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SciPy ebuild broke for latest MKL?
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lednakashim
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Joined: 09 Jun 2010
Posts: 27
PostPosted: Thu Dec 12, 2013 5:18 am    Post subject: SciPy ebuild broke for latest MKL? Reply with quote
Hi,
I installed a copy of MKL, re-emerged the virtual packages for BLAS and set my eselect to the Intel packages. Now I got this error when trying to rebuild SciPy. Anybody know what to do?

Quote:

 * Package: sci-libs/scipy-0.13.1-r2
 * Repository: gentoo
 * Maintainer: sci@gentoo.org
 * USE: amd64 elibc_glibc kernel_linux python_targets_python2_7 python_targets_python3_3 userland_GNU
 * FEATURES: preserve-libs sandbox userpriv usersandbox
* Using following Fortran compiler:
* F77: x86_64-pc-linux-gnu-gfortran
* FC: x86_64-pc-linux-gnu-gfortran
>>> Unpacking source...
>>> Unpacking scipy-0.13.1.tar.gz to /var/tmp/portage/sci-libs/scipy-0.13.1-r2/work
>>> Source unpacked in /var/tmp/portage/sci-libs/scipy-0.13.1-r2/work
>>> Preparing source in /var/tmp/portage/sci-libs/scipy-0.13.1-r2/work/scipy-0.13.1 ...
* Applying scipy-0.12.0-blitz.patch ...
 [ ok ]
* Applying scipy-0.12.0-restore-sys-argv.patch ...
 [ ok ]
* Applying scipy-0.12.0-cephes-missing-include.patch ...
 [ ok ]
* Will copy sources from /var/tmp/portage/sci-libs/scipy-0.13.1-r2/work/scipy-0.13.1
* python3_3: copying to /var/tmp/portage/sci-libs/scipy-0.13.1-r2/work/scipy-0.13.1-python3_3
* python2_7: copying to /var/tmp/portage/sci-libs/scipy-0.13.1-r2/work/scipy-0.13.1-python2_7
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-libs/scipy-0.13.1-r2/work/scipy-0.13.1 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-libs/scipy-0.13.1-r2/work/scipy-0.13.1 ...
* python3_3: running distutils-r1_run_phase python_compile
* python2_7: running distutils-r1_run_phase python_compile
Processing scipy/sparse/csgraph/_traversal.pyx
Processing scipy/sparse/csgraph/_shortest_path.pyx
Processing scipy/sparse/csgraph/_tools.pyx
Processing scipy/sparse/csgraph/_min_spanning_tree.pyx
Processing scipy/interpolate/interpnd.pyx
Processing scipy/signal/_spectral.pyx
Processing scipy/ndimage/src/_ni_label.pyx
Processing scipy/io/matlab/mio5_utils.pyx
Processing scipy/io/matlab/streams.pyx
Processing scipy/io/matlab/mio_utils.pyx
Processing scipy/spatial/ckdtree.pyx
Processing scipy/spatial/qhull.pyx
Processing scipy/special/_ufuncs_cxx.pyx
Processing scipy/special/_ufuncs.pyx
Processing scipy/cluster/_vq_rewrite.pyx
Processing scipy/stats/_rank.pyx
Processing scipy/stats/vonmises_cython.pyx
/usr/bin/python3.3 setup.py build config_fc --noopt --noarch
blas_opt_info:
system_info:
NOT AVAILABLE

blas_info:
libraries mkl_rt,iomp5,mkl_rt,iomp5 not found in ['/opt/intel/composerxe-2013.0.080/mkl/lib/intel64', '/opt/intel/composerxe-2013.0.080/compiler/lib/intel64', '/usr/lib64']
NOT AVAILABLE

