`mamba uninstall cudatoolkit` fails (conda equivalent works) #1770

pierreglaser · 2022-06-29T14:35:33Z

Steps to reproduce: in a shell, run:

mamba create -n condaforgecuda cudatoolkit
mamba uninstall -n condaforgecuda cudatoolkit

First line works fine, second fails with:

Removing specs: ['cudatoolkit']
Transaction

  Prefix: /nfs/nhome/live/pierreg/.local/miniforge/envs/condaforgecuda

  Removing specs:

   - cudatoolkit


  Package          Version  Build        Channel         Size
───────────────────────────────────────────────────────────────
  Remove:
───────────────────────────────────────────────────────────────

  - __glibc           2.31  0            installed
  - _libgcc_mutex      0.1  conda_forge  conda-forge
  - _openmp_mutex      4.5  2_gnu        conda-forge
  - cudatoolkit     11.7.0  hd8887f6_10  conda-forge
  - libgcc-ng       12.1.0  h8d9b700_16  conda-forge
  - libgomp         12.1.0  h8d9b700_16  conda-forge
  - libstdcxx-ng    12.1.0  ha89aaad_16  conda-forge

  Summary:

  Remove: 7 packages

  Total download: 0 B

───────────────────────────────────────────────────────────────

Confirm changes: [Y/n] Y

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/nfs/nhome/live/pierreg/.local/miniforge/lib/python3.9/site-packages/conda/_vendor/boltons/setutils.py", line 247, in remove
        didx = self.item_index_map.pop(item)
    KeyError: PackageRecord(_hash=-1097009890971377200, name='__glibc', version='2.31', build='0', build_number=0, channel=Channel("@"), subdir='linux-64', fn='__glibc', md5='12345678901234567890123456789012', package_type='virtual_system')

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/nfs/nhome/live/pierreg/.local/miniforge/lib/python3.9/site-packages/conda/exceptions.py", line 1114, in __call__
        return func(*args, **kwargs)
      File "/nfs/nhome/live/pierreg/.local/miniforge/lib/python3.9/site-packages/mamba/mamba.py", line 935, in exception_converter
        raise e
      File "/nfs/nhome/live/pierreg/.local/miniforge/lib/python3.9/site-packages/mamba/mamba.py", line 929, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/nfs/nhome/live/pierreg/.local/miniforge/lib/python3.9/site-packages/mamba/mamba.py", line 887, in _wrapped_main
        result = do_call(args, p)
      File "/nfs/nhome/live/pierreg/.local/miniforge/lib/python3.9/site-packages/mamba/mamba.py", line 752, in do_call
        exit_code = remove(args, parser)
      File "/nfs/nhome/live/pierreg/.local/miniforge/lib/python3.9/site-packages/mamba/mamba.py", line 240, in remove
        conda_transaction = to_txn(
      File "/nfs/nhome/live/pierreg/.local/miniforge/lib/python3.9/site-packages/mamba/utils.py", line 432, in to_txn
        final_precs = compute_final_precs(
      File "/nfs/nhome/live/pierreg/.local/miniforge/lib/python3.9/site-packages/mamba/utils.py", line 367, in compute_final_precs
        final_precs.remove(i_rec)
      File "/nfs/nhome/live/pierreg/.local/miniforge/lib/python3.9/site-packages/conda/_vendor/boltons/setutils.py", line 249, in remove
        raise KeyError(item)
    KeyError: PackageRecord(_hash=-1097009890971377200, name='__glibc', version='2.31', build='0', build_number=0, channel=Channel("@"), subdir='linux-64', fn='__glibc', md5='12345678901234567890123456789012', package_type='virtual_system')

