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

Fri Apr 20 11:53:21 EDT 2012

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.