Search found 1573 matches

by hines
Tue Jul 16, 2019 8:34 pm
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 23398

Re: Neurolucida to NEURON best practices?

It appears nothing has been done in this area since late 2007. There was a hook added in python for rxd in 2013 but is not being used. The translation of the soma stack to a centroid of 3-d points with diam continues to be: Approximate each contour of the stack as a circle. Center is the average of ...
by hines
Wed Jun 26, 2019 7:17 pm
Forum: Parallel NEURON
Topic: Using thread-safe source_var/target_var to replace POINTER variables
Replies: 3
Views: 360

Re: Using thread-safe source_var/target_var to replace POINTER variables

computational cost is at each time step of recording into numerous Vectors (for each segment You definitely want only one vector per thread for storage for a recording location. A POINTER for each segment in a thread would all point to the same scalar accumulator and the mod file would add a weight...
by hines
Wed Jun 26, 2019 7:37 am
Forum: Parallel NEURON
Topic: Using thread-safe source_var/target_var to replace POINTER variables
Replies: 3
Views: 360

Re: Using thread-safe source_var/target_var to replace POINTER variables

use POINTER variables for (1) aggregation I don't think you can use the source_var/target_var pattern for this purpose because there is no way for one target to receive an increment from many sources. (the opposite is natural: a source can copy its value to many targets.) This assumes I correctly i...
by hines
Mon May 27, 2019 8:20 am
Forum: MSWin
Topic: Compiling script fails with newer NEURON versions due to $N
Replies: 2
Views: 532

Re: Compiling script fails with newer NEURON versions due to $N

Please try providing N as /cygdrive/c/nrn
The problem with c:/nrn is that the ':' in a pathlist is a separator.
The problem with /c/nrn is that msys2 apparently no longer supports that style.
by hines
Wed May 22, 2019 10:02 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Stochastic gating as a function of external variable (light, membrane tension)
Replies: 3
Views: 430

Re: Stochastic gating as a function of external variable (light, membrane tension)

I'm happy your nmodl mechanism resolves the issue. So this response is a bit stale. The channel builder with ligand would also suffice, Just
invent a ligand name with 0 charge and have another mechanism that modifies the ligand concentration according to your desire function.
by hines
Thu May 09, 2019 10:55 am
Forum: NEURON + Python
Topic: Turn off print messages in NEURON
Replies: 2
Views: 547

Re: Turn off print messages in NEURON

With the most recent master from github, all (or at least most) of printf in c is redirected to the python stdout (if python is the launched program). This was done so that all output with jupyter notebooks goes to the notebook. Note that the statement that actually does the printing is line 687 of ...
by hines
Thu Apr 25, 2019 9:42 pm
Forum: OS X
Topic: Installing Neuron on macOS Mojave
Replies: 5
Views: 1170

Re: Installing Neuron on macOS Mojave

May want to update the xcode command line tools. Mine are Apple LLVM version 10.0.1 (see via gcc -v). Not the latest xcode but recent enough.
My Mojave is 10.14.5
by hines
Wed Apr 24, 2019 10:10 pm
Forum: MSWin
Topic: mknrndll not finding nrnunits.lib
Replies: 6
Views: 1004

Re: mknrndll not finding nrnunits.lib

Yes. You noticed the contradiction Cant open units table in either of: /cygdrive/C/nrn/lib/nrnunits.lib Where that is exactly the correct value for MODLUNIT (and if you export it as MODLUNIT the problem is fixed). I need to do diagnostic runs to trace this to its most elementary source. Will get bac...
by hines
Wed Apr 24, 2019 7:48 pm
Forum: MSWin
Topic: mknrndll not finding nrnunits.lib
Replies: 6
Views: 1004

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: 10
Views: 1436

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: 10
Views: 1436

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: 10
Views: 1436

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: 10
Views: 1436

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: 1170

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