Search found 1703 matches
- Fri Sep 27, 2024 7:36 am
- Forum: MSWin
- Topic: NEURON cann't open hoc
- Replies: 5
- Views: 1438
Re: NEURON cann't open hoc
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...
- Wed Sep 25, 2024 9:59 am
- Forum: UNIX/Linux
- Topic: os.execv
- Replies: 8
- Views: 1791
Re: os.execv
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...
- Wed Sep 25, 2024 7:14 am
- Forum: UNIX/Linux
- Topic: os.execv
- Replies: 8
- Views: 1791
Re: os.execv
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...
- Mon Sep 16, 2024 12:39 pm
- Forum: Parallel NEURON
- Topic: Presyns vs InputPresyns
- Replies: 1
- Views: 1486
Re: Presyns vs InputPresyns
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 ...
- Mon Sep 16, 2024 9:30 am
- Forum: NEURON + Python
- Topic: Type annotation of NEURON objects
- Replies: 3
- Views: 1759
Re: Type annotation of NEURON objects
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...
- Wed Jul 31, 2024 11:50 am
- Forum: UNIX/Linux
- Topic: Python/Neuron model runs on Windows but does not on Linux.(h.finitialize)
- Replies: 1
- Views: 3975
Re: Python/Neuron model runs on Windows but does not on Linux.(h.finitialize)
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...
- Fri Jun 28, 2024 3:39 am
- Forum: UNIX/Linux
- Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
- Replies: 9
- Views: 9844
Re: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
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...
- Fri Jun 28, 2024 2:25 am
- Forum: UNIX/Linux
- Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
- Replies: 9
- Views: 9844
Re: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
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...
- Fri Jun 28, 2024 2:02 am
- Forum: UNIX/Linux
- Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
- Replies: 9
- Views: 9844
Re: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
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...
- Thu Jun 27, 2024 2:46 am
- Forum: UNIX/Linux
- Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
- Replies: 9
- Views: 9844
Re: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
Just want to verify that
works.
Code: Select all
neurondemo
- Thu Jun 27, 2024 2:36 am
- Forum: UNIX/Linux
- Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
- Replies: 9
- Views: 9844
Re: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
This is a bit of flailing around on my part, but I'm curious if the problem goes away if you install the latest neuron-nightly version. Probably best done in a python virtual environment so that subsequent removal of the whole thing becomes straightforward. ie. in the folder where your mod files are...
- Wed Jun 26, 2024 11:47 am
- Forum: UNIX/Linux
- Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
- Replies: 9
- Views: 9844
Re: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
That is a puzzle since I have always been under the impression that later glibc (your 2.35) would resolve earlier versions (2.1). Did you install with
pip install neuron?
pip install neuron?
- Wed May 08, 2024 8:43 am
- Forum: Other questions
- Topic: Show Diameter
- Replies: 8
- Views: 8685
Re: Show Diameter
The above fragments are incomplete and I can't reproduce the figure. Can you send me a zip file with all necessary files and instructions for running?
Please send to Michael.hines@yale.edu
Please send to Michael.hines@yale.edu
- Thu Apr 25, 2024 6:44 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Recording variables from ARTIFICIAL_CELL
- Replies: 14
- Views: 10280
Re: Recording variables from ARTIFICIAL_CELL
I'll be interested to see the example.I'll try to make an example to show the problem.
- Thu Apr 25, 2024 5:09 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Recording variables from ARTIFICIAL_CELL
- Replies: 14
- Views: 10280
Re: Recording variables from ARTIFICIAL_CELL
I applied the pull request change above to the 8.2 branch (for a future 8.2.5 release) and observe better performance than the master (probably due to ARTIFICIAL_CELLS having better performance when the memory layout is "Array of Structures" rather than the newer "Structure of Array&q...