Hello,
I have been trying to compile numpy and scipy against intel MKL. I have been following the following guide to the letter:
https://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl
I am using the versions of numpy and scipy tested with the guide, numpy 1.9.2 and scpy 0.15.1. Numpy installs exactly as I would expect it to and performs well. However, when I run the standard scipy tests, i.e.,
import scipy scipy.test()
I encounter a large number of errors related to missing symbols, such as
ImportError: scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset
Has anyone else experienced this or does anyone have any insight? Thanks in advance for your help.
My LD_LIBRARY_PATH is:
/opt/intel/composer_xe_2015.3.187/compiler/lib/intel64:/opt/intel/composer_xe_2015.3.187/compiler/lib/intel64/:/lib:/usr/local/plc-2.0/lib:/lib64:/opt/intel/composer_xe_2015.3.187/ipp/../compiler/lib/intel64/:/opt/intel/composer_xe_2015.3.187/ipp/../compiler/lib/intel64:/opt/intel/compilers_and_libraries_2016.0.109/linux/compiler/lib/intel64:/opt/intel/compilers_and_libraries_2016.0.109/linux/mpi/intel64/lib:/opt/intel/compilers_and_libraries_2016.0.109/linux/ipp/../compiler/lib/intel64:/opt/intel/compilers_and_libraries_2016.0.109/linux/ipp/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/opt/intel/compilers_and_libraries_2016.0.109/linux/compiler/lib/intel64:/opt/intel/compilers_and_libraries_2016.0.109/linux/mkl/lib/intel64:/opt/intel/compilers_and_libraries_2016.0.109/linux/tbb/lib/intel64/gcc4.4:/opt/intel/debugger_2016/libipt/intel64/lib:/opt/intel/compilers_and_libraries_2016.0.109/linux/daal/lib/intel64_lin:/opt/intel/compilers_and_libraries_2016.0.109/linux/daal/../tbb/lib/intel64_lin/gcc4.4:/opt/intel/compilers_and_libraries_2016.0.109/linux/daal/../compiler/lib/intel64_lin::/usr/local/cuda/lib64:/usr/local/cuda/lib
The full results of the scipy tests are:
======================================================================
ERROR: Failure: ImportError (scipy/fftpack/_fftpack.so: undefined symbol: __intel_avx_rep_memcpy)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/fftpack/__init__.py", line 94, in <module>
from .basic import *
File "scipy/fftpack/basic.py", line 12, in <module>
from . import _fftpack
ImportError: scipy/fftpack/_fftpack.so: undefined symbol: __intel_avx_rep_memcpy
======================================================================
ERROR: Failure: ImportError (scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/integrate/__init__.py", line 51, in <module>
from .quadrature import *
File "scipy/integrate/quadrature.py", line 6, in <module>
from scipy.special.orthogonal import p_roots
File "scipy/special/__init__.py", line 586, in <module>
from ._ufuncs import *
ImportError: scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/interpolate/__init__.py", line 160, in <module>
from .interpolate import *
File "scipy/interpolate/interpolate.py", line 16, in <module>
import scipy.special as spec
File "scipy/special/__init__.py", line 586, in <module>
from ._ufuncs import *
ImportError: scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/io/__init__.py", line 85, in <module>
from .matlab import loadmat, savemat, whosmat, byteordercodes
File "scipy/io/matlab/__init__.py", line 13, in <module>
from .mio import loadmat, savemat, whosmat
File "scipy/io/matlab/mio.py", line 12, in <module>
from .miobase import get_matfile_version, docfiller
File "scipy/io/matlab/miobase.py", line 22, in <module>
from scipy.misc import doccer
File "scipy/misc/__init__.py", line 47, in <module>
from scipy.special import comb, factorial, factorial2, factorialk
File "scipy/special/__init__.py", line 586, in <module>
from ._ufuncs import *
ImportError: scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (scipy/linalg/_interpolative.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/nfs/galaxy/unixhome/jmiller/scipy-to-copy/lib/python2.7/site-packages/scipy/linalg/tests/test_interpolative.py", line 29, in <module>
import scipy.linalg.interpolative as pymatrixid
File "scipy/linalg/interpolative.py", line 386, in <module>
import scipy.linalg._interpolative_backend as backend
File "scipy/linalg/_interpolative_backend.py", line 34, in <module>
import scipy.linalg._interpolative as _id
ImportError: scipy/linalg/_interpolative.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (scipy/sparse/linalg/isolve/_iterative.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/nfs/galaxy/unixhome/jmiller/scipy-to-copy/lib/python2.7/site-packages/scipy/linalg/tests/test_matfuncs.py", line 27, in <module>
from scipy.linalg import _matfuncs_inv_ssq
File "scipy/linalg/_matfuncs_inv_ssq.py", line 15, in <module>
from scipy.sparse.linalg.interface import LinearOperator
File "scipy/sparse/linalg/__init__.py", line 109, in <module>
from .isolve import *
File "scipy/sparse/linalg/isolve/__init__.py", line 6, in <module>
from .iterative import *
File "scipy/sparse/linalg/isolve/iterative.py", line 7, in <module>
from . import _iterative
ImportError: scipy/sparse/linalg/isolve/_iterative.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (cannot import name doccer)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/nfs/galaxy/unixhome/jmiller/scipy-to-copy/lib/python2.7/site-packages/scipy/linalg/tests/test_special_matrices.py", line 12, in <module>
