Containerizing a model

For this step, you will want to navigate back to your Container folder.

1. Verify files

Make sure your folder has all of the necessary files from before.

Reconstruction
├── Container
│   ├── adapter.R
│   ├── main.R
│   ├── predetermined_inputs
│   │   ├── some_data.csv

2. Create the Dockerfile

A Dockerfile is a file that is essentially a list of instructions Docker uses to create a container. Luckily, we don’t need to know much about how to create the file by hand as presto create does it for us! All it takes in is the language we are using and the file that holds all of our reconstruction code.

presto create

emily@VM:~/.../LMRt-container$ presto create
What is the command to run your main file?
Here are some examples:
- python3 main.py
- Rscript main.R
- sh main.sh

> : python3 main.py
Dockerfile created!

You should now see a Dockerfile in your directory:

Reconstruction
├── Container
│   ├── adapter.R
│   ├── Dockerfile
│   ├── main.R
│   ├── predetermined_inputs
│   │   ├── some_data.csv

The Dockerfile should look like the following:

FROM rocker/tidyverse

# Copy all files to the root directory of the container
COPY . /

# Download GitHub packages and their dependencies
RUN apt-get -y update
RUN apt-get -y install libcurl4-gnutls-dev libxml2-dev libssl-dev \
                       libudunits2-dev libgdal-dev gdal-bin libproj-dev \
                       proj-data proj-bin libgeos-dev libfontconfig1-dev \
                       libglpk-dev

RUN R -e 'install.packages(c("usethis", "devtools", "sf", "leaflet", "raster", \
                            "leafem", "pracma", "igraph", "egg", "httpuv", \
                            "rjson", "Rook"))'

RUN R -e 'devtools::install_github("neotomadb/neotoma2")'
RUN R -e 'remotes::install_github("nickmckay/lipdr")'
RUN R -e 'remotes::install_github("nickmckay/compositer")'
RUN R -e 'remotes::install_github("nickmckay/geochronr")'

SHELL ["/bin/bash", "--login", "-c"]

# run the command in the context of the environment we made
CMD Rscript main.R

Add any GitHub packages HERE IN THE DOCKERFILE as pictured above

3. Build the Docker image

More information about what Docker Images are can be found here. Images are essentially what your container uses to run so they need to be built first.

Run presto build <name of your container> to start building the image. This process can take a while. You should get a message when the image is done building.

This process will take time to complete. On my personal machine it took 8-10 minutes but it might take more on other systems. You can leave this running in the background until it has completed.

presto build model

mumbi@WSL:~/.../r-container$ presto build model
Building the image.... This might take a while

Use this command to see the logs for the build process:

docker build --no-cache --progress=plain -t <my-image> .

When the image has finished building you should see a lot of Docker logs as well as the following message Building model image complete

We are now ready to start running the reconstruction model!

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