[SciPy-User] building on Ubuntu Linux from github source : BLAS and LAPACK not getting picked up from environment variable
Keith Hughitt
keith.hughitt at gmail.com
Tue May 1 12:36:32 EDT 2012
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 at 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 at 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 at hari:~/scipy$ export BLAS=/home/hari/blas/BLAS/libblas.a
> hari at hari:~/scipy$ export
> LAPACK=/home/hari/LAPACK/lapack-3.4.0/liblapack.a
> hari at 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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