PETSc sparsity

[Toby Young]

Hello petsc-users and petsc-dev.

I am using PETSc to solve finite element problems. In particular I am
working with the dealii package which has C++ wrappers designed to
interface with PETSc. I am working on developing some of these wrappers.

The difficulty I face is that, after applying boundary conditions to the
matrices, these matrices return as nonsymmetric; I really need them to be
symmetric! I can achieve this by performing the so-called Gauss
elimination step; however this requires access to the sparsity pattern of
the PETSc matrix.

"The gauss elimination step "per se" is not a problem. The problem is
that we don't have access to the sparsity of the matrix, so it is not
so easy to find out which entries are not zero in the petsc matrices."
-- dealii developer

Is there *any* possible way to obtain the sparsity of the PETSc matrix?
Maybe something like GetMatrixSparsity? I have done my research, but I
cannot find any information on this so I am pretty clueless on how
to proceed (sorry if I have missed something obvious).

Any comments or suggests would be greatly appreciated.

Best,
	Toby

-----

Toby D. Young (Adiunkt)
Department of Computational Science
Institute of Fundamental Technological Research
Polish Academy of Science
Room 206, ul. Swietokrzyska 21
00-049 Warszawa, POLAND




Luca.

--
Luca Heltai <luca.heltai at gmail.com>
http://www-dimat.unipv.it/heltai
--
There are no answers, only cross references.



On Jun 15, 2007, at 11:17 AM, Toby D. Young wrote:

> On Thu, 14 Jun 2007 10:55:20 -0400
> Luca Heltai <luca.heltai at gmail.com> wrote:
>
>> Toby, if you do some serious development (like what you are
>> doing... :) ...) I strongly suggest you switch to the subversion
>> tree.
>
> Okay, fair suggestion, and not too tricky to do, I'm running of dealii
> 5.3pre now.
>
>> In the subversion tree that is implemented.
>
> Yet it doesn't seem to be and the problem does not go away. I'll
> have to
> think of a way around this, either that or actually implement Guass
> elimination for the Petsc SParseMatrix < scary thought :-) >.
>
> You can verify this yourself by running step-17, after first changing
> the final flag false->true in apply_boundary_conditions.
>
> Here's what we find:
>
> Cycle 0:
>    Number of active cells        : 1024
>    Number of degrees of freedom  : 1089 (by partition: 1089)
> --------------------------------------------------------
> An error occurred in line <534> of file
> <source/numerics/matrices.all_dimensions.cc>
> in function void dealii::PETScWrappers::apply_boundary_values(const
> std::map<unsigned int, double, std::less<unsigned int>,
> std::allocator<std::pair<const unsigned int, double> > >&,
> PETScMatrix&, PETScVector&, PETScVector&, bool) [with PETScMatrix =
> dealii::PETScWrappers::MPI::SparseMatrix, PETScVector =
> dealii::PETScWrappers::MPI::Vector]
> The violated condition was:
> preserve_symmetry == false
> The name and call sequence of the exception was:
> ExcNotImplemented()
> Additional Information:
> (none)
>
> Stacktrace:
> -----------
> #0  /home/tyoung/fem/deal.II/lib/libdeal_II_1d.g.so: void
> dealii::PETScWrappers::apply_boundary_values<dealii::PETScWrappers::MP
> I::SparseMatrix,
> dealii::PETScWrappers::MPI::Vector>(std::map<unsigned int, double,
> std::less<unsigned int>, std::allocator<std::pair<unsigned int const,
> double> > > const&, dealii::PETScWrappers::MPI::SparseMatrix&,
> double> > > dealii::PETScWrappers::MPI::Vector&,
> double> > > dealii::PETScWrappers::MPI::Vector&, bool)
> double> > > #1  /home/tyoung/fem/deal.II/lib/libdeal_II_1d.g.so:
> double> > > dealii::MatrixTools::apply_boundary_values
> (std::map<unsigned
> double> > > int, double, std::less<unsigned int>,
> double> > > std::allocator<std::pair<unsigned int const, double> > >
> double> > > const&, dealii::PETScWrappers::MPI::SparseMatrix&,
> double> > > dealii::PETScWrappers::MPI::Vector&,
> double> > > dealii::PETScWrappers::MPI::Vector&, bool)
> #2  ./step-75: double> > > InfiniteWellProblem<2>::assemble_system()
> #3  ./step-75: double> > > InfiniteWellProblem<2>::run()
> #4  ./step-75: main
> --------------------------------------------------------
>
>
>
> --
>
> Toby D. Young ( Adiunkt )
> Department of Computational Science
> Institute of Fundamental Technical Research, Polish Academy of
> Sciences
> Room 206, Swietokrzyska 21, 00-049 Warsaw, POLAND