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oneAPI AI Anlytics Toolkit Install via Conda Package Manager on Clean Ubuntu 20.04 LTS

Nathan_Peper
Employee
671 Views

I have a NUC with a fresh Ubuntu 20.04 LTS install that I’m trying to install the Intel oneAPI AI Analytics Toolkit on.  I can get everything to work through the GUI based installer and if I use APT, but if I only install Miniconda and then use the Conda Package Manager I run into some issues. I’m not sure if there is an undocumented step(s) or prereq(s) that I’m missing.  There’s a comment about setting up the environment variables to access the tools, but it doesn’t look like I can use the “source /opt/intel/oneapi/setvars.sh” like in the other install methods when only using conda and no previous oneAPI installs through the other methods.  

 

I’m following the instructions as outlined in the below link on our site, but get the below results in the terminal. I run into this error when I try to import tensorflow in python.

 

Thanks for the help,

Nate

 

 

 

Snapshot of the error:

(oneapi-tf) npeper@TGL-i7-NUC-1:~$ python -c "import tensorflow as tf"

Traceback (most recent call last):

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/numpy/core/__init__.py", line 22, in <module>

    from . import multiarray

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/numpy/core/multiarray.py", line 12, in <module>

    from . import overrides

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/numpy/core/overrides.py", line 7, in <module>

    from numpy.core._multiarray_umath import (

ImportError: libmkl_rt.so.1: cannot open shared object file: No such file or directory

 

 

 

Install instructions on our website:

https://www.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-to...

 

 

 

 

Full terminal steps and output:

 

npeper@TGL-i7-NUC-1:~$ source /home/npeper/miniconda3/bin/activate

(base) npeper@TGL-i7-NUC-1:~$ conda create -n oneapi-tf -c intel intel-aikit-tensorflow

Collecting package metadata (current_repodata.json): done

Solving environment: done

 

## Package Plan ##

 

  environment location: /home/npeper/miniconda3/envs/oneapi-tf

 

  added / updated specs:

    - intel-aikit-tensorflow

 

 

The following NEW packages will be INSTALLED:

 

