Issue with pytables in IntelPython 2021.03 for Mac Os X - removes daal-2021.3.0-intel_555

Bamboos · ‎07-27-2022

I have Intelpython 2021.03 for mac os x (10.13.6 ), the current version of Intelpython (2022.1) can't allow to install tensorflow (2.0 for mac) and py-xgboost (xgboost doesn't install) because of python 3.9.

The following warnings are issued when working with pytables 3.6.1:

/Users/rob/opt/intelpython/latest/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
  return f(*args, **kwds)
/Users/rob/opt/intelpython/latest/lib/python3.7/site-packages/tables/array.py:241: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe. 
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  (oid, self.atom, self.shape, self._v_chunkshape) = self._open_array()

which refers to issue 898 of pytables (see https://github.com/PyTables/PyTables/issues/898) relative to numpy 1.20 (which is installed in intelpython) using lowercase for type (i.e., int instead of Int, float instead of Float) solved as either "Using numpy 1.21.2 and latest pytables" or "updating by hand hdf5extension.cpython-37m-darwin.py" where the call to _g_open() in array.py originates. It seems it has been compiled against an older numpy than is installed (1.20) supposed to be >=1.16.5 as revealed by the average requires.txt in the installation directory (see https://github.com/numpy/numpy/pull/432)

1) The second option is not available since I have "hdf5extension.cpython-37m-darwin.so", a precompiled file for which I don't have the source file.

2) The first option requires updating pytables with conda, adding the following packages AND REMOVING daal-2021.3.0-intel_555 which I dont' want of course:

backcall-0.2.0 | pyhd3eb1b0_0 13 KB

jedi-0.18.1 | py37hecd8cb5_1 978 KB

qtconsole-5.3.1 | py37hecd8cb5_0 177 KB

regex-2022.7.9 | py37hca72f7f_0 313 KB

matplotlib-inline pkgs/main/noarch::matplotlib-inline-0.1.2-pyhd3eb1b0_2

parso pkgs/main/noarch::parso-0.8.3-pyhd3eb1b0_0

prompt-toolkit pkgs/main/noarch::prompt-toolkit-3.0.20-pyhd3eb1b0_0

But the following packages will be REMOVED:

daal-2021.3.0-intel_555

simplegeneric-0.8.1-py37_2

Any help appreciated.

Thanks,

Roberto

AlekhyaV_Intel · ‎07-29-2022

Hi,

Thank you for posting in Intel Communities. And Thank you for sharing all the details with us. We tried reproducing your issue in Mac OS (10.15.6) with Intel core i5 8500 B processor by creating a new environment and installing all the packages mentioned by you.

Set environment variables before creating/activating this below mentioned environment:

source /opt/intel/oneapi/setvars.sh

Conda environment creation and activation:

conda create -n idp intelpython3_full python=3.7

conda activate idp

Installed tensorflow 2.0, xgboost, pytables inside the idp environment with the below command:

pip3 install tensorflow==2.0
pip3 install xgboost
pip3 install tables==3.6.1

And while creating an environment, you will be getting numpy latest version by default.

So we suggest you to create a environment and try working with pytables. Please provide us your processor details if the issue still persists.

If this resolves your issue, make sure to accept this as a solution. This helps other users with similar issue. Thank you!

Regards,

Alekhya

AlekhyaV_Intel · ‎08-08-2022

Hi,

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

Regards,

Alekhya

Bamboos · ‎08-09-2022

Hi there,

thanks for the prompt answer. The issue remains. Here what I did:

source /opt/intel/oneapi/setvars.sh

conda create -n idp intelpython3_full python=3.7

conda activate idp

pip install py_vollib
pip install sklearn-genetic
pip install mplfinance
pip install sdepy
pip install statsmodels
pip install pdfkit and download https://wkhtmltopdf.org/downloads.html

pip install shap
pip install PyALE
Pip install lime

pip3 install tensorflow==2.0
pip3 install xgboost
pip3 install tables==3.6.1

pip install seaborn
pip install jupyter

By the way, I've tried to update pytables to the latest version but then it report the following error:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
~/opt/intelpython/latest/lib/python3.7/site-packages/numpy/core/__init__.py in <module>
     21 try:
---> 22     from . import multiarray
     23 except ImportError as exc:

~/opt/intelpython/latest/lib/python3.7/site-packages/numpy/core/multiarray.py in <module>
     11 
---> 12 from . import overrides
     13 from . import _multiarray_umath

~/opt/intelpython/latest/lib/python3.7/site-packages/numpy/core/overrides.py in <module>
      6 
----> 7 from numpy.core._multiarray_umath import (
      8     add_docstring, implement_array_function, _get_implementing_args)

ImportError: dlopen(/Users/rob/opt/intelpython/latest/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Library not loaded: @rpath/libmkl_rt.1.dylib
  Referenced from: /Users/rob/opt/intelpython/latest/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so
  Reason: image not found

Bamboos · ‎08-09-2022

Model Name: MacBook Pro

Model Identifier: MacBookPro15,2

Processor Name: Intel Core i5

Processor Speed: 2,3 GHz

Number of Processors: 1

Total Number of Cores: 4

L2 Cache (per Core): 256 KB

L3 Cache: 6 MB

Hyper-Threading Technology: Enabled

Memory: 16 GB

Boot ROM Version: 1715.40.15.0.0 (iBridge: 19.16.10548.0.0,0)

Serial Number (system): C02X508KJHD4

Hardware UUID: 64690A9C-88A9-5968-9523-BF074561204E

Bamboos · ‎08-09-2022

System Software Overview:

System Version: macOS 10.14.6 (18G9323)

Kernel Version: Darwin 18.7.0

Boot Volume: Untitled

Boot Mode: Normal

Computer Name: Roberto’s MacBook Pro (2)

Username: Roberto Garrone (rob)

Secure Virtual Memory: Enabled

System Integrity Protection: Enabled

Time since boot: 17:48

AlekhyaV_Intel · ‎08-16-2022

Hi,

Thank you for sharing all the information. We are working on this internally. We will get back to you soon with an update

Regards,

Alekhya

AlekhyaV_Intel · ‎08-18-2022

Hi,

We tried reproducing all the steps that you've provided and we could not find any issues in it.

Below is our system software overview:

Please try upgrading your OS and see if the issue still persists.

Regards,

Alekhya

Bamboos · ‎08-18-2022

Thanks for your support. At the end I resolved to install from 2021.3.0.3043 and then

conda install -c intel intelpython3_full python=3.7

pip install py_vollib
pip install sklearn-genetic
pip install mplfinance
pip install sdepy
pip install statsmodels
pip install pdfkit and download https://wkhtmltopdf.org/downloads.html

pip install shap
pip install PyALE
pip install lime

pip3 install tensorflow==2.0
#pip3 install xgboost #not working, see below
#pip3 install tables==3.6.1 #not working, see below
pip install tables #install 3.7.0

pip install seaborn
sudo conda install jupyter
sudo conda install py-xgboost

Pip install yfinance
Pip install fredapi
Pip install arch
Pip install openpyxl

Now it doesn't complain about removing daal-2021.3.0-intel_555; the issue is solved although one warning remains because numpy is still 1.20.3 but I can live with it.

Many thanks,

Roberto

AlekhyaV_Intel · ‎08-19-2022

Hi,

Glad to know that your issue is resolved. Thanks for sharing all the steps which resolved your issue. If you need any further assistance, please post a new question as this thread will no longer be monitored by Intel.

Regards,

Alekhya