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

[Bastian Löffler]

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/site.
>>>>> 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: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:
>
>