Search found 29 matches

by jaambros
Fri Jun 13, 2008 3:36 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: mechanisms in a section?
Replies: 2
Views: 1681

Re: mechanisms in a section?

I figured out one way of doing this

Code: Select all

strdef mname
proc print_mechs(){ local i localobj mt
  mt = new MechanismType(0)
  for i=0, mt.count()-1 {
    mt.select( i )
    mt.selected( mname )
    if( ismembrane(  mname )) print mname
  }
}
by jaambros
Fri Jun 13, 2008 2:39 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: mechanisms in a section?
Replies: 2
Views: 1681

mechanisms in a section?

Hi, Is there a way to find out programatically the names of the mechanisms in a section? I would of thought that the MechanismType class would have a function for this (it has one for point processes). It does have some (count and select), but they refer to the available mechs, not the ones in a giv...
by jaambros
Fri Jun 06, 2008 3:43 pm
Forum: Other questions
Topic: section arrays in templates
Replies: 1
Views: 1417

section arrays in templates

Hi all, Any ideas on why the following examples don't work? Thanks in advance, Jose Ambros-Ingerson PS. I'm running OSX 10.4.11 on Intel and G5 -------- example 1------------- begintemplate aT proc init(){ create d1[2] } proc many(){ create d1[20] } endtemplate aT objref a a = new aT() a.many() $ nr...
by jaambros
Mon Jan 28, 2008 7:10 pm
Forum: Other questions
Topic: Loglog
Replies: 4
Views: 3065

Is there a simple way to get the axes labels right when plotting as you suggest?

Thanks,
Jose
by jaambros
Thu Sep 27, 2007 1:06 pm
Forum: UNIX/Linux
Topic: libtool segmentation fault when installing Neuron in x86_64
Replies: 3
Views: 3779

I get similar errors with make install: /usr/bin/install -c .libs/liboc.lai /home/ohu0256/Software/src/Neuron/bale/nrn/x86_64/lib/liboc.la PATH="$PATH:/sbin" ldconfig -n /home/ohu0256/Software/src/Neuron/bale/nrn/x86_64/lib ../../libtool: line 6156: 29570 Segmentation fault PATH="$PATH:/sbin" ldconf...
by jaambros
Thu Sep 27, 2007 12:20 pm
Forum: UNIX/Linux
Topic: libtool segmentation fault when installing Neuron in x86_64
Replies: 3
Views: 3779

libtool segmentation fault when installing Neuron in x86_64

Hi, I'm trying to install neuron with no-gui in a Linux x86_64 machine for which I have no root access. $ uname -a Linux bale-login 2.6.18-8.1.8.el5 #1 SMP Mon Jun 25 17:06:07 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux $ tar xzf nrn-6.0.tar.gz $ mv nrn-6.0 nrn $ cd nrn $ ./configure --prefix=`pwd` --wi...
by jaambros
Tue Jul 24, 2007 12:08 pm
Forum: OS X
Topic: Universal binary in 10.4?
Replies: 6
Views: 5579

Building universal Interviews

I tried your suggestion for building Interviews. However, it failed to build a universal libIVhines.3.0.3.dylib $ IDIR=~/Software/bin/nrn-6.0-universal $ cd iv-17/ $ ./configure --prefix=$IDIR/iv --with-x CFLAGS="-arch ppc -arch i386" CXXFLAGS="-arch ppc -arch i386" $ make This failed. I tracked the...
by jaambros
Mon Jul 23, 2007 5:21 pm
Forum: OS X
Topic: Universal binary in 10.4?
Replies: 6
Views: 5579

alpha/nrn-6.0.rel-4-i386-apple-darwin8.10.1.dmg

I tested alpha/nrn-6.0.rel-4-i386-apple-darwin8.10.1.dmg OS X Server 10.4.10 (intel) installed in ~/Applications $ ~/Applications/NEURON-6.0/nrn/i386/bin/nrniv dyld: Library not loaded: /Applications/NEURON-6.0/nrn/i386/lib/libnrnoc.0.dylib Referenced from: /axon/d1/Users/jose/Applications/NEURON-6....
by jaambros
Fri Jul 20, 2007 12:59 pm
Forum: OS X
Topic: Universal binary in 10.4?
Replies: 6
Views: 5579

Universal binary in 10.4?

Has anybody tried to build a NEURON universal binary for 10.4 ? Is there reason that this will or will not work? Presumably, adding the option "-arch ppc -arch i386" to gcc 4.0 should be enough. Is there a simple way of doing this when building NEURON from source? Why do I want to do this? I have a ...
by jaambros
Mon Apr 23, 2007 5:28 pm
Forum: Other questions
Topic: command line options to nrniv
Replies: 2
Views: 4023

command line options to nrniv

I'm looking for some documentation of the command line options of nrniv. I know you can use -NSTACK xxx -NFRAME xxx In particular, I'm looking for a way to tell nrniv not to attempt to set the X11 display variable. Is there such thing? I know you can do this when building nrniv. I'm trying to find o...
by jaambros
Thu Dec 28, 2006 7:00 pm
Forum: Other questions
Topic: bug in strcmp ?
Replies: 2
Views: 3873

bug in strcmp ?

Hi, I'm getting weird results with strcmp. See below. It happens with 5.8 and 5.9 in OSX 3.9 and 4 (details below). However, it seems OK in Linux (details below) Any idea how to fix this? $ uname -a Darwin firestone.sf.osc.edu 8.8.0 Darwin Kernel Version 8.8.0: Fri Sep 8 17:18:57 PDT 2006; root:xnu-...
by jaambros
Fri Nov 03, 2006 3:41 pm
Forum: Other questions
Topic: Cvode corrector convergence failed repeatedly
Replies: 7
Views: 7507

Making sure that h (and n) are not negative solved the problem.

I wasn't aware that the 'h' in the message related to a variable in the mod file. My impression (wrongly) was that it referred to some cvode internal variable.

Thanks very much for your help
by jaambros
Thu Nov 02, 2006 9:37 pm
Forum: Other questions
Topic: Cvode corrector convergence failed repeatedly
Replies: 7
Views: 7507

Cvode corrector convergence failed repeatedly

Hi, I'm getting this error numerous times in my paralle search runs. I was able to isolate it so that it can be reproduced with the following files. Any help in finding out what causes this error would be appreciated. Thanks, Jose Ambros-Ingerson create soma access soma //---------------------------...
by jaambros
Thu Aug 10, 2006 8:32 pm
Forum: OS X
Topic: Problems making nrn-5.9.39 in G5 PowerPC
Replies: 8
Views: 9660

-without-memacs configure option did the trick. I was able to make nrniv with no gui. Thanks. PS. I did get a few warnings firestone:~/Software/src/Neuron/nrn ohu0256$ make > make.out In file included from init.c:59: osxdlfcn.c: In function `dlopen': osxdlfcn.c:118: warning: passing arg 2 of `_dyld...
by jaambros
Sun Jul 30, 2006 6:58 pm
Forum: OS X
Topic: Problems making nrn-5.9.39 in G5 PowerPC
Replies: 8
Views: 9660

Today I tried to install the nrn-5.9.39-powerpc-apple-darwin8.6.0.dmg on the Ohio Supercomputer center (OSC) G5 OSX 10.4. I used $ hdiutil attach nrn-5.9.39-powerpc-apple-darwin8.6.0.dmg to mount the dmg. However, I wasnt able to start the executables. I get the following error: $ /Volumes/NEURON-5....