Search found 10 matches

by rgerkin
Thu Sep 05, 2019 6:13 pm
Forum: Other ways of using NEURON in neuroscience education
Topic: Running NEURON tutorials on webpage
Replies: 5
Views: 44671

Re: Running NEURON tutorials on webpage

Awesome, thanks Robert! Do you think these could be moved to a "NEURON-tutorials" GitHub repo? Then I could git clone whatever was in there everytime I build my server for teaching, and also submit PRs if I see potential improvements. I could set it up and then transfer ownership if you'd ...
by rgerkin
Thu Aug 22, 2019 1:20 pm
Forum: Other ways of using NEURON in neuroscience education
Topic: Running NEURON tutorials on webpage
Replies: 5
Views: 44671

Re: Running NEURON tutorials on webpage

What is the status of this? I have students copying/pasting from https://neuron.yale.edu/neuron/static/d ... steps.html into Jupyter notebooks on our lab JupyterHub and it seems to work great. But just converting this directly to a notebook would be better. Has anyone done this?
by rgerkin
Thu May 09, 2019 11:32 am
Forum: NEURON + Python
Topic: Turn off print messages in NEURON
Replies: 2
Views: 2435

Re: Turn off print messages in NEURON

I was using NEURON 7.5 so I don't think I had this functionality yet. It seems likely that I will be able to redirect stdout as needed entirely with Python calls in NEURON 7.6, since this commit https://github.com/neuronsimulator/nrn/commit/ef4da5dbf293580ee1bf86b3a94d3d2f80226f62 , which contains t...
by rgerkin
Wed May 08, 2019 8:05 pm
Forum: NEURON + Python
Topic: Turn off print messages in NEURON
Replies: 2
Views: 2435

Turn off print messages in NEURON

When using NEURON from Python, I get lots of printed messages that I don't really want to see. If they originate from the NEURON python module, I am able to intercept them and redirect from stdout to another buffer that I can check later (if needed). But the ones coming from the C libraries I am hav...
by rgerkin
Fri Jan 25, 2019 6:37 pm
Forum: UNIX/Linux
Topic: nrnivmodl compiling in Linux
Replies: 8
Views: 26121

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: 27608

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: 27608

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: 27608

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: 27608

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: 8853

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...