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mamba-org / mamba

The Fast Cross-Platform Package Manager
https://mamba.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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libmamba failed to execute pre/post link script for cudatoolkit but works with mamba #2501

Open bastian-f opened 1 year ago

bastian-f commented 1 year ago

Troubleshooting docs

How did you install Mamba?

Micromamba

Search tried in issue tracker

libmamba failed to execute pre/post link script for cudatoolkit

Latest version of Mamba

Tried in Conda?

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

Describe your issue

While building a Docker container from a Dockerfile, when trying to create an environment from a yaml file I get the following error:

#46 333.6 Linking cudatoolkit-11.0.3-h88f8997_11
#46 333.7
#46 333.7 error    libmamba response code: -1 error message: Invalid argument
#46 333.7 critical libmamba failed to execute pre/post link script for cudatoolkit

Interestingly using mamba, it works. For micromamba, I tried the automatic installation and the manual installation described here and also using the mambaorg/micromamba image from the Docker Hub. The error is always the same.

But if during the build, I install conda, and then install mamba in the base environment with conda install mamba -n base -c conda-forge and then doing RUN conda env create -f /home/bastian/environment.yml it works.

mamba info / micromamba info

Not possible because build fails.

Logs

#46 [stage-1 21/21] RUN micromamba install -y -n base -f /tmp/env.yaml &&     micromamba clean --all --yes
#46 0.460
#46 0.460                                            __
#46 0.460           __  ______ ___  ____ _____ ___  / /_  ____ _
#46 0.460          / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
#46 0.460         / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
#46 0.460        / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
#46 0.460       /_/
#46 0.460
#46 34.90 warning  libmamba linux version not found (virtual package skipped)
#46 101.5
#46 101.5 Transaction
#46 101.5
#46 101.5   Prefix: /opt/conda
#46 101.5
#46 101.5   Updating specs:
#46 101.5
#46 101.5    - redis-py
#46 101.5    - pip
#46 101.5    - boto3
#46 101.5    - botocore
#46 101.5    - celery==5.2.1=pyhd8ed1ab_0
#46 101.5    - h5py==3.1.0=nompi_py37h1e651dc_100
#46 101.5    - ipywidgets==7.7.0=pyhd8ed1ab_0
#46 101.5    - librosa==0.9.1=pyhd8ed1ab_0
#46 101.5    - matplotlib==3.5.2=py37h06a4308_0
#46 101.5    - matplotlib-base==3.5.2=py37hf590b9c_0
#46 101.5    - matplotlib-inline==0.1.6=py37h06a4308_0
#46 101.5    - numba==0.55.1=py37h2d894fd_0
#46 101.5    - numpy==1.19.5=py37h3e96413_3
#46 101.5    - pandas==1.3.5=py37he8f5f7f_0
#46 101.5    - peakutils==1.3.3=py_0
#46 101.5    - pymongo==4.1.1=py37hd23a5d3_0
#46 101.5    - pyparsing==3.0.9=py37h06a4308_0
#46 101.5    - qgrid==1.3.1=py37h89c1867_2
#46 101.5    - tensorflow==2.6.2=cuda110py37h4801193_1
#46 101.5    - tensorflow-base==2.6.2=cuda110py37h0ebe739_1
#46 101.5    - tensorflow-estimator==2.6.2=cuda110py37h4801193_1
#46 101.5    - tensorflow-gpu==2.6.2=cuda110py37h5b0ac8e_1
#46 101.5    - tqdm==4.64.1=py37h06a4308_0
#46 101.5    - xgboost==1.6.2=cpu_py37h08536eb_1
#46 101.5
#46 101.5
#46 101.5   Package                               Version  Build                   Channel                   Size
#46 101.5 ─────────────────────────────────────────────────────────────────────────────────────────────────────────
#46 101.5   Install:
#46 101.5 ─────────────────────────────────────────────────────────────────────────────────────────────────────────
#46 101.5
#46 101.5   + _libgcc_mutex                           0.1  conda_forge             conda-forge/linux-64       3kB
#46 101.5   + _openmp_mutex                           4.5  2_gnu                   conda-forge/linux-64      24kB
#46 101.5   + _py-xgboost-mutex                       2.0  cpu_0                   conda-forge/linux-64       8kB
#46 101.5   + abseil-cpp                       20210324.2  h9c3ff4c_0              conda-forge/linux-64       1MB
#46 101.5   + absl-py                              0.15.0  pyhd8ed1ab_0            conda-forge/noarch       100kB
#46 101.5   + aiohttp                               3.8.3  py37h540881e_0          conda-forge/linux-64     442kB
#46 101.5   + aiosignal                             1.3.1  pyhd8ed1ab_0            conda-forge/noarch        13kB
#46 101.5   + alsa-lib                            1.2.3.2  h166bdaf_0              conda-forge/linux-64     567kB
#46 101.5   + amqp                                  5.1.1  pyhd8ed1ab_0            conda-forge/noarch        45kB
#46 101.5   + anyio                                 3.6.2  pyhd8ed1ab_0            conda-forge/noarch        85kB
#46 101.5   + aom                                   3.5.0  h27087fc_0              conda-forge/linux-64       3MB
#46 101.5   + argon2-cffi                          21.3.0  pyhd8ed1ab_0            conda-forge/noarch        16kB
#46 101.5   + argon2-cffi-bindings                 21.2.0  py37h540881e_2          conda-forge/linux-64      35kB
#46 101.5   + astunparse                            1.6.3  pyhd8ed1ab_0            conda-forge/noarch        16kB
#46 101.5   + async-timeout                         4.0.2  pyhd8ed1ab_0            conda-forge/noarch         9kB
#46 101.5   + asynctest                            0.13.0  py_0                    conda-forge/noarch        25kB
#46 101.5   + attrs                                22.2.0  pyh71513ae_0            conda-forge/noarch        54kB
#46 101.5   + audioread                             3.0.0  py37h89c1867_0          conda-forge/linux-64      34kB
#46 101.5   + backcall                              0.2.0  pyh9f0ad1d_0            conda-forge/noarch        14kB
#46 101.5   + backports                               1.0  pyhd8ed1ab_3            conda-forge/noarch         6kB
#46 101.5   + backports.functools_lru_cache         1.6.4  pyhd8ed1ab_0            conda-forge/noarch         9kB
