conda update error on a fresh install of 2020.1

Marc_R_2 · ‎05-11-2020

Hi,

I have a fresh install of Intel Distribution for Python 2020.1 on Windows 10 and am running into the problem that "conda update" is not working. It fails on the Intel packages. e.g. "An error occurred while uninstalling package '<unknown>::intel-openmp-2020.0-intel_166'". (see below)

Is there a work-around for this?

Best,

Marc

(base) C:\intelpython>conda update --all
WARNING conda.core.prefix_data:_load_single_record(183): Ignoring malformed prefix record at: C:\intelpython\conda-meta\tbb-2020.0-intel_166.json
Collecting package metadata (current_repodata.json): done
Solving environment: /
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- <unknown>/win-64::daal==2020.0=intel_166
- intel/win-64::daal4py==2020.0=py37ha68da19_5
- intel/win-64::matplotlib==3.1.1=py37_3
- <unknown>/win-64::mkl==2020.0=intel_166
- intel/win-64::mkl-service==2.3.0=py37_0
- intel/win-64::mkl_fft==1.0.15=py37ha68da19_3
- intel/win-64::mkl_random==1.1.0=py37ha68da19_0
- intel/win-64::numba==0.45.1=np117py37_6
- intel/win-64::numexpr==2.7.0=py37_1
- intel/win-64::numpy==1.17.4=py37ha68da19_4
- intel/win-64::numpy-base==1.17.4=py37_4
- intel/win-64::pandas==0.25.1=py37_3
- intel/win-64::scikit-learn==0.21.3=py37ha68da19_15
- intel/win-64::scipy==1.3.2=py37ha68da19_0
- intel/win-64::tbb4py==2020.0=py37_intel_0
done
## Package Plan ##
environment location: C:\intelpython

