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

[Bastian Löffler]

Well of course i checked that:

eselect blas list
Available providers for blas:
  [1]   acml-gfortran64 *
  [2]   acml-gfortran64-openmp
  [3]   eigen
  [4]   reference

SO my blas is acml-gfortran64.


Am 15.06.2014 23:27, schrieb 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:
>
>