Search found 30 matches

by btorb
Wed Sep 16, 2009 3:13 am
Forum: OS X
Topic: Error compiling even IV on 10.6 Snow Leopard
Replies: 24
Views: 11566

Re: Error compiling even IV on 10.6 Snow Leopard

./configure --prefix=$IDIR/iv --enable-carbon configure: error: cannot run /bin/sh ./config.sub (after installing XTools i can run "nrnivmodl", but the command doesn't work. Collegues (see the other thread about snow leopard) told me to install the latest version of NRN and recompile. but config eve...
by btorb
Mon Jun 01, 2009 5:01 am
Forum: Parallel NEURON
Topic: gap junctions, pointers and multithreading
Replies: 19
Views: 9648

Re: gap junctions, pointers and multithreading

Unfortunately, more difficulties with the gap junctions in combination with ParallelNetwork. I'm building a network that runs on multiple nodes using ParallelContext and ParallelNetwork. Based on the code from the previous post, I implemented a gap junction. It works for a single gap junction betwee...
by btorb
Fri May 22, 2009 1:16 am
Forum: Parallel NEURON
Topic: gap junctions, pointers and multithreading
Replies: 19
Views: 9648

Re: gap junctions, pointers and multithreading

one day later i can tell the problem is caused by the netcon.

nc1= new NetCon(s, cell1.asyn, 0, 0, 0.01) works fine with one thread but doesn't work with n threads.

nc1= new NetCon(s, cell1.asyn, 0, 0.1, 0.01) works with n threads.

But what if i want delay=0???
by btorb
Thu May 21, 2009 3:41 am
Forum: Parallel NEURON
Topic: gap junctions, pointers and multithreading
Replies: 19
Views: 9648

Re: gap junctions, pointers and multithreading

thanks for implementing mutithreaded gapjunctions. it is (or: should be) a step forward to truly parallel gap junctions. However, i encounter different problems when testing my own dummy model with the latest neuron distribution VERSION 7.1 (312:90ceb36c0079). I'll attach all the code. celltemplate....
by btorb
Thu Dec 25, 2008 2:30 am
Forum: Adding new mechanisms and functions to NEURON
Topic: ion-dependent channel
Replies: 1
Views: 1726

ion-dependent channel

first of all, merry christmas to everybody. i'm in a part of the world where they do not celebrate christmas so work continues! I'm in the process of making a ion-dependent channel, a Na-dependent K channel. More specific, i have a system in which there are three currents, (i) Na channel, (ii) K cha...
by btorb
Tue Oct 14, 2008 5:12 am
Forum: Parallel NEURON
Topic: gap junctions, pointers and multithreading
Replies: 19
Views: 9648

Re: gap junctions, pointers and multithreading

ok, but with a global timestep it doesn't work either because the pointer required in the gapjunction is not threadsafe. Any news idea on parallelization of networks with gap junctions? any way to get around this limitation of the current NRN parallelization? Is there a way to force to overrule the ...
by btorb
Wed Sep 24, 2008 9:02 pm
Forum: Parallel NEURON
Topic: gap junctions, pointers and multithreading
Replies: 19
Views: 9648

Re: gap junctions, pointers and multithreading

The local variable time step method is not threadsafe and would not even work correctly with a single thread. you mean that when simulating a network with gap junction, the adaptive time step should always be non local, i.e. NOT cvode.use_local_dt (1)? Or is it a different message you bring across?...
by btorb
Wed Sep 24, 2008 7:49 am
Forum: Other questions
Topic: CVode, more questions (and a bit of GUI)
Replies: 2
Views: 1564

Re: CVode, more questions (and a bit of GUI)

After anohter two hours of thrying, the error becomes more clear and the question can be reformulated as follows: How can i manually (i.e., typing code) set an adaptive time step, with local_step and Mx=b treesolver. the following code has proven NOT to work: objref cvode cvode = new CVode() cvode.a...
by btorb
Wed Sep 24, 2008 5:52 am
Forum: Other questions
Topic: CVode, more questions (and a bit of GUI)
Replies: 2
Views: 1564

CVode, more questions (and a bit of GUI)

I'm trying to find out why my model produces a different output when using cvode (i) started from the GUI with tools -> variablestep control, and (ii) started directly from typed in code. A bit more info: (1) if i start a model and, throught the GUI, set the timestep to adaptive. it all works fine a...
by btorb
Wed Sep 24, 2008 2:09 am
Forum: Parallel NEURON
Topic: gap junctions, pointers and multithreading
Replies: 19
Views: 9648

gap junctions, pointers and multithreading

I'm using nrn 7.0 and want to use several processors. By adding THREADSAFE to the mod files most compilations notifications are resolved. However, pointers are not threadsafe and i need pointers for the gab junction code i'm using. the gab junction is very basic (and probaly taken from another model...
by btorb
Mon Sep 22, 2008 5:19 am
Forum: NEURON + Python
Topic: the `-' in a prompt
Replies: 3
Views: 2028

the `-' in a prompt

Dear, I'm encountering a small but annoying problem.It might be caused be caused by bad programming but still it deserves a solution. Normally when you add the "-" (dash) at the end of a nrniv command, neuron is not quitting after the last command. Now i want to obtain the same result when loading a...
by btorb
Mon Sep 22, 2008 5:07 am
Forum: NEURON + Python
Topic: Neuron GUI with python?
Replies: 7
Views: 4757

Re: Neuron GUI with python?

On my system (ubuntu 4.1.2)the proposed solution doesn't work. the code only seems to work when directly loaded from python (python <py_file_with_nrn_statement>)

Ben
by btorb
Sun Sep 21, 2008 9:11 pm
Forum: MSWin
Topic: neuron 6.2 on XP, mknrndll does not function
Replies: 2
Views: 2602

Re: neuron 6.2 on XP, mknrndll does not function

thanks. removing does files did the job.
by btorb
Fri Sep 19, 2008 4:53 am
Forum: MSWin
Topic: neuron 6.2 on XP, mknrndll does not function
Replies: 2
Views: 2602

neuron 6.2 on XP, mknrndll does not function

Dear, In order to use the python interface with neuron i just switched from neuron 5.9 to neuron 6.2. On my windows computer, this resulted in the fact that i'm unable to compile mod files with mknrndll. (On another computer with linux it works fine). After selecting the directory in which the mod f...
by btorb
Fri Oct 21, 2005 8:16 am
Forum: Anatomically detailed models
Topic: neurolucida file specification
Replies: 1
Views: 4171

neurolucida file specification

Hello,

I'm looking for the file format specification of the neurolucida SWC format. Everybody seems to use this format but a specification is never given. Can someone please give me the specification, or point me where i can find it.

Thanks in advance, Ben