Re: [gentoo-science] Trouble building scipy-0.14.0 against acml

[François Bissey]

I just checked the acml ebuild and it looks like it does the right thing.
Can you give me the output of the following commands:
eselect blas list
pkg-config --libs-only-L blas
cat /usr/lib64/pkgconfig/blas.pc
ls -la /usr/lib64/pkgconfig/blas.pc

Francois 

On Tue, 10 Jun 2014 09:33:37 François Bissey wrote:
> OK, thanks for the file. I think it is a bug in the pkgconfig file for
> blas with acml. You should also have
> library_dirs = //opt/acml5.3.1/gfortran64/lib:/usr/lib64
> in the blas section, not just in the lapack one. Do you have a
> Gentoo bugzilla account? If not I'll fill the report.
>
> Francois
>
> On Mon, 09 Jun 2014 20:41:35 Bastian Löffler wrote:
> > Hi,
> >
> > this is
> >
> > /var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python2_7/site.cf
> > g:
> >
> > [blas]
> > include_dirs =
> > library_dirs = :/usr/lib64
> > blas_libs =
> > [lapack]
> > library_dirs = //opt/acml5.3.1/gfortran64/lib:/usr/lib64
> > lapack_libs = acml
> >
> > Buliding numpy is ago. This is any scipy update.
> >
> > Am 09.06.2014 13:51, schrieb François Bissey:
> > > numpy not bumpy. Sorry for the noise.
> > >
> > > On 9/06/2014, at 23:42, François Bissey <frp.bissey@×××××.com> wrote:
> > >> Hi,
> > >>
> > >> Could you post the file:
> > >> /var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python2_7/site
> > >> .c
> > >> fg
> > >> for our perusal? You obviously managed to merge bumpy which
> > >> fundamentally
> > >> should have the exact same problem.
> > >> Was it just before scipy or a while ago?
> > >>
> > >> François
> > >>
> > >> On 9/06/2014, at 23:25, Bastian Löffler <Bastian_Loeffler@×××××.de>
>
> wrote:
> > >>> Hi all,
> > >>>
> > >>> I can not build scipy 0.14.0 agaonst the currenct aclm since it
> > >>> complains a missing blas:
> > >>>
> > >>> 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.
> > >>>
> > >>> * ERROR: sci-libs/scipy-0.14.0::gentoo failed (compile phase):
> > >>> *   (no error message)
> > >>> *
> > >>> * Call stack:
> > >>> *     ebuild.sh, line   93:  Called src_compile
> > >>> *   environment, line 4075:  Called distutils-r1_src_compile
> > >>> *   environment, line 1421:  Called _distutils-r1_run_foreach_impl
> > >>> 'python_compile'
> > >>> *   environment, line  312:  Called python_parallel_foreach_impl
> > >>> 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line 3808:  Called
> > >>> multibuild_parallel_foreach_variant
> > >>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line 2855:  Called multibuild_foreach_variant
> > >>> '_multibuild_parallel' '_python_multibuild_wrapper'
> > >>> 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line 2798:  Called _multibuild_run
> > >>> '_multibuild_parallel' '_python_multibuild_wrapper'
> > >>> 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line 2796:  Called _multibuild_parallel
> > >>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line 2846:  Called _python_multibuild_wrapper
> > >>> 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line  914:  Called distutils-r1_run_phase
> > >>> 'python_compile'
> > >>> *   environment, line 1412:  Called python_compile
> > >>> *   environment, line 3315:  Called distutils-r1_python_compile
> > >>> 'config_fc' '--noopt' '--noarch'
> > >>> *   environment, line 1292:  Called esetup.py 'build' 'config_fc'
> > >>> '--noopt' '--noarch'
> > >>> *   environment, line 1862:  Called die
> > >>> * The specific snippet of code:
> > >>> *       "${@}" || die
> > >>> *
> > >>> * If you need support, post the output of `emerge --info
> > >>> '=sci-libs/scipy-0.14.0::gentoo'`,
> > >>> * the complete build log and the output of `emerge -pqv
> > >>> '=sci-libs/scipy-0.14.0::gentoo'`.
> > >>> * The complete build log is located at
> > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/build.log'.
> > >>> * The ebuild environment file is located at
> > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/environment'.
> > >>> * Working directory:
> > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python2_7'
> > >>> * S: '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0'
> > >>> /usr/lib64/portage/bin/isolated-functions.sh: line 226: kill: (6675) -
> > >>> No such process
> > >>> blas_opt_info:
> > >>>
> > >>> system_info:
> > >>>  NOT AVAILABLE
> > >>>
> > >>> blas_info:
> > >>>  libraries  not found in ['/usr/lib64']
> > >>>  NOT AVAILABLE
> > >>>
> > >>> blas_src_info:
> > >>>  NOT AVAILABLE
> > >>>
> > >>> /usr/lib64/python3.3/distutils/dist.py:258: UserWarning: Unknown
> > >>> distribution option: 'test_suite'
> > >>>
> > >>>  warnings.warn(msg)
> > >>>
> > >>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:1511
> > >>> :
> > >>>
> > >>> 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__)
> > >>>
> > >>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:566:
> > >>> UserWarning: Specified path  is invalid.
> > >>>
