Search found 1570 matches

by hines
Mon May 27, 2019 8:20 am
Forum: MSWin
Topic: Compiling script fails with newer NEURON versions due to $N
Replies: 2
Views: 149

Re: Compiling script fails with newer NEURON versions due to $N

Please try providing N as /cygdrive/c/nrn
The problem with c:/nrn is that the ':' in a pathlist is a separator.
The problem with /c/nrn is that msys2 apparently no longer supports that style.
by hines
Wed May 22, 2019 10:02 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Stochastic gating as a function of external variable (light, membrane tension)
Replies: 3
Views: 164

Re: Stochastic gating as a function of external variable (light, membrane tension)

I'm happy your nmodl mechanism resolves the issue. So this response is a bit stale. The channel builder with ligand would also suffice, Just
invent a ligand name with 0 charge and have another mechanism that modifies the ligand concentration according to your desire function.
by hines
Thu May 09, 2019 10:55 am
Forum: NEURON + Python
Topic: Turn off print messages in NEURON
Replies: 2
Views: 165

Re: Turn off print messages in NEURON

With the most recent master from github, all (or at least most) of printf in c is redirected to the python stdout (if python is the launched program). This was done so that all output with jupyter notebooks goes to the notebook. Note that the statement that actually does the printing is line 687 of ...
by hines
Thu Apr 25, 2019 9:42 pm
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 504

Re: Installing Neuron on macOS Mojave

May want to update the xcode command line tools. Mine are Apple LLVM version 10.0.1 (see via gcc -v). Not the latest xcode but recent enough.
My Mojave is 10.14.5
by hines
Wed Apr 24, 2019 10:10 pm
Forum: MSWin
Topic: mknrndll not finding nrnunits.lib
Replies: 6
Views: 407

Re: mknrndll not finding nrnunits.lib

Yes. You noticed the contradiction Cant open units table in either of: /cygdrive/C/nrn/lib/nrnunits.lib Where that is exactly the correct value for MODLUNIT (and if you export it as MODLUNIT the problem is fixed). I need to do diagnostic runs to trace this to its most elementary source. Will get bac...
by hines
Wed Apr 24, 2019 7:48 pm
Forum: MSWin
Topic: mknrndll not finding nrnunits.lib
Replies: 6
Views: 407

Re: mknrndll not finding nrnunits.lib

Does the file c:/nrn/lib/nrnunits.lib exist in your installation? Does mknrndll work in the bash terminal if you have export MODLUNIT=/cygdrive/c/nrn/lib/nrnunits.lib Make sure before running that you clean out the *.c and *.o files derived from *.mod Looks like I have a problem with some script usi...
by hines
Wed Apr 24, 2019 7:08 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 10
Views: 541

Re: No module named hoc37

Although my default python3 comes from python.org, I also have anaconda3 (python3.7) installed and I see that the library you need is in /where/you/installed/anaconda3/lib So try export LD_LIBRARY_PATH=/where/you/installed/anaconda3/lib and see if things launch correctly. I mean export LD_LIBRARY_PA...
by hines
Wed Apr 24, 2019 6:48 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 10
Views: 541

Re: No module named hoc37

so copying that file to those two alternative hoc.so and hoc37.made no difference Actually, I'm relieved that I don't have to hunt up further documentation on variations of the python3 shared library module naming standard. libpython3.7m.so.1.0 => not found This is the main anaconda python library ...
by hines
Wed Apr 24, 2019 5:16 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 10
Views: 541

Re: No module named hoc37

I was surprised that there did not seem to be an explicit attempt during import to load the file hoc.cpython-37m-x86_64-linux-gnu.so I would be curious what happens if you temporarily cp hoc.cpython-37m-x86_64-linux-gnu.so hoc.so # be sure to make a copy of hoc.so first!!! cp hoc.cpython-37m-x86_64-...
by hines
Tue Apr 23, 2019 9:03 am
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 10
Views: 541

Re: No module named hoc37

Does your NEURON module have the contents: $ ls /usr/local/nrn/lib/python/neuron crxd hclass3.pyc nonvint_block_supervisor.py doc.py help_data.dat nonvint_block_supervisor.pyc doc.pyc hoc.cpython-35m-x86_64-linux-gnu.so psection.py gui2 hoc.cpython-36m-x86_64-linux-gnu.so psection.pyc gui.py hoc.cpy...
by hines
Tue Apr 23, 2019 8:32 am
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 504

Re: Installing Neuron on macOS Mojave

Please do a git pull for nrn. A multiply defined function was introduced by
https://github.com/neuronsimulator/nrn/ ... e37123aa3c
and fixed by
https://github.com/neuronsimulator/nrn/ ... c586e23e6c
by hines
Wed Mar 27, 2019 4:51 pm
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 1504

Re: Morphology and AP generation

I've run the latest version of NEURON with Anaconda3 with a Jupyter notebook and believe your issue is due to fmc3_1 requiring that stdrun.hoc already be loaded when celldef() is executed. If stdrun.hoc is not already loaded, then celldef() will raise an error at the beginning of geom_nseg() becasu ...
by hines
Mon Mar 25, 2019 10:24 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 1504

Re: Morphology and AP generation

I'm guessing that sometimes nseg=1 and sometimes nseg=5 and somewhere in the jupyter notebook that request is sometimes executed and sometimes not. I'd need to have the notebook and all the external files it is loading to diagnose why/how that is occurring. Also what version of NEURON is being used ...
by hines
Tue Mar 12, 2019 3:43 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL Compile Error: Assertion failed!
Replies: 10
Views: 1080

Re: NMODL Compile Error: Assertion failed!

if those statements (minf, ninf) are in BREAKPOINT, are they undergoing unnecessary recalculations? Yes. And for the fixed step method with secondorder=2, BREAKPOINT and DERIVATIVE blocks are called at different values of t so that voltages are different. CONDUCTANCE is suitable for ohmic currents....