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update docker-stacks, torchviz, dockerhub-image description

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This commit is contained in:
Christoph Schranz
2021-01-05 12:39:30 +01:00
parent 49d0c6f49d
commit c250aea2fe
8 changed files with 183 additions and 225 deletions
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234
.build/Dockerfile
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@@ -2,7 +2,7 @@
# **Please do not change this file directly!** # **Please do not change this file directly!**
# To adapt this Dockerfile, adapt 'generate-Dockerfile.sh' or 'src/Dockerfile.usefulpackages'. # To adapt this Dockerfile, adapt 'generate-Dockerfile.sh' or 'src/Dockerfile.usefulpackages'.
# More information can be found in the documentation. # More information can be found in the README under configuration.
# Use NVIDIA CUDA as base image and run the same installation as in the other packages. # Use NVIDIA CUDA as base image and run the same installation as in the other packages.
@@ -22,7 +22,8 @@ RUN chmod 1777 /tmp && chmod 1777 /var/tmp
# Ubuntu 20.04 (focal) # Ubuntu 20.04 (focal)
# https://hub.docker.com/_/ubuntu/?tab=tags&name=focal # https://hub.docker.com/_/ubuntu/?tab=tags&name=focal
# OS/ARCH: linux/amd64 # OS/ARCH: linux/amd64
ARG ROOT_CONTAINER=ubuntu:focal-20200423@sha256:238e696992ba9913d24cfc3727034985abd136e08ee3067982401acdc30cbf3f ARG ROOT_CONTAINER=ubuntu:focal-20201106@sha256:4e4bc990609ed865e07afc8427c30ffdddca5153fd4e82c20d8f0783a291e241
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>" LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
ARG NB_USER="jovyan" ARG NB_USER="jovyan"
@@ -34,13 +35,33 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
USER root USER root
# ---- Miniforge installer ----
# Default values can be overridden at build time
# (ARGS are in lower case to distinguish them from ENV)
# Check https://github.com/conda-forge/miniforge/releases
# Conda version
ARG conda_version="4.9.2"
# Miniforge installer patch version
ARG miniforge_patch_number="0"
# Miniforge installer architecture
ARG miniforge_arch="x86_64"
# Python implementation to use
# can be either Miniforge3 to use Python or Miniforge-pypy3 to use PyPy
ARG miniforge_python="Miniforge3"
# Miniforge archive to install
ARG miniforge_version="${conda_version}-${miniforge_patch_number}"
# Miniforge installer
ARG miniforge_installer="${miniforge_python}-${miniforge_version}-Linux-${miniforge_arch}.sh"
# Miniforge checksum
ARG miniforge_checksum="6321775eb2c02d7f51d3a9004ce0be839099f126f4099c781531428536669560"
# Install all OS dependencies for notebook server that starts but lacks all # Install all OS dependencies for notebook server that starts but lacks all
# features (e.g., download as all possible file formats) # features (e.g., download as all possible file formats)
ENV DEBIAN_FRONTEND noninteractive ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update \ RUN apt-get update \
&& apt-get install -yq --no-install-recommends \ && apt-get install -yq --no-install-recommends \
wget \ wget \
bzip2 \
ca-certificates \ ca-certificates \
sudo \ sudo \
locales \ locales \
@@ -61,16 +82,21 @@ ENV CONDA_DIR=/opt/conda \
LANG=en_US.UTF-8 \ LANG=en_US.UTF-8 \
LANGUAGE=en_US.UTF-8 LANGUAGE=en_US.UTF-8
ENV PATH=$CONDA_DIR/bin:$PATH \ ENV PATH=$CONDA_DIR/bin:$PATH \
HOME=/home/$NB_USER HOME=/home/$NB_USER \
CONDA_VERSION="${conda_version}" \
MINIFORGE_VERSION="${miniforge_version}"
# Copy a script that we will use to correct permissions after running certain commands # Copy a script that we will use to correct permissions after running certain commands
COPY fix-permissions /usr/local/bin/fix-permissions COPY fix-permissions /usr/local/bin/fix-permissions
RUN chmod a+rx /usr/local/bin/fix-permissions RUN chmod a+rx /usr/local/bin/fix-permissions
