Initial commit, local mode runs

2019-11-12 22:22:20 +01:00
parent 17f3f612dd
commit 87f2e77449
14 changed files with 832 additions and 0 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -102,3 +102,8 @@ venv.bak/

 # mypy
 .mypy_cache/
+
+
+# individual stuff
+/data
+*.save*
--- a/add-to-swarm.sh
+++ b/add-to-swarm.sh
@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
+
+if [[ -n "$1" ]]; then
+    result=$(docker network ls)
+    if [[ "$result" == *" $1 "* ]]; then
+        echo "Adding gpu-jupyter to the swarm in the network $1."
+        export JUPYTER_NETWORK=$1
+        # echo $JUPYTER_NETWORK
+        docker-compose -f docker-compose-swarm.yml build
+        docker-compose -f docker-compose-swarm.yml push
+#        docker stack deploy --compose-file docker-compose-swarm.yml gpu
+    else
+        echo "Could not find network $1. Please provide a valid docker network."
+    fi
+else
+    echo "Usage: $0 network"
+    echo "Please set the network"
+fi
+
--- a/docker-compose-swarm.yml
+++ b/docker-compose-swarm.yml
@@ -0,0 +1,36 @@
+version: "3.4"
+services:
+  gpu-jupyter:
+    image: 127.0.0.1:5001/gpu-jupyter
+    build: ./src/
+    ports:
+      - 8848:8888
+    volumes:
+      - ./data:/home/jovyan/work
+    environment:
+      GRANT_SUDO: "yes"
+      JUPYTER_ENABLE_LAB: "yes"
+    # enable sudo permissions
+    user:
+      "root"
+    networks:
+      - default
+      - $JUPYTER_NETWORK
+    deploy:
+      placement:
+        constraints: [node.hostname == data-science]
+      resources:
+        limits:
+          cpus: "4"
+          memory: 8G
+      replicas: 1
+      update_config:
+        parallelism: 2
+        delay: 10s
+      restart_policy:
+        condition: on-failure
+
+networks:
+  $JUPYTER_NETWORK:
+    external:
+      name: $JUPYTER_NETWORK
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -0,0 +1,28 @@
+version: "3.4"
+services:
+  gpu-jupyter:
+    image: 127.0.0.1:5001/gpu-jupyter
+    build: ./src/
+    ports:
+      - 8848:8888
+    volumes:
+      - ./data:/home/jovyan/work
+    environment:
+      GRANT_SUDO: "yes"
+      JUPYTER_ENABLE_LAB: "yes"
+    # enable sudo permissions
+    user:
+      "root"
+    deploy:
+      placement:
+        constraints: [node.hostname == data-science]
+      resources:
+        limits:
+          cpus: "4"
+          memory: 8G
+      replicas: 1
+      update_config:
+        parallelism: 2
+        delay: 10s
+      restart_policy:
+        condition: on-failure
--- a/remove-from-swarm.sh
+++ b/remove-from-swarm.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
+
+docker stack rm gpu_gpu-jupyter
--- a/src/Dockerfile
+++ b/src/Dockerfile
@@ -0,0 +1,424 @@
+FROM nvidia/cuda:10.1-base-ubuntu18.04
+LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
+
+############################################################################
+#################### Dependency: jupyter/base-image ########################
+############################################################################
+
+ARG NB_USER="jovyan"
+ARG NB_UID="1000"
+ARG NB_GID="100"
+
+USER root
+
+# Install all OS dependencies for notebook server that starts but lacks all
+# features (e.g., download as all possible file formats)
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get update && apt-get -yq dist-upgrade \
+ && apt-get install -yq --no-install-recommends \
+    wget \
+    bzip2 \
+    ca-certificates \
+    sudo \
+    locales \
+    fonts-liberation \
+ && rm -rf /var/lib/apt/lists/*
+
+RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
+    locale-gen
+
+# Configure environment
+ENV CONDA_DIR=/opt/conda \
+    SHELL=/bin/bash \
+    NB_USER=$NB_USER \
+    NB_UID=$NB_UID \
+    NB_GID=$NB_GID \
+    LC_ALL=en_US.UTF-8 \
+    LANG=en_US.UTF-8 \
+    LANGUAGE=en_US.UTF-8
+ENV PATH=$CONDA_DIR/bin:$PATH \
+    HOME=/home/$NB_USER
+
+# Add a script that we will use to correct permissions after running certain commands
+ADD fix-permissions /usr/local/bin/fix-permissions
+
+# 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
+
+# Create NB_USER wtih name jovyan user with UID=1000 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 && \
+    sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
+    useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
+    mkdir -p $CONDA_DIR && \
+    chown $NB_USER:$NB_GID $CONDA_DIR && \
+    chmod g+w /etc/passwd && \
+    fix-permissions $HOME && \
+    fix-permissions "$(dirname $CONDA_DIR)"
+
+USER $NB_UID
+WORKDIR $HOME
+
+# Setup work directory for backward-compatibility
+RUN mkdir /home/$NB_USER/work && \
+    fix-permissions /home/$NB_USER
+
+# Install conda as jovyan and check the md5 sum provided on the download site
+ENV MINICONDA_VERSION=4.6.14 \
+    CONDA_VERSION=4.7.10
+
+RUN cd /tmp && \
