Search found 54 matches

by JimH
Sat Sep 07, 2019 1:20 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: mknrndll fils with undefined reference
Replies: 2
Views: 516

Re: mknrndll fils with undefined reference

That makes perfect sense. Thanks!
by JimH
Sat Sep 07, 2019 10:40 am
Forum: Other questions
Topic: startup python and system path problems
Replies: 0
Views: 310

startup python and system path problems

This is more of a comment than a question. I recently switched to NEURON 7.7 from vs 7.2 and apparently a few things have changed over the past few years! Also important to know, I run NEURON from Matlab (using a Java process and stdin/stdout/stderr) which leads to some of these issues. When first r...
by JimH
Thu Sep 05, 2019 11:40 pm
Forum: MSWin
Topic: cygwin vs msys file path changes, Windows NEURON version
Replies: 1
Views: 254

cygwin vs msys file path changes, Windows NEURON version

For my Windows paths I used to convert them to use the Cygwin path notation of /cygdrive/c/etc. This worked in NEURON 7.2 ... Now in 7.7 I tried using chdir() with Cygwin style pathing and the call fails. Now it seems paths are best represented with forward slashes => C:/Users/etc. This appears to b...
by JimH
Thu Sep 05, 2019 2:50 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: mknrndll fils with undefined reference
Replies: 2
Views: 516

mknrndll fils with undefined reference

I recently updated to NEURON 7.7 from NEURON 7.2 and was trying to recompile a mod file. I tried recompiling one of my mod files and the compilation failed with: undefined reference to 'hoc_register_dparam_size' at line 75 in the mkrndll.mak file (NEURON version 7.7.2.7.7 2b7985ba) After a lot of se...
by JimH
Thu Sep 05, 2019 2:33 pm
Forum: Other questions
Topic: debugging/profiling NEURON execution
Replies: 3
Views: 369

Re: debugging/profiling NEURON execution

The goal was to get a better understanding of how NEURON is running (so debugging NEURON itself), presumably by calling a NEURON simulation. The links Ted have provided are a start, although I was hoping to "see" that code in action. I was assuming this would mean compiling the source code with debu...
by JimH
Thu Aug 29, 2019 9:06 am
Forum: Other questions
Topic: debugging/profiling NEURON execution
Replies: 3
Views: 369

debugging/profiling NEURON execution

I'm interested in stepping through the execution of a NEURON program, line by line, to make sure that I fully understand how it's running. I'm assuming that would require compiling everything from source with debugging enabled. Given the HOC interpreter, the dynamically loaded mechanisms, and my gen...
by JimH
Fri Apr 19, 2013 10:20 pm
Forum: Other questions
Topic: nrniv hide launched process
Replies: 4
Views: 1485

Re: nrniv hide launched process

With regard to the nobanner, I needed to group it with the executable using quotes:

C:\nrn72\bin\bash.exe -c "/cygdrive/c/nrn72/bin/nrniv.exe -nobanner"
by JimH
Fri Apr 19, 2013 12:00 am
Forum: Other questions
Topic: nrniv hide launched process
Replies: 4
Views: 1485

Re: nrniv hide launched process

I think I got what I wanted. I needed the following:

C:\nrn72\bin\bash.exe -c /cygdrive/c/nrn72/bin/nrniv.exe

I'm not sure why it works, but it seems to. I'm having a bit of difficulty getting -nobanner to work, but that might be the way I am running my Java code.
by JimH
Thu Apr 18, 2013 10:28 pm
Forum: Other questions
Topic: nrniv hide launched process
Replies: 4
Views: 1485

Re: nrniv hide launched process

The process you mentioned works but involves opening of the rxvt window. I wasn't sure if there was a way of hiding the rxvt window on execution. Since rxvt and bash are mysteries to me, I was hoping someone might know what's going on behind the scenes and how to disable launching of the windows.
by JimH
Mon Apr 15, 2013 4:11 pm
Forum: Other questions
Topic: nrniv hide launched process
Replies: 4
Views: 1485

nrniv hide launched process

I am using Windows and looking for a way to launch NEURON without opening a window. I am currently using nrniv.exe to interact with NEURON. Would it be possible to do this through rxvt.exe or bash.exe? Using the Windows command window I am unable to launch NEURON without running neuron.exe which ope...
by JimH
Sat Jan 26, 2013 1:42 pm
Forum: Other questions
Topic: nseg shifts depolarization location - extracellular
Replies: 3
Views: 1461

Re: nseg shifts depolarization location - extracellular

Well in the process of cleaning up the code to zip and send I noticed that I was not properly iterating over the play vectors. Even though I was accessing the correct stimulus voltage given the section and segment I had currently accessed, I was assigning it to the wrong vector.
by JimH
Fri Jan 25, 2013 4:15 am
Forum: Other questions
Topic: nseg shifts depolarization location - extracellular
Replies: 3
Views: 1461

nseg shifts depolarization location - extracellular

Hi all, I've created a simple axon model with nodes and internodes. The internodes are modeled with a single section and multiple segments. The nodes are modeled as a single section and a single segment. When I provide an extracellular stimulus that is centered on the axon, the maximum depolarizatio...
by JimH
Fri Jan 25, 2013 2:48 am
Forum: Other questions
Topic: Accessing neuron variables in MATLAB
Replies: 1
Views: 1259

Re: Accessing neuron variables in MATLAB

You can setup communication with NEURON using stdin and stdout (string buffers) in Matlab. I have implemented some code which does this on github. The code has a lot more functionality and is still growing and changing but the basics are there. https://github.com/JimHokanson/matlab_NEURON Setup take...
by JimH
Fri Dec 21, 2012 5:42 pm
Forum: OS X
Topic: isatty vs notatty mac
Replies: 6
Views: 6324

Re: isatty vs notatty mac

When testing the code with the provided alpha version the terminal returns a message about an "Illegal Instruction" and the process closes. The 7.2 code will work fine. Since we were having problems with our stdin parser, we added on a magic string to our stdout following every command, which contai...
by JimH
Thu Dec 20, 2012 12:03 pm
Forum: MSWin
Topic: winio_show
Replies: 1
Views: 5128

winio_show

I tried using this method in version 7.2 and I get an error saying it doesn't exist. I think I can accomplish what I would like to by using the windows api, I just thought perhaps the documentation should up be updated if this is no longer supported, or fixed if it is supported. Thanks, Jim oc>winio...