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

Thomas Markovich thomasmarkovich@gmail....
Tue Aug 2 12:14:02 CDT 2011


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
>>>>>>
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>>>>>>
>>>>>>
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