[petsc-users] Matrix Construction Question

[Adam Byrd]

I have working code that produces the correct answer now, thank you. One
(hopefully) final question, though. The solution is actually transposed.
What causes this? Presumably I can use MatMatSolveTranspose to get around
this, but there's no man page and I want to be sure of what will happen in
all cases.

Respectfully,
Adam

On Thu, Jun 30, 2011 at 4:18 PM, Hong Zhang <hzhang at mcs.anl.gov> wrote:

> Add
>  ierr = MatGetOrdering(testMat,MATORDERING_ND,&isrow,&iscol);CHKERRQ(ierr);
> before the line
>        ierr = MatFactorInfoInitialize(&luinfo);CHKERRQ(ierr);
>
> Somehow, your matrix is numerically singular. With
> MATORDERING_NATURAL
> I get
> [0]PETSC ERROR: Detected zero pivot in LU factorization
>
> even using MATDENSE matrix format, which calls lapack.
> With MATORDERING_ND, I get useless inverseMat.
>
> The modified code I used is attached.
>
> Hong
>
> On Thu, Jun 30, 2011 at 2:30 PM, Adam Byrd <adam1.byrd at gmail.com> wrote:
> > I'm trying to work through what I need to do, again by practicing with a
> > small scale random problem. The general order of events seems to be:
> create
> > a matrix, fill it, assemble it, factor it, then one can use solvers with
> it.
> > When I use MatLUFactor on my matrix before using it with a solver I get
> this
> > error:
> > [0]PETSC ERROR: --------------------- Error Message
> > ------------------------------------
> > [0]PETSC ERROR: Null argument, when expecting valid pointer!
> > [0]PETSC ERROR: Null Object: Parameter # 1!
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48
> > CDT 2011
> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > [0]PETSC ERROR: See docs/index.html for manual pages.
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: ./test on a osx-gnu-c named Macintosh-3.local by adambyrd
> > Thu Jun 30 15:27:30 2011
> > [0]PETSC ERROR: Libraries linked from
> > /Users/adambyrd/soft/petsc-3.1-p8/osx-gnu-cpp/lib
> > [0]PETSC ERROR: Configure run at Tue Jun 28 12:56:55 2011
> > [0]PETSC ERROR: Configure options PETSC_ARCH=osx-gnu-cpp
> --with-fc=gfortran
> > -download-f-blas-lapack=1 --download-mpich=1 --with-scalar-type=complex
> > --with-clanguage=c++
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: ISInvertPermutation() line 209 in
> > src/vec/is/interface/index.c
> > [0]PETSC ERROR: MatLUFactorSymbolic_SeqAIJ() line 306 in
> > src/mat/impls/aij/seq/aijfact.c
> > [0]PETSC ERROR: MatLUFactorSymbolic() line 2534 in
> > src/mat/interface/matrix.c
> > [0]PETSC ERROR: MatLUFactor_SeqAIJ() line 945 in
> > src/mat/impls/aij/seq/aijfact.c
> > [0]PETSC ERROR: MatLUFactor() line 2417 in src/mat/interface/matrix.c
> > [0]PETSC ERROR: main() line 62 in WDtest.cpp
> > application called MPI_Abort(MPI_COMM_WORLD, 85) - process 0[unset]:
> > aborting job:
> > application called MPI_Abort(MPI_COMM_WORLD, 85) - process 0
> > I don't understand what I'm doing wrong.
> > Respectfully,
> > Adam
> > On Wed, Jun 29, 2011 at 1:26 AM, Matthew Knepley <knepley at gmail.com>
> wrote:
> >>
> >> On Tue, Jun 28, 2011 at 10:20 PM, Adam Byrd <adam1.byrd at gmail.com>
> wrote:
> >>>
> >>> Matt,
> >>>
> >>> Alright, that means I need to continue learning how to use
> >>> MatSetValues(). With my 6x6 example I tried filling it with four 3x3
> sub
> >>> matrices, but when I do that I get the error 'sum of local sizes 12
> does not
> >>> equal global size.' I had 4 processors each calling MatSetValues for
> their
> >>> own 3x3. Graphically, I arranged the nodes 0 1
> >>>
> >>>
> 2 3
> >>> where process 0 had global rows 0-2 and global columns 0-2; process 1
> had
> >>> 0-2, 3-5; process 2 had 3-5, 0-2; and process 3 had 3-5, 3-5. From the
> >>> documentation, I think this should be correct, but I'm not sure. Also,
> which
> >>> format would you recommend for storing the matrix?
> >>
> >> 1) With any error, send the Entire error message.
> >> 2) PETSc matrices are divided by rows, not rows and columns, see the
> >> manual section. Rows & columns only makes sense for dense matrices
> >> 3) You can still set arbitrary blocks no matter how the matrix is
> divided
> >> 4) The error means you tried to set both local and global dimensions,
> and
> >> they do not add up correctly. Just set the global dimensions
> >>    Matt
> >>
