Chaster

Dockerfiles for Chaste

Quickstart

To build and launch a contianer with a specific chaste version run:

build_images.sh [VERSION] [REPO_TAG] [NCORES]

e.g.:

For the latest release: build_images.sh
Master branch: build_images.sh master master 4
Older release: build_images.sh 3.4

Installing and running Chaste

Install Docker and increase the number of CPUs as you would like, and amount of RAM to around or above 4GB.

N.B. If you don't increase the amount of available RAM from the default 2GB then compilation will fail with strange errors!

Build the docker container with the chaste dependencies

docker build -t chaste:dependencies .

Run the container

docker run -it -v $(pwd):/usr/chaste chaste:dependencies

TODO

Test GitHub build: docker build https://github.com/docker/rootfs.git#container:docker Setup Travis-CI Consider naming system e.g.:

dependencies/chaste or chaste/dependencies:latest
release/chaste:3.4 or chaste/release:3.4

Creating your own Chaste build

Clone and build the Chaste code

Before running make, set the following options in ccmake:

Change CMAKE_BUILD_TYPE from Debug to Release
Chaste_ERROR_ON_WARNING OFF
Chaste_UPDATE_PROVENANCE OFF Use -D <var>:<type>=<value> The number after -j is the number of cores to use.

git clone -b develop https://chaste.cs.ox.ac.uk/git/chaste.git src
cd build
cmake -DCMAKE_BUILD_TYPE:STRING=Release -DChaste_ERROR_ON_WARNING:BOOL=OFF -DChaste_UPDATE_PROVENANCE:BOOL=OFF /usr/chaste/src
make -j4

This can be achieved by changing to the build directory and running the script: build_chaste.sh

[Optional] Build and run the Continuous Test pack

https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/CmakeFirstRun

make -j4 Continuous
ctest -j4 -L Continuous

Compiling and running simulations

https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/UserProjects

git clone https://github.com/Chaste/template_project.git
cd template_project
python setup_project.py

This can be done with the script: new_project.sh

To check that your user project compiles correctly, at the command line navigate to a build folder (outside the Chaste or project source folder - see ChasteGuides/CmakeBuildGuide) and run

ccmake path/to/Chaste

Create new “Test” header files for simulations in the projects folder then run:

cd ~/build/
cmake ~/src
make -j4 TestProject && ctest -V -R TestProject

This can be achieved by changing to the build directory and running the script: build_project.sh

mirams/chaste-docker