[SciPy-user] numpy installer not finding ATLAS in spite of correct environment variable

[Anand Patil]

Hi all,

I'm trying to install numpy on a machine in which 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4 contains:

libatlas.a  libcblas.a  liblapack.a  libptcblas.a  libtstatlas.a  
Makefile  Make.inc

I've set the relevant environment variables as follows:

setenv ATLAS /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
setenv BLAS /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
setenv LAPACK /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
setenv BLAS_SRC /usr/local/atlas/src/blas
setenv LAPACK_SRC /usr/local/atlas/src/lapack

However, numpy's installer does this:

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack,blas not found in 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries lapack,blas not found in /usr/local/lib
  libraries lapack,blas not found in /usr/lib/sse2
  libraries lapack,blas not found in /usr/lib
  NOT AVAILABLE

atlas_blas_info:
  libraries lapack,blas not found in 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries lapack,blas not found in /usr/local/lib
  libraries lapack,blas not found in /usr/lib/sse2
  libraries lapack,blas not found in /usr/lib
  NOT AVAILABLE

/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1301: 
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/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries blas not found in /usr/local/lib
  libraries blas not found in /usr/lib
  NOT AVAILABLE

/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1310: 
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

/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1313: 
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

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack,blas not found in 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries lapack_atlas not found in 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries lapack,blas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries lapack,blas not found in /usr/lib/sse2
  libraries lapack_atlas not found in /usr/lib/sse2
  libraries lapack,blas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_threads_info
  NOT AVAILABLE

atlas_info:
  libraries lapack,blas not found in 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries lapack_atlas not found in 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries lapack,blas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries lapack,blas not found in /usr/lib/sse2
  libraries lapack_atlas not found in /usr/lib/sse2
  libraries lapack,blas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_info
  NOT AVAILABLE

/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1210: 
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__)
lapack_info:
  FOUND:
    libraries = ['lapack']
    library_dirs = ['/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/']
    language = f77

/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1234: 
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__)
/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1237: 
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

Then, even though it apparently found lapack, it builds lapack_lite:

gcc: numpy/linalg/dlamch.c
gcc: numpy/linalg/lapack_litemodule.c
gcc: numpy/linalg/zlapack_lite.c
gcc: numpy/linalg/dlapack_lite.c
gcc: numpy/linalg/blas_lite.c
gcc: numpy/linalg/f2c_lite.c

What am I doing wrong?

Thanks much,
Anand