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image build fails on Debian 11 when trying follow instructions to build for nvidia/cuda:12.1.0-base-ubuntu20.04 #116

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deepcoder opened this issue Jun 19, 2023 · 3 comments
Closed

image build fails on Debian 11 when trying follow instructions to build for nvidia/cuda:12.1.0-base-ubuntu20.04 #116

deepcoder opened this issue Jun 19, 2023 · 3 comments

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@deepcoder
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When running the command:

sudo docker build -t gpu-jupyter .build/

the error shown below occurs (i believe step 12), full output is at bottom:

#0 92.55 + rm micromamba
#0 92.55 + mamba list python
#0 92.55 + grep '^python '
#0 92.55 + cut -d ' ' -f 1,2
#0 92.55 + tr -s ' '
#0 93.03 'NoneType' object is not iterable
#0 93.03 KeyError('pkgs_dirs')
#0 93.03 Traceback (most recent call last):
#0 93.03   File "/opt/conda/lib/python3.10/site-packages/conda/exception_handler.py", line 16, in __call__



user@gpu02:~/gpu-jupyter$ vi src/Dockerfile.header
user@gpu02:~/gpu-jupyter$ ./generate-Dockerfile.sh --slim
Set docker-stacks to commit 'efa95c2c5b9b095247cd2f5e55bc3b38c85da335'.
Updating efa95c2..799403c
Fast-forward
 .flake8                                                                    |   2 +-
 .github/ISSUE_TEMPLATE/bug_report.yml                                      |  15 +-
 .github/ISSUE_TEMPLATE/feature_request.yml                                 |   1 -
 .github/actions/create-dev-env/action.yml                                  |   4 +-
 .github/actions/download-manifests/action.yml                              |  52 +++++--
 .github/actions/load-image/action.yml                                      |   2 +-
 .github/workflows/docker-build-test-upload.yml                             |  53 ++++++-
 .github/workflows/docker-merge-tags.yml                                    |  61 ++++++++
 .github/workflows/docker-tag-manifest-push.yml                             |  92 ------------
 .github/workflows/docker-tag-push.yml                                      |  58 ++++++++
 .github/workflows/docker-wiki-update.yml                                   |  10 +-
 .github/workflows/docker.yml                                               | 222 ++++++++++++++++++----------
 .github/workflows/hub-overview.yml                                         |  42 ++++--
 .github/workflows/pre-commit.yml                                           |   2 +-
 .github/workflows/sphinx.yml                                               |   6 +-
 .gitignore                                                                 |  10 +-
 .pre-commit-config.yaml                                                    |  38 ++---
 .readthedocs.yaml                                                          |  10 +-
 CONTRIBUTING.md                                                            |  10 +-
 Makefile                                                                   |  15 +-
 README.md                                                                  |  57 +++++---
 aarch64-runner/setup.sh                                                    |   2 +-
 all-spark-notebook/Dockerfile                                              |   2 +-
 base-notebook/Dockerfile                                                   | 127 +++-------------
 base-notebook/docker_healthcheck.py                                        |  21 +++
 base-notebook/jupyter_server_config.py                                     |   4 +-
 binder/Dockerfile                                                          |   4 +-
 datascience-notebook/Dockerfile                                            |  20 +--
 docker-stacks-foundation/.dockerignore                                     |   2 +
 docker-stacks-foundation/Dockerfile                                        | 135 +++++++++++++++++
 docker-stacks-foundation/README.md                                         |  12 ++
 {base-notebook => docker-stacks-foundation}/fix-permissions                |   6 +-
 {base-notebook => docker-stacks-foundation}/initial-condarc                |   0
 {base-notebook => docker-stacks-foundation}/start.sh                       |   0
 docs/conf.py                                                               |  60 ++------
 docs/contributing/features.md                                              |   8 +-
 docs/contributing/issues.md                                                |   8 +-
 docs/contributing/lint.md                                                  |  16 +-
 docs/contributing/packages.md                                              |  10 +-
 docs/contributing/recipes.md                                               |   2 +-
 docs/contributing/stacks.md                                                |  24 +--
 docs/contributing/tests.md                                                 |  18 +--
 docs/images/inherit.svg                                                    |  52 ++++---
 docs/index.rst                                                             |   1 +
 docs/maintaining/aarch64-runner.md                                         |  25 ++--
 docs/maintaining/tasks.md                                                  |  27 ++--
 docs/requirements.txt                                                      |   3 +-
 docs/using/common.md                                                       |  30 ++--
 docs/using/faq.md                                                          |  25 ++++
 docs/using/recipes.md                                                      | 147 +++++++++++++------
 docs/using/running.md                                                      |  36 ++---
 docs/using/selecting.md                                                    | 104 ++++++++-----
