topic Re: Re:numpy incompatibility in Intel® Distribution for Python*

numpy incompatibility

Orion_P_ — Thu, 05 Aug 2021 23:03:42 GMT

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

Re: numpy incompatibility

Orion_P_ — Thu, 05 Aug 2021 23:12:04 GMT

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*.

Re: numpy incompatibility

Orion_P_ — Thu, 05 Aug 2021 23:22:56 GMT

pydaal also appears to require numpy-1.14*

Re:numpy incompatibility

AthiraM_Intel — Fri, 06 Aug 2021 13:18:47 GMT

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.8bnhcp

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

Thanks.

Re: Re:numpy incompatibility

Orion_P_ — Fri, 06 Aug 2021 21:21:18 GMT

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.

Re: numpy incompatibility

AthiraM_Intel — Thu, 12 Aug 2021 13:19:08 GMT

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.

Re:numpy incompatibility

AthiraM_Intel — Thu, 19 Aug 2021 13:57:29 GMT

Hi,

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

Thanks.

Re: numpy incompatibility

Orion_P_ — Fri, 20 Aug 2021 16:53:53 GMT

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.

Re:numpy incompatibility

AthiraM_Intel — Mon, 23 Aug 2021 05:49:02 GMT

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