#46 101.5   + beautifulsoup4                       4.12.2  pyha770c72_0            conda-forge/noarch       115kB
#46 101.5   + billiard                            3.6.4.0  py37h540881e_2          conda-forge/linux-64     147kB
#46 101.5   + bleach                                6.0.0  pyhd8ed1ab_0            conda-forge/noarch       131kB
#46 101.5   + blinker                               1.6.2  pyhd8ed1ab_0            conda-forge/noarch        18kB
#46 101.5   + boto3                              1.26.121  pyhd8ed1ab_0            conda-forge/noarch        78kB
#46 101.5   + botocore                           1.29.121  pyhd8ed1ab_0            conda-forge/noarch         6MB
#46 101.5   + brotli                                1.0.9  h166bdaf_8              conda-forge/linux-64      19kB
#46 101.5   + brotli-bin                            1.0.9  h166bdaf_8              conda-forge/linux-64      20kB
#46 101.5   + brotlipy                              0.7.0  py37h540881e_1004       conda-forge/linux-64     350kB
#46 101.5   + bzip2                                 1.0.8  h7f98852_4              conda-forge/linux-64     496kB
#46 101.5   + c-ares                               1.18.1  h7f98852_0              conda-forge/linux-64     115kB
#46 101.5   + ca-certificates                   2022.12.7  ha878542_0              conda-forge/linux-64     146kB
#46 101.5   + cached-property                       1.5.2  hd8ed1ab_1              conda-forge/noarch         4kB
#46 101.5   + cached_property                       1.5.2  pyha770c72_1            conda-forge/noarch        11kB
#46 101.5   + cachetools                            4.2.4  pyhd8ed1ab_0            conda-forge/noarch        13kB
#46 101.5   + celery                                5.2.1  pyhd8ed1ab_0            conda-forge/noarch       470kB
#46 101.5   + certifi                           2022.12.7  pyhd8ed1ab_0            conda-forge/noarch       151kB
#46 101.5   + cffi                                 1.15.1  py37h43b0acd_1          conda-forge/linux-64     233kB
#46 101.5   + charset-normalizer                    2.1.1  pyhd8ed1ab_0            conda-forge/noarch        36kB
#46 101.5   + click                                 8.1.3  py37h89c1867_0          conda-forge/linux-64     148kB
#46 101.5   + click-didyoumean                      0.3.0  pyhd8ed1ab_0            conda-forge/noarch         7kB
#46 101.5   + click-plugins                         1.1.1  py_0                    conda-forge/noarch         9kB
#46 101.5   + click-repl                            0.2.0  pyhd8ed1ab_0            conda-forge/noarch         9kB
#46 101.5   + cryptography                         38.0.2  py37h38fbfac_1          conda-forge/linux-64       2MB
#46 101.5   + cudatoolkit                          11.0.3  h88f8997_11             conda-forge/linux-64     655MB
#46 101.5   + cudnn                              8.4.1.50  hed8a83a_0              conda-forge/linux-64     648MB
#46 101.5   + cycler                               0.11.0  pyhd8ed1ab_0            conda-forge/noarch        10kB
#46 101.5   + dbus                                 1.13.6  h5008d03_3              conda-forge/linux-64     619kB
#46 101.5   + debugpy                               1.6.3  py37hd23a5d3_0          conda-forge/linux-64       2MB
#46 101.5   + decorator                             5.1.1  pyhd8ed1ab_0            conda-forge/noarch        12kB
#46 101.5   + defusedxml                            0.7.1  pyhd8ed1ab_0            conda-forge/noarch        24kB
#46 101.5   + entrypoints                             0.4  pyhd8ed1ab_0            conda-forge/noarch         9kB
#46 101.5   + expat                                 2.5.0  hcb278e6_1              conda-forge/linux-64     137kB
#46 101.5   + ffmpeg                                5.1.2  gpl_hbd009f3_102        conda-forge/linux-64      11MB
#46 101.5   + flit-core                             3.8.0  pyhd8ed1ab_0            conda-forge/noarch        46kB
#46 101.5   + font-ttf-dejavu-sans-mono              2.37  hab24e00_0              conda-forge/noarch       397kB
#46 101.5   + font-ttf-inconsolata                  3.000  h77eed37_0              conda-forge/noarch        97kB
#46 101.5   + font-ttf-source-code-pro              2.038  h77eed37_0              conda-forge/noarch       701kB
#46 101.5   + font-ttf-ubuntu                        0.83  hab24e00_0              conda-forge/noarch         2MB
#46 101.5   + fontconfig                           2.14.2  h14ed4e7_0              conda-forge/linux-64     272kB
#46 101.5   + fonts-conda-ecosystem                     1  0                       conda-forge/noarch         4kB
#46 101.5   + fonts-conda-forge                         1  0                       conda-forge/noarch         4kB
#46 101.5   + fonttools                            4.38.0  py37h540881e_0          conda-forge/linux-64       2MB
#46 101.5   + freetype                             2.12.1  hca18f0e_1              conda-forge/linux-64     626kB
#46 101.5   + frozenlist                            1.3.1  py37h540881e_0          conda-forge/linux-64      45kB
#46 101.5   + gast                                  0.4.0  pyh9f0ad1d_0            conda-forge/noarch        12kB
#46 101.5   + gettext                              0.21.1  h27087fc_0              conda-forge/linux-64       4MB
#46 101.5   + giflib                                5.2.1  h0b41bf4_3              conda-forge/linux-64      77kB
#46 101.5   + glib                                 2.76.2  hfc55251_0              conda-forge/linux-64     484kB
#46 101.5   + glib-tools                           2.76.2  hfc55251_0              conda-forge/linux-64     112kB
#46 101.5   + gmp                                   6.2.1  h58526e2_0              conda-forge/linux-64     826kB
#46 101.5   + gnutls                                3.7.8  hf3e180e_0              conda-forge/linux-64       2MB
#46 101.5   + google-auth                          1.35.0  pyh6c4a22f_0            conda-forge/noarch        83kB
#46 101.5   + google-auth-oauthlib                  0.4.6  pyhd8ed1ab_0            conda-forge/noarch        19kB