+    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
+    echo "718259965f234088d785cad1fbd7de03 *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
+    /bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
+    rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
+    echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
+    $CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \
+    $CONDA_DIR/bin/conda config --system --set auto_update_conda false && \
+    $CONDA_DIR/bin/conda config --system --set show_channel_urls true && \
+    $CONDA_DIR/bin/conda install --quiet --yes conda && \
+    $CONDA_DIR/bin/conda update --all --quiet --yes && \
+    conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \
+    conda clean --all -f -y && \
+    rm -rf /home/$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 clean --all -f -y && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+# Install Jupyter Notebook, Lab, and Hub
+# Generate a notebook 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
+RUN conda install --quiet --yes \
+    'notebook=6.0.0' \
+    'jupyterhub=1.0.0' \
+    'jupyterlab=1.0.4' && \
+    conda clean --all -f -y && \
+    npm cache clean --force && \
+    jupyter notebook --generate-config && \
+    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
+    rm -rf /home/$NB_USER/.cache/yarn && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+EXPOSE 8888
+
+# Configure container startup
+ENTRYPOINT ["tini", "-g", "--"]
+CMD ["start-notebook.sh"]
+
+# Add local files as late as possible to avoid cache busting
+COPY start.sh /usr/local/bin/
+COPY start-notebook.sh /usr/local/bin/
+COPY start-singleuser.sh /usr/local/bin/
+COPY jupyter_notebook_config.py /etc/jupyter/
+
+# Fix permissions on /etc/jupyter as root
+USER root
+RUN fix-permissions /etc/jupyter/
+
+############################################################################
+################# Dependency: jupyter/minimal-notebook #####################
+############################################################################
+
+# Install all OS dependencies for fully functional notebook server
+RUN apt-get update && apt-get install -yq --no-install-recommends \
+    build-essential \
+    emacs \
+    git \
+    inkscape \
+    jed \
+    libsm6 \
+    libxext-dev \
+    libxrender1 \
+    lmodern \
+    netcat \
+    pandoc \
+    python-dev \
+    texlive-fonts-extra \
+    texlive-fonts-recommended \
+    texlive-generic-recommended \
+    texlive-latex-base \
+    texlive-latex-extra \
+    texlive-xetex \
+    tzdata \
+    unzip \
+    nano \
+    && rm -rf /var/lib/apt/lists/*
+
+
+############################################################################
+################# Dependency: jupyter/scipy-notebook #######################
+############################################################################
+
+# ffmpeg for matplotlib anim
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ffmpeg && \
+    rm -rf /var/lib/apt/lists/*
+
+USER $NB_UID
+
+# Install Python 3 packages
+RUN conda install --quiet --yes \
+    'conda-forge::blas=*=openblas' \
+    'ipywidgets=7.5*' \
+    'pandas=0.24*' \
+    'numexpr=2.6*' \
+    'matplotlib-base=3.1.*' \
+    'scipy=1.2*' \
+    'seaborn=0.9*' \
+    'scikit-learn=0.20*' \
+    'scikit-image=0.14*' \
+    'sympy=1.3*' \
+    'cython=0.29*' \
+    'patsy=0.5*' \
+    'statsmodels=0.9*' \
+    'cloudpickle=0.8*' \
+    'dill=0.2*' \
+    'dask=1.1.*' \
+    'numba=0.42*' \
+    'bokeh=1.0*' \
+    'sqlalchemy=1.3*' \
+    'hdf5=1.10*' \
+    'h5py=2.9*' \
+    'vincent=0.4.*' \
+    'beautifulsoup4=4.7.*' \
+    'protobuf=3.7.*' \
+    'xlrd'  && \
+    conda clean --all -f -y && \
+    # Activate ipywidgets extension in the environment that runs the notebook server
+    jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
+    # Also activate ipywidgets extension for JupyterLab
+    # Check this URL for most recent compatibilities
+    # https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager@^1.0.1 --no-build && \
+    jupyter labextension install jupyterlab_bokeh@1.0.0 --no-build && \
+    jupyter lab build --dev-build=False && \
+    npm cache clean --force && \
+    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
+    rm -rf /home/$NB_USER/.cache/yarn && \
+    rm -rf /home/$NB_USER/.node-gyp && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+# Install facets which does not have a pip or conda package at the moment
+RUN cd /tmp && \
+    git clone https://github.com/PAIR-code/facets.git && \
+    cd facets && \
+    jupyter nbextension install facets-dist/ --sys-prefix && \
+    cd && \
+    rm -rf /tmp/facets && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+# Import matplotlib the first time to build the font cache.
+ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
+RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
+    fix-permissions /home/$NB_USER
+
+
+############################################################################
+################ Dependency: jupyter/datascience-notebook ##################
+############################################################################
+
+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 $HOME
+ENV JULIA_DEPOT_PATH=/opt/julia
+ENV JULIA_PKGDIR=/opt/julia
+ENV JULIA_VERSION=1.1.0
+
+RUN mkdir /opt/julia-${JULIA_VERSION} && \
+    cd /tmp && \
+    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 "80cfd013e526b5145ec3254920afd89bb459f1db7a2a3f21849125af20c05471 *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 \
+    'rpy2=2.9*' \
+    'r-base=3.5.1' \
+    'r-irkernel=0.8*' \
+    'r-plyr=1.8*' \
+    'r-devtools=1.13*' \
+    'r-tidyverse=1.2*' \
+    'r-shiny=1.2*' \
+    'r-rmarkdown=1.11*' \
+    'r-forecast=8.2*' \
+    'r-rsqlite=2.1*' \
+    'r-reshape2=1.4*' \
+    'r-nycflights13=1.0*' \
+    'r-caret=6.0*' \
+    'r-rcurl=1.95*' \
+    'r-crayon=1.3*' \
+    'r-randomforest=4.6*' \
+    'r-htmltools=0.3*' \
+    'r-sparklyr=0.9*' \
+    'r-htmlwidgets=1.2*' \
+    'r-hexbin=1.27*' && \
+    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 Gadfly RDatasets IJulia InstantiateFromURL\"; 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
+
+
+############################################################################
+################ Dependency: jupyter/scipy-notebook ##################
+############################################################################
+
+USER root
+
+# ffmpeg for matplotlib anim
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ffmpeg && \
+    rm -rf /var/lib/apt/lists/*
+
+USER $NB_UID
+
+# Install Python 3 packages
+RUN conda install --quiet --yes \
+    'conda-forge::blas=*=openblas' \
+    'ipywidgets=7.5*' \
+    'pandas=0.24*' \
+    'numexpr=2.6*' \
+    'matplotlib-base=3.1.*' \
+    'scipy=1.2*' \
+    'seaborn=0.9*' \
+    'scikit-learn=0.20*' \
+    'scikit-image=0.14*' \
+    'sympy=1.3*' \
+    'cython=0.29*' \
+    'patsy=0.5*' \
+    'statsmodels=0.9*' \
+    'cloudpickle=0.8*' \
+    'dill=0.2*' \
+    'dask=1.1.*' \
+    'numba=0.42*' \
+    'bokeh=1.0*' \
+    'sqlalchemy=1.3*' \
+    'hdf5=1.10*' \
+    'h5py=2.9*' \
+    'vincent=0.4.*' \
+    'beautifulsoup4=4.7.*' \
+    'protobuf=3.7.*' \
+    'xlrd'  && \
+    conda clean --all -f -y && \
+    # Activate ipywidgets extension in the environment that runs the notebook server
+    jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
+    # Also activate ipywidgets extension for JupyterLab
+    # Check this URL for most recent compatibilities
+    # https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager@^1.0.1 --no-build && \
+    jupyter labextension install jupyterlab_bokeh@1.0.0 --no-build && \
+    jupyter lab build --dev-build=False && \
+    npm cache clean --force && \
+    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
+    rm -rf /home/$NB_USER/.cache/yarn && \
+    rm -rf /home/$NB_USER/.node-gyp && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+# Install facets which does not have a pip or conda package at the moment
+RUN cd /tmp && \
+    git clone https://github.com/PAIR-code/facets.git && \
+    cd facets && \
+    jupyter nbextension install facets-dist/ --sys-prefix && \
+    cd && \
+    rm -rf /tmp/facets && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+# Import matplotlib the first time to build the font cache.
+ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
+RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
+    fix-permissions /home/$NB_USER
+
+
+############################################################################
+############### Dependency: jupyter/tensorflow-notebook ####################
+############################################################################
+
+# Install Tensorflow
+RUN conda install --quiet --yes \
+    'tensorflow=1.13*' \
+    'keras=2.2*' && \
+    conda clean --all -f -y && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+# RUN pip install --upgrade tensorflow-gpu
+
+############################################################################
+########################## Dependency: pytorch #############################
+############################################################################
+
+# Install PyTorch dependencies
+RUN conda install --quiet --yes \
+    pyyaml mkl mkl-include setuptools cmake cffi typing && \
+    conda clean --all -f -y && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+# Install PyTorch
+RUN conda install -y -c pytorch \
+    cudatoolkit=10.1 \
+    'pytorch=1.3.1' \
+    torchvision && \
+    conda clean --all -f -y && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+############################################################################
+############################ Useful packages ###############################
+############################################################################
+
+COPY jupyter_notebook_config.json /etc/jupyter/
+RUN fix-permissions /home/$NB_USER
+
+# Switch back to jovyan to avoid accidental container runs as root
+USER $NB_UID
--- a/src/fix-permissions
+++ b/src/fix-permissions
@@ -0,0 +1,35 @@
+#!/bin/bash
+# set permissions on a directory
+# after any installation, if a directory needs to be (human) user-writable,
+# run this script on it.
+# It will make everything in the directory owned by the group $NB_GID
+# and writable by that group.
+# Deployments that want to set a specific user id can preserve permissions
+# by adding the `--group-add users` line to `docker run`.
+
+# uses find to avoid touching files that already have the right permissions,
+# which would cause massive image explosion
+
+# right permissions are:
+# group=$NB_GID
+# AND permissions include group rwX (directory-execute)
+# AND directories have setuid,setgid bits set
+
+set -e
+
+for d in "$@"; do
+  find "$d" \
+    ! \( \
+      -group $NB_GID \
+      -a -perm -g+rwX  \
+    \) \
+    -exec chgrp $NB_GID {} \; \
+    -exec chmod g+rwX {} \;
+  # setuid,setgid *on directories only*
+  find "$d" \
+    \( \
+        -type d \
+        -a ! -perm -6000  \
+    \) \
+    -exec chmod +6000 {} \;
+done
--- a/src/jupyter_notebook_config.json
+++ b/src/jupyter_notebook_config.json
@@ -0,0 +1,6 @@
+
+{
+  "NotebookApp": {
+    "password": "sha1:e49e73b0eb0e:353c38d87d79527e57da1bba5f65046d0b376d95"
+  }
+}
--- a/src/jupyter_notebook_config.py
+++ b/src/jupyter_notebook_config.py
@@ -0,0 +1,55 @@
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+from jupyter_core.paths import jupyter_data_dir
+import subprocess
+import os
+import errno
+import stat
+
+c = get_config()
+c.NotebookApp.ip = '0.0.0.0'
+c.NotebookApp.port = 8888
+c.NotebookApp.open_browser = False
+
+# https://github.com/jupyter/notebook/issues/3130
+c.FileContentsManager.delete_to_trash = False
+
+# Generate a self-signed certificate
+if 'GEN_CERT' in os.environ:
+    dir_name = jupyter_data_dir()
+    pem_file = os.path.join(dir_name, 'notebook.pem')
+    try:
+        os.makedirs(dir_name)
+    except OSError as exc:  # Python >2.5
+        if exc.errno == errno.EEXIST and os.path.isdir(dir_name):
+            pass
+        else:
+            raise
+
+    # Generate an openssl.cnf file to set the distinguished name
+    cnf_file = os.path.join(os.getenv('CONDA_DIR', '/usr/lib'), 'ssl', 'openssl.cnf')
+    if not os.path.isfile(cnf_file):
+        with open(cnf_file, 'w') as fh:
+            fh.write('''\
+[req]
+distinguished_name = req_distinguished_name
+[req_distinguished_name]
+''')
+
+    # Generate a certificate if one doesn't exist on disk
+    subprocess.check_call(['openssl', 'req', '-new',
+                           '-newkey', 'rsa:2048',
+                           '-days', '365',
+                           '-nodes', '-x509',
+                           '-subj', '/C=XX/ST=XX/L=XX/O=generated/CN=generated',
+                           '-keyout', pem_file,
+                           '-out', pem_file])
