Search found 44 matches

by roybens
Fri Feb 01, 2019 12:41 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 1357

Re: eca calculation

Thanks Micheal,
Now the results i got from ion_style does make sense.
Best
Roy
by roybens
Thu Jan 31, 2019 5:54 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 1357

Re: eca calculation

:-) thanks Ted, ill continue investigating!
by roybens
Thu Jan 31, 2019 2:40 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 1357

Re: eca calculation

I am a bit confused trying to figure this out. From the program reference i get this: The oldstyle value is previous internal setting of c_style + 4*cinit + 8*e_style + 32*einit + 64*eadvance. c_style: 0, 1, 2, 3. Concentrations respectively treated as UNUSED, PARAMETER, ASSIGNED, or STATE variables...
by roybens
Thu Jan 31, 2019 1:54 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 1357

Re: eca calculation

Thank, Ted!
This is very helpful.
by roybens
Wed Jan 30, 2019 7:01 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 1357

eca calculation

Hi, I wanted to ask how does NEURON knows when to calculate eca from cai and cao or not to. For example in Mainen's model https://senselab.med.yale.edu/modeldb/showmodel.cshtml?model=2488&file=%2Fcells%2F#tabs-1 the eca is always 140. But when using one of the BBP models from their portal it is upda...
by roybens
Fri Jun 15, 2018 4:23 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 5367

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

Hi again, I am back in trying to apply this method on a more complicated model - one of the BBP pyramidal neurons https://bbp.epfl.ch/nmc-portal/downloads. For some reason when applying this method to Mainen's model (1996) it works well but when applying to BBP it does not work at all and it is like...
by roybens
Sat Mar 11, 2017 5:38 pm
Forum: UNIX/Linux
Topic: Running neuron with MPI using debian package
Replies: 1
Views: 8278

Running neuron with MPI using debian package

Hi, I am trying to use neuron on a cluster without shared libraries we used the debian package as shifter image and NEURON is runnig well. The problem is when i am trying to use MPI i get only one process. I am trying to use the simple example from the parallelcontext documentation i get nprocs=1 My...
by roybens
Sat Mar 11, 2017 5:33 pm
Forum: UNIX/Linux
Topic: configuring on supercomputer/cluster without shared libs
Replies: 2
Views: 8659

Re: configuring on supercomputer/cluster without shared libs

Thanks!
We eventually used a shifter image using the debian package at http://www.neuron.yale.edu/ftp/neuron/v ... x86_64.deb
by roybens
Thu Jan 05, 2017 11:57 am
Forum: UNIX/Linux
Topic: configuring on supercomputer/cluster without shared libs
Replies: 2
Views: 8659

configuring on supercomputer/cluster without shared libs

Hi, I am trying to build neuron with mpi on supercomputer where we cannot use shared libraries. So building NEURON itself goes smoothly when i use the following configure: ./configure --prefix=`pwd` --with-paranrn --without-iv --enable-shared=no CC=cc CXX=CC But then when i want to add mod file and ...
by roybens
Fri Sep 30, 2016 5:44 pm
Forum: MSWin
Topic: Trying to print _rhs using gdb
Replies: 5
Views: 9227

Re: Trying to print _rhs using gdb

Ha! it worked Thanks!!
by roybens
Fri Sep 30, 2016 3:43 pm
Forum: MSWin
Topic: Trying to print _rhs using gdb
Replies: 5
Views: 9227

Re: Trying to print _rhs using gdb

So i should have mentioned it in the first post, I am using bash on windows - which is a ubuntu linux shell on windows 10 (pretty new feature for win) And i go to '~/neuron/nrn/x86_64/bin$' and run gdb nrniv from there. When trying to set a breakpoint at nrn_rhs i cannot typing (gdb) break nrn (then...
by roybens
Thu Sep 29, 2016 8:21 pm
Forum: MSWin
Topic: Trying to print _rhs using gdb
Replies: 5
Views: 9227

Trying to print _rhs using gdb

Hi, I am trying to print rhs for each time step of my simulation using gdb. I tried to configure with CXXFLAGS='-g' and CFLAGS='-g'. but when executing gdb nrniv i get the symbols load but i cannot access files in the oc folder. I am trying to step through nrn_rhs proc at treeset.c Is there anything...
by roybens
Tue May 24, 2016 5:07 pm
Forum: MSWin
Topic: 'nrniv -python' Not Working
Replies: 1
Views: 9172

'nrniv -python' Not Working

I installed Neuron 7.4 from the binary package from Windows and set up my PYTHONPATH and NEURONHOME so everything points to the correct directories. When I run python 2.7 and import neuron, the import works and I can load files and access information from neuron.h. However, when I try to run 'nrniv ...
by roybens
Tue Jan 06, 2015 11:49 am
Forum: NEURON + Python
Topic: Importing neuron module into Python
Replies: 26
Views: 10992

Re: Importing neuron module into Python

I think I got it, good call on anaconda. So I tried what you suggested by moving the /anaconda/bin to the end of my PATH so I could run default Python, but this still left the hanging prompt. So I decided to uninstall anaconda (which apparently is as simple as rm -rf /anaconda according to its site)...
by roybens
Mon Jan 05, 2015 10:13 pm
Forum: NEURON + Python
Topic: Importing neuron module into Python
Replies: 26
Views: 10992

Re: Importing neuron module into Python

Okay, I have another clue. I uninstalled then reinstalled NEURON from the source code, then set the environmental variables as you mentioned, and I was able to get everything working again. However, once I exited the terminal and tried to open it up again, I got the same issue with the interpreter h...