Intel® Distribution for Python*
Support and discussions for achieving faster Python* applications and core computational packages.
Announcements
Intel Customer Support will be observing the Martin Luther King holiday on Monday, Jan. 17, and will return on Tues. Jan. 18.
For the latest information on Intel’s response to the Log4j/Log4Shell vulnerability, please see Intel-SA-00646

numpy incompatibility

Orion_P_
New Contributor I
744 Views

I've managed to end up with an incompatible environment.  I'm guessing that some package is missing some restriction on the version of numpy it works with.

 

$ python -c 'import scipy.special'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/anaconda/envs/scipy36-intel/lib/python3.6/site-packages/scipy/__init__.py", line 62, in <module>
    from numpy import show_config as show_numpy_config
  File "/opt/anaconda/envs/scipy36-intel/lib/python3.6/site-packages/numpy/__init__.py", line 180, in <module>
    from . import fft
  File "/opt/anaconda/envs/scipy36-intel/lib/python3.6/site-packages/numpy/fft/__init__.py", line 14, in <module>
    import mkl_fft._numpy_fft as _nfft
  File "/opt/anaconda/envs/scipy36-intel/lib/python3.6/site-packages/mkl_fft/__init__.py", line 27, in <module>
    from ._pydfti import (fft, ifft, fft2, ifft2, fftn, ifftn, rfft, irfft,
  File "__init__.pxd", line 918, in init mkl_fft._pydfti
ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject

