www.neuron.yale.edu

A follow up question: how did you install NEURON? From the paths, it looks like you ran in macOS. Doing a "pip install neuron" is supposed to handle all the dependencies, including numpy. (This works for linux and macOS, but unfortunately we don't support pip on Windows.) I believe the und...

I'm not sure if I understand enough of what's happening to be able to say if NEURON's rxd mechanism would be useful... ... but you may want to check out the MOD file in Figure 13 of doi:10.3389/fninf.2022.847108 and the surrounding discussion. There we have a synapse that receives event-driven input...

Just to add one point, the underlying issue here is that Vector.record has to be defined before the simulation is initialized... but yeah, no reason to create a new variable for the second half.

NEURON hasn't supported ./configure since the 7.x series over two years ago. Unless there's a specific reason to use an old version, don't. On a cluster, it's easiest to just do: pip3 install --user neuron In addition to installing the Python libraries, it'll add the binaries (e.g. nrniv, nrnivmodl,...

This appears to be a Windows-specific problem, but I see the same thing with a development version of NEURON (8.2.2+) and Python 3.11.3 on Windows 10: (py311) C:\Users\Robert McDougal>python Python 3.11.3 | packaged by Anaconda, Inc. | (main, Apr 19 2023, 23:46:34) [MSC v.1916 64 bit (AMD64)] on win...

All of that ought to work, but NEURON 7.8 is pretty old. Do you get the same problem in 8.2.2?

(For the purposes of this post, I'm using "M1" as a shorthand for M1, M2, and their variants.) You have an x86_64 version of Python but the M1 version of NEURON and gcc . Uninstall your anaconda, and then get the version labelled "64-Bit (M1) Graphical Installer (564 MB)" from ht...

We have a video on networks and numerical methods on the NEURON YouTube channel: https://youtube.com/watch?v=r9dxBS_e_RI You may also be interested in checking out the ball-and-stick tutorials... they'll step you through creating your first cell to building a ring network: https://nrn.readthedocs.io...

Another way of putting it: the description specified in nmodl400.pdf is still pretty accurate. The text you found refers to something very specific to xtra.mod... most models will still use BREAKPOINT instead. See hh.mod for how NEURON implemented Hodgkin-Huxley itself. A few suggestions for modern ...

Sounds like NEURON might have been built without dynamic MPI, in which case it'll try to use whichever version of MPI was picked at compile time. Before we try debugging the compilation instructions for 7.6, have you tested to see if the current release (8.2.1) binary works? Even if you want the old...

Not sure why it doesn't like nrniv -python , but launching nrniv when you really want to run python complicates things unnecessarily. As long as your script initializes MPI before setting up the model, either via mpi4py or via: h.nrnmpi_init() it suffices to just: mpiexec -n 2 python run_model_to_st...

Unfortunately, the []s will cause problems for trying to read/write them from mod files.

specs0, specs1, ... specs19 would work for names (and then you could have e.g. specs0i, ispecs0, etc)

setpointer literally sets a double* that's allocated inside of the MOD file. Once the assignment has been made, there is no explicit semantic information obtainable from the pointer. That is, h.setpointer(secA(0.5)._ref_v, 'V_pre', synAB) is 100% equivalent to: synAB._ref_V_pre = secA(0.5)._ref_v Bo...

The binaries for NEURON 7.7 would not work with Python 3.8, which did not exist at the time 7.7 was released. I imagine it would work if it was compiled specifically for 3.8, but I would strongly suggest using a more recent version of NEURON. My guess is that it's saying there's a folder called &quo...

Here's a possible clue... it's looking for a .so file. Usually on Windows, the equivalent is a .dll Are you using the regular Windows version of NEURON or a version the windows subsystem for linux (WSL)? Either way, if you try running with python -i myprogram.py (that is, add the -i flag so it doesn...