Search found 34 matches

by bschneiders
Tue Apr 07, 2020 11:27 am
Forum: The GUI
Topic: PlotShape colormap
Replies: 1
Views: 8751

PlotShape colormap

Hi, is there are way to make PlotShapes have different colormaps? I changed the color scheme for one plotshape (for fluorescence - I want it to be a single hue) and it ended up changing the rest of them. Is there any way around this, or is colormap a global setting? Thanks! Also, my method for doing...
by bschneiders
Wed Feb 05, 2020 3:29 pm
Forum: Reaction-diffusion in NEURON
Topic: length scales and SparseEfficiencyWarning
Replies: 5
Views: 9823

Re: length scales and SparseEfficiencyWarning

Hmm. This got weirder. I replaced the PlotShape code with your suggestion, and now the warning goes away, but the seg fault does not. That is, when I enter the code manually, I don't get that syntax warning anymore and can make sw5, sw6 etc. no problem. However, if I run the code all at once ("...
by bschneiders
Tue Feb 04, 2020 2:30 pm
Forum: Reaction-diffusion in NEURON
Topic: length scales and SparseEfficiencyWarning
Replies: 5
Views: 9823

Re: length scales and SparseEfficiencyWarning

A quick follow-up. I did finally update to 7.7, but I am still getting frequent seg faults. It now seg faults every time I run my full code (i.e. execfile("driver.py")) but if I run every line manually, it doesn't seg fault. The only warning I get is the following, whether it segfaults or ...
by bschneiders
Tue Nov 12, 2019 12:34 pm
Forum: Reaction-diffusion in NEURON
Topic: length scales and SparseEfficiencyWarning
Replies: 5
Views: 9823

Re: length scales and SparseEfficiencyWarning

That's good to know about 7.7, thanks! As for the lengths scales and tolerance, I figured that was the case but it was worth a shot. I have set atolscales appropriately I believe (the Atol Scale Tool caught some that I had missed - very handy), but I don't think that catches the discretization I'm t...
by bschneiders
Fri Nov 08, 2019 7:02 pm
Forum: Reaction-diffusion in NEURON
Topic: length scales and SparseEfficiencyWarning
Replies: 5
Views: 9823

length scales and SparseEfficiencyWarning

Hi. I have two likely related questions. The first is, I sometimes get the following warning: /Applications/NEURON-7.6/nrn/lib/python/neuron/rxd/section1d.py:155: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil_matrix is more efficient. g[io, io] += rate_r ...
by bschneiders
Mon Apr 29, 2019 4:53 pm
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 11534

Re: Installing Neuron on macOS Mojave

By the way, thanks to help from Robert McDougal, I do have the packaged version of 7.6 working! For anyone else who was having issues with that on a Mac, it has been updated and it fixed what was causing my seg faults.
by bschneiders
Mon Apr 29, 2019 3:53 pm
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 11534

Re: Installing Neuron on macOS Mojave

Hmm. My xcode command line tools are Apple LLVM version 10.0.1, but my Mojave is 10.14.4, so maybe that needs to be updated. I'll see if that does it. Thanks!
by bschneiders
Tue Apr 23, 2019 3:15 pm
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 11534

Re: Installing Neuron on macOS Mojave

Thank you. With that, I get past the make error. Then, in the make install, I first was getting this error: clang: error: linker command failed with exit code 1 (use -v to see invocation) error: command 'g++' failed with exit status 1 I didn't see this error on the Neuron forum, but on other forums ...
by bschneiders
Mon Apr 22, 2019 12:22 pm
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 11534

Installing Neuron on macOS Mojave

Hi, I updated to Mojave a couple months ago (unfortunately) and have not been able to get my model to run on Neuron since then. I've been using a Linux machine in the meantime, but I decided to give it a shot again on my own machine this past week - it'd be convenient to run it on my own laptop. Las...
by bschneiders
Fri Mar 01, 2019 9:48 am
Forum: Reaction-diffusion in NEURON
Topic: USEION in mod files for RxD species I created
Replies: 3
Views: 9001

USEION in mod files for RxD species I created

Hi, I am trying to keep track of the maximum value of several concentrations using mod files (so that I don't have to record in a bunch of locations). This worked really well for calcium, but the same syntax doesn't work for species that I created with RxD. Here is what worked for calcium: NEURON { ...
by bschneiders
Fri Jan 18, 2019 3:08 pm
Forum: Reaction-diffusion in NEURON
Topic: updating Species and Rates inputs
Replies: 2
Views: 3277

Re: updating Species and Rates inputs

Thank you, I will try that!
by bschneiders
Wed Jan 16, 2019 2:41 pm
Forum: Reaction-diffusion in NEURON
Topic: updating Species and Rates inputs
Replies: 2
Views: 3277

updating Species and Rates inputs

Hi, I have a question about updating rxd.Species inputs. Up until now, I simply restart python when I need to update initial concentrations, etc. However, I'm now running scripts to rapidly run through parameter values, and it would be very convenient not to exit Python between runs. First of all, l...
by bschneiders
Tue Nov 27, 2018 12:48 pm
Forum: OS X
Topic: Segmentation fault with alpha version of 7.6
Replies: 0
Views: 13283

Segmentation fault with alpha version of 7.6

Hi, I am wondering if I can get help with a segmentation fault when I run the new Neuron 7.6. I updated to Mojave, and therefore downloaded the alpha version of Neuron 7.6. I got past the issues from the installation forum page and have it running, but my model only works sometimes . I often get a s...
by bschneiders
Thu Nov 15, 2018 5:42 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 36
Views: 55094

Re: Installation problem Neuron

I ended up getting mine to work. I did the following: -added the same 3 flags mentioned by aaronmil to my bash_profile -deleted Neuron again and built it from source code -used the configure option --with-readline=no -did the following step after "make after_install" to make sure python an...
by bschneiders
Wed Nov 14, 2018 9:45 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 36
Views: 55094

Re: Installation problem Neuron

Hi all, I'm getting a similar issue. I updated to Mojave, and got the "ImportError: No module named hoc27" error when I tried to run Neuron again. Per this forum topic, I uninstalled anaconda, deleted Neuron 7.5, and then reinstalled anaconda 2.7 and downloaded Neuron 7.6. I updated Xcode,...