#46 101.5   + google-pasta                          0.2.0  pyh8c360ce_0            conda-forge/noarch        43kB
#46 101.5   + grpc-cpp                             1.41.1  h75e9d12_2              conda-forge/linux-64       4MB
#46 101.5   + grpcio                               1.41.1  py37hb27c1af_1          conda-forge/linux-64       2MB
#46 101.5   + gst-plugins-base                     1.20.2  hcf0ee16_0              conda-forge/linux-64       3MB
#46 101.5   + gstreamer                            1.20.3  hd4edc92_2              conda-forge/linux-64       2MB
#46 101.5   + h5py                                  3.1.0  nompi_py37h1e651dc_100  conda-forge/linux-64       1MB
#46 101.5   + hdf5                                 1.10.6  nompi_h6a2412b_1114     conda-forge/linux-64       3MB
#46 101.5   + icu                                    69.1  h9c3ff4c_0              conda-forge/linux-64      14MB
#46 101.5   + idna                                    3.4  pyhd8ed1ab_0            conda-forge/noarch        57kB
#46 101.5   + importlib-metadata                   4.11.4  py37h89c1867_0          conda-forge/linux-64      34kB
#46 101.5   + importlib_resources                  5.12.0  pyhd8ed1ab_0            conda-forge/noarch        31kB
#46 101.5   + ipykernel                            6.14.0  py37h25bab4e_0          conda-forge/linux-64     190kB
#46 101.5   + ipython                              7.33.0  py37h89c1867_0          conda-forge/linux-64       1MB
#46 101.5   + ipython_genutils                      0.2.0  py_1                    conda-forge/noarch        22kB
#46 101.5   + ipywidgets                            7.7.0  pyhd8ed1ab_0            conda-forge/noarch       106kB
#46 101.5   + jedi                                 0.18.2  pyhd8ed1ab_0            conda-forge/noarch       804kB
#46 101.5   + jinja2                                3.1.2  pyhd8ed1ab_1            conda-forge/noarch       101kB
#46 101.5   + jmespath                              1.0.1  pyhd8ed1ab_0            conda-forge/noarch        21kB
#46 101.5   + joblib                                1.2.0  pyhd8ed1ab_0            conda-forge/noarch       210kB
#46 101.5   + jpeg                                     9e  h0b41bf4_3              conda-forge/linux-64     240kB
#46 101.5   + jsonschema                           4.17.3  pyhd8ed1ab_0            conda-forge/noarch        70kB
#46 101.5   + jupyter_client                        7.4.9  pyhd8ed1ab_0            conda-forge/noarch        99kB
#46 101.5   + jupyter_core                         4.11.1  py37h89c1867_0          conda-forge/linux-64      83kB
#46 101.5   + jupyter_server                       1.23.4  pyhd8ed1ab_0            conda-forge/noarch       244kB
#46 101.5   + jupyterlab_pygments                   0.2.2  pyhd8ed1ab_0            conda-forge/noarch        17kB
#46 101.5   + jupyterlab_widgets                    1.1.4  pyhd8ed1ab_0            conda-forge/noarch       114kB
#46 101.5   + keras                                 2.6.0  pyhd8ed1ab_1            conda-forge/noarch       842kB
#46 101.5   + keras-preprocessing                   1.1.2  pyhd8ed1ab_0            conda-forge/noarch        35kB
#46 101.5   + keyutils                              1.6.1  h166bdaf_0              conda-forge/linux-64     118kB
#46 101.5   + kiwisolver                            1.4.4  py37h7cecad7_0          conda-forge/linux-64      75kB
#46 101.5   + kombu                                 5.2.4  py37h89c1867_1          conda-forge/linux-64     292kB
#46 101.5   + krb5                                 1.20.1  hf9c8cef_0              conda-forge/linux-64       1MB
#46 101.5   + lame                                  3.100  h166bdaf_1003           conda-forge/linux-64     508kB
#46 101.5   + lcms2                                  2.14  h6ed2654_0              conda-forge/linux-64     262kB
#46 101.5   + ld_impl_linux-64                       2.40  h41732ed_0              conda-forge/linux-64     705kB
#46 101.5   + lerc                                  4.0.0  h27087fc_0              conda-forge/linux-64     282kB
#46 101.5   + libblas                               3.9.0  16_linux64_openblas     conda-forge/linux-64      13kB
#46 101.5   + libbrotlicommon                       1.0.9  h166bdaf_8              conda-forge/linux-64      67kB
#46 101.5   + libbrotlidec                          1.0.9  h166bdaf_8              conda-forge/linux-64      34kB
#46 101.5   + libbrotlienc                          1.0.9  h166bdaf_8              conda-forge/linux-64     295kB
#46 101.5   + libcblas                              3.9.0  16_linux64_openblas     conda-forge/linux-64      13kB
#46 101.5   + libclang                             13.0.1  default_had23c3d_1      conda-forge/linux-64       9MB
#46 101.5   + libcurl                              7.87.0  h6312ad2_0              conda-forge/linux-64     347kB
#46 101.5   + libdeflate                             1.14  h166bdaf_0              conda-forge/linux-64      83kB
#46 101.5   + libdrm                              2.4.114  h166bdaf_0              conda-forge/linux-64     305kB
#46 101.5   + libedit                        3.1.20191231  he28a2e2_2              conda-forge/linux-64     124kB
#46 101.5   + libev                                  4.33  h516909a_1              conda-forge/linux-64     106kB
#46 101.5   + libevent                             2.1.10  h9b69904_4              conda-forge/linux-64       1MB
#46 101.5   + libexpat                              2.5.0  hcb278e6_1              conda-forge/linux-64      78kB
#46 101.5   + libffi                                3.4.2  h7f98852_5              conda-forge/linux-64      58kB
#46 101.5   + libflac                               1.4.2  h27087fc_0              conda-forge/linux-64     421kB
#46 101.5   + libgcc-ng                            12.2.0  h65d4601_19             conda-forge/linux-64     954kB
#46 101.5   + libgfortran-ng                       12.2.0  h69a702a_19             conda-forge/linux-64      23kB
#46 101.5   + libgfortran5                         12.2.0  h337968e_19             conda-forge/linux-64       2MB
