Search found 87 matches

by patoorio
Tue Aug 13, 2024 3:22 pm
Forum: NEURON + Python
Topic: can't run without GUI in Linux + slurm
Replies: 2
Views: 1595

Re: can't run without GUI in Linux + slurm

Found a solution. (there are others)

Adding

Code: Select all

export NEURON_MODULE_OPTIONS="-nogui"
to the slurm script file did the trick
by patoorio
Mon Aug 12, 2024 11:36 am
Forum: NEURON + Python
Topic: can't run without GUI in Linux + slurm
Replies: 2
Views: 1595

can't run without GUI in Linux + slurm

Hi, A while ago I used to run Python+Neuron scripts and models in a computing cluster without the need of GUI. But now I can't; I don't know what may have changed. I have this simple code: import matplotlib matplotlib.use('Agg') from neuron import h print("h imported") h.load_file("st...
by patoorio
Wed Jul 31, 2024 3:46 pm
Forum: NEURON + Python
Topic: Non-uniform parameter with colon notation?
Replies: 2
Views: 1954

Re: Non-uniform parameter with colon notation?

Thanks for you answer! In summary, there is no equivalent to the 'colon notation' and its use should be discouraged in hoc as well. Message received and appreciated! BTW, I was being a little ironic with the difficulty of figuring out the 'interpolation function', but your help is (and will always b...
by patoorio
Wed Jul 31, 2024 10:31 am
Forum: NEURON + Python
Topic: Non-uniform parameter with colon notation?
Replies: 2
Views: 1954

Non-uniform parameter with colon notation?

Hello, In HOC, I was used to write something like section diam(0:1) = 2.0:1.0 which would yield an interpolated diameter between 2 and 1 accross the section's segments. But I am not able to find the way to do this in Python! Any similar syntax that I tried gives an invalid syntax error. I have looke...
by patoorio
Fri May 31, 2024 5:08 pm
Forum: MSWin
Topic: Python cannot import neuron library on Windows install
Replies: 7
Views: 28672

Re: Python cannot import neuron library on Windows install

Yes, I thought about setting an environment with Python 3.11, but since I already have Python(3.12)+Neuron working under the WSL, it is kind of the same.
We'll have to wait for an update, I guess.

EDIT: in another computer I have Python 3.11 + Neuron working perfectly in Windows
by patoorio
Thu May 30, 2024 5:41 pm
Forum: MSWin
Topic: Python cannot import neuron library on Windows install
Replies: 7
Views: 28672

Re: Python cannot import neuron library on Windows install

Hi, I am having the same issue with my Python/Windows installation: from neuron import h Traceback (most recent call last): File c:\nrn\lib\python\neuron\__init__.py:135 from . import hoc ImportError: cannot import name 'hoc' from partially initialized module 'neuron' (most likely due to a circular ...
by patoorio
Mon Apr 29, 2019 9:21 am
Forum: MSWin
Topic: mknrndll not finding nrnunits.lib
Replies: 6
Views: 18994

Re: mknrndll not finding nrnunits.lib

Great, thanks!
by patoorio
Fri Apr 26, 2019 3:30 pm
Forum: MSWin
Topic: mknrndll not finding nrnunits.lib
Replies: 6
Views: 18994

Re: mknrndll not finding nrnunits.lib

Thank you!
I'll stay tuned
by patoorio
Wed Apr 24, 2019 10:04 pm
Forum: MSWin
Topic: mknrndll not finding nrnunits.lib
Replies: 6
Views: 18994

Re: mknrndll not finding nrnunits.lib

Does the file c:/nrn/lib/nrnunits.lib exist in your installation? Yes it does! Does mknrndll work in the bash terminal if you have export MODLUNIT=/cygdrive/c/nrn/lib/nrnunits.lib yes it works!! (Previously I made the stupid mistake of using 'set' instead of 'export'... sorry, too much time away fr...
by patoorio
Tue Apr 23, 2019 9:14 pm
Forum: MSWin
Topic: mknrndll not finding nrnunits.lib
Replies: 6
Views: 18994

mknrndll not finding nrnunits.lib

Hi, I wasn't sure whether to post this here or under the NMODL sub-forum, but finally posted here because it seems to be a Windows-specific issue. With the last Neuron version (7.6.6), I'm getting the following error when trying to compile a .mod file that contains a UNITS block: c:\nrn/mingw/usr/bi...
by patoorio
Tue Jul 04, 2017 2:15 pm
Forum: NEURON + Python
Topic: nseg not a USEPROPERTY
Replies: 8
Views: 16918

Re: nseg not a USEPROPERTY

Oh, I see.
Thanks for the explanation!!
by patoorio
Tue Jul 04, 2017 1:17 pm
Forum: NEURON + Python
Topic: nseg not a USEPROPERTY
Replies: 8
Views: 16918

Re: nseg not a USEPROPERTY

Great! Thanks Still, when I do autocompletion on a Section's name, 'diam' does not appear as an option: In [2]: soma=h.Section() In [3]: soma. allseg() diam3d() L parentseg() trueparentseg() arc3d() has_membrane() n3d() push() uninsert() cell() hname() name() Ra x3d() children() hoc_internal_name() ...
by patoorio
Mon Jul 03, 2017 1:00 pm
Forum: NEURON + Python
Topic: nseg not a USEPROPERTY
Replies: 8
Views: 16918

Re: nseg not a USEPROPERTY

Hi, I'm getting the same error under a completely different circumstance. Windows+Python3+Neuron7.5 (See below the details), if I'm within iPython and press TAB for autocompletion of h.IClamp, or h.load_file, the kernel dies with that same message. Autocompletion for other things like h.Section(), w...
by patoorio
Sun Apr 23, 2017 5:14 pm
Forum: MSWin
Topic: NRN 7.4 on windows 10
Replies: 24
Views: 55459

Re: NRN 7.4 on windows 10

Hi, I'm running into the same issue. My workaround has been to replace the association of .hoc files to make them be opened with 'nrniv.exe' instead of neuron.exe. I think it works OK that way, though I don't know if some unexpected problem may arise later. I'm wondering if this is related to the fa...
by patoorio
Fri Apr 25, 2014 2:20 pm
Forum: UNIX/Linux
Topic: Error compiling in Ubuntu 14.04
Replies: 13
Views: 13992

Error compiling in Ubuntu 14.04

Hi, I'm compiling Neuron 7.3 under the new Ubuntu 14.04 and get this error: In file included from ./ACG.h:21:0, from ACG.cpp:24: ./RNG.h:48:5: error: '_G_uint32_t' does not name a type _G_uint32_t u; ^ ./RNG.h:53:5: error: '_G_uint32_t' does not name a type _G_uint32_t u[2]; ^ And the errors continu...