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

["François Bissey" <frp.bissey@gmail.com>]

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.cfg:
> 
> [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@gmail.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@arcor.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: