I checked out numpy from svn few hours ago, and created a site.cfg following
site.cfg.example. During the build process I am getting an warning that
unoptimized lapack in being used.
Machine: dual core amd64 running gentoo linux.
Relevant packages: python 2.5.1, blas-atlas-3.8.0, lapack-atlas-3.8.0
# site.cfg
[ALL]
library_dirs = /usr/lib64/lapack/atlas:/usr/lib64/blas/threaded-atlas:/usr/lib
include_dirs = /usr/include/atlas:/usr/include
[blas_opt]
library_dirs = /usr/lib64/blas/threaded-atlas:/usr/lib64
libraries = blas, cblas, atlas
[lapack_opt]
library_dirs = /usr/lib64/lapack/atlas:/usr/lib64
libraries = lapack, blas, cblas, atlas
[fftw]
libraries = fftw3
I added the following print lines in system_info class:
def __init__ (self,
default_lib_dirs=default_lib_dirs,
default_include_dirs=default_include_dirs,
verbosity = 1,
):
print '\n\n====================================='
print ' class: ',self.__class__
print ' libs: ', default_lib_dirs
print ' includes: ', default_include_dirs
print '=====================================\n\n'
A partial dump out of "python setup.py build":
Running from numpy source directory.
F2PY Version 2_4971
=====================================
class: numpy.distutils.system_info.blas_opt_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
blas_opt_info:
=====================================
class: numpy.distutils.system_info.blas_mkl_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
blas_mkl_info:
libraries mkl,vml,guide not found in /usr/lib
libraries mkl,vml,guide not found in /usr/local/lib
NOT AVAILABLE
=====================================
class: numpy.distutils.system_info.atlas_blas_threads_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
NOT AVAILABLE
=====================================
class: numpy.distutils.system_info.atlas_blas_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
atlas_blas_info:
NOT AVAILABLE
/home/nadav/numpy/numpy/distutils/system_info.py:1345: 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__)
=====================================
class: numpy.distutils.system_info.blas_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
blas_info:
NOT AVAILABLE
/home/nadav/numpy/numpy/distutils/system_info.py:1354: 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__)
=====================================
class: numpy.distutils.system_info.blas_src_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
blas_src_info:
NOT AVAILABLE
/home/nadav/numpy/numpy/distutils/system_info.py:1357: 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__)
NOT AVAILABLE
=====================================
class: numpy.distutils.system_info.lapack_opt_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
lapack_opt_info:
=====================================
class: numpy.distutils.system_info.lapack_mkl_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
lapack_mkl_info:
=====================================
class: numpy.distutils.system_info.mkl_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
mkl_info:
libraries mkl,vml,guide not found in /usr/lib
libraries mkl,vml,guide not found in /usr/local/lib
NOT AVAILABLE
NOT AVAILABLE
=====================================
class: numpy.distutils.system_info.atlas_threads_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
atlas_threads_info:
Setting PTATLAS=ATLAS
numpy.distutils.system_info.atlas_threads_info
NOT AVAILABLE
=====================================
class: numpy.distutils.system_info.atlas_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
atlas_info:
numpy.distutils.system_info.atlas_info
NOT AVAILABLE
/home/nadav/numpy/numpy/distutils/system_info.py:1252: 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__)
=====================================
class: numpy.distutils.system_info.lapack_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
lapack_info:
NOT AVAILABLE
/home/nadav/numpy/numpy/distutils/system_info.py:1263: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
=====================================
class: numpy.distutils.system_info.lapack_src_info
libs: ['/usr/local/lib', '/usr/lib']
includes: ['/usr/local/include', '/usr/include']
=====================================
lapack_src_info:
NOT AVAILABLE
/home/nadav/numpy/numpy/distutils/system_info.py:1266: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
NOT AVAILABLE
running build
running scons
.
.
.
building extension "numpy.core._dotblas" sources
building extension "numpy.lib._compiled_base" sources
building extension "numpy.numarray._capi" sources
building extension "numpy.fft.fftpack_lite" sources
building extension "numpy.linalg.lapack_lite" sources
creating build/src.linux-x86_64-2.5/numpy/linalg
### Warning: Using unoptimized lapack ###
adding 'numpy/linalg/lapack_litemodule.c' to sources.
adding 'numpy/linalg/zlapack_lite.c' to sources.
adding 'numpy/linalg/dlapack_lite.c' to sources.
adding 'numpy/linalg/blas_lite.c' to sources.
adding 'numpy/linalg/dlamch.c' to sources.
adding 'numpy/linalg/f2c_lite.c' to sources.
-------------------------------------------
* Why /usr/local/lib and /usr/local/include are there although they are not in
site.cfg?
* Why lapack library was not found?
* site.cfg.example is located in ~/numpy but the UserWarning indicates
numpy/distutils/site.cfg. I copied site.cfg also to ~/numpy/numpy/distutils but
it did not help.
Nadav
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