from scipy.misc import comb
File "scipy/misc/__init__.py", line 44, in <module>
from . import doccer
ImportError: cannot import name doccer
======================================================================
ERROR: Failure: ImportError (cannot import name doccer)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/misc/__init__.py", line 44, in <module>
from . import doccer
ImportError: cannot import name doccer
======================================================================
ERROR: Failure: ImportError (cannot import name doccer)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/ndimage/__init__.py", line 172, in <module>
from .filters import *
File "scipy/ndimage/filters.py", line 37, in <module>
from scipy.misc import doccer
File "scipy/misc/__init__.py", line 44, in <module>
from . import doccer
ImportError: cannot import name doccer
======================================================================
ERROR: Failure: ImportError (scipy/odr/__odrpack.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/odr/__init__.py", line 114, in <module>
from .odrpack import *
File "scipy/odr/odrpack.py", line 42, in <module>
from scipy.odr import __odrpack
ImportError: scipy/odr/__odrpack.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (scipy/optimize/_lbfgsb.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/optimize/__init__.py", line 176, in <module>
from ._minimize import *
File "scipy/optimize/_minimize.py", line 31, in <module>
from .lbfgsb import _minimize_lbfgsb
File "scipy/optimize/lbfgsb.py", line 40, in <module>
from . import _lbfgsb
ImportError: scipy/optimize/_lbfgsb.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/signal/__init__.py", line 264, in <module>
from .bsplines import *
File "scipy/signal/bsplines.py", line 4, in <module>
import scipy.special
File "scipy/special/__init__.py", line 586, in <module>
from ._ufuncs import *
ImportError: scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (scipy/sparse/linalg/isolve/_iterative.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/sparse/linalg/__init__.py", line 109, in <module>
from .isolve import *
File "scipy/sparse/linalg/isolve/__init__.py", line 6, in <module>
from .iterative import *
File "scipy/sparse/linalg/isolve/iterative.py", line 7, in <module>
from . import _iterative
ImportError: scipy/sparse/linalg/isolve/_iterative.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (scipy/sparse/linalg/isolve/_iterative.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/nfs/galaxy/unixhome/jmiller/scipy-to-copy/lib/python2.7/site-packages/scipy/sparse/tests/test_base.py", line 44, in <module>
from scipy.sparse.linalg import splu, expm, inv
File "scipy/sparse/linalg/__init__.py", line 109, in <module>
from .isolve import *
File "scipy/sparse/linalg/isolve/__init__.py", line 6, in <module>
from .iterative import *
File "scipy/sparse/linalg/isolve/iterative.py", line 7, in <module>
from . import _iterative
ImportError: scipy/sparse/linalg/isolve/_iterative.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/special/__init__.py", line 586, in <module>
from ._ufuncs import *
ImportError: scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset
======================================================================
ERROR: Failure: ImportError (scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 411, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "scipy/stats/__init__.py", line 338, in <module>
from .stats import *
File "scipy/stats/stats.py", line 184, in <module>
import scipy.special as special
File "scipy/special/__init__.py", line 586, in <module>
from ._ufuncs import *
ImportError: scipy/special/_ufuncs.so: undefined symbol: __intel_avx_rep_memset
======================================================================
FAIL: test_qhull.TestDelaunay.test_incremental('pathological-1-chunk-1',)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/nfs/galaxy/unixhome/jmiller/scipy-to-copy/lib/python2.7/site-packages/scipy/spatial/tests/test_qhull.py", line 507, in check
np.arange(points.shape[0]))
File "/usr/local/numpy-1.9.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 739, in assert_array_equal
verbose=verbose, header='Arrays are not equal')
File "/usr/local/numpy-1.9.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 620, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not equal
(shapes (79,), (81,) mismatch)
x: array([ 0, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,...
y: array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,...
======================================================================
FAIL: test_qhull.TestUtilities.test_degenerate_barycentric_transforms
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/numpy-1.9.2/lib/python2.7/site-packages/numpy/testing/decorators.py", line 146, in skipper_func
return f(*args, **kwargs)
File "/nfs/galaxy/unixhome/jmiller/scipy-to-copy/lib/python2.7/site-packages/scipy/spatial/tests/test_qhull.py", line 296, in test_degenerate_barycentric_transforms
assert_(bad_count < 20, bad_count)
File "/usr/local/numpy-1.9.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 53, in assert_
raise AssertionError(smsg)
AssertionError: 26
----------------------------------------------------------------------
Ran 1760 tests in 13.580s