MKL and NumPy incompatibility (test fails)

rex — Mon, 19 May 2008 00:02:00 GMT

Numpy svn 1.1.0rc1 compiles w/o error with MKL 10.0.3.020, but the normal test fails. The identical failure has been reported by another user who is using the lib/em64t library. I'm using lib/32. Any pointers as to what may be going on would be much appreciated. Relevant data are below. Thanks.

Numpy was compiled with the command:

python setup.py config build_clib build_ext install --prefix=/usr/local > build.log

# python
Python 2.5 (release25-maint, Dec 9 2006, 14:35:53)
[GCC 4.1.2 20061115 (prerelease) (Debian 4.1.1-20)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.test()
Numpy is installed in /usr/local/lib/python2.5/site-packages/numpy
Numpy version 1.1.0rc1
Python version 2.5 (release25-maint, Dec 9 2006, 14:35:53) [GCC 4.1.2 20061115 (prerelease) (Debian 4.1.1-20)]
Found 18/18 tests for numpy.core.defmatrix
Found 3/3 tests for numpy.core.memmap
Found 283/283 tests for numpy.core.multiarray
Found 70/70 tests for numpy.core.numeric
Found 36/36 tests for numpy.core.numerictypes
Found 12/12 tests for numpy.core.records
Found 7/7 tests for numpy.core.scalarmath
Found 16/16 tests for numpy.core.umath
Found 5/5 tests for numpy.ctypeslib
Found 5/5 tests for numpy.distutils.misc_util
Found 2/2 tests for numpy.fft.fftpack
Found 3/3 tests for numpy.fft.helper
Found 24/24 tests for numpy.lib._datasource
Found 10/10 tests for numpy.lib.arraysetops
Found 1/1 tests for numpy.lib.financial
Found 0/0 tests for numpy.lib.format
Found 53/53 tests for numpy.lib.function_base
Found 5/5 tests for numpy.lib.getlimits
Found 6/6 tests for numpy.lib.index_tricks
Found 15/15 tests for numpy.lib.io
Found 1/1 tests for numpy.lib.machar
Found 4/4 tests for numpy.lib.polynomial
Found 49/49 tests for numpy.lib.shape_base
Found 15/15 tests for numpy.lib.twodim_base
Found 43/43 tests for numpy.lib.type_check
Found 1/1 tests for numpy.lib.ufunclike
Found 89/89 tests for numpy.linalg
Found 94/94 tests for numpy.ma.core
Found 15/15 tests for numpy.ma.extras
Found 7/7 tests for numpy.random
Found 16/16 tests for numpy.testing.utils
Found 0/0 tests for __main__
MKL FATAL ERROR: /opt/intel/mkl/10.0.3.020/lib/32/: cannot read file data: Is a directory

I have been unable to determine what file MKL is attemping to read.

The error occurs with both icc and gcc. The relevant .bashrc calls are these:

source /opt/intel/cc/10.1.015/bin/iccvars.sh
source /opt/intel/fc/10.1.015/bin/ifortvars.sh
export PYTHONPATH=/usr/local/lib/python2.5/site-packages:/usr/lib/python2.5
source /opt/intel/mkl/10.0.3.020/tools/environment/mklvars32.sh

The relevant environment variables set by the above are:

CPATH=/opt/intel/mkl/10.0.3.020/include
DYLD_LIBRARY_PATH=/opt/intel/fc/10.1.015/lib:/opt/intel/cc/10.1.015/lib
FPATH=/opt/intel/mkl/10.0.3.020/include
INCLUDE=/opt/intel/mkl/10.0.3.020/include
LD_LIBRARY_PATH=/opt/intel/mkl/10.0.3.020/lib/32:/opt/intel/fc/10.1.015/lib:/opt/intel/cc/10.1.015/lib
LIBRARY_PATH=/opt/intel/mkl/10.0.3.020/lib/32
MKLROOT=/opt/intel/mkl/10. 0.3.020
PYTHONPATH=/usr/local/lib/python2.5/site-packages:/usr/lib/python2.5

When Numpy is compiled w/o MKL it passes the tests:

$python
Python 2.5 (release25-maint, Dec 9 2006, 14:35:53)
[GCC 4.1.2 20061115 (prerelease) (Debian 4.1.1-20)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.test()
Numpy is installed in /usr/local/lib/python2.5/site-packages/numpy
Numpy version 1.1.0rc1
Python version 2.5 (release25-maint, Dec 9 2006, 14:35:53) [GCC 4.1.2 20061115 (prerelease) (Debian 4.1.1-20)]
Found 18/18 tests for numpy.core.defmatrix
Found 3/3 tests for numpy.core.memmap
Found 283/283 tests for numpy.core.multiarray
Found 70/70 tests for numpy.core.numeric
Found 36/36 tests for numpy.core.numerictypes
Found 12/12 tests for numpy.core.records
Found 7/7 tests for numpy.core.scalarmath
Found 16/16 tests for numpy.core.umath
Found 5/5 tests for numpy.ctypeslib
Found 5/5 tests for numpy.distutils.misc_util
Found 2/2 tests for numpy.fft.fftpack
Found 3/3 tests for numpy.fft.helper
Found 24/24 tests for numpy.lib._datasource
Found 10/10 tests for numpy.lib.arraysetops
Found 1/1 tests for numpy.lib.financial
Found 0/0 tests for numpy.lib.format
Found 53/53 tests for numpy.lib.function_base
Found 5/5 tests for numpy.lib.getlimits
Found 6/6 tests for numpy.lib.index_tricks
Found 15/15 tests for numpy.lib.io
Found 1/1 tests for numpy.lib.machar
Found 4/4 tests for numpy.lib.polynomial
Found 49/49 tests for numpy.lib.shape_base
Found 15/15 tests for numpy.lib.twodim_base
Found 43/43 tests for numpy.lib.type_check
Found 1/1 tests for numpy.lib.ufunclike
Found 89/89 tests for numpy.linalg
Found 94/94 tests for numpy.ma.core
Found 15/15 tests for numpy.ma.extras
Found 7/7 tests for numpy.random
Found 16/16 tests for numpy.testing.utils
Found 0/0 tests for __main__
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 1004 tests in 1.054s

OK

>>>

Re: MKL and NumPy incompatibility (test fails)

rex — Mon, 19 May 2008 15:36:26 GMT

Either there is a bug in MKL 10.0.3.020 or I have a corrupted copy. The error below does not appear when MKL 10.0.1.014 is used.

MKL FATAL ERROR: /opt/intel/mkl/10.0.3.020/lib/32/: cannot read file data: Is a directory

-rex

topic MKL and NumPy incompatibility (test fails) in Intel® oneAPI Math Kernel Library

MKL and NumPy incompatibility (test fails)

Re: MKL and NumPy incompatibility (test fails)