www.neuron.yale.edu

XQuartz is one of those installations that requires one to logout and log back in in order to activate it.

A work around for now for readline problems is to try
nrn-7.8.1-2-gdfe33e60-osx-27-36-37-38-39.pkg
or
nrn-8.0.dev-239-g8f2aaaa9.w64-mingw-py-27-36-37-38-39-setup.exe
at
https://neuron.yale.edu/ftp/neuron/versions/alpha/
These use NEURON's internal readline sources.

Because of these perennial problems with readline when binary distributions are installed, we will be taking the tack during build of compiling a recent version of readline ourselves as a libreadline.a file along with ncurses and incorporating that into the libnrniv.dylib. I hope after that I'll nev...

Please try https://neuron.yale.edu/ftp/neuron/vers ... -setup.exe
If there are any difficulties that is the best place for me to resolve. I'm not experiencing any $N issue with that.

I would re-install software from xquartz.org. (After installing, logout and log back in). If that does not fix the issue, it may be a good idea to update the xcode command line tools and redo your mod files with nrnivmodl after removing the x86_64 folder. WIth regard to updating the xcode command li...

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 limited s...

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 the first ...

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...