#46 101.5   + libglib                              2.76.2  hebfc3b9_0              conda-forge/linux-64       3MB
#46 101.5   + libgomp                              12.2.0  h65d4601_19             conda-forge/linux-64     466kB
#46 101.5   + libiconv                               1.17  h166bdaf_0              conda-forge/linux-64       1MB
#46 101.5   + libidn2                               2.3.4  h166bdaf_0              conda-forge/linux-64     160kB
#46 101.5   + liblapack                             3.9.0  16_linux64_openblas     conda-forge/linux-64      13kB
#46 101.5   + libllvm11                            11.1.0  he0ac6c6_5              conda-forge/linux-64      30MB
#46 101.5   + libllvm13                            13.0.1  hf817b99_2              conda-forge/linux-64      35MB
#46 101.5   + libnghttp2                           1.51.0  hdcd2b5c_0              conda-forge/linux-64     623kB
#46 101.5   + libnsl                                2.0.0  h7f98852_0              conda-forge/linux-64      31kB
#46 101.5   + libogg                                1.3.4  h7f98852_1              conda-forge/linux-64     211kB
#46 101.5   + libopenblas                          0.3.21  pthreads_h78a6416_3     conda-forge/linux-64      11MB
#46 101.5   + libopus                               1.3.1  h7f98852_1              conda-forge/linux-64     261kB
#46 101.5   + libpciaccess                           0.17  h166bdaf_0              conda-forge/linux-64      40kB
#46 101.5   + libpng                               1.6.39  h753d276_0              conda-forge/linux-64     283kB
#46 101.5   + libpq                                  14.5  h2baec63_5              conda-forge/linux-64       2MB
#46 101.5   + libprotobuf                          3.18.1  h780b84a_0              conda-forge/linux-64       3MB
#46 101.5   + librosa                               0.9.1  pyhd8ed1ab_0            conda-forge/noarch       157kB
#46 101.5   + libsndfile                            1.2.0  hb75c966_0              conda-forge/linux-64     350kB
#46 101.5   + libsodium                            1.0.18  h36c2ea0_1              conda-forge/linux-64     375kB
#46 101.5   + libsqlite                            3.40.0  h753d276_1              conda-forge/linux-64     804kB
#46 101.5   + libssh2                              1.10.0  haa6b8db_3              conda-forge/linux-64     239kB
#46 101.5   + libstdcxx-ng                         12.2.0  h46fd767_19             conda-forge/linux-64       4MB
#46 101.5   + libtasn1                             4.19.0  h166bdaf_0              conda-forge/linux-64     117kB
#46 101.5   + libtiff                               4.4.0  h82bc61c_5              conda-forge/linux-64     485kB
#46 101.5   + libunistring                         0.9.10  h7f98852_0              conda-forge/linux-64       1MB
#46 101.5   + libuuid                              2.38.1  h0b41bf4_0              conda-forge/linux-64      34kB
#46 101.5   + libva                                2.18.0  h0b41bf4_0              conda-forge/linux-64     187kB
#46 101.5   + libvorbis                             1.3.7  h9c3ff4c_0              conda-forge/linux-64     286kB
#46 101.5   + libvpx                               1.11.0  h9c3ff4c_3              conda-forge/linux-64       1MB
#46 101.5   + libwebp-base                          1.3.0  h0b41bf4_0              conda-forge/linux-64     357kB
#46 101.5   + libxcb                                 1.13  h7f98852_1004           conda-forge/linux-64     400kB
#46 101.5   + libxgboost                            1.6.2  cpu_ha3b9936_1          conda-forge/linux-64       4MB
#46 101.5   + libxkbcommon                          1.0.3  he3ba5ed_0              conda-forge/linux-64     595kB
#46 101.5   + libxml2                              2.9.14  haae042b_4              conda-forge/linux-64     737kB
#46 101.5   + libzlib                              1.2.13  h166bdaf_4              conda-forge/linux-64      66kB
#46 101.5   + llvmlite                             0.38.1  py37h0761922_0          conda-forge/linux-64       2MB
#46 101.5   + markdown                              3.4.3  pyhd8ed1ab_0            conda-forge/noarch        71kB
#46 101.5   + markupsafe                            2.1.1  py37h540881e_1          conda-forge/linux-64      23kB
#46 101.5   + matplotlib                            3.5.2  py37h06a4308_0          pkgs/main/linux-64         7kB
#46 101.5   + matplotlib-base                       3.5.2  py37hf590b9c_0          pkgs/main/linux-64         6MB
#46 101.5   + matplotlib-inline                     0.1.6  py37h06a4308_0          pkgs/main/linux-64        16kB
#46 101.5   + mistune                               2.0.5  pyhd8ed1ab_0            conda-forge/noarch        74kB
#46 101.5   + mpg123                               1.31.3  hcb278e6_0              conda-forge/linux-64     485kB
#46 101.5   + multidict                             6.0.2  py37h540881e_1          conda-forge/linux-64      50kB
#46 101.5   + munkres                               1.1.4  pyh9f0ad1d_0            conda-forge/noarch        12kB
#46 101.5   + mysql-common                         8.0.32  h14678bc_0              conda-forge/linux-64     803kB
#46 101.5   + mysql-libs                           8.0.32  h54cf53e_0              conda-forge/linux-64       2MB
#46 101.5   + nbclassic                             0.5.6  pyhb4ecaf3_1            conda-forge/noarch         6MB
#46 101.5   + nbclient                              0.7.0  pyhd8ed1ab_0            conda-forge/noarch        67kB
#46 101.5   + nbconvert                             7.3.1  pyhd8ed1ab_0            conda-forge/noarch         8kB
#46 101.5   + nbconvert-core                        7.3.1  pyhd8ed1ab_0            conda-forge/noarch       208kB
#46 101.5   + nbconvert-pandoc                      7.3.1  pyhd8ed1ab_0            conda-forge/noarch         7kB
#46 101.5   + nbformat                              5.8.0  pyhd8ed1ab_0            conda-forge/noarch       101kB
#46 101.5   + nccl                               2.15.5.1  h17a0586_0              conda-forge/linux-64      90MB
#46 101.5   + ncurses                                 6.3  h27087fc_1              conda-forge/linux-64       1MB
#46 101.5   + nest-asyncio                          1.5.6  pyhd8ed1ab_0            conda-forge/noarch        10kB
#46 101.5   + nettle                                3.8.1  hc379101_1              conda-forge/linux-64       1MB
#46 101.5   + notebook                              6.5.4  pyha770c72_0            conda-forge/noarch       306kB
#46 101.5   + notebook-shim                         0.2.3  pyhd8ed1ab_0            conda-forge/noarch        17kB
#46 101.5   + nspr                                   4.35  h27087fc_0              conda-forge/linux-64     227kB
#46 101.5   + nss                                    3.89  he45b914_0              conda-forge/linux-64       2MB
#46 101.5   + numba                                0.55.1  py37h2d894fd_0          conda-forge/linux-64       4MB
#46 101.5   + numpy                                1.19.5  py37h3e96413_3          conda-forge/linux-64       6MB
#46 101.5   + oauthlib                              3.2.2  pyhd8ed1ab_0            conda-forge/noarch        92kB
#46 101.5   + openh264                              2.3.1  hcb278e6_2              conda-forge/linux-64     719kB
#46 101.5   + openjpeg                              2.5.0  h7d73246_1              conda-forge/linux-64     546kB
#46 101.5   + openssl                              1.1.1t  h0b41bf4_0              conda-forge/linux-64       2MB
#46 101.5   + opt_einsum                            3.3.0  pyhd8ed1ab_1            conda-forge/noarch        54kB
#46 101.5   + p11-kit                              0.24.1  hc5aa10d_0              conda-forge/linux-64       5MB
#46 101.5   + packaging                              23.1  pyhd8ed1ab_0            conda-forge/noarch        46kB
#46 101.5   + pandas                                1.3.5  py37he8f5f7f_0          conda-forge/linux-64      13MB
#46 101.5   + pandoc                               2.19.2  h32600fe_2              conda-forge/linux-64      27MB
#46 101.5   + pandocfilters                         1.5.0  pyhd8ed1ab_0            conda-forge/noarch        12kB
#46 101.5   + parso                                 0.8.3  pyhd8ed1ab_0            conda-forge/noarch        71kB
#46 101.5   + pcre2                                 10.40  hc3806b6_0              conda-forge/linux-64       2MB
#46 101.5   + peakutils                             1.3.3  py_0                    conda-forge/noarch        10kB
#46 101.5   + pexpect                               4.8.0  pyh1a96a4e_2            conda-forge/noarch        49kB
#46 101.5   + pickleshare                           0.7.5  py_1003                 conda-forge/noarch         9kB
#46 101.5   + pillow                                9.2.0  py37h850a105_2          conda-forge/linux-64      47MB
#46 101.5   + pip                                  23.1.2  pyhd8ed1ab_0            conda-forge/noarch         1MB
#46 101.5   + pkgutil-resolve-name                 1.3.10  pyhd8ed1ab_0            conda-forge/noarch         9kB
#46 101.5   + platformdirs                          2.6.0  pyhd8ed1ab_0            conda-forge/noarch        17kB
#46 101.5   + pooch                                 1.7.0  pyha770c72_3            conda-forge/noarch        51kB
#46 101.5   + prometheus_client                    0.16.0  pyhd8ed1ab_0            conda-forge/noarch        52kB
#46 101.5   + prompt-toolkit                       3.0.38  pyha770c72_0            conda-forge/noarch       269kB
#46 101.5   + prompt_toolkit                       3.0.38  hd8ed1ab_0              conda-forge/noarch         6kB
#46 101.5   + protobuf                             3.18.1  py37hcd2ae1e_0          conda-forge/linux-64     353kB
#46 101.5   + psutil                                5.9.3  py37h540881e_0          conda-forge/linux-64     357kB
#46 101.5   + pthread-stubs                           0.4  h36c2ea0_1001           conda-forge/linux-64       6kB
#46 101.5   + ptyprocess                            0.7.0  pyhd3deb0d_0            conda-forge/noarch        17kB
#46 101.5   + py-xgboost                            1.6.2  cpu_py37h08536eb_1      conda-forge/linux-64     161kB
#46 101.5   + pyasn1                                0.4.8  py_0                    conda-forge/noarch        54kB
#46 101.5   + pyasn1-modules                        0.2.7  py_0                    conda-forge/noarch        61kB
#46 101.5   + pycparser                              2.21  pyhd8ed1ab_0            conda-forge/noarch       103kB
#46 101.5   + pygments                             2.15.1  pyhd8ed1ab_0            conda-forge/noarch       841kB
#46 101.5   + pyjwt                                 2.6.0  pyhd8ed1ab_0            conda-forge/noarch        21kB
#46 101.5   + pymongo                               4.1.1  py37hd23a5d3_0          conda-forge/linux-64       1MB
#46 101.5   + pyopenssl                            23.1.1  pyhd8ed1ab_0            conda-forge/noarch       128kB
#46 101.5   + pyparsing                             3.0.9  py37h06a4308_0          pkgs/main/linux-64       154kB
#46 101.5   + pyqt                                 5.12.3  py37h89c1867_8          conda-forge/linux-64      22kB
#46 101.5   + pyqt-impl                            5.12.3  py37hac37412_8          conda-forge/linux-64       6MB
#46 101.5   + pyqt5-sip                           4.19.18  py37hcd2ae1e_8          conda-forge/linux-64     317kB
#46 101.5   + pyqtchart                              5.12  py37he336c9b_8          conda-forge/linux-64     263kB
#46 101.5   + pyqtwebengine                        5.12.1  py37he336c9b_8          conda-forge/linux-64     179kB
#46 101.5   + pyrsistent                           0.18.1  py37h540881e_1          conda-forge/linux-64      93kB
#46 101.5   + pysocks                               1.7.1  py37h89c1867_5          conda-forge/linux-64      28kB
#46 101.5   + pysoundfile                          0.12.1  pyhd8ed1ab_0            conda-forge/noarch        28kB
