NEURON not working properly after update to Catalina and major troubleshooting!
Posted: Thu Nov 21, 2019 12:36 pm
Hello all,
I am experiencing a very odd issue with NEURON after updating my Macbook Pro to the newest OS (Catalina).
At first, it appeared that something was awry with Python, so I went through a long and arduous process of uninstalling and reinstalling Anaconda (both versions 2 and 3). When this didn't appear to be working, I found this thread on the forum here: viewtopic.php?t=3806
After reading through that, and running
multiple times, and using
to make the relevant changes, at the very minimum Python appears to be working (I can run "python" and "python3" from my Terminal and it appears to run... Anaconda still isn't working, but that's a separate issue potentially).
If I run nrngui from my home terminal window, it's also able to run. HOWEVER, as soon as I move to ANY different folder, particularly where my NEURON code is stored, this no longer works. In particular, if I run nrngui init_final.hoc (which opens the model I want to use) I get the following:
If it is of importance, "python" and "python3" both still appear to be working in this new folder. Additionally, the output of running nrnpyenv.sh is the same:
I'm at my absolute wits end trying to figure this out, and have exhausted essentially every troubleshooting resource available to me... and since I need access to my code (as I'm nearing the completion of a project) this issue is a major problem. Any help in fixing this would be GREATLY appreciated!
EDIT: I should have mentioned that I've also uninstalled and reinstalled NEURON multiple times, so I'm running NEURON 7.7
I am experiencing a very odd issue with NEURON after updating my Macbook Pro to the newest OS (Catalina).
At first, it appeared that something was awry with Python, so I went through a long and arduous process of uninstalling and reinstalling Anaconda (both versions 2 and 3). When this didn't appear to be working, I found this thread on the forum here: viewtopic.php?t=3806
After reading through that, and running
Code: Select all
unset PYTHONHOME
unset NRN_PYLIB
nrnpyenv.sh
Code: Select all
sudo nano $HOME/.bash_profile
If I run nrngui from my home terminal window, it's also able to run. HOWEVER, as soon as I move to ANY different folder, particularly where my NEURON code is stored, this no longer works. In particular, if I run nrngui init_final.hoc (which opens the model I want to use) I get the following:
Code: Select all
/Users/scottrich/OneDrive - UHN/3) NEURON stuff/Human Cell/x86_64/special: line 13: /Applications/NEURON-7.6/nrn/x86_64/bin/nrniv: No such file or directory
Code: Select all
nrnpyenv.sh
# PYTHON=/usr/bin/python3
# nrn_pylib from lsof: /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.7/Python3
# items in sys.path = 7
# beginning with sys.prefix = 4
# site-3 same as sys.prefix
# in neither location ['.', '/Applications/NEURON-7.7/nrn/lib/python', '/Users/scottrich/OneDrive - UHN/3) NEURON stuff/Human Cell']
# sys.prefix = /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.7
# site-3 = /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.7
# if launch python, then need:
export PYTHONPATH="/Applications/NEURON-7.7/nrn/lib/python:."
# if launch nrniv, then likely need:
export PYTHONHOME="/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.7"
export NRN_PYLIB="/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.7/Python3"
EDIT: I should have mentioned that I've also uninstalled and reinstalled NEURON multiple times, so I'm running NEURON 7.7