www.neuron.yale.edu

Posted: **Wed Sep 09, 2009 9:06 pm**

I recently discovered from http://www.neuron.yale.edu/phpBB/viewto ... f=16&t=489 that cvode should work with kinetic models (but does it work with LONGITUDINAL_DIFFUSION?) My first couple attempts ended in mysterious "bus error(s)," so I decided to start over from the beginning, and I discovered a weird quirk.

Running i686/special, I'm told "cvode_active undefined function"

Code: Select all

MacBook:2009-09-09a robert$ i686/special 
NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

loading membrane mechanisms from /Users/robert/math/research/rd/images/2009-09-09a/i686/.libs/libnrnmech.so
Additional mechanisms from files
 d3.mod wf2.mod
oc>cvode_active()
/Applications/NEURON-7.0/nrn/i686/bin/nrniv.app/Contents/MacOS/nrniv: cvode_active undefined function
 near line 1
 cvode_active()
               ^
        cvode_active()
oc>quit()

but typing the same thing in nrngui works just fine

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MacBook:2009-09-09a robert$ nrngui
-e 
NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

oc>cvode_active()
	0 
oc>quit()

I actually want to use cvode via python, but what is going on here?

I'm running
MacBook:2009-09-09a robert$ uname -a
Darwin MacBook.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

Posted: **Thu Sep 10, 2009 10:49 am**

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[ted@loki ~]$ grep cvode_active /usr/local/nrn71numpy/share/nrn/lib/hoc/stdrun.hoc 
func cvode_active() {

so cvode_active() is not built into the executable but is part of the standard run library. Execute
load_file('noload.hoc")
first, and then you will be able to call cvode_active()

www.neuron.yale.edu

cvode quirks

cvode quirks

Re: cvode quirks