Problem using PyNN with Neuron

[Szabolcs Káli]

Dear All,

We are trying to use PyNN with Neuron on Ubuntu 14.04 (Python 2.7). Installation of Neuron from source seems to be fine; we can run either the standalone version, or import it as a Python module. We then installed PyNN either using pip or from source; we have also tried both version 0.8 and 0.7.5. When we then try "from pyNN.neuron import *" in Python, we get the following error:

NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09

Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015

See http://www.neuron.yale.edu/neuron/credits

loading membrane mechanisms from /usr/local/lib/python2.7/dist-packages/pyNN/neuron/nmodl/x86_64/.libs/libnrnmech.so

dlopen failed - 

/usr/local/lib/python2.7/dist-packages/pyNN/neuron/nmodl/x86_64/.libs/libnrnmech.so: undefined symbol: nrnmpi_myid

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/usr/local/lib/python2.7/dist-packages/pyNN/neuron/__init__.py", line 18, in <module>

    from pyNN.neuron.standardmodels.cells import *

  File "/usr/local/lib/python2.7/dist-packages/pyNN/neuron/standardmodels/cells.py", line 13, in <module>

    from pyNN.neuron.cells import StandardIF, SingleCompartmentTraub, RandomSpikeSource, VectorSpikeSource, BretteGerstnerIF, GsfaGrrIF

  File "/usr/local/lib/python2.7/dist-packages/pyNN/neuron/cells.py", line 43, in <module>

    class SingleCompartmentNeuron(nrn.Section):

  File "/usr/local/lib/python2.7/dist-packages/pyNN/neuron/cells.py", line 47, in SingleCompartmentNeuron

    'current':      { 'exp': h.ExpISyn, 'alpha': h.AlphaISyn },

AttributeError: 'hoc.HocObject' object has no attribute 'ExpISyn'

Do you have any idea what might be going wrong?

Thank you, best regards,

Szabolcs

-------------------------------------------------------

Szabolcs Káli

Laboratory of Cerebral Cortex Research
Institute of Experimental Medicine
Hungarian Academy of Sciences

H-1083 Budapest Szigony utca 43.
Phone: +36-1-2109413
Fax: +36-1-2109412
E-mail: kali.s...@koki.mta.hu
www.koki.mta.hu