The following packages will be downloaded:
package | build
---------------------------|-----------------
asn1crypto-1.3.0 | py37_0 171 KB intel
bzip2-1.0.8 | vc14_1 83 KB intel
certifi-2019.11.28 | py37_0 147 KB intel
cffi-1.13.2 | py37_2 216 KB intel
conda-package-handling-1.4.0| py37_1 289 KB intel
cryptography-2.8 | py37_0 356 KB intel
cython-0.29.14 | py37ha68da19_0 2.4 MB intel
icc_rt-2020.1 | intel_216 13.3 MB intel
idna-2.8 | py37_0 101 KB intel
impi_rt-2019.7 | intel_216 8.3 MB intel
intel-openmp-2020.1 | intel_216 2.0 MB intel
intelpython-2020.1 | 0 502 KB intel
ipp-2020.1 | intel_216 74.7 MB intel
kiwisolver-1.1.0 | py37h6538335_0 61 KB intel
libarchive-3.4.2 | h2fa13f4_2 5.6 MB intel
libpng-1.6.37 | 2 590 KB intel
llvmlite-0.31.0 | py37ha1f5b8b_1 8.2 MB intel
lzo-2.10 | hfa6e2cd_4 170 KB intel
mpi4py-3.0.3 | py37_6 450 KB intel
numba-0.48.0 | np117py37_0 3.3 MB intel
openssl-1.1.1d | vc14_1 5.9 MB intel
pip-19.3.1 | py37_2 1.9 MB intel
pycparser-2.19 | py37_1 171 KB intel
pyopenssl-19.1.0 | py37_1 81 KB intel
pyparsing-2.4.5 | py37_1 108 KB intel
pysocks-1.7.0 | py37_1 25 KB intel
python-3.7.7 | h21ff451_0 17.6 MB intel
python-dateutil-2.8.1 | py37_1 276 KB intel
pytz-2019.3 | py37_1 274 KB intel
pyyaml-5.3 | py37_0 192 KB intel
requests-2.22.0 | py37_1 84 KB intel
ruamel_yaml-0.15.99 | py37_4 280 KB intel
setuptools-45.2.0 | py37_0 682 KB intel
six-1.13.0 | py37_2 22 KB intel
sqlite-3.30.1 | vc14_6 974 KB intel
tbb-2020.2 | vc14_intel_216 276 KB intel
tcl-8.6.9 | vc14_24 1.5 MB intel
tk-8.6.9 | vc14_29 1.3 MB intel
tqdm-4.39.0 | py37_2 94 KB intel
urllib3-1.25.7 | py37_0 160 KB intel
wheel-0.33.6 | py37_4 61 KB intel
win_inet_pton-1.1.0 | py37_0 7 KB intel
xz-5.2.4 | vc14_5 345 KB intel
yaml-0.1.7 | 5 111 KB intel
zlib-1.2.11.1 | vc14hfa6e2cd_1 351 KB intel
------------------------------------------------------------
Total: 153.5 MB
The following NEW packages will be INSTALLED:
tbb intel/win-64::tbb-2020.2-vc14_intel_216
The following packages will be UPDATED:
asn1crypto 0.24.0-py37_3 --> 1.3.0-py37_0
bzip2 1.0.8-vc14_0 --> 1.0.8-vc14_1
certifi 2019.9.11-py37_0 --> 2019.11.28-py37_0
cffi 1.12.3-py37_2 --> 1.13.2-py37_2
conda-package-han~ 1.4.0-py37_0 --> 1.4.0-py37_1
cryptography 2.7-py37_0 --> 2.8-py37_0
cython 0.29.13-py37ha68da19_0 --> 0.29.14-py37ha68da19_0
icc_rt <unknown>::icc_rt-2020.0-intel_166 --> intel::icc_rt-2020.1-intel_216
idna 2.6-py37_3 --> 2.8-py37_0
impi_rt <unknown>::impi_rt-2019.6-intel_166 --> intel::impi_rt-2019.7-intel_216
intel-openmp <unknown>::intel-openmp-2020.0-intel_~ --> intel::intel-openmp-2020.1-intel_216
intelpython 2020.0-1 --> 2020.1-0
ipp <unknown>::ipp-2020.0-intel_166 --> intel::ipp-2020.1-intel_216
kiwisolver 1.0.1-py37_2 --> 1.1.0-py37h6538335_0
libarchive 3.4.0-h2fa13f4_0 --> 3.4.2-h2fa13f4_2
libpng 1.6.36-2 --> 1.6.37-2
llvmlite 0.29.0-py37_9 --> 0.31.0-py37ha1f5b8b_1
lzo 2.10-hfa6e2cd_0 --> 2.10-hfa6e2cd_4
mpi4py 3.0.0-py37_6 --> 3.0.3-py37_6
numba 0.45.1-np117py37_6 --> 0.48.0-np117py37_0
openssl 1.1.1d-vc14_0 --> 1.1.1d-vc14_1
pip 19.1.1-py37_0 --> 19.3.1-py37_2
pycparser 2.18-py37_2 --> 2.19-py37_1
pyopenssl 17.5.0-py37_2 --> 19.1.0-py37_1
pyparsing 2.2.0-py37_2 --> 2.4.5-py37_1
pysocks 1.6.7-py37_1 --> 1.7.0-py37_1
python 3.7.4-h21ff451_3 --> 3.7.7-h21ff451_0
python-dateutil 2.8.0-py37_0 --> 2.8.1-py37_1
pytz 2019.1-py37_0 --> 2019.3-py37_1
pyyaml 5.1.1-py37_0 --> 5.3-py37_0
requests 2.20.1-py37_1 --> 2.22.0-py37_1
ruamel_yaml 0.15.64-py37_1 --> 0.15.99-py37_4
setuptools 41.0.1-py37_0 --> 45.2.0-py37_0
six 1.12.0-py37_0 --> 1.13.0-py37_2
sqlite 3.29.0-vc14_0 --> 3.30.1-vc14_6
tcl 8.6.4-vc14_24 --> 8.6.9-vc14_24
tk 8.6.4-vc14_29 --> 8.6.9-vc14_29
tqdm 4.32.1-py37_0 --> 4.39.0-py37_2
urllib3 1.24.1-py37_2 --> 1.25.7-py37_0
wheel 0.31.0-py37_3 --> 0.33.6-py37_4
win_inet_pton 1.0.1-py37_4 --> 1.1.0-py37_0
yaml 0.1.7-2 --> 0.1.7-5
zlib 1.2.11-vc14hfa6e2cd_7 --> 1.2.11.1-vc14hfa6e2cd_1
The following packages will be DOWNGRADED:
xz 5.2.4-h2fa13f4_7 --> 5.2.4-vc14_5