# Enable prompt color in the skeleton .bashrc before creating the default NB_USER # Enable prompt color in the skeleton .bashrc before creating the default NB_USER
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc # hadolint ignore=SC2016
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
# Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
# Create NB_USER wtih name jovyan user with UID=1000 and in the 'users' group # Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
# and make sure these dirs are writable by 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 && \ RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \ sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
@@ -83,42 +109,34 @@ RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
fix-permissions $CONDA_DIR fix-permissions $CONDA_DIR
USER $NB_UID USER $NB_UID
WORKDIR $HOME
ARG PYTHON_VERSION=default ARG PYTHON_VERSION=default
# Setup work directory for backward-compatibility # Setup work directory for backward-compatibility
RUN mkdir /home/$NB_USER/work && \ RUN mkdir "/home/$NB_USER/work" && \
fix-permissions /home/$NB_USER fix-permissions "/home/$NB_USER"
# Install conda as jovyan and check the md5 sum provided on the download site
ENV MINICONDA_VERSION=4.8.2 \
MINICONDA_MD5=87e77f097f6ebb5127c77662dfc3165e \
CONDA_VERSION=4.8.2
# Install conda as jovyan and check the sha256 sum provided on the download site
WORKDIR /tmp WORKDIR /tmp
RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh && \
echo "${MINICONDA_MD5} *Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \ # Prerequisites installation: conda, pip, tini
/bin/bash Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \ RUN wget --quiet "https://github.com/conda-forge/miniforge/releases/download/${miniforge_version}/${miniforge_installer}" && \
rm Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh && \ echo "${miniforge_checksum} *${miniforge_installer}" | sha256sum --check && \
/bin/bash "${miniforge_installer}" -f -b -p $CONDA_DIR && \
rm "${miniforge_installer}" && \
# Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \ echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
conda config --system --prepend channels conda-forge && \
conda config --system --set auto_update_conda false && \ conda config --system --set auto_update_conda false && \
conda config --system --set show_channel_urls true && \ conda config --system --set show_channel_urls true && \
conda config --system --set channel_priority strict && \
if [ ! $PYTHON_VERSION = 'default' ]; then conda install --yes python=$PYTHON_VERSION; fi && \ if [ ! $PYTHON_VERSION = 'default' ]; then conda install --yes python=$PYTHON_VERSION; fi && \
conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \ conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \
conda install --quiet --yes conda && \ conda install --quiet --yes \
conda install --quiet --yes pip && \ "conda=${CONDA_VERSION}" \
'pip' \
'tini=0.18.0' && \
conda update --all --quiet --yes && \ conda update --all --quiet --yes && \
conda clean --all -f -y && \
rm -rf /home/$NB_USER/.cache/yarn && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
# Install Tini
RUN conda install --quiet --yes 'tini=0.18.0' && \
conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \ conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
conda clean --all -f -y && \ conda clean --all -f -y && \
rm -rf /home/$NB_USER/.cache/yarn && \
fix-permissions $CONDA_DIR && \ fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER fix-permissions /home/$NB_USER
@@ -129,9 +147,9 @@ RUN conda install --quiet --yes 'tini=0.18.0' && \
# Do all this in a single RUN command to avoid duplicating all of the # Do all this in a single RUN command to avoid duplicating all of the
# files across image layers when the permissions change # files across image layers when the permissions change
RUN conda install --quiet --yes \ RUN conda install --quiet --yes \
'notebook=6.0.3' \ 'notebook=6.1.6' \
'jupyterhub=1.1.0' \ 'jupyterhub=1.3.0' \
'jupyterlab=2.1.3' && \ 'jupyterlab=2.2.9' && \
