[yt-users] SciPy and YT problem

trobolo dinni trobolo.trobolo.dinni5 at gmail.com
Sat Aug 25 08:11:45 PDT 2012


Hi Jeff,

I already tried that way and I get the same error about Alias and Blas
libraries missing (attached)...
My question is: since SciPy works fine with the system python, don't those
libraries should be already in the system?


Thanks,
                Roberto


2012/8/25 j s oishi <jsoishi at gmail.com>

> Hi Roberto,
>
> Try activating yt and then typing
>
> pip install scipy
>
> I am not sure that will work, but if it does, scipy will certainly be in
> the right place.
>
> Jeff
> On Aug 25, 2012 10:42 AM, "roberto iaconi" <robertoiaconi at yahoo.it> wrote:
>
>> Dear YT users,
>>
>> I have a problem in installing the SciPy library when using YT python,
>> what happens is that:
>>
>> -when installing from packages, also after activating yt (i.e. through
>> the command sudo apt-get install python-scipy) I get the confirmation
>> that SciPy is correctly installed but i cannot import it in YT python,
>> since probably the installation is connected to the system python instead.
>> -when installing from source (by downloading the packages) I get a lot of
>> errors concerning missing libraries (mainly blas and atlas).
>> I installed them and added the paths to a "site.cfg" file, but I am still
>> getting the same error.
>>
>> Also, I appended the system SciPy path through the sys.path.append()
>> function, in this way I can succesfully import SciPy, but I cannot import
>> any sublibrary such as SciPy.optimize (which is the one I particularly
>> need).
>>
>> By browsing the YT Mailing List I found a user with a similar problem (
>> http://lists.spacepope.org/htdig.cgi/yt-users-spacepope.org/2011-July/001694.html),
>> but there are no suggestions in reply.
>>
>> I would like to ask if there is a way to get SciPy installed under YT or
>> make it available to be included.
>>
>> Cheers,
>>                 Roberto
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20120825/9203ad5e/attachment.htm>
-------------- next part --------------
(yt-x86_64)sith at ubuntu:~$ pip install scipy
Downloading/unpacking scipy
  Downloading scipy-0.10.1.zip (7.8Mb): 7.8Mb downloaded
  Running setup.py egg_info for package scipy
    Running from scipy source directory.
    blas_opt_info:
    blas_mkl_info:
      libraries mkl,vml,guide not found in /home/sith/yt-x86_64/lib
      libraries mkl,vml,guide not found in /usr/local/lib
      libraries mkl,vml,guide not found in /usr/lib
      NOT AVAILABLE
    
    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
      libraries ptf77blas,ptcblas,atlas not found in /home/sith/yt-x86_64/lib
      libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib
      NOT AVAILABLE
    
    atlas_blas_info:
      libraries f77blas,cblas,atlas not found in /home/sith/yt-x86_64/lib
      libraries f77blas,cblas,atlas not found in /usr/local/lib
      libraries f77blas,cblas,atlas not found in /usr/lib
      NOT AVAILABLE
    
    /home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py:1414: UserWarning:
        Atlas (http://math-atlas.sourceforge.net/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [atlas]) or by setting
        the ATLAS environment variable.
      warnings.warn(AtlasNotFoundError.__doc__)
    blas_info:
      libraries blas not found in /home/sith/yt-x86_64/lib
      libraries blas not found in /usr/local/lib
      libraries blas not found in /usr/lib
      NOT AVAILABLE
    
    /home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py:1423: UserWarning:
        Blas (http://www.netlib.org/blas/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [blas]) or by setting
        the BLAS environment variable.
      warnings.warn(BlasNotFoundError.__doc__)
    blas_src_info:
      NOT AVAILABLE
    
