PETSc sparsity

[Mark Adams]

Toby,

If I understand you correctly, a trick we use for this is to use  
MatGetRow to get the sparcity pattern of each row (where you are  
applying BCs) and then create a vector of zeros and use MatSetValues  
using the *row* sparcity from MatGetRow and SET the *column* values  
with this vector of zeros.  This assumes that your matrix has  
symmetric structure.  This zeros out the column and now you can just  
zero out the row as you now do.

Hope that helps,
Mark

On Jun 15, 2007, at 2:19 PM, Toby Young wrote:

>
>
> 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::M 
>> P
>> 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
>

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