Search found 1595 matches

by hines
Wed Jun 10, 2020 11:07 am
Forum: Other questions
Topic: spFactor error: Zero Diagonal
Replies: 5
Views: 2234

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: 287

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: 287

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: 287

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: 287

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: 176

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: 655

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: 738

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: 738

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: 392

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: 2298

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...
by hines
Fri Feb 07, 2020 6:26 pm
Forum: OS X
Topic: NEURON installation on macOS Catalina
Replies: 8
Views: 2298

Re: NEURON installation on macOS Catalina

If you start a terminal and launch python or python3 what is the result of
import sys
sys.version
by hines
Thu Jan 23, 2020 2:04 pm
Forum: OS X
Topic: NEURON installation on macOS Catalina
Replies: 8
Views: 2298

Re: NEURON installation on macOS Catalina

ld: library not found for -lX11
It appears that XQuartz is not installed. You can do that from xquartz.org
by hines
Wed Jan 15, 2020 7:20 am
Forum: Modeling networks
Topic: Simulation with external feedback
Replies: 1
Views: 568

Re: Simulation with external feedback

The problem with VecStim is that the mod file implementation did not envision this style of usage. I would recommend adding a restart procedure which, after you replace the Vector in the middle of a simulation, would set the counter to the first element of the Vector and do a net_send to activate th...
by hines
Mon Dec 23, 2019 8:48 am
Forum: OS X
Topic: NEURON installation on macOS Catalina
Replies: 8
Views: 2298

Re: NEURON installation on macOS Catalina

Yes. It is not enough any longer that the package be signed, it must also be notarized (now a $100 annual fee). Notarization means that Apple scanned the app for known malicious software. From https://support.apple.com/en-us/HT202491 How to open an app that hasn’t been notarized or is from an uniden...