# packages in environment at /opt/anaconda/envs/scipy36-intel:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    main
absl-py                   0.13.0           py36h06a4308_0    main
alembic                   1.6.4              pyhd3eb1b0_0    main
appdirs                   1.4.4                      py_0    main
asn1crypto                0.24.0                   py36_3    intel
astor                     0.8.1            py36h06a4308_0    main
astropy                   3.2.3            py36h7b6447c_0    main
async_generator           1.10             py36h28b3542_0    main
atomicwrites              1.4.0                      py_0    main
attrs                     21.2.0             pyhd3eb1b0_0    main
backcall                  0.1.0                    py36_2    intel
backports                 1.0                      py36_9    intel
basemap                   1.2.0            py36h705c2d8_0    main
beautifulsoup4            4.9.3              pyha847dfd_0    main
black                     19.10b0                    py_0    main
blas                      1.0                    openblas    main
bleach                    2.1.3                    py36_2    intel
bzip2                     1.0.8                hb9a14ef_8    intel
c-ares                    1.17.1               hff3d592_1    intel
certifi                   2018.1.18                py36_2    intel
cffi                      1.11.5                   py36_3    intel
chardet                   3.0.4                    py36_3    intel
click                     8.0.0              pyhd3eb1b0_0    main
common_cmplr_lib_rt       2021.3.0             intel_3350    intel
common_cmplr_lic_rt       2021.3.0             intel_3350    intel
configurable-http-proxy   4.0.1                   node6_0    main
contextlib2               0.6.0.post1                py_0    main
cryptography              2.3                      py36_2    intel
curl                      7.61.0               h84994c4_0    main
cycler                    0.10.0                   py36_7    intel
daal                      2018.0.3.20180405               0    intel
decorator                 4.3.0                    py36_3    intel
dpcpp-cpp-rt              2021.3.0             intel_3350    intel
dpcpp_cpp_rt              2021.3.0             intel_3350    intel
drms                      0.5.7                      py_0    conda-forge
entrypoints               0.2.3                    py36_2    intel
freetype                  2.9                           4    intel
gast                      0.5.1              pyhd3eb1b0_0    main
geos                      3.6.2                heeff764_2    main
get_terminal_size         1.0.0                    py36_7    intel
ghost.py                  0.2.3                    py36_0    conda-forge
grpcio                    1.14.1           py36h9ba97e2_0    main
h5py                      2.7.1           np114py36_intel_0  [intel]  intel
hdf4                      4.2.13               h3ca952b_2    main
hdf5                      1.10.1                  intel_0  [intel]  intel
html5lib                  1.0.1                    py36_4    intel
hypothesis                6.14.1             pyhd3eb1b0_0    main
icc_rt                    2021.3.0             intel_3350    intel
icu                       59.1                    intel_0  [intel]  intel
idna                      2.6                      py36_3    intel
importlib_metadata        1.5.0                    py36_0    main
importlib_resources       5.2.0              pyhd3eb1b0_1    main
intel-cmplr-lib-rt        2021.3.0             intel_3350    intel
intel-cmplr-lic-rt        2021.3.0             intel_3350    intel
intel-opencl-rt           2021.3.0             intel_3350    intel
intel-openmp              2021.3.0             intel_3350    intel
intelpython               2021.3.0                      7    intel
ipykernel                 4.6.1                    py36_2    intel
ipython                   6.3.1                    py36_3    intel
ipython_genutils          0.2.0                    py36_2    intel
ipywidgets                7.0.0                    py36_2    intel
jedi                      0.12.0                   py36_2    intel
jinja2                    2.9.6                    py36_2    intel
jpeg                      9d                   h36c2ea0_0    intel
jsonschema                2.6.0                    py36_2    intel
jupyter                   1.0.0                    py36_7    intel
jupyter_client            5.1.0                    py36_5    intel
jupyter_console           5.1.0                    py36_2    intel
jupyter_core              4.4.0                    py36_6    intel
keras-applications        1.0.8                      py_1    main
keras-preprocessing       1.1.2              pyhd3eb1b0_0    main
kiwisolver                1.0.1                    py36_2    intel
libblas                   3.8.0               17_openblas    conda-forge
libcblas                  3.8.0               17_openblas    conda-forge
libcurl                   7.61.0               h1ad7b7a_0    main
libedit                   3.1.20210216         h27cfd23_1    main
libffi                    3.3                          13    intel
libgcc                    7.2.0                h69d50b8_2    main
libgcc-ng                 9.3.0              hdf63c60_101    intel
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.5.0               ha8ba4b0_17    main
libgfortran4              7.5.0               ha8ba4b0_17    main
liblapack                 3.8.0               17_openblas    conda-forge
libnetcdf                 4.5.0                hc9a163a_7    main
libopenblas               0.3.10               h5a2b251_0    main
libpng                    1.6.37                        7    intel
libprotobuf               3.6.0                hdbcaa40_0    main
libsodium                 1.0.16                        3    intel
libssh2                   1.8.0                h9cfc8f7_4    main
libstdcxx-ng              9.3.0              hdf63c60_101    intel
libtiff                   4.0.9                   intel_2  [intel]  intel
libxml2                   2.9.12               h7681594_0    intel
llvmlite                  0.24.0                   py36_0    intel
mako                      1.1.4              pyhd3eb1b0_0    main
markdown                  3.1.1                    py36_0    main
markupsafe                1.0                      py36_3    intel
matplotlib                2.2.2               np114py36_4    intel
metis                     5.1.0                hf484d3e_4    main
metpy                     0.9.2                 py36_1001    conda-forge
mistune                   0.8.3                    py36_2    intel
mkl                       2021.3.0              intel_520    intel
mkl-service               2.1.0                    py36_2    intel
mkl_fft                   1.0.14           py36ha68da19_1    intel
mkl_random                1.0.4            py36ha68da19_2    intel
mock                      2.0.0              py36_intel_4  [intel]  intel
more-itertools            8.8.0              pyhd3eb1b0_0    main
mpmath                    1.0.0                    py36_2    intel
mypy_extensions           0.4.3                    py36_0    main
mysql-connector-c         6.1.11               hf4847fb_0    main
mysql-connector-python    8.0.18           py36h9c95fcb_1    main
nbbrowserpdf              0.2.0                    py36_0    conda-forge
nbconvert                 5.2.1                    py36_2    intel
nbformat                  4.4.0                    py36_2    intel
ncurses                   6.2                  he6710b0_1    main
netcdf4                   1.3.1            py36h73d701b_2    main
networkx                  2.0                py36_intel_0  [intel]  intel
nodejs                    6.11.2               h3db8ef7_0    main
