Thanks a lot, Barry! I see that you had implemented the bs=3 special case.
I will play with these codes and add at least bs=2 case and try to get it
working for parallel baij. I will let you know the update.

Thank you.

Xiangdong

On Wed, Feb 14, 2018 at 2:57 PM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote:

>
>   In the PETSc git branch barry/feature-baij-blockdiagonal-scale I have
> done the "heavy lifting" for what you need. See
> https://bitbucket.org/petsc/petsc/branch/barry/feature-
> baij-blockdiagonal-scale
>
>   It scales the Seq BAIJ matrix by its block diagonal. You will need to
> write a routine to also scale the right hand side vector by the block
> diagonal and then you can try the preconditioner for sequential code. Write
> something like VecBlockDiagonalScale(Vec,const PetscScalar *). You get
> the block size from the vector.
>
>
>   Later you or I can add the parallel version (not much more difficult). I
> don't have time to work on it now.
>
>   Let us know if you have any difficulties.
>
>
>   Barry
>
>
> > On Feb 14, 2018, at 9:10 AM, Xiangdong <epsco...@gmail.com> wrote:
> >
> > The idea goes back to the alternate-block-factorization (ABF) method
> >
> > https://link.springer.com/article/10.1007/BF01932753
> >
> > and is widely used in the reservoir simulation, where the unknowns are
> pressure and saturation. Although the coupled equations are parabolic, the
> pressure equations/variables are more elliptic and the saturation equations
> are more hyperbolic. People always decouple the transformed linear equation
> to obtain a better (more elliptical) pressure matrix and then apply the AMG
> preconditioner on the decoupled matrix.
> >
> > https://link.springer.com/article/10.1007/s00791-016-0273-3
> >
> > Thanks.
> >
> > Xiangdong
> >
> > On Wed, Feb 14, 2018 at 9:49 AM, Smith, Barry F. <bsm...@mcs.anl.gov>
> wrote:
> >
> >   Hmm, I never had this idea presented to me, I have no way to know if
> it is particularly good or bad. So essentially you transform the matrix
> "decoupling the physics alone the diagonal" and then do PCFIELDSPLIT
> instead of using PCFIELDSPLIT directly on the original equations.
> >
> >   Maybe in the long run this should be an option to PCFIEDLSPLIT. In
> general we like the solvers to manage any transformations, not require
> transformations before calling the solvers. I have to think about this.
> >
> >    Barry
> >
> >
> > > On Feb 14, 2018, at 8:29 AM, Xiangdong <epsco...@gmail.com> wrote:
> > >
> > > The reason for the operation invdiag(A)*A is to have a decoupled
> matrix/physics for preconditioning. For example, after the transformation,
> the diagonal block is identity matrix ( e.g. [1,0,0;0,1,0;0,0,1]  for
> bs=3). One can extract a submatrix (e.g. corresponding to only first
> unknown) and apply special preconditioners for the extracted/decoupled
> matrix. The motivation is that after the transformation, one can get a
> better decoupled matrix to preserve the properties of the unknowns.
> > >
> > > Thanks.
> > >
> > > Xiangdong
> > >
> > > On Tue, Feb 13, 2018 at 6:27 PM, Smith, Barry F. <bsm...@mcs.anl.gov>
> wrote:
> > >
> > >  In general you probably don't want to do this. Most good
> preconditioners (like AMG) rely on the matrix having the "natural" scaling
> that arises from the discretization and doing a scaling like you describe
> destroys that natural scaling. You can use PCPBJACOBI to use point block
> Jacobi preconditioner on the matrix without needing to do the scaling up
> front. The ILU preconditioners for BAIJ matrices work directly with the
> block structure so again pre-scaling the matrix buys you nothing. PETSc
> doesn't have any particularly efficient routines for computing what you
> desire, the only way to get something truly efficient is to write the code
> directly using the BAIJ data structure, doable but probably not worth it.
> > >
> > >   Barry
> > >
> > >
> > > > On Feb 13, 2018, at 5:21 PM, Xiangdong <epsco...@gmail.com> wrote:
> > > >
> > > > Hello everyone,
> > > >
> > > > I have a block sparse matrices A created from the DMDA3d. Before
> passing the matrix to ksp solver, I want to apply a transformation to this
> matrix: namely A:= invdiag(A)*A. Here invdiag(A) is the inverse of the
> block diagonal of A. What is the best way to get the transformed matrix?
> > > >
> > > > At this moment, I created a new mat IDA=inv(diag(A)) by looping
> through each row and call MatMatMult to get B=invdiag(A)*A, then destroy
> the temporary matrix B. However, I prefer the in-place transformation if
> possible, namely, without the additional matrix B for memory saving purpose.
> > > >
> > > > Do you have any suggestion on compute invdiag(A)*A for mpibaij
> matrix?
> > > >
> > > > Thanks for your help.
> > > >
> > > > Best,
> > > > Xiangdong
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> >
> >
>
>

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