Merge pull request #154 from iot-salzburg/v1.8_cuda-12.5_ubuntu-22.04

Updated packages V1.8 with cuda 12.5 ubuntu 22.04

.build/Dockerfile

@@ -7,8 +7,9 @@
 
 # Use NVIDIA CUDA as base image and run the same installation as in the other packages.
 # The version of cuda must match those of the packages installed in src/Dockerfile.gpulibs
-FROM nvidia/cuda:12.2.2-cudnn8-runtime-ubuntu22.04
-LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
+FROM nvidia/cuda:12.5.1-cudnn-runtime-ubuntu22.04
+LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
+
 # This is a concatenated Dockerfile, the maintainers of subsequent sections may vary.
 RUN chmod 1777 /tmp && chmod 1777 /var/tmp
 
@@ -41,7 +42,7 @@ USER root
 
 # Install all OS dependencies for the Server that starts
 # but lacks all features (e.g., download as all possible file formats)
-ENV DEBIAN_FRONTEND noninteractive
+ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update --yes && \
     # - `apt-get upgrade` is run to patch known vulnerabilities in system packages
     #   as the Ubuntu base image is rebuilt too seldom sometimes (less than once a month)
@@ -51,6 +52,10 @@ RUN apt-get update --yes && \
     bzip2 \
     ca-certificates \
     locales \
+    # - `netbase` provides /etc/{protocols,rpc,services}, part of POSIX
+    #   and required by various C functions like getservbyname and getprotobyname
+    #   https://github.com/jupyter/docker-stacks/pull/2129
+    netbase \
     sudo \
     # - `tini` is installed as a helpful container entrypoint,
     #   that reaps zombie processes and such of the actual executable we want to start
@@ -85,7 +90,7 @@ RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashr
     # and docs: https://docs.conda.io/projects/conda/en/latest/dev-guide/deep-dives/activation.html
     echo 'eval "$(conda shell.bash hook)"' >> /etc/skel/.bashrc
 
-# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
+# Create "${NB_USER}" user (`jovyan` by default) with UID="${NB_UID}" (`1000` by default) and in the 'users' group
 # and make sure these dirs are writable by the `users` group.
 RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
     sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
@@ -134,9 +139,9 @@ RUN set -x && \
         --root-prefix="${CONDA_DIR}" \
         --prefix="${CONDA_DIR}" \
         --yes \
-        "${PYTHON_SPECIFIER}" \
+        'jupyter_core' \
         'mamba' \
-        'jupyter_core' && \
+        "${PYTHON_SPECIFIER}" && \
     rm -rf /tmp/bin/ && \
     # Pin major.minor version of python
     # https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-pkgs.html#preventing-packages-from-updating-pinning
@@ -199,18 +204,18 @@ RUN apt-get update --yes && \
 
 USER ${NB_UID}
 
-# Install JupyterLab, Jupyter Notebook, JupyterHub and NBClassic
+# Install JupyterHub, JupyterLab, NBClassic and Jupyter Notebook
 # Generate a Jupyter Server config
 # Cleanup temporary files
 # Correct permissions
 # Do all this in a single RUN command to avoid duplicating all of the
 # files across image layers when the permissions change
 WORKDIR /tmp
 RUN mamba install --yes \
-    'jupyterlab' \
-    'notebook' \
     'jupyterhub' \
-    'nbclassic' && \
+    'jupyterlab' \
+    'nbclassic' \
+    'notebook' && \
     jupyter server --generate-config && \
     mamba clean --all -f -y && \
     npm cache clean --force && \
@@ -339,7 +344,7 @@ RUN mamba install --yes \
     'dask' \
     'dill' \
     'h5py' \
-    'ipympl'\
+    'ipympl' \
     'ipywidgets' \
     'jupyterlab-git' \
     'matplotlib-base' \
@@ -357,7 +362,7 @@ RUN mamba install --yes \
     'sqlalchemy' \
     'statsmodels' \
     'sympy' \
-    'widgetsnbextension'\
+    'widgetsnbextension' \
     'xlrd' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
@@ -383,7 +388,7 @@ WORKDIR "${HOME}"
 ########################## Dependency: gpulibs #############################
 ############################################################################
 
-LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
+LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
 
 # Install dependencies for e.g. PyTorch
 RUN mamba install --quiet --yes \
@@ -399,7 +404,7 @@ RUN mamba install --quiet --yes \
 # using device_lib.list_local_devices() the cudNN version is shown, adapt version to tested compat
 USER ${NB_UID}
 RUN pip install --upgrade pip && \
-    pip install --no-cache-dir tensorflow==2.15.1 keras==2.15.0 && \
+    pip install --no-cache-dir tensorflow==2.18.0 keras==3.6.0 && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
@@ -410,11 +415,11 @@ RUN pip install --upgrade pip && \
 #  && torchviz==0.0.2 --extra-index-url https://download.pytorch.org/whl/cu121
 RUN set -ex \
  && buildDeps=' \
-    torch==2.2.2 \
-    torchvision==0.17.2 \
-    torchaudio==2.2.2 \
+    torch==2.5.1 \
+    torchvision==0.20.1 \
+    torchaudio==2.5.1 \
 ' \
- && pip install --no-cache-dir $buildDeps  --extra-index-url https://download.pytorch.org/whl/cu121 \
+ && pip install --no-cache-dir $buildDeps  --extra-index-url https://download.pytorch.org/whl/cu124 \
  && fix-permissions "${CONDA_DIR}" \
  && fix-permissions "/home/${NB_USER}"
 