nomkl                     3.0                           0    main
notebook                  5.2.2                    py36_1    intel
numba                     0.39.0              np114py36_0    intel
numexpr                   2.6.5               np114py36_2    intel
numpy                     1.14.3                   py36_5    intel
numpy-base                1.17.0                  py36_13    intel
oct2py                    5.2.0                    pypi_0    pypi
octave-kernel             0.32.0                   pypi_0    pypi
olefile                   0.44               py36_intel_0  [intel]  intel
openblas                  0.3.10                        0    main
openblas-devel            0.3.10                        0    main
opencl_rt                 2021.3.0             intel_3350    intel
openjpeg                  2.3.0                h05c96fa_1    main
openssl                   1.0.2s                        0    intel
packaging                 21.0               pyhd3eb1b0_0    main
pamela                    1.0.0                      py_0    main
pandas                    0.23.0              np114py36_1    intel
pandocfilters             1.4.1                    py36_2    intel
parso                     0.2.0                    py36_2    intel
path.py                   11.0.1                   py36_2    intel
pathspec                  0.7.0                      py_0    main
patsy                     0.5.1                    py36_0    main
pbr                       1.10.0             py36_intel_4  [intel]  intel
pexpect                   4.2.1                    py36_4    intel
pickleshare               0.7.4                    py36_3    intel
pillow                    5.1.0              py36_intel_2  [intel]  intel
pint                      0.17               pyhd8ed1ab_0    conda-forge
pip                       19.1.1                   py36_0    intel
pluggy                    0.13.1           py36h06a4308_0    main
pooch                     0.2.1                 py36_1000    conda-forge
portpicker                1.1.1                    py36_0    intel
proj4                     5.2.0                he6710b0_1    main
prometheus_client         0.11.0             pyhd3eb1b0_0    main
prompt_toolkit            1.0.15                   py36_2    intel
protobuf                  3.5.2              py36_intel_0  [intel]  intel
psutil                    5.8.0            py36h27cfd23_1    main
ptyprocess                0.5.2                    py36_2    intel
py                        1.10.0             pyhd3eb1b0_0    main
pycparser                 2.18                     py36_2    intel
pycurl                    7.43.0.2         py36hb7f436b_0    main
pydaal                    2018.0.3.20180405 np114py36_intel_0  [intel]  intel
pyepsg                    0.4.0                    py36_0    main
pygments                  2.2.0                    py36_5    intel
pymp-pypi                 0.4.3                    pypi_0    pypi
pyodbc                    4.0.31           py36h295c915_0    main
pyopenssl                 17.5.0                   py36_2    intel
pyparsing                 2.2.0                    py36_2    intel
pypdf2                    1.26.0                   py36_1    conda-forge
pyproj                    1.9.6            py36h14380d9_0    main
pyshp                     2.1.3              pyhd3eb1b0_0    main
pysocks                   1.6.7                    py36_1    intel
pytest                    5.4.3            py36h06a4308_0    main
pytest-arraydiff          0.3              py36h39e3cac_0    main
pytest-astropy            0.8.0              pyhd3eb1b0_0    main
pytest-astropy-header     0.1.2              pyhd3eb1b0_0    main
pytest-doctestplus        0.9.0              pyhd3eb1b0_0    main
pytest-openfiles          0.5.0              pyhd3eb1b0_0    main
pytest-remotedata         0.3.2                    py36_0    main
python                    3.6.3                  intel_12  [intel]  intel
python-dateutil           2.8.0                    py36_0    intel
python-editor             1.0.4                      py_0    main
python-oauth2             1.1.1                      py_0    main
pytz                      2019.1                   py36_0    intel
pywavelets                0.5.2           np114py36_intel_3  [intel]  intel
pyyaml                    5.1.1                    py36_0    intel
pyzmq                     16.0.2                   py36_6    intel
regex                     2021.7.6         py36h7f8727e_0    main
requests                  2.20.1                   py36_1    intel
scikit-image              0.13.1          np114py36_intel_3  [intel]  intel
scikit-learn              0.19.1          np114py36_intel_29  [intel]  intel
scikit-umfpack            0.3.2           py36h8b7e671_1001    conda-forge
scipy                     1.1.0               np114py36_6    intel
seaborn                   0.11.1             pyhd3eb1b0_0    main
setuptools                41.0.1                   py36_0    intel
shapely                   1.6.4            py36h7ef4460_0    main
simplegeneric             0.8.1                    py36_7    intel
six                       1.12.0                   py36_0    intel
sortedcontainers          2.4.0              pyhd3eb1b0_0    main
soupsieve                 2.2.1              pyhd3eb1b0_0    main
sqlalchemy                1.4.4            py36h27cfd23_0    main
sqlite                    3.23.1                        1    intel
statsmodels               0.10.1           py36hdd07704_0    main
suds-jurko                0.6              py36h06a4308_3    main
suitesparse               5.2.0                h2ffa06c_0    main
sunpy                     0.7.7                    py36_1    conda-forge
sympy                     1.3                      py36_1    intel
tbb                       2021.3.0              intel_511    intel
tbb4py                    2021.3.0         py36_intel_511    intel
tcl                       8.6.4                        24    intel
tensorboard               1.12.2           py36he6710b0_0    main
tensorflow                1.3.1               np114py36_5    intel
tensorflow-base           2.3.0                         0    intel
tensorflow-estimator      2.3.0              pyheb71bc4_0    main
termcolor                 1.1.0            py36h06a4308_1    main
terminado                 0.8.1                    py36_2    intel
testpath                  0.3.1                    py36_2    intel
tk                        8.6.4                        29    intel
toml                      0.10.2             pyhd3eb1b0_0    main
tornado                   4.5.2                    py36_5    intel
traitlets                 4.3.2                    py36_3    intel
typed-ast                 1.4.3            py36h7f8727e_1    main
typing_extensions         3.7.4.3            pyha847dfd_0    intel
unixodbc                  2.3.9                h7b6447c_0    main
urllib3                   1.24.1                   py36_2    intel
wcwidth                   0.1.7                    py36_6    intel
weakref                   1.0.post1                py36_0    intel
webencodings              0.5.1                    py36_0    intel
werkzeug                  0.14.1                   py36_0    intel
wheel                     0.31.0                   py36_3    intel
widgetsnbextension        3.2.0                    py36_1    intel
xarray                    0.13.0                     py_0    main
xz                        5.2.5                h74280d8_2    intel
yaml                      0.1.7                         7    intel
zeromq                    4.2.3                         2    intel
zipp                      3.5.0              pyhd3eb1b0_0    main
zlib                      1.2.11.1             h047b5d8_3    intel
0 Kudos
1 Solution
AthiraM_Intel
Moderator
657 Views

