mm/jupyterhub-deploy-docker
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merge conflict failed. lab default.

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This commit is contained in:
Michael Pilosov 2019-04-10 18:52:55 -06:00
commit c52699a6f1
6 changed files with 73 additions and 24 deletions
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8
Dockerfile.jupyterhub
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@ -8,8 +8,14 @@ RUN /opt/conda/bin/conda install -yq psycopg2=2.7 && \
/opt/conda/bin/conda clean -tipsy && \
/opt/conda/bin/pip install --no-cache-dir \
oauthenticator==0.8.*
RUN apt-get update && \
apt-get install -y --no-install-recommends \
vim
RUN pip install jupyterhub-hashauthenticator git+https://github.com/jupyterhub/dockerspawner.git@master
RUN apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN pip install jupyterhub-hashauthenticator dockerspawner==0.10.0
# Copy TLS certificate and key
#ENV SSL_CERT /srv/jupyterhub/secrets/jupyterhub.crt

8
groups.sh Executable file
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@ -0,0 +1,8 @@
#!/bin/bash
source .env
NUM_GROUPS=4
for i in `seq 1 $NUM_GROUPS`; do
docker volume create shared-$HUB_NAME-group$i
sudo chmod 777 $(docker inspect shared-$HUB_NAME-group$i | grep "Mountpoint" | awk '{print $2}' | sed 's/"//g' | sed 's/,//g')
done

27
jupyterhub_config.py
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@ -1,5 +1,6 @@
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
# Major edits by MathematicalMichael(.com) 02-2019
# Configuration file for JupyterHub
import os
@ -32,20 +33,26 @@ class MyDockerSpawner(DockerSpawner):
for i in range(1,len(parts)):
group_id = parts.pop()
if group_id != 'admin': # no need for an admin group.
group_map[user_name].append(group_id)
def start(self):
if self.user.name in self.group_map:
group_list = self.group_map[self.user.name]
# add team volume to volumes
for group_id in group_list:
self.volumes['shared-{}'.format(group_id)] = {
'bind': '/home/jovyan/%s'%(group_id),
'mode': 'rw', # or ro for read-only
}
if self.user.name == 'hub-admin': # if admin, allow userlist access
self.volumes[os.path.join(pwd,'userlist')] = { 'bind': '/home/jovyan/userlist',
'mode': 'rw' }
for group_id in group_list: # admins in userlist get to write files.
if group_id != 'admin':
if 'admin' in group_list:
self.volumes['shared-{}'.format(group_id)] = \
{ 'bind': '/home/jovyan/%s'%(group_id),
'mode': 'rw' } # or ro for read-only
else: # this "shared-" is part of the naming convention
self.volumes['shared-{}'.format(group_id)] = \
{'bind': '/home/jovyan/%s'%(group_id),
'mode': 'ro' } # or rw for write (can cause conflicts)
else: # if admin is one of the groups in userlist, mount the following:
self.volumes['%s/userlist'%(os.environ['HUB_LOC'])] = \
{ 'bind': '/home/jovyan/userlist', 'mode': 'rw' }
self.volumes['%s/jupyterhub_config.py'%(os.environ['HUB_LOC'])] = \
{ 'bind': '/home/jovyan/jupyterhub_config.py', 'mode': 'rw' }
self.environment['JUPYTER_ENABLE_LAB'] = 'yes'
return super().start()
@ -75,7 +82,7 @@ spawn_cmd = os.environ.get('DOCKER_SPAWN_CMD', "start-singleuser.sh")
c.DockerSpawner.extra_create_kwargs.update({ 'command': spawn_cmd })
# Memory limit
c.Spawner.mem_limit = '2G' # RAM limit
c.Spawner.mem_limit = '4G' # RAM limit
c.Spawner.cpu_limit = 0.0001
# Connect containers to this Docker network

2
makefile
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@ -17,7 +17,7 @@ secrets/postgres.env:
@echo "POSTGRES_PASSWORD=$(shell openssl rand -hex 32)" > $@
secrets/oauth.env:
@echo "Generating postgres password in $@"
@echo "Generating hash key in $@"
@echo "HASH_SECRET_KEY=$(shell openssl rand -hex 32)" > $@
login:

