merge conflict failed. lab default.

Dockerfile.jupyterhub

@@ -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

groups.sh

@@ -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
+

jupyterhub_config.py

@@ -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:
+            for group_id in group_list: # admins in userlist get to write files.
-                self.volumes['shared-{}'.format(group_id)] = {
+                if group_id != 'admin':
-                    'bind': '/home/jovyan/%s'%(group_id),
+                    if 'admin' in group_list: 
-                    'mode': 'rw',  # or ro for read-only
+                        self.volumes['shared-{}'.format(group_id)] = \
-                    }
+                            { 'bind': '/home/jovyan/%s'%(group_id),
-        if self.user.name == 'hub-admin': # if admin, allow userlist access
+                                'mode': 'rw' } # or ro for read-only
-            self.volumes[os.path.join(pwd,'userlist')] = { 'bind': '/home/jovyan/userlist',
+                    else: # this "shared-" is part of the naming convention
-                                                            'mode': 'rw' }
+                        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

makefile

@@ -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:

setup.sh

@@ -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}}"

singleuser/Dockerfile

@@ -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 && \
+    gcc
-    rm -rf /var/lib/apt/lists/*
+
+# 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 
+# If you do not need parallelism, delete the following. 
-RUN conda install -c conda-forge fenics
+RUN python3 -m pip install ipyparallel mpi4py
-
-RUN python3 -m pip install ipyparallel
 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