Hi,

 

You can uninstall the numpy and reinstall the same. This helps to resolve the version issue. Same for other packages also.

 

If you have any further issue, please let us know.

 

Thanks.

 

 

View solution in original post

8 Replies
Orion_P_
New Contributor I
742 Views

I'm guessing that numpy and numpy-base really need to be at the same version, but there doesn't seem to be any requirement on that in the packages, at least in the numpy-1.14 packages which predate numpy-base.

 

Looks like it's the h5py package that is limiting me to numpy-1.14*.

 

Orion_P_
New Contributor I
739 Views

pydaal also appears to require numpy-1.14*

AthiraM_Intel
Moderator
722 Views

Hi,


Thanks for reaching out to us.


The version changes are due to the installation of too many packages in your environment. Also we could see that the some of the packages are outdated. 


We suggest you to either install packages in a new environment or to install Intel® oneAPI AI Analytics Toolkit.


To insatll Intel® oneAPI AI Analytics Toolkit using conda, please refer the below link:


https://software.intel.com/content/www/us/en/develop/articles/installing-ai-kit-with-conda.html#gs.8...



If you have any further issue, please let us know.


Thanks.


Orion_P_
New Contributor I
703 Views

With the morass of packages that compromise the full anaconda universe, I can appreciate you wanting to limit use to specific, well defined cases.  But I think that side steps issues within the intel channel - namely the ability to install incompatible packages like numpy-1.14.3 and numpy-base-1.17.0 or tensorflow 1.3.1 and tensorflow-base 2.3.0 that really should be addressed.

AthiraM_Intel
Moderator
658 Views

Hi,

 

You can uninstall the numpy and reinstall the same. This helps to resolve the version issue. Same for other packages also.

 

If you have any further issue, please let us know.

 

Thanks.

 

 

View solution in original post

Orion_P_
New Contributor I
604 Views

I think there are still issues with being able to install incompatible packages, but I'm not able to easily reproduce at the moment.  Reinstalling has worked for now.

AthiraM_Intel
Moderator
618 Views

Hi,


Could you please give us an update? Has the solution provided helped?


Thanks.


AthiraM_Intel
Moderator
574 Views

Hi,


Thanks for accepting our solution. If you need any additional information, please post a new question as this thread will no longer be monitored by Intel. 



Thanks


Reply