#46 101.5   + python                               3.7.12  hb7a2778_100_cpython    conda-forge/linux-64      60MB
#46 101.5   + python-dateutil                       2.8.2  pyhd8ed1ab_0            conda-forge/noarch       246kB
#46 101.5   + python-fastjsonschema                2.16.3  pyhd8ed1ab_0            conda-forge/noarch       225kB
#46 101.5   + python-flatbuffers                     1.12  pyhd8ed1ab_1            conda-forge/noarch        20kB
#46 101.5   + python_abi                              3.7  3_cp37m                 conda-forge/linux-64       6kB
#46 101.5   + pytz                                 2023.3  pyhd8ed1ab_0            conda-forge/noarch       187kB
#46 101.5   + pyu2f                                 0.1.5  pyhd8ed1ab_0            conda-forge/noarch        32kB
#46 101.5   + pyzmq                                24.0.1  py37h0c0c2a8_0          conda-forge/linux-64     512kB
#46 101.5   + qgrid                                 1.3.1  py37h89c1867_2          conda-forge/linux-64       2MB
#46 101.5   + qt                                   5.12.9  h1304e3e_6              conda-forge/linux-64     103MB
#46 101.5   + re2                              2021.11.01  h9c3ff4c_0              conda-forge/linux-64     227kB
#46 101.5   + readline                                8.2  h8228510_1              conda-forge/linux-64     281kB
#46 101.5   + redis-py                              4.5.4  pyhd8ed1ab_0            conda-forge/noarch       164kB
#46 101.5   + requests                             2.29.0  pyhd8ed1ab_0            conda-forge/noarch        57kB
#46 101.5   + requests-oauthlib                     1.3.1  pyhd8ed1ab_0            conda-forge/noarch        22kB
#46 101.5   + resampy                               0.4.2  pyhd8ed1ab_0            conda-forge/noarch         3MB
#46 101.5   + rsa                                     4.9  pyhd8ed1ab_0            conda-forge/noarch        30kB
#46 101.5   + s3transfer                            0.6.0  pyhd8ed1ab_0            conda-forge/noarch        57kB
#46 101.5   + scikit-learn                          1.0.2  py37hf9e9bfc_0          conda-forge/linux-64       8MB
#46 101.5   + scipy                                 1.7.3  py37hf2a6cf1_0          conda-forge/linux-64      23MB
#46 101.5   + send2trash                            1.8.0  pyhd8ed1ab_0            conda-forge/noarch        18kB
#46 101.5   + setuptools                           59.8.0  py37h89c1867_1          conda-forge/linux-64       1MB
#46 101.5   + six                                  1.15.0  pyh9f0ad1d_0            conda-forge/noarch        14kB
#46 101.5   + snappy                               1.1.10  h9fff704_0              conda-forge/linux-64      39kB
#46 101.5   + sniffio                               1.3.0  pyhd8ed1ab_0            conda-forge/noarch        14kB
#46 101.5   + soupsieve                       2.3.2.post1  pyhd8ed1ab_0            conda-forge/noarch        35kB
#46 101.5   + sqlite                               3.40.0  h4ff8645_1              conda-forge/linux-64     791kB
#46 101.5   + svt-av1                               1.3.0  h27087fc_0              conda-forge/linux-64       4MB
#46 101.5   + tensorboard                           2.6.0  pyhd8ed1ab_1            conda-forge/noarch         5MB
#46 101.5   + tensorboard-data-server               0.6.0  py37h38fbfac_2          conda-forge/linux-64       3MB
#46 101.5   + tensorboard-plugin-wit                1.8.1  pyhd8ed1ab_0            conda-forge/noarch       685kB
#46 101.5   + tensorflow                            2.6.2  cuda110py37h4801193_1   conda-forge/linux-64      30kB
#46 101.5   + tensorflow-base                       2.6.2  cuda110py37h0ebe739_1   conda-forge/linux-64     299MB
#46 101.5   + tensorflow-estimator                  2.6.2  cuda110py37h4801193_1   conda-forge/linux-64     667kB
#46 101.5   + tensorflow-gpu                        2.6.2  cuda110py37h5b0ac8e_1   conda-forge/linux-64      30kB
#46 101.5   + termcolor                             1.1.0  pyhd8ed1ab_3            conda-forge/noarch         9kB
#46 101.5   + terminado                            0.15.0  py37h89c1867_0          conda-forge/linux-64      28kB
#46 101.5   + threadpoolctl                         3.1.0  pyh8a188c0_0            conda-forge/noarch        18kB
#46 101.5   + tinycss2                              1.2.1  pyhd8ed1ab_0            conda-forge/noarch        23kB
#46 101.5   + tk                                   8.6.12  h27826a3_0              conda-forge/linux-64       3MB
#46 101.5   + tornado                                 6.2  py37h540881e_0          conda-forge/linux-64     666kB
#46 101.5   + tqdm                                 4.64.1  py37h06a4308_0          pkgs/main/linux-64       129kB
#46 101.5   + traitlets                             5.9.0  pyhd8ed1ab_0            conda-forge/noarch        98kB
#46 101.5   + typing-extensions                   3.7.4.3  0                       conda-forge/noarch         8kB
#46 101.5   + typing_extensions                   3.7.4.3  py_0                    conda-forge/noarch        26kB
#46 101.5   + unicodedata2                         14.0.0  py37h540881e_1          conda-forge/linux-64     508kB
#46 101.5   + urllib3                             1.26.15  pyhd8ed1ab_0            conda-forge/noarch       113kB
#46 101.5   + vine                                  5.0.0  pyhd8ed1ab_1            conda-forge/noarch        12kB
#46 101.5   + wcwidth                               0.2.6  pyhd8ed1ab_0            conda-forge/noarch        29kB
#46 101.5   + webencodings                          0.5.1  py_1                    conda-forge/noarch        12kB
#46 101.5   + websocket-client                      1.5.1  pyhd8ed1ab_0            conda-forge/noarch        44kB
#46 101.5   + werkzeug                              2.2.3  pyhd8ed1ab_0            conda-forge/noarch       253kB
#46 101.5   + wheel                                0.40.0  pyhd8ed1ab_0            conda-forge/noarch        56kB
#46 101.5   + widgetsnbextension                    3.6.4  pyhd8ed1ab_0            conda-forge/noarch       645kB
