Building using docker

Author

Fulton, Beth (Environment, Hobart)

The Atlantis truck code now includes a Dockerfile that can be used to build an environment to build and run Atlantis. It will not pull an existing container but build the container and run it using the Dockerfile.

You will first need a working docker install - see https://docs.docker.com/install/ for information on this. Then just use the following (Note from Beth: on a Mac I have to have the Docker open and then do the following at the command line in the terminal):

# build the docker image

make build


# run the example model

make run

Changing the model run:

To change the model run in the docker image you will need to edit the Makefile - the default version should look like:

IMAGE=atlantis_docker
USER=$(id -u)
GROUP=$(id -g)

run: build
     docker run -v $(PWD)/example:/app/model --user $(USER):$(GROUP) atlantis_docker

build:
    docker build --build-arg REGISTRY=docker-registry.it.csiro.au -t $(IMAGE) .

clean:
    docker system prune -f

Looking at the existing dockerfile:

FROM debian:jessie
RUN apt-get update && apt-get install -yq build-essential autoconf libnetcdf-dev libxml2-dev libproj-dev subversion valgrind


COPY atlantis /app/src
RUN cd /app/src && aclocal && autoheader && autoconf && automake -a && ./configure && make && make install

RUN mkdir -p /app/model
CMD  cd /app/model/ && ./RunAtlantis.sh

You can see the last line will run a script called RunAtlantis.sh in the /app/model folder within the docker image. You can use bind mount a volume to point to your model files. In the make file change the run: build line to point to the directory where your run is, for example:

run_settas: build
     docker run -v /home/bec/BackedUp/Atlantis/runFiles/SETas_model_New_trunk_Pristine/SETas_model_New_Trunk:/app/model --user $(id -u):$(id -g) atlantis_docker

This assumes that you have a script called runAtlantis.sh in the /home/bec/BackedUp/Atlantis/runFiles/SETas_model_New_trunk_Pristine/SETas_model_New_Trunk folder . This script should not contain any code to compile Atlantis, just the command to run it:

#!/bin/bash

#valgrind --log-file=valgrind%p.log --track-origins=yes --leak-check=full --track-fds=yes --show-reachable=yes 
atlantisMerged -i INIT_VMPA_Jan2015.nc 0 -o outputSETAS.nc -r VMPA_setas_run_fishing_F_Trunk.prm -f VMPA_setas_force_fish_Trunk.prm -p VMPA_setas_physics.prm -b VMPA_setas_biol_fishing_Trunk.prm -h VMPA_setas_harvest_F_Trunk.prm  -s SETasGroupsDem.csv -q SETasFisheries.csv -d outputFolderPristine

Note - if you want to use valgrind to check the code just uncomment the valgrind line. Valgrind is already installed in the docker image.