ImportError: cannot import name fft_ on OSX (Python+MKL)

John_O_ · ‎04-05-2017

I installed MKL and the Intel Python Distribution for OSX and I'm having trouble importing scipy.signal:

$ python
Python 2.7.12 |Intel Corporation| (default, Feb 5 2017, 00:31:58)
[GCC 4.2.1 Compatible Apple LLVM 7.3.0 (clang-703.0.31)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Intel(R) Distribution for Python is brought to you by Intel Corporation.
Please check out: https://software.intel.com/en-us/python-distribution
>>> import scipy.signal
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/intel/intelpython27/lib/python2.7/site-packages/scipy/signal/__init__.py", line 298, in <module>
from .windows import *
File "/opt/intel/intelpython27/lib/python2.7/site-packages/scipy/signal/windows.py", line 7, in <module>
from scipy import fftpack, linalg, special
File "/opt/intel/intelpython27/lib/python2.7/site-packages/scipy/fftpack/__init__.py", line 98, in <module>
from numpy.fft import fft_ as fft
ImportError: cannot import name fft_

I get a similar failure when I run scipy.test():

$ python
Python 2.7.12 |Intel Corporation| (default, Feb 5 2017, 00:31:58)
[GCC 4.2.1 Compatible Apple LLVM 7.3.0 (clang-703.0.31)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Intel(R) Distribution for Python is brought to you by Intel Corporation.
Please check out: https://software.intel.com/en-us/python-distribution
>>> import scipy
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.12.1
NumPy relaxed strides checking option: True
NumPy is installed in /opt/intel/intelpython27/lib/python2.7/site-packages/numpy
SciPy version 0.18.1
SciPy is installed in /opt/intel/intelpython27/lib/python2.7/site-packages/scipy
Python version 2.7.12 |Intel Corporation| (default, Feb 5 2017, 00:31:58) [GCC 4.2.1 Compatible Apple LLVM 7.3.0 (clang-703.0.31)]
nose version 1.3.7
[snip]
ERROR: Failure: ImportError (cannot import name fft_)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/opt/intel/intelpython27/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
addr.filename, addr.module)
File "/opt/intel/intelpython27/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/opt/intel/intelpython27/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/opt/intel/intelpython27/lib/python2.7/site-packages/scipy/fftpack/__init__.py", line 98, in <module>
from numpy.fft import fft_ as fft
ImportError: cannot import name fft_
[snip]
----------------------------------------------------------------------
Ran 22144 tests in 515.705s

FAILED (KNOWNFAIL=59, SKIP=1834, errors=3, failures=3)
<nose.result.TextTestResult run=22144 errors=3 failures=3>

I assume I made a mistake during my install. I would appreciate any guidance. Thanks in advance.

Oleksandr_P_Intel · ‎04-05-2017

Hi John,

I was attempting to recreate the problem you experience as follows:

# install Miniconda3 downloaded with curl -O https://repo.continuum.io/miniconda/Miniconda3-4.2.12-MacOSX-x86_64.sh
./Miniconda3-4.2.12-MacOSX-x86_64.sh
# activate
source ./miniconda3/bin/activate
# create environment
conda create --name idp_2017u2_py2 -c intel python=2 intelpython2_core --yes
# activate it
source activate idp_2017u2_py2

With this setup I can not reproduce the problem:

# try to reproduce
(idp_2017u2_py2) [20:40:25 fxsatmac02 opavlyk]$ python
Python 2.7.12 |Intel Corporation| (default, Feb  5 2017, 00:31:58)
[GCC 4.2.1 Compatible Apple LLVM 7.3.0 (clang-703.0.31)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Intel(R) Distribution for Python is brought to you by Intel Corporation.
Please check out: https://software.intel.com/en-us/python-distribution
>>> import scipy.signal
>>> exit()

Did you download the distribution as an installer from registrationcenter.intel.com?

Perhaps the method I tried could be used as a work-around. I will try to reproduce the issue using the installer.

Best regards, Oleksandr

gaston-hillar · ‎04-05-2017

Hi John,

If you run the following commands in a Terminal window on macOS, do you see any results?

conda list | grep scipy

conda list | grep mkl

Oleksandr_P_Intel · ‎04-06-2017

Please try running

python -c "import numpy.fft as m; print dir(m)"

This what I get by running this line:

(idp_2017u2_py2) [21:18:02 fxsatmac02 opavlyk]$ python -c "import numpy.fft as m; print dir(m)"
['__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', '_numpy_tester', 
'absolute_import', 'bench', 'division', 'fft', 'fft2', 'fft2_', 'fft_', 'fftfreq', 'fftn', 'fftn_', 
'fftshift', 'helper', 'hfft', 'ifft', 'ifft2', 'ifft2_', 'ifft_', 'ifftn', 'ifftn_', 'ifftshift', 
'ihfft', 'info', 'irfft', 'irfft2', 'irfftn', 'print_function', 'rfft', 'rfft2', 'rfftfreq', 'rfftn', 'test']

It would also be useful if you included the full output of

/opt/intel/intelpython27/bin/conda list --explicit

Thank you,
Oleksandr

John_O_ · ‎04-06-2017

Here you go Gastón:

(root) mini:tmp john$ conda list | grep scipy
scipy 0.18.1 np111py27_intel_10 [intel] intel
(root) mini:tmp john$ conda list | grep mkl
mkl 2017.0.2 intel_1 [intel] intel

And for you Oleksandr:

Let me know if you have any other commands to try. In a few hours, I'll uninstall and reinstall per Oleksandr's original reply. Thank you for your assistance!

gaston-hillar · ‎04-06-2017

Hi John,

It seems to me you have everything that is needed. I'm working with 2017 Update 2 on macOS El Capitan, formerly known as OS X El Capitan.

