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.
Search found 32 matches
- 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: 9353
- 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: 9353
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...
- Fri Nov 30, 2018 8:59 am
- Forum: NEURON + Python
- Topic: Nested for loops over SectionList objects
- Replies: 5
- Views: 3805
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.
- Wed Nov 28, 2018 3:12 am
- Forum: NEURON + Python
- Topic: Nested for loops over SectionList objects
- Replies: 5
- Views: 3805
Re: Nested for loops over SectionList objects
Much obliged. I will compile NEURON on my end here and try it out.
- Tue Nov 27, 2018 8:00 am
- Forum: NEURON + Python
- Topic: Nested for loops over SectionList objects
- Replies: 5
- Views: 3805
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...
- Sat Nov 14, 2015 12:31 pm
- Forum: UNIX/Linux
- Topic: Issue compiling ...geometry3d/surfaces.cpp NEURON v7.4
- Replies: 3
- Views: 11729
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,...
- Thu Feb 16, 2012 9:37 am
- Forum: NEURON + Python
- Topic: Import MorphML file in Python RuntimeError
- Replies: 3
- Views: 4565
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...
- Wed Feb 15, 2012 6:16 am
- Forum: NEURON + Python
- Topic: Import MorphML file in Python RuntimeError
- Replies: 3
- Views: 4565
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...
- Tue Dec 13, 2011 5:12 am
- Forum: OS X
- Topic: Python module error in Mac OS X Lion
- Replies: 9
- Views: 14394
Re: Python module error in Mac OS X Lion
Works for me!
Espen.
Espen.
- Mon Dec 12, 2011 5:51 am
- Forum: OS X
- Topic: Python module error in Mac OS X Lion
- Replies: 9
- Views: 14394
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...
- Mon Dec 05, 2011 8:52 am
- Forum: OS X
- Topic: Python module error in Mac OS X Lion
- Replies: 9
- Views: 14394
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
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
- Tue Jun 07, 2011 6:00 am
- Forum: Getting started
- Topic: Problem encountered using Vector.play and somatic traces
- Replies: 3
- Views: 4454
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...
- Mon Jun 06, 2011 8:56 am
- Forum: Getting started
- Topic: Problem encountered using Vector.play and somatic traces
- Replies: 3
- Views: 4454
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...
- Fri May 06, 2011 7:47 am
- Forum: NEURON + Python
- Topic: neuron.h.Vector() size argument has no effect
- Replies: 4
- Views: 3402
Re: neuron.h.Vector() size argument has no effect
Thanks, I was able to resolve our memory consumption problems.
Best,
Espen
Best,
Espen
- Thu May 05, 2011 3:52 am
- Forum: NEURON + Python
- Topic: neuron.h.Vector() size argument has no effect
- Replies: 4
- Views: 3402
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 ...