[petsc-users] Mat preallocation in case of variable stencils

[Jed Brown]

Matteo Semplice <matteo.semplice at uninsubria.it> writes:

> Hi.
>
> We are writing a code for a FD scheme on an irregular domain and thus 
> the local stencil is quite variable: we have inner nodes, boundary nodes 
> and inactive nodes, each with their own stencil type and offset with 
> respect to the grid node. We currently create a matrix with 
> DMCreateMatrix on a DMDA and for now have set the option 
> MAT_NEW_NONZERO_LOCATIONS to PETSC_TRUE, but its time to render the code 
> memory-efficient. The layout created automatically is correct for inner 
> nodes, wrong for boundary ones (off-centered stencils) and redundant for 
> outer nodes.
>
> After the preprocessing stage (including stencil creation) we'd be in 
> position to set the nonzero pattern properly.
>
> Do we need to start from a Mat created by CreateMatrix? Or is it ok to 
> call DMCreateMatrix (so that the splitting among CPUs and the block size 
> are set by PETSc) and then call a MatSetPreallocation routine?

You can call MatXAIJSetPreallocation after. It'll handle all matrix types so you don't have to shepherd data for all the specific preallocations.

> Also, I've seen in some examples that you call the Seq and the MPI 
> preallocation routines in a row. Does this work because 
> MatMPIAIJSetPreallocation silently does nothing on a Seq matrix and 
> viceversa?
>
> Thanks
>
>      Matteo