blas_src_info:
NOT AVAILABLE

/usr/lib64/python3.3/distutils/dist.py:257: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
/usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:1512: 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:1521: 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:1524: 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 230, in <module>
setup_package()
File "setup.py", line 227, 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 170, 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-0.13.1-r2::gentoo failed (compile phase):
* (no error message)
*
* Call stack:
* ebuild.sh, line 93: Called src_compile
* environment, line 4307: Called distutils-r1_src_compile
* environment, line 1450: Called _distutils-r1_run_foreach_impl 'python_compile'
* environment, line 319: Called python_parallel_foreach_impl 'distutils-r1_run_phase' 'python_compile'
* environment, line 4044: Called multibuild_parallel_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
* environment, line 3229: Called multibuild_foreach_variant '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
* environment, line 3177: Called _multibuild_run '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
* environment, line 3175: Called _multibuild_parallel '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
* environment, line 3220: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile'
* environment, line 912: Called distutils-r1_run_phase 'python_compile'
* environment, line 1441: Called python_compile
* environment, line 3633: Called distutils-r1_python_compile 'config_fc' '--noopt' '--noarch'
* environment, line 1325: Called esetup.py 'build' 'config_fc' '--noopt' '--noarch'
* environment, line 2245: Called die
* The specific snippet of code:
* "${@}" || die
*
* If you need support, post the output of `emerge --info '=sci-libs/scipy-0.13.1-r2::gentoo'`,
* the complete build log and the output of `emerge -pqv '=sci-libs/scipy-0.13.1-r2::gentoo'`.
* The complete build log is located at '/var/tmp/portage/sci-libs/scipy-0.13.1-r2/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-0.13.1-r2/temp/environment'.
* Working directory: '/var/tmp/portage/sci-libs/scipy-0.13.1-r2/work/scipy-0.13.1-python3_3'
* S: '/var/tmp/portage/sci-libs/scipy-0.13.1-r2/work/scipy-0.13.1'
Processing scipy/sparse/csgraph/_traversal.pyx
Processing scipy/sparse/csgraph/_shortest_path.pyx
Processing scipy/sparse/csgraph/_tools.pyx
Processing scipy/sparse/csgraph/_min_spanning_tree.pyx
Processing scipy/interpolate/interpnd.pyx
Processing scipy/signal/_spectral.pyx
Processing scipy/ndimage/src/_ni_label.pyx
Processing scipy/io/matlab/mio5_utils.pyx
Processing scipy/io/matlab/streams.pyx
Processing scipy/io/matlab/mio_utils.pyx
Processing scipy/spatial/ckdtree.pyx
Processing scipy/spatial/qhull.pyx
Processing scipy/special/_ufuncs_cxx.pyx
Processing scipy/special/_ufuncs.pyx
Processing scipy/cluster/_vq_rewrite.pyx
Processing scipy/stats/_rank.pyx
Processing scipy/stats/vonmises_cython.pyx
/usr/bin/python2.7 setup.py build config_fc --noopt --noarch
/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
blas_opt_info:
system_info:
NOT AVAILABLE

/usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:1512: 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__)
blas_info:
libraries mkl_rt,iomp5,mkl_rt,iomp5 not found in ['/opt/intel/composerxe-2013.0.080/mkl/lib/intel64', '/opt/intel/composerxe-2013.0.080/compiler/lib/intel64', '/usr/lib64']
NOT AVAILABLE

/usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:1521: 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__)
blas_src_info:
NOT AVAILABLE

/usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:1524: 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 230, in <module>
setup_package()
File "setup.py", line 227, in setup_package
setup(**metadata)
File "/usr/lib64/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup
config = configuration()
File "setup.py", line 170, in configuration
config.add_subpackage('scipy')
File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/usr/lib64/python2.7/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/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/usr/lib64/python2.7/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/python2.7/site-packages/numpy/distutils/system_info.py", line 340, in get_info
return cl().get_info(notfound_action)
File "/usr/lib64/python2.7/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-0.13.1-r2::gentoo failed (compile phase):
* (no error message)
*
* Call stack:
* ebuild.sh, line 93: Called src_compile
* environment, line 4307: Called distutils-r1_src_compile
* environment, line 1450: Called _distutils-r1_run_foreach_impl 'python_compile'
* environment, line 319: Called python_parallel_foreach_impl 'distutils-r1_run_phase' 'python_compile'
* environment, line 4044: Called multibuild_parallel_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
* environment, line 3229: Called multibuild_foreach_variant '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
* environment, line 3177: Called _multibuild_run '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
* environment, line 3175: Called _multibuild_parallel '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
* environment, line 3220: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile'
* environment, line 912: Called distutils-r1_run_phase 'python_compile'
* environment, line 1441: Called python_compile
* environment, line 3633: Called distutils-r1_python_compile 'config_fc' '--noopt' '--noarch'
* environment, line 1325: Called esetup.py 'build' 'config_fc' '--noopt' '--noarch'
* environment, line 2245: Called die
* The specific snippet of code:
* "${@}" || die
*
* If you need support, post the output of `emerge --info '=sci-libs/scipy-0.13.1-r2::gentoo'`,
* the complete build log and the output of `emerge -pqv '=sci-libs/scipy-0.13.1-r2::gentoo'`.
* The complete build log is located at '/var/tmp/portage/sci-libs/scipy-0.13.1-r2/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-0.13.1-r2/temp/environment'.
* Working directory: '/var/tmp/portage/sci-libs/scipy-0.13.1-r2/work/scipy-0.13.1-python2_7'
* S: '/var/tmp/portage/sci-libs/scipy-0.13.1-r2/work/scipy-0.13.1'
>>> Source compiled.



