Search found 30 matches

by btorb
Mon Mar 03, 2014 8:48 pm
Forum: OS X
Topic: Compilation failure on Mavericks
Replies: 13
Views: 10275

Re: Compilation failure on Mavericks

Unfortunately, copying that library also doesn't help. The complete error reads: btorb:~> python Python 2.7.5 |Anaconda 1.7.0 (x86_64)| (default, Jun 28 2013, 22:20:13) [GCC 4.0.1 (Apple Inc. build 5493)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import neu...
by btorb
Mon Mar 03, 2014 8:03 pm
Forum: OS X
Topic: Compilation failure on Mavericks
Replies: 13
Views: 10275

Re: Compilation failure on Mavericks

Hi Mike, No compiled files in that directory. I found my previous post about this here: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=4&t=2957&p=12112&hilit=libreadline#p12112 The current status is that I can run "import neuron" only if I'm calling python in the directory that contains the readl...
by btorb
Mon Mar 03, 2014 7:41 pm
Forum: OS X
Topic: Compilation failure on Mavericks
Replies: 13
Views: 10275

Re: Compilation failure on Mavericks

I was too quick! The tarball linked above does not work. Pulling the latest code from mercurial does. So start with hg clone http://www.neuron.yale.edu/hg/neuron/nrn I still have one more error because afterwards, if I start python and run "import neuron", the readline library cannot be found. I con...
by btorb
Mon Mar 03, 2014 7:06 pm
Forum: OS X
Topic: Compilation failure on Mavericks
Replies: 13
Views: 10275

Re: Compilation failure on Mavericks

Thanks for the prompt reply. Unfortunately, I still get the same error, and, I still need the compiler flags. (If not, compilation crashes even earlier) So I unpack the latest tarball you linked above, run ./build.sh, then ./configure ./configure --prefix=`pwd` --with-iv=/Users/btorb/local/neuron/iv...
by btorb
Mon Mar 03, 2014 7:18 am
Forum: OS X
Topic: Compilation failure on Mavericks
Replies: 13
Views: 10275

Re: Compilation failure on Mavericks

Is there any solution to this problem? I get the same error: Rand::Rand(unsigned long seed = 0, int size = 55, Object* obj = nil) { ^ ~ ./random1.h:11:3: note: previous declaration is here Rand(unsigned long seed, int size, Object*); ^ ivocrand.cpp:202:3: warning: delete called on 'Random' that is a...
by btorb
Sun Nov 10, 2013 1:15 am
Forum: OS X
Topic: Trouble during 'make install'
Replies: 15
Views: 14298

Re: Trouble during 'make install'

Oops. Forgot that one. But now I run into another problem. Typically mac osx in my opinion: ImportError: dlopen(/Users/btorb/local/lib/python2.7/site-packages/neuron/hoc.so, 2): Library not loaded: libreadline.6.2.dylib At this point I compile without any LDFLAGS. Now nrniv works, but I cannot load ...
by btorb
Fri Nov 08, 2013 6:56 pm
Forum: OS X
Topic: Trouble during 'make install'
Replies: 15
Views: 14298

Re: Trouble during 'make install'

Sorry to enter this discussion but the topic seemed most relevant. I don't even get to the stage of compiling on Maverick (10.9). "-bash: ./configure: No such file or directory" I did install xcode and afterwards the command-line-tool (late cotober 2013). So I'm not sure what is going on (and it is ...
by btorb
Sun Mar 11, 2012 11:52 am
Forum: Other questions
Topic: computing impedances...
Replies: 15
Views: 14391

Re: computing impedances...

Hi Ted, so, in short the answer is that we have to use the Impedance tool included and toggle the "full" computation of the impedance compute(loc,1) ? If I understand the explanation in the programmers manual correctly the toggle has to be used when the membrane contains voltage-gated conductances? ...
by btorb
Thu Feb 23, 2012 7:51 am
Forum: NEURON + Python
Topic: NetCon
Replies: 1
Views: 1163

NetCon

Hi, I just noticed something annoying while setting the threshold of a NetCon in PyNRN. def _initRecordingSpikes(self): self.SpikesRec = h.Vector() self.nc = h.NetCon(self.soma(0.5)._ref_v,None,sec=self.soma,threshold=-10) self.nc.record(self.SpikesRec) With the above code the netcon threshold will ...
by btorb
Thu Oct 27, 2011 9:51 am
Forum: Adding new mechanisms and functions to NEURON
Topic: integration in NEURON (and differences with Brian)
Replies: 2
Views: 1865

Re: integration in NEURON (and differences with Brian)

A tempest in a teapot. thanks to the alertness of Mike and Ted it was found that a time-constant was missing a factor in one of the files.
by btorb
Mon Oct 24, 2011 12:41 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: integration in NEURON (and differences with Brian)
Replies: 2
Views: 1865

integration in NEURON (and differences with Brian)

I stumbled upon some issue related to the way of integration in NEURON and don't exactly know what's going behind the scenes. I made a simple one-compartmental model that has one current (some fast K current) and simulated this model both in NEURON and in brian (as well as, actually, analytically in...
by btorb
Mon Aug 08, 2011 3:03 am
Forum: NEURON + Python
Topic: reset NEURON
Replies: 10
Views: 6526

reset NEURON

Hi, Is there a way to "reset" NEURON? In Nest there is a ResetKernel() method. Since i experience some issues with the scope of NEURON in Python, it would be nice to see such a method. Did i overlook it until now? Or, is there a python way of completely reloading the NEURON module during execution? ...
by btorb
Fri Jun 25, 2010 3:42 am
Forum: NEURON + Python
Topic: access GLOBAL from Python
Replies: 1
Views: 892

Re: access GLOBAL from Python

tried some things for the last hour, wrote a post a minute ago and now i found the answer:

h.<globalname>_<mechname> = <value>
by btorb
Fri Jun 25, 2010 3:39 am
Forum: NEURON + Python
Topic: access GLOBAL from Python
Replies: 1
Views: 892

access GLOBAL from Python

Hi, A quick question: how do you access a NMODL GLOBAL parameter in python.

In hoc (and h("")) you can do:
<global_name>_<process_name>=<value>
for instance gnabar_hh = 0.12

What is the pythonic way of doing this?
by btorb
Thu Sep 17, 2009 8:41 pm
Forum: OS X
Topic: An error in 10.6 Snow Leopard
Replies: 8
Views: 5236

Re: An error in 10.6 Snow Leopard

shhong and wvangeit came up with this solution which seems to work. (which works for the latest development code downloaded with mercurial) ./build.sh at this point, automake fails to create the "config.sub" and "config.guess". copy these two files from either the downloadable tarball or from a prev...