Search found 1691 matches
- Thu Apr 15, 2021 11:37 am
- Forum: OS X
- Topic: If you can't compile mod files . . .
- Replies: 26
- Views: 80453
Re: If you can't compile mod files . . .
Did you launch using a terminal from the parent folder of the x86_64 folder?
- Thu Apr 15, 2021 7:45 am
- Forum: OS X
- Topic: If you can't compile mod files . . .
- Replies: 26
- Views: 80453
Re: If you can't compile mod files . . .
The web page referred to needs to be updated. The library is present in the x86_64 folder and will be automatically loaded if you launch nrniv in the
parent folder.
parent folder.
- Mon Mar 29, 2021 10:05 am
- Forum: Other questions
- Topic: spFactor error: Zero Diagonal
- Replies: 7
- Views: 16500
Re: spFactor error: Zero Diagonal
I need to reproduce the problem on my machine if possible. Can you send me (michael dot hines at yale dot edu) a zip file with all the needed hoc,ses,mod,py files that comprise the simulation? No guarantee that I'll succeed or that my diagnostic path will generalize, but I'll take notes on the proce...
- Tue Mar 23, 2021 7:47 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: calling a function from NMODL
- Replies: 10
- Views: 14908
Re: calling a function from NMODL
I hope you are doing a sanity check when you have problems by printing some details. e.g print(seg.sec.name(), seg.x, seg.v, seg.Kv1.alphan) Anyway, one problem I see is that for seg in sec.allseg(): includes in the iteration sec(0) and sec(1) which are zero area nodes and do not contain Kv1. The li...
- Mon Mar 22, 2021 5:14 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: calling a function from NMODL
- Replies: 10
- Views: 14908
Re: calling a function from NMODL
I see you have a def wrapper(alphan, betan, n, noise) but in your recording_callback = (wrapper, (seg.alphan_Kv1 , seg.betan_Kv1, seg.n_Kv1 , 0 )) the arguments to wrapper are just constant values computed at the time the recording_callback assignment statement is executed. In your mod file, alpahn ...
- Thu Mar 18, 2021 9:50 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: calling a function from NMODL
- Replies: 10
- Views: 14908
Re: calling a function from NMODL
My opinion is that findnoiseterm should not be the callback but instead the callback should be a wrapper python function that for every instance of Kv1, the wrapper would call findnoiseterm and assign the return value into z1_Kv1 (which should be a regular RANGE variable instead of a POINTER.) If th...
- Wed Mar 17, 2021 10:08 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: calling a function from NMODL
- Replies: 10
- Views: 14908
Re: calling a function from NMODL
Forgot to show the usage of the mod file... Note that the callback happens at the end of finitialize and at the beginning of a step. nrnivmodl beforestep_py.mod $ cat temp.py from neuron import h #enough model for the point process to have a home s = h.Section() # and for something interesting to ha...
- Wed Mar 17, 2021 9:53 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: calling a function from NMODL
- Replies: 10
- Views: 14908
Re: calling a function from NMODL
I think that CVode.extra_scatter_gather is fine (in the after scatter direction) for your purpose because, since you are dealing with channel noise, you are most likely using only the fixed step method. In general we need to introduce something like Cvode.before_step(python_callback) which, for vari...
- Mon Jan 25, 2021 4:42 pm
- Forum: MSWin
- Topic: Issues with Anaconda install
- Replies: 2
- Views: 21045
Re: Issues with Anaconda install
From a terminal which can run the specific conda environment, do you have a PYTHOPATH that mentions c:\nrn\lib\python ? If you launch python (in your specific conda environment and without such a PYTHONPATH) can you import sys sys.path.append("c:/nrn/lib/python") import neuron neuron.test(...
- Thu Jan 21, 2021 10:28 am
- Forum: Parallel NEURON
- Topic: Efficient way of debugging Python scripts with MPI library
- Replies: 4
- Views: 11176
Re: Efficient way of debugging Python scripts with MPI library
I was accessing a cell that is not associated with the rank it was made This wording puzzles me as I don't know anyway for a cell not to be associated with the rank it was made on. (although if you are using multisplit there may be parts of a cell that are on ranks that are different from the rank ...
- Mon Nov 23, 2020 6:53 am
- Forum: Getting started
- Topic: Display environment error
- Replies: 2
- Views: 10785
Re: Display environment error
XQuartz is one of those installations that requires one to logout and log back in in order to activate it.
- Mon Nov 23, 2020 6:50 am
- Forum: Getting started
- Topic: Compiling Mod Files on Catalina
- Replies: 8
- Views: 13989
Re: Compiling Mod Files on Catalina
A work around for now for readline problems is to try
nrn-7.8.1-2-gdfe33e60-osx-27-36-37-38-39.pkg
or
nrn-8.0.dev-239-g8f2aaaa9.w64-mingw-py-27-36-37-38-39-setup.exe
at
https://neuron.yale.edu/ftp/neuron/versions/alpha/
These use NEURON's internal readline sources.
nrn-7.8.1-2-gdfe33e60-osx-27-36-37-38-39.pkg
or
nrn-8.0.dev-239-g8f2aaaa9.w64-mingw-py-27-36-37-38-39-setup.exe
at
https://neuron.yale.edu/ftp/neuron/versions/alpha/
These use NEURON's internal readline sources.
- Sat Nov 21, 2020 11:52 am
- Forum: Getting started
- Topic: Compiling Mod Files on Catalina
- Replies: 8
- Views: 13989
Re: Compiling Mod Files on Catalina
Because of these perennial problems with readline when binary distributions are installed, we will be taking the tack during build of compiling a recent version of readline ourselves as a libreadline.a file along with ncurses and incorporating that into the libnrniv.dylib. I hope after that I'll nev...
- Wed Nov 11, 2020 6:34 pm
- Forum: MSWin
- Topic: Compiling script fails with newer NEURON versions due to $N
- Replies: 6
- Views: 23348
Re: Compiling script fails with newer NEURON versions due to $N
Please try https://neuron.yale.edu/ftp/neuron/vers ... -setup.exe
If there are any difficulties that is the best place for me to resolve. I'm not experiencing any $N issue with that.
If there are any difficulties that is the best place for me to resolve. I'm not experiencing any $N issue with that.
- Thu Oct 22, 2020 7:01 pm
- Forum: OS X
- Topic: Gui Freezing
- Replies: 5
- Views: 21106
Re: Gui Freezing
I would re-install software from xquartz.org. (After installing, logout and log back in). If that does not fix the issue, it may be a good idea to update the xcode command line tools and redo your mod files with nrnivmodl after removing the x86_64 folder. WIth regard to updating the xcode command li...