[petsc-users] Conversion between AIJ & BAIJ

[Chung-Kan Huang]

Thanks, I will definitely take a look.

Kan

On Wed, Jan 21, 2015 at 4:44 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>   Since you have various "physics" in the same matrix you can use the
> PCFIELDSPLIT preconditioner to tack each of the physics separately and then
> combine them together within the same overall preconditioner. For example
> the pressure subproblem inside the large matrix should likely be solved
> with PCGAMG while the other parts not. Take a look at the manual page.
> Loosely speaking PCFIELDSPLIT is kind of like using an operator splitting
> only within the preconditioner.
>
>    Barry
>
> > On Jan 21, 2015, at 4:21 PM, Chung-Kan Huang <ckhuangf at gmail.com> wrote:
> >
> >
> > On Wed, Jan 21, 2015 at 4:03 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Wed, Jan 21, 2015 at 3:16 PM, Chung-Kan Huang <ckhuangf at gmail.com>
> wrote:
> >
> > On Wed, Jan 21, 2015 at 2:36 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Wed, Jan 21, 2015 at 2:29 PM, Chung-Kan Huang <ckhuangf at gmail.com>
> wrote:
> >
> > On Wed, Jan 21, 2015 at 2:15 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Wed, Jan 21, 2015 at 2:07 PM, Chung-Kan Huang <ckhuangf at gmail.com>
> wrote:
> >
> > On Wed, Jan 21, 2015 at 2:01 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Wed, Jan 21, 2015 at 1:55 PM, Chung-Kan Huang <ckhuangf at gmail.com>
> wrote:
> >
> > On Wed, Jan 21, 2015 at 1:44 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Wed, Jan 21, 2015 at 1:40 PM, Chung-Kan Huang <ckhuangf at gmail.com>
> wrote:
> > Then A & AB are not longer the same matrix.  They become complete two
> individuals aren't they?
> > If I do whatever to AB after AB is created the A is still the same old A
> and not going to be affected by the operations I do to AB.
> >
> > Yes.
> >
> >
> > What I am really looking for is a way to create two interfaces (one as
> AIJ and one as BAIJ) but they both refer to the same matrix.
> >
> > Why would you ever want this? Why not just using BAIJ?
> > As I mentioned in the beginning.  There are parts of the code gets
> benifit when AIJ is used and the other part gets benifit  if BAIJ is used.
> >
> > For instance,
> >
> > I'd like to use MatSetValuesBlocked but I also want to use ilu
> constructed by AIJ instead of BAIJ (our experience found ilu from BAIJ
> behaves funny sometimes.
> >
> > If the blocks truly are dense, then ILU(0) is identical on both.
> >
> > Unfortunately the life is not that easy.  The blocks are spares and we
> found ILU(1) works better for our case.
> > And besides that is not the only reason I want to have AIJ & BAIJ
> interfaces, we have some code management issue and I am looking for short
> cut to unite them.
> >
> > So go back to the original question the short answer is no way?
> >
> > Yes, it would not make sense.
> >
> > What problem are you using ILU(1) for?
> >
> > I am using it for flow simulation for reservoir problems.
> >
> > Have you considered trying algebraic multigrid?
> >
> > I am solving PDE fully implicitly and as far as I know algebraic
> multigrid only good for pressure equations
> > I will need 2 stages PC while AMG is for pressure stage but I will still
> need something like ILU for second stage.
> >
> > So you are using a mixed-formulation of Darcy? What equations do you
> have?
> > After some steps of reduction, the system equation solved in linear
> solver is basically the convervations of masses and energy.
> > Together I am solving the equations with natrual variables (pressure,
> temperature, saturations and molar fractions) .
> >
> > It might have variable block size depend on local state and physics that
> considered.  For instant, I can skip mass transfer if it is impermeable to
> fluid locally but I still need to solve for conduction in energy balance
> equations.  I might also have some zones do not have some components so I
> can skip them as well.  Ideally I should have used variable size of block
