[IPython-dev] Numpy with OpenBLAS vs. IPython
Florian M. Wagner
wagnerfl at student.ethz.ch
Fri Nov 1 08:40:31 EDT 2013
Thanks Jens,
you were right. numpy.__file__ was not the same. It works now!
Best regards
Florian
Am 01.11.2013 11:01, schrieb Jens Nielsen:
> Hi
>
> I have just tried this using openblas 0.2.8 and numpy 1.8.0 on mac OSx
> with ipython 1.1.0 and I can't reproduce your issue.
> What is the output of numpy.show_config() from python and IPython?
>
> Is the same install of numpy being picked up and used. I.e. what is
> the output of numpy.__file__ in python and IPython?
>
> best regards
> Jens
>
>
>
>
> On Fri, Nov 1, 2013 at 9:42 AM, Florian M. Wagner
> <wagnerfl at student.ethz.ch <mailto:wagnerfl at student.ethz.ch>> wrote:
>
> Any ideas? Has someone here a functioning setup with
> Numpy-OpenBlas and the scientific (I)Python stack on Linux and is
> willing to share the necessary installation steps?
>
> Am 30.10.2013 <tel:30.10.2013> 09:46, schrieb Florian M. Wagner:
>> I reproduced the error with the latest IPython source:
>>
>> fwagner at fwagner-notebook ~/Downloads/ipython $ ipython
>> Python 2.7.4 (default, Sep 26 2013, 03:20:26)
>> Type "copyright", "credits" or "license" for more information.
>>
>> IPython 2.0.0-dev -- An enhanced Interactive Python.
>> ? -> Introduction and overview of IPython's features.
>> %quickref -> Quick reference.
>> help -> Python's own help system.
>> object? -> Details about 'object', use 'object??' for extra
>> details.
>>
>> In [1]: A = np.random.randn(50,50)
>>
>> In [2]: A[0,0]
>> Out[2]: 0.62268531821589967
>>
>> In [3]: A.T.dot(A)
>> Speicherzugriffsfehler
>>
>> Compared to:
>>
>> Python 2.7.4 (default, Sep 26 2013, 03:20:26)
>> [GCC 4.7.3] on linux2
>> Type "help", "copyright", "credits" or "license" for more
>> information.
>> >>> import numpy as np
>> >>> A = np.random.randn(50,50)
>> >>> A.T.dot(A)
>> array([[ 4.61866860e+01, 1.97714469e+00, 8.78842173e+00, ...,
>> -9.65143259e+00, 4.74312877e+00, -1.85163266e+01],
>> [ 1.97714469e+00, 4.50113072e+01, -1.13105045e+01, ...,
>> 2.31604581e+00, 4.93068512e+00, 1.29316267e+01],
>> [ 8.78842173e+00, -1.13105045e+01, 6.02859864e+01, ...,
>> -2.65040891e+00, 3.98374437e+00, -1.54860323e+01],
>> ...,
>> [ -9.65143259e+00, 2.31604581e+00, -2.65040891e+00, ...,
>> 3.81774984e+01, 1.63768677e+00, 1.16681961e+01],
>> [ 4.74312877e+00, 4.93068512e+00, 3.98374437e+00, ...,
>> 1.63768677e+00, 5.11159138e+01, 6.56039753e-02],
>> [ -1.85163266e+01, 1.29316267e+01, -1.54860323e+01, ...,
>> 1.16681961e+01, 6.56039753e-02, 6.61061915e+01]])
>>
>>
>>
>> Am 30.10.2013 <tel:30.10.2013> 09:33, schrieb Florian M. Wagner:
>>> Thanks guys,
>>>
>>> @Julian: Reducing the thread number did not help
>>> @Thomas: dap is mpl-basemap dependency, fixed the import issue, but the
>>> error still occurs
>>>
>>> It is really weird that it is occuring only when printing the array, or
>>> slicing the array. And whats more weird, that it works in plain Python
>>> as I understood that IPython has no numpy dependency?
>>>
>>> Thanks and regards
>>> Florian
>>>
>>> Am29.10.2013 <tel:29.10.2013> 19:39, schrieb Julian Taylor:
>>>> does this also happen if you do this before starting ipython?
>>>>
>>>> export OPENBLAS_NUM_THREADS=1
>>>> (assuming bash shell)
>>>>
>>>> On29.10.2013 <tel:29.10.2013> 17:19, Florian M. Wagner wrote:
>>>>> Dear all,
>>>>>
>>>>> I recently compiled numpy with OpenBlas for faster matrix-matrix
>>>>> multiplication. Everything works fine, but IPython seems to dislike it.
>>>>> I get a Segmentation Fault error when trying this (I reinstalled IPython
>>>>> 1.1.0 after numpy compilation):
>>>>>
>>>>> fwagner at fwagner-notebook ~ $ ipython -c "import numpy as np; print
>>>>> np.__version__; import IPython; print IPython.__version__; A =
>>>>> np.random.randn(600, 600); print A[20,53]; print A"
>>>>> /usr/local/bin/ipython:5: UserWarning: Module dap was already
>>>>> imported from None, but /usr/lib/python2.7/dist-packages is being
>>>>> added to sys.path
>>>>> from pkg_resources import load_entry_point
>>>>> 1.9.0.dev-54d3559
>>>>> 1.1.0
>>>>> -2.1004055886
>>>>> Speicherzugriffsfehler
>>>>>
>>>>> In comparison, this works fine (just python instead of ipython):
>>>>>
>>>>> fwagner at fwagner-notebook ~ $ python -c "import numpy as np; print
>>>>> np.__version__; import IPython; print IPython.__version__; A =
>>>>> np.random.randn(600, 600); print A[20,53]; print A"
>>>>> 1.9.0.dev-54d3559
>>>>> 1.1.0
>>>>> -1.10282239744
>>>>> [[ 0.13798084 -0.39195796 -0.15309986 ..., 1.47471232 -0.9158455
>>>>> 0.97060671]
>>>>> [ 0.25720169 0.51895478 0.55175787 ..., -0.02010573 0.78047754
>>>>> -1.07891961]
>>>>> [ 1.59478156 0.81245486 -0.03959768 ..., -0.04816659 -0.03356907
>>>>> -0.11860379]
>>>>> ...,
>>>>> [-0.06299817 -0.0956477 -0.32987518 ..., -1.47714386 1.66736916
>>>>> -0.47704276]
>>>>> [-0.93769589 1.50006542 0.97782803 ..., -0.5034154 1.31592011
>>>>> -0.74482995]
>>>>> [-0.24661336 -0.98979706 -0.39366363 ..., 0.20507632 0.8701609
>>>>> -1.10449957]]
>>>>>
>>>>> Any ideas what might cause this problem?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Florian
>>>>>
>>>>>
>>>>>
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