#46 101.5   + wrapt                                1.12.1  py37h5e8e339_3          conda-forge/linux-64      48kB
#46 101.5   + x264                             1!164.3095  h166bdaf_2              conda-forge/linux-64     898kB
#46 101.5   + x265                                    3.5  h924138e_3              conda-forge/linux-64       3MB
#46 101.5   + xgboost                               1.6.2  cpu_py37h08536eb_1      conda-forge/linux-64      13kB
#46 101.5   + xorg-fixesproto                         5.0  h7f98852_1002           conda-forge/linux-64       9kB
#46 101.5   + xorg-kbproto                          1.0.7  h7f98852_1002           conda-forge/linux-64      27kB
#46 101.5   + xorg-libx11                           1.8.4  h0b41bf4_0              conda-forge/linux-64     830kB
#46 101.5   + xorg-libxau                           1.0.9  h7f98852_0              conda-forge/linux-64      13kB
#46 101.5   + xorg-libxdmcp                         1.1.3  h7f98852_0              conda-forge/linux-64      19kB
#46 101.5   + xorg-libxext                          1.3.4  h0b41bf4_2              conda-forge/linux-64      50kB
#46 101.5   + xorg-libxfixes                        5.0.3  h7f98852_1004           conda-forge/linux-64      18kB
#46 101.5   + xorg-xextproto                        7.3.0  h0b41bf4_1003           conda-forge/linux-64      30kB
#46 101.5   + xorg-xproto                          7.0.31  h7f98852_1007           conda-forge/linux-64      75kB
#46 101.5   + xz                                    5.2.6  h166bdaf_0              conda-forge/linux-64     418kB
#46 101.5   + yarl                                  1.7.2  py37h540881e_2          conda-forge/linux-64     135kB
#46 101.5   + zeromq                                4.3.4  h9c3ff4c_1              conda-forge/linux-64     360kB
#46 101.5   + zipp                                 3.15.0  pyhd8ed1ab_0            conda-forge/noarch        17kB
#46 101.5   + zlib                                 1.2.13  h166bdaf_4              conda-forge/linux-64      94kB
#46 101.5   + zstd                                  1.5.2  h3eb15da_6              conda-forge/linux-64     420kB
#46 101.5
#46 101.5   Summary:
#46 101.5
#46 101.5   Install: 309 packages
#46 101.5
#46 101.5   Total download: 2GB
#46 101.5
#46 101.5 ─────────────────────────────────────────────────────────────────────────────────────────────────────────
#46 101.5
#46 101.5
#46 101.5
#46 101.5 Transaction starting
#46 331.5 Linking _libgcc_mutex-0.1-conda_forge
#46 331.5 Linking libstdcxx-ng-12.2.0-h46fd767_19
#46 331.5 Linking python_abi-3.7-3_cp37m
#46 331.5 Linking ld_impl_linux-64-2.40-h41732ed_0
#46 331.5 Linking _py-xgboost-mutex-2.0-cpu_0
#46 331.5 Linking ca-certificates-2022.12.7-ha878542_0
#46 331.5 Linking libgfortran5-12.2.0-h337968e_19
#46 331.5 Linking libgomp-12.2.0-h65d4601_19
#46 331.5 Linking libgfortran-ng-12.2.0-h69a702a_19
#46 331.5 Linking _openmp_mutex-4.5-2_gnu
#46 331.5 Linking libgcc-ng-12.2.0-h65d4601_19
#46 331.5 Linking libunistring-0.9.10-h7f98852_0
#46 331.5 Linking xorg-libxdmcp-1.1.3-h7f98852_0
#46 331.5 Linking xorg-libxau-1.0.9-h7f98852_0
#46 331.5 Linking pthread-stubs-0.4-h36c2ea0_1001
#46 331.5 Linking libsodium-1.0.18-h36c2ea0_1
#46 331.5 Linking xorg-xproto-7.0.31-h7f98852_1007
#46 331.5 Linking xorg-kbproto-1.0.7-h7f98852_1002
#46 331.5 Linking libuuid-2.38.1-h0b41bf4_0
#46 331.5 Linking xorg-xextproto-7.3.0-h0b41bf4_1003
#46 331.5 Linking x265-3.5-h924138e_3
#46 331.5 Linking x264-1!164.3095-h166bdaf_2
#46 331.5 Linking openh264-2.3.1-hcb278e6_2
#46 331.5 Linking libvpx-1.11.0-h9c3ff4c_3
#46 331.5 Linking libpciaccess-0.17-h166bdaf_0
#46 331.5 Linking gmp-6.2.1-h58526e2_0
#46 331.5 Linking libtasn1-4.19.0-h166bdaf_0
#46 331.5 Linking bzip2-1.0.8-h7f98852_4
#46 331.5 Linking nspr-4.35-h27087fc_0
#46 331.5 Linking libev-4.33-h516909a_1
#46 331.5 Linking nettle-3.8.1-hc379101_1
#46 331.6 Linking svt-av1-1.3.0-h27087fc_0
#46 331.6 Linking aom-3.5.0-h27087fc_0
#46 331.6 Linking libexpat-2.5.0-hcb278e6_1
#46 331.6 Linking libbrotlicommon-1.0.9-h166bdaf_8
#46 331.6 Linking libiconv-1.17-h166bdaf_0
#46 331.6 Linking libwebp-base-1.3.0-h0b41bf4_0
#46 331.6 Linking libdeflate-1.14-h166bdaf_0
#46 331.6 Linking lerc-4.0.0-h27087fc_0
#46 331.6 Linking alsa-lib-1.2.3.2-h166bdaf_0
#46 331.6 Linking abseil-cpp-20210324.2-h9c3ff4c_0
#46 331.7 Linking c-ares-1.18.1-h7f98852_0
#46 331.7 Linking libopenblas-0.3.21-pthreads_h78a6416_3
#46 331.7 Linking xz-5.2.6-h166bdaf_0
#46 331.7 Linking ncurses-6.3-h27087fc_1
#46 333.6 Linking libnsl-2.0.0-h7f98852_0
#46 333.6 Linking libffi-3.4.2-h7f98852_5
#46 333.6 Linking snappy-1.1.10-h9fff704_0
#46 333.6 Linking keyutils-1.6.1-h166bdaf_0
#46 333.6 Linking jpeg-9e-h0b41bf4_3
#46 333.6 Linking re2-2021.11.01-h9c3ff4c_0
#46 333.6 Linking giflib-5.2.1-h0b41bf4_3
#46 333.6 Linking openssl-1.1.1t-h0b41bf4_0
#46 333.6 Linking cudatoolkit-11.0.3-h88f8997_11
#46 333.7
#46 333.7 error    libmamba response code: -1 error message: Invalid argument
#46 333.7 critical libmamba failed to execute pre/post link script for cudatoolkit
#46 ERROR: process "/usr/local/bin/_dockerfile_shell.sh micromamba install -y -n base -f /tmp/env.yaml &&     micromamba clean --all --yes" did not complete successfully: exit code: 1
------
 > [stage-1 21/21] RUN micromamba install -y -n base -f /tmp/env.yaml &&     micromamba clean --all --yes:
#46 333.6 Linking snappy-1.1.10-h9fff704_0
#46 333.6 Linking keyutils-1.6.1-h166bdaf_0
#46 333.6 Linking jpeg-9e-h0b41bf4_3
#46 333.6 Linking re2-2021.11.01-h9c3ff4c_0
#46 333.6 Linking giflib-5.2.1-h0b41bf4_3
#46 333.6 Linking openssl-1.1.1t-h0b41bf4_0
#46 333.6 Linking cudatoolkit-11.0.3-h88f8997_11
#46 333.7
#46 333.7 error    libmamba response code: -1 error message: Invalid argument
#46 333.7 critical libmamba failed to execute pre/post link script for cudatoolkit
------
ERROR: failed to solve: process "/usr/local/bin/_dockerfile_shell.sh micromamba install -y -n base -f /tmp/env.yaml &&     micromamba clean --all --yes" did not complete successfully: exit code: 1

