Search found 1697 matches

by hines
Fri Jun 17, 2022 12:15 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: 'y' is a reserved word?
Replies: 2
Views: 12490

Re: 'y' is a reserved word?

y cannot be the name of a STATE as that automatically declares y0 for the initial value. Unfortunately y0() is the Bessel function of the first order and is declared in math.h.
by hines
Fri Jun 17, 2022 12:06 pm
Forum: Other questions
Topic: h.finitialize() fails with a hocobj call error
Replies: 5
Views: 13419

Re: h.finitialize() fails with a hocobj call error

Running the model requires the 8.swc file. Please send that to michael.hines@yale.edu as a an attachment. Or zip file if there are are other files needed to run the model.
by hines
Fri May 20, 2022 7:07 am
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 56032

Re: NEURON 7.6.7 - Permission denied. Python not available.

https://github.com/chlubba/PyPNS/pull/6 has been merged to master. The expectation is that all versions of NEURON will now produce the same results modulo nondeterministic use of random variables.
by hines
Thu May 19, 2022 2:16 pm
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 56032

Re: NEURON 7.6.7 - Permission denied. Python not available.

When I use NEURON-8.1.0 with python3.9 on my linux desktop and install PyPNS from github and run python -i test.py I get (pypns-39) hines@hines-t7500:~/tmp/pypns$ python -i test.py 1 Creating axon 0 Myelinated fiber diameter: [0.97982345] Number of segments for myelinated axon: 2208 Starting simulat...
by hines
Thu May 19, 2022 6:12 am
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 56032

Re: NEURON 7.6.7 - Permission denied. Python not available.

Yes, I got this message but for version 8.0. NEURON -- VERSION 7.6.7-3-gef035d9b 7.6 (ef035d9b) 2019-04-28 That confuses me.I can't reconcile the "version 8.0" with the 7.6.7 banner. Anyway, I suppose it is potentially possible for me to rebuild a version of 7.6.7 that has a python 3.8 in...
by hines
Thu May 19, 2022 5:59 am
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 56032

Re: NEURON 7.6.7 - Permission denied. Python not available.

i.e. nrn-7.6.7.w64-mingw-py-37-36-35-27-setup.exe

Sorry, it was staring me in the face the whole time. That installer does not have an interface dll for Python3.8
by hines
Wed May 18, 2022 9:17 pm
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 56032

Re: NEURON 7.6.7 - Permission denied. Python not available.

When you temporarily installed the most recent version of NEURON, were you able to successfully launch
nrniv -python
from a command prompt?
by hines
Wed May 18, 2022 8:20 pm
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 56032

Re: NEURON 7.6.7 - Permission denied. Python not available.

The syntax for set statements in a command prompt terminal does not allow spaces surrounding the '=' . I don't know how they crept into the code fragment above. Please try again in a command prompt the following set NRN_PYTHONHOME=C:/Users/amalu/anaconda3 set NRN_PYLIB=C:/Users/amalu/anaconda3/pytho...
by hines
Wed May 18, 2022 4:04 pm
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 56032

Re: NEURON 7.6.7 - Permission denied. Python not available.

try the following. Be careful about the distinction between / and \ Start a windows command line terminal and type nrniv quit() I just want to verify that you can launch nrniv but also get the error. Then set NRN_PYTHONHOME = C:/Users/amalu/anaconda3 set NRN_PYLIB = C:/Users/amalu/anaconda3/python38...
by hines
Wed May 18, 2022 2:13 pm
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 56032

Re: NEURON 7.6.7 - Permission denied. Python not available.

If you use the bash terminal that is installed with NEURON, it suffices to copy/paste into that terminal window export NRN_PYTHONHOME = "C:/Users/amalu/anaconda3" export NRN_PYLIB = "C:/Users/amalu/anaconda3/python38.dll" And, by the way none of this is needed if you launch pytho...
by hines
Wed May 18, 2022 8:55 am
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 56032

Re: NEURON 7.6.7 - Permission denied. Python not available.

nrnpyenv.sh has changed a bit over the past few years as it occasionally needs tweaking when new python installations become available. I suggest the experiment of replacing c:\nrn\bin\nrnpyenv.sh with https://github.com/neuronsimulator/nrn/blob/master/bin/nrnpyenv.sh The purpose of the script is to...
by hines
Fri Mar 25, 2022 12:38 pm
Forum: NetPyNE
Topic: After updating to MacOS 12.3 Monterey
Replies: 5
Views: 23871

Re: After updating to MacOS 12.3 Monterey

Perhaps you have not installed the xcode command line tools. From a Terminal, type xcode-select --install and see if that fixes the problem. Although I'm curious about why you had a import error when importing neuron after a package install. No need to pursue that now since your pip install fixed th...
by hines
Thu Mar 17, 2022 8:55 am
Forum: OS X
Topic: MacOS 12.3; Application "Terminal" can't be opened. -1703
Replies: 4
Views: 24030

Re: MacOS 12.3; Application "Terminal" can't be opened. -1703

Have to admit I'm stuck. See: https://github.com/neuronsimulator/nrn/issues/1708 I can see the Terminal via the Finder in /Applications/Utilities But from a Terminal hines@Michaels-MacBook-Pro-2 ~ % ls -al /Applications/Utilities total 0 drwxr-xr-x 4 root wheel 128 Mar 16 18:45 . drwxrwxr-x 18 root ...
by hines
Wed Mar 16, 2022 8:47 pm
Forum: OS X
Topic: MacOS 12.3; Application "Terminal" can't be opened. -1703
Replies: 4
Views: 24030

Re: MacOS 12.3; Application "Terminal" can't be opened. -1703

I just upgraded to 12.3 and am experiencing the same issue when double clicking the nrngui or neurondemo icon. I'll try to diagnose and fix this. Meanwhile, a possible work around is to manually start a terminal window and launch neurondemo or nrngui from there by typing those names into the termina...