11
setup.sh
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@ -3,10 +3,17 @@
# this script is meant to be run only the first time a hub is being set up.
# create a default userlist
echo "hub-admin admin shared" > userlist
# Use the format \"studentname HUB_NAME-group1\" on each line to add students to groups (10 by default have already been created and permissions appropriately set)"
echo "hub-admin admin shared" >> userlist
# change permissions so that admins can edit these.
sudo chmod 777 userlist
sudo chmod 777 jupyterhub_config.py
mkdir secrets
make secrets/oauth.env
make secrets/postgres.env
echo "HUB_LOC=$(pwd)" >> .env
source .env
# show what is needed to be added to /etc/nginx/sites-enabled/hub.conf
@ -19,7 +26,7 @@ docker-compose up -d
echo -en "\n\nWe create a default shared volume and set its permissions to be read/write. You may have to enter your password now:\n"
docker volume create shared-shared
sudo chmod 777 $(docker inspect shared-shared | grep "Mountpoint" | awk '{print $2}' | sed 's/"//g' | sed 's/,//g')
echo -en "Volume has been created."
echo -en "Globally shared volume has been created."
echo -en "\n\nHub has been launched. Here are the Docker processes running right now:"
docker ps --format "table {{.Names}}\t{{.Status}}\t{{.Ports}}"

39
singleuser/Dockerfile
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@ -1,7 +1,9 @@
ARG DOCKER_NOTEBOOK_IMAGE
ARG DISPLAY
FROM $DOCKER_NOTEBOOK_IMAGE
ARG JUPYTERHUB_VERSION
#any additional installations go here.
RUN export DISPLAY=$DISPLAY
USER root
@ -12,27 +14,45 @@ RUN apt-get update && \
fonts-dejavu \
tzdata \
gfortran \
gcc && \
rm -rf /var/lib/apt/lists/*
gcc
# finish off with MPI dependencies (only required if not installing fenics)
#RUN sudo apt-get install mpich libmpich-dev -y
RUN rm -rf /var/lib/apt/lists/*
USER jovyan
RUN conda update --all
RUN conda install fenics
RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse
RUN conda install -c conda-forge fenics
RUN python3 -m pip install ipyparallel
# If you do not need parallelism, delete the following.
RUN python3 -m pip install ipyparallel mpi4py
RUN ipython profile create --parallel --profile=mpi
RUN ipython profile create --parallel --profile=default
RUN echo "c.IPClusterEngines.engine_launcher_class = 'MPIEngineSetLauncher'" >> /home/jovyan/.ipython/profile_mpi/ipcluster_config.py
RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 ipython ipykernel kernda numpy pandas matplotlib ipywidgets yaml
# Python 2 environment
RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 ipython ipykernel kernda numpy pandas matplotlib ipywidgets yaml ipyparallel mpi4py scipy pyDOE
RUN /opt/conda/envs/python2/bin/ipython profile create --parallel --profile=mpi
USER root
# Create a global kernelspec in the image and modify it so that it properly activates
# the python2 conda environment.
RUN $CONDA_DIR/envs/python2/bin/python -m ipykernel install && \
$CONDA_DIR/envs/python2/bin/kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json
USER $NB_UID
# Jupyterhub and memory monitoring
RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse && \
jupyter labextension install jupyterlab-topbar-extension && \
jupyter labextension install jupyterlab-system-monitor && \
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
# R environment
USER root
RUN apt-get update && \
@ -63,6 +83,7 @@ ENV PATH="${PATH}:/usr/lib/rstudio-server/bin"
ENV LD_LIBRARY_PATH="/usr/lib/R/lib:/lib:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/opt/conda/lib/R/lib"
#ENV LD_LIBRARY_PATH="/usr/lib/R/lib:/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/opt/conda/lib/R/lib"
# USER SETTINGS
USER jovyan
RUN echo "export EDITOR=/usr/bin/vim" >> /home/jovyan/.bashrc
RUN echo "source /home/jovyan/work/.bash_custom" >> /home/jovyan/.bashrc