CentOS with RxD and NEURON build from source

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Posts: 43
Joined: Thu May 23, 2019 8:02 am
Location: Warsaw, Poland

CentOS with RxD and NEURON build from source

Post by ziemek »


I try to run NEURON on cluster for parallel computing with CentOS. I built the code from source, with iv (even though I can't use GUI through console).

NEURON is working in general, but when I try to execute code with rxd - it crashes on the line:

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from neuron import rxd
The error message looks like this:

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Warning: no DISPLAY environment variable.
--No graphics will be displayed.
Traceback (most recent call last):
  File "morpho_diffusion.py", line 7, in <module>
    from cells.cell_rxd import CellRxD
  File "/home/ziemek/projects/morpho_neuro_rxd/cells/cell_rxd.py", line 1, in <module>
    from neuron.rxd import rxd
  File "/home/ziemek/nrn/lib/python/neuron/rxd/__init__.py", line 7, in <module>
    from . import rxd
  File "/home/ziemek/nrn/lib/python/neuron/rxd/rxd.py", line 2, in <module>
    from . import species, node, section1d, region
  File "/home/ziemek/nrn/lib/python/neuron/rxd/species.py", line 3, in <module>
    from .section1d import Section1D
  File "/home/ziemek/nrn/lib/python/neuron/rxd/section1d.py", line 3, in <module>
    from . import node, rxdsection, nodelist
  File "/home/ziemek/nrn/lib/python/neuron/rxd/node.py", line 3, in <module>
    from . import region
  File "/home/ziemek/nrn/lib/python/neuron/rxd/region.py", line 10, in <module>
    from . import geometry as geo
  File "/home/ziemek/nrn/lib/python/neuron/rxd/geometry.py", line 129, in <module>
    inside.volumes3d = geometry3d.voxelize2
AttributeError: module 'neuron.rxd.geometry3d' has no attribute 'voxelize2'
I have NEURON 7.7.2 and iv 1.9.

Does anyone know what's wrong here?

Posts: 214
Joined: Fri Nov 28, 2008 3:38 pm
Location: Yale School of Public Health

Re: CentOS with RxD and NEURON build from source

Post by ramcdougal »

Looks like something went wrong with the Cython part of the compilation (which provides voxelize2).

If you're using Centos 7 and Python 3.4, try recompiling after something like:

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yum -y install python34-Cython
(I understand you may not have sudo rights on this machine, but you ought to be able to install locally... modify the above line for different versions of CentOS and Python as needed, but the point is to make sure you have a working Cython install.)

Our linux compilation instructions are at: https://www.neuron.yale.edu/neuron/down ... pile_linux

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