www.neuron.yale.edu

Oh I see, that explanation makes perfect sense. Thank you very much for the help. And yes, this model has been used to generate published results. I am currently going back and re-running with gmax_IhPyrKop = 0.1, and I will see whether this affects simulation results. Thank you both again for the h...

I am translating a hoc model (that I inherited) into Python, and I am having some trouble with a custom mod file. The hoc code references the mod file (which defines a mechanism named "IhPyrKop") in the following way: insert IhPyrKop soma{ gh_IhPyrKop = 0.1 v50_IhPyrKop = -82 } The only pr...

Great, thanks so much for the thorough explanation. I feel like when it comes to NEURON's integration schemes, I now harbor fewer unknown unknowns, more known unknowns, and maybe even one or two known knowns. :-)

Thanks, this works perfectly now. I really appreciate the help. I am curious why importing gui automatically creates an instance of CVode. I know CVode implements adaptive time step numerical integration, with a separate "stream" for each neuron in the simulation. Is CVode the default nume...

That is really helpful--thank you! One more question, though. I am having trouble getting this newly-crated NetCon to actually do anything. Using the following code from neuron import h, gui soma=h.Section() soma.insert('pas') syn=h.ExpSyn(soma(0.5)) #create netcon h("objref nil") nil=h.ni...

I am trying to translate the following hoc code into Python (where nil is an unassigned objref, and syn is some generic synapse): nc=new NetCon(nil, syn) I initially tried nc=h.NetCon(None,syn) but I received a "hoc error" . Then, after reading https://www.neuron.yale.edu/phpBB/viewtopic.p...

I am attempting to install NEURON in Linux for the first time, and I need it to work with mpich2. I've searched the documentation, but I can't find which version is best for NEURON 7.4. Does it matter?

Whoops...yes, I meant /usr/lib64/openmpi/lib was in LD_LIBRARY_PATH. Okay, I re-installed openmpi from source, putting it in /usr/local/openmpi. Then I installed interviews in ~/local/iv. No problem. Then I tried installing nrn in ~/local/nrn, so that I would not have to use sudo to install it. Unfo...

I checked, and /usr/lib64/openmpi/bin is already included in LD_LIBRARY_PATH. To install openmpi, I simply executed the command yum install openmpi openmpi-devel, and it apparently installed it in /usr/lib64. Should I perhaps uninstall it and then re-install in /usr/local ?

I am trying to install NEURON on CentOS 7. I need it to have parallel capabilities and work with Python, so I am following these steps: 1. Clone InterViews and NEURON sources into the current directory: hg clone http://www.neuron.yale.edu/hg/neuron/iv hg clone http://www.neuron.yale.edu/hg/neuron/nr...

Thanks for all the help, Michael. Just so everyone else can benefit, the solution was to issue the following installation commands in the /share/apps directory (installing in this directory makes the program available to all compute nodes in Rocks): ./configure --prefix=/share/apps/neuron-73 --with-...

It turns out I spoke too soon. I *thought* everything was working fine because my simulations seemed to start all right, but then they crashed with the error message ./special: line 13: 18039 Killed “${NRNIV}” –dll “/share_home/cgfink/Documents/hfo/base_code/mod/x86_64/.libs/libnrnmech.so” “$@” Base...

I figured out a simple solution. I just deleted the installation from the /exports/apps directory, and re-installed in the /share/apps directory. Everything works fine now.

I recently installed NEURON 7.3 on our small ROCKS cluster (running CentOS). I can run simulations just fine on the head node, but I cannot get NEURON to work on any other nodes. I get the following error message: /export/apps/neuron-73/x86_64/bin/nrniv: No such file or directory I believe the issue...

A few years ago I went to the NEURON tutorial in La Jolla and received help writing a mod file which stimulated noisy synaptic events to a cell. It uses Random123, but there are no hoc calls to Random123--everything is done within the mod file. Within the INITIAL section, the two "identifier&qu...