And

Code:
emerge -pqv =sci-libs/scipy-0.13.1-r2::gentoo
[ebuild   R   ] sci-libs/scipy-0.13.1-r2  USE="-doc -sparse {-test}" PYT


Obvious question is if the libraries are there.
Quote:

libmkl_avx2.so libmkl_intel_lp64.a
libmkl_avx.so libmkl_intel_lp64.so
libmkl_blacs_ilp64.a libmkl_intel_thread.a
libmkl_blacs_intelmpi_ilp64.a libmkl_intel_thread.so
libmkl_blacs_intelmpi_ilp64.so libmkl_lapack95_ilp64.a
libmkl_blacs_intelmpi_lp64.a libmkl_lapack95_lp64.a
libmkl_blacs_intelmpi_lp64.so libmkl_mc3.so
libmkl_blacs_lp64.a libmkl_mc.so
libmkl_blacs_openmpi_ilp64.a libmkl_p4n.so
libmkl_blacs_openmpi_lp64.a libmkl_pgi_thread.a
libmkl_blacs_sgimpt_ilp64.a libmkl_pgi_thread.so
libmkl_blacs_sgimpt_lp64.a libmkl_rt.so
libmkl_blas95_ilp64.a libmkl_scalapack_ilp64.a
libmkl_blas95_lp64.a libmkl_scalapack_ilp64.so
libmkl_cdft_core.a libmkl_scalapack_lp64.a
libmkl_cdft_core.so libmkl_scalapack_lp64.so
libmkl_core.a libmkl_sequential.a
libmkl_core.so libmkl_sequential.so
libmkl_def.so libmkl_vml_avx2.so
libmkl_gf_ilp64.a libmkl_vml_avx.so
libmkl_gf_ilp64.so libmkl_vml_cmpt.so
libmkl_gf_lp64.a libmkl_vml_def.so
libmkl_gf_lp64.so libmkl_vml_mc2.so
libmkl_gnu_thread.a libmkl_vml_mc3.so
libmkl_gnu_thread.so libmkl_vml_mc.so
libmkl_intel_ilp64.a libmkl_vml_p4n.so
libmkl_intel_ilp64.so locale


So, the two libraries it is looking for are in the right directories, I can only assume something is broken with the script that locates them?

Later, following Intel's MKL numpy guide, I set my configuration to
Quote:
[blas]
include_dirs = /opt/intel/composerxe-2013.0.080/mkl/include
library_dirs = /opt/intel/composerxe-2013.0.080/mkl/lib/intel64
blas_libs = mkl_rt,iomp5#,mkl_rt,iomp5
[lapack]
library_dirs = /opt/intel/composerxe-2013.0.080/mkl/lib/intel64
lapack_libs = mkl_rt,iomp5
[mkl]
library_dirs = /opt/intel/composerxe-2013.0.080/mkl/lib/intel64
include_dirs = /opt/intel/composerxe-2013.0.080/mkl/include
mkl_libs = mkl_intel_lp64,mkl_intel_thread,mkl_core
lapack_libs =
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