Proceed (/n)? y

Downloading and Extracting Packages
certifi-2019.11.28 | 147 KB | ############################################################################ | 100%
conda-package-handli | 289 KB | ############################################################################ | 100%
llvmlite-0.31.0 | 8.2 MB | ############################################################################ | 100%
ruamel_yaml-0.15.99 | 280 KB | ############################################################################ | 100%
six-1.13.0 | 22 KB | ############################################################################ | 100%
pycparser-2.19 | 171 KB | ############################################################################ | 100%
intelpython-2020.1 | 502 KB | ############################################################################ | 100%
win_inet_pton-1.1.0 | 7 KB | ############################################################################ | 100%
xz-5.2.4 | 345 KB | ############################################################################ | 100%
pysocks-1.7.0 | 25 KB | ############################################################################ | 100%
requests-2.22.0 | 84 KB | ############################################################################ | 100%
urllib3-1.25.7 | 160 KB | ############################################################################ | 100%
python-3.7.7 | 17.6 MB | ############################################################################ | 100%
mpi4py-3.0.3 | 450 KB | ############################################################################ | 100%
pytz-2019.3 | 274 KB | ############################################################################ | 100%
tbb-2020.2 | 276 KB | ############################################################################ | 100%
lzo-2.10 | 170 KB | ############################################################################ | 100%
tk-8.6.9 | 1.3 MB | ############################################################################ | 100%
sqlite-3.30.1 | 974 KB | ############################################################################ | 100%
libpng-1.6.37 | 590 KB | ############################################################################ | 100%
cython-0.29.14 | 2.4 MB | ############################################################################ | 100%
pyparsing-2.4.5 | 108 KB | ############################################################################ | 100%
intel-openmp-2020.1 | 2.0 MB | ############################################################################ | 100%
tqdm-4.39.0 | 94 KB | ############################################################################ | 100%
ipp-2020.1 | 74.7 MB | ############################################################################ | 100%
icc_rt-2020.1 | 13.3 MB | ############################################################################ | 100%
pyopenssl-19.1.0 | 81 KB | ############################################################################ | 100%
bzip2-1.0.8 | 83 KB | ############################################################################ | 100%
yaml-0.1.7 | 111 KB | ############################################################################ | 100%
cryptography-2.8 | 356 KB | ############################################################################ | 100%
python-dateutil-2.8. | 276 KB | ############################################################################ | 100%
libarchive-3.4.2 | 5.6 MB | ############################################################################ | 100%
pip-19.3.1 | 1.9 MB | ############################################################################ | 100%
idna-2.8 | 101 KB | ############################################################################ | 100%
asn1crypto-1.3.0 | 171 KB | ############################################################################ | 100%
zlib-1.2.11.1 | 351 KB | ############################################################################ | 100%
kiwisolver-1.1.0 | 61 KB | ############################################################################ | 100%
impi_rt-2019.7 | 8.3 MB | ############################################################################ | 100%
openssl-1.1.1d | 5.9 MB | ############################################################################ | 100%
tcl-8.6.9 | 1.5 MB | ############################################################################ | 100%
setuptools-45.2.0 | 682 KB | ############################################################################ | 100%
cffi-1.13.2 | 216 KB | ############################################################################ | 100%
wheel-0.33.6 | 61 KB | ############################################################################ | 100%
numba-0.48.0 | 3.3 MB | ############################################################################ | 100%
pyyaml-5.3 | 192 KB | ############################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(700): An error occurred while uninstalling package '<unknown>::intel-openmp-2020.0-intel_166'.
Rolling back transaction: done
ValueError('Attempted to make prefix record for unknown package type: intel-openmp-2020.0-intel_166')
()

(base) C:\intelpython>

ChithraJ_Intel · ‎05-12-2020

Hi Marc,

Thanks for reaching out to us.

