README_ver2_java-hello-world.md

How to run a Java program in DevContainer on the LIS Cluster

Getting started

Prerequisite: Ubuntu Terminal

Tutorial source:

• “Manuals.” Docker Documentation. https://docs.docker.com/manuals/. Published March 5, 2025. Accessed March 18, 2025.
• Fabrice Daian. "Create, manage and deploy DevContainers | DevContainer Formation." LIS GitLab. https://gitlab.lis-lab.fr/sicomp/devcontainer_formation. Published December 5, 2024. Accessed March 18, 2025.

Step by step

Installation

Install Docker

1. Uninstalling any potential conflicting packages already installed on your computer:

   for pkg in docker.io docker-doc docker-compose docker-compose-v2 podman-docker containerd runc; do sudo apt-get remove $pkg; done

2. Set up Docker's apt repository:

   # Add Docker's official GPG key:    
   sudo apt-get update
   sudo apt-get install ca-certificates curl
   sudo install -m 0755 -d /etc/apt/keyrings
   sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
   sudo chmod a+r /etc/apt/keyrings/docker.asc
   
   # Add the repository to Apt sources:
   echo \
       "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
       $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
       sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
   sudo apt-get update

3. Install the Docker packages:

   sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

4. Configure docker in rootless mode

   sudo groupadd docker
   sudo usermod -aG docker $USER

5. Verify that the installation is successful by running the hello-world image:

   docker run hello-world

   This command downloads a test image and runs it in a container. When the container runs, it prints a confirmation message and exits.

   Hello from Docker!
   This message shows that your installation appears to be working correctly.
   ...

Install Squashfs tools

sudo apt-get update && sudo apt-get install squashfs-tools

Install Devcontainer Command Line Interface (DCLI)

DCLI is a tool which will help you manage DevContainers (https://gitlab.lis-lab.fr/sicomp/dcli)

1. If you don't already have git installed, type:

   sudo apt install git

2. Once done clone the DCLI directory:

   git clone https://gitlab.lis-lab.fr/sicomp/dcli

3. Proceed to the install:

   cd dcli
   chmod +x install.sh
   ./install.sh

4. Once installation is complete, you have to source your bashrc:

   source ~/.bashrc

5. Check that dcli is working properly by typing:

   dcli --version

Create Java project and Write dockerfile

Now, we will start with a simple Java program: Hello World. The file structure and content are organized as follows:

hello-world/
│── src/
│   └── main.java
└── Dockerfile

main.java

public class main {
    public static void main(String[] args) {
        System.out.println("Hello, World!");
    }
}

Dockerfile

Create a Dockerfile in the hello-world directory:

FROM openjdk
COPY src hello-world/src
WORKDIR hello-world
RUN mkdir -p bin
RUN javac -d bin ./src/main.java
WORKDIR bin
CMD ["java", "main"]

Note: Make sure that the scripts is named exactly as Dockerfile or dockerfile.

Create docker image

To create a Docker image from the Dockerfile, run the following command in the hello-world directory:

docker build -t hello:test .    

with hello:test assigns the image a name hello and a tag test.

Run the Docker Container

Once the image is built, you can run the container using:

docker run -it hello:test

Initialize a project using a customized Devcontainer configuration

On Terminal, type:

dcli init

Insert image name of docker created:

Image Name: hello:test

Test running the DevContainer

Type :

dcli start

You will see the VSCode workspace opened. Test running the java program inside the DevContainer, type:

java main.java

Stop the container:

dcli stop 

Push DevContainer to the LIS Cluster

1. Export the DevContainer

Type:

dcli export

Once finished, you should see a squashfs file created.

Note: Ignore the error on permission denied, or type:

dcli export | chmod -R 777 tmp

2. Push your Devcontainer on LIS Cluster

On the first teminal window, connect to the cluster:

ssh thi-phuong.kieu@sms

Then create new folders:

mkdir devcontainer_images # for the squashfs file
mkdir hello-world       # for your soucre code

On the second window, type:

dcli config

Please provide the following information to create the .cluster_config file.
Cluster server name/address [sms]: sms
LIS cluster username []: thi-phuong.kieu
Devcontainer workspace directory path [/workspace]: /workspace
Project directory (absolute path) to mount inside the devcontainer located on the cluster []: /home/thi-phuong.kieu/hello-world/
Directory containing squashfs images (absolute path) located on the cluster []: /home/thi-phuong.kieu/devcontainer_images/

.cluster_config file created successfully in the .devcontainer directory.

Now, push the squashfs file to the cluster push your squashfs fil inside the cluster:

dcli push

Then, push your source code to the cluster. E.g:

scp -r -o ProxyJump="thi-phuong.kieu@139.124.22.4" ./src/main.java thi-phuong.kieu@sms:/home/thi-phuong.kieu/hello-world/src/main.java

Run your DevContainer on LIS Cluster

On the termianl, type:

dcli irun

Once connect successfully, type:

java main.java

Note: To run manually, connect to the cluster first, then type:

srun --container-image=/home/thi-phuong.kieu/devcontainer_images//dcli_hello-world.squashfs --container-mounts=/home/thi-phuong.kieu/hello-world/:/workspace --container-workdir=/workspace --cpus-per-task=12 --pty bash

Appendix

With the DEv-CF project, the dockerfile is written as follow:

FROM openjdk:17

# Copy all necessary project folders into the container
COPY src/ /devs-dclitest/src/      
COPY lib/ /devs-dclitest/lib/
COPY input/ /devs-dclitest/input/
COPY output/ /devs-dclitest/output/

WORKDIR /devs-dclitest
RUN mkdir -p /devs-dclitest/bin

# Compile Java source files with the required library
RUN javac -cp "/devs-dclitest/lib/fwkdevs-v0.7" -d /devs-dclitest/bin /devs-dclitest/src/*.java

# Run the Java application with the bin and lib path
CMD ["java", "-cp", "/devs-dclitest/bin:/devs-dclitest/lib/fwkdevs-v0.7", "Simulator"]