petsc_parallel_sparse_matrix.cc

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// ---------------------------------------------------------------------
//
// Copyright (C) 2004 - 2020 by the deal.II authors
//
// This file is part of the deal.II library.
//
// The deal.II library is free software; you can use it, redistribute
// it, and/or modify it under the terms of the GNU Lesser General
// Public License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
// The full text of the license can be found in the file LICENSE.md at
// the top level directory of deal.II.
//
// ---------------------------------------------------------------------
 
#include <deal.II/lac/petsc_sparse_matrix.h>
 
#ifdef DEAL_II_WITH_PETSC
 
#  include <deal.II/base/mpi.h>
 
#  include <deal.II/lac/dynamic_sparsity_pattern.h>
#  include <deal.II/lac/exceptions.h>
#  include <deal.II/lac/petsc_compatibility.h>
#  include <deal.II/lac/petsc_vector.h>
#  include <deal.II/lac/sparsity_pattern.h>
 
DEAL_II_NAMESPACE_OPEN
 
namespace PETScWrappers
{
  namespace MPI
  {
    SparseMatrix::SparseMatrix()
      : communicator(MPI_COMM_SELF)
    {
      // just like for vectors: since we
      // create an empty matrix, we can as
      // well make it sequential
      const int            m = 0, n = 0, n_nonzero_per_row = 0;
      const PetscErrorCode ierr = MatCreateSeqAIJ(
        PETSC_COMM_SELF, m, n, n_nonzero_per_row, nullptr, &matrix);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
    }
 
 
    SparseMatrix::~SparseMatrix()
    {
      destroy_matrix(matrix);
    }
 
    SparseMatrix::SparseMatrix(const MPI_Comm &communicator,
                               const size_type m,
                               const size_type n,
                               const size_type local_rows,
                               const size_type local_columns,
                               const size_type n_nonzero_per_row,
                               const bool      is_symmetric,
                               const size_type n_offdiag_nonzero_per_row)
      : communicator(communicator)
    {
      do_reinit(m,
                n,
                local_rows,
                local_columns,
                n_nonzero_per_row,
                is_symmetric,
                n_offdiag_nonzero_per_row);
    }
 
 
 
    SparseMatrix::SparseMatrix(
      const MPI_Comm &              communicator,
      const size_type               m,
      const size_type               n,
      const size_type               local_rows,
      const size_type               local_columns,
      const std::vector<size_type> &row_lengths,
      const bool                    is_symmetric,
      const std::vector<size_type> &offdiag_row_lengths)
      : communicator(communicator)
    {
      do_reinit(m,
                n,
                local_rows,
                local_columns,
                row_lengths,
                is_symmetric,
                offdiag_row_lengths);
    }
 
 
 
    template <typename SparsityPatternType>
    SparseMatrix::SparseMatrix(
      const MPI_Comm &              communicator,
      const SparsityPatternType &   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)
      : communicator(communicator)
    {
      do_reinit(sparsity_pattern,
                local_rows_per_process,
                local_columns_per_process,
                this_process,
                preset_nonzero_locations);
    }
 
 
    void
    SparseMatrix::reinit(const SparseMatrix &other)
    {
      if (&other == this)
        return;
 
      this->communicator = other.communicator;
 
      PetscErrorCode ierr = destroy_matrix(matrix);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      ierr = MatDuplicate(other.matrix, MAT_DO_NOT_COPY_VALUES, &matrix);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
    }
 
 
    SparseMatrix &
    SparseMatrix::operator=(const value_type d)
    {
      MatrixBase::operator=(d);
      return *this;
    }
 
    void
    SparseMatrix::copy_from(const SparseMatrix &other)
    {
      if (&other == this)
        return;
 
      this->communicator = other.communicator;
 
      const PetscErrorCode ierr =
        MatCopy(other.matrix, matrix, SAME_NONZERO_PATTERN);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
    }
 
    void
    SparseMatrix::reinit(const MPI_Comm &communicator,
                         const size_type m,
                         const size_type n,
                         const size_type local_rows,
                         const size_type local_columns,
                         const size_type n_nonzero_per_row,
                         const bool      is_symmetric,
                         const size_type n_offdiag_nonzero_per_row)
    {
      this->communicator = communicator;
 
      // get rid of old matrix and generate a new one
      const PetscErrorCode ierr = destroy_matrix(matrix);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      do_reinit(m,
                n,
                local_rows,
                local_columns,
                n_nonzero_per_row,
                is_symmetric,
                n_offdiag_nonzero_per_row);
    }
 