We are investigating on the issue.Meanwhile, could you please try installing Intel® Distribution for Python* using anaconda as follows:
Step 1: Create a virtual environment in Anaconda with required Intel Distribution for python. For that, You need at least conda 4.1.11, so first update your conda using :

conda update conda

Step 2: To get Intel packages over default packages, add the Intel channel as follows :

conda config --add channels intel

Step 3: To install the latest full Intel python distribution :

conda create -n idp intelpython3_full python=3

Step 4: Activate your virtual environment with:

activate idp

Now, you have the virtual environment with intelpython installed, including numpy, scipy etc. You can use the usual conda install commands for additional packages. For example, to install intel sympy do:

conda install sympy

Hopes this workaround will help you.

ChithraJ_Intel · ‎05-13-2020

Hi Marc,

We also tried to install Intel Distribution for Python 2020.1 on Windows 10 using the installer and tried to update the conda packages as you did. We were able to find that it's updating all the packages without any issues with the below steps:

Step 1: Register and download the latest Intel® Distribution for Python zip file from the link: https://software.intel.com/content/www/us/en/develop/tools/distribution-for-python/choose-download/windows.html
[Note: Skip the step, if it's done already]
Step 2: Extract Intel distribution for Python ZIP file. Open a command prompt and run setup_intel_python.bat in that directory.
Step 3: Update the conda packages as:
conda update --all

Could you please confirm whether you are doing the same steps or not.If not, please try the above steps and feel free to reach out to us in case of any issues.

Thanks.

Marc_R_2 · ‎05-13-2020

Hi,

I did almost exactly the same. I only called activate.bat after the setup in order to get conda into the path.

Best,

Marc

ChithraJ_Intel · ‎05-14-2020

Hi Marc,

Please let me know whether the workaround helped for you. Since, we are not able to reproduce the issue, we will contact with the SME on this issue and get back to you soon.

Thanks.

Marc_R_2 · ‎05-17-2020

Hi,

I can confirm that the work-around (with env idp) with a stock Anaconda 2020.02 works.

Best,

Marc

ChithraJ_Intel · ‎05-18-2020

Hi Marc,

Thanks for the confirmation. Since the workaround resolved your issue, shall we close this case? Or do you want to keep this as open until your conda update issue get resolved?

Marc_R_2 · ‎05-21-2020

HI,

I would prefer this issues to remain open, since it is not resolved. Although, the work-around works it forces me to install the stock Anaconda distribution and use conda envs. Two things I really prefer *not* to do.

Best,

Marc

ChithraJ_Intel · ‎05-22-2020

Hi Marc,

We are forwarding this case for SME to check. They will get back to you on this.

Marc_R_2 · ‎06-03-2020

I have reloaded he distribution today and tried again. The output below is from a fresh installation. I unzipped the distribution with 7zip directly to c:\.

I tried with and without support for longnames turned on in Windows. Same problem. Is there anything else I could try or provide?

C:\>cd intelpython3

C:\intelpython3>dir
Volume in drive C is Windows
Volume Serial Number is AAD8-4535

Directory of C:\intelpython3

24/03/2020 10:16 <DIR> .
24/03/2020 10:16 <DIR> ..
24/03/2020 10:16 41 184 condainstall.py
24/03/2020 10:16 5 996 generate_urlstxt.bat
24/03/2020 10:16 <DIR> licensing
24/03/2020 10:17 <DIR> pkgs
24/03/2020 10:16 163 ReleaseNotes.txt
24/03/2020 10:16 460 setup_intel_python.bat
4 File(s) 47 803 bytes
4 Dir(s) 310 282 493 952 bytes free

C:\intelpython3>cmd /c setup_intel_python.bat

INSTALLED PACKAGE OF SCIKIT-LEARN CAN BE ACCELERATED USING DAAL4PY.

