- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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.
Link Copied
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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:
(root) mini:tmp john$ python -c "import numpy.fft as m; print dir(m)"
['__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', '_numpy_tester', 'absolute_import', 'bench', 'division', 'fft', 'fft2', 'fftfreq', 'fftn', 'fftpack', 'fftpack_lite', 'fftshift', 'helper', 'hfft', 'ifft', 'ifft2', 'ifftn', 'ifftshift', 'ihfft', 'info', 'irfft', 'irfft2', 'irfftn', 'print_function', 'rfft', 'rfft2', 'rfftfreq', 'rfftn', 'test']
(root) mini:tmp john$ /opt/intel/intelpython27/bin/conda list --explicit
# This file may be used to create an environment using:
# $ conda create --name
# platform: osx-64
@EXPLICIT
https://conda.anaconda.org/intel/osx-64/appnope-0.1.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/backports-1.0-py27_intel_6.tar.bz2
https://conda.anaconda.org/intel/osx-64/backports_abc-0.4-py27_intel_7.tar.bz2
https://conda.anaconda.org/intel/osx-64/conda-4.2.12-py27_intel_0.tar.bz2
https://conda.anaconda.org/intel/osx-64/conda-env-2.6.0-0.tar.bz2
https://conda.anaconda.org/intel/osx-64/configparser-3.5.0-py27_intel_3.tar.bz2
https://conda.anaconda.org/intel/osx-64/cycler-0.10.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/cython-0.24-py27_intel_16.tar.bz2
https://conda.anaconda.org/intel/osx-64/decorator-4.0.10-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/entrypoints-0.2.2-py27_intel_1.tar.bz2
https://conda.anaconda.org/intel/osx-64/enum34-1.1.6-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/freetype-2.5.5-intel_9.tar.bz2
https://conda.anaconda.org/intel/osx-64/funcsigs-1.0.2-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/functools32-3.2.3.2-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/get_terminal_size-1.0.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/hdf5-1.8.17-intel_0.tar.bz2
https://conda.anaconda.org/intel/osx-64/icc_rt-16.0.3-intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/intelpython-2017.0.2-0.tar.bz2
https://conda.anaconda.org/intel/osx-64/ipykernel-4.5.0-py27_intel_4.tar.bz2
https://conda.anaconda.org/intel/osx-64/ipython-4.2.0-py27_intel_8.tar.bz2
https://conda.anaconda.org/intel/osx-64/ipython_genutils-0.1.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/ipywidgets-5.2.2-py27_intel_1.tar.bz2
https://conda.anaconda.org/intel/osx-64/jinja2-2.8-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/jsonschema-2.5.1-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/jupyter-1.0.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/jupyter_client-4.4.0-py27_intel_2.tar.bz2
https://conda.anaconda.org/intel/osx-64/jupyter_console-5.0.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/jupyter_core-4.2.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/libpng-1.6.28-intel_10.tar.bz2
https://conda.anaconda.org/intel/osx-64/llvmlite-0.15.0-py27_intel_0.tar.bz2
https://conda.anaconda.org/intel/osx-64/markupsafe-0.23-py27_intel_6.tar.bz2
https://conda.anaconda.org/intel/osx-64/matplotlib-1.5.3-py27_intel_3.tar.bz2
https://conda.anaconda.org/intel/osx-64/mistune-0.7.3-py27_intel_1.tar.bz2
https://conda.anaconda.org/intel/osx-64/mkl-2017.0.2-intel_1.tar.bz2
https://conda.anaconda.org/intel/osx-64/mpmath-0.19-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/nbconvert-4.2.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/nbformat-4.1.0-py27_intel_1.tar.bz2
https://conda.anaconda.org/intel/osx-64/nose-1.3.7-py27_intel_12.tar.bz2
https://conda.anaconda.org/intel/osx-64/notebook-4.2.3-py27_intel_7.tar.bz2
https://conda.anaconda.org/intel/osx-64/numba-0.30.1-py27_intel_11.tar.bz2
https://conda.anaconda.org/intel/osx-64/numexpr-2.6.1-np111py27_intel_11.tar.bz2
https://conda.anaconda.org/intel/osx-64/numpy-1.11.2-py27_intel_51.tar.bz2