conda clean --all -f -y && \ conda clean --all -f -y && \
npm cache clean --force && \ npm cache clean --force && \
jupyter notebook --generate-config && \ jupyter notebook --generate-config && \
@@ -148,10 +166,16 @@ CMD ["start-notebook.sh"]
# Copy local files as late as possible to avoid cache busting # Copy local files as late as possible to avoid cache busting
COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/ COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
# Currently need to have both jupyter_notebook_config and jupyter_server_config to support classic and lab
COPY jupyter_notebook_config.py /etc/jupyter/ COPY jupyter_notebook_config.py /etc/jupyter/
# Fix permissions on /etc/jupyter as root # Fix permissions on /etc/jupyter as root
USER root USER root
# Prepare upgrade to JupyterLab V3.0 #1205
RUN sed -re "s/c.NotebookApp/c.ServerApp/g" \
/etc/jupyter/jupyter_notebook_config.py > /etc/jupyter/jupyter_server_config.py
RUN fix-permissions /etc/jupyter/ RUN fix-permissions /etc/jupyter/
# Switch back to jovyan to avoid accidental container runs as root # Switch back to jovyan to avoid accidental container runs as root
@@ -173,29 +197,27 @@ USER root
# Install all OS dependencies for fully functional notebook server # Install all OS dependencies for fully functional notebook server
RUN apt-get update && apt-get install -yq --no-install-recommends \ RUN apt-get update && apt-get install -yq --no-install-recommends \
build-essential \ build-essential \
emacs-nox \
vim-tiny \ vim-tiny \
git \ git \
inkscape \ inkscape \
jed \
libsm6 \ libsm6 \
libxext-dev \ libxext-dev \
libxrender1 \ libxrender1 \
lmodern \ lmodern \
netcat \ netcat \
python-dev \
# ---- nbconvert dependencies ---- # ---- nbconvert dependencies ----
texlive-xetex \ texlive-xetex \
texlive-fonts-recommended \ texlive-fonts-recommended \
texlive-plain-generic \ texlive-plain-generic \
# Optional dependency
texlive-fonts-extra \
# ---- # ----
tzdata \ tzdata \
unzip \ unzip \
nano \ nano-tiny \
&& apt-get clean && rm -rf /var/lib/apt/lists/* && apt-get clean && rm -rf /var/lib/apt/lists/*
# Create alternative for nano -> nano-tiny
RUN update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 10
# Switch back to jovyan to avoid accidental container runs as root # Switch back to jovyan to avoid accidental container runs as root
USER $NB_UID USER $NB_UID
@@ -210,10 +232,10 @@ LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
USER root USER root
# ffmpeg for matplotlib anim & dvipng for latex labels # ffmpeg for matplotlib anim & dvipng+cm-super for latex labels
RUN apt-get update && \ RUN apt-get update && \
apt-get install -y --no-install-recommends ffmpeg dvipng && \ apt-get install -y --no-install-recommends ffmpeg dvipng cm-super && \
rm -rf /var/lib/apt/lists/* apt-get clean && rm -rf /var/lib/apt/lists/*
USER $NB_UID USER $NB_UID
@@ -221,31 +243,29 @@ USER $NB_UID
RUN conda install --quiet --yes \ RUN conda install --quiet --yes \
'beautifulsoup4=4.9.*' \ 'beautifulsoup4=4.9.*' \
'conda-forge::blas=*=openblas' \ 'conda-forge::blas=*=openblas' \
'bokeh=2.0.*' \ 'bokeh=2.2.*' \
'bottleneck=1.3.*' \ 'bottleneck=1.3.*' \
'cloudpickle=1.4.*' \ 'cloudpickle=1.6.*' \
'cython=0.29.*' \ 'cython=0.29.*' \
'dask=2.15.*' \ 'dask=2020.12.*' \
'dill=0.3.*' \ 'dill=0.3.*' \
'h5py=2.10.*' \ 'h5py=3.1.*' \
'hdf5=1.10.*' \ 'ipywidgets=7.6.*' \
'ipywidgets=7.5.*' \
'ipympl=0.5.*'\ 'ipympl=0.5.*'\
'matplotlib-base=3.2.*' \ 'matplotlib-base=3.3.*' \
# numba update to 0.49 fails resolving deps. 'numba=0.52.*' \
'numba=0.48.*' \
'numexpr=2.7.*' \ 'numexpr=2.7.*' \
'pandas=1.0.*' \ 'pandas=1.1.*' \
'patsy=0.5.*' \ 'patsy=0.5.*' \
'protobuf=3.11.*' \ 'protobuf=3.14.*' \
'pytables=3.6.*' \ 'pytables=3.6.*' \
'scikit-image=0.16.*' \ 'scikit-image=0.18.*' \
'scikit-learn=0.22.*' \ 'scikit-learn=0.24.*' \
'scipy=1.4.*' \ 'scipy=1.5.*' \
'seaborn=0.10.*' \ 'seaborn=0.11.*' \
'sqlalchemy=1.3.*' \ 'sqlalchemy=1.3.*' \
'statsmodels=0.11.*' \ 'statsmodels=0.12.*' \
