www.neuron.yale.edu

Posted: **Thu Sep 17, 2015 12:25 pm**

Hello, I have just started using a Mac with Yosemite 10.10.5, but I am having a little NEURON trouble (or maybe it's actually MATLAB trouble?).

I installed NEURON 7.4 and it is working fine. But then when I try to run it from MATLAB 2015a using a system call (which I can do just fine in Linux or Windows), I am having trouble. Here's what happens:

NEURON -- Release 7.4 (1341:2ccabed20677) 2ccabed20677
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits

oc>load_file("nrngui.hoc")

nrniv: Couldn't find: nrngui.hoc

near line 1

load_file("nrngui.hoc")

^

0

Even though I can see it exists at /Applications/NEURON-7.4/nrn/share/nrn/lib/hoc/nrngui.hoc and invoking NEURON from Mac's Terminal works just fine and gives no error. If I define the whole path to the file, I get a Python error (I didn't think I was invoking Python, though I did do the standard Mac install which I guess installs NEURON with Python?):

oc>load_file("/Applications/NEURON-7.4/nrn/share/nrn/lib/hoc/nrngui.hoc")

first instance of j

first instance of itmp

first instance of using_cvode_

first instance of movie_frame_dur_

first instance of realtime

first instance of running_

first instance of rtstart

first instance of stdrun_quiet

first instance of screen_update_invl

first instance of tstop

first instance of steps_per_ms

first instance of nstep_steprun

first instance of runStopAt

first instance of runStopIn

first instance of global_ra

first instance of mapped_nrnmainmenu_

first instance of v_init

first instance of n_graph_lists

first instance of i

first instance of eventslow

first instance of eventcount

first instance of cnt

Traceback (most recent call last):

File "<string>", line 1, in <module>

ImportError: No module named neuron

1

Here are my current environmental variables (I've tried a lot of combinations of these, but apparently just not the right one):

>> disp(getenv('PATH'))
/usr/local/bin:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin:/Applications/NEURON-7.4/nrn/x86_64/bin:/Applications/NEURON-7.4/nrn/x86_64/bin
>> disp(getenv('PYTHONPATH'))
/System/Library/Frameworks/Python.framework/Versions/2.7/lib
>> disp(getenv('PYTHONHOME'))
/System/Library/Frameworks/Python.framework/Versions/2.7
>> disp(getenv('NEURONHOME'))
/Applications/NEURON-7.4/nrn/x86_64/bin
>> disp(getenv('N'))
/Applications/NEURON-7.4/nrn/x86_64/bin

And here is a bash script I call when issuing system commands from MATLAB or launching Mac's Terminal:

Code: Select all

export PATH=/usr/local/bin:$PATH:/Applications/NEURON-7.4/nrn/x86_64/bin
export PYTHONPATH=/System/Library/Frameworks/Python.framework/Versions/2.7/lib
export PYTHONHOME=/System/Library/Frameworks/Python.framework/Versions/2.7
export NEURONHOME=/Applications/NEURON-7.4/nrn/x86_64/bin
export N=/Applications/NEURON-7.4/nrn/x86_64/bin

Posted: **Thu Sep 17, 2015 4:29 pm**

The NEURONHOME environment variable is incorrect. If it exists at all, it should be /Applications/NEURON-7.4/nrn/share/nrn
At any rate, without that variable, what is the result, after a launch, of the hoc function
print neuronhome()

I believe this is irrelevant, but if you launch python and wish to import neuron they your PYTHONPATH should also contain
/Applications/NEURON-7.4/nrn/lib/python
but check to see if that is lib64 or lib.
You might try unsetting the NEUROHOME, PYTHONPATH, and PYTHONHOME variables and see what is suggested by executing
nrnpyenv.sh

Posted: **Tue Sep 22, 2015 10:26 am**

The NEURONHOME environment variable is incorrect. If it exists at all, it should be /Applications/NEURON-7.4/nrn/share/nrn

That was it, everything works fine after setting NEURONHOME correctly!

At any rate, without that variable, what is the result, after a launch, of the hoc function
print neuronhome()

This turns up blank if I have not set NEURONHOME environmental variable

Thank you for the PYTHONPATH info. I have added that to my variable as I will want to experiment with python and NEURON soon.

Thank you, Michael!

www.neuron.yale.edu

NEURON and MATLAB on Mac

NEURON and MATLAB on Mac

Re: NEURON and MATLAB on Mac

Re: NEURON and MATLAB on Mac