www.neuron.yale.edu

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.

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.

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 ...

https://neuron.yale.edu/ftp/neuron/vers ... -setup.exe
fixes the problem.

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

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...

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...

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...

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 ...

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-...

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...

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

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 ...

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 ...

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....