'sympy=1.5.*' \ 'sympy=1.7.*' \
'vincent=0.4.*' \ 'vincent=0.4.*' \
'widgetsnbextension=3.5.*'\ 'widgetsnbextension=3.5.*'\
'xlrd=1.2.*' \ 'xlrd=1.2.*' \
@@ -283,102 +303,6 @@ RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
USER $NB_UID USER $NB_UID
WORKDIR $HOME
############################################################################
################ Dependency: jupyter/datascience-notebook ##################
############################################################################
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
# Set when building on Travis so that certain long-running build steps can
# be skipped to shorten build time.
ARG TEST_ONLY_BUILD
# Fix DL4006
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
USER root
# R pre-requisites
RUN apt-get update && \
apt-get install -y --no-install-recommends \
fonts-dejavu \
gfortran \
gcc && \
rm -rf /var/lib/apt/lists/*
# Julia dependencies
# install Julia packages in /opt/julia instead of $HOME
ENV JULIA_DEPOT_PATH=/opt/julia
ENV JULIA_PKGDIR=/opt/julia
ENV JULIA_VERSION=1.4.1
WORKDIR /tmp
# hadolint ignore=SC2046
RUN mkdir "/opt/julia-${JULIA_VERSION}" && \
wget -q https://julialang-s3.julialang.org/bin/linux/x64/$(echo "${JULIA_VERSION}" | cut -d. -f 1,2)"/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" && \
echo "fd6d8cadaed678174c3caefb92207a3b0e8da9f926af6703fb4d1e4e4f50610a *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \
tar xzf "julia-${JULIA_VERSION}-linux-x86_64.tar.gz" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
rm "/tmp/julia-${JULIA_VERSION}-linux-x86_64.tar.gz"
RUN ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia
# Show Julia where conda libraries are \
RUN mkdir /etc/julia && \
echo "push!(Libdl.DL_LOAD_PATH, \"$CONDA_DIR/lib\")" >> /etc/julia/juliarc.jl && \
# Create JULIA_PKGDIR \
mkdir "${JULIA_PKGDIR}" && \
chown "${NB_USER}" "${JULIA_PKGDIR}" && \
fix-permissions "${JULIA_PKGDIR}"
USER $NB_UID
# R packages including IRKernel which gets installed globally.
RUN conda install --quiet --yes \
'r-base=3.6.3' \
'r-caret=6.0*' \
'r-crayon=1.3*' \
'r-devtools=2.3*' \
'r-forecast=8.12*' \
'r-hexbin=1.28*' \
'r-htmltools=0.4*' \
'r-htmlwidgets=1.5*' \
'r-irkernel=1.1*' \
'r-nycflights13=1.0*' \
'r-plyr=1.8*' \
'r-randomforest=4.6*' \
'r-rcurl=1.98*' \
'r-reshape2=1.4*' \
'r-rmarkdown=2.1*' \
'r-rsqlite=2.2*' \
'r-shiny=1.4*' \
'r-tidyverse=1.3*' \
'rpy2=3.1*' \
&& \
conda clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
# Add Julia packages. Only add HDF5 if this is not a test-only build since
# it takes roughly half the entire build time of all of the images on Travis
# to add this one package and often causes Travis to timeout.
#
# Install IJulia as jovyan and then move the kernelspec out
# to the system share location. Avoids problems with runtime UID change not
# taking effect properly on the .local folder in the jovyan home dir.
RUN julia -e 'import Pkg; Pkg.update()' && \
(test $TEST_ONLY_BUILD || julia -e 'import Pkg; Pkg.add("HDF5")') && \
julia -e "using Pkg; pkg\"add IJulia\"; pkg\"precompile\"" && \
# move kernelspec out of home \
mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/" && \
chmod -R go+rx "${CONDA_DIR}/share/jupyter" && \
rm -rf "${HOME}/.local" && \
fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"
WORKDIR $HOME WORKDIR $HOME
############################################################################ ############################################################################
@@ -403,6 +327,8 @@ RUN conda install --quiet --yes \
torchvision \ torchvision \
cudatoolkit=10.1 -c pytorch cudatoolkit=10.1 -c pytorch
# pip install torch_nightly -f https://download.pytorch.org/whl/nightly/cu90/torch_nightly.html && \ # pip install torch_nightly -f https://download.pytorch.org/whl/nightly/cu90/torch_nightly.html && \
RUN pip install --no-cache-dir torchviz
# Clean installation # Clean installation
RUN conda clean --all -f -y && \ RUN conda clean --all -f -y && \