 docs/using/specifics.md                                                    |  31 ++--
 docs/using/troubleshooting.md                                              |  31 +++-
 examples/README.md                                                         |   4 +
 examples/docker-compose/README.md                                          |   2 +-
 examples/docker-compose/bin/letsencrypt.sh                                 |   2 +-
 examples/docker-compose/notebook/Dockerfile                                |   4 +-
 examples/make-deploy/Dockerfile                                            |   4 +-
 examples/make-deploy/Makefile                                              |   6 +-
 examples/make-deploy/letsencrypt.makefile                                  |   4 +-
 minimal-notebook/Dockerfile                                                |   9 +-
 minimal-notebook/Rprofile.site                                             |   4 +
 pyspark-notebook/Dockerfile                                                |  36 +++--
 r-notebook/Dockerfile                                                      |  14 +-
 scipy-notebook/Dockerfile                                                  |   4 +-
 tagging/README.md                                                          |  24 +--
 tagging/apply_tags.py                                                      |  68 +++++++++
 tagging/get_platform.py                                                    |  14 ++
 tagging/get_tags_prefix.py                                                 |   8 -
 tagging/images_hierarchy.py                                                |  11 +-
 tagging/merge_tags.py                                                      |  72 +++++++++
 tagging/tag_image.py                                                       |  56 -------
 tagging/taggers.py                                                         |   7 +
 tagging/write_manifest.py                                                  |  22 +--
 tagging/write_tags_file.py                                                 |  65 +++++++++
 tensorflow-notebook/Dockerfile                                             |   7 +-
 tests/R_mimetype_check.py                                                  |  21 +++
 tests/all-spark-notebook/test_spark_notebooks.py                           |   3 +-
 tests/base-notebook/test_container_options.py                              | 325 +++++++----------------------------------
 tests/base-notebook/test_healthcheck.py                                    | 112 ++++++++++++++
 tests/base-notebook/test_npm_package_manager.py                            |  14 ++
 tests/base-notebook/test_packages.py                                       |   2 +-
 tests/conftest.py                                                          |   6 +
 tests/datascience-notebook/test_mimetypes.py                               |  10 ++
 tests/{base-notebook => docker-stacks-foundation}/test_outdated.py         |   0
 tests/{base-notebook => docker-stacks-foundation}/test_package_managers.py |  15 +-
 tests/{base-notebook => docker-stacks-foundation}/test_python.py           |   2 +-
 tests/{base-notebook => docker-stacks-foundation}/test_units.py            |   0
 tests/docker-stacks-foundation/test_user_options.py                        | 290 ++++++++++++++++++++++++++++++++++++
 tests/images_hierarchy.py                                                  |   3 +-
 tests/minimal-notebook/test_inkscape.py                                    |  19 ---
 tests/package_helper.py                                                    |  15 ++
 tests/r-notebook/test_R_mimetypes.py                                       |  10 ++
 tests/run_tests.py                                                         |   6 +-
 95 files changed, 1945 insertions(+), 1110 deletions(-)
 create mode 100644 .github/workflows/docker-merge-tags.yml
 delete mode 100644 .github/workflows/docker-tag-manifest-push.yml
 create mode 100644 .github/workflows/docker-tag-push.yml
 create mode 100755 base-notebook/docker_healthcheck.py
 create mode 100644 docker-stacks-foundation/.dockerignore
 create mode 100644 docker-stacks-foundation/Dockerfile
 create mode 100644 docker-stacks-foundation/README.md
 rename {base-notebook => docker-stacks-foundation}/fix-permissions (89%)
 rename {base-notebook => docker-stacks-foundation}/initial-condarc (100%)
 rename {base-notebook => docker-stacks-foundation}/start.sh (100%)
 create mode 100644 docs/using/faq.md
 create mode 100644 examples/README.md
 create mode 100644 minimal-notebook/Rprofile.site
 create mode 100755 tagging/apply_tags.py
 create mode 100644 tagging/get_platform.py
 delete mode 100644 tagging/get_tags_prefix.py
 create mode 100755 tagging/merge_tags.py
 delete mode 100755 tagging/tag_image.py
 create mode 100755 tagging/write_tags_file.py
 create mode 100644 tests/R_mimetype_check.py
 create mode 100644 tests/base-notebook/test_healthcheck.py
 create mode 100644 tests/base-notebook/test_npm_package_manager.py
 create mode 100644 tests/datascience-notebook/test_mimetypes.py
 rename tests/{base-notebook => docker-stacks-foundation}/test_outdated.py (100%)
 rename tests/{base-notebook => docker-stacks-foundation}/test_package_managers.py (59%)
 rename tests/{base-notebook => docker-stacks-foundation}/test_python.py (95%)
 rename tests/{base-notebook => docker-stacks-foundation}/test_units.py (100%)
 create mode 100644 tests/docker-stacks-foundation/test_user_options.py
 delete mode 100644 tests/minimal-notebook/test_inkscape.py
 create mode 100644 tests/r-notebook/test_R_mimetypes.py
/home/user/gpu-jupyter

Set head to given commit.
Set 'no-datascience-notebook' = 'python-only', not installing the datascience-notebook with Julia and R.
Set 'no-useful-packages', not installing stuff within src/Dockerfile.usefulpackages.

