Search found 24 matches

by agmccrei
Fri Dec 06, 2019 2:50 pm
Forum: Parallel NEURON
Topic: Making Random Processes Threadsafe
Replies: 0
Views: 627

Making Random Processes Threadsafe

Hello, I have a question about using mod files that utilize random number generators in parallelized network simulations. Specifically I use Gfluct.mod ( https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=8115&file=/fluct/Gfluct.mod#tabs-2 - from what I've read, this file also appears to h...
by agmccrei
Wed Oct 09, 2019 4:20 pm
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 9
Views: 1946

Re: MOD Files Compile But Fail To Load

Just an update to this. I recently updated to macOS Catalina vs10.15, and had a lot of problems with my anaconda installation as a result. In getting fed up with it and just deleting anaconda (I only had it installed to test it out - was never really dependent on it) and then re-installing all the p...
by agmccrei
Sun Sep 29, 2019 8:19 pm
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 9
Views: 1946

Re: MOD Files Compile But Fail To Load

I'm also curious why it's not finding and linking ncurses through "@rpath/libncursesw.6.dylib". When I run a search, only 1 libncursesw.6.dylib pops up: (base) Alexandres-MacBook-Pro:.libs agmccrei$ mdfind libncursesw.6.dylib /anaconda3/lib/libncursesw.6.dylib /Users/agmccrei/Downloads/PurkReduction...
by agmccrei
Sun Sep 29, 2019 7:52 pm
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 9
Views: 1946

Re: MOD Files Compile But Fail To Load

When I run neurondemo, the gui pops up fine and all the demos appear to run fine with no errors. I don't see a "Release" button in any of the GUI windows, but clicking on "Init & Run" in any of the demos does not generate any errors and the simulations run to completion. My mod files and x86_64 fold...
by agmccrei
Fri Sep 27, 2019 4:37 pm
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 9
Views: 1946

Re: MOD Files Compile But Fail To Load

Update: I can fix the problem in a very manual way. From the directory: nrnivmodl cd x86_64/.libs/ -L libnrnmech.0.so This outputs the following: libnrnmech.0.so: /Applications/NEURON-7.7/nrn/x86_64/lib/libnrnoc.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Applications/NEURON-7.7/nr...
by agmccrei
Fri Sep 27, 2019 12:08 pm
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 9
Views: 1946

Re: MOD Files Compile But Fail To Load

Thanks. 1. It's a new laptop (about a week old now). No previous installations of NEURON. When I first installed everything it worked fine. Seemingly out of the blue yesterday, I started getting that error message when I tried to load a model from modeldb (at first I thought it was just that model b...
by agmccrei
Thu Sep 26, 2019 9:12 pm
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 9
Views: 1946

MOD Files Compile But Fail To Load

Hello, I'm running into some strange errors in loading my channel mechanisms with my Python/NEURON installation. I have tried re-installing NEURON and XQuartz but the error report persists. Here are my system details: macOS Mojave (10.14.6) NEURON VERSION 7.7.2 Python 3.7.3 XQuartz 2.7.11 Xcode vers...
by agmccrei
Mon May 13, 2019 6:06 pm
Forum: Parallel NEURON
Topic: Bulletin-Style Grid-Like Simulations: Indexing Getting Mixed Up
Replies: 4
Views: 1280

Re: Bulletin-Style Grid-Like Simulations: Indexing Getting Mixed Up

UPDATE: Turns out my error was pretty trivial (as is usually the case). I was using code from a previous project, and I had forgotten to adjust it for conditions where the input spike rate was 0 Hz. The problem was that I had a conditional statement in my hoc code that prevented the NetStim paramete...
by agmccrei
Mon May 13, 2019 5:13 pm
Forum: Parallel NEURON
Topic: Bulletin-Style Grid-Like Simulations: Indexing Getting Mixed Up
Replies: 4
Views: 1280

Re: Bulletin-Style Grid-Like Simulations: Indexing Getting Mixed Up

Thanks Ted, I return both the index values as well as the actual parameters values (i.e. injected current and input frequency). The odd thing about my problem is that everything gets indexed in the correct order, despite the results appearing out of order. When I print out output lists (i.e. that we...
by agmccrei
Sun May 12, 2019 1:23 pm
Forum: Parallel NEURON
Topic: Bulletin-Style Grid-Like Simulations: Indexing Getting Mixed Up
Replies: 4
Views: 1280

Bulletin-Style Grid-Like Simulations: Indexing Getting Mixed Up

Hello, I am doing a grid-like set of simulations on a single-neuron model (python/neuron) with increasing holding currents (i.e. using IClamp at the soma; all spike-generating current levels) and increasing synaptic input frequencies (i.e. using Exp2Syn processes at various dendritic locations). I'v...
by agmccrei
Wed Jan 24, 2018 1:37 pm
Forum: Other questions
Topic: NetStim Fractional Randomness: Mathematical Notation?
Replies: 3
Views: 1787

Re: NetStim Fractional Randomness: Mathematical Notation?

Right, so my understanding of how fractional randomness is implemented is that for each interspike interval, the interval is dependent on the values set for s.interval and s.noise (assuming s = new NetStim(x)). Specifically, the magnitude of the value of s.noise (from 0 to 1) will control the propor...
by agmccrei
Fri Jan 19, 2018 4:19 pm
Forum: Other questions
Topic: NetStim Fractional Randomness: Mathematical Notation?
Replies: 3
Views: 1787

NetStim Fractional Randomness: Mathematical Notation?

Hello, I don't have a strong formal background in mathematics here, but I want to describe some of the mechanisms used in NEURON. Specifically, I am not sure if I have the correct mathematical notation for describing how fractional randomness is implemented in NEURON's NetStim function. So far, I ha...
by agmccrei
Sun Feb 26, 2017 2:18 am
Forum: Parallel NEURON
Topic: Accessing ParallelContext() while in Python
Replies: 2
Views: 5862

Re: Accessing ParallelContext() while in Python

I actually found what looks to be a (embarrassingly) simple solution to my initial query. In fact, I am somewhat embarrassed I had not realized this before. Instead of running the ParallelContext twice for two separate problems, I could just run my hoc "simulation" function (i.e. h.f()) at the begin...
by agmccrei
Thu Feb 23, 2017 6:21 pm
Forum: Parallel NEURON
Topic: Accessing ParallelContext() while in Python
Replies: 2
Views: 5862

Re: Accessing ParallelContext() while in Python

One quick thing to add is that in the simplified code, when I do not create the ParallelContext in the hoc file (i.e. I comment out execution of the "SynParamSearch.hoc" file in the "init.py" file) and I create it in the python code with pc = h.ParallelContext(), the parallelization works fine. Simi...
by agmccrei
Thu Feb 23, 2017 5:36 pm
Forum: Parallel NEURON
Topic: Accessing ParallelContext() while in Python
Replies: 2
Views: 5862

Accessing ParallelContext() while in Python

Hello, I am fairly new to parallel processing and I am running into a somewhat odd problem while trying to access and re-use a previously used ParallelContext(). When I first use a ParallelContext in my hoc code to run a parameter search (i.e. simulate many iterations of my models) using a bulletin ...