Neuron parallel installation on Clusters

General issues of interest both for network and
individual cell parallelization.

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Rahul123
Posts: 1
Joined: Wed Jun 27, 2018 7:42 am

Neuron parallel installation on Clusters

Post by Rahul123 » Thu Jun 28, 2018 1:08 am

I have installed Neuron on the cluster.
1. After installation of neuron paralleI got an error like:
>>>import neuron
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/__init__.py", line 112, in <module>
exec("import neuron.hoc%d%d as hoc" % (sys.version_info[0], sys.version_info[1]))
File "<string>", line 1, in <module>
ImportError: No module named hoc27





IangularMesh.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/geometry3d/voxelize2.py to voxelize2.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/geometry3d/surface.py to surface.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/geometry3d/setup_local.py to setup_local.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/geometry3d/voxelize.py to voxelize.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/geometry3d/setup.py to setup.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/geometry3d/scalarField.py to scalarField.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/morphology.py to morphology.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/region.py to region.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/generalizedReaction.py to generalizedReaction.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/rxd.py to rxd.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/species.py to species.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/rxdsection.py to rxdsection.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/initializer.py to initializer.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/rxd/rate.py to rate.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/hclass2.py to hclass2.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/neuroml/__init__.py to __init__.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/neuroml/rdxml.py to rdxml.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/neuroml/biophysics.py to biophysics.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/neuroml/morphml.py to morphml.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/neuroml/xml2nrn.py to xml2nrn.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/neuroml/metadata.py to metadata.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/neuroml/neuroml.py to neuroml.pyc
byte-compiling /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/sections.py to sections.pyc
running install_data
copying ../.././share/lib/python/neuron/help_data.dat -> /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron
running install_egg_info
Writing /home/ug/15/ugraees/package/lib/python2.7/site-packages/NEURON-7.5-py2.7.egg-info

[ugraees@tyrone-cluster site-packages]$ vi ~/.cshrc
[ugraees@tyrone-cluster site-packages]$ source ~/.cshrc
[ugraees@tyrone-cluster site-packages]$ python
Python 2.7.13 (default, Jun 28 2017, 10:53:26)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import neuron
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "neuron/__init__.py", line 112, in <module>
exec("import neuron.hoc%d%d as hoc" % (sys.version_info[0], sys.version_info[1]))
File "<string>", line 1, in <module>
ImportError: No module named hoc27
>>>
[ugraees@tyrone-cluster site-packages]$ exit
logout
[root@tyrone-cluster ugraees]# su - ugraees
[ugraees@tyrone-cluster ~]$ pyth
python python2 python2.6 python2.6-config python2.7 python2.7-config python2-config python-config
[ugraees@tyrone-cluster ~]$ python2.7
Python 2.7.13 (default, Jun 28 2017, 10:53:26)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import neoron
Traceback (most recent call last):>>>import neuron
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/__init__.py", line 112, in <module>
exec("import neuron.hoc%d%d as hoc" % (sys.version_info[0], sys.version_info[1]))
File "<string>", line 1, in <module>
ImportError: No module named hoc27

File "<stdin>", line 1, in <module>
ImportError: No module named neoron
>>> import neuron
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/__init__.py", line 112, in <module>
exec("import neuron.hoc%d%d as hoc" % (sys.version_info[0], sys.version_info[1]))
File "<string>", line 1, in <module>
ImportError: No module named hoc27>>>import neuron
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/__init__.py", line 112, in <module>
exec("import neuron.hoc%d%d as hoc" % (sys.version_info[0], sys.version_info[1]))
File "<string>", line 1, in <module>
ImportError: No module named hoc27

>>>
[ugraees@tyrone-cluster ~]$ vi /home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/__init__.py
[ugraees@tyrone-cluster ~]$ python2.7
Python 2.7.13 (default, Jun 28 2017, 10:53:26)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import nrn
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named nrn
>>> import neuron
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/ug/15/ugraees/package/lib/python2.7/site-packages/neuron/__init__.py", line 114
import nrn
^

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