Search found 1705 matches

by hines
Tue Oct 22, 2024 1:49 pm
Forum: UNIX/Linux
Topic: Flags to enable Avx256 and 512 compiling
Replies: 3
Views: 304

Re: Flags to enable Avx256 and 512 compiling

I wrote to pkumbhar and hope Pramod can chime in on this.
by hines
Tue Oct 22, 2024 1:38 pm
Forum: MSWin
Topic: Python cannot import neuron library on Windows install
Replies: 9
Views: 29194

Re: Python cannot import neuron library on Windows install

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....
by hines
Fri Sep 27, 2024 7:36 am
Forum: MSWin
Topic: NEURON cann't open hoc
Replies: 5
Views: 1729

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...
by hines
Wed Sep 25, 2024 9:59 am
Forum: UNIX/Linux
Topic: os.execv
Replies: 8
Views: 2095

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...
by hines
Wed Sep 25, 2024 7:14 am
Forum: UNIX/Linux
Topic: os.execv
Replies: 8
Views: 2095

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...
by hines
Mon Sep 16, 2024 12:39 pm
Forum: Parallel NEURON
Topic: Presyns vs InputPresyns
Replies: 1
Views: 1838

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 ...
by hines
Mon Sep 16, 2024 9:30 am
Forum: NEURON + Python
Topic: Type annotation of NEURON objects
Replies: 3
Views: 2203

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...
by hines
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: 4181

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...
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: 10136

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: 10136

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: 10136

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: 10136

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: 10136

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: 10136

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: 10473

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