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

[François Bissey]

It looks like one of my messages didn't make it to the list but that one did:
http://article.gmane.org/gmane.linux.gentoo.science/2148

My final opinion on the matter looking at your site.cfg is that you don't have
a blas eselected at all and that's not a valid configuration.
eselect blas list
will tell you all the implementation of blas available choose the one
that match your current lapack one.

Francois

On Sun, 15 Jun 2014 23:20:30 Bastian Löffler wrote:
> I did. I posted site.cfg an regarding numpy: Installing this was some
> time ago. Its an scipy update making trouble.
>
> Regards Bastian
>
> Am 15.06.2014 23:13, schrieb François Bissey:
> > You obviously didn't read my last two emails.
> >
> > Francois
> >
> > On Sun, 15 Jun 2014 16:22:43 Bastian Löffler wrote:
> >> I still have this problem when updating to scipy-0.14.0. Ideas?
> >>
> >> Am 09.06.2014 20:41, schrieb Bastian Löffler:
> >>> 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/sit
> >>>>> e.
> >>>>> cfg
> >>>>> 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:151
> >>>>>> 1:
> >>>>>>
> >>>>>> 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:152
> >>>>>> 0:
> >>>>>>
> >>>>>> 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:152
> >>>>>> 3:
> >>>>>>
> >>>>>> 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: