Cross compiling NeuroML2 support into NEURON using nrnivmodl

[Peter Sussman]

Hello,

I am trying to run the openworm connectome on a board I'm using for a robot I'm building. The board is ARM based, and running a stripped down version of GNU/Linux. As the board does not have make or gcc on it, software must be cross compiled. I succeeded in cross compiling NEURON, however, NEURON does not ship with support for NeuroML or NeuroML2 files. Rather, it uses its own HOC format. NEURON provides a utility, nrnivmodl, for compiling modules (such as the nml2 support module) into NEURON, however, it doesn't appear to have any configure flags. When I try to run nrnivmodl in ./share/nrn/lib/python I get:

KConductance.mod LeakConductance.mod NaConductance.mod KConductance.mod LeakConductance.mod NaConductance.mod "/home/psussman/neuron/install/share/nrn/libtool" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I"/home/psussman/neuron/install/include/nrn" -I"/home/psussman/neuron/install/x86_64/lib" -g -O2 -c -o KConductance.lo `test -f 'KConductance.c' || echo '/'`KConductance.c
libtool: compile: unable to infer tagged configuration
libtool: compile: specify a tag with `--tag'
make: *** [KConductance.lo] Error 1

[Padraig Gleeson]

Hi,

Great that you're trying out the code on a new architecture. I don't think the problem here is anything OW specific though. Try using nrnivmodl to compile any other *.mod files and see if they work. There are some in /share/nrn/demo/release. If this fails it's an issue with the build/setup of neuron on your system and its interactions with your locally installed build tools. If it is still a problem, I'd advise asking a question on the Neuron forum (http://www.neuron.yale.edu/phpBB), they're usually quite quick to respond.

Regards,
Padraig

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Padraig Gleeson
Room 321, Anatomy Building
Department of Neuroscience, Physiology&  Pharmacology
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[Peter Sussman]

Padraig,

First of all, thanks for the reply.

Indeed, this is an issue with NEURON and not OpenWorm. I created an account at neuron.yale.edu/phpBB before I came here, but my account has not been approved yet, so I can not post to the forums.