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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:
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
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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.
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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
- pip uninstall -y numpy
- pip uninstall -y setuptools
- pip install setuptools
- pip install numpy
- 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!
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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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