 
 
    void
    SparseMatrix::reinit(const MPI_Comm &              communicator,
                         const size_type               m,
                         const size_type               n,
                         const size_type               local_rows,
                         const size_type               local_columns,
                         const std::vector<size_type> &row_lengths,
                         const bool                    is_symmetric,
                         const std::vector<size_type> &offdiag_row_lengths)
    {
      this->communicator = communicator;
 
      // get rid of old matrix and generate a
      // new one
      const PetscErrorCode ierr = destroy_matrix(matrix);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      do_reinit(m,
                n,
                local_rows,
                local_columns,
                row_lengths,
                is_symmetric,
                offdiag_row_lengths);
    }
 
 
 
    template <typename SparsityPatternType>
    void
    SparseMatrix::reinit(
      const MPI_Comm &              communicator,
      const SparsityPatternType &   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)
    {
      this->communicator = communicator;
 
      // get rid of old matrix and generate a new one
      const PetscErrorCode ierr = destroy_matrix(matrix);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
 
      do_reinit(sparsity_pattern,
                local_rows_per_process,
                local_columns_per_process,
                this_process,
                preset_nonzero_locations);
    }
 
    template <typename SparsityPatternType>
    void
    SparseMatrix::reinit(const IndexSet &           local_rows,
                         const IndexSet &           local_columns,
                         const SparsityPatternType &sparsity_pattern,
                         const MPI_Comm &           communicator)
    {
      this->communicator = communicator;
 
      // get rid of old matrix and generate a new one
      const PetscErrorCode ierr = destroy_matrix(matrix);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      do_reinit(local_rows, local_columns, sparsity_pattern);
    }
 
    void
    SparseMatrix::do_reinit(const size_type m,
                            const size_type n,
                            const size_type local_rows,
                            const size_type local_columns,
                            const size_type n_nonzero_per_row,
                            const bool      is_symmetric,
                            const size_type n_offdiag_nonzero_per_row)
    {
      Assert(local_rows <= m, ExcLocalRowsTooLarge(local_rows, m));
 
      // use the call sequence indicating only
      // a maximal number of elements per row
      // for all rows globally
      const PetscErrorCode ierr = MatCreateAIJ(communicator,
                                               local_rows,
                                               local_columns,
                                               m,
                                               n,
                                               n_nonzero_per_row,
                                               nullptr,
                                               n_offdiag_nonzero_per_row,
                                               nullptr,
                                               &matrix);
      set_matrix_option(matrix, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      // set symmetric flag, if so requested
      if (is_symmetric == true)
        {
          set_matrix_option(matrix, MAT_SYMMETRIC, PETSC_TRUE);
        }
    }
 
 
 
    void
    SparseMatrix::do_reinit(const size_type               m,
                            const size_type               n,
                            const size_type               local_rows,
                            const size_type               local_columns,
                            const std::vector<size_type> &row_lengths,
                            const bool                    is_symmetric,
                            const std::vector<size_type> &offdiag_row_lengths)
    {
      Assert(local_rows <= m, ExcLocalRowsTooLarge(local_rows, m));
 
      Assert(row_lengths.size() == m,
             ExcDimensionMismatch(row_lengths.size(), m));
 
      // For the case that local_columns is smaller than one of the row lengths
      // MatCreateMPIAIJ throws an error. In this case use a
      // PETScWrappers::SparseMatrix
      for (const size_type row_length : row_lengths)
        {
          (void)row_length;
          Assert(row_length <= local_columns,
                 ExcIndexRange(row_length, 1, local_columns + 1));
        }
 
      // use the call sequence indicating a
      // maximal number of elements for each
      // row individually. annoyingly, we
      // always use unsigned ints for cases
      // like this, while PETSc wants to see
      // signed integers. so we have to
      // convert, unless we want to play dirty
      // tricks with conversions of pointers
      const std::vector<PetscInt> int_row_lengths(row_lengths.begin(),
                                                  row_lengths.end());
      const std::vector<PetscInt> int_offdiag_row_lengths(
        offdiag_row_lengths.begin(), offdiag_row_lengths.end());
 
      // TODO: There must be a significantly better way to provide information
      // about the off-diagonal blocks of the matrix. this way, petsc keeps
      // allocating tiny chunks of memory, and gets completely hung up over this
      const PetscErrorCode ierr =
        MatCreateAIJ(communicator,
                     local_rows,
                     local_columns,
                     m,
                     n,
                     0,
                     int_row_lengths.data(),
                     0,
                     offdiag_row_lengths.size() ?
                       int_offdiag_row_lengths.data() :
                       nullptr,
                     &matrix);
 
