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Minutes 19 June 2006

Present: Shane, Karl, Travis, Poul.

An "audio recording": is available.

MPI Test problem proposal and implementation

  • Karl updated the suggested test problem:
    • made the time step implicit as a linear solve is required for the non-diagonal mass-matrix anyway.
    • changed the solution to make boundary conditions homogeneous.
    • No feedback, so will go ahead with this problem.
  • libmesh has example that is very close to what we want.
    • Easy to change solver, preconditioner, tolerance, and probably maxiterations.
    • One thing we would want to change is that matrix assembly is done at each time step.
    • Another thing is the penalty method as discussed on OpenCMISS/libMesh Development Notes.
      • Travis is happy with the method.
      • Karl is not.
    • but can get something going fairly quickly and improve after we have a base to improve on.
  • Need to set up cm examples as well.
    • cm has time-dependent heat equation.
    • Could also possibly use "grid-based fem" monodomain model with a cell model that does nothing.

Libmesh and visualization

  • Shane investigated visualization for libmesh.
    • Where is solution information collated before writing out the solution?
    • cmgui currently knows when a (some component of) field has changed and can automatically update aspects that depend on this.
    • Integrating with libmesh might require an explicit function to update graphics from libmesh data. e.g. create isosurface from mesh and solution.
  • GMV is a gui (executable only) available to display libmesh output.


  • provides a debugger that has MPI support. development

  • job description for new position may be moving away from web development as Gareth may be looking after web stuff.
  • Gareth (logged in as stevens) fixed the long-standing "Missing emails for this tracker" bug which meant no notification of new bugs.


  • Shane: want to make a decision on a framework ASAP (last February).
    • Shane away next week but keen to set up some criteria to make decisions on framework.
  • Criteria
    • execution speed
    • language
    • time to develop
    • user community for support
    • flexibility

SUR cluster

  • meant to arrive in NZ on 30 June.


  • We should buy a microphone for the meeting room.