Search found 32 matches

by selfdestructo
Thu Dec 06, 2018 4:25 pm
Forum: UNIX/Linux
Topic: BUG.am: error: 'install.sh' is an anachronism; use 'install-sh' instead
Replies: 1
Views: 1243

Re: BUG.am: error: 'install.sh' is an anachronism; use 'install-sh' instead

Hi,
I found out why this happens. There was a file /<neuron-sources>/../install.sh confusing automake. Don't know why it would look for it in a location not in $PATH or outside of the NEURON source code directory.
by selfdestructo
Tue Dec 04, 2018 5:39 am
Forum: UNIX/Linux
Topic: BUG.am: error: 'install.sh' is an anachronism; use 'install-sh' instead
Replies: 1
Views: 1243

BUG.am: error: 'install.sh' is an anachronism; use 'install-sh' instead

Dear Neuron developers, I'm experiencing some issues with the build.sh script and the configure step of NEURON on a cluster. I've compiled it previously on the same machine, so I'm a bit confused why it doesn't work now. These are the loaded modules (seems pretty ordinary): $ module list Currently L...
by selfdestructo
Fri Nov 30, 2018 8:59 am
Forum: NEURON + Python
Topic: Nested for loops over SectionList objects
Replies: 5
Views: 1795

Re: Nested for loops over SectionList objects

Hi, I can confirm that your fix pushed to the github repository works for me. Thanks a lot.
by selfdestructo
Wed Nov 28, 2018 3:12 am
Forum: NEURON + Python
Topic: Nested for loops over SectionList objects
Replies: 5
Views: 1795

Re: Nested for loops over SectionList objects

Much obliged. I will compile NEURON on my end here and try it out.
by selfdestructo
Tue Nov 27, 2018 8:00 am
Forum: NEURON + Python
Topic: Nested for loops over SectionList objects
Replies: 5
Views: 1795

Nested for loops over SectionList objects

Dear NEURON devs; The most recent version of NEURON v7.6.3 appears to have caused some problems in LFPy (github.com/LFPy/LFPy) over v7.6.2 as the SectionList class lost its allsec method (in this particular commit from the look of it: https://github.com/neuronsimulator/nrn/commit/25482fad3a7ea01aac6...
by selfdestructo
Sat Nov 14, 2015 12:31 pm
Forum: UNIX/Linux
Topic: Issue compiling ...geometry3d/surfaces.cpp NEURON v7.4
Replies: 3
Views: 9969

Issue compiling ...geometry3d/surfaces.cpp NEURON v7.4

Dear Neuron developers, I'm facing an issue compiling share/lib/python/neuron/rxd/geometry3d/surfaces.cpp during make install with more recent versions of gcc and intel compilers, also across different machines. I did not see other encountering this issue, but I'm getting it on OSX w. macports gcc5,...
by selfdestructo
Thu Feb 16, 2012 9:37 am
Forum: NEURON + Python
Topic: Import MorphML file in Python RuntimeError
Replies: 3
Views: 3058

Re: Import MorphML file in Python RuntimeError

Thanks a lot, that solved my problem, files with the NeuroML v 1.8.1 specification can now be loaded. There is another problem though, which should perhaps be discussed elsewhere; somatic sections are apperently missing/renamed, so the root of the morphology is on the first dendritic section, like n...
by selfdestructo
Wed Feb 15, 2012 6:16 am
Forum: NEURON + Python
Topic: Import MorphML file in Python RuntimeError
Replies: 3
Views: 3058

Import MorphML file in Python RuntimeError

Hi, I'm having a problem here importing a MorphoML file generated by NEURON itself (NEURON -- VERSION 7.3 (581:b1b7836b8bab) b1b7836b8bab) in Python. I've built nrnpython against a macports build of Python 2.7 using this recipe: http://compneuro.umb.no/LFPy/information.html#dependencies-and-installa...
by selfdestructo
Tue Dec 13, 2011 5:12 am
Forum: OS X
Topic: Python module error in Mac OS X Lion
Replies: 9
Views: 7684

Re: Python module error in Mac OS X Lion

Works for me!
Espen.
by selfdestructo
Mon Dec 12, 2011 5:51 am
Forum: OS X
Topic: Python module error in Mac OS X Lion
Replies: 9
Views: 7684

Re: Python module error in Mac OS X Lion

I'm not sure if it helps or not, but I was able to use the patch as copied and paste with the --ignore-whitespace flag to rev 536, i.e; hg update -r 536:c4eed98bb84b patch -Np1 --ignore-whitespace < environ_patch This will build correctly for me using sh build.sh ./configure --prefix=/Applications/N...
by selfdestructo
Mon Dec 05, 2011 8:52 am
Forum: OS X
Topic: Python module error in Mac OS X Lion
Replies: 9
Views: 7684

Re: Python module error in Mac OS X Lion

Hi,
Will sshong's patch make it into the alpha-repository?
I'm experiencing the same problem here and had to roll back to my previous install;
NEURON -- VERSION 7.2 (504:f8e1ebea86e4) f8e1ebea86e4

Then, it loads just fine

Best,
Espen
by selfdestructo
Tue Jun 07, 2011 6:00 am
Forum: Getting started
Topic: Problem encountered using Vector.play and somatic traces
Replies: 3
Views: 3543

Re: Problem encountered using Vector.play and somatic traces

Suggestion and hint: instead of trying to drive soma.v, attach an SEClamp to the soma, set its series resistance parameter to something very small (0.01 or 0.001 megohm would be good), set its dur1 to 1e9, and drive its amp1 parameter. What happens now? Hi Ted, I'm aware that SEClamp can be used fo...
by selfdestructo
Mon Jun 06, 2011 8:56 am
Forum: Getting started
Topic: Problem encountered using Vector.play and somatic traces
Replies: 3
Views: 3543

Problem encountered using Vector.play and somatic traces

Hi, I'm encountering an issue obtaining the results I expect using the Vector.play method. As in Pettersen & Einevoll (Biophys J, 94, 784-802, 2008), considering some multi-compartment neuron with passive channels on all dendrites and a single active somatic compartment with somatic stimuli, the som...
by selfdestructo
Fri May 06, 2011 7:47 am
Forum: NEURON + Python
Topic: neuron.h.Vector() size argument has no effect
Replies: 4
Views: 2301

Re: neuron.h.Vector() size argument has no effect

Thanks, I was able to resolve our memory consumption problems.

Best,
Espen
by selfdestructo
Thu May 05, 2011 3:52 am
Forum: NEURON + Python
Topic: neuron.h.Vector() size argument has no effect
Replies: 4
Views: 2301

Re: neuron.h.Vector() size argument has no effect

It is generally the case that Hoc does not take keyword arguments. The exceptions are sec=... to specify the currently accessed section during the scope of the function, and several optional named arguments to the Section constructor. Those named arguments must follow the unnamed arguments. So use ...