  absl-py            intel/linux-64::absl-py-0.12.0-py37h06a4308_0

  aiohttp            intel/linux-64::aiohttp-3.7.4-py37h27cfd23_1

  asn1crypto         intel/linux-64::asn1crypto-1.4.0-py37hcd5400e_2

  astor              intel/linux-64::astor-0.8.1-py37h06a4308_0

  astunparse         intel/noarch::astunparse-1.6.3-py_0

  async-timeout      intel/linux-64::async-timeout-3.0.1-py37h06a4308_0

  attrs              intel/noarch::attrs-21.2.0-pyhd3eb1b0_0

  blinker            intel/linux-64::blinker-1.4-py37h06a4308_0

  bzip2              intel/linux-64::bzip2-1.0.8-hb9a14ef_9

  c-ares             intel/linux-64::c-ares-1.17.1-h14c3975_3

  ca-certificates    intel/linux-64::ca-certificates-2021.10.26-h06a4308_2

  cached-property    intel/noarch::cached-property-1.5.2-py_0

  cachetools         intel/noarch::cachetools-4.2.2-pyhd3eb1b0_0

  certifi            intel/linux-64::certifi-2021.10.8-py37h06a4308_0

  cffi               intel/linux-64::cffi-1.14.6-py37h400218f_0

  chardet            intel/linux-64::chardet-3.0.4-py37h82fad40_4

  click              intel/noarch::click-8.0.3-pyhd3eb1b0_0

  cloudpickle        intel/noarch::cloudpickle-1.6.0-py_0

  contextlib2        intel/noarch::contextlib2-0.5.5-py_2

  coverage           intel/linux-64::coverage-5.5-py37h27cfd23_2

  cryptography       intel/linux-64::cryptography-3.3.2-py37h3d3d174_1

  cython             intel/linux-64::cython-0.29.24-py37hbf8da92_2

  daal4py            intel/linux-64::daal4py-2021.5.1-py37_intel_803

  dal                intel/linux-64::dal-2021.5.1-intel_803

  dataclasses        intel/noarch::dataclasses-0.8-pyh6d0b6a4_7

  dpcpp-cpp-rt       intel/linux-64::dpcpp-cpp-rt-2022.0.1-intel_3633

  dpcpp_cpp_rt       intel/linux-64::dpcpp_cpp_rt-2022.0.1-intel_3633

  flatbuffers        intel/linux-64::flatbuffers-2.0.0-h2531618_0

  fortran_rt         intel/linux-64::fortran_rt-2022.0.1-intel_3633

  future             intel/linux-64::future-0.18.2-py37_1

  gast               intel/noarch::gast-0.4.0-py_0

  google-auth        intel/noarch::google-auth-1.33.0-pyhd3eb1b0_0

  google-auth-oauth~ intel/noarch::google-auth-oauthlib-0.4.1-py_2

  google-pasta       intel/noarch::google-pasta-0.2.0-py_0

  grpcio             intel/linux-64::grpcio-1.36.1-py37h2157cd5_1

  h5py               intel/linux-64::h5py-3.2.1-py37h6c542dc_0

  hdf5               intel/linux-64::hdf5-1.10.6-hb1b8bf9_0

  hyperopt           intel/noarch::hyperopt-0.2.5-pyh9f0ad1d_0

  icc_rt             intel/linux-64::icc_rt-2022.0.1-intel_3633

  idna               intel/linux-64::idna-3.1-py37hf52dec2_0

  impi-devel         intel/linux-64::impi-devel-2021.5.0-intel_497

  impi_rt            intel/linux-64::impi_rt-2021.5.0-intel_pycpuinfo_496

  importlib-metadata intel/linux-64::importlib-metadata-3.10.0-py37h06a4308_0

  intel-aikit-tenso~ intel/linux-64::intel-aikit-tensorflow-2021.3.0-0

  intel-cmplr-lib-rt intel/linux-64::intel-cmplr-lib-rt-2022.0.1-intel_3633

  intel-cmplr-lic-rt intel/linux-64::intel-cmplr-lic-rt-2022.0.1-intel_3633

  intel-fortran-rt   intel/linux-64::intel-fortran-rt-2022.0.1-intel_3633

  intel-opencl-rt    intel/linux-64::intel-opencl-rt-2022.0.1-intel_3633

  intel-openmp       intel/linux-64::intel-openmp-2022.0.1-intel_3633

  intelpython        intel/linux-64::intelpython-2022.0.0-0

  joblib             intel/linux-64::joblib-1.0.1-py37h3f38642_0

  keras-preprocessi~ intel/noarch::keras-preprocessing-1.1.2-pyhd3eb1b0_0

  libffi             intel/linux-64::libffi-3.3-14

  libgcc-ng          intel/linux-64::libgcc-ng-9.3.0-hdf63c60_101

  libgfortran-ng     intel/linux-64::libgfortran-ng-7.3.0-hdf63c60_0

  libprotobuf        intel/linux-64::libprotobuf-3.14.0-he78db7b_1

  libstdcxx-ng       intel/linux-64::libstdcxx-ng-9.3.0-hdf63c60_101

  lpot               intel/noarch::lpot-1.0-py_0

  markdown           intel/linux-64::markdown-3.3.4-py37h06a4308_0

  mkl                intel/linux-64::mkl-2022.0.1-intel_117

