www.neuron.yale.edu

On my machine (macOS Catalina Version10.15 Beta (19A573a)) (my most recent build in /Applications/NEURON-7.7 is NEURON -- VERSION 7.7.1-38-g1f3d46d9+ master (1f3d46d9+) 2019-09-13 ) I'm seeing for a typical libnrnmech.so created by nrnivmodl $ otool -L x86_64/.libs/libnrnmech.so ... /usr/lib/libncur...

An old way of getting the PARAMETER names of a mechanism is from neuron import h ms = h.MechanismStandard("hh", 1) parm_name = h.ref("") for i in range(ms.count()): ms.name(parm_name, i) print(parm_name[0]) https://www.neuron.yale.edu/neuron/static/py_doc/programming/mechstan.html#MechanismStandard....

Segmentation Fault errors under MPI with gap junctions when I had h.cvode.cache_efficient(1) I'd like to attempt to fix this bug. Can you send me a (hopefully small) version of your model that exhibits this error. (Michael.hines@yale.edu) An unrelated point is that it is now possible to avoid the "...

It appears nothing has been done in this area since late 2007. There was a hook added in python for rxd in 2013 but is not being used. The translation of the soma stack to a centroid of 3-d points with diam continues to be: Approximate each contour of the stack as a circle. Center is the average of ...

computational cost is at each time step of recording into numerous Vectors (for each segment You definitely want only one vector per thread for storage for a recording location. A POINTER for each segment in a thread would all point to the same scalar accumulator and the mod file would add a weight...

use POINTER variables for (1) aggregation I don't think you can use the source_var/target_var pattern for this purpose because there is no way for one target to receive an increment from many sources. (the opposite is natural: a source can copy its value to many targets.) This assumes I correctly i...

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 ...