2
.build/docker-stacks

Submodule .build/docker-stacks updated: d676cdf9b4...703d8b2dcb

2
.build/fix-permissions
View File

@@ -25,7 +25,7 @@ for d in "$@"; do
\) \ \) \
-exec chgrp $NB_GID {} \; \ -exec chgrp $NB_GID {} \; \
-exec chmod g+rwX {} \; -exec chmod g+rwX {} \;
# setuid,setgid *on directories only* # setuid, setgid *on directories only*
find "$d" \ find "$d" \
\( \ \( \
-type d \ -type d \

2
.build/jupyter_notebook_config.py
View File

@@ -7,7 +7,7 @@ import os
import errno import errno
import stat import stat
c = get_config() c = get_config() # noqa: F821
c.NotebookApp.ip = '0.0.0.0' c.NotebookApp.ip = '0.0.0.0'
c.NotebookApp.port = 8888 c.NotebookApp.port = 8888
c.NotebookApp.open_browser = False c.NotebookApp.open_browser = False

30
.build/start.sh
View File

@@ -47,19 +47,6 @@ if [ $(id -u) == 0 ] ; then
usermod -d /home/$NB_USER -l $NB_USER jovyan usermod -d /home/$NB_USER -l $NB_USER jovyan
fi fi
# Handle case where provisioned storage does not have the correct permissions by default
# Ex: default NFS/EFS (no auto-uid/gid)
if [[ "$CHOWN_HOME" == "1" || "$CHOWN_HOME" == 'yes' ]]; then
echo "Changing ownership of /home/$NB_USER to $NB_UID:$NB_GID with options '${CHOWN_HOME_OPTS}'"
chown $CHOWN_HOME_OPTS $NB_UID:$NB_GID /home/$NB_USER
fi
if [ ! -z "$CHOWN_EXTRA" ]; then
for extra_dir in $(echo $CHOWN_EXTRA | tr ',' ' '); do
echo "Changing ownership of ${extra_dir} to $NB_UID:$NB_GID with options '${CHOWN_EXTRA_OPTS}'"
chown $CHOWN_EXTRA_OPTS $NB_UID:$NB_GID $extra_dir
done
fi
# handle home and working directory if the username changed # handle home and working directory if the username changed
if [[ "$NB_USER" != "jovyan" ]]; then if [[ "$NB_USER" != "jovyan" ]]; then
# changing username, make sure homedir exists # changing username, make sure homedir exists
@@ -76,11 +63,24 @@ if [ $(id -u) == 0 ] ; then
fi fi
fi fi
# Handle case where provisioned storage does not have the correct permissions by default
# Ex: default NFS/EFS (no auto-uid/gid)
if [[ "$CHOWN_HOME" == "1" || "$CHOWN_HOME" == 'yes' ]]; then
echo "Changing ownership of /home/$NB_USER to $NB_UID:$NB_GID with options '${CHOWN_HOME_OPTS}'"
chown $CHOWN_HOME_OPTS $NB_UID:$NB_GID /home/$NB_USER
fi
if [ ! -z "$CHOWN_EXTRA" ]; then
for extra_dir in $(echo $CHOWN_EXTRA | tr ',' ' '); do
echo "Changing ownership of ${extra_dir} to $NB_UID:$NB_GID with options '${CHOWN_EXTRA_OPTS}'"
chown $CHOWN_EXTRA_OPTS $NB_UID:$NB_GID $extra_dir
done
fi
# Change UID:GID of NB_USER to NB_UID:NB_GID if it does not match # Change UID:GID of NB_USER to NB_UID:NB_GID if it does not match
if [ "$NB_UID" != $(id -u $NB_USER) ] || [ "$NB_GID" != $(id -g $NB_USER) ]; then if [ "$NB_UID" != $(id -u $NB_USER) ] || [ "$NB_GID" != $(id -g $NB_USER) ]; then
echo "Set user $NB_USER UID:GID to: $NB_UID:$NB_GID" echo "Set user $NB_USER UID:GID to: $NB_UID:$NB_GID"
if [ "$NB_GID" != $(id -g $NB_USER) ]; then if [ "$NB_GID" != $(id -g $NB_USER) ]; then
groupadd -g $NB_GID -o ${NB_GROUP:-${NB_USER}} groupadd -f -g $NB_GID -o ${NB_GROUP:-${NB_USER}}
fi fi
userdel $NB_USER userdel $NB_USER
useradd --home /home/$NB_USER -u $NB_UID -g $NB_GID -G 100 -l $NB_USER useradd --home /home/$NB_USER -u $NB_UID -g $NB_GID -G 100 -l $NB_USER
@@ -101,7 +101,7 @@ if [ $(id -u) == 0 ] ; then
echo "Executing the command: ${cmd[@]}" echo "Executing the command: ${cmd[@]}"
exec sudo -E -H -u $NB_USER PATH=$PATH XDG_CACHE_HOME=/home/$NB_USER/.cache PYTHONPATH=${PYTHONPATH:-} "${cmd[@]}" exec sudo -E -H -u $NB_USER PATH=$PATH XDG_CACHE_HOME=/home/$NB_USER/.cache PYTHONPATH=${PYTHONPATH:-} "${cmd[@]}"
else else
if [[ "$NB_UID" == "$(id -u jovyan)" && "$NB_GID" == "$(id -g jovyan)" ]]; then if [[ "$NB_UID" == "$(id -u jovyan 2>/dev/null)" && "$NB_GID" == "$(id -g jovyan 2>/dev/null)" ]]; then
# User is not attempting to override user/group via environment # User is not attempting to override user/group via environment
# variables, but they could still have overridden the uid/gid that # variables, but they could still have overridden the uid/gid that
# container runs as. Check that the user has an entry in the passwd # container runs as. Check that the user has an entry in the passwd

