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Mamba 1.4.7 installed within conda base env throws libmamba ZSTD decompression error: Unknown frame descriptor #2667

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KnightArthurRen opened this issue Jul 12, 2023 · 2 comments
Closed
2 tasks done

Mamba 1.4.7 installed within conda base env throws libmamba ZSTD decompression error: Unknown frame descriptor #2667

KnightArthurRen opened this issue Jul 12, 2023 · 2 comments

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@KnightArthurRen
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Troubleshooting docs

  • My problem is not solved in the Troubleshooting docs

How did you install Mamba?

Mambaforge

Search tried in issue tracker

libmamba ZSTD decompression error

Latest version of Mamba

  • My problem is not solved with the latest version

Tried in Conda?

I do not have this problem with Conda, just with Mamba

Describe your issue

We are currently building our environment by installing mamba in conda via

conda install -n base --override-channels -c conda-forge mamba 'python_abi=*=*cp*'

After recent 1.4.7 update mamba installed this way broke with error msg
error libmamba ZSTD decompression error: Unknown frame descriptor on our build agents

I was able to reproduce it on our linux machines by

  1. Install Miniconda via https://docs.conda.io/en/latest/miniconda.html#linux-installers
  2. Install mamba via conda install -n base --override-channels -c conda-forge mamba 'python_abi=*=*cp*'
    3.conda activate (activated base)
  3. mamba env create -f environment.yml (The environment.yml below)

I tried it with mamba 1.4.5 and it looks good, I think this is related with mamba adding support to ZSTD with 1.4.7 update.
I'm wondering what should be the fix here, or should I just switch to install mamba using mambaforge?

Thank you!

mamba info / micromamba info

mamba version : 1.4.7
     active environment : base
    active env location : /home/ubuntu/miniconda3
            shell level : 1
       user config file : /home/ubuntu/.condarc
 populated config files : /home/ubuntu/.condarc
          conda version : 23.5.0
    conda-build version : not installed
         python version : 3.11.4.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.31=0
                          __linux=5.11.15=0
                          __unix=0=0
       base environment : /home/ubuntu/miniconda3  (writable)
      conda av data dir : /home/ubuntu/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/ubuntu/miniconda3/pkgs
                          /home/ubuntu/.conda/pkgs
       envs directories : /home/ubuntu/miniconda3/envs
                          /home/ubuntu/.conda/envs
               platform : linux-64
             user-agent : conda/23.5.0 requests/2.29.0 CPython/3.11.4 Linux/5.11.15-xanmod1 ubuntu/20.04.4 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Logs

info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/conda-forge/linux-64/repodata.json'
warning  libmamba Could not parse mod/etag header
info     libmamba Invalid json cache found, ignoring
info     libmamba No valid cache found
info     libmamba All targets to download are cached
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/conda-forge/noarch/repodata.json'
warning  libmamba Could not parse mod/etag header
info     libmamba Invalid json cache found, ignoring
info     libmamba No valid cache found
info     libmamba All targets to download are cached
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/anaconda/linux-64/repodata.json'
info     libmamba No valid cache found
info     libmamba All targets to download are cached
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/anaconda/noarch/repodata.json'
info     libmamba No valid cache found
info     libmamba All targets to download are cached
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/gurobi/linux-64/repodata.json'
info     libmamba No valid cache found
info     libmamba Starting to download targets
[+] 0.4s
gurobi/linux-64 (check zst) ━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0.0 B /  ??.?MB @  ??.?MB/s Checking  0.4sinfo     libmamba Transfer done for 'gurobi/linux-64 (check zst)'
info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/gurobi/linux-64/repodata.json.zst] 0 bytes
gurobi/linux-64 (check zst)                         Checked  0.5s
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/gurobi/noarch/repodata.json'
info     libmamba No valid cache found
info     libmamba Starting to download targets
[+] 0.1s
gurobi/noarch (check zst) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━   0.0 B /  ??.?MB @  ??.?MB/s Checking  0.1sinfo     libmamba Transfer done for 'gurobi/noarch (check zst)'
info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/gurobi/noarch/repodata.json.zst] 0 bytes
gurobi/noarch (check zst)                           Checked  0.2s
info     libmamba Searching index cache file for repo 'https://repo.anaconda.com/pkgs/main/linux-64/repodata.json'
info     libmamba No valid cache found
info     libmamba Expired cache (or invalid mod/etag headers) found at '/home/ubuntu/miniconda3/pkgs'
info     libmamba Starting to download targets
[+] 0.0s
info     libmamba Transfer done for 'pkgs/main/linux-64 (check zst)'
info     libmamba Transfer finalized, status: 200 [https://repo.anaconda.com/pkgs/main/linux-64/repodata.json.zst] 0 bytes
pkgs/main/linux-64 (check zst)                     Checked  0.0s
info     libmamba Searching index cache file for repo 'https://repo.anaconda.com/pkgs/main/noarch/repodata.json'
info     libmamba No valid cache found
info     libmamba Expired cache (or invalid mod/etag headers) found at '/home/ubuntu/miniconda3/pkgs'
info     libmamba Starting to download targets
[+] 0.0s
pkgs/main/noarch (check zst) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0.0 B /  ??.?MB @  ??.?MB/s Checking  0.0sinfo     libmamba Transfer done for 'pkgs/main/noarch (check zst)'
info     libmamba Transfer finalized, status: 200 [https://repo.anaconda.com/pkgs/main/noarch/repodata.json.zst] 0 bytes
pkgs/main/noarch (check zst)                        Checked  0.0s
info     libmamba Searching index cache file for repo 'https://repo.anaconda.com/pkgs/r/linux-64/repodata.json'
info     libmamba No valid cache found
info     libmamba Expired cache (or invalid mod/etag headers) found at '/home/ubuntu/miniconda3/pkgs'
info     libmamba Starting to download targets
[+] 0.0s
info     libmamba Transfer done for 'pkgs/r/linux-64 (check zst)'
info     libmamba Transfer finalized, status: 200 [https://repo.anaconda.com/pkgs/r/linux-64/repodata.json.zst] 0 bytes
pkgs/r/linux-64 (check zst)                        Checked  0.0s
info     libmamba Searching index cache file for repo 'https://repo.anaconda.com/pkgs/r/noarch/repodata.json'
info     libmamba No valid cache found
info     libmamba Expired cache (or invalid mod/etag headers) found at '/home/ubuntu/miniconda3/pkgs'
info     libmamba Starting to download targets
[+] 0.0s
pkgs/r/noarch (check zst) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0.0 B /  ??.?MB @  ??.?MB/s Checking  0.0sinfo     libmamba Transfer done for 'pkgs/r/noarch (check zst)'
info     libmamba Transfer finalized, status: 404 [https://repo.anaconda.com/pkgs/r/noarch/repodata.json.zst] 0 bytes
pkgs/r/noarch (check zst)                           Checked  0.1s
info     libmamba Starting to download targets
[+] 0.1s
conda-forge/linux-64 ━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   1.3MB /  29.1MB @  22.4MB/s  0.1s
conda-forge/noarch   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0.0 B /  ??.?MB @  ??.?MB/s  0.1s
anaconda/linux-64    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0.0 B /  ??.?MB @  ??.?MB/s  0.1s
anaconda/noarch      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0.0 B /  ??.?MB @  ??.?MB/s  0.1s
gurobi/linux-64      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━   0.0 B /  ??.?MB @  ??.?MB/s  0.1serror    libmamba ZSTD decompression error: Unknown frame descriptor
error    libmamba ZSTD decompression error: Unknown frame descriptor
info     libmamba Download error (23) Failed writing received data to disk/application [https://conda.anaconda.org/anaconda/linux-64/repodata.json.zst]
    Failure writing output to destination
anaconda/linux-64                                   ??.?MB @  ??.?MB/s 404 failed  0.2s