The GPU Dockerfile was generated successfully in file .build/Dockerfile.
To start the GPU-based Juyterlab instance, run:
  docker build -t gpu-jupyter .build/  # will take a while
  docker run --gpus all -d -it -p 8848:8888 -v /home/user/gpu-jupyter/data:/home/jovyan/work -e GRANT_SUDO=yes -e JUPYTER_ENABLE_LAB=yes -e NB_UID=1000 -e NB_GID=1000 --user root --restart always --name gpu-jupyter_1 gpu-jupyter
user@gpu02:~/gpu-jupyter$ sudo docker build -t gpu-jupyter .build/
[+] Building 86.9s (16/34)
 => [internal] load build definition from Dockerfile                                                                   0.0s
 => => transferring dockerfile: 13.69kB                                                                                0.0s
 => [internal] load .dockerignore                                                                                      0.0s
 => => transferring context: 2B                                                                                        0.0s
 => [internal] load metadata for docker.io/nvidia/cuda:12.1.0-base-ubuntu20.04                                         0.0s
 => [ 1/30] FROM docker.io/nvidia/cuda:12.1.0-base-ubuntu20.04                                                         0.0s
 => [internal] load build context                                                                                      0.0s
 => => transferring context: 16.38kB                                                                                   0.0s
 => CACHED [ 2/30] RUN chmod 1777 /tmp && chmod 1777 /var/tmp                                                          0.0s
 => CACHED [ 3/30] RUN apt-get update &&     apt-get -y install apt-utils                                              0.0s
 => CACHED [ 4/30] RUN apt-get update --yes &&     apt-get upgrade --yes &&     apt-get install --yes --no-install-re  0.0s
 => CACHED [ 5/30] COPY fix-permissions /usr/local/bin/fix-permissions                                                 0.0s
 => CACHED [ 6/30] RUN chmod a+rx /usr/local/bin/fix-permissions                                                       0.0s
 => CACHED [ 7/30] RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc &&    echo 'eval  0.0s
 => CACHED [ 8/30] RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su &&     sed -i.bak -e 's/^%admin/#%admin/' /  0.0s
 => CACHED [ 9/30] RUN mkdir "/home/jovyan/work" &&     fix-permissions "/home/jovyan"                                 0.0s
 => CACHED [10/30] COPY --chown=1000:100 initial-condarc /opt/conda/.condarc                                           0.0s
 => CACHED [11/30] WORKDIR /tmp                                                                                        0.0s
 => ERROR [12/30] RUN set -x &&     arch=$(uname -m) &&     if [ "${arch}" = "x86_64" ]; then         arch="64";      86.7s
------
 > [12/30] RUN set -x &&     arch=$(uname -m) &&     if [ "${arch}" = "x86_64" ]; then         arch="64";     fi &&     wget -qO /tmp/micromamba.tar.bz2         "https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" &&     tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba &&     rm /tmp/micromamba.tar.bz2 &&     PYTHON_SPECIFIER="python=3.10" &&     if [[ "3.10" == "default" ]]; then PYTHON_SPECIFIER="python"; fi &&     ./micromamba install         --root-prefix="/opt/conda"         --prefix="/opt/conda"         --yes         "${PYTHON_SPECIFIER}"         'mamba'         'notebook'         'jupyterhub'         'jupyterlab' &&     rm micromamba &&     mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "/opt/conda/conda-meta/pinned" &&     jupyter notebook --generate-config &&     mamba clean --all -f -y &&     npm cache clean --force &&     jupyter lab clean &&     rm -rf "/home/jovyan/.cache/yarn" &&     fix-permissions "/opt/conda" &&     fix-permissions "/home/jovyan":
#0 0.293 ++ uname -m
#0 0.295 + arch=x86_64
#0 0.295 + '[' x86_64 = x86_64 ']'
#0 0.295 + arch=64
#0 0.295 + wget -qO /tmp/micromamba.tar.bz2 https://micromamba.snakepit.net/api/micromamba/linux-64/latest
#0 12.07 + tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba
#0 12.09 bin/micromamba
#0 12.55 + rm /tmp/micromamba.tar.bz2
#0 12.55 + PYTHON_SPECIFIER=python=3.10
#0 12.55 + [[ 3.10 == \d\e\f\a\u\l\t ]]
#0 12.55 + ./micromamba install --root-prefix=/opt/conda --prefix=/opt/conda --yes python=3.10 mamba notebook jupyterhub jupyterlab
#0 12.56
#0 12.56                                            __
#0 12.56           __  ______ ___  ____ _____ ___  / /_  ____ _
#0 12.56          / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
