setup matrix using petsc and metis in 3D

[Jose Javier Muñoz Criollo]

Hi

I'm using deal.ii-8.0.0.

I'm trying to setup a parallel sparse matrix:

 PETScWrappers::MPI::SparseMatrix system_matrix;

Until now I was working in 2D, so I had been initializing the matrix like this:

   const types::global_dof_index n_local_dofs
      = DoFTools::count_dofs_with_subdomain_association (dof_handler,
                                                         this_mpi_process);

 

    system_matrix.reinit      (mpi_communicator,
                               dof_handler.n_dofs (),
                               dof_handler.n_dofs (),
                               n_local_dofs,
                               n_local_dofs,
                               dof_handler.max_couplings_between_dofs());

I'm currently working on the 3D model. According to the documentation of the function max_couplings_between_dofs(), it shouldn't be used in a 3D case and in fact it throws an error if this is attempted. I'm trying to initialize the matrix in a similar way to step-40 (although it uses p4est for the grid). Like this:

    IndexSet locally_owned_dofs = dof_handler.locally_owned_dofs ();
    CompressedSimpleSparsityPattern compressed_pattern (dof_handler.n_dofs());
    DoFTools::make_sparsity_pattern (dof_handler,
                                                      compressed_pattern);
    constraints.condense (compressed_pattern);
    SparsityPattern sp;
    sp.copy_from (compressed_pattern);

    system_matrix.reinit (locally_owned_dofs,
                                   locally_owned_dofs,
                                   sp,
                                   mpi_communicator);

But when I compile I receive an error like this:

undefined reference to `void dealii::PETScWrappers::MPI::SparseMatrix::reinit<dealii::SparsityPattern>(dealii::IndexSet const&, dealii::IndexSet const&, dealii::SparsityPattern const&, ompi_communicator_t* const&)'
make: *** [trl_3d_petsc_03_03_2014] Error 1

Is it related with the fact that I'm not using p4est? If so, which would be the correct way to reinit the matrix? Maybe using this other reinit function?

PETScWrappers::MPI::SparseMatrix::SparseMatrix
( const MPI_Comm &  communicator,
  const SparsityType &  sparsity_pattern,
  const std::vector< size_type > &  local_rows_per_process,
  const std::vector< size_type > &  local_columns_per_process,
  const unsigned int  this_process,
  const bool  preset_nonzero_locations = true )

Best Regards

javier

--
José Javier Muñoz Criollo
PhD Student | Cardiff University School of Engineering
E-mail: josejm...@gmail.com

[Timo Heister]

>> SparsityPattern sp;

>> system_matrix.reinit (locally_owned_dofs,
>> locally_owned_dofs,
>> sp,
>> mpi_communicator);

You don't need the dealii::SparsityPattern. Try feeding the
CompressedSimpleSparsityPattern as argument 3 into reinit(). Also see
step-18.

--
Timo Heister
http://www.math.clemson.edu/~heister/

[Jose Javier Muñoz Criollo]

Yes, you're right. How did I miss step 18? Thanks for your help.

Javier

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