100
README.md
View File

@@ -21,62 +21,81 @@ The image of this repository is available on [Dockerhub](https://hub.docker.com/
## Requirements ## Requirements
1. A NVIDIA GPU 1. A computer with a NVIDIA GPU
2. Install [Docker](https://www.docker.com/community-edition#/download) version **1.10.0+** 2. Install [Docker](https://www.docker.com/community-edition#/download) version **1.10.0+**
and [Docker Compose](https://docs.docker.com/compose/install/) version **1.6.0+**. and [Docker Compose](https://docs.docker.com/compose/install/) version **1.6.0+**.
3. Get access to your GPU via CUDA drivers within Docker containers. Therfore, check out this 3. Get access to your GPU via CUDA drivers within Docker containers.
[medium article](https://medium.com/@christoph.schranz/set-up-your-own-gpu-based-jupyterlab-e0d45fcacf43).
The CUDA toolkit is not required on the host system, as it will be deployed
in [NVIDIA-docker](https://github.com/NVIDIA/nvidia-docker).
You can be sure that you can access your GPU within Docker, You can be sure that you can access your GPU within Docker,
if the command `docker run --gpus all nvidia/cuda:10.1-base-ubuntu18.04 nvidia-smi` if the command `docker run --gpus all nvidia/cuda:10.1-cudnn7-runtime-ubuntu18.04 nvidia-smi`
returns a result similar to this one: returns a result similar to this one:
```bash ```bash
Mon Jun 22 09:06:28 2020 Tue Jan 5 09:38:21 2021
+-----------------------------------------------------------------------------+ +-----------------------------------------------------------------------------+
| NVIDIA-SMI 440.82 Driver Version: 440.82 CUDA Version: 10.1 | | NVIDIA-SMI 450.80.02 Driver Version: 450.80.02 CUDA Version: 10.1 |
|-------------------------------+----------------------+----------------------+ |-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================| |===============================+======================+======================|
| 0 GeForce RTX 207... Off | 00000000:01:00.0 On | N/A | | 0 GeForce RTX 207... Off | 00000000:01:00.0 On | N/A |
| 0% 46C P8 9W / 215W | 424MiB / 7974MiB | 6% Default | | 0% 40C P8 7W / 215W | 360MiB / 7974MiB | 1% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+ +-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+ +-----------------------------------------------------------------------------+
| Processes: GPU Memory | | Processes: |
| GPU PID Type Process name Usage | | GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================| |=============================================================================|
+-----------------------------------------------------------------------------+ +-----------------------------------------------------------------------------+
``` ```
4. Clone the Repository or pull the image from If you don't get an output similar than this one, follow the installation steps in this
[Dockerhub](https://hub.docker.com/repository/docker/cschranz/gpu-jupyter): [medium article](https://medium.com/@christoph.schranz/set-up-your-own-gpu-based-jupyterlab-e0d45fcacf43).
The CUDA toolkit is not required on the host system, as it will be
installed within the Docker containers using [NVIDIA-docker](https://github.com/NVIDIA/nvidia-docker).
It is also important to keep your installed CUDA version in mind, when you pull images.
**You can't run images based on `nvidia/cuda:11.1` if you have only CUDA version 10.1 installed.**
Check your host's CUDA-version with `nvcc --version` and update to at least
the same version you want to pull.
4. Pull and run the image. This can last some hours, as a whole data-science
environment will be downloaded:
```bash ```bash
git clone https://github.com/iot-salzburg/gpu-jupyter.git cd your-working-directory
cd gpu-jupyter docker run --gpus all -d -it -p 8848:8888 -v data:/home/jovyan/work -e GRANT_SUDO=yes -e JUPYTER_ENABLE_LAB=yes --user root cschranz/gpu-jupyter:v1.1_cuda-10.1_ubuntu-18.04_python-only
``` ```
This starts a new instance of the GPU-Jupyter service on at [http://localhost:8848](http://localhost:8848) (port `8484`).
The default password is `asdf` which should be changed as described [below](#set-password).
Furthermore, data within the host's `data` directory is shared with the container.
## Quickstart Within the Jupyterlab instance, you can check if you can access your GPU by opening a new terminal window and running
`nvidia-smi`. In terminal windows, you can also install new packages for your own projects.
Some example code can be found in the repository under `extra/Getting_Started`.
If you want to learn more about Jupyterlab, check out this [tutorial](https://www.youtube.com/watch?v=7wfPqAyYADY).
First of all, it is necessary to generate the `Dockerfile` that is based on
## Build a modified version
First, it is necessary to generate the `Dockerfile` in `.build`, that is based on
the NIVIDA base image and the [docker-stacks](https://github.com/jupyter/docker-stacks). the NIVIDA base image and the [docker-stacks](https://github.com/jupyter/docker-stacks).
As soon as you have access to your GPU within Docker containers As soon as you have access to your GPU within Docker containers
(make sure the command `docker run --gpus all nvidia/cuda:10.1-base-ubuntu18.04 nvidia-smi` (make sure the command `docker run --gpus all nvidia/cuda:10.1-cudnn7-runtime-ubuntu18.04 nvidia-smi`
