Modify NB Dockerfile and start scripts to detect PVC mount for /home/…

…jovyan

bootstrap/cmd/bootstrap/app/server.go

@@ -388,7 +388,7 @@ func Run(opt *options.ServerOption) error {
 
 	pvcMount := ""
 	if hasDefault {
-		pvcMount = "/home/jovyan/work"
+		pvcMount = "/home/jovyan"
 	}
 
 	err = actions.RunParamSet(map[string]interface{}{

components/tensorflow-notebook-image/Dockerfile

@@ -16,7 +16,7 @@ ENV DEBIAN_FRONTEND noninteractive
 ENV NB_USER jovyan
 ENV NB_UID 1000
 ENV HOME /home/$NB_USER
-ENV CONDA_DIR=$HOME/.conda
+ENV CONDA_DIR=/opt/conda
 ENV PATH $CONDA_DIR/bin:$PATH
 
 # Use bash instead of sh
@@ -50,8 +50,11 @@ ENV LANG en_US.UTF-8
 ENV LANGUAGE en_US.UTF-8
 
 # Create jovyan user with UID=1000 and in the 'users' group
-RUN useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
-    chown -R ${NB_USER}:users /usr/local/bin
+# but allow for non-initial launches of the notebook to have
+# $HOME provided by the contents of a PV
+RUN useradd -M -s /bin/bash -N -u $NB_UID $NB_USER && \
+    chown -R ${NB_USER}:users /usr/local/bin && \
+    mkdir -p $HOME
 
 RUN export CLOUD_SDK_REPO="cloud-sdk-$(lsb_release -c -s)" && \
     echo "deb https://packages.cloud.google.com/apt $CLOUD_SDK_REPO main" > /etc/apt/sources.list.d/google-cloud-sdk.list && \
@@ -62,16 +65,6 @@ RUN export CLOUD_SDK_REPO="cloud-sdk-$(lsb_release -c -s)" && \
     gcloud config set component_manager/disable_update_check true && \
     gcloud config set metrics/environment github_docker_image
 
-RUN chown -R ${NB_USER}:users /home/${NB_USER}
-
-# Run everything below this as $NB_USER
-USER $NB_USER
-
-WORKDIR $HOME
-
-# Setup work directory for backward-compatibility
-RUN mkdir /home/$NB_USER/work
-
 # Install Tini - used as entrypoint for container
 RUN cd /tmp && \
     wget --quiet https://github.com/krallin/tini/releases/download/v0.10.0/tini && \
@@ -126,23 +119,33 @@ RUN conda create -n py2 python=2 && \
       pip install --no-cache-dir tensorflow-model-analysis && \
       jupyter nbextension install --py --symlink tensorflow_model_analysis --user && \
       jupyter nbextension enable --py tensorflow_model_analysis --user; \
-    fi
-
-# Install jupyterlab-manager
-RUN conda install --quiet --yes \
+    fi \
+    && \
+    # Install jupyterlab-manager
+    conda install --quiet --yes \
     # nodejs required for jupyterlab-manager
     nodejs && \
-    jupyter labextension install @jupyter-widgets/jupyterlab-manager
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager && \
+    # Do chown in this layer for significant size savings
+    chown -R ${NB_USER}:users $HOME && \
+    chown -R ${NB_USER}:users $CONDA_DIR
 
 # Install common packages from requirements.txt for both python2 and python3
+# NB: the COPY chown can't expand a bash variable for NB_USER
 COPY --chown=jovyan:users requirements.txt $HOME/requirements.txt
+COPY --chown=jovyan:users  jupyter_notebook_config.py $HOME/.jupyter/
 RUN pip --no-cache-dir install -r $HOME/requirements.txt && \
     source activate py2 && \
     pip --no-cache-dir install -r $HOME/requirements.txt
 
