Search found 1589 matches

by hines
Fri Apr 03, 2020 5:44 pm
Forum: NEURON + Python
Topic: Copy a nrn object in Python?
Replies: 5
Views: 475

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: 568

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: 568

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: 309

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: 1211

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: 1211

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: 1211

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: 487

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: 1211

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...
by hines
Mon Dec 23, 2019 8:34 am
Forum: UNIX/Linux
Topic: Which environmental variables do I need to setup for NEURON to work after rpm installation without sudo with cpio
Replies: 1
Views: 505

Re: Which environmental variables do I need to setup for NEURON to work after rpm installation without sudo with cpio

MODLUNIT and NEURONHOME should be export MODLUNIT=/home/ziemek/usr/local/nrn/share/nrn/lib/nrnunits.lib export NEURONHOME=/home/ziemek/usr/local/nrn/share/nrn (I'm not sure but if you have NEURONHOME set, you may not need MODLUNIT) If you want to launch python and import neuron then export PYTHONPAT...
by hines
Wed Nov 06, 2019 6:34 am
Forum: Adding new mechanisms and functions to NEURON
Topic: adrunge not thread safe
Replies: 2
Views: 499

Re: adrunge not thread safe

I had forgotten about that. It was the default for SCoP. The fix on our part will be to replace the existing adrunge implementation with a thread safe version. Nevertheless, adrunge generally makes little sense in a NEURON context since the extra accuracy does not translate into a more accurate simu...
by hines
Fri Nov 01, 2019 9:29 am
Forum: Parallel NEURON
Topic: parallel simulation hang on permanently at some loops
Replies: 1
Views: 521

Re: parallel simulation hang on permanently at some loops

You did not mention whether the 7.7 version hangs on your Macbook pro and on comet. Or if NEURON 7.5 has no problem on Manjaro linux. There have been a lot of mpi changes since 7.5. If it does not take too long to run an example, you can send me a zip file with sufficient code to exhibit the problem...
by hines
Fri Nov 01, 2019 9:17 am
Forum: UNIX/Linux
Topic: PyNeuron + Ubuntu + Python 3.6
Replies: 5
Views: 1842

Re: PyNeuron + Ubuntu + Python 3.6

So I assume that I can just add libs by hand to the PYTHONPATH, but could you tell me where I can find export PYTHONPATH=/where/you/installed/nrn/lib #often /usr/local/nrn/lib The default build installs the NEURON module in <prefix>/lib/python in order to be python independent of the python version...
by hines
Sun Sep 29, 2019 3:56 am
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 9
Views: 1588

Re: MOD Files Compile But Fail To Load

On my machine (macOS Catalina Version10.15 Beta (19A573a)) (my most recent build in /Applications/NEURON-7.7 is NEURON -- VERSION 7.7.1-38-g1f3d46d9+ master (1f3d46d9+) 2019-09-13 ) I'm seeing for a typical libnrnmech.so created by nrnivmodl $ otool -L x86_64/.libs/libnrnmech.so ... /usr/lib/libncur...
by hines
Fri Sep 20, 2019 1:47 pm
Forum: NEURON + Python
Topic: Filter Mechanism params by NMODL PARAMETER
Replies: 8
Views: 1321

Re: Filter Mechanism params by NMODL PARAMETER

An old way of getting the PARAMETER names of a mechanism is from neuron import h ms = h.MechanismStandard("hh", 1) parm_name = h.ref("") for i in range(ms.count()): ms.name(parm_name, i) print(parm_name[0]) https://www.neuron.yale.edu/neuron/static/py_doc/programming/mechstan.html#MechanismStandard....