[SciPy-User] Scipy with pip compliation problems on Centos 6.6

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[SciPy-User] Scipy with pip compliation problems on Centos 6.6

Robinson, Roger

Hi,

 

I am on CentOS 6.6. I have compiled BLAS+ATLAS+LAPACK separately on a network drive.

 

I have python 2.7.9 compiled.

 

Im using this command to install + complie scipy

pip install --target=/apps_shared/python/scipy/scipy-0.15.1 scipy

 

I get this error

 

Python 2.7.9 (default, Feb 16 2015, 11:29:23)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-11)] on linux2

Type "help", "copyright", "credits" or "license" for more information.

>>> from scipy.stats import genextreme

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/apps_shared/python/scipy/current/scipy/stats/__init__.py", line 338, in <module>

    from .stats import *

  File "/apps_shared/python/scipy/current/scipy/stats/stats.py", line 184, in <module>

    import scipy.special as special

  File "/apps_shared/python/scipy/current/scipy/special/__init__.py", line 586, in <module>

    from ._ufuncs import *

ImportError: /apps_shared/python/scipy/current/scipy/special/_ufuncs.so: undefined symbol: dstevr_

 

Any advice ?

 

Thanks Roger

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Re: Scipy with pip compliation problems on Centos 6.6

ralfgommers


On Tue, Feb 24, 2015 at 5:11 PM, Robinson, Roger <[hidden email]> wrote:

Hi,

 

I am on CentOS 6.6. I have compiled BLAS+ATLAS+LAPACK separately on a network drive.

 

I have python 2.7.9 compiled.

 

Im using this command to install + complie scipy

pip install --target=/apps_shared/python/scipy/scipy-0.15.1 scipy

 

I get this error

 

Python 2.7.9 (default, Feb 16 2015, 11:29:23)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-11)] on linux2

Type "help", "copyright", "credits" or "license" for more information.

>>> from scipy.stats import genextreme

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/apps_shared/python/scipy/current/scipy/stats/__init__.py", line 338, in <module>

    from .stats import *

  File "/apps_shared/python/scipy/current/scipy/stats/stats.py", line 184, in <module>

    import scipy.special as special

  File "/apps_shared/python/scipy/current/scipy/special/__init__.py", line 586, in <module>

    from ._ufuncs import *

ImportError: /apps_shared/python/scipy/current/scipy/special/_ufuncs.so: undefined symbol: dstevr_

 

Any advice ?


Looks like a problem with the LAPACK (or ATLAS) you compiled. I'm not sure if the network drive and unusual pip command have anything to do with it. To test that, you could first try compiling scipy against a precompiled ATLAS binary for your distribution that is known to work.

 Ralf



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