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

[Matteo Semplice]

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?

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