www.neuron.yale.edu

The issues mentioned by Ted have been fixed and are available with the current neuron-nightly wheel. Also neurondemo should work when the
neuron-nightly wheel is installed in a location for which the user does not have write permission (eg. sudo pip...).

If you are using extracellular, make sure you have that inserted in every node as well as the myelin sections. Otherwise the extracellular current balance boundary conditions may not be as expected.

File "C:\Users\17186\py3env\Lib\site-packages\neuron\__init__.py", line 90 I'm puzzled by this because on windows 10 the neuron module is in c:\nrn\lib\python\neuron Do you have an old installation from pip install from a third party? It has been a long time since __init__.py had python 2...

VERBATIM is still the only way to implement an array of pointers.

You probably think this is a bug, I think we need to expand the documentation about ion_style a bit in this area. ie. from neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/ions.html?highlight=ion_style Warning: if other mechanisms are inserted subsequent to a call of this function, the s...

The exp function is often used for channel rates where the arg is some function of voltage. As the arg is 1.8...e184 that could be far downstream from the cause of such a large arg. Also it sometimes occurs under conditions of temporary instability while the variable time step method is busy reducin...

2008, 2012, and now 2020. I wonder what happened in 2016 :) Please send me a zip file with the hoc,ses,mod,py files so I can reproduce the error and try to diagnose. The error message means the matrix had no inverse. I wonder if two matrix rows started out the same. I wonder if the (sub?)problem it ...

openmpi was not installed "over" the old version That is better. One can safely update or remove the system version with apt and one can safely update your source compiled version without them interfering with each other. From the perspective of a NEURON build, one by default always gets ...

was the --DNRN_ENABLE_MPI_DYNAMIC=ON option part of the build I just did? No. Default of NRN_ENABLE_MPI_DYNAMIC is OFF. Dynamic MPI and PYTHON (and InterViews) is most useful for binary installations where one does not a priori know if mpi or python (or XQuartz for mac) is installed at all on the u...

I guess that I should have rebuilt neuron after installing open mpi anyways? Building from sources with mpi enabled requires a pre-existing version of mpi, ie openmpi or mpich. Installing a binary distribution which we built with --DNRN_ENABLE_MPI_DYNAMIC=ON does not require an mpi on the user mach...

Let's see if this problem disappears with a cmake build. If you don't have cmake, then sudo apt install cmake Then with a fresh nrn repository clone git clone https://github.com/neuronsimulator/nrn nrncmake cd nrncmake mkdir build cd build cmake .. -DCMAKE_INSTALL_PREFIX=install make -j install expo...

Please see https://github.com/nrnhines/dcmdt in particular the comment in hhdcdt.mod

You're right, there are no __deepcopy__ method implementations for NEURON objects like sections, segments, mechanisms, point processes, NetCon, or other potentially relevant info such as gid in parallel models. In some cases, a copy is not valid such as for top level hoc Section (constructed by the ...

I think the easiest installation is to try to remove all of what you have done and download https://neuron.yale.edu/ftp/neuron/versions/alpha/nrn-7.8.0-82-g5104c2e7-osx-py-27-36-37-38.pkg and double click on it. If that works and you then want to build from github sources, I can give the recipe for ...

You didn't mention whether you installed from sources or a pkg file? I'll assume the former. You didn't mention how you configured. So I don't know where the neuron module was installed. Or where the bulk of neuron itself was installed. With your PATH=$HOME/local/bin I assume you used cmake (configu...