miricle_docker

Scripts to create Docker images with Anaconda (https://www.continuum.io/what-is-anaconda) and MIRICLE (www.miricle.org).

The "Dockerfile_<xyz>" are files required by Docker to build images. The shell scripts provide examples of docker commands that will build the images from the Dockerfiles.

Installing Docker

These scripts require Docker to be pre-installed. To get started, visit: https://www.docker.com/get-docker

Available MIRICLE Docker images

These scripts provide 4 different MIRICLE Docker images:

• stable : installs the current stable build of MIRICLE.
• test : installs the "test" build of MIRICLE, used for testing of upcoming releases.
• devel : installs the latest "developer" build of MIRICLE, used in development.
• prep : installs requirements for MIRICLE, and downloads MIRICLE install script; used for debugging install script and for interactive / custom installs.

How Docker works

The scripts provided here can be used to create a so-called Docker "image", which in these case will represent a template version of a Unix-machine with MIRICLE pre-installed, together with its key dependencies (Anaconda, gcc, etc.).

Once a Docker image has been built, you can create as many instances (so-called Docker "containers") of this pre-build machine to use for running the MIRICLE software.

Building a MIRICLE Docker image

To get started:

1. Ensure Docker is installed and running.
2. In Docker Preferences, ensure it has 4-8 GB RAM allocated, to run MIRI simulations.
3. Download / clone this repo, and step into directory.

git clone https://github.com/vcgeers/miricle_docker

cd miricle_docker

4. To build e.g. the "stable" MIRICLE image, run:

build_miricle_stable.sh

Running a MIRICLE Docker container

A simple example to launch an instance of the MIRICLE "stable" image:

docker run -it --rm miriec/miricle_stable /bin/bash

Example to launch an instance of MIRICLE "test" image, while creating a link between a "scratch" directory on host machine, and the "simulations" path inside the Docker container. By default, simulations run within the Docker container will store output under the "/root/simulations" path, and the link will ensure that those simulations are available on the host machine, and will persist even after the container is removed.

docker run -it --rm -v <absolute_path_to_local_scratch_directory>:/root/simulations miriec/miricle_test /bin/bash

Example to launch an instance of MIRICLE "devel" image, while creating a link between local repository checkouts and the "repos" path inside the Docker container. This can be used by developers to e.g. install a custom revision into conda / MIRICLE.

docker run -it --rm -v <absolute_path_to_local_repositories>:/root/repos miriec/miricle_devel /bin/bash

Building and running a specific version of MIRICLE

By default, the build scripts will install the latest available version of MIRICLE. To build and run a specific version, e.g. 30, of MIRICLE:

1. build_miricle_test.sh 30
2. docker run -it --rm miriec/miricle_stable:30 /bin/bash

To find available versions:

• Linux: Stable, Test, Devel
• Mac: Stable, Test, Devel

Useful Docker commands

Command line help:

docker help

To check which Docker images are available on your system:

docker images

To check which Docker containers are running/stopped:

docker ps -a

To remove a stopped container:

docker rm <id_of_container>

To remove an image:

docker rmi <id_of_image>

To remove unused data from Docker cache (unused images, containers, volumes, networks):

docker system prune