`$ /nfs/nhome/live/pierreg/.local/miniforge/bin/mamba uninstall -n condaforgecuda cudatoolkit`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/nfs/nhome/live/pierreg/.local/miniforge/bin/conda
             CONDA_PREFIX=/nfs/nhome/live/pierreg/.local/miniforge
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/nfs/nhome/live/pierreg/.local/miniforge/bin/python
               CONDA_ROOT=/nfs/nhome/live/pierreg/.local/miniforge
              CONDA_SHLVL=1
           CURL_CA_BUNDLE=<not set>
                  MANPATH=::/opt/puppetlabs/puppet/share/man
               MODULEPATH=/etc/environment-modules/modules:/usr/share/modules/versions:/usr/shar
                          e/modules/modulefiles:/ceph/apps/ubuntu-20/modulefiles
                     PATH=/nfs/nhome/live/pierreg/.local/miniforge/bin:/nfs/nhome/live/pierreg/.
                          local/bin:/nfs/nhome/live/pierreg/.local/bin:/nfs/nhome/live/pierreg/.
                          local/bin:/nfs/nhome/live/pierreg/.local/miniforge/bin:/nfs/nhome/live
                          /pierreg/.local/miniforge/condabin:/usr/local/sbin:/usr/local/bin:/usr
                          /sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/p
                          uppetlabs/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /nfs/nhome/live/pierreg/.local/miniforge
            shell level : 1
       user config file : /nfs/nhome/live/pierreg/.condarc
 populated config files : /nfs/nhome/live/pierreg/.local/miniforge/.condarc
          conda version : 4.13.0
    conda-build version : not installed
         python version : 3.9.9.final.0
       virtual packages : __cuda=11.6=0
                          __linux=5.4.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /nfs/nhome/live/pierreg/.local/miniforge  (writable)
      conda av data dir : /nfs/nhome/live/pierreg/.local/miniforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /nfs/nhome/live/pierreg/.local/miniforge/pkgs
                          /nfs/nhome/live/pierreg/.conda/pkgs
       envs directories : /nfs/nhome/live/pierreg/.local/miniforge/envs
                          /nfs/nhome/live/pierreg/.conda/envs
               platform : linux-64
             user-agent : conda/4.13.0 requests/2.28.0 CPython/3.9.9 Linux/5.4.0-109-generic ubuntu/20.04.2 glibc/2.31
                UID:GID : 801150913:801150913
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

conda uninstall -n condaforgecuda cudatoolkit works fine.

Base env spec (shortened):

conda                     4.13.0           py39hf3d152e_1    conda-forge
conda-package-handling    1.8.1            py39hb9d737c_1    conda-forge
mamba                     0.24.0           py39hfa8f2c8_1    conda-forge

The text was updated successfully, but these errors were encountered:

hmaarrfk · 2023-02-20T14:05:16Z

I've seen this problem with non-cuda packages too.

It seems that mamba is trying to uninstall __glibc a virtual package, which is breaking things. That is my guess.

ihnorton · 2023-03-29T01:51:48Z

Seeing this with distributed due to __unix virtual package.

Removing specs: ['distributed']
Transaction

  Prefix: /Users/inorton/opt/conda/envs/pydev

  Removing specs:

   - distributed


  Package                Version  Build               Channel         Size
────────────────────────────────────────────────────────────────────────────
  Remove:
────────────────────────────────────────────────────────────────────────────

  - __unix                     0  0                   installed
  - bokeh                  2.4.3  pyhd8ed1ab_3        conda-forge
  - brotlipy               0.7.0  py310h8e9501a_1005  conda-forge
  - cryptography          38.0.4  py310hfc83b78_0     conda-forge
  - cytoolz               0.12.0  py310h8e9501a_1     conda-forge
  - dask               2022.12.0  pyhd8ed1ab_0        conda-forge
  - dask-core          2022.12.0  pyhd8ed1ab_0        conda-forge
  - distributed        2022.12.0  pyhd8ed1ab_0        conda-forge
  - fsspec             2022.11.0  pyhd8ed1ab_0        conda-forge
  - heapdict               1.0.1  py_0                conda-forge
  - idna                     3.4  pyhd8ed1ab_0        conda-forge
  - locket                 1.0.0  pyhd8ed1ab_0        conda-forge
  - lz4                    4.0.2  py310ha6df754_0     conda-forge
  - msgpack-python         1.0.4  py310h2887b22_1     conda-forge
  - partd                  1.3.0  pyhd8ed1ab_0        conda-forge
  - pyopenssl             22.1.0  pyhd8ed1ab_0        conda-forge
  - pysocks                1.7.1  pyha2e5f31_6        conda-forge
  - pyyaml                   6.0  py310h8e9501a_5     conda-forge
  - tblib                  1.7.0  pyhd8ed1ab_0        conda-forge
  - toolz                 0.12.0  pyhd8ed1ab_0        conda-forge
  - typing_extensions      4.4.0  pyha770c72_0        conda-forge
  - urllib3              1.26.13  pyhd8ed1ab_0        conda-forge
  - yaml                   0.2.5  h3422bc3_2          conda-forge
  - zict                   2.2.0  pyhd8ed1ab_0        conda-forge

  Summary:

  Remove: 24 packages

  Total download: 0 B

────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y
PackageRecord(_hash=-711664884171206039, name='__unix', version='0', build='0', build_number=0, channel=Channel("@"), subdir='osx-arm64', fn='__unix', md5='12345678901234567890123456789012', package_type='virtual_system')

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/Users/inorton/opt/conda/lib/python3.9/site-packages/conda/_vendor/boltons/setutils.py", line 206, in remove
        didx = self.item_index_map.pop(item)
    KeyError: PackageRecord(_hash=-711664884171206039, name='__unix', version='0', build='0', build_number=0, channel=Channel("@"), subdir='osx-arm64', fn='__unix', md5='12345678901234567890123456789012', package_type='virtual_system')