+    # Restrict access to the file
+    os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
+    c.NotebookApp.certfile = pem_file
+
+# Change default umask for all subprocesses of the notebook server if set in
+# the environment
+if 'NB_UMASK' in os.environ:
+    os.umask(int(os.environ['NB_UMASK'], 8))
--- a/src/start-notebook.sh
+++ b/src/start-notebook.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+set -e
+
+if [[ ! -z "${JUPYTERHUB_API_TOKEN}" ]]; then
+  # launched by JupyterHub, use single-user entrypoint
+  exec /usr/local/bin/start-singleuser.sh "$@"
+elif [[ ! -z "${JUPYTER_ENABLE_LAB}" ]]; then
+  . /usr/local/bin/start.sh jupyter lab "$@"
+else
+  . /usr/local/bin/start.sh jupyter notebook "$@"
+fi
+
--- a/src/start-singleuser.sh
+++ b/src/start-singleuser.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+set -e
+
+# set default ip to 0.0.0.0
+if [[ "$NOTEBOOK_ARGS $@" != *"--ip="* ]]; then
+  NOTEBOOK_ARGS="--ip=0.0.0.0 $NOTEBOOK_ARGS"
+fi
+
+# handle some deprecated environment variables
+# from DockerSpawner < 0.8.
+# These won't be passed from DockerSpawner 0.9,
+# so avoid specifying --arg=empty-string
+if [ ! -z "$NOTEBOOK_DIR" ]; then
+  NOTEBOOK_ARGS="--notebook-dir='$NOTEBOOK_DIR' $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_PORT" ]; then
+  NOTEBOOK_ARGS="--port=$JPY_PORT $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_USER" ]; then
+  NOTEBOOK_ARGS="--user=$JPY_USER $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_COOKIE_NAME" ]; then
+  NOTEBOOK_ARGS="--cookie-name=$JPY_COOKIE_NAME $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_BASE_URL" ]; then
+  NOTEBOOK_ARGS="--base-url=$JPY_BASE_URL $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_HUB_PREFIX" ]; then
+  NOTEBOOK_ARGS="--hub-prefix=$JPY_HUB_PREFIX $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_HUB_API_URL" ]; then
+  NOTEBOOK_ARGS="--hub-api-url=$JPY_HUB_API_URL $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JUPYTER_ENABLE_LAB" ]; then
+  NOTEBOOK_BIN="jupyter labhub"
+else
+  NOTEBOOK_BIN="jupyterhub-singleuser"
+fi
+
+. /usr/local/bin/start.sh $NOTEBOOK_BIN $NOTEBOOK_ARGS "$@"
+
--- a/src/start.sh
+++ b/src/start.sh
@@ -0,0 +1,152 @@
+#!/bin/bash
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+set -e
+
+# Exec the specified command or fall back on bash
+if [ $# -eq 0 ]; then
+    cmd=( "bash" )
+else
+    cmd=( "$@" )
+fi
+
+run-hooks () {
+    # Source scripts or run executable files in a directory
+    if [[ ! -d "$1" ]] ; then
+        return
+    fi
+    echo "$0: running hooks in $1"
+    for f in "$1/"*; do
+        case "$f" in
+            *.sh)
+                echo "$0: running $f"
+                source "$f"
+                ;;
+            *)
+                if [[ -x "$f" ]] ; then
+                    echo "$0: running $f"
+                    "$f"
+                else
+                    echo "$0: ignoring $f"
+                fi
+                ;;
+        esac
+    done
+    echo "$0: done running hooks in $1"
+}
+
+run-hooks /usr/local/bin/start-notebook.d
+
+# Handle special flags if we're root
+if [ $(id -u) == 0 ] ; then
+
+    # Only attempt to change the jovyan username if it exists
+    if id jovyan &> /dev/null ; then
+        echo "Set username to: $NB_USER"
+        usermod -d /home/$NB_USER -l $NB_USER jovyan
+    fi
+
+    # Handle case where provisioned storage does not have the correct permissions by default
+    # Ex: default NFS/EFS (no auto-uid/gid)
+    if [[ "$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 $extra_dir
+        done
+    fi
+
+    # handle home and working directory if the username changed
+    if [[ "$NB_USER" != "jovyan" ]]; then
+        # changing username, make sure homedir exists
+        # (it could be mounted, and we shouldn't create it if it already exists)
+        if [[ ! -e "/home/$NB_USER" ]]; then
+            echo "Relocating home dir to /home/$NB_USER"
+            mv /home/jovyan "/home/$NB_USER"
+        fi
+        # if workdir is in /home/jovyan, cd to /home/$NB_USER
+        if [[ "$PWD/" == "/home/jovyan/"* ]]; then
+            newcwd="/home/$NB_USER/${PWD:13}"
+            echo "Setting CWD to $newcwd"
+            cd "$newcwd"
+        fi
+    fi
+
+    # Change UID of NB_USER to NB_UID if it does not match
+    if [ "$NB_UID" != $(id -u $NB_USER) ] ; then
+        echo "Set $NB_USER UID to: $NB_UID"
+        usermod -u $NB_UID $NB_USER
+    fi
+
+    # Set NB_USER primary gid to NB_GID (after making the group).  Set
+    # supplementary gids to NB_GID and 100.