> but I used the same size anyway in my previous BAIJ configuration as you
> pointed out some optimization can be done with the same size blocked matrix.
> >
> > I switched to AIJ for reason related to ILU that I explained already. I
> didn't see the same problem in AIJ.
> >
> > I am looking for room to improve linear solver performance in all
> aspects including CPU time to assemble the matrix and also good PC that are
> provided by PETSc.
> > Currently I am using AIJ + ILU(1) + overlay(1) +BCGS.  I am not so happy
> about scalbility but that is not in the scope of the problem I brought
> initially.  But I am interested if you have any good suggestions that I
> should test.
> >
> > Thanks,
> >
> > Kan
> >
> >   Thanks,
> >
> >      MAtt
> >
> >
> > Some issues we found is that
> > 1) for a * x = 0 it doesn't return x = 0
> >
> > This is impossible. There must be a bug in the code.
> >
> >   Thanks,
> >
> >      Matt
> >
> > 2) After compared ILU(1) with BAIJ against with ILU(1) with AIJ I found
> latter one is better.  I could not find anything wrong with my BAIJ version
> though.  However, experiences suggested that BAIJ's ILU(1) should be better.
> >
> >
> > Thanks,
> >
> > Kan
> >
> >   Thanks,
> >
> >      Matt
> >
> > Thanks,
> >
> > Kan
> >
> >   Matt
> >
> > Thanks,
> >
> > Kan
> >
> >   Thanks,
> >
> >       Matt
> >
> > Thanks,
> >
> > Kan
> > On Wed, Jan 21, 2015 at 1:20 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Wed, Jan 21, 2015 at 12:56 PM, Chung-Kan Huang <ckhuangf at gmail.com>
> wrote:
> > Hi,
> >
> > So if I do
> >
> > Mat A, AB;
> > MatCreateAIJ(comm,m,n,M,N,d_nz, d_nnz,o_nz, o_nnz, &A);
> > MatConvert(A, MATBAIJ, MAT_INITAL_MATRIX, &AB);
> > MatSetBlockSize(AB, bs)
> > I can create AB as a BAIJ with block size of bs from A which is a AIJ
> matrix.
> >
> > So from this point I can use both A and AB and they will mean the same
> matrix. Am I right?
> >
> > Yes
> >
> > At the end of the program do I only destory one of them or both?
> >
> > Both
> >
> > Do I need to worry about anything in terms of memory penalty?
> >
> > It is twice the memory. Its another matrix.
> >
> > Did you catch when Jed said you could jsut create the BAIJ up front?
> >
> >   Thanks,
> >
> >     Matt
> >
> >
> > Thanks,
> >
> > Kan
> >
> >
> > On Tue, Jan 20, 2015 at 4:39 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> >   You can do a MatConvert() (requires another copy of the matrix) for
> the parts that benefit from BAIJ.
> >
> >   Barry
> >
> > > On Jan 20, 2015, at 4:33 PM, Chung-Kan Huang <ckhuangf at gmail.com>
> wrote:
> > >
> > > Hi,
> > >
> > > Does PETSc provide means for conversion between AIJ & BAIJ.
> > >
> > > My matrix is created as AIJ because it makes life easy for most part
> of the applications but some part of applications actually get some
> benefits with BAIJ.  So I wonder if a matrix can exist as two idenfities
> and I can use either format depend on which one is more convenient at run
> time.
> > >
> > > So in my case the block size is fixed and identical for all blocks.
> > >
> > >
> > > Thanks,
> > >
> > >
> > > Kan
> >
> >
> >
> >
> > --
> > Cheers
> >
> >
> >
> >
> > --
> > What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> > -- Norbert Wiener
> >
> >
> >
> > --
> > Cheers
> >
> >
> >
> >
> > --
> > What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> > -- Norbert Wiener
> >
> >
> >
> > --
> > Cheers
> >
> >
> >
> >
> > --
> > What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> > -- Norbert Wiener
> >
> >
> >
> > --
> > Cheers
> >
> >
> >
> >
> > --
> > What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> > -- Norbert Wiener
> >
> >
> >
> > --
> > Cheers
> >
> >
> >
> >
> > --
> > What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> > -- Norbert Wiener
> >
> >
> >
> > --
> > Cheers
> >
> >
> >
> >
> > --
> > What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> > -- Norbert Wiener
> >
> >
> >
> > --
> > Cheers
> >
>
>


-- 

*Cheers*
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