  mkl-service        intel/linux-64::mkl-service-2.4.0-py37h4119f30_11

  mkl_fft            intel/linux-64::mkl_fft-1.2.0-py37hb9c2cde_4

  mkl_random         intel/linux-64::mkl_random-1.2.0-py37h90a4e38_4

  mkl_umath          intel/linux-64::mkl_umath-0.1.0-py37hb46b53c_0

  multidict          intel/linux-64::multidict-5.1.0-py37h27cfd23_2

  networkx           intel/noarch::networkx-2.6.2-pyhd3eb1b0_2

  numpy              intel/linux-64::numpy-1.19.2-py37h02626c5_0

  numpy-base         intel/linux-64::numpy-base-1.19.2-py37h591eb60_0

  oauthlib           intel/noarch::oauthlib-3.1.1-pyhd3eb1b0_0

  openssl            intel/linux-64::openssl-1.1.1l-h7f8727e_0

  opt_einsum         intel/noarch::opt_einsum-3.3.0-pyhd3eb1b0_1

  pandas             intel/linux-64::pandas-1.2.0-py37hef31ef9_2

  pip                intel/linux-64::pip-21.2.2-py37h06a4308_0

  protobuf           intel/linux-64::protobuf-3.14.0-py37h2531618_1

  py-cpuinfo         intel/noarch::py-cpuinfo-8.0.0-pyhd3eb1b0_0

  pyasn1             intel/noarch::pyasn1-0.4.8-py_0

  pyasn1-modules     intel/noarch::pyasn1-modules-0.2.8-py_0

  pycparser          intel/noarch::pycparser-2.21-pyhd3eb1b0_0

  pyjwt              intel/noarch::pyjwt-2.1.0-pyhd8ed1ab_0

  pymongo            intel/linux-64::pymongo-3.11.4-py37h2531618_0

  pyopenssl          intel/noarch::pyopenssl-21.0.0-pyhd3eb1b0_1

  pysocks            intel/linux-64::pysocks-1.7.1-py37_1

  python             intel/linux-64::python-3.7.11-h6ca7d21_6

  python-dateutil    intel/linux-64::python-dateutil-2.8.2-py37_1

  pytz               intel/noarch::pytz-2021.3-pyhd3eb1b0_0

  pyyaml             intel/linux-64::pyyaml-6.0-py37h7f8727e_1

  requests           intel/linux-64::requests-2.25.1-py37h6282448_1

  requests-oauthlib  intel/noarch::requests-oauthlib-1.3.0-py_0

  rsa                intel/noarch::rsa-4.7.2-pyhd3eb1b0_1

  schema             intel/noarch::schema-0.7.4-pyh44b312d_0

  scikit-learn       intel/linux-64::scikit-learn-0.24.2-py37h8411759_4

  scikit-learn-inte~ intel/linux-64::scikit-learn-intelex-2021.5.1-py37_intel_803

  scipy              intel/linux-64::scipy-1.5.2-py37h83b3cbf_0

  setuptools         intel/linux-64::setuptools-58.0.4-py37h06a4308_0

  six                intel/linux-64::six-1.16.0-py37_0

  sqlite             intel/linux-64::sqlite-3.36.0-hb9a14ef_3

  tbb                intel/linux-64::tbb-2021.5.0-intel_707

  tbb4py             intel/linux-64::tbb4py-2021.5.0-py37_intel_707

  tensorboard        intel/noarch::tensorboard-2.5.0-py_0

  tensorboard-plugi~ intel/noarch::tensorboard-plugin-wit-1.6.0-py_0

  tensorflow         intel/linux-64::tensorflow-2.5.0-py37_1

  tensorflow-estima~ intel/noarch::tensorflow-estimator-2.5.0-pyh7b7c402_0

  termcolor          intel/linux-64::termcolor-1.1.0-py37h06a4308_1

  threadpoolctl      intel/noarch::threadpoolctl-2.2.0-pyh0d69192_0

  tk                 intel/linux-64::tk-8.6.10-h8e2d9d6_3

  tqdm               intel/noarch::tqdm-4.62.3-pyhd3eb1b0_1

  typing-extensions  intel/noarch::typing-extensions-3.7.4.3-hd3eb1b0_0

  typing_extensions  intel/noarch::typing_extensions-3.7.4.3-pyh06a4308_0

  urllib3            intel/linux-64::urllib3-1.26.6-py37h6fed32d_1

  werkzeug           intel/noarch::werkzeug-2.0.2-pyhd3eb1b0_0

  wheel              intel/noarch::wheel-0.37.0-pyhd3eb1b0_1

  wrapt              intel/linux-64::wrapt-1.12.1-py37h7b6447c_1

  xz                 intel/linux-64::xz-5.2.5-h74280d8_2

  yaml               intel/linux-64::yaml-0.2.5-h7b6447c_0

  yarl               intel/linux-64::yarl-1.6.3-py37h27cfd23_0

  zipp               intel/noarch::zipp-3.6.0-pyhd3eb1b0_0

  zlib               intel/linux-64::zlib-1.2.11.1-h1e99aa7_5

 

 

Proceed ([y]/n)? y

 

Preparing transaction: done

Verifying transaction: done

Executing transaction: /

    Installed package of scikit-learn can be accelerated using scikit-learn-intelex.