#0 12.56         / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
#0 12.56        / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
#0 12.56       /_/
#0 12.56
#0 35.94
#0 35.94 Transaction
#0 35.94
#0 35.94   Prefix: /opt/conda
#0 35.94
#0 35.94   Updating specs:
#0 35.94
#0 35.94    - python=3.10
#0 35.94    - mamba
#0 35.94    - notebook
#0 35.94    - jupyterhub
#0 35.94    - jupyterlab
#0 35.94
#0 35.94
#0 35.96   Package                               Version  Build               Channel          Size
#0 35.96 ────────────────────────────────────────────────────────────────────────────────────────────
#0 35.96   Install:
#0 35.96 ────────────────────────────────────────────────────────────────────────────────────────────
#0 35.96
#0 35.96   + _libgcc_mutex                           0.1  conda_forge         conda-forge       3kB
#0 35.96   + _openmp_mutex                           4.5  2_gnu               conda-forge      24kB
#0 35.96   + alembic                              1.11.1  pyhd8ed1ab_0        conda-forge     154kB
#0 35.96   + anyio                                 3.7.0  pyhd8ed1ab_1        conda-forge      97kB
#0 35.96   + argon2-cffi                          21.3.0  pyhd8ed1ab_0        conda-forge      16kB
#0 35.96   + argon2-cffi-bindings                 21.2.0  py310h5764c6d_3     conda-forge      35kB
#0 35.96   + asttokens                             2.2.1  pyhd8ed1ab_0        conda-forge      28kB
#0 35.96   + async-lru                             2.0.2  pyhd8ed1ab_0        conda-forge      14kB
#0 35.96   + async_generator                        1.10  py_0                conda-forge      18kB
#0 35.96   + attrs                                23.1.0  pyh71513ae_1        conda-forge      55kB
#0 35.96   + babel                                2.12.1  pyhd8ed1ab_1        conda-forge       7MB
#0 35.96   + backcall                              0.2.0  pyh9f0ad1d_0        conda-forge      14kB
#0 35.96   + backports                               1.0  pyhd8ed1ab_3        conda-forge       6kB
#0 35.96   + backports.functools_lru_cache         1.6.4  pyhd8ed1ab_0        conda-forge       9kB
#0 35.96   + beautifulsoup4                       4.12.2  pyha770c72_0        conda-forge     115kB
#0 35.96   + bleach                                6.0.0  pyhd8ed1ab_0        conda-forge     131kB
#0 35.96   + blinker                               1.6.2  pyhd8ed1ab_0        conda-forge      18kB
#0 35.96   + boltons                              23.0.0  pyhd8ed1ab_0        conda-forge     303kB
#0 35.96   + brotli                                1.0.9  h166bdaf_8          conda-forge      19kB
#0 35.96   + brotli-bin                            1.0.9  h166bdaf_8          conda-forge      20kB
#0 35.96   + bzip2                                 1.0.8  h7f98852_4          conda-forge     496kB
#0 35.96   + c-ares                               1.19.1  hd590300_0          conda-forge     113kB
#0 35.96   + ca-certificates                    2023.5.7  hbcca054_0          conda-forge     148kB
#0 35.96   + certifi                            2023.5.7  pyhd8ed1ab_0        conda-forge     152kB
#0 35.96   + certipy                               0.1.3  py_0                conda-forge      17kB
#0 35.96   + cffi                                 1.15.1  py310h255011f_3     conda-forge     237kB
#0 35.96   + charset-normalizer                    3.1.0  pyhd8ed1ab_0        conda-forge      45kB
#0 35.96   + colorama                              0.4.6  pyhd8ed1ab_0        conda-forge      25kB
#0 35.96   + comm                                  0.1.3  pyhd8ed1ab_0        conda-forge      11kB
#0 35.96   + conda                                23.5.0  py310hff52083_1     conda-forge       1MB
#0 35.96   + conda-package-handling                2.0.2  pyh38be061_0        conda-forge     253kB
#0 35.96   + conda-package-streaming               0.8.0  pyhd8ed1ab_0        conda-forge      19kB
#0 35.96   + configurable-http-proxy               4.5.4  he2f69ee_2          conda-forge       1MB
#0 35.96   + cryptography                         41.0.1  py310h75e40e8_0     conda-forge       2MB
#0 35.96   + debugpy                               1.6.7  py310heca2aa9_0     conda-forge       2MB
#0 35.96   + decorator                             5.1.1  pyhd8ed1ab_0        conda-forge      12kB
#0 35.96   + defusedxml                            0.7.1  pyhd8ed1ab_0        conda-forge      24kB
#0 35.96   + entrypoints                             0.4  pyhd8ed1ab_0        conda-forge       9kB
#0 35.96   + exceptiongroup                        1.1.1  pyhd8ed1ab_0        conda-forge      19kB