https://conda.anaconda.org/intel/osx-64/openssl-1.0.2k-intel_3.tar.bz2
https://conda.anaconda.org/intel/osx-64/pandas-0.19.2-py27_intel_1.tar.bz2
https://conda.anaconda.org/intel/osx-64/path.py-8.2.1-py27_intel_7.tar.bz2
https://conda.anaconda.org/intel/osx-64/pathlib2-2.1.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/pexpect-4.0.1-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/pickleshare-0.7.4-py27_intel_1.tar.bz2
https://conda.anaconda.org/intel/osx-64/pip-8.1.2-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/prompt_toolkit-1.0.3-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/ptyprocess-0.5.1-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/pycosat-0.6.1-py27_intel_6.tar.bz2
https://conda.anaconda.org/intel/osx-64/pydaal-2017.0.2.20170126-py27_intel_0.tar.bz2
https://conda.anaconda.org/intel/osx-64/pygments-2.1.3-py27_intel_6.tar.bz2
https://conda.anaconda.org/intel/osx-64/pyparsing-2.1.4-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/pytables-3.2.3.1-py27_intel_8.tar.bz2
https://conda.anaconda.org/intel/osx-64/python-2.7.12-intel_20.tar.bz2
https://conda.anaconda.org/intel/osx-64/python-dateutil-2.5.3-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/pytz-2016.6.1-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/pyzmq-15.4.0-py27_intel_3.tar.bz2
https://conda.anaconda.org/intel/osx-64/requests-2.11.1-py27_intel_1.tar.bz2
https://conda.anaconda.org/intel/osx-64/ruamel_yaml-0.11.14-py27_intel_1.tar.bz2
https://conda.anaconda.org/intel/osx-64/scikit-learn-0.18.1-py27_intel_4.tar.bz2
https://conda.anaconda.org/intel/osx-64/scipy-0.18.1-np111py27_intel_10.tar.bz2
https://conda.anaconda.org/intel/osx-64/setuptools-23.0.0-py27_intel_4.tar.bz2
https://conda.anaconda.org/intel/osx-64/simplegeneric-0.8.1-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/singledispatch-3.4.0.3-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/six-1.10.0-py27_intel_7.tar.bz2
https://conda.anaconda.org/intel/osx-64/sqlite-3.13.0-intel_13.tar.bz2
https://conda.anaconda.org/intel/osx-64/ssl_match_hostname-3.5.0.1-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/sympy-1.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/tbb-2017.0.4-py27_intel_0.tar.bz2
https://conda.anaconda.org/intel/osx-64/tcl-8.6.4-intel_16.tar.bz2
https://conda.anaconda.org/intel/osx-64/terminado-0.6-py27_intel_6.tar.bz2
https://conda.anaconda.org/intel/osx-64/tk-8.6.4-intel_18.tar.bz2
https://conda.anaconda.org/intel/osx-64/tornado-4.4.1-py27_intel_3.tar.bz2
https://conda.anaconda.org/intel/osx-64/traitlets-4.2.2-py27_intel_3.tar.bz2
https://conda.anaconda.org/intel/osx-64/wcwidth-0.1.7-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/wheel-0.29.0-py27_intel_5.tar.bz2
https://conda.anaconda.org/intel/osx-64/widgetsnbextension-1.2.6-py27_0.tar.bz2
https://conda.anaconda.org/intel/osx-64/yaml-0.1.6-intel_10.tar.bz2
https://conda.anaconda.org/intel/osx-64/zlib-1.2.11-intel_0.tar.bz2
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!
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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.
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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.
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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_
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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.
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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.
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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.
- Mark as New
- Bookmark
- Subscribe
- Mute
- Subscribe to RSS Feed
- Permalink
- Report Inappropriate Content
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.

- Subscribe to RSS Feed
- Mark Topic as New
- Mark Topic as Read
- Float this Topic for Current User
- Bookmark
- Subscribe
- Printer Friendly Page