Search found 14 matches

by jtmoyer
Fri May 23, 2008 5:30 pm
Forum: Parallel NEURON
Topic: nrn_timeout error
Replies: 2
Views: 2950

The problem turned out to be load imbalance. I was using variable dt (cvode.active(1)); one processor would finish much sooner than another, and would have to wait for the other to catch up. Turning off variable dt solved the problem and also reduced simulation time. It seemed to owe primarily to hi...
by jtmoyer
Thu Jan 24, 2008 5:44 pm
Forum: Parallel NEURON
Topic: nrn_timeout error
Replies: 2
Views: 2950

nrn_timeout error

Hi - I'm having a problem with a large network simulation that we are running on our XServe cluster. I think it might be a memory error but I'm not sure. We're running NEURON release 6.1.1 (1894), using the Inquiry system, on Mac OS 10.4 with 32 processors on 8 nodes. The simulation runs ok with 512...
by jtmoyer
Sun Dec 09, 2007 1:59 pm
Forum: Other questions
Topic: mpicc: command not found using nrnivmodl
Replies: 3
Views: 5290

The problem was that the mpi directory was not properly added to my path for some reason - i fixed it by adding the directory to my path in the .bash_login file in my home directory. For me, it looked like this:

export PATH="/usr/local/bin:/usr/local/sbin:/Applications/mpi/bin:$PATH"
by jtmoyer
Sun Dec 09, 2007 12:19 pm
Forum: Other questions
Topic: mpicc: command not found using nrnivmodl
Replies: 3
Views: 5290

orion:~ jtmoyer$ which mpicc
no mpicc in /usr/local/bin /Applications/NEURON-6.1/nrn/i686/bin /usr/local/bin /usr/local/sbin /Applications/NEURON-6.1/nrn/i686/bin /bin /sbin /usr/bin /usr/sbin
by jtmoyer
Sat Dec 08, 2007 8:49 pm
Forum: Other questions
Topic: mpicc: command not found using nrnivmodl
Replies: 3
Views: 5290

mpicc: command not found using nrnivmodl

Hello- I have Release 6.1.1 (1894) on my MacBook Pro, and I compiled it with MPI. When I try to compile my mod files by invoking nrnivmodl I get this error: /Applications/NEURON-6.1/nrn/share/nrn/libtool: line 1: mpicc: command not found make: *** [fsi_AMPA.lo] Error 1 Any idea what this could be? T...
by jtmoyer
Thu Sep 21, 2006 6:38 pm
Forum: The GUI
Topic: Turn Keep Lines on in hoc and preserve color info
Replies: 1
Views: 4312

Turn Keep Lines on in hoc and preserve color info

How can I turn on Keep Lines from the hoc code without using the Graph.family() command? Specifically I have a bunch of different variables being plotted in different colors, and calling family() changes all the colors to black.
by jtmoyer
Fri May 19, 2006 10:10 am
Forum: Other questions
Topic: changing a variable at specific times
Replies: 2
Views: 3781

that is pretty cool.
by jtmoyer
Thu May 18, 2006 4:27 pm
Forum: Other questions
Topic: Poisson distributed synaptic input
Replies: 5
Views: 14180

poisson spikes using matlab

This is the matlab code we use for generating gamma/poisson distributions. We save the times out into a text file, then import them into neuron using the netcon.event command. I got this off the web somewhere, but unfortunately I didn't keep track of where... function [t,s] = fastgammatrain(duration...
by jtmoyer
Thu May 18, 2006 4:25 pm
Forum: Other questions
Topic: changing a variable at specific times
Replies: 2
Views: 3781

changing a variable at specific times

what's the most efficient way to turn change a variable at a given time? i want to up-regulate a current at a specific time, leave it there for a few milliseconds, and then turn it back down. the best i can come up with is putting a few if statements in the advance block, but it seems like there mus...
by jtmoyer
Thu May 18, 2006 12:04 pm
Forum: OS X
Topic: Installing 5.8/InterViews 17 from source code
Replies: 1
Views: 4331

Installing 5.8/InterViews 17 from source code

I'm trying to install NEURON 5.8 from source code onto a dual 2.5 GHz Mac G5. When I try to "make" InteViews I get the error pasted below. Any idea why it can't find the LibUnidrawhines.la library? It doesn't appear to be in the referenced directory, or anywhere in the IV directory for that matter. ...
by jtmoyer
Thu Mar 23, 2006 12:24 pm
Forum: Suggestions and Feedback
Topic: Possible Workshop for 2006 Meeting
Replies: 1
Views: 11148

Possible Workshop for 2006 Meeting

I'd like to submit a request for a tutorial or workshop for the NEURON 2006 Simulator meeting in Austin - I would be very interested in a workshop on model reduction. That is, how do you take a very complicated model (in our case, 169 compartments, 15 currents) and reduce it to a much smaller one (s...
by jtmoyer
Tue Sep 20, 2005 2:41 pm
Forum: Other questions
Topic: Survey: need for large-scale computational support
Replies: 6
Views: 7306

Re: Survey: need for large-scale computational support

2 Simulating large scale models, i.e. the model itself is so complex that it's hard to fit onto a single computer, and even a single run takes a long time. Time per run is ___5 min______ Total number of simulations is ____480_____ Total simulation time ___40 hrs______ (i.e. time per run X number of ...
by jtmoyer
Wed Jun 29, 2005 1:53 pm
Forum: OS X
Topic: Is NEURON 5.7.159 slow compared to the previous 5.7?
Replies: 2
Views: 5725

It turns out that my trouble was an artifact of the screen update interval, which replaced the Quiet button in previous versions. Setting the interval to 0.5 or 1 second (instead of 0.05) fixed the problem.
by jtmoyer
Fri Jun 17, 2005 10:13 am
Forum: OS X
Topic: Is NEURON 5.7.159 slow compared to the previous 5.7?
Replies: 2
Views: 5725

Is NEURON 5.7.159 slow compared to the previous 5.7?

I installed the carbonized version of 5.7.159 and was comparing my results to the previous standard release (5.7.71, I think). I noticed that the same simulation took twice as long (43 seconds vs. 22)! Is this inherent to the version, or could it be something else? I installed 5.7.71 from the source...