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

    Traceback (most recent call last):
      File "/home/ubuntu/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 16, in __call__
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/miniconda3/lib/python3.11/site-packages/conda_env/cli/main.py", line 49, in do_call
        exit_code = getattr(module, func_name)(args, parser)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/miniconda3/lib/python3.11/site-packages/conda/notices/core.py", line 123, in wrapper
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/miniconda3/lib/python3.11/site-packages/conda_env/cli/main_create.py", line 163, in execute
        result[installer_type] = installer.install(
                                 ^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/miniconda3/lib/python3.11/site-packages/mamba/mamba_env.py", line 55, in mamba_install
        index = load_channels(pool, channel_urls, repos, prepend=False)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/miniconda3/lib/python3.11/site-packages/mamba/utils.py", line 142, in load_channels
        index = get_index(
                ^^^^^^^^^^
      File "/home/ubuntu/miniconda3/lib/python3.11/site-packages/mamba/utils.py", line 123, in get_index
        is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    RuntimeError: Download error (23) Failed writing received data to disk/application [https://conda.anaconda.org/anaconda/noarch/repodata.json.zst]
    Failure writing output to destination

`$ /home/ubuntu/miniconda3/bin/mamba create -f environment.yml -v`

  environment variables:
                 CIO_TEST=<not set>
  CONDA_AUTO_UPDATE_CONDA=false
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/home/ubuntu/miniconda3/bin/conda
             CONDA_PREFIX=/home/ubuntu/miniconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/home/ubuntu/miniconda3/bin/python
               CONDA_ROOT=/home/ubuntu/miniconda3
              CONDA_SHLVL=1
           CURL_CA_BUNDLE=<not set>
               LD_PRELOAD=<not set>
                     PATH=/home/ubuntu/miniconda3/bin:/home/ubuntu/miniconda3/bin:/home/ubuntu/.
                          local/bin:/home/ubuntu/miniconda3/condabin:/usr/local/sbin:/usr/local/
                          bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bi
                          n
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /home/ubuntu/miniconda3
            shell level : 1
       user config file : /home/ubuntu/.condarc
 populated config files : /home/ubuntu/.condarc
          conda version : 23.5.0
    conda-build version : not installed
         python version : 3.11.4.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.31=0
                          __linux=5.11.15=0
                          __unix=0=0
       base environment : /home/ubuntu/miniconda3  (writable)
      conda av data dir : /home/ubuntu/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/ubuntu/miniconda3/pkgs
                          /home/ubuntu/.conda/pkgs
       envs directories : /home/ubuntu/miniconda3/envs
                          /home/ubuntu/.conda/envs
               platform : linux-64
             user-agent : conda/23.5.0 requests/2.29.0 CPython/3.11.4 Linux/5.11.15-xanmod1 ubuntu/20.04.4 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False


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

environment.yml

name: test_env
channels:
  - conda-forge
  - anaconda
  - gurobi
  - defaults
dependencies:
  - python==3.10.9
  - poetry==1.4.2
  - gdal==3.6.2

~/.condarc

auto_activate_base: false
channels:
  - conda-forge
  - defaults
@JohanMabille
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JohanMabille commented Jul 12, 2023 •
edited
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This issue has been fixed on master (see #2661). I have another important fix to push and I will release a new version (tonight or tomorrow morning).

@KnightArthurRen
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This issue has been fixed on master (see #2661). I have another important fix to push and I will release a new version (tonight or tomorrow morning).
Awesome thank you!

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@jonashaag @JohanMabille @KnightArthurRen