PLEASE SET 'USE_DAAL4PY_SKLEARN' ENVIRONMENT VARIABLE TO 'YES' TO ENABLE THE ACCELERATION.

FOR EXAMPLE:

$ set USE_DAAL4PY_SKLEARN=YES
$ python -c 'import sklearn'

Warning: 'intel' already in 'channels' list, moving to the top

C:\intelpython3>Scripts\activate

(base) C:\intelpython3>conda update --all
WARNING conda.core.prefix_data:_load_single_record(183): Ignoring malformed prefix record at: C:\intelpython3\conda-meta\tbb-2020.2-intel_216.json
Collecting package metadata (current_repodata.json): done
Solving environment: \
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

- <unknown>/win-64::daal==2020.1=intel_216
- intel/win-64::daal4py==2020.1=py37ha68da19_0
- intel/win-64::matplotlib==3.1.2=py37_3
- <unknown>/win-64::mkl==2020.1=intel_216
- intel/win-64::mkl-service==2.3.0=py37_0
- intel/win-64::mkl_fft==1.1.0=py37ha68da19_0
- intel/win-64::mkl_random==1.1.0=py37ha68da19_0
- intel/win-64::numba==0.48.0=np117py37_0
- intel/win-64::numexpr==2.7.0=py37_1
- intel/win-64::numpy==1.17.5=py37ha68da19_1
- intel/win-64::numpy-base==1.17.5=py37_1
- intel/win-64::pandas==0.25.3=py37_4
- intel/win-64::scikit-learn==0.22.1=py37ha68da19_10
- intel/win-64::scipy==1.3.3=py37ha68da19_2
- intel/win-64::tbb4py==2020.2=py37_intel_0
done

## Package Plan ##

environment location: C:\intelpython3

The following packages will be downloaded:

package | build
---------------------------|-----------------
icc_rt-2020.1 | intel_216 13.3 MB intel
impi_rt-2019.7 | intel_216 8.3 MB intel
intel-openmp-2020.1 | intel_216 2.0 MB intel
ipp-2020.1 | intel_216 74.7 MB intel
tbb-2020.2 | vc14_intel_216 276 KB intel
xz-5.2.4 | vc14_5 345 KB intel
------------------------------------------------------------
Total: 98.9 MB

The following NEW packages will be INSTALLED:

tbb intel/win-64::tbb-2020.2-vc14_intel_216

The following packages will be SUPERSEDED by a higher-priority channel:

icc_rt <unknown> --> intel
impi_rt <unknown> --> intel
intel-openmp <unknown> --> intel
ipp <unknown> --> intel

The following packages will be DOWNGRADED:

xz 5.2.4-h2fa13f4_7 --> 5.2.4-vc14_5

Proceed (/n)? y

Downloading and Extracting Packages
xz-5.2.4 | 345 KB | ############################################################## | 100%
tbb-2020.2 | 276 KB | ############################################################## | 100%
ipp-2020.1 | 74.7 MB | ############################################################## | 100%
impi_rt-2019.7 | 8.3 MB | ############################################################## | 100%
intel-openmp-2020.1 | 2.0 MB | ############################################################## | 100%
icc_rt-2020.1 | 13.3 MB | ############################################################## | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(700): An error occurred while uninstalling package '<unknown>::intel-openmp-2020.1-intel_216'.
Rolling back transaction: done

ValueError('Attempted to make prefix record for unknown package type: intel-openmp-2020.1-intel_216')
()

(base) C:\intelpython3>

AthiraM_Intel · ‎06-22-2021

Hi,

Could you please check if the issue is reproducible with the new version (Intel Distribution for Python 2021.2)?

You can install the Intel Distribution for Python 2021.2 from the below link:

https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html

We are able to update conda successfully with the latest version.

If the issue still persists for you, please let us know.

Thanks.

AthiraM_Intel · ‎06-29-2021

Hi,

We have not heard back from you. Could you please give us an update?

Thanks.

AthiraM_Intel · ‎07-06-2021

Hi,

We have not heard back from you, so we will close this inquiry now. If you need further assistance, please post a new question.

Thanks.