[Numpy-discussion] Segmentation Fault in Numpy.test()

Olivier Delalleau shish@keba...
Tue Aug 2 12:21:59 CDT 2011


Maybe specify which scipy superpack. Your issue was probably because the
superpack you installed was not meant to be used with Python 2.7.

-=- Olivier

2011/8/2 Thomas Markovich <thomasmarkovich@gmail.com>

> Oh okay, that's unfortunate but I guess not unexpected. Regardless, thank
> you so much for all your help Ralf, Bruce, and Oliver! You guys are great.
>
> Just to recap, the issue appears to stem from using the scipy superpack
> with python 2.7 from python.org. This was solved by using the apple python
> along with the scipy superpack.
>
> Thomas
>
>
> On Tue, Aug 2, 2011 at 12:06 PM, Ralf Gommers <ralf.gommers@googlemail.com
> > wrote:
>
>>
>>
>> On Tue, Aug 2, 2011 at 6:57 PM, Thomas Markovich <
>> thomasmarkovich@gmail.com> wrote:
>>
>>> It appears that uninstalling python 2.7 and installing the scipy
>>> superpack with the apple standard python removes the segfaulting behavior
>>> from numpy. Now it appears that just scipy is segfaulting at test
>>> "test_arpack.test_hermitian_modes(True, <std-hermitian>, 'F', 2, 'SM', None,
>>> 0.5, <function aslinearoperator at 0x1043b1848>) ... Segmentation fault"
>>>
>>> That is a known problem (unfortunately hard to fix), see
>> http://projects.scipy.org/scipy/ticket/1472
>> Everything else besides arpack should work fine for you.
>>
>> Cheers,
>> Ralf
>>
>>
>>>
>>>
>>>
>>> On Tue, Aug 2, 2011 at 11:28 AM, Ralf Gommers <
>>> ralf.gommers@googlemail.com> wrote:
>>>
>>>>
>>>>
>>>> On Tue, Aug 2, 2011 at 6:14 PM, Thomas Markovich <
>>>> thomasmarkovich@gmail.com> wrote:
>>>>
>>>>> I just have the default "apple" version of python that comes with Snow
>>>>> Leopard (Python 2.6.1 (r261:67515, Aug  2 2010, 20:10:18)) and python 2.7
>>>>> (Python 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34) ) installed.
>>>>>
>>>>> Should I just remove 2.7 and reinstall everything with the standard
>>>>> apple python?
>>>>>
>>>>> Did you get it from http://stronginference.com/scipy-superpack/? The
>>>> info on the 10.6 installer has disappeared, but the 10.7 one is built
>>>> against Apple's Python. So conflicting Pythons makes sense. Even if you find
>>>> the right one, it may be worth emailing Chris to ask him to put back the
>>>> info for the 10.6 installer.
>>>>
>>>> Ralf
>>>>
>>>>
>>>> On Tue, Aug 2, 2011 at 11:08 AM, Olivier Delalleau <shish@keba.be>wrote:
>>>>>
>>>>>> It's a wild guess, but in the past I've had seg faults issues on Mac
>>>>>> due to conflicting versions of Python. Do you have multiple Python installs
>>>>>> on your Mac?
>>>>>>
>>>>>> -=- Olivier
>>>>>>
>>>>>>
>>>>>> 2011/8/2 Thomas Markovich <thomasmarkovich@gmail.com>
>>>>>>
>>>>>>> Hi All,
>>>>>>>
>>>>>>> I installed numpy from the scipy superpack on Snow Leopard with
>>>>>>> python 2.7 and it all appears to work but when I do the following, I get a
>>>>>>> segmentation fault.
>>>>>>>
>>>>>>> >>> import numpy
>>>>>>> >>> print numpy.__version__, numpy.__file__
>>>>>>> 2.0.0.dev-b5cdaee
>>>>>>> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-2.0.0.dev_b5cdaee_20110710-py2.6-macosx-10.6-universal.egg/numpy/__init__.pyc
>>>>>>> >>> numpy.test()
>>>>>>> Running unit tests for numpy
>>>>>>> NumPy version 2.0.0.dev-b5cdaee
>>>>>>> NumPy is installed in
>>>>>>> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-2.0.0.dev_b5cdaee_20110710-py2.6-macosx-10.6-universal.egg/numpy
>>>>>>> Python version 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34)
>>>>>>> [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
>>>>>>> nose version 1.1.2
>>>>>>> ............................................................................................................................................................................................................................................................................................................................Segmentation
>>>>>>> fault
>>>>>>> thomasmarkovich:~ Thomas$
>>>>>>>
>>>>>>> What is the best way to trouble shoot this? Do you guys have any
>>>>>>> suggestions? I have also included the core dump in this email as a pastie
>>>>>>> link.
>>>>>>>
>>>>>>> http://pastie.org/2309652
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Thomas
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> NumPy-Discussion mailing list
>>>>>>> NumPy-Discussion@scipy.org
>>>>>>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>>>>>>
>>>>>>>
>>>>>>
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