In the previous two recipes, we prepared and tested the train, serve, and api.r files. With these ready, we can now proceed with crafting the Dockerfile and building the custom algorithm container image.
Tip
Wait! What's a Dockerfile? It is a text document containing the directives (commands) used to prepare and build a container image. This container image then serves as the blueprint when running containers. Feel free to check out https://docs.docker.com/engine/reference/builder/ for more information.
In this recipe, we will prepare a Dockerfile for the custom R container image. We will make use of the api.r file, as well as the train and serve scripts we prepared in the Preparing and testing the train script in R and Preparing and testing the serve script in R recipes. After that, we will use the docker build command to prepare the image before pushing it to an Amazon ECR repository.
Getting ready
Make sure you have completed the Preparing and testing the serve script in R recipe.
How to do it...
The initial steps in this recipe focus on preparing the Dockerfile. Let's get started:
- Double-click the
Dockerfile file in the file tree to open it in the Editor pane. Make sure that this is the same Dockerfile that's inside the ml-r directory:Figure 2.92 – Opening the Dockerfile inside the ml-r directory
Here, we can see that there's a Dockerfile inside the ml-r directory. Remember that we created an empty Dockerfile in the Setting up the Python and R experimentation environments recipe. Clicking on it in the file tree should open an empty file in the Editor pane:
Figure 2.93 – Empty Dockerfile
Here, we have an empty Dockerfile. In the next step, we will update this by adding four lines of code.
- Update the
Dockerfile with the following block of configuration code:FROM arvslat/amazon-sagemaker-cookbook-r-base:1
COPY train /usr/local/bin/train
COPY serve /usr/local/bin/serve
COPY api.r /usr/local/bin/api.r
Here, we are planning to build on top of an existing image called amazon-sagemaker-cookbook-r-base. This image already has a few prerequisites installed. These include the rjson, here, and plumber packages so that you don't have to worry about getting the installation steps working properly in this recipe. For more details on this image, check out https://hub.docker.com/r/arvslat/amazon-sagemaker-cookbook-r-base:
Figure 2.94 – Docker Hub page for the amazon-sagemaker-cookbook-r-base image
Here, we can see the Docker Hub page for the amazon-sagemaker-cookbook-r-base image.
Tip
You can access a working copy of this Dockerfile in the Amazon SageMaker Cookbook GitHub repository: https://github.com/PacktPublishing/Machine-Learining-with-Amazon-SageMaker-Cookbook/blob/master/Chapter02/ml-r/Dockerfile.
With our Dockerfile ready, we will proceed by using the Terminal until the end of this recipe.
- You may use a new Terminal tab or an existing one to run the next set of commands:
Figure 2.95 – New Terminal
The preceding screenshot shows how to create a new Terminal. Note that the Terminal pane is right under the Editor pane in the AWS Cloud9 IDE.
- Navigate to the
ml-python directory containing our Dockerfile:cd /home/ubuntu/environment/opt/ml-r
- Specify the image name and the tag number:
IMAGE_NAME=chap02_r
TAG=1
- Build the Docker container using the
docker build command:docker build --no-cache -t $IMAGE_NAME:$TAG .
The docker build command makes use of what is written inside our Dockerfile. We start with the image specified in the FROM directive and then proceed by copying the file files into the container image.
- Use the
docker run command to test if the train script works:docker run --name rtrain --rm -v /opt/ml:/opt/ml $IMAGE_NAME:$TAG train
Let's quickly discuss some of the different options that are used in this command. The --rm flag makes Docker clean up the container after the container exits, while the -v flag allows us to mount the /opt/ml directory from the host system to the /opt/ml directory of the container:
Figure 2.96 – Result of the docker run command (train)
Here, we can see the logs and results after running the docker run command.
- Use the
docker run command to test if the serve script works:docker run --name rserve --rm -v /opt/ml:/opt/ml $IMAGE_NAME:$TAG serve
After running this command, the plumber API server will start successfully, as shown in the following screenshot:
Figure 2.97 – Result of the docker run command (serve)
Here, we can see that the API is running on port 8080. In the base image we used, we added EXPOSE 8080 to allow us to access this port in the running container.
- Open a new Terminal tab:
Figure 2.98 – New Terminal
As the API is running already in the first Terminal, we have created a new Terminal here.
- In the new Terminal tab, run the following command to get the IP address of the running Plumber API:
SERVE_IP=$(docker network inspect bridge | jq -r ".[0].Containers[].IPv4Address" | awk -F/ '{print $1}')
echo $SERVE_IPWhat happened here? Check out the How it works… section of this recipe for a detailed explanation of what happened in the previous block of code! In the meantime, let's think of this line as using multiple commands to get the IP address of the running API server. We should get an IP address equal or similar to 172.17.0.2. Of course, we may get a different IP address value altogether.
- Next, test the
ping endpoint URL using the curl command:curl http://$SERVE_IP:8080/ping
We should get an OK after running this command.
- Finally, test the
invocations endpoint URL using the curl command:curl -d "1" -X POST http://$SERVE_IP:8080/invocations
We should get a value similar or close to 881.342840085751 after invoking the invocations endpoint.
Now, let's see how this works!
How it works…
In this recipe, we built a custom container image with our Dockerfile. In our Dockerfile, we did the following:
Using the arvslat/amazon-sagemaker-cookbook-r-base image as the base image allowed us to write a shorter Dockerfile that focuses only on copying the train, serve, and api.r files to the directory inside the container image. Behind the scenes, we have already pre-installed the rjson, plumber, and here packages, along with their prerequisites, inside this container image so that we will not run into issues when building the custom container image. Here is a quick look at the Dockerfile file that was used for the base image that we are using in this recipe:
FROM r-base:4.0.2
RUN apt-get -y update
RUN apt-get install -y --no-install-recommends wget
RUN apt-get install -y --no-install-recommends libcurl4-openssl-dev
RUN apt-get install -y --no-install-recommends libsodium-dev
RUN R -e "install.packages('rjson',repos='https://cloud.r-project.org')"
RUN R -e "install.packages('plumber',repos='https://cloud.r-project.org')"
RUN R -e "install.packages('here',repos='https://cloud.r-project.org')"
ENV PATH "/opt/ml:$PATH"
WORKDIR /usr/local/bin
EXPOSE 8080
In this Dockerfile, we can see that we are using r-base:4.0.2 as the base image. If we were to use a higher version, there's a chance that the plumber package will not install properly, which is why we had to stick with a lower version of this base image.
With these potential blockers out of the way, we were able to build a custom container image in a short amount of time. In the Using the custom R algorithm container image for training and inference with Amazon SageMaker Local Mode recipe of this chapter, we will use this custom container image when we do training and deployment with reticulate so that we can use the SageMaker Python SDK with our R code.
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