Search found 48 matches

by roybens
Thu Sep 29, 2016 8:21 pm
Forum: MSWin
Topic: Trying to print _rhs using gdb
Replies: 5
Views: 10110

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: 10100

'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: 13523

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: 13523

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...
by roybens
Sun Jan 04, 2015 10:40 pm
Forum: NEURON + Python
Topic: Importing neuron module into Python
Replies: 26
Views: 13523

Re: Importing neuron module into Python

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...
by roybens
Wed Dec 24, 2014 8:21 am
Forum: NEURON + Python
Topic: Importing neuron module into Python
Replies: 26
Views: 13523

Re: Importing neuron module into Python

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/libreadline...
by roybens
Sat Dec 20, 2014 9:49 am
Forum: NEURON + Python
Topic: Importing neuron module into Python
Replies: 26
Views: 13523

Re: Importing neuron module into Python

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...
by roybens
Fri Dec 19, 2014 3:12 pm
Forum: NEURON + Python
Topic: Importing neuron module into Python
Replies: 26
Views: 13523

Re: Importing neuron module into Python

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...
by roybens
Wed Dec 17, 2014 5:17 pm
Forum: NEURON + Python
Topic: Importing neuron module into Python
Replies: 26
Views: 13523

Re: Importing neuron module into Python

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/NEURON-7.3/nrn/...
by roybens
Wed Dec 17, 2014 1:12 pm
Forum: NEURON + Python
Topic: Importing neuron module into Python
Replies: 26
Views: 13523

Re: Importing neuron module into Python

Michael, Is anything about readline mentioned when, from a terminal window, you execute otool -L //anaconda/lib/python2.7/site-packages/neuron/hoc.so The result from that command is as follows (note the "libreadline" about 3/4 the way down): kjb:~ ken$ otool -L //anaconda/lib/python2.7/site-packages...
by roybens
Mon Dec 15, 2014 3:21 pm
Forum: NEURON + Python
Topic: Importing neuron module into Python
Replies: 26
Views: 13523

Importing neuron module into Python

Hello all, I am having difficulty importing neuron into python. After launching python... Last login: Mon Dec 15 12:16:56 on ttys000 kjb:~ ken$ cd neuron/nrn/src/nrnpython/ kjb:nrnpython ken$ python Python 2.7.8 |Anaconda 1.9.0 (x86_64)| (default, Jul 2 2014, 15:36:00) [GCC 4.2.1 (Apple Inc. build 5...
by roybens
Wed Dec 04, 2013 1:58 am
Forum: Other questions
Topic: Derivative block calculation per segment or per section
Replies: 3
Views: 1639

Re: Derivative block calculation per segment or per section

Hi Ted,
Your question
Exactly what did the "check" consist of?
made me look over my code again, and i realized my mistake i did not add (x) i did for(x) m_hh instead of m_hh(x) thats why i got the same result (the value in the middle of the section).
Thanks for your answer
Roy
by roybens
Tue Dec 03, 2013 6:56 pm
Forum: Other questions
Topic: Derivative block calculation per segment or per section
Replies: 3
Views: 1639

Derivative block calculation per segment or per section

Hi When the derivative block is called for a specific mechanism does the state variable have different values for each segment or the same value for the whole section? When i checked this in a toy model i got the same value for all the segments, if this is true i wonder what is the voltage that is u...
by roybens
Sat Nov 23, 2013 1:10 am
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 7243

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

Thanks so much for this solution now the connection works well. Next i set the NODEA and NODEB of the children using GETA and SETA in the branching.mod file as you recommended. I am having difficulties now setting NODEA and NODEB of the Exts' nodes appropriately. If i dont touch them they get a very...
by roybens
Mon Nov 18, 2013 10:26 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 7243

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

I am checking if nchild>1 so if the section does have more than one children there is a scenario where there are two children in the same segment(now that i can use the verbatim i should probably do a better check - that there is no segment that appears more than twice in the v_parent_node array). B...