Search found 18 matches

by JBall
Thu Sep 29, 2016 11:29 pm
Forum: NEURON + Python
Topic: Interviews graphing in Python
Replies: 1
Views: 8976

Interviews graphing in Python

Hello, I'm getting back into Neuron after a few years' hiatus...this time teaching myself Python in the process. I'm generally picking things up well, but I'm banging my head against graphing variables using the IV interface from python. I apologize--I wouldn't have created a forum topic if I'd had ...
by JBall
Fri Jul 08, 2011 11:17 pm
Forum: Parallel NEURON
Topic: parallel save/restore state
Replies: 4
Views: 2313

Re: parallel save/restore state

I am bumping this thread because I have a similar problem as the user in the first post. I have a network with plasticity, and I would like to put it through a series of training events and test it between each training session. Thinking that the savestate class would work perfectly for this, I set ...
by JBall
Thu May 12, 2011 5:43 pm
Forum: UNIX/Linux
Topic: Problems installing Neuron on a supercluster
Replies: 10
Views: 14626

Re: Problems installing Neuron on a supercluster

Alright, I'm having an issue that I have asked Ferlin support about, but I'm going to post it here in case you know something: When I do an mpirun on an interactive node (say, using spattach -i -p3), a fair amount of the time, I get a message like this: rsh: connect(a11c11n13 [193.11.170.105]): No r...
by JBall
Thu May 12, 2011 2:19 pm
Forum: UNIX/Linux
Topic: Problems installing Neuron on a supercluster
Replies: 10
Views: 14626

Re: Problems installing Neuron on a supercluster

I need to contact Ferlin support anyway for a couple of Ferlin-related things, so I'll ask about that error message. I suspect it's related to abnormal termination of the job after the script runs. You and Ted continue to astound me with how thoroughly you maintain and support Neuron. Thanks again f...
by JBall
Thu May 12, 2011 12:49 pm
Forum: UNIX/Linux
Topic: Problems installing Neuron on a supercluster
Replies: 10
Views: 14626

Re: Problems installing Neuron on a supercluster

Ok, wow! Your instructions have been immensely helpful so far. Neuron has been successfully installed and I can run nrniv on single nodes as well as run mpi jobs on an interactive node (I'm still figuring out the "esubmit" procedure, but I will talk to ferlin support for that). One issue I do have, ...
by JBall
Wed May 11, 2011 7:14 pm
Forum: UNIX/Linux
Topic: Problems installing Neuron on a supercluster
Replies: 10
Views: 14626

Re: Problems installing Neuron on a supercluster

...yes, using the wrong directory would be an issue. I've had issues with iv as well as Neuron, and while I have mostly given up on iv, I seem to have pasted the wrong make output here. I've pasted the results for the make of Neuron below. Also, I am trying to install Neuron on Ferlin and not Lindgr...
by JBall
Wed May 11, 2011 5:20 pm
Forum: UNIX/Linux
Topic: Problems installing Neuron on a supercluster
Replies: 10
Views: 14626

Problems installing Neuron on a supercluster

Hello, I've been banging my head against this problem for a couple of days now, and I'm not sure how to proceed. Disclaimer: I'm very much a novice in this. I've been following the instructions for downloading and installing Neuron on a supercluster to which we just recently gained access. When tryi...
by JBall
Thu Oct 21, 2010 1:44 pm
Forum: Parallel NEURON
Topic: Passing parameters using pack/post, etc.
Replies: 18
Views: 16218

Passing parameters using pack/post, etc.

Hello, I've been trying to get some model optimization going in parallel neuron. This involves, among other things, the ability to pass numbers between nodes to set model parameters and to compare fitness scores for different parameter sets. As a starting point, the code below is built to generate a...
by JBall
Mon Jul 05, 2010 8:20 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Implementing delays with continuous variables
Replies: 10
Views: 3492

Re: Implementing delays with continuous variables

The new version is extrapolating future values of the output variable from its two most recently calculated values. This is equivalent to the forward Euler method, which becomes unstable if the time step is too large. As far as the abrupt jump of the output variable that occurs at each sampling tim...
by JBall
Sat Jul 03, 2010 10:43 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Very odd problem with NMODL files
Replies: 3
Views: 1606

Re: Very odd problem with NMODL files

I just sent you an e-mail with the files in a zip called "BugTest.zip."

I forgot to mention my OS and version, though: I'm using Windows Vista Home SP1 with NEURON v7.1; however, I had the exact problem on Windows XP SP3 as well with the same files.

Thanks again!
by JBall
Fri Jul 02, 2010 3:33 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Implementing delays with continuous variables
Replies: 10
Views: 3492

Re: Implementing delays with continuous variables

I've implemented this into my simulation routine, and it works well. However, in the process I've had to completely scrap using cvode, because the net_send interval and the time-step optimization routine fight each other and really slow the simulation down in order to land on the right point in time...
by JBall
Thu Jul 01, 2010 8:55 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Very odd problem with NMODL files
Replies: 3
Views: 1606

Very odd problem with NMODL files

Hello again, Today I spent six hours debugging a pair of .mod files. Functionally they were identical with different parameters, but one calculates numbers correctly and the other doesn't. In the process of debugging, I got to the point where these mod files were completely identical, character by c...
by JBall
Thu Jul 01, 2010 10:37 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Implementing delays with continuous variables
Replies: 10
Views: 3492

Re: Implementing delays with continuous variables

Ted, Thanks so much for your help. After some fiddling I think I understand how this works. I think this really highlights how new I am to the software--for instance, I had no idea that using arrays in NMODL code was allowed. Anyway, I sat down and created this modified version of the mod file that ...
by JBall
Mon Jun 28, 2010 1:08 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Implementing delays with continuous variables
Replies: 10
Views: 3492

Re: Implementing delays with continuous variables

I've thought about this based on your advice, but I haven't figured out how to make it happen. An idea that came to me was the possibility of using an nmodl TABLE with a time (modulus delay) dependency as a sort of ring buffer, but this would require writing individual values of my delay variable at...
by JBall
Thu Jun 24, 2010 12:11 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Implementing delays with continuous variables
Replies: 10
Views: 3492

Implementing delays with continuous variables

I have an interesting problem I'm trying to work with here, and I've tackled it several times conceptually with no luck, but I am hoping someone here can help. I need to implement a delay for a continuous value during simulations. I won't get into the details of the project, but an equivalent exerci...