Search found 6 matches

by rgerkin
Fri Jan 25, 2019 6:37 pm
Forum: UNIX/Linux
Topic: nrnivmodl compiling in Linux
Replies: 8
Views: 9976

Re: nrnivmodl compiling in Linux

If anyone gets here running NEURON with a miniconda installation, this is why it is happening and how to solve it: Your default gcc may be on the miniconda path (/path/to/miniconda/bin), and it will look in your miniconda path for libraries, too (/path/to/miniconda/lib). apt-get won't install the nc...
by rgerkin
Fri Nov 10, 2017 2:31 am
Forum: OS X
Topic: NEURON 7.5 + Python 3 installation on OSX 10.12.5
Replies: 4
Views: 14652

Re: NEURON 7.5 + Python 3 installation on OSX 10.12.5

For simple NEURON scripts like the one in https://neuron.yale.edu/neuron/static/docs/neuronpython/firststeps.html , the instructions I gave seem to work, but for others I run into: dyld: Library not loaded: @rpath/libpython3.5m.dylib I can fix this with: sudo install_name_tool -change @rpath/libpyth...
by rgerkin
Tue Oct 31, 2017 12:04 am
Forum: OS X
Topic: NEURON 7.5 + Python 3 installation on OSX 10.12.5
Replies: 4
Views: 14652

Re: NEURON 7.5 + Python 3 installation on OSX 10.12.5

I've created a minimal installation verified using Travis CI and tested against a simple example from the Neuron website.
https://github.com/rgerkin/neuron-python3-miniconda
by rgerkin
Tue Oct 24, 2017 2:21 am
Forum: OS X
Topic: NEURON 7.5 + Python 3 installation on OSX 10.12.5
Replies: 4
Views: 14652

Re: NEURON 7.5 + Python 3 installation on OSX 10.12.5

Thanks, Ted. This is also probably a good idea since setting the PYTHONHOME environment variable, which I think NEURON needs for installation if not for execution, can screw up the version of python that it is not set to. Which means that in the example above Python2 can get screwed up and so best t...
by rgerkin
Tue Oct 17, 2017 11:36 am
Forum: OS X
Topic: NEURON 7.5 + Python 3 installation on OSX 10.12.5
Replies: 4
Views: 14652

NEURON 7.5 + Python 3 installation on OSX 10.12.5

Since the instructions on the webpage didn't work for me, I want to document here commands that allowed me to install NEURON 7.5 from source with Python 3 support on OSX 10.12.5. I hope this will be useful to someone. For simplicity, this installation excludes Interviews, MPI support, and everything...
by rgerkin
Tue Oct 10, 2017 2:51 am
Forum: Other questions
Topic: NEURON Python segmentation fault on OSX
Replies: 1
Views: 7653

NEURON Python segmentation fault on OSX

On OSX (fresh installation of NEURON 7.5 but similar results with 7.4), but not on Linux, I observe the following problem with a python file LEMS_2007One_nrn.py (source here https://gist.github.com/rgerkin/e4867fbf22b455ca0f1517e9e2f88d2e ) import LEMS_2007One_nrn # runs fine however... def foo(): i...