Search found 1599 matches

by hines
Thu Aug 13, 2020 10:56 am
Forum: MSWin
Topic: DLL load failed in Windows10
Replies: 4
Views: 269

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 limited s...
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: 7056

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: 340

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: 211

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: 5
Views: 3096

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: 1457

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 the first ...
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: 1457

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: 1457

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: 1457

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: 2
Views: 985

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: 870

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 ...
by hines
Wed Mar 25, 2020 5:26 pm
Forum: OS X
Topic: Installation Help: Fail to "import neuron" in Python
Replies: 4
Views: 972

Re: Installation Help: Fail to "import neuron" in Python

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 ...
by hines
Wed Mar 25, 2020 12:41 pm
Forum: OS X
Topic: Installation Help: Fail to "import neuron" in Python
Replies: 4
Views: 972

Re: Installation Help: Fail to "import neuron" in Python

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...
by hines
Wed Mar 11, 2020 9:19 am
Forum: Other questions
Topic: Cannot load compiled mod files from python
Replies: 1
Views: 498

Re: Cannot load compiled mod files from python

The symbol that is not found would be in the interviews library and it is not clear to me why that is needed to successfully load the libnrnmech.so file. Can you try the following test which loads the mod files for the neurondemo python3 from neuron import h h.nrn_load_dll("/Applications/NEURON-7.7/...
by hines
Mon Feb 10, 2020 11:54 am
Forum: OS X
Topic: NEURON installation on macOS Catalina
Replies: 8
Views: 2736

Re: NEURON installation on macOS Catalina

Check the output of otool -L /Applications/NEURON-7.7/nrn/lib/python/neuron/hoc.so to see if it cannot find any of the libraries that library is trying to load. It may be that you need to install/upgrade your command line tools and XQuartz. The latter comes from xquartz.org. For the former, when I t...