#0 35.96   + executing                             1.2.0  pyhd8ed1ab_0        conda-forge      25kB
#0 35.96   + flit-core                             3.9.0  pyhd8ed1ab_0        conda-forge      49kB
#0 35.96   + fmt                                   9.1.0  h924138e_0          conda-forge     190kB
#0 35.96   + gmp                                   6.2.1  h58526e2_0          conda-forge     826kB
#0 35.96   + greenlet                              2.0.2  py310hc6cd4ac_1     conda-forge     191kB
#0 35.96   + icu                                    72.1  hcb278e6_0          conda-forge      12MB
#0 35.96   + idna                                    3.4  pyhd8ed1ab_0        conda-forge      57kB
#0 35.96   + importlib-metadata                    6.7.0  pyha770c72_0        conda-forge      26kB
#0 35.96   + importlib_metadata                    6.7.0  hd8ed1ab_0          conda-forge       9kB
#0 35.96   + importlib_resources                  5.12.0  pyhd8ed1ab_0        conda-forge      31kB
#0 35.96   + ipykernel                            6.23.1  pyh210e3f2_0        conda-forge     113kB
#0 35.96   + ipython                              8.14.0  pyh41d4057_0        conda-forge     583kB
#0 35.96   + ipython_genutils                      0.2.0  py_1                conda-forge      22kB
#0 35.96   + jedi                                 0.18.2  pyhd8ed1ab_0        conda-forge     804kB
#0 35.96   + jinja2                                3.1.2  pyhd8ed1ab_1        conda-forge     101kB
#0 35.96   + json5                                 0.9.5  pyh9f0ad1d_0        conda-forge      21kB
#0 35.96   + jsonpatch                              1.32  pyhd8ed1ab_0        conda-forge      15kB
#0 35.96   + jsonpointer                             2.0  py_0                conda-forge       9kB
#0 35.96   + jsonschema                           4.17.3  pyhd8ed1ab_0        conda-forge      70kB
#0 35.96   + jupyter-lsp                           2.2.0  pyhd8ed1ab_0        conda-forge      53kB
#0 35.96   + jupyter_client                        8.2.0  pyhd8ed1ab_0        conda-forge     104kB
#0 35.96   + jupyter_core                          5.3.1  py310hff52083_0     conda-forge      92kB
#0 35.96   + jupyter_events                        0.6.3  pyhd8ed1ab_0        conda-forge      77kB
#0 35.96   + jupyter_server                        2.6.0  pyhd8ed1ab_0        conda-forge     316kB
#0 35.96   + jupyter_server_terminals              0.4.4  pyhd8ed1ab_1        conda-forge      19kB
#0 35.96   + jupyter_telemetry                     0.1.0  pyhd8ed1ab_1        conda-forge      10kB
#0 35.96   + jupyterhub                            4.0.1  pyh2a2186d_0        conda-forge       8kB
#0 35.96   + jupyterhub-base                       4.0.1  pyh2a2186d_0        conda-forge       2MB
#0 35.96   + jupyterlab                            4.0.2  pyhd8ed1ab_0        conda-forge       7MB
#0 35.96   + jupyterlab_pygments                   0.2.2  pyhd8ed1ab_0        conda-forge      17kB
#0 35.96   + jupyterlab_server                    2.23.0  pyhd8ed1ab_0        conda-forge      60kB
#0 35.96   + keyutils                              1.6.1  h166bdaf_0          conda-forge     118kB
#0 35.96   + krb5                                 1.20.1  h81ceb04_0          conda-forge       1MB
#0 35.96   + ld_impl_linux-64                       2.40  h41732ed_0          conda-forge     705kB
#0 35.96   + libarchive                            3.6.2  h039dbb9_1          conda-forge     844kB
#0 35.96   + libbrotlicommon                       1.0.9  h166bdaf_8          conda-forge      67kB
#0 35.96   + libbrotlidec                          1.0.9  h166bdaf_8          conda-forge      34kB
#0 35.96   + libbrotlienc                          1.0.9  h166bdaf_8          conda-forge     295kB
#0 35.96   + libcurl                               8.1.2  h409715c_0          conda-forge     373kB
#0 35.96   + libedit                        3.1.20191231  he28a2e2_2          conda-forge     124kB
#0 35.96   + libev                                  4.33  h516909a_1          conda-forge     106kB
#0 35.96   + libffi                                3.4.2  h7f98852_5          conda-forge      58kB
#0 35.96   + libgcc-ng                            13.1.0  he5830b7_0          conda-forge     776kB
#0 35.96   + libgomp                              13.1.0  he5830b7_0          conda-forge     419kB
#0 35.96   + libiconv                               1.17  h166bdaf_0          conda-forge       1MB
#0 35.96   + libmamba                              1.4.4  h658169a_1          conda-forge       2MB
