www.neuron.yale.edu

I see that >>> for sec in secList: print(f"{sec}_spine_neck") ... soma[0]_spine_neck dend[0]_spine_neck dend[1]_spine_neck dend[2]_spine_neck ... So you can see that those are all invalid variable names. You need a bit more text processing to get the array index at the end of the name or e...

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spine_neck = h.Section(name= f''{sec}_spine_neck'')

Just curious. What is the value of the string By the way, I didn't try to run your code fragment in your initiating message as it seemed incomplete (what is secList) and improperly indented.

For several years now, we've been having a great deal of trouble maintaining the neuron.yale.edu website.It crashes every 8 days for an unknown reason. Only one or two persons, not me, know how to change content (and not all the types of content at that). Almost all user facing information, the exce...

nrniv.exe: stack underflow The connect child, parent syntax is unfortunately limited in that the parent cannot be of the form obj.sec as the sequence of tokens syntactically conflicts with other syntax in the HOC language. That is, with that form of the connect statement, the parent must be a liter...

I wrote to pkumbhar and hope Pramod can chime in on this.

NEURON + python can work only if the python version is one of those listed in the name of the neuron installer. Presently the installer one gets from https://nrn.readthedocs.io/en/latest/ or https://nrn.readthedocs.io/en/8.2.6/ is https://github.com/neuronsimulator/nrn/releases/download/8.2.6/nrn-8....

Just to help isolate the problem... Please remove the two spaces from the "data driven model" folder name and try again (you can replace with - or _). If your model involves mod files, you may also have to rerun mknrndll or nrnivmodl. When you launch neuron, what banner is printed. Our int...

Another detail that gave me a bit of an itch but we can ignore for now is File "/home/pfortier/project/x86_64/special.nrn", line 123, in <module> os.execv(exe, sys.argv) FileNotFoundError: [Errno 2] No such file or directory I interpret that as a failure with respect to the value of exe. I...

The only change made was to the file permission of gstim.mod from 664 to 750 so I must assume that this was the problem. I glad the problem went away. That's not a bad reason to move on. However I'm quite puzzled how that change could fix a FileNotFoundError: [Errno 2] No such file or directory whe...

Different numbers of InputPresyn are expected. InputPresyn is a memory optimized version of PreSyn and does not need to act as a threshold detector as it receives a spike from a PreSyn that was generated on another MPI rank. The number of InputPresyn on a rank is equal to the number of distinct gid ...

Types for built in hoc classes (eg. Vector, File, etc.) have been augmented with a HocClass metaclass in order to recover the HOC internal indexing for object indexing of classes that had been broken by the change to the development version mentioned by ramcdougal above . The original (up through ve...

I'm afraid the code you copied above is incomplete. After installing the necessary modules in a python virtual environment, I'm stuck at $ python -i test.py NEURON: Couldn't find: kim.hoc near line 0 objref hoc_obj_[2] ^ I Started multiprocessing.pool.RemoteTraceback: """ Traceback (m...

I see that comments are starting to arrive https://github.com/neuronsimulator/nrn/issues/2949#issuecomment-2196286531 I'd say that we should move this discussion to that GitHub issue, but I'm not certain if you have permission to comment there. If so and it merely requires a GitHub account, then gre...

A colleague mentions: Ubuntu 22.04 is recent and I don’t think issue is about the system glibc+compiler compatibility. Seeing below, I see the compiler toolchain is coming from conda env and I suspect issue is coming from there: /home/kedoxey/.conda/envs/python3_9-NEW/bin/../lib/gcc/x86_64-conda-lin...

So the issue seems generic with respect to our wheel build environment. I think the fact that you can launch neurondemo with its libnrniv and the libnrnmech built when the installer was created is an important clue. The issue seems focused on the nrnivmodl make process. I imagine some detail is miss...