shows your GPU statistics), you can generate the Dockerfile, build and run it. shows your GPU statistics), you can generate the Dockerfile, build and run it.
The following commands will start *GPU-Jupyter* on [localhost:8848](http://localhost:8848) The following commands will start *GPU-Jupyter* on [localhost:8848](http://localhost:8848)
with the default password `asdf`. with the default password `asdf`.
```bash ```bash
git clone https://github.com/iot-salzburg/gpu-jupyter.git
cd gpu-jupyter
# generate a Dockerfile with python and without Julia and R # generate a Dockerfile with python and without Julia and R
./generate-Dockerfile.sh --no-datascience-notebook ./generate-Dockerfile.sh --no-datascience-notebook
docker build -t gpu-jupyter .build/ # will take a while docker build -t gpu-jupyter .build/ # will take a while
docker run -d -p [port]:8888 gpu-jupyter # starts gpu-jupyter WITHOUT GPU support docker run --gpus all -d -it -p 8848:8888 -v $pwd/data:/home/jovyan/work -e GRANT_SUDO=yes -e JUPYTER_ENABLE_LAB=yes --user root --restart always --name gpu-jupyter_1 gpu-jupyter
``` ```
To run the container WITH GPU support, a local data volume and some other configurations, run: This starts a container WITH GPU support, a shared local data volume `data`
```bash and some other configurations like root permissions which are necessary to install packages within the container.
docker run --gpus all -d -it -p 8848:8888 -v $(pwd)/data:/home/jovyan/work -e GRANT_SUDO=yes -e JUPYTER_ENABLE_LAB=yes --user root --restart always --name gpu-jupyter_1 gpu-jupyter For more configurations, scroll down to [Configuration of the Dockerfile-Generation](#configuration-of-the-dockerfile-generation).
```
### Start via Docker Compose ### Start via Docker Compose
@@ -92,14 +111,16 @@ underlying `docker-compose.yml`:
With these commands we can see if everything worked well: With these commands we can see if everything worked well:
```bash ```bash
bash show-local.sh # a env-var safe wrapper for 'docker-compose logs -f'
docker ps docker ps
docker logs [service-name] docker logs [service-name] # or
bash show-local.sh # a env-var safe wrapper for 'docker-compose logs -f'
``` ```
In order to stop the local deployment, run: In order to stop the local deployment, run:
```bash ```bash
docker ps
docker rm -f [service-name] # or
./stop-local.sh ./stop-local.sh
``` ```
@@ -134,13 +155,16 @@ the essential `gpulibs` are installed, but not the packages within `src/Dockerfi
### Custom Installations ### Custom Installations
**As `.build/Dockerfile` is overwritten, it is suggested to append custom installations either Custom packages can be installed within a container, or by modifying the file
`src/Dockerfile.usefulpackages`.
**As `.build/Dockerfile` is overwritten each time a Dockerfile is generated,
it is suggested to append custom installations either
within `src/Dockerfile.usefulpackages` or in `generate-Dockerfile.sh`.** within `src/Dockerfile.usefulpackages` or in `generate-Dockerfile.sh`.**
If you think some package is missing in the default stack, please let us know! If an essential package is missing in the default stack, please let us know!
### Set the Password ### Set Password
Please set a new password using `src/jupyter_notebook_config.json`. Please set a new password using `src/jupyter_notebook_config.json`.
Therefore, hash your password in the form (password)(salt) using a sha1 hash generator, e.g., the sha1 generator of [sha1-online.com](http://www.sha1-online.com/). Therefore, hash your password in the form (password)(salt) using a sha1 hash generator, e.g., the sha1 generator of [sha1-online.com](http://www.sha1-online.com/).
@@ -162,24 +186,30 @@ Then update the config file as shown below and restart the service.
#### Update CUDA to another version #### Update CUDA to another version
Please check version compatibilities for [CUDA and Pytorch](https://pytorch.org/get-started/locally/) The host's CUDA-version must be equal or higher than that of the
respectively [CUDA and Tensorflow](https://www.tensorflow.org/install/gpu) previously. container itself (in `Dockerfile.header`).
To update CUDA to another version, change in `Dockerfile.header` Check the host's version with `nvcc --version` and the version compatibilities
for CUDA-dependent packages as [Pytorch](https://pytorch.org/get-started/locally/)
respectively [Tensorflow](https://www.tensorflow.org/install/gpu) previously.
Then modify, if supported, the CUDA-version in `Dockerfile.header` to, e.g.:
the line: the line:
FROM nvidia/cuda:10.1-base-ubuntu18.04 FROM nvidia/cuda:11.1-base-ubuntu20.04
and in the `Dockerfile.pytorch` the line: and in the `Dockerfile.pytorch` the line:
cudatoolkit=10.1 cudatoolkit=11.1
Then re-generate and re-run the image, as closer described above: Then re-generate, re-build and run the updated image, as closer described above:
Note that a change in the first line of the Dockerfile will re-build the whole image.
```bash ```bash
./generate-Dockerfile.sh ./generate-Dockerfile.sh
./start-local.sh -p 8848 docker build -t gpu-jupyter .build/ # will take a while
docker run --gpus all -d -it -p 8848:8888 -v $pwd/data:/home/jovyan/work -e GRANT_SUDO=yes -e JUPYTER_ENABLE_LAB=yes --user root --restart always --name gpu-jupyter_1 gpu-jupyter
``` ```
#### Update Docker-Stack #### Update Docker-Stack
The [docker-stacks](https://github.com/jupyter/docker-stacks) are used as a The [docker-stacks](https://github.com/jupyter/docker-stacks) are used as a

