Docker for Clawpack¶
Using Version 5.9.0 or above¶
A new docker image has been created for v5.9.x. This image includes Clawpack v5.9.0 and a number of packages of primary interest to GeoClaw users.
It also now includes the packages and files needed to execute the Jupyter notebooks from the book Riemann Problems and Jupyter Solutions. These notebooks can be found in the riemann_book directory.
To download an image:
$ docker pull clawpack/v5.9.0_dockerimage:release
To create a container and run it:
$ docker run -i -t -p 8889:8889 --name clawpack-v5.9.0_container \
You can change the container name if you wish, and also the port 8889 (on which jupyter notebooks might be served, see below).
You should now see a prompt like:
indicating that you are in the container, logged in as user jovyan.
Once logged in to the container, you should find a directory $HOME/clawpack-v5.9.0 that contains the Clawpack installation (including the current master branch of the Clawpack Applications repository).
Stopping a container¶
You can exit a container (after using ctrl-C to quit the jupyter server if one is running) via:
at the jovyan $ prompt.
Restarting a container¶
You can restart the container via:
docker start -a -i clawpack-v5.9.0_container
Running Jupyter notebooks¶
The form of run command suggested above also allows you to run Jupyter notebooks from port 8889 on your own computer (or whatever port you specified when creating the container).
To start the sever, in the docker container (at the jovyan $ prompt) run this command:
jupyter notebook --ip=0.0.0.0 --port=8889 --no-browser
Then open a browser (on the host machine) to:
replacing TOKEN with the token that should have printed out when you started the server.
This will open to the top level of $HOME, and you can then navigate to wherever the notebooks are you want to run, e.g. the sample ones in the apps repository can be found at clawpack-v5.9.0/apps/notebooks.
PyClaw users might want to start with clawpack-v5.9.0/apps/notebooks/pyclaw/Acoustics-1D.ipynb.
GeoClaw users might want to try running clawpack-v5.9.0/apps/notebooks/geoclaw/chile2010a.ipynb, which exercises most aspects of GeoClaw.
Moving files between the docker container and the host machine¶
Often you want to run the code on Docker and then transfer the resulting output files, and/or the plots generated, back to the host machine (e.g. some directory on your laptop). You can use the –volume flag when running a container to accomplish this, see docker volume documentation.
For example, if you have created a directory $HOME/docker/volumes/work on your computer (it can have a different name but should be in $HOME/docker/volumes/) then adding:
to your docker run command will map this directory to /home/jovyan/work in the docker container. So you can move Clawpack output or plots to that directory in order to have access to them from your host computer.
Putting this together with previous options, here’s a sample command that creates and runs a geoclaw-based container with this mapping and also allowing us to start a Jupyter server:
$ docker run -i -t -p 8889:8889 \
-v $HOME/docker/volumes/work:/home/jovyan/work \
--name clawpack-v5.9.0_container \
Some other useful docker commands¶
See the docker command line documentation or any of the tutorials available on-line for more details, but here are a few particularly useful commands:
docker ps -a # list all containsers
docker rm clawpack-v5.7.1_container # remove a container
docker images -a # list all images
docker rmi clawpack/v5.7.1_dockerimage:release # remove an image
docker prune # remove all images not used by any container
Creating your own docker image¶
If you want to create a new docker image that includes other software in addition to Clawpack, you can find the Dockerile used to create the docker image on dockerhub in the repository https://github.com/clawpack/docker-files.
This might be useful if you want to distribute your own code that depends on Clawpack in a form that’s easy for others to use.
You can also create a Dockerfile that uses the already-build Clawpack 5.9.0 on Dockerhub by starting the Dockerfile with:
and then adding anything addition you want in the image, such as other Python modules you need or your own application code. You may need to specify USER root in order to install some things, and then switch back to USER jovyan at the end. For an example, see how clawpack/docker-files/Dockerfile_v5.7.0_geoclaw is built on top of clawpack/v5.7.0_dockerimage:release.
Dockerfiles for binder¶
The username jovyan was chosen so that you can use this docker image also for starting up a Jupyter notebook server on binder. You can do this by including a simple Dockerfile at the top level of your repository that uses the dockerhub image, as above. See this repository for a simple example: https://github.com/rjleveque/test_binder.
The repository for the book Riemann Problems and Jupyter Solutions also uses this approach.
See the binder documentation for more details on using Dockerfiles there.