Search found 1579 matches

by hines
Tue Mar 05, 2019 5:56 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 3236

Re: Errors importing neuron

What is the name of the *.so file in <prefix>lib/python/neuron When i installed on comet with "module load python" it turned out to be hoc.so . However python3 builds a name like hoc.cpython-35m-x86_64-linux-gnu.so Also what was your configure line? It seems quite strange that the path to the neuron...
by hines
Tue Mar 05, 2019 3:52 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 3236

Re: Errors importing neuron

Good. I'm glad that is resolved. In my own attempt on comet I first used the configure option --with-nrnpython
which ended up building against Python 3.5.0 (default, Feb 1 2016, 14:14:54) so, of course, I had to start over with
--with-nrnpython=python
by hines
Sat Mar 02, 2019 12:24 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 3236

Re: Errors importing neuron

I have obtained a guest account for comet and will be able to login on Monday to see if I can resolve your issue. I have been told that the
proper python to use is python 2.7.10 which is activated by
module load python
by hines
Fri Mar 01, 2019 5:05 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 3236

Re: Errors importing neuron

The PYTHONPATH should be export PYTHONPATH=$HOME/local/lib64/python2.6/site-packages. But are you sure the $HOME got expanded and there is not a OME folder in nrn/src/nrnpython The latter is what happened to me on my desktop with I used your configure options and I needed hines@hines-T7500:~/neuron/...
by hines
Thu Feb 28, 2019 12:06 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 3236

Re: Errors importing neuron

which installed two folders in $HOME/local That is because a default build and make install installs the neuron module by default in <prefix>/lib/python . This can be turned off with the configure option --disable-pysetup Alternatively, you can avoid the manual execution of setup.py with the config...
by hines
Thu Feb 28, 2019 12:06 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 3236

Re: Errors importing neuron

which installed two folders in $HOME/local That is because a default build and make install installs the neuron module by default in <prefix>/lib/python . This can be turned off with the configure option --disable-pysetup Alternatively, you can avoid the manual execution of setup.py with the config...
by hines
Mon Feb 18, 2019 12:08 pm
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 11139

Re: Driving synaptic event using vecStim

vecevent.mod has been updated to be compatible with CoreNEURON. See https://github.com/neuronsimulator/nrn/commit/7adabc176763386031a9c88ef5218a64f9402219 This kind of VERBATIM code is quite painful. I need to consider an NMODL syntax for easily describing the use of Random variables and Vectors in ...
by hines
Mon Feb 18, 2019 11:47 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 11139

Re: Driving synaptic event using vecStim

i've updated vecevent.mod (VecStim)
Just need to test with coreneuron.
When it is working I'll push to the github repository and mention that here.
by hines
Thu Feb 14, 2019 8:53 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 11139

Re: Driving synaptic event using vecStim

look at nrn/src/nrnoc/netstim.mod for an analogy. You need to replace POINTER with BBCOREPOINTER and introduce
bbcore_write and bbcore_read implementations. Anything containing the string BBCORE is of interest.
I should update vecstim.mod to make it compatible with CoreNEURON.
by hines
Fri Feb 01, 2019 6:48 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 1692

Re: eca calculation

Using
neurondemo -python
#select release model

Code: Select all

from neuron import h
bin(int(h.ion_style("ca_ion", sec=h.terminal)))
yields
'0b11110111'
If you send me the code fragment that returns

Code: Select all

>>> bin(136)
'0b10001000'
I can look into it in more detail.
by hines
Fri Feb 01, 2019 8:53 am
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 1692

Re: eca calculation

from nrn/src/nrnoc/eion.c /*the bitmap is 03 concentration unused, nrnocCONST, DEP, STATE 04 initialize concentrations 030 reversal potential unused, nrnocCONST, DEP, STATE 040 initialize reversal potential 0100 calc reversal during fadvance 0200 ci being written by a model 0400 co being written by ...
by hines
Mon Jan 28, 2019 4:46 pm
Forum: NEURON + Python
Topic: how to delete a Point Process object
Replies: 11
Views: 4597

Re: how to delete a Point Process object

is there a reason
I don't know the reason yet.
In my notebook, the output from that function shows up in the terminal
Today I pushed a fix in the master branch of github.com/neuronsimulator/nrn that directs the output of
h.allobjects() to stdout of Python.
by hines
Mon Jan 28, 2019 9:00 am
Forum: NEURON + Python
Topic: how to delete a Point Process object
Replies: 11
Views: 4597

Re: how to delete a Point Process object

Something mysterious is going on with jupyter that I can't yet quite figure out. Can you work around the problem with print (soma.psection()) Everytime Jupyter default pretty prints the result of soma.psection(), the hoc reference count of the POINT_PROCESS is incremented and never gets decremented ...
by hines
Sat Jan 26, 2019 10:31 am
Forum: Modeling networks
Topic: Running secondary networks in isolation
Replies: 11
Views: 1964

Re: Running secondary networks in isolation

You only need to call sec.simulate(0) for one section in a cell and all the sections in that cell will follow along. However, if you call sec.simulate(0) for several or all of the sections in a cell it should not matter as any after the first will do nothing. for sec in neuron.h.allsec(): sec.simula...
by hines
Thu Jan 24, 2019 9:00 pm
Forum: Modeling networks
Topic: Running secondary networks in isolation
Replies: 11
Views: 1964

Re: Running secondary networks in isolation

Ok. The do-not-simulate branch is ready to try. the log message is commit 0ebc0f8ff10ddd68b8cd3fe12cfb5e78bd9dd6a5 (HEAD -> do-not-simulate, origin/do-not-simulate) Author: Michael Hines <michael.hines@yale.edu> Date: Thu Jan 24 13:38:54 2019 -0500 nrn.Section.simulate(False) causes the entire tree ...