+    if [ "$NB_GID" != $(id -g $NB_USER) ] ; then
+        echo "Add $NB_USER to group: $NB_GID"
+        groupadd -g $NB_GID -o ${NB_GROUP:-${NB_USER}}
+        usermod  -g $NB_GID -aG 100 $NB_USER
+    fi
+
+    # Enable sudo if requested
+    if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then
+        echo "Granting $NB_USER sudo access and appending $CONDA_DIR/bin to sudo PATH"
+        echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/notebook
+    fi
+
+    # Add $CONDA_DIR/bin to sudo secure_path
+    sed -r "s#Defaults\s+secure_path=\"([^\"]+)\"#Defaults secure_path=\"\1:$CONDA_DIR/bin\"#" /etc/sudoers | grep secure_path > /etc/sudoers.d/path
+
+    # Exec the command as NB_USER with the PATH and the rest of
+    # the environment preserved
+    run-hooks /usr/local/bin/before-notebook.d
+    echo "Executing the command: ${cmd[@]}"
+    exec sudo -E -H -u $NB_USER PATH=$PATH XDG_CACHE_HOME=/home/$NB_USER/.cache PYTHONPATH=${PYTHONPATH:-} "${cmd[@]}"
+else
+    if [[ "$NB_UID" == "$(id -u jovyan)" && "$NB_GID" == "$(id -g jovyan)" ]]; then
+        # User is not attempting to override user/group via environment
+        # variables, but they could still have overridden the uid/gid that
+        # container runs as. Check that the user has an entry in the passwd
+        # file and if not add an entry.
+        STATUS=0 && whoami &> /dev/null || STATUS=$? && true
+        if [[ "$STATUS" != "0" ]]; then
+            if [[ -w /etc/passwd ]]; then
+                echo "Adding passwd file entry for $(id -u)"
+                cat /etc/passwd | sed -e "s/^jovyan:/nayvoj:/" > /tmp/passwd
+                echo "jovyan:x:$(id -u):$(id -g):,,,:/home/jovyan:/bin/bash" >> /tmp/passwd
+                cat /tmp/passwd > /etc/passwd
+                rm /tmp/passwd
+            else
+                echo 'Container must be run with group "root" to update passwd file'
+            fi
+        fi
+
+        # Warn if the user isn't going to be able to write files to $HOME.
+        if [[ ! -w /home/jovyan ]]; then
+            echo 'Container must be run with group "users" to update files'
+        fi
+    else
+        # Warn if looks like user want to override uid/gid but hasn't
+        # run the container as root.
+        if [[ ! -z "$NB_UID" && "$NB_UID" != "$(id -u)" ]]; then
+            echo 'Container must be run as root to set $NB_UID'
+        fi
+        if [[ ! -z "$NB_GID" && "$NB_GID" != "$(id -g)" ]]; then
+            echo 'Container must be run as root to set $NB_GID'
+        fi
+    fi
+
+    # Warn if looks like user want to run in sudo mode but hasn't run
+    # the container as root.
+    if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then
+        echo 'Container must be run as root to grant sudo permissions'
+    fi
+
+    # Execute the command
+    run-hooks /usr/local/bin/before-notebook.d
+    echo "Executing the command: ${cmd[@]}"
+    exec "${cmd[@]}"
+fi
+
--- a/start-local.sh
+++ b/start-local.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
+
+docker-compose up --build -d
--- a/stop-local.sh
+++ b/stop-local.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
+
+docker-compose down