www.neuron.yale.edu

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...

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...

Thanks!
We eventually used a shifter image using the debian package at http://www.neuron.yale.edu/ftp/neuron/v ... x86_64.deb

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 ...

Ha! it worked Thanks!!

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...

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...

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 ...

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)...

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...

Hi Michael, Unfortunately this fix does not seem to work anymore, after restarting my computer. Even though I had incorporated the command I mentioned earlier into my .bashrc file before restarting.... export DYLD_LIBRARY_PATH=/anaconda/lib/ ... when I attempted to replicate what I did in my previou...

Hi Michael, Yes I am using Yosemite. I think I found a temporary solution! When I do a "find . -name libreadline.6.2\*" from the root directory I now find it (I assume it's because of the dmg install I recently did): ./anaconda/lib/libreadline.6.2.dylib ./anaconda/pkgs/readline-6.2-2/lib/l...

2) otool shows no mention of libreadline in regard to nrniv and launching 'nrniv -python' works fine and you can successfully 'import neuron'. Yes, this appears to be true... strange. Last login: Fri Dec 19 21:36:38 on ttys000 kjb:~ ken$ nrniv -python NEURON -- VERSION 7.4 (1198:03358d02fbc4) 03358...

Michael, Commenting out that line did not solve the problem. The result of the grep command is as follows: # Generated by configure. # Compiler output produced by configure, useful for debugging # configure, is in config.log if it exists. configured by ../nrn/configure, generated by GNU Autoconf 2.6...

Michael: I didn't see anything relating to "libreadline.6.2.dylib" this time... kjb:~ ken$ otool -L `which nrniv` /Applications/NEURON-7.3/nrn/x86_64/bin/nrniv: /Applications/NEURON-7.3/nrn/x86_64/lib/libnrnoc.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Applications/NEURO...