Oleksandr_P_Intel · ‎04-06-2017

John,

I copy-pasted the output of your run of `conda list --explicit`, commented out two entries about conda and conda-env (lines 4 and 5) after the line `@EXPLICIT`, saved the file into `john_env.txt`, and then ran

conda create --name john --file john_env.txt

This recreated your environment as conda thought it was. Even here the problem could not reproduced:

(root) [14:29:34 fxsatmac02 opavlyk]$ . activate john
(john) [14:29:59 fxsatmac02 opavlyk]$ python -c "import numpy.fft as m; print dir(m)"
['__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', 
'_numpy_tester', 'absolute_import', 'bench', 'division', 'fft', 'fft2', 'fft2_', 
'fft_', 'fftfreq', 'fftn', 'fftn_', 'fftshift', 'helper', 'hfft', 'ifft', 'ifft2', 
'ifft2_', 'ifft_', 'ifftn', 'ifftn_', 'ifftshift', 'ihfft', 'info', 'irfft', 
'irfft2', 'irfftn', 'print_function', 'rfft', 'rfft2', 'rfftfreq', 'rfftn', 'test']

It is best to reinstall the distribution to see if the problem fixes itself.

John_O_ · ‎04-06-2017

I reinstalled using Oleksandr instructions and importing scipy.signal works fine, but when I try to run my production code, an import cv2 fails. I tried installing via "conda install opencv-python" but I get a PackageNotFoundError, so I used "pip install opencv-python". That works but it reinstalls numpy and my problem reappears!

(idp_2017u2_py2) mini:registrar john$ conda install opencv-python
PackageNotFoundError: Package not found: '' Package missing in current osx-64 channels:
- opencv-python
(idp_2017u2_py2) mini:registrar john$ pip install opencv-python
Installing collected packages: numpy, opencv-python
Found existing installation: numpy 1.11.2
Uninstalling numpy-1.11.2:
Successfully uninstalled numpy-1.11.2
Successfully installed numpy-1.12.1 opencv-python-3.2.0.6

(idp_2017u2_py2) mini:registrar john$ python
Python 2.7.12 |Intel Corporation| (default, Feb 5 2017, 00:31:58)
[GCC 4.2.1 Compatible Apple LLVM 7.3.0 (clang-703.0.31)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Intel(R) Distribution for Python is brought to you by Intel Corporation.
Please check out: https://software.intel.com/en-us/python-distribution
>>> import scipy.signal
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/john/miniconda3/envs/idp_2017u2_py2/lib/python2.7/site-packages/scipy/signal/__init__.py", line 298, in <module>
from .windows import *
File "/Users/john/miniconda3/envs/idp_2017u2_py2/lib/python2.7/site-packages/scipy/signal/windows.py", line 7, in <module>
from scipy import fftpack, linalg, special
File "/Users/john/miniconda3/envs/idp_2017u2_py2/lib/python2.7/site-packages/scipy/fftpack/__init__.py", line 98, in <module>
from numpy.fft import fft_ as fft
ImportError: cannot import name fft_

John_O_ · ‎04-06-2017

I could not use conda to install opencv because that version of opencv depends on numpy 1.7 so I ended up using "conda install opencv -c conda-forge". I'm making progress again, but if there is a better way to get opencv with Intel Python, please let me know. Thanks.

Oleksandr_P_Intel · ‎04-06-2017

John Otken wrote:

I could not use conda to install opencv because that version of opencv depends on numpy 1.7 so I ended up using "conda install opencv -c conda-forge". I'm making progress again, but if there is a better way to get opencv with Intel Python, please let me know. Thanks.

I just tried installing opencv into Intel Distribution for Python3, got the instructions on StackOverflow

(idp_2017u2) [15:39:32 fxsatlin04 opavlyk]$ conda install -c https://conda.binstar.org/menpo opencv
Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /localdisk/work/opavlyk/miniconda3/envs/idp_2017u2:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    opencv-3.1.0               |      np111py35_1        36.5 MB

The following NEW packages will be INSTALLED:

    opencv: 3.1.0-np111py35_1

Proceed (/n)?

which appeared to work fine. I have not found opencv for Python 2 yet.

John_O_ · ‎04-06-2017

I'm currently using Python 2.7. When I installed using conde-forge, it displays:

opencv: 3.2.0-np111py27_blas_openblas_200 conda-forge [blas_openblas]

I assume that means opencv is using the non-optimal BLAS library as opposed to MKL.

gaston-hillar · ‎04-06-2017

Hi John,

The initial problem you mentioned in this thread has been solved by reinstalling. So, this thread is solved. Now, you are trying to install a different package to run your code. When this happens, instead of adding additional questions on the same thread, it is a good idea to open another thread with the specific problem / question. This way, the forum has a better organization.

I'm not working with opencv on Pyton 2.7 on macOS. So, I won't be able to help you with your new question. It's great to know the first issue is solved.