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Building Options

.. seealso:: `docker build <https://docs.docker.com/engine/reference/commandline/build/>`_
             reference documentation |br|
             (Probably a safer choice for information!)

ApPredict-related Containers

This section refers to :

  1. appredict-no-emulators
  2. appredict-with-emulators

Warning

It's important to note that even when using 32 processors it can 30+ mins to build! |br| Equally, building appredict-with-emulators uses a lot of RAM as |ApPredict| loads files >1Gb into RAM. So better not to use all available processors for this step.

Note

Within the :file:`Dockerfile`s we have not enforced version-controlling of images or dependencies (e.g. by specifying the base image tag with hash, or by using specific versions of software, e.g. libhdf5-dev version X), as the built container represents a unique snapshot in time. See No version-controlling in appredict-chaste-libs Dockerfile.

Note

These instructions cover the case for building and testing |ApPredict| containers locally, rather than for uploading to DockerHub.

user@host:~> mkdir tmp && cd tmp
user@host:~/tmp> git clone https://github.com/CardiacModelling/appredict-docker
user@host:~/tmp> cd appredict-docker/appredict-no-emulators
user@host:~/tmp/appredict-docker/appredict-no-emulators>

          Edit the Dockerfile to a new appredict tag value

user@host:~/tmp/appredict-docker/appredict-no-emulators> docker build --build-arg build_processors=<processors> -t appredict-no-emulators:<new version, e.g. mytest1> .
user@host:~/tmp/appredict-docker/appredict-no-emulators> docker run -it --rm appredict-no-emulators:<new version, e.g. mytest1>

          Verify below the ApPredict commit value against the commit hashes at https://github.com/Chaste/ApPredict/tags

bash-4.4$ apps/ApPredict/ApPredict 2> /dev/null | grep 'ApPredict is based on commit'
bash-4.4$ exit

user@host:~/tmp/appredict-docker/appredict-no-emulators> cd ../appredict-with-emulators
user@host:~/tmp/appredict-docker/appredict-with-emulators>

          Edit the Dockerfile `FROM` clause to appredict-no-emulators:<new version, e.g. mytest1>

user@host:~/tmp/appredict-docker/appredict-with-emulators> docker build --build-arg build_processors=<processors> -t appredict-with-emulators:<new version, e.g. mytest1> .

|ap-nimbus-client-direct| Container

This section refers to :

  1. ap-nimbus-client-direct

Perhaps the most important thing to keep in mind when building a local container is to temporarily modify the :file:`docker/Dockerfile` to copy the content of the local dir (which you've probably just modified a bit for this change), e.g.

user@host:~> mkdir tmp && cd tmp
user@host:~/tmp> git clone https://github.com/CardiacModelling/ap-nimbus-client
user@host:~/tmp> cd ap-nimbus-client
user@host:~/tmp/ap-nimbus-client>

          Edit the docker/Dockerfile to copy the local content
          e.g. #RUN git clone --recursive --branch master --depth 1 https://github.com/CardiacModelling/ap-nimbus-client.git
               COPY / /opt/django/ap-nimbus-client

user@host:~/tmp/ap-nimbus-client> docker build -f docker/Dockerfile -t ap-nimbus-client-direct:<new version, e.g. mytest1> .

Why not use Chaste/chaste-docker?

It would be possible to use the "offical" Chaste-endorsed dependency container as a base image to build |appredict-no-emulators|, etc., on -- and up to around 2021 we'd been using an Alpine Linux distribution base. Now, however, we're using the preferred Debian container to enable easy install of dependency packages.