www.neuron.yale.edu

With respect to cmake, I've asked my more knowledgable colleague to weigh in. That may save some flailing around on my part. CoreNEURON should be able to use MPI with either CPU or GPU. That is, in either case the cpu manages spike exchange and the event will be processed by the GPU in the latter ca...

cvode.active(1) is primarily for using cvode with fadvance() and ParallelContext.psolve(tstop). It is merely inadvertent that cvode.solve(tstop) does its work independently of the value of cvode.active(). Note, though, that cvode.solve does not make sense without a precursor call to cvode.re_init() ...

NEURON only loads mod files by default if you start in the folder where you executed nrnivmodl. SInce you executed the latter in the mod folder, if you wanted to load from the parent of the mod folder you would need nrniv -dll mod/x86_64/.libs/libnrnmech.so mosinit.hoc However, much better is to rem...

You should check whether a section has a parent using sref.has_parent() before actually trying to reference the parent. Also when many sections are connected to the same rootnode or parent section, it may be useful to use sref.has_trueparent() and sref.trueparent(). Parent and trueparent can differ ...

In nrn/src/nrnoc/treeset.c there is a lengthy comment (beginning line 81) that discusses how NEURON is doing the calculation.

ARTIFICIAL_CELL does not fit will with the concept of a ratio between integration time and real time since there is no integration per (fixed) time step but only computation on each incoming event. At the no incoming event extreme, there is no computation. However, if you replace ARTIFICIAL_CELL wit...

It turned out that to fix the import rxd problem for python 3.5, it was necessary to compile the neuron.rxd.geometry3d cython constructed
cpp files using Microsoft visual c. That is now being done when distributions are constructed.

I've reproduced the results of your code. An alternative to your fix using t.restore(0), which restores the event queue to the time of save. is to realize that the save phase did not have any knowledge of rv.play(t.ic._ref_amp, tv, 1) and in particular that on restore there needs to be an event for ...

I'll need to look into this a bit more but for now I just want to caution that if SaveState is chosen so that events on the queue are part of the state, that one cannot in general set h.t = 0 because all the outstanding events will be delivered at a time after the save time. Also many ArtificialCell...

The problem remains after changing the init file as you suggested. ... now does not work anymore in an ipython console (without spyder, after reinstallation of neuron). The "embedded" variable is certainly the cause of failure to print due to import hoc being executed prior to import neuron. I did ...

It would be interesting to see if the problem goes away by demanding that embedded = False in neuron/__init__.py . Ie. just add a
embedded = False
line after the check about whether the hoc module is already loaded.

I believe the problem will resolve if you always import neuron prior to import hoc (import neuron also imports hoc so you can replace any import hoc with from neuron import hoc. The reason for this is the code in the neuron/__init__.py file that reads: if not embedded: try: # callback in place of ho...

just to be clear about the difference between h and hoc in the neuron module... hines@hines-T7500:~$ python Python 2.7.12 (default, Dec 4 2017, 14:50:18) [GCC 5.4.0 20160609] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from neuron import h, hoc NEURON -- VERS...

hoc.execute(1/2) prints ".5" in the working case, before returning 1 in the console. In spyder, it returns 1 without printing anything before. I'm guessing you mean hoc.execute('1/2') as otherwise it raises "NEURON: Expecting string argument" RuntimeError: hoc error I use from neuron import h and I...

I have not yet been able to reproduce the problem hines@hines-T7500:~/tmp$ ipython2 Python 2.7.12 (default, Dec 4 2017, 14:50:18) Type "copyright", "credits" or "license" for more information. IPython 5.2.2 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %qui...