Search found 1558 matches

by hines
Wed Mar 27, 2019 4:51 pm
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 858

Re: Morphology and AP generation

I've run the latest version of NEURON with Anaconda3 with a Jupyter notebook and believe your issue is due to fmc3_1 requiring that stdrun.hoc already be loaded when celldef() is executed. If stdrun.hoc is not already loaded, then celldef() will raise an error at the beginning of geom_nseg() becasu ...
by hines
Mon Mar 25, 2019 10:24 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 858

Re: Morphology and AP generation

I'm guessing that sometimes nseg=1 and sometimes nseg=5 and somewhere in the jupyter notebook that request is sometimes executed and sometimes not. I'd need to have the notebook and all the external files it is loading to diagnose why/how that is occurring. Also what version of NEURON is being used ...
by hines
Tue Mar 12, 2019 3:43 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL Compile Error: Assertion failed!
Replies: 10
Views: 708

Re: NMODL Compile Error: Assertion failed!

if those statements (minf, ninf) are in BREAKPOINT, are they undergoing unnecessary recalculations? Yes. And for the fixed step method with secondorder=2, BREAKPOINT and DERIVATIVE blocks are called at different values of t so that voltages are different. CONDUCTANCE is suitable for ohmic currents....
by hines
Tue Mar 12, 2019 8:37 am
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL Compile Error: Assertion failed!
Replies: 10
Views: 708

Re: NMODL Compile Error: Assertion failed!

Is it advisable to write the expression which are not differential equations in the DERIVATIVE instead of BREAKPOINT? For models that compute current, the only assignment statements that should be in the BREAKPOINT block are statements that aid in computing the current under the assumption that the...
by hines
Mon Mar 11, 2019 4:31 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL Compile Error: Assertion failed!
Replies: 10
Views: 708

Re: NMODL Compile Error: Assertion failed!

I'm afraid that the parser that analyzes the right hand side of ode's for derivimplicit does not allow the power operation. You can write the relevant ode's as atpi' = (nu - atpi*(1+k*adpi)*(1+k*adpi))/tauc adpi' = (atpi*(1+k*adpi)*(1+k*adpi) - eta*adpi)/tauc The syntax of an expression e for derivi...
by hines
Wed Mar 06, 2019 4:36 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 570

Re: Errors importing neuron

I would not keep things in scratch as they are deleted automatically at some interval. I know of no reason why you cannot install under $HOME. The only reason I installed in /oasis/scratch is because my temporary account does not have a $HOME. I think it is likely that a build in your $HOME will be ...
by hines
Wed Mar 06, 2019 11:11 am
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 570

Re: Errors importing neuron

I don't see any clear reason for the problem. To my surprise, I was able to install anaconda2 on comet despite the fact I have no $HOME directory. And I'm seeing no problem running on the login node. -bash-4.1$ nrniv -python NEURON -- VERSION 7.7.0-23-gd28247f9 master (d28247f9) 2019-03-02 Duke, Yal...
by hines
Tue Mar 05, 2019 8:15 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 570

Re: Errors importing neuron

I believe the neuron module did in fact try to import hoc.so and it failed, thus falling back to try hoc27.so which does not exist. So the next step in the diagnostic process is to determine the hidden error that prevented hoc.so from importing. Is your anaconda installation available for use by oth...
by hines
Tue Mar 05, 2019 6:15 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 570

Re: Errors importing neuron

Ok. Then i'd like to know the name of the .so file in
/home/latimerb/utils/nrn/lib/python/neuron/
and are you sure that 'which python' is anaconda?
Ie what is the value of NRNPYTHON_LIBS in config.status
When you ran configure, I presume `pwd` was
/home/latimerb/utils/nrn
by hines
Tue Mar 05, 2019 5:56 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 570

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: 570

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: 570

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: 570

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: 570

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: 570

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...