[petsc-users] Variable Block Row format in PETSc

[Jed Brown]

It's not the same data layout, but I recommend that you just use AIJ and
let it optimize internally. Partition the graph first, then allocate the
matrix, then compute the Jacobian entries and use MatSetValues.
On May 14, 2013 5:11 PM, "Satish Balay" <balay at mcs.anl.gov> wrote:

> AIJ matrix format internally supports VBR listed below [called inodes in
> PETSc]
>
> So I'm not sure what problem you are having.
>
> Satish
>
> On Tue, 14 May 2013, Longxiang Chen wrote:
>
> > VBR like in this link, use 6 arrays to represent a matrix.
> >
> http://docs.oracle.com/cd/E19061-01/hpc.cluster5/817-0086-10/prog-sparse-support.html
> >
> > Each row is a vertex in the graph, , and use parmetis to partition the
> > graph to minimize the number of cuts between different processors.
> (reduce
> > communication when calculate Matrix-Vector)
> > The matrix is calculated from Jacobian and construct the A and b from the
> > result of Jacobian (in VBR).
> >
> >
> > Best regards,
> > Longxiang Chen
> >
> > Do something every day that gets you closer to being done.
> > --------------------------------------------------------------
> > 465 Winston Chung Hall
> > Computer Science Engineering
> > University of California, Riverside
> >
> >
> >
> > On Tue, May 14, 2013 at 2:51 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
> >
> > > What kind of VBR matrix? What are you partitioning using parmetis? A
> mesh?
> > > The blocks of the matrix? How do you create the entries in the matrix?
> > > On May 14, 2013 4:36 PM, "Longxiang Chen" <suifengls at gmail.com> wrote:
> > >
> > >> To whom it may concern,
> > >>
> > >> I use parmetis to partition a mesh for a sparse matrix.
> > >> Then I distribute the data to the  appropriate processors according to
> > >> the result of partition.
> > >>
> > >> The sparse matrix is stored in Variable Block Row(VBR) format.
> > >> After the distribution, I want to call PETSc KSP solver to solve Ax =
> b.
> > >> I tried to convert VBR to AIJ or CSR format, but the data would be
> > >> re-distributed.
> > >>
> > >> The ideal method is to keep the distribution result from parmetis.
> > >> For example, after parmetis, processor 0 has 0, 1, 4, and processor 1
> > >> has 2, 3, 5. I wish the PETSc would not change this distribution and
> > >> solve Ax = b.
> > >>
> > >> Are there any approaches to call KSP solver in VBR format from PETSc?
> > >> Or any suggestions for solving Ax = b?
> > >>
> > >> Thanks in advance.
> > >>
> > >> Regards,
> > >> Longxiang Chen
> > >>
> > >>
> >
>
>
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