#0 35.96   + libmambapy                            1.4.4  py310h8aae740_1     conda-forge     289kB
#0 35.96   + libnghttp2                           1.52.0  h61bc06f_0          conda-forge     622kB
#0 35.96   + libnsl                                2.0.0  h7f98852_0          conda-forge      31kB
#0 35.96   + libsodium                            1.0.18  h36c2ea0_1          conda-forge     375kB
#0 35.96   + libsolv                              0.7.24  h3eb15da_0          conda-forge     463kB
#0 35.96   + libsqlite                            3.42.0  h2797004_0          conda-forge     829kB
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#0 35.96
#0 35.96   Summary:
#0 35.96
#0 35.96   Install: 192 packages
#0 35.96
#0 35.96   Total download: 154MB
#0 35.96
#0 35.96 ────────────────────────────────────────────────────────────────────────────────────────────
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#0 84.25 Linking conda-package-streaming-0.8.0-pyhd8ed1ab_0
#0 84.27 Linking argon2-cffi-21.3.0-pyhd8ed1ab_0
#0 84.28 Linking pyopenssl-23.2.0-pyhd8ed1ab_1
#0 84.30 Linking oauthlib-3.2.2-pyhd8ed1ab_0
#0 84.32 Linking jupyter_events-0.6.3-pyhd8ed1ab_0
#0 84.35 Linking nbformat-5.9.0-pyhd8ed1ab_0
#0 84.36 Linking jupyter_telemetry-0.1.0-pyhd8ed1ab_1
#0 84.37 Linking alembic-1.11.1-pyhd8ed1ab_0
#0 84.42 Linking jupyter_server_terminals-0.4.4-pyhd8ed1ab_1
#0 84.44 Linking ipykernel-6.23.1-pyh210e3f2_0
#0 84.48 Linking conda-package-handling-2.0.2-pyh38be061_0
#0 84.49 Linking certipy-0.1.3-py_0
#0 84.50 Linking nbclient-0.8.0-pyhd8ed1ab_0
#0 84.51 Linking jupyterhub-base-4.0.1-pyh2a2186d_0
#0 84.84 Linking nbconvert-core-7.5.0-pyhd8ed1ab_0
#0 84.91 Linking jupyterhub-4.0.1-pyh2a2186d_0
#0 84.94 Linking jupyter_server-2.6.0-pyhd8ed1ab_0
#0 84.99 Linking nbconvert-pandoc-7.5.0-pyhd8ed1ab_0
#0 85.00 Linking jupyterlab_server-2.23.0-pyhd8ed1ab_0
#0 85.02 Linking jupyter-lsp-2.2.0-pyhd8ed1ab_0
#0 85.08 Linking notebook-shim-0.2.3-pyhd8ed1ab_0
#0 85.10 Linking nbconvert-7.5.0-pyhd8ed1ab_0
#0 85.10 Linking jupyterlab-4.0.2-pyhd8ed1ab_0
#0 85.26 Linking nbclassic-1.0.0-pyhb4ecaf3_1
#0 85.50 Linking notebook-6.5.4-pyha770c72_0
#0 85.56 Linking conda-23.5.0-py310hff52083_1
#0 85.75 Linking mamba-1.4.4-py310h51d5547_1
#0 85.78
#0 85.78 Transaction finished
#0 85.78
#0 85.78 To activate this environment, use:
#0 85.78
#0 85.78     micromamba activate base
#0 85.78
#0 85.78 Or to execute a single command in this environment, use:
#0 85.78
#0 85.78     micromamba run -n base mycommand
#0 85.78
#0 85.81 + rm micromamba
#0 85.82 + mamba list python
#0 85.82 + cut -d ' ' -f 1,2
#0 85.82 + tr -s ' '
#0 85.82 + grep '^python '
#0 86.19 'NoneType' object is not iterable
#0 86.20 KeyError('pkgs_dirs')
#0 86.20 Traceback (most recent call last):
#0 86.20   File "/opt/conda/lib/python3.10/site-packages/conda/exception_handler.py", line 16, in __call__
#0 86.20     return func(*args, **kwargs)
#0 86.20   File "/opt/conda/lib/python3.10/site-packages/mamba/mamba.py", line 968, in exception_converter
#0 86.20     raise e
#0 86.20   File "/opt/conda/lib/python3.10/site-packages/mamba/mamba.py", line 961, in exception_converter
#0 86.20     exit_code = _wrapped_main(*args, **kwargs)
#0 86.20   File "/opt/conda/lib/python3.10/site-packages/mamba/mamba.py", line 901, in _wrapped_main
#0 86.20     p = generate_parser()
#0 86.20   File "/opt/conda/lib/python3.10/site-packages/conda/cli/main.py", line 60, in generate_parser
#0 86.20     return generate_parser(*args, **kwargs)
#0 86.20   File "/opt/conda/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 65, in generate_parser
#0 86.20     p = ArgumentParser(
#0 86.20   File "/opt/conda/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 152, in __init__
#0 86.20     self._subcommands = context.plugin_manager.get_hook_results("subcommands")
#0 86.20   File "/opt/conda/lib/python3.10/site-packages/conda/plugins/manager.py", line 104, in get_hook_results
#0 86.20     (item for items in hook() for item in items),
#0 86.20 TypeError: 'NoneType' object is not iterable
#0 86.20
#0 86.20 During handling of the above exception, another exception occurred:
#0 86.20
#0 86.20 Traceback (most recent call last):
#0 86.20   File "/opt/conda/lib/python3.10/site-packages/conda/exception_handler.py", line 165, in print_unexpected_error_report
#0 86.20     get_main_info_str(error_report["conda_info"])
#0 86.20   File "/opt/conda/lib/python3.10/site-packages/conda/cli/main_info.py", line 250, in get_main_info_str
#0 86.20     info_dict["_" + key] = ("\n" + 26 * " ").join(info_dict[key])
#0 86.20 KeyError: 'pkgs_dirs'
#0 86.20
#0 86.20 # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
