Glossia FEniCS Example

Requirements

• docker

• Python3 (via pip3)

  • glot
  • glossia.comparator

Instructions

Running without Glossia

• Clone this repository, containing toy surfaces and a basic FEniCS solver

• Run

  glot setup . code/*
  

  This prepares the directory with the necessary tools for running a Glossia container offline.

• Run

  sudo ./setup.sh
  sudo ./run.sh
  

This should download the necessary image from DockerHub and execute the simulation in the container. Output should appear in output/run/. The code outputs most run-time numerics into the results/ subdirectory.

Running with local Glossia

Once you have <https://github.com/go-smart/glossia-server-side/> up and running, from the previous layout, run

glot launch -i input/tumour.stl -i input/vessel1.stl -i input/vessel2.stl -i input/organ.stl --tmp-directory ${GLOSSIA_SERVER_SIDE_LOCATION}/transferrer original.xml code/*

This is actually a similar command to the launch above, but as glot does not process the original.xml definition, (it leaves this to be done by Glossia) the user must specify the locations of any needed input surfaces. Moreover, the tmp directory is given to allow exchange of files without a Glossia-side file server.

The results may be retrieved, as usual for Glossia, with the command,

glot results ${SIMULATIONID}

If successful, this will output a TGZ bundle of simulation results in the local directory. For more diagnostic data, check the glot documentation for glot diagnostic.