FEniCS'15 Workshop at Imperial College London, 29th June - 1st July 2015

Hale, Jack S.

Li, Lizao (Larry)

Wells, Garth N.

Apollo (Cambridge)

FEniCS in Linux ContainersJack S. Hale (University of Luxembourg), Lizao Larry Li (University of Minnesota),Garth N. Wells (University of Cambridge)jack.hale@uni.lu, lixx1445@umn.edu, gnw20@cam.ac.ukIntroductionDocker allows application developers to build, ship and run their application nearly any-where. We have built three Docker images with FEniCS that are suitable for both end-users and developers:1. fenicsproject/stable-ppa: The latest version from the Ubuntu PPA.2. fenicsproject/dev-env: An environment for building FEniCS from source.3. fenicsproject/dev: FEniCS compiled weekly from master.With one command, you can launch a lightweight container that provides a consistentand performant environment for developing or using FEniCS.You will like using FEniCS with Docker because you can: Run the same image on any platform. See precisely how an image is built. Add to or modify the image, or use them as a base for your own custom image. Tag an image and send it to your colleagues so that they can run your complex applica-tion immediately. Push your image to your favourite commercial cloud computing service and run itthere. Distribute your image with your paper so that others can reproduce your results.Try it yourselfDocker is available on most platforms, including Linux, Mac OS X and Windows. Youcan install it by following the instructions for your platform at http://docker.com. Youcan then launch a FEniCS environment using the command:docker run -ti fenicsproject/stable -ppa:latestHow do I . . . ?Share a folder with the containerWhen you launch the container for the first time you can share any directory on the hostinto the container:docker run -ti -v $(pwd ):/ shared \fenicsproject/stable -ppa:latestThis will share the current working directory into the container.Launch another terminal in a running containerFirst, check which containers are runningdocker psUsing the CONTAINER ID field, launch a new bash session using:docker exec -ti b8f51c sudo -u fenics /bin/bashBuild FEniCS from sourceWe provide an image with a ready-to-go development environment for building FEniCS,including an easy-to-modify script to build FEniCS from the master repositories.Launch a development container using the command:docker run -ti fenicsproject/dev -env:latestThen update the FEniCS build in the container using:$ update_fenicsFEniCS is built against up-to-date and optimised stable versions of PETSc and SLEPc.See how you built the imagesOur Docker images are automatically built in the cloud on Dockerhub directly from theDockerfile, the ‘recipe’ that defines every Docker image. The FEniCS Dockerfiles aremaintained at https://github.com/FEniCS/docker. Every time we change the Docker-file, a new image is automatically built. If you visit https://registry.hub.docker.com/u/fenicsproject/stable-ppa/dockerfile/ and click on ‘Dockerfile’ you can see precisely whichsteps were used to build the image that you are running.Install more software into the containerYou have two options. The first is to manually install the software into the container,stop the container, then commit and tag the a new image. The second way is to learn howto write your own Dockerfile. For brevity, we only cover the first approach here. If youwant to learn about writing your own Dockerfile using ours as a base then take a look athttp://docker.com.Begin by launching a container with a name:docker run -ti --name="mycontainer" \fenicsproject/stable -ppa:latestNow install the software you want and exit the container:$ sudo apt -get install python -pandas$ exitCommit the image:docker commit mycontainerThe above command gives you a hash of the commit. You can tag this hash so that it iseasy to remember.docker tag f749 jhale/mycontainer:latestNow you can push it to Dockerhub so your colleague can use it too:docker push jhale/mycontainer:latestYour colleague just has to run:docker run -ti jhale/mycontainer:latestNo performance penaltyWe tested our Ubuntu-based Docker image against a bare-metal Ubuntu build, with bothcompiled against the same system packages on the same Intel Xeon-based machine. For arange of benchmarks that tested assembly, linear solvers and IO, we have found almost nomeasurable performance difference between the Docker and bare-metal builds, in serialor in parallel using MPI.IOPoissonelasticitymultigridbenchmark01020304050time (s)Docker vs native for various FEniCS benchmarksDockernativeBecause of Docker’s layered filesystem, additional containers take up only a few kilobytesof extra space and launch almost instantly. This means you can happily have hundreds ofcontainers, one for every project if you like, on your development laptop.ConclusionsWe have covered a small number of ways that you can integrate Docker into a powerfulworkflow for repeatable, easy-to-use and portable scientific computing using FEniCS. Forfurther reading we recommend the Docker documentation at http://docker.com and theDocker cheat sheet at https://github.com/wsargent/docker-cheat-sheet.

FEniCS in Linux Containers

We present a collection of Docker images for running FEniCS in Linux containers. With one command, a user can launch a lightweight container that provides a consistent environment for using or developing FEniCS. Once the initial image has been fetched, 'FEniCS terminals' can be launched near-instantly. We show through a range of tests that performance within a container is to equal to that on the host system. Moreover, MPI programs can be run from inside the container, and host CPU vectorisation features can be exploited. In practice, container versions of FEniCS will be faster than user installations as the container images can be carefully tuned for performance. Live demonstrations of user and developer container use will be presented. The containers are built and hosted on Docker Hu

Hale, Jack

Li, Lizao

Open Repository and Bibliography - Luxembourg

http://creativecommons.org/licenses/by-nc-nd/2.0/uk/

FEniCS in Linux Containers

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Apollo (Cambridge)

Open Repository and Bibliography - Luxembourg