[SciPy-User] site.cfg problems : scipy can't find BLAS

John Reid j.reid@mail.cryst.bbk.ac...
Thu Apr 8 07:38:11 CDT 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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