> > >>>  warnings.warn('Specified path %s is invalid.' % d)
> > >>>
> > >>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:1520
> > >>> :
> > >>>
> > >>> 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__)
> > >>>
> > >>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:1523
> > >>> :
> > >>>
> > >>> 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 237, in <module>
> > >>>
> > >>>    setup_package()
> > >>>
> > >>>  File "setup.py", line 234, in setup_package
> > >>>
> > >>>    setup(**metadata)
> > >>>
> > >>>  File "/usr/lib64/python3.3/site-packages/numpy/distutils/core.py",
> > >>>
> > >>> line 135, in setup
> > >>>
> > >>>    config = configuration()
> > >>>
> > >>>  File "setup.py", line 173, in configuration
> > >>>
> > >>>    config.add_subpackage('scipy')
> > >>>
> > >>>  File
> > >>>
> > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py",
> > >>> line
> > >>> 966, in add_subpackage
> > >>>
> > >>>    caller_level = 2)
> > >>>
> > >>>  File
> > >>>
> > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py",
> > >>> line
> > >>> 935, in get_subpackage
> > >>>
> > >>>    caller_level = caller_level + 1)
> > >>>
> > >>>  File
> > >>>
> > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py",
> > >>> line
> > >>> 872, in _get_configuration_from_setup_py
> > >>>
> > >>>    config = setup_module.configuration(*args)
> > >>>
> > >>>  File "scipy/setup.py", line 12, in configuration
> > >>>
> > >>>    config.add_subpackage('integrate')
> > >>>
> > >>>  File
> > >>>
> > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py",
> > >>> line
> > >>> 966, in add_subpackage
> > >>>
> > >>>    caller_level = 2)
> > >>>
> > >>>  File
> > >>>
> > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py",
> > >>> line
> > >>> 935, in get_subpackage
> > >>>
> > >>>    caller_level = caller_level + 1)
> > >>>
> > >>>  File
> > >>>
> > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py",
> > >>> line
> > >>> 872, in _get_configuration_from_setup_py
> > >>>
> > >>>    config = setup_module.configuration(*args)
> > >>>
> > >>>  File "scipy/integrate/setup.py", line 12, in configuration
> > >>>
> > >>>    blas_opt = get_info('blas_opt',notfound_action=2)
> > >>>
> > >>>  File
> > >>>
> > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py",
> > >>> line 340, in get_info
> > >>>
> > >>>    return cl().get_info(notfound_action)
> > >>>
> > >>>  File
> > >>>
> > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py",
> > >>> line 499, 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.
> > >>>
> > >>> * ERROR: sci-libs/scipy-0.14.0::gentoo failed (compile phase):
> > >>> *   (no error message)
> > >>> *
> > >>> * Call stack:
> > >>> *     ebuild.sh, line   93:  Called src_compile
> > >>> *   environment, line 4075:  Called distutils-r1_src_compile
> > >>> *   environment, line 1421:  Called _distutils-r1_run_foreach_impl
> > >>> 'python_compile'
> > >>> *   environment, line  312:  Called python_parallel_foreach_impl
> > >>> 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line 3808:  Called
> > >>> multibuild_parallel_foreach_variant
> > >>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line 2855:  Called multibuild_foreach_variant
> > >>> '_multibuild_parallel' '_python_multibuild_wrapper'
> > >>> 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line 2798:  Called _multibuild_run
> > >>> '_multibuild_parallel' '_python_multibuild_wrapper'
> > >>> 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line 2796:  Called _multibuild_parallel
> > >>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line 2846:  Called _python_multibuild_wrapper
> > >>> 'distutils-r1_run_phase' 'python_compile'
> > >>> *   environment, line  914:  Called distutils-r1_run_phase
> > >>> 'python_compile'
> > >>> *   environment, line 1412:  Called python_compile
> > >>> *   environment, line 3315:  Called distutils-r1_python_compile
> > >>> 'config_fc' '--noopt' '--noarch'
> > >>> *   environment, line 1292:  Called esetup.py 'build' 'config_fc'
> > >>> '--noopt' '--noarch'
> > >>> *   environment, line 1862:  Called die
> > >>> * The specific snippet of code:
> > >>> *       "${@}" || die
> > >>> *
> > >>> * If you need support, post the output of `emerge --info
> > >>> '=sci-libs/scipy-0.14.0::gentoo'`,
> > >>> * the complete build log and the output of `emerge -pqv
> > >>> '=sci-libs/scipy-0.14.0::gentoo'`.
> > >>> * The complete build log is located at
> > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/build.log'.
> > >>> * The ebuild environment file is located at
> > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/environment'.
> > >>> * Working directory:
> > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python3_3'
> > >>> * S: '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0'
> > >>> /usr/lib64/portage/bin/isolated-functions.sh: line 226: kill: (6675) -
> > >>> No such process
> > >>>
> > >>>>>> Failed to emerge sci-libs/scipy-0.14.0, Log file: