Update docs about GraalVM compiler switches and tidy up docker relate…

…d scripts: create docker user and enable running Jupyter inside the container and be able to create notebooks.
jd-13 · Sep 10, 2019 · 863e4bf · 863e4bf
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diff --git a/examples/JuPyteR/.gitignore b/examples/JuPyteR/.gitignore
@@ -1,3 +1,3 @@
-jupyter/
+notebooks/
 vulnerabilities/
 dockerfileScan/
diff --git a/examples/JuPyteR/Docker-container-instructions.md b/examples/JuPyteR/Docker-container-instructions.md
@@ -51,22 +51,25 @@ which runs the container and the [runLocal.sh](runLocal.sh) is executed inside t
 
 #### Scripts provided:
 
+All the scripts will be found on the `build-docker-image` folder:
+
 - [buildDockerImage.sh](buildDockerImage.sh): build the docker image using Dockerfile
     - [Dockerfile](Dockerfile): a dockerfile script to help build a docker image of Jupyter with the IJava kernel running on Java 9 (with Graal enabled)
         - [install-jupyter-notebooks.sh](install-jupyter-notebooks.sh): installs Jupyter notebook and its dependencies
         - [install-java-kernel.sh](install-java-kernel.sh): executed during building of the Docker container
+    - [removeUnusedContainersAndImages.sh](removeUnusedContainersAndImages.sh)  - clean up after a build, removes dangling images and closed/exited containers
 - [runDockerContainer.sh](runDockerContainer.sh): run the Jupyter docker image, exposing port 8888 to point your browser to (http://localhost:8888)
     - [runLocal.sh](runLocal.sh): runs inside the docker container but can be also run on any local environment with the necessary dependencies installed
-- [push-jupyter-java-docker-image-to-hub.sh](push-jupyter-java-docker-image-to-hub.sh): push the built docker image to Docker Hub. `DOCKER_USER_NAME` must be set in the environment or passed in on CLI, otherwise a default user name is assumed.
+- [push-jupyter-java-docker-image-to-hub.sh](push-jupyter-java-docker-image-to-hub.sh): push the built docker image to Docker Hub. `DOCKER_USER_NAME` must be set in the environment or passed in on CLI, otherwise a default user name is assumed
 
-Note: the GraalVM compiler can be enabled starting Java 9 and this currently only works for Linux. But later versions support Linux, MacOS and Windows.
+Note: the GraalVM compiler can be enabled starting Java 9 and this currently only works for Linux. But later versions support Linux, MacOS and Windows. See [Switches to enable the GraalVM compiler in Java 9](./README.md#switches-to-enable-the-graalvm-compiler-in-java-9) in [README.md](README.md).
 
 ### Debug your running container
 
 Set the environment variable `DEBUG` to `true` and it should do the job:
 
 ```
-$ cd build-docker-image
+$ [stay or switch into the project root folder]
 ```
 
 ```
@@ -87,7 +90,7 @@ You will be provided with the below `bash` prompt:
 * Running in Debug mode *
 *************************
 
-root@a659f75885b0:/jupyter-notebooks#
+root@a659f75885b0:/home/jupyter#
 ```
 
-The `jupyter-notebook` instance will need to be started manually.
+The `/home/jupyter` instance will need to be started manually.
diff --git a/examples/JuPyteR/README.md b/examples/JuPyteR/README.md
@@ -17,6 +17,22 @@ GraalVM compiler can be enabled for JDK 9 and higher, for platforms where it is
 |Java 10          | Linux and MacOS       |
 |Java 11 or higher| Linux, MacOS, Windows |
 
+#### Switches to enable the GraalVM compiler in Java 9
+
+```
+  export JAVA_OPTS="-XX:+UnlockExperimentalVMOptions -XX:+EnableJVMCI -XX:+UseJVMCICompiler"
+  export JAVA_TOOL_OPTIONS="${JAVA_TOOL_OPTIONS} ${JAVA_OPTS}"
+```
+
+or
+
+```
+  export ENABLE_GRAALVM_COMPILER="-XX:+UnlockExperimentalVMOptions -XX:+EnableJVMCI -XX:+UseJVMCICompiler"
+
+  java [-cp] [...] [-jar] [...] \
+       ${ENABLE_GRAALVM_COMPILER}
+```
+
 ### Additional source of kernels
 - [beakerx](http://beakerx.com/) - Is another source where a wider range of kernels can be found (covering many JVM languages).
 

diff --git a/examples/JuPyteR/build-docker-image/Dockerfile b/examples/JuPyteR/build-docker-image/Dockerfile
@@ -13,9 +13,19 @@ EXPOSE 8888
 
 RUN rm -f *.sh *.zip install.py
 
-COPY runLocal.sh runLocal.sh
+ARG USER
+RUN groupadd -r ${USER} \
+    && useradd -r -s /bin/false \
+               -g ${USER} ${USER}
 
 ARG WORKDIR
 WORKDIR ${WORKDIR}
 
-ENTRYPOINT ["./../runLocal.sh"]
+COPY runLocal.sh runLocal.sh
+RUN mv -f /root/.local ${WORKDIR}
+
+RUN chown -R ${USER}:${USER} ${WORKDIR}
+
+USER ${USER}
+
+ENTRYPOINT ["./runLocal.sh"]
diff --git a/examples/JuPyteR/build-docker-image/buildDockerImage.sh b/examples/JuPyteR/build-docker-image/buildDockerImage.sh
@@ -13,9 +13,12 @@ if [[ -z ${DOCKER_USER_NAME:-""} ]]; then
 fi
 
 DOCKER_FULL_TAG_NAME="${DOCKER_USER_NAME}/${IMAGE_NAME}"
+USER=jupyter
+JUPYTER_HOME=/home/${USER}
 
 time docker build \
-                 --build-arg WORKDIR=/jupyter-notebooks      \
+                 --build-arg USER=jupyter                    \
+                 --build-arg WORKDIR=${JUPYTER_HOME}         \
                  -t ${DOCKER_FULL_TAG_NAME}:${IMAGE_VERSION} \
                  .
 

diff --git a/examples/JuPyteR/runDockerContainer.sh b/examples/JuPyteR/runDockerContainer.sh
@@ -16,7 +16,7 @@ if [[ "${DEBUG}" == "true" ]]; then
     echo "*************************"
 fi
 
-[ ! ${PWD}/jupyter/notebooks ] && mkdir -p ${PWD}/jupyter/notebooks
+[ ! ${PWD}/notebooks ] && mkdir -p ${PWD}/notebooks
 
 IMAGE_NAME=${IMAGE_NAME:-jupyter-java}
 IMAGE_VERSION=${IMAGE_VERSION:-$(cat version.txt)}
@@ -30,6 +30,6 @@ DOCKER_FULL_TAG_NAME="${DOCKER_USER_NAME}/${IMAGE_NAME}"
 
 docker run --rm                                                  \
            ${DOCKER_DEBUG_PARAMS}                                \
-           --volume ${PWD}/jupyter/notebooks:/jupyter-notebooks  \
+           --volume ${PWD}/notebooks:/home/jupyter/notebooks     \
            -p 8888:8888                                          \
            ${DOCKER_FULL_TAG_NAME}:${IMAGE_VERSION}