IPython import segmentation fault...
Posted: Thu Jul 03, 2008 4:52 pm
I have the latest code from the NEURON subversion repository built and installed. I have built neuron with both --with-numpy and --enable-numpy, but it doesn't seem to matter, either way I get the same error *only* when I try to import neuron from within IPython. at the python prompt it seems to work fine. Here is what my terminal looks like:
Is this possibly a problem with the PyRun_SimpleString() in IPython? I don't know, but I just fixed it by commenting out that whole 'if' block. I'm not sure why the function useful since for me the path "neuronhome/lib/python" ("/home/gartland/neuron/nrn/lib/python") doesn't exist.
Anyway I just thought you should be aware.
Code: Select all
gartland@komodo:~$ ipython
Python 2.5.2 (r252:60911, Apr 21 2008, 11:12:42)
Type "copyright", "credits" or "license" for more information.
IPython 0.8.1 -- An enhanced Interactive Python.
? -> Introduction to IPython's features.
%magic -> Information about IPython's 'magic' % functions.
help -> Python's own help system.
object? -> Details about 'object'. ?object also works, ?? prints more.
In [1]: import neuron
NEURON -- VERSION 6.2.1036 (2163) 2008-07-02
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007
See http://www.neuron.yale.edu/credits.html
---------------------------------------------------------------------------
<type 'exceptions.ImportError'> Traceback (most recent call last)
/home/gartland/<string> in <module>()
<type 'exceptions.ImportError'>: __import__ not found
Assertion failed: file nrnpython.cpp, line 38
NEURON: PyRun_SimpleString("import sys") == 0
near line 0
objref hoc_obj_[2]
^
Segmentation fault
gartland@komodo:~$ nrniv -python
NEURON -- VERSION 6.2.1036 (2163) 2008-07-02
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007
See http://www.neuron.yale.edu/credits.html
>>> import neuron
>>>
gartland@komodo:~$ python
Python 2.5.2 (r252:60911, Apr 21 2008, 11:12:42)
[GCC 4.2.3 (Ubuntu 4.2.3-2ubuntu7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import neuron
NEURON -- VERSION 6.2.1036 (2163) 2008-07-02
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007
See http://www.neuron.yale.edu/credits.html
>>> import sys
>>> sys.version
'2.5.2 (r252:60911, Apr 21 2008, 11:12:42) \n[GCC 4.2.3 (Ubuntu 4.2.3-2ubuntu7)]'
Anyway I just thought you should be aware.