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/Users/inorton/opt/conda/lib/python3.9/site-packages/conda/exceptions.py", line 1082, in __call__
        return func(*args, **kwargs)
      File "/Users/inorton/opt/conda/lib/python3.9/site-packages/mamba/mamba.py", line 935, in exception_converter
        raise e
      File "/Users/inorton/opt/conda/lib/python3.9/site-packages/mamba/mamba.py", line 928, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/Users/inorton/opt/conda/lib/python3.9/site-packages/mamba/mamba.py", line 886, in _wrapped_main
        result = do_call(parsed_args, p)
      File "/Users/inorton/opt/conda/lib/python3.9/site-packages/mamba/mamba.py", line 752, in do_call
        exit_code = remove(args, parser)
      File "/Users/inorton/opt/conda/lib/python3.9/site-packages/mamba/mamba.py", line 240, in remove
        conda_transaction = to_txn(
      File "/Users/inorton/opt/conda/lib/python3.9/site-packages/mamba/utils.py", line 436, in to_txn
        final_precs = compute_final_precs(
      File "/Users/inorton/opt/conda/lib/python3.9/site-packages/mamba/utils.py", line 371, in compute_final_precs
        final_precs.remove(i_rec)
      File "/Users/inorton/opt/conda/lib/python3.9/site-packages/conda/_vendor/boltons/setutils.py", line 208, in remove
        raise KeyError(item)
    KeyError: PackageRecord(_hash=-711664884171206039, name='__unix', version='0', build='0', build_number=0, channel=Channel("@"), subdir='osx-arm64', fn='__unix', md5='12345678901234567890123456789012', package_type='virtual_system')

`$ /Users/inorton/opt/conda/condabin/mamba uninstall distributed`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=pydev
                CONDA_EXE=/Users/inorton/opt/conda/bin/conda
             CONDA_PREFIX=/Users/inorton/opt/conda/envs/pydev
           CONDA_PREFIX_1=/Users/inorton/opt/conda
    CONDA_PROMPT_MODIFIER=
         CONDA_PYTHON_EXE=/Users/inorton/opt/conda/bin/python
               CONDA_ROOT=/Users/inorton/opt/conda
              CONDA_SHLVL=2
           CURL_CA_BUNDLE=<not set>
                 INFOPATH=/opt/homebrew/share/info:
                  MANPATH=/opt/homebrew/share/man::
                     PATH=/Users/inorton/.sdkman/candidates/java/current/bin:/Users/inorton/.bun
                          /bin:/Users/inorton/.deno/bin:/Users/inorton/opt/conda/envs/pydev/bin:
                          /Users/inorton/opt/conda/condabin:/Users/inorton/.cargo/bin:/Users/ino
                          rton/bin:/Users/inorton/go/bin:/Users/inorton/.npm-global/bin:/opt/hom
                          ebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/s
                          bin:/usr/local/share/dotnet:~/.dotnet/tools:/Library/Apple/usr/bin:/Ap
                          plications/Wireshark.app/Contents/MacOS:/Users/inorton/.dotnet/tools
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : pydev
    active env location : /Users/inorton/opt/conda/envs/pydev
            shell level : 2
       user config file : /Users/inorton/.condarc
 populated config files : /Users/inorton/opt/conda/.condarc
                          /Users/inorton/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.13.final.0
       virtual packages : __osx=12.6=0
                          __unix=0=0
                          __archspec=1=arm64
       base environment : /Users/inorton/opt/conda  (writable)
      conda av data dir : /Users/inorton/opt/conda/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/inorton/opt/conda/pkgs
                          /Users/inorton/.conda/pkgs
       envs directories : /cmn/condaenvs
                          /Users/inorton/opt/conda/envs
                          /Users/inorton/.conda/envs
               platform : osx-arm64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.13 Darwin/21.6.0 OSX/12.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

[edit]: x-ref #2129 (comment) which looks to be the same issue.
[edit2]: did the uninstall with conda succesfully (which removed much more than mamba was planning to) and then reinstalled w/ mamba

vipcxj · 2023-04-11T09:06:48Z

The same issue! Any news?

jonashaag · 2023-04-12T10:31:45Z

Can you try upgrading Mamba and Conda to the latest versions?

oliver-batchelor · 2023-04-17T05:53:42Z

Can you try upgrading Mamba and Conda to the latest versions?

