When Python is the interpreter, what is a good
design for the interface to the basic NEURON

Moderator: hines

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Posts: 39
Joined: Sat Mar 15, 2008 10:32 am


Post by sec6 » Sun Jun 29, 2008 10:12 pm

I'm getting "bus errors" (KERN_PROTECTION_FAILURE) when I try to use NetCons from Python.

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[1] neuron -python
NEURON -- VERSION 6.2.1028 (2151) 2008-06-18
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007

>>> import neuron
>>> h = neuron.h
>>> import nrn
>>> h.nrn_load_dll('/Users/foo/bar/myMech/i686/.libs/')
loading membrane mechanisms from /Users/foo/bar/myMech/i686/.libs/
Additional mechanisms from files
 expSyn1.mod myMechBad.mod myMechGood.mod myMechSimple.mod
>>> postCell = nrn.Section()
>>> postCell.L = 20
>>> postCell(0.5).diam=20
>>> myMech = nrn.myMechSimple(postCell(0.5))
>>> preCell0 = nrn.Section()
>>> preCell0.L = 20
>>> preCell0(0.5).diam = 20
>>> preCell0.insert('pas')
<nrn.Section object at 0x7a4060>
>>> preCell0.insert('hh')
<nrn.Section object at 0x7a4060>
>>> h.NetCon(preCell0(0.5)._ref_v,myMech)
Bus error
I can provide a CrashLog dump if it would be helpful, but it's too bulky to post on the forum.

I suppose I may be doing something wrong, but it still seems like I ought to get an error message rather than crashing NEURON.

I'm using NEURON 6.2.1028 (unthreaded version) built from source, on a MacBook Pro running OSX 10.5.2

Here is the .mod file for the myMechSimple mechanism:

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I've also tried this using the ExpSyn1 mechanism, copied from _The NEURON Book_ (just to be sure the problem wasn't with the myMechSimple .mod file) with exactly the same result.

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Post by hines » Mon Jun 30, 2008 2:13 pm

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>>> myMech = nrn.myMechSimple(postCell(0.5))
I'm surprised you were not getting an error here since myMechSimple
is a POINT_PROCESS. The correct idiom is

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myMech = h.ExpSyn(0.5, sec = postCell)
However, I realize that the first statement is in fact a very natural way to
specify the location of the point process, ie. via a compartment, and I will
see if that can be allowed in the future. By the way, also in the future I will
be deprecating the nrn module in favor of doing everything from the h = neuron.HocObject().
See ... /nrn/trunk

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>>> h.NetCon(preCell0(0.5)._ref_v,myMech)

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nc = h.NetCon(preCell0(0.5)._ref_v, myMech, sec = preCell0)
without storing the return value, the new NetCon will be immediately destroyed.
Without the third arg (or an accidentally consistent currently accessed section) you will get
nrniv: NetCon pointer not associated with currently accessed section
Use section ... (&var(x)...) intead of ...(&section.var(x)...)
error message.

Note that on my linux machine

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myMech = nrn.ExpSyn(postCell(0.5))
gives the error
AttributeError: 'module' object has no attribute 'ExpSyn'
so I don't know how you were able to get beyond that line.
I will have to try to reproduce this on the mac and if I can, fix the problem
with not producing the correct error messages.

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