Search found 1589 matches

by hines
Wed Sep 12, 2018 7:10 am
Forum: OS X
Topic: Installation problem Neuron
Replies: 36
Views: 20554

Re: Installation problem Neuron

one last diagnostic test using a terminal window. What is the output of
otool -L /Applications/NEURON-7.6/nrn/x86_64/bin/nrniv
The executable expects to get those variables from /usr/lib/libedit.3.dylib
Also what is the result of
ls -l /usr/lib/libedit*
ls -l /usr/lib/libreadline*
by hines
Tue Sep 11, 2018 8:34 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 36
Views: 20554

Re: Installation problem Neuron

I'd like to know the result of the terminal experiment I mentioned earlier. That will generate several further questions.
by hines
Mon Sep 10, 2018 9:39 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 36
Views: 20554

Re: Installation problem Neuron

I tried to install the mojave beta on a virtual box clone of high sierra. Gets what seems to be close to success but will not boot. Hangs at the
boot message
/dev/disk0s2 on / (hfs, local, journaled)
by hines
Mon Sep 10, 2018 6:10 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 36
Views: 20554

Re: Installation problem Neuron

Did you build from sources or use the pkg file distribution. If the latter, have you intalled the software from xquartz.org and the command line tools. If the latter what configure line did you use. What python do you have installed. Does the following work? Start a terminal window and in the termin...
by hines
Wed Aug 29, 2018 8:20 am
Forum: Neurons in Action
Topic: NIA 2 crashes Firefox
Replies: 1
Views: 6272

Re: NIA 2 crashes Firefox

I'm not actually certain the following is relevant but you might try (from a terminal window) curl https://nia2.sinauer.com/nrngui.forNIA2EX.txt > /Applications/NIA2Ex.app/Contents/MacOS/HelperApps/NEURON/nrn/i686/bin/nrngui.sh Probably a good idea to first make a copy of the original nrngui.sh Plea...
by hines
Mon Aug 27, 2018 6:41 pm
Forum: Anatomically detailed models
Topic: area() function -- stylized method -- 3d-method
Replies: 4
Views: 2110

Re: area() function -- stylized method -- 3d-method

When there are 3-d points the area of a segment is the sum of all frusta between adjacent 3-d points that intersect the segment. No curvature effects are taken into account but effects of the sqrt(dradius^2 + darc^2) are taken into account (notice that if there are two points at the same position wi...
by hines
Mon Jul 30, 2018 10:09 am
Forum: Parallel NEURON
Topic: How to execute CoreNEURON with GPU?
Replies: 11
Views: 5951

Re: How to execute CoreNEURON with GPU?

With respect to cmake, I've asked my more knowledgable colleague to weigh in. That may save some flailing around on my part. CoreNEURON should be able to use MPI with either CPU or GPU. That is, in either case the cpu manages spike exchange and the event will be processed by the GPU in the latter ca...
by hines
Sat Jul 07, 2018 6:14 pm
Forum: Other questions
Topic: Using event delivery system with fixed time step method.
Replies: 7
Views: 3508

Re: Using event delivery system with fixed time step method.

cvode.active(1) is primarily for using cvode with fadvance() and ParallelContext.psolve(tstop). It is merely inadvertent that cvode.solve(tstop) does its work independently of the value of cvode.active(). Note, though, that cvode.solve does not make sense without a precursor call to cvode.re_init() ...
by hines
Tue Jun 19, 2018 6:31 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: "My mechanisms don't load!"
Replies: 21
Views: 33276

Re: "My mechanisms don't load!"

NEURON only loads mod files by default if you start in the folder where you executed nrnivmodl. SInce you executed the latter in the mod folder, if you wanted to load from the parent of the mod folder you would need nrniv -dll mod/x86_64/.libs/libnrnmech.so mosinit.hoc However, much better is to rem...
by hines
Fri Jun 15, 2018 5:59 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 6950

Re: Getting the full topology (segments level) from hoc

You should check whether a section has a parent using sref.has_parent() before actually trying to reference the parent. Also when many sections are connected to the same rootnode or parent section, it may be useful to use sref.has_trueparent() and sref.trueparent(). Parent and trueparent can differ ...
by hines
Tue Jun 12, 2018 9:43 am
Forum: Other questions
Topic: Numerical methods in NEURON
Replies: 6
Views: 2298

Re: Numerical methods in NEURON

In nrn/src/nrnoc/treeset.c there is a lengthy comment (beginning line 81) that discusses how NEURON is doing the calculation.
by hines
Fri Jun 08, 2018 8:24 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Making a timer dummy cell for benchmarking
Replies: 3
Views: 1797

Re: Making a timer dummy cell for benchmarking

ARTIFICIAL_CELL does not fit will with the concept of a ratio between integration time and real time since there is no integration per (fixed) time step but only computation on each incoming event. At the no incoming event extreme, there is no computation. However, if you replace ARTIFICIAL_CELL wit...
by hines
Fri May 25, 2018 1:16 am
Forum: NEURON + Python
Topic: Python NEURON
Replies: 15
Views: 20897

Re: Python NEURON

It turned out that to fix the import rxd problem for python 3.5, it was necessary to compile the neuron.rxd.geometry3d cython constructed
cpp files using Microsoft visual c. That is now being done when distributions are constructed.
by hines
Tue Apr 10, 2018 4:47 am
Forum: NEURON + Python
Topic: Cannot get Vector.play() and NetCon/NetStim work with CVODE and SaveState.restore()
Replies: 4
Views: 2636

Re: Cannot get Vector.play() and NetCon/NetStim work with CVODE and SaveState.restore()

I've reproduced the results of your code. An alternative to your fix using t.restore(0), which restores the event queue to the time of save. is to realize that the save phase did not have any knowledge of rv.play(t.ic._ref_amp, tv, 1) and in particular that on restore there needs to be an event for ...
by hines
Sat Apr 07, 2018 8:31 am
Forum: NEURON + Python
Topic: Cannot get Vector.play() and NetCon/NetStim work with CVODE and SaveState.restore()
Replies: 4
Views: 2636

Re: Cannot get Vector.play() and NetCon/NetStim work with CVODE and SaveState.restore()

I'll need to look into this a bit more but for now I just want to caution that if SaveState is chosen so that events on the queue are part of the state, that one cannot in general set h.t = 0 because all the outstanding events will be delivered at a time after the save time. Also many ArtificialCell...