    More details are available here: https://intel.github.io/scikit-learn-intelex

    For example:

        $ conda install scikit-learn-intelex

        $ python -m sklearnex my_application.py

   

 

done

#

# To activate this environment, use

#

#     $ conda activate oneapi-tf

#

# To deactivate an active environment, use

#

#     $ conda deactivate

 

(base) npeper@TGL-i7-NUC-1:~$ conda activate oneapi-tf

(oneapi-tf) npeper@TGL-i7-NUC-1:~$ python -c "import tensorflow as tf"

Traceback (most recent call last):

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/numpy/core/__init__.py", line 22, in <module>

    from . import multiarray

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/numpy/core/multiarray.py", line 12, in <module>

    from . import overrides

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/numpy/core/overrides.py", line 7, in <module>

    from numpy.core._multiarray_umath import (

ImportError: libmkl_rt.so.1: cannot open shared object file: No such file or directory

 

During handling of the above exception, another exception occurred:

 

Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/tensorflow/__init__.py", line 41, in <module>

    from tensorflow.python.tools import module_util as _module_util

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/tensorflow/python/__init__.py", line 40, in <module>

    from tensorflow.python.eager import context

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/tensorflow/python/eager/context.py", line 29, in <module>

    import numpy as np

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/numpy/__init__.py", line 156, in <module>

    from . import core

  File "/home/npeper/miniconda3/envs/oneapi-tf/lib/python3.7/site-packages/numpy/core/__init__.py", line 48, in <module>

    raise ImportError(msg)

ImportError:

 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

 

Importing the numpy C-extensions failed. This error can happen for

many reasons, often due to issues with your setup or how NumPy was

installed.

 

We have compiled some common reasons and troubleshooting tips at:

 

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

 

Please note and check the following:

 

  * The Python version is: Python3.7 from "/home/npeper/miniconda3/envs/oneapi-tf/bin/python"

  * The NumPy version is: "1.19.2"

 

and make sure that they are the versions you expect.

Please carefully study the documentation linked above for further help.

 

Original error was: libmkl_rt.so.1: cannot open shared object file: No such file or directory

 

(oneapi-tf) npeper@TGL-i7-NUC-1:~$ cd /opt

(oneapi-tf) npeper@TGL-i7-NUC-1:/opt$ ls

google

 

Labels (3)
0 Kudos
3 Replies
VaradJ_Intel
Moderator
629 Views

Hi,


Thank you for posting in Intel communities. 


We could reproduce your issue and we have a workaround for that. Try locating the libmkl_rt.so with the below command:


locate libmkl_rt.so 


If locate command is not found, try installing with the following command:


sudo apt install mlocate


Try renaming all the files to libmkl_rt.so.1 with the below command:


mv <path>/libmkl_rt.so <path>/libmkl_rt.so.1


You would be getting an error that flatbuffers module is not found. You could resolve it by simply installing that package with the below command:


conda install -c conda-forge python-flatbuffers


Try importing tensorflow again & let us know if the issue still persists.


Thank You.


Nathan_Peper
Employee
605 Views

Thank you so much for the help on this, it looks like that method works for the tensorflow import. While continuing to troubleshoot, I also found this as a fix to the issue:

 

https://stackoverflow.com/questions/58868528/importing-the-numpy-c-extensions-failed

  1. pip uninstall -y numpy
  2. pip uninstall -y setuptools
  3. pip install setuptools
  4. pip install numpy
  5. conda install -c conda-forge python-flatbuffers

 

Is one fix more robust or proper than the other here when looking to have all of the oneAPI features enabled? 

 

Thank you!

VaradJ_Intel
Moderator
584 Views

Hi,


Glad to know that your issue is resolved. Thanks for sharing the solution with us. Both the workarounds solves the issue but the workaround suggested by you looks more robust or proper. If you need any additional information, please post a new question as this thread will no longer be monitored by Intel.


Thank You.


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