environment.yml

name: machine_learning
channels:
  - conda-forge
  - defaults
dependencies:
  - redis-py
  - pip
  - boto3
  - botocore
  - celery=5.2.1=pyhd8ed1ab_0
  - h5py=3.1.0=nompi_py37h1e651dc_100
  - ipywidgets=7.7.0=pyhd8ed1ab_0
  - librosa=0.9.1=pyhd8ed1ab_0
  - matplotlib=3.5.2=py37h06a4308_0
  - matplotlib-base=3.5.2=py37hf590b9c_0
  - matplotlib-inline=0.1.6=py37h06a4308_0
  - numba=0.55.1=py37h2d894fd_0
  - numpy=1.19.5=py37h3e96413_3
  - pandas=1.3.5=py37he8f5f7f_0
  - peakutils=1.3.3=py_0
  - pymongo=4.1.1=py37hd23a5d3_0
  - pyparsing=3.0.9=py37h06a4308_0
  - qgrid=1.3.1=py37h89c1867_2
  - tensorflow=2.6.2=cuda110py37h4801193_1
  - tensorflow-base=2.6.2=cuda110py37h0ebe739_1
  - tensorflow-estimator=2.6.2=cuda110py37h4801193_1
  - tensorflow-gpu=2.6.2=cuda110py37h5b0ac8e_1
  - tqdm=4.64.1=py37h06a4308_0
  - xgboost=1.6.2=cpu_py37h08536eb_1
prefix: /home/bastian/.conda/envs/machine_learning

~/.condarc

No response

chrisburr commented 1 year ago

This is due to MAX_FD_LIMIT in reproc++:

https://github.com/DaanDeMeyer/reproc/blob/9f399675b821e175f85ac3ee6e3fd2e6056573eb/reproc/src/process.posix.c#L266-L270

Setting a ulimit -n XXX to a number less than 1024*1024 works around the issue.

jonashaag commented 1 year ago

Is this something we can fix in libmamba?

chrisburr commented 1 year ago

I think the right solution is to fix it in reproc: https://github.com/DaanDeMeyer/reproc/pull/103