Minutes 10 July 2006

Present: Shane, Karl, Travis.

An "audio recording":ftp://ftp.bioeng.auckland.ac.nz/cmiss/opencmiss/meeting-2006-07-10.ogg is available.

Audio recording of meetings

• This is the last meeting that will be recorded unless more interest is shown.

MPI Test problem proposal and implementation

• cm performs much better with "grid-based fem" than with the original advection-diffusion fem code.
  • The problem solved is not the test problem (initial conditions are not set, boundary conditions are Neumann, and there is an Euler integration of a cubic cell model) but provides an indication of what to expect if the test problem were solved similarly.
    • a 1000x1000 element problem with 50 time steps of 0.001 and a maximum of 4 iterations in each CG solve took 82 seconds using 1.1 GB resident memory (2.6 virtual). The single matrix assembly took 19.4 seconds.
    • A similar libmesh problem but with matrix assembly at each time step took 379 seconds using 1.3 GB resident memory (1.4 virtual).
• Sundance
  • Doesn't have a high level time-stepping object.
  • Nice high level classes for describing the mathematics of the problem (in a variation form).
  • Easy to get it to work, even for a problem for which it may not have been intended.
  • Results on Using Sundance seem reasonable in comparison to libmesh given that it is doing more iterations in each linear solve.
  • Code that uses Sundance can be written in an easy to read manner.
  • Currently provides only Triangular/tet elements but quads/hexs shouldn't be a problem.
  • Not sure about basis functions in addition to Lagrange.
  • No AMR.
  • A few seg faults happening
    • solver reaches max iterations
    • running with 4 processes
  • Feels a bit like still an academic project; not sure what applications it is being used for.
  • Used for Navier Stokes.
  • High level operators provided by epetera
    • Perhaps this could be imported to other packages.

Libmesh

• Shane wants to establish a dialog with libmesh developers and suggests asking about assembling only once.
  • Karl says this might be in documentation; we should read this first. If we want to establish a dialog then we should get to the point and explain our position.
• We want to appear as developers (not like people building a Windows gui).
• We could ask what would be involved in parallelization of mesh

What about other packages?

• LifeV and freepooma have not yet been considered.
• Do we check these out now before spending more time on libmesh?
• Have we enough evidence that using an existing package is sensible?

Next meeting 11am Thursday 20 July.