#0 86.20
#0 86.20     Traceback (most recent call last):
#0 86.20       File "/opt/conda/lib/python3.10/site-packages/conda/exception_handler.py", line 16, in __call__
#0 86.20         return func(*args, **kwargs)
#0 86.20       File "/opt/conda/lib/python3.10/site-packages/mamba/mamba.py", line 968, in exception_converter
#0 86.20         raise e
#0 86.20       File "/opt/conda/lib/python3.10/site-packages/mamba/mamba.py", line 961, in exception_converter
#0 86.20         exit_code = _wrapped_main(*args, **kwargs)
#0 86.20       File "/opt/conda/lib/python3.10/site-packages/mamba/mamba.py", line 901, in _wrapped_main
#0 86.20         p = generate_parser()
#0 86.20       File "/opt/conda/lib/python3.10/site-packages/conda/cli/main.py", line 60, in generate_parser
#0 86.20         return generate_parser(*args, **kwargs)
#0 86.20       File "/opt/conda/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 65, in generate_parser
#0 86.20         p = ArgumentParser(
#0 86.20       File "/opt/conda/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 152, in __init__
#0 86.20         self._subcommands = context.plugin_manager.get_hook_results("subcommands")
#0 86.20       File "/opt/conda/lib/python3.10/site-packages/conda/plugins/manager.py", line 104, in get_hook_results
#0 86.20         (item for items in hook() for item in items),
#0 86.20     TypeError: 'NoneType' object is not iterable
#0 86.20
#0 86.20 `$ /opt/conda/bin/mamba list python`
#0 86.20
#0 86.20   environment variables:
#0 86.20 conda info could not be constructed.
#0 86.20 KeyError('pkgs_dirs')
#0 86.20
#0 86.20 An unexpected error has occurred. Conda has prepared the above report.
#0 86.20
------
Dockerfile:129
--------------------
 128 |     WORKDIR /tmp
 129 | >>> RUN set -x && \
 130 | >>>     arch=$(uname -m) && \
 131 | >>>     if [ "${arch}" = "x86_64" ]; then \
 132 | >>>         # Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
 133 | >>>         arch="64"; \
 134 | >>>     fi && \
 135 | >>>     wget -qO /tmp/micromamba.tar.bz2 \
 136 | >>>         "https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
 137 | >>>     tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
 138 | >>>     rm /tmp/micromamba.tar.bz2 && \
 139 | >>>     PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
 140 | >>>     if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
 141 | >>>     # Install the packages
 142 | >>>     ./micromamba install \
 143 | >>>         --root-prefix="${CONDA_DIR}" \
 144 | >>>         --prefix="${CONDA_DIR}" \
 145 | >>>         --yes \
 146 | >>>         "${PYTHON_SPECIFIER}" \
 147 | >>>         'mamba' \
 148 | >>>         'notebook' \
 149 | >>>         'jupyterhub' \
 150 | >>>         'jupyterlab' && \
 151 | >>>     rm micromamba && \
 152 | >>>     # Pin major.minor version of python
 153 | >>>     mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
 154 | >>>     jupyter notebook --generate-config && \
 155 | >>>     mamba clean --all -f -y && \
 156 | >>>     npm cache clean --force && \
 157 | >>>     jupyter lab clean && \
 158 | >>>     rm -rf "/home/${NB_USER}/.cache/yarn" && \
 159 | >>>     fix-permissions "${CONDA_DIR}" && \
 160 | >>>     fix-permissions "/home/${NB_USER}"
 161 |
--------------------
ERROR: failed to solve: process "/bin/bash -o pipefail -c set -x &&     arch=$(uname -m) &&     if [ \"${arch}\" = \"x86_64\" ]; then         arch=\"64\";     fi &&     wget -qO /tmp/micromamba.tar.bz2         \"https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest\" &&     tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba &&     rm /tmp/micromamba.tar.bz2 &&     PYTHON_SPECIFIER=\"python=${PYTHON_VERSION}\" &&     if [[ \"${PYTHON_VERSION}\" == \"default\" ]]; then PYTHON_SPECIFIER=\"python\"; fi &&     ./micromamba install         --root-prefix=\"${CONDA_DIR}\"         --prefix=\"${CONDA_DIR}\"         --yes         \"${PYTHON_SPECIFIER}\"         'mamba'         'notebook'         'jupyterhub'         'jupyterlab' &&     rm micromamba &&     mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> \"${CONDA_DIR}/conda-meta/pinned\" &&     jupyter notebook --generate-config &&     mamba clean --all -f -y &&     npm cache clean --force &&     jupyter lab clean &&     rm -rf \"/home/${NB_USER}/.cache/yarn\" &&     fix-permissions \"${CONDA_DIR}\" &&     fix-permissions \"/home/${NB_USER}\"" did not complete successfully: exit code: 1
user@gpu02:~/gpu-jupyter$
@ChristophSchranz
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ChristophSchranz commented Jul 14, 2023 •
edited
Loading

