Search found 1589 matches

by hines
Sat Dec 22, 2018 1:10 pm
Forum: NEURON + Python
Topic: Compling Problem
Replies: 21
Views: 18888

Re: Compling Problem

Looks like I have a bad substitution line in nrn/src/nrnpython/setup.py.in which reads @setup_extra_link_args@ = [ epre+libdirs[0],epre+libdirs[1] ], and should get replaced in setup.py with either extra_link_args = [ epre+libdirs[0],epre+libdirs[1] ], or #extra_link_args = [ epre+libdirs[0],epre+li...
by hines
Thu Dec 20, 2018 3:09 pm
Forum: MSWin
Topic: Windows 10 install problem
Replies: 2
Views: 3692

Re: Windows 10 install problem

NEURON -- VERSION 7.6.2 master (f5a1284) 2018-08-15
The latest standard distribution is 7.6.3.
I have hope but not certainty that that will fix your problem. At any rate it makes sense to begin diagnosing with that as there have
been a few changes in the files that would be related to your issues.
by hines
Fri Dec 14, 2018 10:53 am
Forum: Other questions
Topic: Impedance methods change the location
Replies: 5
Views: 2105

Re: Impedance methods change the location

The extended impedance behavior is now the same as for the default impedance calculation. That is, interleaved calculations of transfer and input impedance work properly without having to reset the input stimulus location for transfer. So the behavior now corresponds to the existing documentation. N...
by hines
Tue Dec 11, 2018 8:40 am
Forum: Other questions
Topic: Impedance methods change the location
Replies: 5
Views: 2105

Re: Impedance methods change the location

The documentation needs to be updated to reflect this behavior. The default calculation is able to efficiently combine the calculation of transfer impedance everywhere given a specific current stimulus location and input impedance everywhere. After a compute, it is possible just read off the values ...
by hines
Wed Nov 28, 2018 8:17 am
Forum: NEURON + Python
Topic: Nested for loops over SectionList objects
Replies: 5
Views: 2314

Re: Nested for loops over SectionList objects

Please try the latest version. I inadvertently reffed the section list iterators twice which prevents deletion of the SectionList
See commit a3d1233b
by hines
Tue Nov 27, 2018 11:29 am
Forum: NEURON + Python
Topic: Nested for loops over SectionList objects
Replies: 5
Views: 2314

Re: Nested for loops over SectionList objects

A fix for nested SectionList iteration in python has been pushed to the github repository. I use the test: $ cat slseq.py from neuron import h a = [h.Section(name='s%d'%i) for i in range(3)] sl = h.SectionList() for s in a: sl.append(sec=s) for s in sl: print(s) print("") for x in sl: for y in sl: p...
by hines
Tue Nov 27, 2018 9:03 am
Forum: NEURON + Python
Topic: Nested for loops over SectionList objects
Replies: 5
Views: 2314

Re: Nested for loops over SectionList objects

The following is intended behavior >>> sl = h.SectionList() >>> sl.allsec() Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'hoc.HocObject' object has no attribute 'allsec' that is, the allsec method is restricted to the <HocTopLevelInterpreter>. The changeset ...
by hines
Fri Nov 02, 2018 9:02 am
Forum: Getting started
Topic: Program functions between Mac and Windows
Replies: 3
Views: 1988

Re: Program functions between Mac and Windows

Please email me a zip file with all the mod, py, ses, hoc files needed along with instructions on launching the model to produce the result to michael.hines@yale.edu . I will try to reproduce the problem, diagnose, and fix the issue. There are two dimensions here: (mac, mswin) and (7.4, 7.6) as well...
by hines
Tue Oct 30, 2018 5:11 pm
Forum: Getting started
Topic: compiling issues on Mac
Replies: 6
Views: 2830

Re: compiling issues on Mac

Instead of dragging the mod file, try dragging the folder containing the two mod files on to the mknrndll icon
by hines
Fri Oct 26, 2018 9:29 pm
Forum: Getting started
Topic: compiling issues on Mac
Replies: 6
Views: 2830

Re: compiling issues on Mac

Is the hoc file in the same folder as the mod file? Dragging the mod file (or its folder) onto the mknrndll icon should create an x86_64 folder in the folder that contained the mod file. Verify this is the case. If you launch nrniv in this folder (now containing the x86_64) folder from a terminal, y...
by hines
Fri Oct 26, 2018 3:03 pm
Forum: Getting started
Topic: compiling issues on Mac
Replies: 6
Views: 2830

Re: compiling issues on Mac

It is not hard to build from sources on the mac, but be aware that there is an installation pkg available that does not require the "brew" developer tool hints alluded to below and also attempts to install xquartz and command line tools if they are not already installed. See: https://neuron.yale.edu...
by hines
Thu Oct 25, 2018 1:00 pm
Forum: MSWin
Topic: Compile Neuron
Replies: 5
Views: 3524

Re: Compile Neuron

Please try: https://neuron.yale.edu/ftp/neuron/versions/alpha/nrn-7.6.2-29-g8e63a96+.w64-mingw-py-27-35-36-37-setup.exe (note the '+' at the end of g8e63a96) Extracellular and LinearMechanism are compatible with MPI but not with multisplit. I.e. for whole cells on a single process where all the gaus...
by hines
Wed Oct 24, 2018 9:44 am
Forum: MSWin
Topic: Compile Neuron
Replies: 5
Views: 3524

Re: Compile Neuron

Informaiton about the build environment used to construct a neuron setup.exe distribution is scattered in the nrn/mingw_files folder. Given a valid build environment, I construct a setup.exe using sh howto 37 36 27 Setting up a build environment is explained in the msys2 file. mingwnotes has some ve...
by hines
Fri Oct 12, 2018 1:58 pm
Forum: Other questions
Topic: Conflict between CVode.maxstep, NetCon instances, and extracellular
Replies: 1
Views: 1527

Re: Conflict between CVode.maxstep, NetCon instances, and extracellular

That is an oversight. cvode wraps ida and the former is persistent while the latter is destroyed/created whenever the model topology, or if the model requires a differential algebraic solver, changes. Extacellular requires ida. I forgot to make all the ida calls to reflect the existing cvode style f...
by hines
Wed Oct 10, 2018 10:39 am
Forum: OS X
Topic: Installation problem Neuron
Replies: 36
Views: 20556

Re: Installation problem Neuron

Ok. so there is no problem with command line tools and readline. I think the next diagnostic test is to install a distributed pkg file for NEURON and see if that works with your python3.7. Please try https://neuron.yale.edu/ftp/neuron/versions/alpha/nrn-7.6.2-18-gcfe5f00.x86_64-osx-py-37-36-27.pkg J...