Search found 88 matches

by breakwave922
Fri Nov 13, 2015 6:31 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Hi, Hines, Thanks for the help. Yes, I've been trying to debug this issue step-by-step. I created a small network with only 100 cells. I printed out the sequences saved and restored. But I'm not sure whether I did it correctly. Below is what I did. For the first part of the simulation, I saved the s...
by breakwave922
Wed Nov 11, 2015 6:27 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Hines, Sorry, I realize that randomlist is empty just now. And here is what I modified: for m = 0, 799{ if(!pc.gid_exists(m)) { continue } // Can't connect to target if it doesn't exist // on the node ("continue") skips rest of code bggen[m] = new BgGen(3,0,tstop,30,dt,m,pc.id) cellid = pc.gid2cell(...
by breakwave922
Wed Nov 11, 2015 5:45 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Hines, Here is what I did according to your advise. Remove pc.id from the Random123, use three args instead of one. One of the three args is cell's global id, other twos are zero. begintemplate BgGen proc init() { ... r = new Random() r.Random123(1000*($6+12),0,0) r.negexp(1) noise_netstim = new Net...
by breakwave922
Wed Nov 11, 2015 1:32 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Hines, If I use the same number of nodes to run the simulation, maybe using pc.id in a random stream is not a problem? But you are right, running on different pc.nhost would definitely have problems. Could you please let me know what should I do to this? Or can you show me some reference codes that ...
by breakwave922
Wed Nov 11, 2015 1:59 am
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Hi, Hines, Thanks for the reply. Here is what I modified to my code, according to your last threads: I changed MCellRan4 to Random123, and also both gid and pc.id are used to encode the stream and sequence. See code below begintemplate BgGen proc init() { ... r = new Random() r.Random123(1000*($6+$7...
by breakwave922
Tue Nov 10, 2015 7:38 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Hines, Thanks for helping me to solve my SaveState() problem on the single cell model, so now I'm moving on to the network level. I have some questions to ask. In my network, each cell receives random noise inputs, based on their cell id, see codes below begintemplate BgGen proc init() { ... r = new...
by breakwave922
Mon Nov 09, 2015 7:33 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Hines, Thank you for your reply. Yes, the code works now. But it's very strange that, the spikes only matches for some values of stim.interval. For example, when I set stim.interval=25 or 30, I can match the number of spikes. But when I set stim.interval=333 or 3, the second part of the simulation d...
by breakwave922
Mon Nov 09, 2015 1:23 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Hines, Thank you so much for you reply. But sorry for my not understanding your suggestion quite well. Here is what I did so far: In random generator, I switched to Random123, replacing my previous MCellRan4 generator r = new Random() r.Random123(1000) //r.MCellRan4(1000) r.negexp(1) stim = new NetS...
by breakwave922
Sun Nov 08, 2015 10:38 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Hi, Hines, I found that once if I set random noise in the netstim to the synapses, the second simulation results couldn't match the corresponding part in the original one that is before segmentation of the simulation. The first simulation matches well. If I turned off the random noise, both two part...
by breakwave922
Tue Oct 27, 2015 4:14 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Thanks, Hines, This works.
by breakwave922
Fri Oct 23, 2015 7:10 pm
Forum: Modeling networks
Topic: How to run the simulation in-between?
Replies: 28
Views: 14444

Re: How to run the simulation in-between?

Hi, Hines, I still have some problems in using SaveState(). I created a small program to test: Single cell with current injection for 800ms, and split this into 200+600ms. For this setup, SaveState works perfectly. But then I use netstim instead of current injection, once I use svstate.restore(), NE...
by breakwave922
Thu Oct 08, 2015 12:40 am
Forum: NEURON + Python
Topic: how to install Python+NEURON in Windows
Replies: 1
Views: 2217

how to install Python+NEURON in Windows

Are anyone here familiar with how to install Python and build and install the NEURON shared library for Python in Window? I've been stuck in it for almost 1 week and couldn't make any progress. I followed some instructions in the forum, but got too many errors. And I think those instructions is for ...
by breakwave922
Thu Oct 08, 2015 12:21 am
Forum: NEURON + Python
Topic: Introducing LFPy, a Python module for simulating LFPs
Replies: 3
Views: 5742

Re: Introducing LFPy, a Python module for simulating LFPs

Hi, Hagen,

I would like to use LFPy in my project. I have strong interests in using it.
But I found http://compneuro.umb.no/LFPy is no longer available.
Did you move the website?
Or can you send me related materials?
Thank you so much.
by breakwave922
Tue Oct 06, 2015 10:39 pm
Forum: MSWin
Topic: After updated to NEURON 7.4 on MSWin
Replies: 14
Views: 12374

Re: After updated to NEURON 7.4 on MSWin

Hi, Hines, Thank you so much for you reply. After you start your main.hoc by clicking on it and after the error message. Check your current working folder from the interpreter window by typing the command print getcwd() Is that the folder that contains XX.hoc? Tying print getcwd(), under 7.4, I got ...
by breakwave922
Mon Oct 05, 2015 11:16 pm
Forum: MSWin
Topic: After updated to NEURON 7.4 on MSWin
Replies: 14
Views: 12374

Re: After updated to NEURON 7.4 on MSWin

OK, and just to be quite sure, after you installed 7.4, you deleted all of your old nrnmech.dll and .o and .c files, then ran mknrndll to compile your mod files. Then you tried your hoc program, and got the "Entry Point Not Found" error message? Ted, Yes, I deleted all the old dll,.o and .c files a...