Search found 97 matches

by eacheon
Tue Aug 25, 2009 2:16 pm
Forum: NEURON + Python
Topic: pointprocess does not know its own type/name
Replies: 2
Views: 1577

pointprocess does not know its own type/name

Using p = neuron.new_point_process('ExpSyn') I can get the name of p by access name attribute. But since neuron.new_point_process is becoming obsolete, from the correspondent usage a = h.ExpSyn(0.5, sec = dend)) nc = h.NetCon(stim, a) I cannot get the name (or type) of a (as an ExpSyn): >> a.__str__...
by eacheon
Wed Dec 24, 2008 12:47 am
Forum: Modeling networks
Topic: variable weight of a NetCon
Replies: 0
Views: 1975

variable weight of a NetCon

Is it possible to have the weight of a NetCon pointing to a "reference of a variable"? No. That way the weight of the NetCon can vary during a simulation (to account for use-dependent plasticity for example). This can already be done with code in the synaptic mechanism's NET_RECEIVE block. all the ...
by eacheon
Sat Dec 13, 2008 3:44 pm
Forum: UNIX/Linux
Topic: mercurial changeset 266 openmpi+python problem
Replies: 5
Views: 3834

Re: mercurial changeset 266 openmpi+python problem

Yes, you fixed it. Thanks a lot for this quick fix!
hines wrote:The problem seems to be fixed (and building with mpich continues to work) by including
mpi.h before stdio.h. Do an hg pull;hg update to get the change.
by eacheon
Sat Dec 13, 2008 3:19 pm
Forum: UNIX/Linux
Topic: mercurial changeset 266 openmpi+python problem
Replies: 5
Views: 3834

Re: mercurial changeset 266 openmpi+python problem

I tried using an objdir in the same directory level with the srcdir, but get the same error. I was doing the build in an objdir different from srcdir, configured with ../configure --prefix=/path/to/nrnhg/nrnmpi --with-iv=/path/to/nrnhg/iv --srcdir=.. --with-nrnpython --with-paranrn in a subdirectory...
by eacheon
Sat Dec 13, 2008 4:48 am
Forum: UNIX/Linux
Topic: mercurial changeset 266 openmpi+python problem
Replies: 5
Views: 3834

mercurial changeset 266 openmpi+python problem

A while ago NEURON was able to be compiled with python and openmpi, but not in the newest mercurial repository, nrniv compiles fine though: $ python setup.py build ... creating build/temp.linux-i686-2.5 mpicc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I../../../src...
by eacheon
Thu Dec 11, 2008 1:27 pm
Forum: Getting started
Topic: weird segmentation violation
Replies: 4
Views: 2945

Re: Strategy for debugging segmentation violations

Thanks for the tips, Dr. Hines. I tried a bit with gdb with "run /path/to/nrngui.hoc test.hoc -" and got the following traceback that points me to hoc_object_asgn () from /usr/lib/libnrnoc.so.0. Maybe I need to recompile NEURON with debug symbols. At the same time I find "run test.hoc -" finishes su...
by eacheon
Wed Dec 10, 2008 3:14 pm
Forum: Getting started
Topic: weird segmentation violation
Replies: 4
Views: 2945

Re: weird segmentation violation

Localization is the first task. Usually this means answering the question "where in my code does the problem lie?" but occasionally the bug is in NEURON itself. The most recent revision of 6.2 is dated August 28; you might try updating to that, if you are reasonably sure of the correctness of your ...
by eacheon
Wed Dec 10, 2008 5:37 am
Forum: Getting started
Topic: weird segmentation violation
Replies: 4
Views: 2945

weird segmentation violation

:~/tmp/neuronoo$ nrngui test.hoc NEURON -- VERSION 6.2.1006 (2048) 2008-04-07 (2051M) Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007 See http://www.neuron.yale.edu/credits.html nrniv: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed" loading membrane mechanisms fro...
by eacheon
Mon Sep 29, 2008 12:49 am
Forum: Getting started
Topic: NetCon.event doesn't respect NetCon.active
Replies: 6
Views: 3234

Re: accept certificate permanently

We will update our certificate soon to be un-expired but still not (externally) certified. You can get around the extra certificate dialog boxes when visiting the forum by accepting the certificate **permanently** rather than choosing to **temporarily** accept the certificate. Once you have selecte...
by eacheon
Fri May 16, 2008 2:33 am
Forum: Getting started
Topic: NetCon.event doesn't respect NetCon.active
Replies: 6
Views: 3234

I agree that in this case the event should not be placed onto the queue. I committed the change to the subversion repository. http://www.neuron.yale.edu/cgi-bin/trac.cgi/changeset/2087 Thank you! BTW, everytime when I use firefox to browse this forum, the browser reminds me that some SSL certificat...
by eacheon
Sun May 11, 2008 10:49 pm
Forum: Getting started
Topic: NetCon.event doesn't respect NetCon.active
Replies: 6
Views: 3234

NetCon.event doesn't respect NetCon.active

Hi, I am using NetCon.event in a FinitializeHandler to schedule events time for this NetCon object, and was hoping by setting NetCon.active(0), I can run a simulation with this NetCon silent. fih = FInitializeHandler("e.event(10)") e.active(0) run() However, .event() doesn't seem to respect .active(...
by eacheon
Sat May 10, 2008 12:59 pm
Forum: NEURON + Python
Topic: Compling Problem
Replies: 21
Views: 16802

Re: no module named hoc

in neuron/__init__.py, if import hoc is changed to from neuron import hoc Then the problem goes away. after make install I switched to the src/nrnpython dir and typed python setup.py install in super user mode: ... Python 2.5.1 (r251:54863, May 2 2007, 16:56:35) [GCC 4.1.2 (Ubuntu 4.1.2-0ubuntu4)] o...
by eacheon
Fri Mar 14, 2008 1:10 am
Forum: Getting started
Topic: Impedance-class with point-processes?
Replies: 8
Views: 4173

point 2 first. The freq arg is call by value in both cases. You'll have to send me an example where passing a reference did not give an immediate error. I only have examples that gives immediate errors. Now point 1. I direct your attention to the longer discussion for the Impedance class itself: ht...
by eacheon
Thu Mar 13, 2008 8:44 pm
Forum: Getting started
Topic: Impedance-class with point-processes?
Replies: 8
Views: 4173

Here, membrane mechanisms refers to both density mechanisms and point processes. If there is any context in the documentation where it is restricted to density mechanisms, let me know so I can disambiguate it. There may be some places where I include artificial cells as well and that would be a mis...
by eacheon
Thu Mar 13, 2008 5:19 am
Forum: Getting started
Topic: Impedance-class with point-processes?
Replies: 8
Views: 4173

Impedance-class with point-processes?

Since version 5.3, when the second argument is 1, an extended impedance calculation is performed which takes into account the effect of differential gating states. ie. the linearized cy' = f(y) system is used where y is all the membrane potentials plus all the states in KINETIC and DERIVATIVE block...