conda update error on a fresh install of 2020.1

conda update error on a fresh install of 2020.1


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 ([y]/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>
 

10 posts / 0 new

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. 


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.


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


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.


Hi,

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

 

Best,

Marc


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?


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


Hi Marc,

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


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 ([y]/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>

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