • Err, PYTHONPATH='/Users/wernop/anaconda3/bin/python3.7' doesn't do what you expect. PYTHONPATH should point to library roots, not executables. Run the following: python3.7 -c "import encodings; print(encodings.__file__). Make sure you use the right executable from anaconda installation. This should print you a path like /usr/lib64/python3.7/encodings/__init__.py. You thus set PYTHONPATH="/usr/lib64/python3.7". Print the contents of sys.path in your code to see whether PYTHONPATH was applied correctly. Commented Apr 16, 2020 at 17:02
  • Aside from that, check what flags you'll need for compilation by running python3-config --cflags --ldflags. Commented Apr 16, 2020 at 17:02
  • Yes, I am using the conda base environment Don't! Using a single environment for everything, especially the base environment, is a surefire way to end up with a bunch of issues. I wouldn't be surprised if it's at least partially responsible for the problems you're experiencing. Should my environment variables be set differently? I think there should be no need to mess with environment variables manually. How did you install Conda? Commented Apr 16, 2020 at 20:12

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I don't know if I answer to your question, but when I call Python from C, I use PyObjects and it works really fine

You have some examples here : https://docs.python.org/3.8/extending/embedding.html

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3 Comments

Thanks for your reply. I also used PyObjects in my C code. I think my problem is not so much about the C code, but about the Python environment.
Could you run your compilation with the -Wall option. This option show sometimes more details about compilation warning.
No warnings were given even with the -Wall option

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