Currently, Docker is required to run FEniCS-MyoSim. Docker is a program that creates “containers” that allows code to be run in a controlled environment using the host computer’s resources. A switch from Docker to Singularity may be made in the future to allow the code to be executed on a computing cluster. To get started, follow these steps (Note, command line text can be copied and pasted into a terminal, but items in < > need to be replaced with user specific information):

• Install Docker
• Clone Repository
• Load Image
• Create Container
• Enter Container Command Line

Install Docker

Install the latest version of Docker.

Clone the FEniCS-MyoSim Repository

All of the source code to run FEniCS-MyoSim is located on a GitHub repository. Users experienced with Git can do this through a command line approach. Otherwise, a .zip file from the repository can be downloaded. Unzip the folder in your desired directory.

Load Image

A Docker image is a copy of the environment used to execute the code. This allows standardization of the modules and their versions used by FEniCS-MyoSim. The image that needs to be loaded by Docker is in the MMotH-Fenics-UK repository, saved as MMotH-Vent.tar. We need a way to distribute this outside of our lab From the command line, with Docker running, navigate to where this file is saved on your machine, and execute the following:

docker load < MMotH-Vent.tar

Note, this step takes time. Once the step is complete, execute:

docker images

to check that the MMotH-Vent image has been loaded correctly.

Create Container

Once Docker has loaded the image, a container can be created in which FEniCS-MyoSim will be executed. To access the cloned repository, the directory containing FEniCS-MyoSim source code needs to be shared with the container. To create the container, and mount the directory to be shared, execute the following at the command line:

sudo docker run -it --mount src=</path_to_FEniCS-MyoSim_directory_on_machine>,target=/home/fenics/shared/,type=bind <image_name>

The directory structure within the new container is

/home/  
|  +-- fenics/  
|  |  +-- demo/  
|  |  +-- local/  
|  |  +-- shared/  

and the contents of the FEniCS-MyoSim repository will be located under the shared directory.
Verify that the container has been created by executing the following at the command line:

docker ps -a

This displays a list of all containers created on the local machine.
Once the container has been created, it needs to be started. Using “Container ID” from the previous command output,

docker start <CONTAINER_ID>

Enter Container Command Line

Now that the container is created and started, the following command takes the user to a command line within the container to execute the FEniCS-MyoSim code. Replace CONTAINER_NAME with the name of the container as seen from the docker ps -a command.

sudo docker exec -ti -u fenics <CONTAINER_NAME> /bin/bash -l

It is recommended to create an alias shortcut to issue this command regularly. Once the container is created from the image, the regular workflow to use FEniCS-MyoSim is:

• Start Docker
• From the command line, start the created container using docker start <CONTAINER_ID>
• Enter the command line in the container using sudo docker exec -ti -u fenics <CONTAINER_NAME> /bin/bash -l.
• When finished, exit the container by issuing the exit command.

Demos »