2
generate-Dockerfile.sh
View File

@@ -5,7 +5,7 @@ cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
export DOCKERFILE=".build/Dockerfile" export DOCKERFILE=".build/Dockerfile"
export STACKS_DIR=".build/docker-stacks" export STACKS_DIR=".build/docker-stacks"
# please test the build of the commit in https://github.com/jupyter/docker-stacks/commits/master in advance # please test the build of the commit in https://github.com/jupyter/docker-stacks/commits/master in advance
export HEAD_COMMIT="04f7f60d34a674a2964d96a6cb97c57a7870a828" export HEAD_COMMIT="703d8b2dcb886be2fe5aa4660a48fbcef647e7aa"
while [[ "$#" -gt 0 ]]; do case $1 in while [[ "$#" -gt 0 ]]; do case $1 in
-c|--commit) HEAD_COMMIT="$2"; shift;; -c|--commit) HEAD_COMMIT="$2"; shift;;

2
src/Dockerfile.gpulibs
View File

@@ -16,6 +16,8 @@ RUN conda install --quiet --yes \
torchvision \ torchvision \
cudatoolkit=10.1 -c pytorch cudatoolkit=10.1 -c pytorch
# pip install torch_nightly -f https://download.pytorch.org/whl/nightly/cu90/torch_nightly.html && \ # pip install torch_nightly -f https://download.pytorch.org/whl/nightly/cu90/torch_nightly.html && \
RUN pip install --no-cache-dir torchviz
# Clean installation # Clean installation
RUN conda clean --all -f -y && \ RUN conda clean --all -f -y && \