Search found 1697 matches

by hines
Fri Jun 28, 2024 3:39 am
Forum: UNIX/Linux
Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
Replies: 9
Views: 7509

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...
by hines
Fri Jun 28, 2024 2:25 am
Forum: UNIX/Linux
Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
Replies: 9
Views: 7509

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...
by hines
Fri Jun 28, 2024 2:02 am
Forum: UNIX/Linux
Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
Replies: 9
Views: 7509

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...
by hines
Thu Jun 27, 2024 2:46 am
Forum: UNIX/Linux
Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
Replies: 9
Views: 7509

Re: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error

Just want to verify that

Code: Select all

neurondemo
works.
by hines
Thu Jun 27, 2024 2:36 am
Forum: UNIX/Linux
Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
Replies: 9
Views: 7509

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...
by hines
Wed Jun 26, 2024 11:47 am
Forum: UNIX/Linux
Topic: undefined reference to ‘memcpy@GLIBC_2.1’ compiling error
Replies: 9
Views: 7509

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?
by hines
Wed May 08, 2024 8:43 am
Forum: Other questions
Topic: Show Diameter
Replies: 8
Views: 6459

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
by hines
Thu Apr 25, 2024 6:44 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Recording variables from ARTIFICIAL_CELL
Replies: 14
Views: 7272

Re: Recording variables from ARTIFICIAL_CELL

I'll try to make an example to show the problem.
I'll be interested to see the example.
by hines
Thu Apr 25, 2024 5:09 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Recording variables from ARTIFICIAL_CELL
Replies: 14
Views: 7272

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...
by hines
Thu Apr 25, 2024 4:04 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Recording variables from ARTIFICIAL_CELL
Replies: 14
Views: 7272

Re: Recording variables from ARTIFICIAL_CELL

I've started a pull request https://github.com/neuronsimulator/nrn/pull/2858 . For now, you can work around the "Optional first arg is not a POINT_PROCESS" error by using hpc.nthread(1) or else creating a section for each thread and putting a POINT_PROCESS in the middle of each Section. On...
by hines
Thu Apr 25, 2024 11:38 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Recording variables from ARTIFICIAL_CELL
Replies: 14
Views: 7272

Re: Recording variables from ARTIFICIAL_CELL

First, it seems to me to be a mistake in the internal NEURON implementation that the following generates an error trec.record(wcs, h._ref_t) erec.record(wcs, wcs._ref_e) That is, I believe the thread that wcs (an ARTIFICIAL CELL) is in is definitely known just as any POINT_PROCESS. An extra section ...
by hines
Tue Apr 09, 2024 6:10 pm
Forum: NEURON + Python
Topic: Python Code Continues Execution Despite HOC Error
Replies: 4
Views: 5779

Re: Python Code Continues Execution Despite HOC Error

when an error occurs in the HOC code during a simulation executed from Python, the execution should halt That is what is supposed to happen. Sorry, h('hoc code') does not raise an exception on a hoc error, it returns 0 on failure and 1 on success. It's behavior is similar to https://nrn.readthedocs...
by hines
Wed Apr 03, 2024 10:34 am
Forum: Other questions
Topic: Show Diameter
Replies: 8
Views: 6459

Re: Show Diameter

Your example code above worked for me (after prefixing "from neuron import h"). The show diameter feature for pyplot is only available in version 9. For mac, linux you can pip install NEURON-nightly For windows the latest master build is (see the first master label at https://github.com/ne...
by hines
Wed Apr 03, 2024 8:20 am
Forum: Other questions
Topic: Show Diameter
Replies: 8
Views: 6459

Re: Show Diameter

After looking around a bit in the github history for nrn, my first impression is that show diameter is supposed to work with plotly. I.e. https://github.com/neuronsimulator/nrn/pull/2404 at the end of June 2023 with the same mode call as works for InterViews GUI PlotShape. After some experimenting, ...
by hines
Tue Apr 02, 2024 11:49 am
Forum: NEURON + Python
Topic: Python Code Continues Execution Despite HOC Error
Replies: 4
Views: 5779

Re: Python Code Continues Execution Despite HOC Error

when an error occurs in the HOC code during a simulation executed from Python, the execution should halt That is what is supposed to happen. What kind of computer are you using and what is the NEURON version. A short example would be helpful. E.g. from neuron import h h(''' proc test() { print 1/0 ...