    /home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py:1426: UserWarning:
        Blas (http://www.netlib.org/blas/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [blas_src]) or by setting
        the BLAS_SRC environment variable.
      warnings.warn(BlasSrcNotFoundError.__doc__)
    Traceback (most recent call last):
      File "<string>", line 14, in <module>
      File "/home/sith/build/scipy/setup.py", line 196, in <module>
        setup_package()
      File "/home/sith/build/scipy/setup.py", line 187, in setup_package
        configuration=configuration )
      File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/core.py", line 152, in setup
        config = configuration()
      File "/home/sith/build/scipy/setup.py", line 138, in configuration
        config.add_subpackage('scipy')
      File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage
        caller_level = 2)
      File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage
        caller_level = caller_level + 1)
      File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/setup.py", line 8, in configuration
        config.add_subpackage('integrate')
      File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage
        caller_level = 2)
      File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage
        caller_level = caller_level + 1)
      File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/integrate/setup.py", line 10, in configuration
        blas_opt = get_info('blas_opt',notfound_action=2)
      File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 311, in get_info
        return cl().get_info(notfound_action)
      File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 462, in get_info
        raise self.notfounderror(self.notfounderror.__doc__)
    numpy.distutils.system_info.BlasNotFoundError:
        Blas (http://www.netlib.org/blas/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [blas]) or by setting
        the BLAS environment variable.
    Complete output from command python setup.py egg_info:
    Running from scipy source directory.

blas_opt_info:

blas_mkl_info:

  libraries mkl,vml,guide not found in /home/sith/yt-x86_64/lib

  libraries mkl,vml,guide not found in /usr/local/lib

  libraries mkl,vml,guide not found in /usr/lib

  NOT AVAILABLE



atlas_blas_threads_info:

Setting PTATLAS=ATLAS

  libraries ptf77blas,ptcblas,atlas not found in /home/sith/yt-x86_64/lib

  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib

  libraries ptf77blas,ptcblas,atlas not found in /usr/lib

  NOT AVAILABLE



atlas_blas_info:

  libraries f77blas,cblas,atlas not found in /home/sith/yt-x86_64/lib

  libraries f77blas,cblas,atlas not found in /usr/local/lib

  libraries f77blas,cblas,atlas not found in /usr/lib

  NOT AVAILABLE



/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py:1414: UserWarning:

    Atlas (http://math-atlas.sourceforge.net/) libraries not found.

    Directories to search for the libraries can be specified in the

    numpy/distutils/site.cfg file (section [atlas]) or by setting

    the ATLAS environment variable.

  warnings.warn(AtlasNotFoundError.__doc__)

blas_info:

  libraries blas not found in /home/sith/yt-x86_64/lib

  libraries blas not found in /usr/local/lib

  libraries blas not found in /usr/lib

  NOT AVAILABLE



/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py:1423: UserWarning:

    Blas (http://www.netlib.org/blas/) libraries not found.

    Directories to search for the libraries can be specified in the

    numpy/distutils/site.cfg file (section [blas]) or by setting

    the BLAS environment variable.

  warnings.warn(BlasNotFoundError.__doc__)

blas_src_info:

  NOT AVAILABLE



/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py:1426: UserWarning:

    Blas (http://www.netlib.org/blas/) sources not found.

    Directories to search for the sources can be specified in the

    numpy/distutils/site.cfg file (section [blas_src]) or by setting

    the BLAS_SRC environment variable.

  warnings.warn(BlasSrcNotFoundError.__doc__)

Traceback (most recent call last):

  File "<string>", line 14, in <module>

  File "/home/sith/build/scipy/setup.py", line 196, in <module>

    setup_package()

  File "/home/sith/build/scipy/setup.py", line 187, in setup_package

    configuration=configuration )

  File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/core.py", line 152, in setup

    config = configuration()

  File "/home/sith/build/scipy/setup.py", line 138, in configuration

    config.add_subpackage('scipy')

  File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage

    caller_level = 2)

  File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage

    caller_level = caller_level + 1)

  File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py

    config = setup_module.configuration(*args)

  File "scipy/setup.py", line 8, in configuration

    config.add_subpackage('integrate')

  File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage

    caller_level = 2)

  File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage

    caller_level = caller_level + 1)

  File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py

    config = setup_module.configuration(*args)

  File "scipy/integrate/setup.py", line 10, in configuration

    blas_opt = get_info('blas_opt',notfound_action=2)

  File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 311, in get_info

    return cl().get_info(notfound_action)

  File "/home/sith/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 462, in get_info

    raise self.notfounderror(self.notfounderror.__doc__)

numpy.distutils.system_info.BlasNotFoundError:

    Blas (http://www.netlib.org/blas/) libraries not found.

    Directories to search for the libraries can be specified in the

    numpy/distutils/site.cfg file (section [blas]) or by setting

    the BLAS environment variable.

----------------------------------------
Command python setup.py egg_info failed with error code 1 in /home/sith/build/scipy
Storing complete log in /home/sith/.pip/pip.log


More information about the yt-users mailing list