[SciPy-User] scipy test error: undefined symbol: ATL_buildinfo

[Ralf Gommers]

On Sat, May 19, 2012 at 12:46 AM, Sergio Rojas <sergio_r at mail.com> wrote:

>
> Hello guys,
>
> After struggling for a while, I just finished the installation
> of scipy using the intel mkl library.
>
> Ungracefully the tests ended with an error regarding
> "undefined symbol: ATL_buildinfo" (see below)


> Can this scipy installation live with this error? or
> Is it  prone to throw out wrong computations?
>

The only failure is a check of the ATLAS version, that shouldn't yield
incorrect results.


> Also, why the number of ran test is not a fix number
>

Not sure. Perhaps nose isn't counting the one ATLAS test when it passes,
due to that file not having any actual tests in it.


> (running the tests using a scipy/Atlas installation
> finished succesfully indicating: Ran 5832 tests in 422.155s
> OK (KNOWNFAIL=14, SKIP=42), but the scipy/mkl tests ended with
> Ran 5833 tests in 448.386s FAILED (KNOWNFAIL=14, SKIP=34, errors=1))?
>
> what is the meaning of KNOWNFAIL=14?
>

Knownfail indicates tests that are known to fail under some conditions
(usually hardware/compiler dependent), so they aren't reported as new
errors/failures. If we wouldn't do this, we would keep getting the same bug
reports over and over again.

Ralf



> Sergio
>
> >$ python_mkl
> Python 2.7.2 (default, May 16 2012, 13:06:17)
> [GCC 4.6.1] on linux3
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scipy
> >>> scipy.show_config()
> umfpack_info:
>   NOT AVAILABLE
> lapack_opt_info:
>     libraries = ['mkl_lapack95_ilp64', 'mkl_lapack95_lp64', 'mkl_rt',
> 'mkl_intel
> _lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
>     library_dirs =
> ['/home/srojas/myPROG/IntelC/composer_xe_2011_sp1.7.256/mkl/l
> ib/intel64']
>     define_macros = [('SCIPY_MKL_H', None)]
>     include_dirs =
> ['/home/srojas/myPROG/IntelC/composer_xe_2011_sp1.7.256/mkl/i
> nclude']
> blas_opt_info:
>     libraries = ['mkl_rt', 'mkl_intel_lp64', 'mkl_intel_thread',
> 'mkl_core', 'pt
> hread']
>     library_dirs =
> ['/home/srojas/myPROG/IntelC/composer_xe_2011_sp1.7.256/mkl/l
> ib/intel64']
>     define_macros = [('SCIPY_MKL_H', None)]
>     include_dirs =
> ['/home/srojas/myPROG/IntelC/composer_xe_2011_sp1.7.256/mkl/i
> nclude']
> lapack_mkl_info:
>     libraries = ['mkl_lapack95_ilp64', 'mkl_lapack95_lp64', 'mkl_rt',
> 'mkl_intel
> _lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
>     library_dirs =
> ['/home/srojas/myPROG/IntelC/composer_xe_2011_sp1.7.256/mkl/l
> ib/intel64']
>     define_macros = [('SCIPY_MKL_H', None)]
>     include_dirs =
> ['/home/srojas/myPROG/IntelC/composer_xe_2011_sp1.7.256/mkl/i
> nclude']
> blas_mkl_info:
>     libraries = ['mkl_rt', 'mkl_intel_lp64', 'mkl_intel_thread',
> 'mkl_core', 'pt
> hread']
>     library_dirs =
> ['/home/srojas/myPROG/IntelC/composer_xe_2011_sp1.7.256/mkl/l
> ib/intel64']
>     define_macros = [('SCIPY_MKL_H', None)]
>     include_dirs =
> ['/home/srojas/myPROG/IntelC/composer_xe_2011_sp1.7.256/mkl/i
> nclude']
> mkl_info:
>     libraries = ['mkl_rt', 'mkl_intel_lp64', 'mkl_intel_thread',
> 'mkl_core', 'pt
> hread']
>     library_dirs =
> ['/home/srojas/myPROG/IntelC/composer_xe_2011_sp1.7.256/mkl/l
> ib/intel64']
>     define_macros = [('SCIPY_MKL_H', None)]
>     include_dirs =
> ['/home/srojas/myPROG/IntelC/composer_xe_2011_sp1.7.256/mkl/i
> nclude']
> >>> scipy.test('full', verbose=2)
> Running unit tests for scipy
> NumPy version 1.6.1
> NumPy is installed in
> /home/srojas/myPROG/Python272GnuMKL/lib/python2.7/site-pac
> kages/numpy
> SciPy version 0.10.1
> SciPy is installed in
> /home/srojas/myPROG/Python272GnuMKL/lib/python2.7/site-pac
> kages/scipy
> Python version 2.7.2 (default, May 16 2012, 13:06:17) [GCC 4.6.1]
> nose version 1.1.2
> ...
> ... (DELETED OUTPUT)
> ...
> ======================================================================
> ERROR: Failure: ImportError
> (/home/srojas/myPROG/Python272GnuMKL/lib/python2.7/s
> ite-packages/scipy/linalg/atlas_version.so: undefined symbol:
> ATL_buildinfo)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/home/srojas/myPROG/Python272GnuMKL/lib/python2.7/site-packages/nose/loa
> der.py", line 390, in loadTestsFromName
>     addr.filename, addr.module)
>   File
> "/home/srojas/myPROG/Python272GnuMKL/lib/python2.7/site-packages/nose/imp
> orter.py", line 39, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File
> "/home/srojas/myPROG/Python272GnuMKL/lib/python2.7/site-packages/nose/imp
> orter.py", line 86, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File
> "/home/srojas/myPROG/Python272GnuMKL/lib/python2.7/site-packages/scipy/li
> nalg/tests/test_atlas_version.py", line 6, in <module>
>     import scipy.linalg.atlas_version
> ImportError:
> /home/srojas/myPROG/Python272GnuMKL/lib/python2.7/site-packages/sci
> py/linalg/atlas_version.so: undefined symbol: ATL_buildinfo
>
> ----------------------------------------------------------------------
> Ran 5833 tests in 448.386s
>
> FAILED (KNOWNFAIL=14, SKIP=34, errors=1)
> <nose.result.TextTestResult run=5833 errors=1 failures=0>
>
>
> _______________________________________________
> SciPy-User mailing list
> SciPy-User at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-user
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20120520/f6541361/attachment.html>