Hi @deepcoder
It seems like there is already a problem in the part of installing docker-stacks:

gpu-jupyter/.build/Dockerfile

Lines 128 to 159 in 5d8443c

RUN set -x && \
arch=$(uname -m) && \
if [ "${arch}" = "x86_64" ]; then \
# Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
arch="64"; \
fi && \
wget -qO /tmp/micromamba.tar.bz2 \
"https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
rm /tmp/micromamba.tar.bz2 && \
PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
# Install the packages
./micromamba install \
--root-prefix="${CONDA_DIR}" \
--prefix="${CONDA_DIR}" \
--yes \
"${PYTHON_SPECIFIER}" \
'mamba' \
'notebook' \
'jupyterhub' \
'jupyterlab' && \
rm micromamba && \
# Pin major.minor version of python
mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
jupyter notebook --generate-config && \
mamba clean --all -f -y && \
npm cache clean --force && \
jupyter lab clean && \
rm -rf "/home/${NB_USER}/.cache/yarn" && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"

In order to debug the problem:

  • Can you build the minimal-notebook of docker-stacks? (see here)
  • Can you generate another version of the Dockerfile, like --python-only? 
    ./generate-Dockerfile.sh --python-only
docker build -t gpu-jupyter .build/  # will take a while
  • Try to find a solution to install mamba (and maybe other packages) using your base image nvidia/cuda:12.1.0-base-ubuntu20.04. You might have to install some additional packages. In case it doesn't work as expected, consider using the original and tested base image.

@benz0li
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benz0li commented Sep 4, 2023 •
edited
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@deepcoder @ChristophSchranz Regarding CUDA versions 11.6.0 and version 12.1.0: Please be aware of the CUDA Container Tag Support EOL Chart.

@ChristophSchranz
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Hi,

I've noticed docker-stacks should have solved this issue for the 12.0.1-cudnn8-devel-ubuntu22.04 base image.
It builds and runs appropriately for the GPU-Jupyter version tagged with v1.5_cuda-12.0_ubuntu-22.04_python-only. See PR #124.

Also, note @benz0li's hint to prefer supported CUDA tags.

Please let me know and reopen this issue if there are still problems.

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@deepcoder @ChristophSchranz @benz0li