Search found 1697 matches

by hines
Tue Apr 02, 2024 11:38 am
Forum: Other questions
Topic: Show Diameter
Replies: 8
Views: 6509

Re: Show Diameter

ps.show(1) At least for the classical InterViews nrn gui, the diameter is shown when the arg to show is 0. (as specified in https://nrn.readthedocs.io/en/8.2.3/python/visualization/shape.html#Shape.show ) Often times, the neurites ar so slender compared to length, it is not easy to see the diameter...
by hines
Thu Feb 22, 2024 9:35 am
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 10472

Re: can't open DISPLAY

A terminal window does open but does not offer a prompt for commands: The launch mechanism dates back to Macos 9. I never learned xcode sufficiently to bring it into the 21st century. Anyway, double clicking on nrngui.app after a few intermediate steps ultimately starts a terminal window that execu...
by hines
Thu Feb 22, 2024 6:44 am
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 10472

Re: can't open DISPLAY

That's great progress. Sadly, I don't know how to diagnose issues at the DISPLAY level of XQuartz so am at a loss as to how to extend the working behavior to launching by double clicking the app icons. When the app icon is launched, does a terminal window pop up? And is the value of DISPLAY in that ...
by hines
Tue Feb 20, 2024 4:54 pm
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 10472

Re: can't open DISPLAY

Yes. The graphics work when nrngui is launched from an xterm. (the xterm was launched from a terminal window)
by hines
Tue Feb 20, 2024 1:42 pm
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 10472

Re: can't open DISPLAY

After installing Sonoma, neurondemo started from a terminal and the graphics works. I do see the <stdin>:149: SyntaxWarning: invalid escape sequence '\.' <stdin>:197: SyntaxWarning: invalid escape sequence '\.' oc> and will try to trace that down. But it does not seem related to the GUI issue. In my...
by hines
Tue Feb 20, 2024 12:46 pm
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 10472

Re: can't open DISPLAY

I have an Apple M1 Ventura 13.6, xquartz 2.8.5, and a bunch of pythons including python-3.12.2. I'll upgrade to Sonoma 14.3.1 and see what happens.
by hines
Tue Feb 20, 2024 11:37 am
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 10472

Re: can't open DISPLAY

I just uploaded a mac pkg file at https://github.com/neuronsimulator/nrn/releases/tag/8.2.4 It is called nrn-8.2.4-12-g64efe0a14-macosx-10.9-universal2-py-38-39-310-311-312.pkg Please try that and let me know if it is not fully functional I think we are in the middle of fixing a newest xquartz/pytho...
by hines
Tue Feb 13, 2024 5:51 pm
Forum: Parallel NEURON
Topic: Calling MPI_Abort() from HOC
Replies: 5
Views: 23757

Re: Calling MPI_Abort() from HOC

You didn't mention how you launched the program. I'm guessing that you are running a NEURON version that dynamically loads mpi when you give it the -mpi arg. Otherwise the memory for nrnmpi_abort is NULL (hence the seg fault). Do you have a problem if you try mpiexec -n 1 nrniv -mpi -c 'mpiabort(-1)'
by hines
Wed Jan 03, 2024 1:06 pm
Forum: Parallel NEURON
Topic: Calling MPI_Abort() from HOC
Replies: 5
Views: 23757

Re: Calling MPI_Abort() from HOC

Try

Code: Select all

NEURON {SUFFIX nothing}

VERBATIM
extern void nrnmpi_abort(int);        
ENDVERBATIM

PROCEDURE mpiabort(errcode) {
VERBATIM
  {
    nrnmpi_abort((int)_lerrcode);  
  }
ENDVERBATIM
}
by hines
Fri Dec 15, 2023 1:36 pm
Forum: Parallel NEURON
Topic: Calling MPI_Abort() from HOC
Replies: 5
Views: 23757

Re: Calling MPI_Abort() from HOC

The internal wrapper for MPI_Abort is not exposed to the interpreter. You can do that with a mod file $ cat abrt.mod NEURON {SUFFIX nothing} VERBATIM extern "C" { void nrnmpi_abort(int); } ENDVERBATIM PROCEDURE mpiabort(errcode) { VERBATIM { nrnmpi_abort(int(_lerrcode)); } ENDVERBATIM } Th...
by hines
Fri Dec 15, 2023 1:20 pm
Forum: The GUI
Topic: Programmatic GUI control (pressing buttons, etc.)
Replies: 3
Views: 22758

Re: Programmatic GUI control (pressing buttons, etc.)

From the interpreter, there is no way to control the GUI directly. One can only execute the button/menu actions.
by hines
Wed Aug 30, 2023 8:02 pm
Forum: Reaction-diffusion in NEURON
Topic: MultiCompartmentReaction across sections
Replies: 6
Views: 23574

Re: MultiCompartmentReaction across sections

I've run the address sanitizer several times and upon ^C have always ended up at nrn-enable-sanitizer --preload python3 -i test.py ... Adding flux to exc. synapse 500/500 in spine 2/2: prend seg = spine[1](0.5), postnd seg = dend[65](0.5) Starting simulation ^CAddressSanitizer:DEADLYSIGNAL =========...
by hines
Wed Aug 30, 2023 4:35 pm
Forum: MSWin
Topic: MSWin11 + Anaconda, Neuron 8.2.2
Replies: 6
Views: 26521

Re: MSWin11 + Anaconda, Neuron 8.2.2

Perhaps this is now somewhat stale. But if your windows11 computer is available, I would be happy to have a zoom meeting where you could share your screen and we might work through the issue. If you wish to proceed, contact me at michael dot hines at yale dot edu. The first thing to diagnose is the ...
by hines
Wed Aug 30, 2023 2:23 pm
Forum: Other questions
Topic: Analyzing pointers
Replies: 1
Views: 21289

Re: Analyzing pointers

I'm sorry to say that in NEURON version 8 and before , the interpreters do not store the information used to determine the address. And in the internal implementation the only way to know what a pointer was pointing to was to search all internal data structures. This, of course, made it very inconve...
by hines
Wed Aug 30, 2023 1:37 pm
Forum: Reaction-diffusion in NEURON
Topic: MultiCompartmentReaction across sections
Replies: 6
Views: 23574

Re: MultiCompartmentReaction across sections

Code: Select all

python3 mycode.py 2 10
Gives me a segfault for NEURON version 8.1.0 but not for 8.2.2 or current master.

I also built the master using the address sanitizer and there were no substantive complaints (only some memory leaks), so there is a possibility that the bug was fixed after 8.1.0.