libnrnpython3 and libnrnpython2 on High Sierra

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wpettine
Posts: 2
Joined: Fri Jan 05, 2018 11:12 am

libnrnpython3 and libnrnpython2 on High Sierra

Post by wpettine » Wed Jan 10, 2018 10:45 am

I am trying to install neuron on High Sierra and am running into an issue with libnrnpython3 and libnrnpython2. Specifically, it is showing the output below upon startup. It then cannot run neuron files.
NEURON -- VERSION 7.5 master (b14b5dd) 2017-12-21
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2016
See http://neuron.yale.edu/neuron/credits

loading membrane mechanisms from /Applications/NEURON-7.5/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so
Additional mechanisms from files
cabpump.mod cachan1.mod camchan.mod capump.mod invlfire.mod khhchan.mod mcna.mod nacaex.mod nachan.mod release.mod
Could not load either libnrnpython3 or libnrnpython2
pyver10=0 pylib=/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
Prior to installation of neuron through the package, I installed the following dependencies
- Xquartz
- Command line tools
- open MPI
- Anaconda (I had a pre-existing full installation)

I tried installing from the package provided on the following link:
https://www.neuron.yale.edu/neuron/download

I also tried compiling based on the instructions given here:
https://www.neuron.yale.edu/neuron/down ... ilestd_osx

Furthermore, libnrnpython3 and libnrnpython2 both exist on my machine, and appear entirely intact.

Any suggestions?

hines
Site Admin
Posts: 1467
Joined: Wed May 18, 2005 3:32 pm

Re: libnrnpython3 and libnrnpython2 on High Sierra

Post by hines » Wed Jan 10, 2018 11:32 am

I'm a little confused by
NEURON -- VERSION 7.5 master (b14b5dd) 2017-12-21
because this change is later than the latest alpha distribution of
https://neuron.yale.edu/ftp/neuron/vers ... 64-osx.pkg
which is

Code: Select all

#define GIT_DATE "2017-12-07"
#define GIT_BRANCH "master"
#define GIT_CHANGESET "c693a84"
#define GIT_LOCAL "1670"
I don not recall distributing as a package...

Code: Select all

#define GIT_DATE "2017-12-21"
#define GIT_BRANCH "master"
#define GIT_CHANGESET "b14b5dd"
#define GIT_LOCAL "1673"
Anyway, perhaps the problem will go away if you download and install the above package since there was a fix to nrnpyenv.sh which is a bit
more robust. ie.
https://github.com/nrnhines/nrn/commit/ ... d678c72b4d
or download the nrnpyenv.sh from there and use it to replace your present version of that file (in /Applications/NEURON-7.5/nrn/x86_64/bin)

wpettine
Posts: 2
Joined: Fri Jan 05, 2018 11:12 am

Re: libnrnpython3 and libnrnpython2 on High Sierra

Post by wpettine » Tue Jan 16, 2018 3:34 pm

Thanks for the reply! I set it up to notify me with replies now, so will respond faster.

I think the line
NEURON -- VERSION 7.5 master (b14b5dd) 2017-12-21
probably had something to do with installing by compilation.

I tried replacing the file nrnpyenv.sh in the relevent folder and continued getting the error. I also deleted everything, and reinstalled from the package you recommended, and continue to get the error. Here's the output
-e
NEURON -- VERSION 7.5 master (c693a84) 2017-12-07
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2016
See http://neuron.yale.edu/neuron/credits

loading membrane mechanisms from /Applications/NEURON-7.5/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so
Additional mechanisms from files
cabpump.mod cachan1.mod camchan.mod capump.mod invlfire.mod khhchan.mod mcna.mod nacaex.mod nachan.mod release.mod
Could not load either libnrnpython3 or libnrnpython2
pyver10=0 pylib=/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
oc>

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