scipy test error: undefined symbol: ATL_buildinfo
$ 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:
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? Also, why the number of ran test is not a fix number (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? Sergio 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>
On Sat, May 19, 2012 at 12:46 AM, Sergio Rojas <sergio_r@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
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
$ 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. 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>
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participants (2)
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Ralf Gommers -
Sergio Rojas