Search found 1618 matches

by hines
Wed Nov 11, 2020 6:34 pm
Forum: MSWin
Topic: Compiling script fails with newer NEURON versions due to $N
Replies: 6
Views: 2656

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

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.
by hines
Thu Oct 22, 2020 7:01 pm
Forum: OS X
Topic: Gui Freezing
Replies: 5
Views: 648

Re: Gui Freezing

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...
by hines
Thu Oct 22, 2020 5:25 pm
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 1634

Re: Installing on Ubuntu 20.04 (GUI not working)

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...).
by hines
Sat Oct 03, 2020 7:05 am
Forum: Other questions
Topic: Temperature Dependent Membrane Capacitance
Replies: 4
Views: 1866

Re: Temperature Dependent Membrane Capacitance

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.
by hines
Thu Aug 13, 2020 10:56 am
Forum: MSWin
Topic: DLL load failed in Windows10
Replies: 4
Views: 1062

Re: DLL load failed in Windows10

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...
by hines
Tue Aug 11, 2020 8:43 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Defining a POINTER to be a list
Replies: 16
Views: 8456

Re: Defining a POINTER to be a list

VERBATIM is still the only way to implement an array of pointers.
by hines
Thu Jul 30, 2020 7:00 am
Forum: Other questions
Topic: initialization of calcium concentration in a segment with attached point process
Replies: 5
Views: 1326

Re: initialization of calcium concentration in a segment with attached point process

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...
by hines
Tue Jul 28, 2020 4:47 pm
Forum: NEURON + Python
Topic: Is it possible to track "value explosions" and out of range errors
Replies: 2
Views: 679

Re: Is it possible to track "value explosions" and out of range errors

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...
by hines
Wed Jun 10, 2020 11:07 am
Forum: Other questions
Topic: spFactor error: Zero Diagonal
Replies: 7
Views: 4198

Re: spFactor error: Zero Diagonal

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 ...
by hines
Wed Jun 03, 2020 9:08 am
Forum: UNIX/Linux
Topic: Open MPI error with h.nrnmpi_init(): mca_base_component_repository_open: unable to open mca_patcher_overwrite
Replies: 7
Views: 3067

Re: Open MPI error with h.nrnmpi_init(): mca_base_component_repository_open: unable to open mca_patcher_overwrite

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 ...
by hines
Tue Jun 02, 2020 4:15 pm
Forum: UNIX/Linux
Topic: Open MPI error with h.nrnmpi_init(): mca_base_component_repository_open: unable to open mca_patcher_overwrite
Replies: 7
Views: 3067

Re: Open MPI error with h.nrnmpi_init(): mca_base_component_repository_open: unable to open mca_patcher_overwrite

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...
by hines
Tue Jun 02, 2020 3:26 pm
Forum: UNIX/Linux
Topic: Open MPI error with h.nrnmpi_init(): mca_base_component_repository_open: unable to open mca_patcher_overwrite
Replies: 7
Views: 3067

Re: Open MPI error with h.nrnmpi_init(): mca_base_component_repository_open: unable to open mca_patcher_overwrite

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...
by hines
Mon Jun 01, 2020 1:50 pm
Forum: UNIX/Linux
Topic: Open MPI error with h.nrnmpi_init(): mca_base_component_repository_open: unable to open mca_patcher_overwrite
Replies: 7
Views: 3067

Re: Open MPI error with h.nrnmpi_init(): mca_base_component_repository_open: unable to open mca_patcher_overwrite

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...
by hines
Mon Jun 01, 2020 11:50 am
Forum: Other questions
Topic: Temperature Dependent Membrane Capacitance
Replies: 4
Views: 1866

Re: Temperature Dependent Membrane Capacitance

Please see https://github.com/nrnhines/dcmdt in particular the comment in hhdcdt.mod
by hines
Fri Apr 03, 2020 5:44 pm
Forum: NEURON + Python
Topic: Copy a nrn object in Python?
Replies: 5
Views: 1637

Re: Copy a nrn object in Python?

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 ...