Search found 28 matches

by nikkip
Mon Sep 11, 2017 9:02 am
Forum: Parallel NEURON
Topic: Parallelization of a single cell
Replies: 7
Views: 9557

Re: Parallelization of a single cell

Hi Mike,

I do need to use the extracellular method. Thanks for clarifying.

Nikki
by nikkip
Thu Sep 07, 2017 8:44 pm
Forum: Parallel NEURON
Topic: Parallelization of a single cell
Replies: 7
Views: 9557

Re: Parallelization of a single cell

Hi again, In looking more carefully at the multisplit documentation, it says that it cannot be used with the extracellular mechanism. Is that correct? In which case there's no way to split a single cell across multiple processors if using extracellular? https://www.neuron.yale.edu/neuron/static/new_...
by nikkip
Wed Sep 06, 2017 1:57 pm
Forum: Parallel NEURON
Topic: Parallelization of a single cell
Replies: 7
Views: 9557

Re: Parallelization of a single cell

Thanks Ted. I'm already doing #1, so looking to add on #2. I'll work from Hines 2008 & associated ModelDB entry.

Thanks,

Nikki
by nikkip
Tue Sep 05, 2017 6:52 pm
Forum: Parallel NEURON
Topic: Parallelization of a single cell
Replies: 7
Views: 9557

Re: Parallelization of a single cell

Thanks for the quick reply!! Good question. I have not tried multithreaded, although I don't grasp the pros/cons/implications of multithreading vs using multisplit. To provide some more context about my task: We currently use a bash script to post a large number of independent NEURON jobs on a compu...
by nikkip
Mon Sep 04, 2017 10:22 pm
Forum: Parallel NEURON
Topic: Parallelization of a single cell
Replies: 7
Views: 9557

Parallelization of a single cell

Hi Ted and Mike, I was wondering if it's possible to parallelize an unbranched single cell (with many compartments). If yes, I assume it involves using multisplit: https://www.neuron.yale.edu/neuron/static/new_doc/modelspec/programmatic/network/parcon.html#ParallelContext.multisplit. Is there a simp...
by nikkip
Thu Jun 29, 2017 4:41 pm
Forum: MSWin
Topic: NRN 7.4 on windows 10
Replies: 24
Views: 21823

Re: NRN 7.4 on windows 10

I just realized that I installed a v7.4 as per my earlier post, but using that alpha link you sent: nrn-7.4.rel-1390.x86_64-w64-mingw32-setup.exe I didn't use the nrn-7.5 installer because it seemed to include python (as alluded to in your last post), which I don't use. But I didn't realize that the...
by nikkip
Thu Jun 29, 2017 10:24 am
Forum: MSWin
Topic: NRN 7.4 on windows 10
Replies: 24
Views: 21823

Re: NRN 7.4 on windows 10

Follow-up: I'm still getting the error sometimes. Not clear what causes it to happen or not. I can repeatedly double-click my HOC (associated with neuron.exe from v7.5), and sometimes I get the bash error window, other times the code will run.

Thanks,

Nikki
by nikkip
Wed Jun 28, 2017 6:08 pm
Forum: MSWin
Topic: NRN 7.4 on windows 10
Replies: 24
Views: 21823

Re: NRN 7.4 on windows 10

Thanks Mike! V7.5 seems to have resolved the issue. I'm using:

nrn-7.4.rel-1390.x86_64-w64-mingw32-setup.exe

I don't think it's the registry issue you mentioned since this computer is new from a few months ago.

Thanks!

Nikki
by nikkip
Wed Jun 21, 2017 11:37 am
Forum: MSWin
Topic: NRN 7.4 on windows 10
Replies: 24
Views: 21823

Re: NRN 7.4 on windows 10

Hi Ted and Mike, I am also getting an error running NEURON v7.4 (64 bit) on Windows 10 (64 bit). When double-clicking a HOC file (with the blue AP icon, i.e. associated with neuron.exe), I get the following error: bash.exe - Application Error The application was unable to start correctly (0xc0000142...
by nikkip
Mon Sep 15, 2014 9:33 am
Forum: Getting started
Topic: Issues with underscores in variable or procedure names
Replies: 2
Views: 1410

Re: Issues with underscores in variable or procedure names

Interesting... If you replace batch_run() with batch_gun(), it works fine. So some conflict with the built-in run() function?
by nikkip
Sun Sep 14, 2014 8:29 pm
Forum: Getting started
Topic: Issues with underscores in variable or procedure names
Replies: 2
Views: 1410

Issues with underscores in variable or procedure names

Hi Ted, I use underscores in almost all of my variable/procedure/function names. But I've just recently that sometimes these underscores make NEURON crash. For instance: proc batchrun() { print "testing 1" } batchrun() proc batch_run() { print "testing 2" } batch_run() The first procedure runs fine,...
by nikkip
Thu Jul 24, 2014 9:36 am
Forum: Getting started
Topic: Action potential with SEclamp
Replies: 5
Views: 4450

Re: Action potential with SEclamp

First realize that NEURON uses the central difference approximation for the second derivative of v with respect to distance along a cable. Then realize that this means each compartment is properly represented by an equivalent T circuit where each compartment's axial resistance is divided into two p...
by nikkip
Wed Jul 23, 2014 12:41 pm
Forum: Getting started
Topic: Action potential with SEclamp
Replies: 5
Views: 4450

Re: Action potential with SEclamp

Thanks for the quick reply! So I'm trying to understand the two issues from a circuits perspective. http://i.imgur.com/9hqSJy9.png My model is a single compartment (i.e. space-clamped). That being said, I realize that NEURON computes voltages at 0 and 1, even though there are only membrane propertie...
by nikkip
Tue Jul 22, 2014 4:18 pm
Forum: Getting started
Topic: Action potential with SEclamp
Replies: 5
Views: 4450

Action potential with SEclamp

Hello,

I'm using an SEclamp to obtain Vm and Im data. However, if the clamp's rs is too big or if my cell is too big, I'm getting an action potential at sufficiently depolarized clamp values. How/why is the clamp allowing the cell to fire an action potential?

Thanks!

Nikki
by nikkip
Mon Jun 16, 2014 10:18 am
Forum: Getting started
Topic: CVODE: record, play, events
Replies: 16
Views: 7193

Re: CVODE: record, play, events

ted wrote:The examples are of the Vector class's record method. Did you mean to include an example of the use of cvode.record?

Oops! No, I never ended up using cvode.record(). Thanks for catching that.