I'm seeing the same thing with the latest mamba 1.4.2. Mamba is trying to uninstall __unix

oliver-batchelor · 2023-04-17T05:56:41Z

It also occurs with the libmamba solver on conda:

conda uninstall torchvision torchaudio 
Channels:
 - nvidia
 - pytorch
 - conda-forge
 - defaults
 - anaconda
 - robostack
 - omnia
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: - WARNING conda.conda_libmamba_solver.solver:_export_solved_records(685): Tried to unlink __unix but it is not installed or manageable?
done

peppapighs · 2023-06-12T09:49:44Z

I encounter this problem trying to remove gdb as well. It tries to remove __glibc.

ziyuanzhao2000 · 2023-08-02T03:31:21Z

Any solution? I encountered this while trying to remove a custom built package.

It tries to remove __linux:

KeyError: PackageRecord(_hash=-6054808270103221154, name='__linux', version='4.18.0', build='0', build_number=0, channel=Channel("@"), subdir='linux-64', fn='__linux', md5='12345678901234567890123456789012', package_type='virtual_system')

Edit: after updating mamba from 1.1.0 to 1.4.9 the problem goes away. So perhaps other people seeing related problems can try updating their mamba and see if it works.

iamthebot · 2023-09-13T17:23:23Z

I can confirm this is still an issue with mamba 1.5.1 with the __glibc virtual package. This occurs when uninstalling matplotlib. The only workaround for now is to keep conda around without libmamba-solver and use it for uninstallation.

Interestingly the ARM build doesn't seem to have this issue.

ogrisel · 2023-10-19T12:36:36Z

I believe I experienced the same problem when trying to use conda-lock for a macOS build (same KeyError message). #2923 should fix this.

asw28 · 2023-11-18T18:59:56Z

Same problem here with huggingface datasets on macos:

KeyError: PackageRecord(_hash=-5592555481460673488, name='__osx', version='12.1', build='0', build_number=0, channel=Channel("@"), subdir='osx-64', fn='__osx', md5='12345678901234567890123456789012', package_type='virtual_system')

jonashaag mentioned this issue Jul 15, 2022

Bug in mamba remove [package] when [package] depends on cuda #1794

Open

vipcxj mentioned this issue Apr 11, 2023

package is incompatbile with nvidia and pytorch channel conda-forge/opencv-feedstock#353

Closed

1 task

jonashaag mentioned this issue Apr 17, 2023

A KeyError Exception occurs when uninstalling flask #2464

Closed

2 tasks

jonashaag mentioned this issue Aug 21, 2023

Issue when removing package #2767

Closed

2 tasks

ogrisel mentioned this issue Oct 19, 2023

Fix support for the PackageType.VIRTUAL_SYSTEM enum #2923

Merged

jmoralez mentioned this issue Jan 22, 2024

[ci] fix conda env creation in 'regular' CI job (fixes #6282) microsoft/LightGBM#6283

Merged

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`mamba uninstall cudatoolkit` fails (conda equivalent works) #1770

`mamba uninstall cudatoolkit` fails (conda equivalent works) #1770

pierreglaser commented Jun 29, 2022

hmaarrfk commented Feb 20, 2023

ihnorton commented Mar 29, 2023 •

edited

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vipcxj commented Apr 11, 2023 •

edited

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jonashaag commented Apr 12, 2023

oliver-batchelor commented Apr 17, 2023

oliver-batchelor commented Apr 17, 2023

peppapighs commented Jun 12, 2023 •

edited

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ziyuanzhao2000 commented Aug 2, 2023 •

edited

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iamthebot commented Sep 13, 2023 •

edited

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ogrisel commented Oct 19, 2023

asw28 commented Nov 18, 2023

mamba uninstall cudatoolkit fails (conda equivalent works) #1770

mamba uninstall cudatoolkit fails (conda equivalent works) #1770

Comments

pierreglaser commented Jun 29, 2022

hmaarrfk commented Feb 20, 2023

ihnorton commented Mar 29, 2023 • edited Loading

vipcxj commented Apr 11, 2023 • edited Loading

jonashaag commented Apr 12, 2023

oliver-batchelor commented Apr 17, 2023

oliver-batchelor commented Apr 17, 2023

peppapighs commented Jun 12, 2023 • edited Loading

ziyuanzhao2000 commented Aug 2, 2023 • edited Loading

iamthebot commented Sep 13, 2023 • edited Loading

ogrisel commented Oct 19, 2023

asw28 commented Nov 18, 2023

`mamba uninstall cudatoolkit` fails (conda equivalent works) #1770

`mamba uninstall cudatoolkit` fails (conda equivalent works) #1770

ihnorton commented Mar 29, 2023 •

edited

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vipcxj commented Apr 11, 2023 •

edited

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peppapighs commented Jun 12, 2023 •

edited

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ziyuanzhao2000 commented Aug 2, 2023 •

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iamthebot commented Sep 13, 2023 •

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