> >>>
> >>> Jack,
> >>>
> >>> I'm a summer intern just getting started with this project, so I don't
> >>> know all the details yet (I can ask though). I know I need to find the
> >>> Green's function which will involve the trace of the inverted
> Hamiltonian,
> >>> as well as the rest of the matrix. I have inquired about avoiding the
> >>> inversion altogether, but my instructor doesn't believe there is a way
> >>> around it. Once I've worked through the math I want to explore other
> options
> >>> though.
> >>>
> >>> Respectfully,
> >>> Adam
> >>>
> >>> On Tue, Jun 28, 2011 at 6:08 PM, Matthew Knepley <knepley at gmail.com>
> >>> wrote:
> >>>>
> >>>> On Tue, Jun 28, 2011 at 5:01 PM, Adam Byrd <adam1.byrd at gmail.com>
> wrote:
> >>>>>
> >>>>> Actually, it's quite sparse. In the 3600x3600 there are only just 4
> >>>>> nonzero entries in each row. This means it's 99.9% empty. My smaller
> 6x6
> >>>>> example is dense, but it's only practice building and manipulating
> matrices.
> >>>>
> >>>> Ah, then its easy. Just call MatSetValues() with each block. Then use
> >>>> MUMPS to do a sparse direct solve.
> >>>>   Matt
> >>>>
> >>>>>
> >>>>> Respectfully,
> >>>>> Adam
> >>>>>
> >>>>> On Tue, Jun 28, 2011 at 5:55 PM, Matthew Knepley <knepley at gmail.com>
> >>>>> wrote:
> >>>>>>
> >>>>>> It sounds like you have a dense matrix (from your example). Is this
> >>>>>> true? If so, you should use Elemental (on Google Code).
> >>>>>>   Thanks,
> >>>>>>      Matt
> >>>>>>
> >>>>>> On Tue, Jun 28, 2011 at 8:55 AM, Adam Byrd <adam1.byrd at gmail.com>
> >>>>>> wrote:
> >>>>>>>
> >>>>>>> Hi,
> >>>>>>> I'm rather new to PETSc and trying to work out the best way to
> create
> >>>>>>> and fill a large sparse matrix distributed over many processors.
> Currently,
> >>>>>>> my goal is to create a 3600x3600 matrix in units of 12x12 blocks
> with
> >>>>>>> several blocks on any given node. I'd like to create the matrix in
> such a
> >>>>>>> way that each node only holds the information in it's handful of
> blocks and
> >>>>>>> not the entire matrix. Eventually, this matrix is to be inverted (I
> know,
> >>>>>>> inversion should be avoided, but as this is a Hamiltonian matrix
> from which
> >>>>>>> I need the Green's function, I'm unaware of a way to forgo carrying
> out the
> >>>>>>> inversion). Additionally, the values will be changed slightly and
> the matrix
> >>>>>>> will be repeatedly inverted. It's structure will remain the same.
> In order
> >>>>>>> to learn how to do this is I am starting with a small 6x6 matrix
> broken into
> >>>>>>> four 3x3 blocks and distributed one block per node. I've been able
> to create
> >>>>>>> a local 3x3 matrix on each node, with it's own values, and with the
> global
> >>>>>>> row/column IDs correctly set to [0, 1, 2] or [3, 4, 5] depending on
> where
> >>>>>>> the block is in the matrix. My problem manifests when I try to
> create the
> >>>>>>> larger matrix from the individual smaller ones. When the matrix is
> >>>>>>> constructed I'm trying to use MatSetValues and having each node
> pass in it's
> >>>>>>> 3x3 block. I end up with an error that the sum of local lengths
> 12x12 does
> >>>>>>> not match the global length 6x6. It appears as though this is from
> passing
> >>>>>>> in four 3x3s and the program interpreting that as a 12x12 instead
> of as a
> >>>>>>> 6x6 with the blocks in a grid.
> >>>>>>> My question is then: is it possible to fill a matrix as a grid of
> >>>>>>> blocks, or can I only fill it in groups of rows or columns? Also,
> am I
> >>>>>>> approaching this problem the correct way, or are there more
> efficient ways
> >>>>>>> of building this matrix with the ultimate goal of inverting it?
> >>>>>>> I have included my copy of a modified example if it helps. I do
> >>>>>>> apologize if this is answered somewhere in the documentation, I
> have been
> >>>>>>> unable to find a solution.
> >>>>>>> Respectfully,
> >>>>>>> Adam
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> 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
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> 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
> >>>
> >>
> >>
> >>
> >> --
> >> 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
> >
> >
>
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