installing editable hnn-core - dlopen fail

[dylansdaniels]

Running (intel) MacOS Venture 13.2.1

I'm running into a path issue with NEURON probably related to older installations. I'm getting 'dlopen fail' when running my 'make test', but it's also looking in the wrong location.

dlopen failed -
dlopen(/Users/dylandaniels/Documents/github-repos/hnn-core/hnn_core/mod/x86_64/.libs/libnrnmech.0.so, 0x0002): Library not loaded: /Applications/NEURON-7.7/nrn/x86_64/lib/libnrnoc.0.dylib
Referenced from: <959875B6-5E4B-374A-8C93-23C300F47E54> /Users/dylandaniels/Documents/github-repos/hnn-core/hnn_core/mod/x86_64/.libs/libnrnmech.0.so
Reason: tried: '/Applications/NEURON-7.7/nrn/x86_64/lib/libnrnoc.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Applications/NEURON-7.7/nrn/x86_64/lib/libnrnoc.0.dylib' (no such file), '/Applications/NEURON-7.7/nrn/x86_64/lib/libnrnoc.0.dylib' (no such file), '/usr/local/lib/libnrnoc.0.dylib' (no such file), '/usr/lib/libnrnoc.0.dylib' (no such file, not in dyld cache)

I had everything working before trying to install the editable version of core, though in notebook I had to run sys.path.insert(0, '/usr/local/nrn/lib/python/') to get it to work (and also had to remove 'DISPLAY' from os.environ or i'd get a 'can't open DISPLAY' error from neruon)

[jasmainak]

Just to be clear, did you install Neuron using pip or did you use a different method?

[dylansdaniels]

several months back i deleted my old neuron installation (not pip) and installed via pip. now that i think about it, i'm not sure that /usr/local/nrn/lib/python is doing anything? i copied the solutions here https://doc.cocalc.com/howto/neuron.html to get things running in notebook before trying to install the editable version, but it may have just been solving the display issue

my neuron lives here: /Users/dylandaniels/anaconda3/envs/hnn/lib/python3.7/site-packages/neuron

[jasmainak]

I think those instructions might be outdated. Can you delete all copies of Neuron you have and do a fresh editable install of hnn-core in a fresh environment? So delete:

/usr/local/nrn/lib/python

and then make a new environment and try installing in there. Make sure to not touch any environment variables. It should just work out of the box without editing any environmental variables

[jasmainak]

This seems like a Python 3.11 issue. Instead of downgrading, I wonder if this could be your first PR @dylansdaniels to fix these tests :)

[dylansdaniels]

[dylansdaniels]

Also, all of the workflows run, but the plot wasn't showing correctly in the final example of the alpha workflow where you have the 3 subplots. It was drawing the first plot from plot_spikes_hist and not drawing the final fig after adding the dipole and psd subplots.

It displays properly when adding the show=False arg to plot_spikes_hist. Just wanted to flag that

[rythorpe]

Oh, good catch. Would you mind opening an issue for that?

[dylansdaniels]

Sure!

[jasmainak]

Also I hope you don't have NEURONHOME or PYTHONPATH or any such environment variables already set in your .bashrc or .bash_profile ?

[dylansdaniels]

.bashrc is empty and .bash_profile has the following but it's commented out:

unset __conda_setup
#<<< conda initialize <<<
#export PYTHONPATH=/Applications/NEURON-7.7/nrn/lib/python:$PYTHONPATH
#export PATH=/Applications/NEURON-7.7/nrn/x86_64/bin:$PATH