[SciPy-User] building on Ubuntu Linux from github source : BLAS and LAPACK not getting picked up from environment variable

hari jayaram harijay@gmail....
Tue May 1 13:56:13 CDT 2012


Thanks Keith,
My problem was that I had installed numpy from the git repository
before I had installed BLAS.

Once I uninstalled numpy , then installed LAPACK and BLAS.
Then I could install numpy and scipy using "sudo python setup.py install"

Thanks
Hari

On Tue, May 1, 2012 at 12:36 PM, Keith Hughitt <keith.hughitt@gmail.com> wrote:
> Hi hari,
>
> Try:
>
> sudo apt-get build-dep python-scipy
>
> That should fetch and install all of the dependencies needed to build SciPy.
>
> Best,
> Keith
>
> On Fri, Apr 20, 2012 at 11:53 AM, hari jayaram <harijay@gmail.com> wrote:
>>
>> Hi
>> I am on 64 bit Ubuntu , python  2.6.5 , GCC 4.4.3. I want to compile
>> my own scipy since the ubuntu package on lucid installs a scipy which
>> does not have the scipy.optimize.curve_fit
>>
>> I followed the build instructions at the url below to install from the
>> git source .
>>
>> http://www.scipy.org/Installing_SciPy/BuildingGeneral
>>
>> I could install numpy from the git source . Then I installed lapack
>> and blas libraries in my home directory following the instructions at
>> BuildingGeneral.
>> I set the environment variables BLAS and LAPACK in my ~/.bashrc and
>> sourced them and then tried the setup.py for scipy
>>
>> sudo python setup.py install
>>
>>
>> I get the following errors implying that BLAS was not getting picked
>> up.  I even copied the libblas.a and liblapack.a files to /usr/lib,
>> linked it to liblapack.so ...but none of these helped find lapack or
>> blas
>>
>>
>> "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."
>>
>> I am wondering if  the build instructions are different for the github
>> tree. The detailed error is given below.
>> Thanks for your help
>>
>> Hari
>>
>>
>>
>>
>>
>>
>>
>>
>> hari@hari:~/scipy$ sudo python setup.py install --prefix=/usr/local
>> blas_opt_info:
>> blas_mkl_info:
>>  libraries mkl,vml,guide not found in ['/usr/local/lib',
>> '/usr/lib64', '/usr/lib']
>>  NOT AVAILABLE
>>
>> atlas_blas_threads_info:
>> Setting PTATLAS=ATLAS
>>  libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib',
>> '/usr/lib64', '/usr/lib']
>>  NOT AVAILABLE
>>
>> atlas_blas_info:
>>  libraries f77blas,cblas,atlas not found in ['/usr/local/lib',
>> '/usr/lib64', '/usr/lib']
>>  NOT AVAILABLE
>>
>>
>> /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1474:
>> 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 ['/usr/local/lib', '/usr/lib64', '/usr/lib']
>>  NOT AVAILABLE
>>
>>
>> /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1483:
>> 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
>>
>>
>> /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1486:
>> 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 "setup.py", line 208, in <module>
>>    setup_package()
>>  File "setup.py", line 199, in setup_package
>>    configuration=configuration )
>>  File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/core.py",
>> line 152, in setup
>>    config = configuration()
>>  File "setup.py", line 136, in configuration
>>    config.add_subpackage('scipy')
>>  File
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py",
>> line 1002, in add_subpackage
>>    caller_level = 2)
>>  File
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py",
>> line 971, in get_subpackage
>>    caller_level = caller_level + 1)
>>  File
>> "/usr/local/lib/python2.6/dist-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
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py",
>> line 1002, in add_subpackage
>>    caller_level = 2)
>>  File
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py",
>> line 971, in get_subpackage
>>    caller_level = caller_level + 1)
>>  File
>> "/usr/local/lib/python2.6/dist-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
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py",
>> line 325, in get_info
>>    return cl().get_info(notfound_action)
>>  File
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py",
>> line 484, 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.
>> hari@hari:~/scipy$ export BLAS=/home/hari/blas/BLAS/libblas.a
>> hari@hari:~/scipy$ export
>> LAPACK=/home/hari/LAPACK/lapack-3.4.0/liblapack.a
>> hari@hari:~/scipy$ sudo python setup.py install --prefix=/usr/local
>> blas_opt_info:
>> blas_mkl_info:
>>  libraries mkl,vml,guide not found in ['/usr/local/lib',
>> '/usr/lib64', '/usr/lib']
>>  NOT AVAILABLE
>>
>> atlas_blas_threads_info:
>> Setting PTATLAS=ATLAS
>>  libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib',
>> '/usr/lib64', '/usr/lib']
>>  NOT AVAILABLE
>>
>> atlas_blas_info:
>>  libraries f77blas,cblas,atlas not found in ['/usr/local/lib',
>> '/usr/lib64', '/usr/lib']
>>  NOT AVAILABLE
>>
>>
>> /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1474:
>> 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 ['/usr/local/lib', '/usr/lib64', '/usr/lib']
>>  NOT AVAILABLE
>>
>>
>> /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1483:
>> 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
>>
>>
>> /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1486:
>> 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 "setup.py", line 208, in <module>
>>    setup_package()
>>  File "setup.py", line 199, in setup_package
>>    configuration=configuration )
>>  File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/core.py",
>> line 152, in setup
>>    config = configuration()
>>  File "setup.py", line 136, in configuration
>>    config.add_subpackage('scipy')
>>  File
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py",
>> line 1002, in add_subpackage
>>    caller_level = 2)
>>  File
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py",
>> line 971, in get_subpackage
>>    caller_level = caller_level + 1)
>>  File
>> "/usr/local/lib/python2.6/dist-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
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py",
>> line 1002, in add_subpackage
>>    caller_level = 2)
>>  File
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py",
>> line 971, in get_subpackage
>>    caller_level = caller_level + 1)
>>  File
>> "/usr/local/lib/python2.6/dist-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
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py",
>> line 325, in get_info
>>    return cl().get_info(notfound_action)
>>  File
>> "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py",
>> line 484, 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.
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