@@ -435,8 +440,9 @@ RUN pip install --no-cache-dir nvidia-pyindex && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Install cuda-nvcc with sepecific version, see here: https://anaconda.org/nvidia/cuda-nvcc/labels
-RUN mamba install -c nvidia cuda-nvcc=12.2.140 -y && \
+# Install cuda-nvcc with sepecific version, see here:
+# https://anaconda.org/nvidia/cuda-nvcc/labels
+RUN mamba install -c nvidia cuda-nvcc=12.5.82 -y && \
     mamba clean --all -f -y && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER
@@ -450,7 +456,7 @@ USER $NB_UID
   ############################ Useful packages ###############################
   ############################################################################
 
-LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
+LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
 
 USER root
 
@@ -463,7 +469,7 @@ USER $NB_UID
 RUN set -ex \
  && buildDeps=' \
     graphviz==0.20.3 \
-    pytest==8.1.1 \
+    pytest==8.3.3 \
  ' \
  && pip install --no-cache-dir $buildDeps \
  && fix-permissions "${CONDA_DIR}" \
@@ -472,8 +478,8 @@ RUN set -ex \
 # upgrade jupyter-server for compatibility
 RUN set -ex \
  && buildDeps=' \
-    distributed==2024.4.1 \
-    jupyter-server==2.13 \
+    distributed==2024.11.2 \
+    jupyter-server==2.14.2 \
  ' \
  && pip install --no-cache-dir $buildDeps \
  && fix-permissions "${CONDA_DIR}" \
@@ -483,15 +489,15 @@ RUN set -ex \
  && buildDeps=' \
     # install extension manager
     jupyter_contrib_nbextensions==0.7.0 \
-    jupyter_nbextensions_configurator==0.6.3 \
+    jupyter_nbextensions_configurator==0.6.4 \
     # install git extension
-    jupyterlab-git==0.50.0 \
+    jupyterlab-git==0.50.2 \
     # install plotly extension
-    plotly==5.20.0 \
+    plotly==5.24.1 \
     # install drawio and graphical extensions, not compatible with Jupyterlab 4.X yet
     # ipydrawio==1.3.0 \
-    ipyleaflet==0.18.2 \
-    ipywidgets==8.1.2 \
+    ipyleaflet==0.19.2 \
+    ipywidgets==8.1.5 \
     # install spell checker
     jupyterlab-spellchecker==0.8.4 \
     ' \

.build/docker_healthcheck.py

@@ -9,9 +9,9 @@
 import requests
 
 # Several operations below deliberately don't check for possible errors
-# As this is a healthcheck, it should succeed or raise an exception on error
+# As this is a health check, it should succeed or raise an exception on error
 
-# Docker runs healtchecks using an exec
+# Docker runs health checks using an exec
 # It uses the default user configured when running the image: root for the case of a custom NB_USER or jovyan for the case of the default image user.
 # We manually change HOME to make `jupyter --runtime-dir` report a correct path
 # More information: <https://github.com/jupyter/docker-stacks/pull/2074#issuecomment-1879778409>

.build/start.sh

@@ -155,11 +155,14 @@ if [ "$(id -u)" == 0 ]; then
     unset_explicit_env_vars
 
     _log "Running as ${NB_USER}:" "${cmd[@]}"
-    exec sudo --preserve-env --set-home --user "${NB_USER}" \
-        LD_LIBRARY_PATH="${LD_LIBRARY_PATH}" \
-        PATH="${PATH}" \
-        PYTHONPATH="${PYTHONPATH:-}" \
-        "${cmd[@]}"
+    if [ "${NB_USER}" = "root" ] && [ "${NB_UID}" = "$(id -u "${NB_USER}")" ] && [ "${NB_GID}" = "$(id -g "${NB_USER}")" ]; then
+        HOME="/home/root" exec "${cmd[@]}"
+    else
+        exec sudo --preserve-env --set-home --user "${NB_USER}" \
+            LD_LIBRARY_PATH="${LD_LIBRARY_PATH}" \
+            PATH="${PATH}" \
+            PYTHONPATH="${PYTHONPATH:-}" \
+            "${cmd[@]}"
         # Notes on how we ensure that the environment that this container is started
         # with is preserved (except vars listed in JUPYTER_ENV_VARS_TO_UNSET) when
         # we transition from running as root to running as NB_USER.
@@ -187,6 +190,7 @@ if [ "$(id -u)" == 0 ]; then
         #   above in /etc/sudoers.d/path. Thus PATH is irrelevant to how the above
         #   sudo command resolves the path of `${cmd[@]}`. The PATH will be relevant
         #   for resolving paths of any subprocesses spawned by `${cmd[@]}`.
+    fi
 
 # The container didn't start as the root user, so we will have to act as the
 # user we started as.