Issue with two versions of python

Question

Problem having two versions of python on my Mac and them interacting. I have the following python locations

python is /anaconda3/envs/fenicsproject/bin/python

python is /usr/bin/python

and when I try to run a script. I get the following error:

Fatal Python error: PyThreadState_Get: no current thread

Abort trap: 6

I have googled some solutions and have found some posts saying I should try

env PYTHON_CONFIGURE_OPTS="--enable-framework"  #or 
env PYTHON_CONFIGURE_OPTS="--enable-shared" 

This is they type of code I try to run

#Import packages 
import dolfin as dl

I installed the env fenics by following the directions here

Answer 1

The google search possibly found Homebrew + Python on mac os x 10.8: Fatal Python error: PyThreadState_Get: no current thread importing mapnik however I was unable to find the library that links to a wrong version of python using otool.

I also found https://github.com/enthought/mayavi/issues/552 which suggests pinning to a different version of python.

Based on the install notes for hippy, https://hippylib.readthedocs.io/en/latest/installation.html then where they say conda create -n fenicproject ... you need to substitute the following:

conda create -n fenicsproject python==3.5.1
conda install -n fenicsproject -c conda-forge fenics==2017.2.0 \
               mpi4py matplotlib scipy sympy==1.1.1 jupyter

After this, python -c 'import dolfin' no longer fails. It might also be possible to use a later version of python (I only tried 3.5.1).

Answer 2

What OS are you using? That will largely determine the specifics of how to go about correcting this issue, but the key here is which Python version the system path points to and what Python version your IDE is pointing to.

What you largely want to avoid is a situation where you are running Python scripts via your native system Python (2, likely).

Check which version of Python your IDE is using (from: How do I check what version of Python is running my script?):

import sys
print(sys.version)

Is the first number a 2? Did you want to use Python 2?

Next, let's check what version your system currently defaults to. If Ubuntu/Linux, use:

python -V

Is this expected? If not, you may need to change your system environmental variables to point to the correct Python version. The solution to this is OS dependent. If Windows, search "Edit Environmental Variables for Your Account" -> "Environmental Variables" -> "Path" , be sure it either points to Anaconda or the correct Python version; if Ubuntu/Linux, check your .bashrc file:

gedit ~/.bashrc

to see if the system points to the correct Python variable. If using a Mac, I formally apologize.