Stokes flow in porous media

Gerard Gorman

Summary

• Unstructured mesh generation.• Finite element model for single phase Stokes

flow.• Research data management and deep

integration.• Apps for the lab.

Unstructured mesh generation• Very active community in bioengineering and medicine

developing methods for generating high quality unstructured meshes from 3D images.

• First tried Tarantula meshing software. Generates good quality meshes based on an octree approach. However, it is proprietary software which is actually being discontinued by the developer. Unclear if it would be possible to mesh large images,

• Developed bespoke tool using the CGAL library. Generates high quality meshes. Straightforward to develop. Open source license.

• May get very demanding for memory. However, we have a SGI Altix UV100 at IC with 5TB of RAM.

Finite element model

• For fast exploration of different numerical discretisations and solvers we used FEniCS.– Solved implicitly (ie single matric for pressure and velocity).– The MINI element proved to be the most robust for this

application.– Iterative solvers, including AMG, did not perform

satisfactory. Used direct solver (MUMPS).– Runs in parallel using MPI.

• IC developing alternative backend that will also support accelerators (e.g. GPU’s, Intel Phi).– This will replace the core of Fluidity in the future.

Research data management and deep integration.

• Open data access getting lots of attending and technology is catching up.– Figshare free offers storage, DOI referencing for data and

much more. Pay option for private data.• Aim is to curate primary data products (micro-CT

images) and derived data (flow calculations) making them accessible, persistent and citable.

• Integrate with lab and analysis software so that data can be uploaded and interacted with seamlessly – make it routine, not troublesome.

Apps for the lab.

• The platform would be used for both open research and commercial purposes.– In research mode:

• Micro-CT image data is uploaded along with meta-data and a DOI is generated.• Mesh generation, flow calculations and analysis are triggered on Cloud compute

resources.• Derived data uploaded, DOI’s generated and linked to primary data source.• Provided as a service to the community so anyone can upload image data, get the

analysis in return for free access to this data for the community.

– In commercial mode:• An enterprise version of the platform is installed on a private Cloud.• Primary data and analysis only available to the owner.

• Interface developed using HTML5 and ParaViewWeb allowing deployment on desktop’s and handheld devices. ParaViewWeb will allow visualisation of massive datasets on handheld devices.