update readme with openjdk

README.md

@@ -10,7 +10,7 @@ Tutorial source:
 
 ## Step by step
 
-### Installation
+### 1. Installation
 
 #### Install Docker
 
@@ -94,96 +94,69 @@ DCLI is a tool which will help you manage DevContainers (https://gitlab.lis-lab.
     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:
+### 2. Initialize a project with DevContainer
 
-```css
-hello-world/
-│── src/
-│   └── main.java
-└── Dockerfile
-```
+Create a new project named `hello-world`. 
 
-#### main.java
-```java
-public class main {
-    public static void main(String[] args) {
-        System.out.println("Hello, World!");
-    }
-}
-```
-
-#### Dockerfile
-Create a `Dockerfile` in the hello-world directory:
-
-```dockerfile
-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:
+Open Terminal, type:
 
 ```bash
-docker build -t hello:test .    
+dcli init
 ```
 
-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:
-
+Insert the image name `openjdk` to import environment to execute Java:
 
 ```bash
-docker run -it hello:test
+Image Name: openjdk
 ```
 
-### Initialize a project using a customized Devcontainer configuration
+#### Run the DevContainer
 
-On Terminal, type:
+Type : 
 
 ```bash
-dcli init
+dcli start
 ```
 
-Insert image name of docker created:
+You will see the VSCode workspace opened. The enviroment inclues Java. To test, run:
 
 ```bash
-Image Name: hello:test
+java --version
 ```
 
-### Test running the DevContainer
+#### Create Java file
 
-Type : 
+On the VSCode workspace, we create a simple Java program: Hello World.
+The file structure and content are organized as follows:
 
-```bash
-dcli start
+```css
+hello-world/
+└── main.java
+```
+
+##### main.java
+```java
+public class main {
+    public static void main(String[] args) {
+        System.out.println("Hello, World!");
+    }
+}
 ```
 
-You will see the VSCode workspace opened. Test running the java program inside the DevContainer, type:
+#### Run java program inside the DevContainer
 
 ```bash
 java main.java
 ```
 
-Stop the container: 
+#### Stop the container: 
 
 ```bash 
 dcli stop 
 ```
 
-### Push DevContainer to the LIS Cluster
+### 3. Push DevContainer to the LIS Cluster
 
 #### 1. Export the DevContainer
 
@@ -243,10 +216,10 @@ dcli push
 Then, push your source code to the cluster. E.g: 
 
 ```bash
-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
+scp -r -o ProxyJump="thi-phuong.kieu@139.124.22.4" * thi-phuong.kieu@sms:/home/thi-phuong.kieu/hello-world/*
 ```
 
-### Run your DevContainer on LIS Cluster
+### 4. Run your DevContainer on LIS Cluster
 
 On the termianl, type:
 
@@ -265,26 +238,3 @@ java main.java
 ```bash
 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
 ```
\ No newline at end of file
-
-## Appendix
-
-With the [DEv-CF project](~/code/devs-dclitest.zip), the dockerfile is written as follow:
-
-```dockerfile
-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"]
-```
\ No newline at end of file

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:
+    ```bash
+    for pkg in docker.io docker-doc docker-compose docker-compose-v2 podman-docker containerd runc; do sudo apt-get remove $pkg; done
+    ```
+
+2. Set up Docker's apt repository:
+    ```bash
+    # Add Docker's official GPG key:    
+    sudo apt-get update
+    sudo apt-get install ca-certificates curl
+    sudo install -m 0755 -d /etc/apt/keyrings
+    sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
+    sudo chmod a+r /etc/apt/keyrings/docker.asc
+
+    # Add the repository to Apt sources:
+    echo \
+        "deb [arch=$(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:
+    ```bash
+    sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
+    ```
+
+4. Configure docker in rootless mode
+    ```bash
+    sudo groupadd docker
+    sudo usermod -aG docker $USER
+    ```
+
+5. Verify that the installation is successful by running the hello-world image:
+    ```bash
+    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.
+    ```txt
+    Hello from Docker!
+    This message shows that your installation appears to be working correctly.
+    ...
+    ```
+
+#### Install Squashfs tools
+
+```bash
+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:
+    ```bash
+    sudo apt install git
+    ```
+
+2. Once done clone the DCLI directory:
+    ```bash
+    git clone https://gitlab.lis-lab.fr/sicomp/dcli
+    ```
+
+3. Proceed to the install:
+    ```bash
+    cd dcli
+    chmod +x install.sh
+    ./install.sh
+    ```
+
+4. Once installation is complete, you have to source your bashrc:
+    ```bash
+    source ~/.bashrc
+    ```
+
+5. Check that dcli is working properly by typing:
+    ```bash
+    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:
+
+```css
+hello-world/
+│── src/
+│   └── main.java
+└── Dockerfile
+```
+
+#### main.java
+```java
+public class main {
+    public static void main(String[] args) {
+        System.out.println("Hello, World!");
+    }
+}
+```
+
+#### Dockerfile
+Create a `Dockerfile` in the hello-world directory:
+
+```dockerfile
+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:
+
+```bash
+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:
+
+
+```bash   
+docker run -it hello:test
+```
+
+### Initialize a project using a customized Devcontainer configuration
+
+On Terminal, type:
+
+```bash
+dcli init
+```
+
+Insert image name of docker created:
+
+```bash
+Image Name: hello:test
+```
+
+### Test running the DevContainer
+
+Type : 
+
+```bash
+dcli start
+```
+
+You will see the VSCode workspace opened. Test running the java program inside the DevContainer, type:
+
+```bash
+java main.java
+```
+
+Stop the container: 
+
+```bash 
+dcli stop 
+```
+
+### Push DevContainer to the LIS Cluster
+
+#### 1. Export the DevContainer
+
+Type: 
+
+```bash
+dcli export
+```
+
+Once finished, you should see a squashfs file created.
+
+**Note:** Ignore the error on permission denied, or type: 
+
+```bash
+dcli export | chmod -R 777 tmp
+```
+
+#### 2. Push your Devcontainer on LIS Cluster
+
+On the first teminal window, connect to the cluster:
+
+```bash
+ssh thi-phuong.kieu@sms
+```
+
+Then create new folders:
+
+```bash 
+mkdir devcontainer_images # for the squashfs file
+mkdir hello-world       # for your soucre code
+```
+
+On the second window, type:
+
+```bash
+dcli config
+```
+
+```txt
+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:
+
+```bash
+dcli push
+```
+
+Then, push your source code to the cluster. E.g: 
+
+```bash
+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:
+
+```bash
+dcli irun
+```
+
+Once connect successfully, type:
+
+```bash
+java main.java
+```
+
+**Note:** To run manually, connect to the cluster first, then type:
+
+```bash
+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](~/code/devs-dclitest.zip), the dockerfile is written as follow:
+
+```dockerfile
+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"]
+```
\ No newline at end of file