[SciPy-User] site.cfg problems : scipy can't find BLAS
John Reid
j.reid at mail.cryst.bbk.ac.uk
Thu Apr 8 08:38:11 EDT 2010
Hi,
I'm trying to build numpy and scipy from the latest svn source. I have
followed the instructions in site.cfg.example to configure my own
site.cfg and I'm using the same site.cfg for both numpy and scipy. numpy
builds and installs fine and the tests pass. scipy won't build and
throws out lots of warnings about the BLAS libraries and source. I have
GotoBLAS2 installed in /usr/local/lib but it doesn't seem to find it.
Here is my site.cfg:
# Defaults
# ========
# The settings given here will apply to all other sections if not
overridden.
# This is a good place to add general library and include directories like
# /usr/local/{lib,include}
#
[DEFAULT]
library_dirs =
/usr/local/lib:/home/john/local/src/SuiteSparse-3.4.0/UMFPACK/Lib:/home/john/local/src/SuiteSparse-3.4.0/AMD/Lib
include_dirs =
/usr/local/include:/home/john/local/src/SuiteSparse-3.4.0/AMD/Include:/home/john/local/src/SuiteSparse-3.4.0/UMFPACK/Include
# Optimized BLAS and LAPACK
# -------------------------
# Use the blas_opt and lapack_opt sections to give any settings that are
# required to link against your chosen BLAS and LAPACK, including the
regular
# FORTRAN reference BLAS and also ATLAS. Some other sections still exist for
# linking against certain optimized libraries (e.g. [atlas],
[lapack_atlas]),
# however, they are now deprecated and should not be used.
#
# These are typical configurations for ATLAS (assuming that the library and
# include directories have already been set in [DEFAULT]; the include
directory
# is important for the BLAS C interface):
#
[blas_opt]
libraries = goto2_penrynp-r1.13
#
[lapack_opt]
libraries = goto2_penrynp-r1.13
#
# If your ATLAS was compiled with pthreads, the names of the libraries
might be
# different:
#
#[blas_opt]
#libraries = ptf77blas, ptcblas, atlas
#
#[lapack_opt]
#libraries = lapack, ptf77blas, ptcblas, atlas
# UMFPACK
# -------
# The UMFPACK library is used to factor large sparse matrices. It, in turn,
# depends on the AMD library for reordering the matrices for better
performance.
# Note that the AMD library has nothing to do with AMD (Advanced Micro
Devices),
# the CPU company.
#
# http://www.cise.ufl.edu/research/sparse/umfpack/
# http://www.cise.ufl.edu/research/sparse/amd/
#
#[amd]
amd_libs = amd
#
#[umfpack]
umfpack_libs = umfpack
and here are the errors from "python2.5 setup.py build" for scipy:
Warning: No configuration returned, assuming unavailable.blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in /usr/local/lib
libraries mkl,vml,guide not found in
/home/john/local/src/SuiteSparse-3.4.0/UMFPACK/Lib
libraries mkl,vml,guide not found in
/home/john/local/src/SuiteSparse-3.4.0/AMD/Lib
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in
/home/john/local/src/SuiteSparse-3.4.0/UMFPACK/Lib
libraries ptf77blas,ptcblas,atlas not found in
/home/john/local/src/SuiteSparse-3.4.0/AMD/Lib
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries f77blas,cblas,atlas not found in
/home/john/local/src/SuiteSparse-3.4.0/UMFPACK/Lib
libraries f77blas,cblas,atlas not found in
/home/john/local/src/SuiteSparse-3.4.0/AMD/Lib
NOT AVAILABLE
/usr/lib/python2.5/site-packages/numpy/distutils/system_info.py:1399:
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
libraries blas not found in
/home/john/local/src/SuiteSparse-3.4.0/UMFPACK/Lib
libraries blas not found in
/home/john/local/src/SuiteSparse-3.4.0/AMD/Lib
NOT AVAILABLE
/usr/lib/python2.5/site-packages/numpy/distutils/system_info.py:1408:
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/lib/python2.5/site-packages/numpy/distutils/system_info.py:1411:
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 160, in <module>
setup_package()
File "setup.py", line 152, in setup_package
configuration=configuration )
File "/usr/lib/python2.5/site-packages/numpy/distutils/core.py", line
152, in setup
config = configuration()
File "setup.py", line 118, in configuration
config.add_subpackage('scipy')
File "/usr/lib/python2.5/site-packages/numpy/distutils/misc_util.py",
line 972, in add_subpackage
caller_level = 2)
File "/usr/lib/python2.5/site-packages/numpy/distutils/misc_util.py",
line 941, in get_subpackage
caller_level = caller_level + 1)
File "/usr/lib/python2.5/site-packages/numpy/distutils/misc_util.py",
line 878, 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/lib/python2.5/site-packages/numpy/distutils/misc_util.py",
line 972, in add_subpackage
caller_level = 2)
File "/usr/lib/python2.5/site-packages/numpy/distutils/misc_util.py",
line 941, in get_subpackage
caller_level = caller_level + 1)
File "/usr/lib/python2.5/site-packages/numpy/distutils/misc_util.py",
line 878, 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/lib/python2.5/site-packages/numpy/distutils/system_info.py", line
310, in get_info
return cl().get_info(notfound_action)
File
"/usr/lib/python2.5/site-packages/numpy/distutils/system_info.py", line
461, 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.
Can anyone tell me what I'm doing wrong?
Thanks,
John.
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