Search found 39 matches

by sec6
Sun Aug 23, 2009 9:44 pm
Forum: Other questions
Topic: time intervals using vec.record()...
Replies: 3
Views: 1802

Re: time intervals using vec.record()...

Is there any way to record only during a period of time much shorter than t stop I mean something like if(t>=tstart &&t<=tstp){vec.record(..)...} ? No. I think there is, actually. First, create an FInitializeHandler instance FInitializeHandler(1, init) next, write the "init" routine which invokes t...
by sec6
Mon Jun 29, 2009 7:22 am
Forum: NEURON + Python
Topic: Memory leak (?) in NEURON/Python
Replies: 5
Views: 7702

Re: Memory leak (?) in NEURON/Python

That is a large block. Do you know where and why it is being requested? Yes, it occurs while "loading" NEURON's event queue, i.e. within the following set of nested loops: for i in range(numCells): for j in range(numExCells): if exNetConArray[i,j] != None: for (k,spikeTime) in enumerate(exTrains[j]...
by sec6
Fri Jun 26, 2009 12:15 pm
Forum: NEURON + Python
Topic: Memory leak (?) in NEURON/Python
Replies: 5
Views: 7702

Re: Memory leak (?) in NEURON/Python

1) I installed version 7.1 (much easier than I expected: thanks for the precompiled binaries), and I get the same behavior. 2) I only *think* the requested block size is 1048580096, based on the error message (quoted above) which I may be misunderstanding. 3) I, too, thought of the "two fold size in...
by sec6
Thu Jun 25, 2009 5:15 pm
Forum: NEURON + Python
Topic: Memory leak (?) in NEURON/Python
Replies: 5
Views: 7702

Re: Memory leak (?) in NEURON/Python

Thanks, will do.
I thought updating to 7.1 might be the thing to do, but when I searched the Hg repository for "leak," I didn't find anything newer than 7.0.
by sec6
Wed Jun 24, 2009 4:40 pm
Forum: NEURON + Python
Topic: Memory leak (?) in NEURON/Python
Replies: 5
Views: 7702

Memory leak (?) in NEURON/Python

My model seems to be leaking memory. I've had no success, so far, debugging it myself. Results so far seem to implicate NEURON, rather than Python, but I'm not 100% confident of that. Unless I'm very lucky, nobody's going to be able to tell me the solution, but I'd like suggestions about how to proc...
by sec6
Thu Jun 04, 2009 3:56 pm
Forum: NEURON + Python
Topic: Error msg: "Event arrived out of order"
Replies: 1
Views: 1326

Error msg: "Event arrived out of order"

I am trying to do something complicated with the event delivery system, and clearly not doing it right: I'd like to know what I'm doing wrong. The full error message is: /Applications/NEURON-7.0/nrn/umac/bin/nrniv: GABAa_S[599] :Event arrived out of order. Must call ParallelContext.set_maxstep AFTER...
by sec6
Mon Mar 02, 2009 2:53 pm
Forum: NEURON + Python
Topic: standard run system hooks from Python
Replies: 2
Views: 2535

standard run system hooks from Python

My questions, from specific to general, are: Is there a way to call a Python method from inside a Hoc proc? If I modify advance() as described below, will I slow down execution horribly? Is there some other better, or more conventional way than the one described below to accumulate output on disk, r...
by sec6
Sat Dec 27, 2008 3:50 pm
Forum: Modeling networks
Topic: Accessing Netcon.weight from NMODL before first Netcon event
Replies: 4
Views: 3745

Re: Accessing Netcon.weight from NMODL before first Netcon event

Alright, I've replicated the problem with a toy program. It boils down to an instance of unexpected behavior at the interface between NEURON and NMODL when combining NET_RECEIVE{INITIAL{}} with Netcon.event() The elements are as follows: One cell template simpleCell 2 presynaptic cells, instances of...
by sec6
Thu Dec 18, 2008 9:34 am
Forum: Modeling networks
Topic: Accessing Netcon.weight from NMODL before first Netcon event
Replies: 4
Views: 3745

Accessing Netcon.weight from NMODL before first Netcon event

In a synaptic mechanism I wrote in NMODL, I attempted to read the value of the connecting Netcon.weight at intialization time. Specifically, my NET_RECEIVE block contained this line: gmax = weight which executed *before* the first Netcon event occurred. This didn't work. If I understand correctly, t...
by sec6
Mon Aug 25, 2008 5:51 pm
Forum: NEURON + Python
Topic: NEURON-6.2 rev 2195 apparently requires Python 2.5.2
Replies: 2
Views: 2376

Re: NEURON-6.2 rev 2195 apparently requires Python 2.5.2

when you built with 2.5.1, that the python library that got linked was a 2.3 or 2.4? Right, that's probably the explanation. Sorry. I've got multiple copies of various versions of Python in various places, and have had problems before with NEURON finding the wrong one -- in particular 2.4 when I wa...
by sec6
Sat Aug 23, 2008 11:47 pm
Forum: NEURON + Python
Topic: NEURON-6.2 rev 2195 apparently requires Python 2.5.2
Replies: 2
Views: 2376

NEURON-6.2 rev 2195 apparently requires Python 2.5.2

I checked out & built revision 2195, and, when I ran neuron with the -python switch, got this warning: sys:1: RuntimeWarning: Python C API version mismatch for module nrn: This Python has API version 1012, module nrn has version 1013. I was using Python 2.5.1 I installed Python 2.5.2 and the warning...
by sec6
Thu Aug 21, 2008 7:15 pm
Forum: NEURON + Python
Topic: Vector.record() & RANGE variable of a point process
Replies: 2
Views: 2392

Re: Vector.record() & RANGE variable of a point process

Hang on a minute: I just noticed there's apparently a trac ticket for this. Is this the issue that was fixed in revision 2192?
If so, do I need to get the source from the SVN repository, or is it enough to download the latest precompiled installer for the current standard distribution?
by sec6
Thu Aug 21, 2008 6:01 pm
Forum: NEURON + Python
Topic: Vector.record() & RANGE variable of a point process
Replies: 2
Views: 2392

Vector.record() & RANGE variable of a point process

I'm debugging the Python-port of a model originally coded in hoc. Of course, I'm aiming to get the Python version to generate the same output as the hoc version. There's still a subtle difference, which I've tracked down to a particular synapse. I need a way to look more closely at that synapse, to ...
by sec6
Thu Aug 07, 2008 7:32 pm
Forum: OS X
Topic: Program editors for OS X
Replies: 7
Views: 7503

Re: Program editors for OS X

Some Mac users prefer BBEdit. It costs about $200. I wouldn't bother with it; has too many extraneous features and is far too expensive. I use BBedit, and like it a lot, but I concede that a really high-powered text editor is only useful if you do a lot of programming, and I definitely conceed that...
by sec6
Thu Aug 07, 2008 7:16 pm
Forum: NEURON + Python
Topic: hoc.NULLObject != Python.None
Replies: 1
Views: 2416

hoc.NULLObject != Python.None

Sometimes, in NEURON one needs a NULLObject, for example, when creating a NetCon with a source, but no target, or vice versa. (In the following toy example, I create a NetCon with no source *and* no target, which is legal, 'though useless.) oc>objref nil,nc oc>nc = new NetCon(nil,nil) oc>nc.event(5)...