Search found 1582 matches

by hines
Wed Jan 15, 2020 7:20 am
Forum: Modeling networks
Topic: Simulation with external feedback
Replies: 1
Views: 77

Re: Simulation with external feedback

The problem with VecStim is that the mod file implementation did not envision this style of usage. I would recommend adding a restart procedure which, after you replace the Vector in the middle of a simulation, would set the counter to the first element of the Vector and do a net_send to activate th...
by hines
Mon Dec 23, 2019 8:48 am
Forum: OS X
Topic: NEURON installation on macOS Catalina
Replies: 1
Views: 170

Re: NEURON installation on macOS Catalina

Yes. It is not enough any longer that the package be signed, it must also be notarized (now a $100 annual fee). Notarization means that Apple scanned the app for known malicious software. From https://support.apple.com/en-us/HT202491 How to open an app that hasn’t been notarized or is from an uniden...
by hines
Mon Dec 23, 2019 8:34 am
Forum: UNIX/Linux
Topic: Which environmental variables do I need to setup for NEURON to work after rpm installation without sudo with cpio
Replies: 1
Views: 140

Re: Which environmental variables do I need to setup for NEURON to work after rpm installation without sudo with cpio

MODLUNIT and NEURONHOME should be export MODLUNIT=/home/ziemek/usr/local/nrn/share/nrn/lib/nrnunits.lib export NEURONHOME=/home/ziemek/usr/local/nrn/share/nrn (I'm not sure but if you have NEURONHOME set, you may not need MODLUNIT) If you want to launch python and import neuron then export PYTHONPAT...
by hines
Wed Nov 06, 2019 6:34 am
Forum: Adding new mechanisms and functions to NEURON
Topic: adrunge not thread safe
Replies: 2
Views: 244

Re: adrunge not thread safe

I had forgotten about that. It was the default for SCoP. The fix on our part will be to replace the existing adrunge implementation with a thread safe version. Nevertheless, adrunge generally makes little sense in a NEURON context since the extra accuracy does not translate into a more accurate simu...
by hines
Fri Nov 01, 2019 9:29 am
Forum: Parallel NEURON
Topic: parallel simulation hang on permanently at some loops
Replies: 1
Views: 301

Re: parallel simulation hang on permanently at some loops

You did not mention whether the 7.7 version hangs on your Macbook pro and on comet. Or if NEURON 7.5 has no problem on Manjaro linux. There have been a lot of mpi changes since 7.5. If it does not take too long to run an example, you can send me a zip file with sufficient code to exhibit the problem...
by hines
Fri Nov 01, 2019 9:17 am
Forum: UNIX/Linux
Topic: PyNeuron + Ubuntu + Python 3.6
Replies: 5
Views: 474

Re: PyNeuron + Ubuntu + Python 3.6

So I assume that I can just add libs by hand to the PYTHONPATH, but could you tell me where I can find export PYTHONPATH=/where/you/installed/nrn/lib #often /usr/local/nrn/lib The default build installs the NEURON module in <prefix>/lib/python in order to be python independent of the python version...
by hines
Sun Sep 29, 2019 3:56 am
Forum: Other questions
Topic: MOD Files Compile But Fail To Load
Replies: 8
Views: 906

Re: MOD Files Compile But Fail To Load

On my machine (macOS Catalina Version10.15 Beta (19A573a)) (my most recent build in /Applications/NEURON-7.7 is NEURON -- VERSION 7.7.1-38-g1f3d46d9+ master (1f3d46d9+) 2019-09-13 ) I'm seeing for a typical libnrnmech.so created by nrnivmodl $ otool -L x86_64/.libs/libnrnmech.so ... /usr/lib/libncur...
by hines
Fri Sep 20, 2019 1:47 pm
Forum: NEURON + Python
Topic: Filter Mechanism params by NMODL PARAMETER
Replies: 8
Views: 737

Re: Filter Mechanism params by NMODL PARAMETER

An old way of getting the PARAMETER names of a mechanism is from neuron import h ms = h.MechanismStandard("hh", 1) parm_name = h.ref("") for i in range(ms.count()): ms.name(parm_name, i) print(parm_name[0]) https://www.neuron.yale.edu/neuron/static/py_doc/programming/mechstan.html#MechanismStandard....
by hines
Sat Sep 14, 2019 2:47 am
Forum: Parallel NEURON
Topic: Minimal Working Example of MPI Gap Junctions (in python)
Replies: 17
Views: 10515

Re: Minimal Working Example of MPI Gap Junctions (in python)

Segmentation Fault errors under MPI with gap junctions when I had h.cvode.cache_efficient(1) I'd like to attempt to fix this bug. Can you send me a (hopefully small) version of your model that exhibits this error. (Michael.hines@yale.edu) An unrelated point is that it is now possible to avoid the "...
by hines
Tue Jul 16, 2019 8:34 pm
Forum: Anatomically detailed models
Topic: Neurolucida to NEURON best practices?
Replies: 26
Views: 26914

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: 875

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: 875

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: 1125

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: 923

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: 1024

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 ...