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Anders Logg wrote:
On Fri, May 22, 2009 at 09:01:25AM +0100, Garth N. Wells wrote:Anders Logg wrote:These look too low level to me. They look appropriate for creating a PETSc matrix from data underlying a CSR matrix (using what is returned by GenericMatrix::data().On Fri, May 22, 2009 at 08:10:11AM +0100, Garth N. Wells wrote:Anders Logg wrote:I'm looking at how to extend GenericSparsityPattern for parallel assembly. Currently, the interface allows the number of nonzeros per row to be retrieved when initializing a matrix (through the common interface). For PETSc, the interface needs to be extended to include both the number of nonzeros in the diagonal block and offdiagonal blocks for each row. This is already in the subclass SparsityPattern and a cast is used in PETScMatrix to convert the GenericSparsityPattern to a SparsityPattern so the offdiagonal nonzeros may be retrieved. For Epetra, we have a subclass EpetraSparsityPattern and also a cast in EpetraMatrix. So, what would be a sensible way to design/implement the different sparsity patterns? One option could be to extend GenericSparsityPattern with the stuff needed for PETSc, and just have those functions return an error for Epetra. There would then be a single cast (in EpetraMatrix) and all backends except Epetra would use the SparsityPattern implementation. If so, I can go ahead and make the required changes so it works with PETSc. Epetra should work as is I guess, assuming Epetra_FECrsGraph& does the right thing. On a side note, we build much more information in SparsityPattern than we actually need for PETSc. We know all the nonzero columns but just count the total number and throw away the more fine-grained information. Is there a way to pass this on to PETSc and have PETSc use it?This might be what you want. http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/Mat/MatSeqAIJSetColumnIndices.html#MatSeqAIJSetColumnIndices GarthLooks like these might be more interesting (can't find SetColumnIndices for MPI matrix): http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/Mat/MatSeqAIJSetPreallocationCSR.html http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/Mat/MatMPIAIJSetPreallocationCSR.htmlPerhaps. But it would be fairly easy to add the required data to SparsityPattern so I might try to see if it improves performance. It's not necessarily a low-level format. It's just that PETSc uses low-level data structures for describing the sparsity pattern. It might has well have been std::vector<std::map<uint, uint> >. But do we agree that we design GenericSparsityPattern after what PETSc needs and let the Epetra backend use a dynamic cast and give an error for all the functions it does not implement?
Yes. Garth
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