Search found 1579 matches

by hines
Wed Apr 24, 2019 7:48 pm
Forum: MSWin
Topic: mknrndll not finding nrnunits.lib
Replies: 6
Views: 1681

Re: mknrndll not finding nrnunits.lib

Does the file c:/nrn/lib/nrnunits.lib exist in your installation? Does mknrndll work in the bash terminal if you have export MODLUNIT=/cygdrive/c/nrn/lib/nrnunits.lib Make sure before running that you clean out the *.c and *.o files derived from *.mod Looks like I have a problem with some script usi...
by hines
Wed Apr 24, 2019 7:08 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 11
Views: 2520

Re: No module named hoc37

Although my default python3 comes from python.org, I also have anaconda3 (python3.7) installed and I see that the library you need is in /where/you/installed/anaconda3/lib So try export LD_LIBRARY_PATH=/where/you/installed/anaconda3/lib and see if things launch correctly. I mean export LD_LIBRARY_PA...
by hines
Wed Apr 24, 2019 6:48 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 11
Views: 2520

Re: No module named hoc37

so copying that file to those two alternative hoc.so and hoc37.made no difference Actually, I'm relieved that I don't have to hunt up further documentation on variations of the python3 shared library module naming standard. libpython3.7m.so.1.0 => not found This is the main anaconda python library ...
by hines
Wed Apr 24, 2019 5:16 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 11
Views: 2520

Re: No module named hoc37

I was surprised that there did not seem to be an explicit attempt during import to load the file hoc.cpython-37m-x86_64-linux-gnu.so I would be curious what happens if you temporarily cp hoc.cpython-37m-x86_64-linux-gnu.so hoc.so # be sure to make a copy of hoc.so first!!! cp hoc.cpython-37m-x86_64-...
by hines
Tue Apr 23, 2019 9:03 am
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 11
Views: 2520

Re: No module named hoc37

Does your NEURON module have the contents: $ ls /usr/local/nrn/lib/python/neuron crxd hclass3.pyc nonvint_block_supervisor.py doc.py help_data.dat nonvint_block_supervisor.pyc doc.pyc hoc.cpython-35m-x86_64-linux-gnu.so psection.py gui2 hoc.cpython-36m-x86_64-linux-gnu.so psection.pyc gui.py hoc.cpy...
by hines
Tue Apr 23, 2019 8:32 am
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 1803

Re: Installing Neuron on macOS Mojave

Please do a git pull for nrn. A multiply defined function was introduced by
https://github.com/neuronsimulator/nrn/ ... e37123aa3c
and fixed by
https://github.com/neuronsimulator/nrn/ ... c586e23e6c
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: 5601

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: 5601

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: 2387

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: 2387

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: 2387

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: 3068

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: 3068

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: 3068

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: 3068

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