[SciPy-dev] newcore build problem on Ubuntu / Debian

[Stephen Walton]

Ed Schofield wrote:

>Hi all,
>
>SciPy core fails to find ATLAS or LAPACK libraries with Ubuntu's (and
>Debian's?) default installation.
>  
>
I have the following packages installed on my Athlon laptop (just 
updated to Ubuntu 5.10):

atlas3-base, atlas3-base-dev, atlas3-headers, atlas3-sse, atlas3-sse-dev

The lapack packages do not seem to be needed with this setup.  However, 
the *-dev packages are needed so that you have the *.a libraries in 
addition to the *.so so that linking works.

Having said that, there may other issues.  Attached to the end of this 
is the first part of the output I get when I build newcore.  Notice that 
atlas_blas_info finds the versions in /usr/lib/sse, but 
scipy.distutils.system_info.atlas_info seems to find the versions in 
/usr/lib.  In addition, it seems to think the version of ATLAS I have is 
3.5.19 although "dpkg -p atlas3-base" and so on say that it is version 
3.6.0.  Further down in the file (not shown here) shows that _dotblas.so 
is linked using -L/usr/lib/sse on the command line, while lapack_lite.so 
is linked with -L/usr/lib/atlas.   If I remove atlas3-base and 
atlas3-base-dev, lapack_lite.so is not linked with ATLAS at all, because 
it reports that we have ATLAS but not LAPACK libraries.

atlas_blas_info:
  FOUND:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib/sse']
    language = c

running build_src
building extension "atlas_version" sources
creating build
creating build/src
  adding 'build/src/atlas_version_-0x7408d8b6.c' to sources.
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'atlas_version' extension
compiling C sources
gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall 
-Wstrict-prototypes -fPIC'
creating build/temp.linux-i686-2.4
creating build/temp.linux-i686-2.4/build
creating build/temp.linux-i686-2.4/build/src
compile options: '-Iscipy/base/include -I/usr/include/python2.4 -c'
gcc: build/src/atlas_version_-0x7408d8b6.c
gcc -pthread -shared 
build/temp.linux-i686-2.4/build/src/atlas_version_-0x7408d8b6.o 
-L/usr/lib/sse -lf77blas -lcblas -latlas -o 
build/temp.linux-i686-2.4/atlas_version.so
  FOUND:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib/sse']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.5.19\\""')]

lapack_opt_info:
atlas_threads_info:
Setting PTATLAS=ATLAS
scipy.distutils.system_info.atlas_threads_info
  NOT AVAILABLE

atlas_info:
scipy.distutils.system_info.atlas_info
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib/atlas', '/usr/lib']
    language = f77

running build_src
building extension "atlas_version" sources
  adding 'build/src/atlas_version_0x3bb31a54.c' to sources.
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using build_ext
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib/atlas', '/usr/lib']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.5.19\\""')]