+# Tar and delete staged content
+WORKDIR $HOME
+RUN tar -cf /tmp/${NB_USER}.tar -C $HOME . && \
+    chown ${NB_USER}:users /tmp/${NB_USER}.tar && \
+    rm -fr $(ls -A $HOME)
+
 # Copy over init scripts
-COPY --chown=jovyan:users start-singleuser.sh start-notebook.sh start.sh /usr/local/bin/
-COPY --chown=jovyan:users  jupyter_notebook_config.py $HOME/.jupyter/
+COPY --chown=jovyan:users start-singleuser.sh start-notebook.sh start.sh pvc-check.sh /usr/local/bin/
 RUN chmod a+rx /usr/local/bin/*
 
 # Configure container startup

components/tensorflow-notebook-image/pvc-check.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+# Copyright 2016 The Kubeflow Authors All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# stored in the NB Dockerfile
+SRC_TAR=/tmp/$NB_USER.tar
+WORK_DIR=$HOME/work
+
+echo "checking if $HOME volume needs init..."
+
+if [ "$(ls -A $HOME)" ]; then
+    # assume we are working with an existing volume via a PVC
+    echo "...$HOME already has content. Reinstalling packages..."
+    cd $HOME
+    pip install -q -r $HOME/requirements.txt
+    source activate py2 && pip install -q -r $HOME/requirements.txt
+else
+    # clean volume, needs init
+    echo "...creating $WORK_DIR"
+    mkdir $WORK_DIR
+
+    echo "...load initial content into $HOME..."
+    tar --no-overwrite-dir -xf $SRC_TAR -C $HOME .
+
+    chown -R $NB_USER:users $(ls -A $HOME)
+fi
+
+echo "...done"

components/tensorflow-notebook-image/start-singleuser.sh

@@ -46,4 +46,7 @@ if [ ! -z "$JPY_HUB_API_URL" ]; then
   NOTEBOOK_ARGS="--hub-api-url=$JPY_HUB_API_URL $NOTEBOOK_ARGS"
 fi
 
+# check to see if a PV has been mounted 
+. /usr/local/bin/pvc-check.sh
+
 . /usr/local/bin/start.sh jupyterhub-singleuser $NOTEBOOK_ARGS $@

kubeflow/core/kubeform_spawner.py

@@ -98,14 +98,18 @@ def extra_resource_limits(self):
 c.KubeSpawner.start_timeout = 60 * 30
 # Increase timeout to 5 minutes to avoid HTTP 500 errors on JupyterHub
 c.KubeSpawner.http_timeout = 60 * 5
+
+# Volume setup
+c.KubeSpawner.singleuser_uid = 1000
+c.KubeSpawner.singleuser_fs_gid = 100
+c.KubeSpawner.singleuser_working_dir = '/home/jovyan'
 volumes = []
 volume_mounts = []
 ###################################################
 # Persistent volume options
 ###################################################
 # Using persistent storage requires a default storage class.
 # TODO(jlewi): Verify this works on minikube.
-# TODO(jlewi): Should we set c.KubeSpawner.singleuser_fs_gid = 1000
 # see https://github.com/kubeflow/kubeflow/pull/22#issuecomment-350500944
 pvc_mount = os.environ.get('NOTEBOOK_PVC_MOUNT')
 if pvc_mount and pvc_mount != 'null':

kubeflow/core/tests/jupyterhub_test.jsonnet

@@ -5,7 +5,7 @@ local params = {
   jupyterHubAuthenticator:: null,
   jupyterHubServiceType:: "ClusterIP",
   jupyterHubImage: "gcr.io/kubeflow/jupyterhub-k8s:1.0.1",
-  jupyterNotebookPVCMount: "/home/jovyan/work",
+  jupyterNotebookPVCMount: "/home/jovyan",
   cloud: null,
 };
 

user_guide.md

@@ -123,10 +123,10 @@ kubectl get storageclass
   parameter to create a volume that will be mounted within the notebook
 
   ```
-  ks param set kubeflow-core jupyterNotebookPVCMount /home/jovyan/work
+  ks param set kubeflow-core jupyterNotebookPVCMount /home/jovyan
   ```
 
-  * Here we mount the volume at `/home/jovyan/work` because the notebook
+  * Here we mount the volume at `/home/jovyan` because the notebook
     always executes as user jovyan
   * The selected directory will be stored on whatever storage is the default
     for the cluster (typically some form of persistent disk)