      // TODO: Sometimes the actual number of nonzero entries allocated is
      // greater than the number of nonzero entries, which petsc will complain
      // about unless explicitly disabled with MatSetOption. There is probably a
      // way to prevent a different number nonzero elements being allocated in
      // the first place. (See also previous TODO).
      set_matrix_option(matrix, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      // set symmetric flag, if so requested
      if (is_symmetric == true)
        {
          set_matrix_option(matrix, MAT_SYMMETRIC, PETSC_TRUE);
        }
    }
 
 
    template <typename SparsityPatternType>
    void
    SparseMatrix::do_reinit(const IndexSet &           local_rows,
                            const IndexSet &           local_columns,
                            const SparsityPatternType &sparsity_pattern)
    {
      Assert(sparsity_pattern.n_rows() == local_rows.size(),
             ExcMessage(
               "SparsityPattern and IndexSet have different number of rows"));
      Assert(
        sparsity_pattern.n_cols() == local_columns.size(),
        ExcMessage(
          "SparsityPattern and IndexSet have different number of columns"));
      Assert(local_rows.is_contiguous() && local_columns.is_contiguous(),
             ExcMessage("PETSc only supports contiguous row/column ranges"));
      Assert(local_rows.is_ascending_and_one_to_one(communicator),
             ExcNotImplemented());
 
#  ifdef DEBUG
      {
        // check indexsets
        types::global_dof_index row_owners =
          Utilities::MPI::sum(local_rows.n_elements(), communicator);
        types::global_dof_index col_owners =
          Utilities::MPI::sum(local_columns.n_elements(), communicator);
        Assert(row_owners == sparsity_pattern.n_rows(),
               ExcMessage(
                 std::string(
                   "Each row has to be owned by exactly one owner (n_rows()=") +
                 std::to_string(sparsity_pattern.n_rows()) +
                 " but sum(local_rows.n_elements())=" +
                 std::to_string(row_owners) + ")"));
        Assert(
          col_owners == sparsity_pattern.n_cols(),
          ExcMessage(
            std::string(
              "Each column has to be owned by exactly one owner (n_cols()=") +
            std::to_string(sparsity_pattern.n_cols()) +
            " but sum(local_columns.n_elements())=" +
            std::to_string(col_owners) + ")"));
      }
#  endif
 
 
      // create the matrix. We do not set row length but set the
      // correct SparsityPattern later.
      PetscErrorCode ierr = MatCreate(communicator, &matrix);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      ierr = MatSetSizes(matrix,
                         local_rows.n_elements(),
                         local_columns.n_elements(),
                         sparsity_pattern.n_rows(),
                         sparsity_pattern.n_cols());
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      ierr = MatSetType(matrix, MATMPIAIJ);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
 
      // next preset the exact given matrix
      // entries with zeros. this doesn't avoid any
      // memory allocations, but it at least
      // avoids some searches later on. the
      // key here is that we can use the
      // matrix set routines that set an
      // entire row at once, not a single
      // entry at a time
      //
      // for the usefulness of this option
      // read the documentation of this
      // class.
      // if (preset_nonzero_locations == true)
      if (local_rows.n_elements() > 0)
        {
          // MatMPIAIJSetPreallocationCSR
          // can be used to allocate the sparsity
          // pattern of a matrix
 
          const PetscInt local_row_start = local_rows.nth_index_in_set(0);
          const PetscInt local_row_end =
            local_row_start + local_rows.n_elements();
 
 
          // first set up the column number
          // array for the rows to be stored
          // on the local processor. have one
          // dummy entry at the end to make
          // sure petsc doesn't read past the
          // end
          std::vector<PetscInt>
 
            rowstart_in_window(local_row_end - local_row_start + 1, 0),
            colnums_in_window;
          {
            unsigned int n_cols = 0;
            for (PetscInt i = local_row_start; i < local_row_end; ++i)
              {
                const PetscInt row_length = sparsity_pattern.row_length(i);
                rowstart_in_window[i + 1 - local_row_start] =
                  rowstart_in_window[i - local_row_start] + row_length;
                n_cols += row_length;
              }
            colnums_in_window.resize(n_cols + 1, -1);
          }
 
          // now copy over the information
          // from the sparsity pattern.
          {
            PetscInt *ptr = colnums_in_window.data();
            for (PetscInt i = local_row_start; i < local_row_end; ++i)
              for (typename SparsityPatternType::iterator p =
                     sparsity_pattern.begin(i);
                   p != sparsity_pattern.end(i);
                   ++p, ++ptr)
                *ptr = p->column();
          }
 
 
          // then call the petsc function
          // that summarily allocates these
          // entries:
          ierr = MatMPIAIJSetPreallocationCSR(matrix,
                                              rowstart_in_window.data(),
                                              colnums_in_window.data(),
                                              nullptr);
          AssertThrow(ierr == 0, ExcPETScError(ierr));
        }
      else
        {
          PetscInt i = 0;
          ierr       = MatMPIAIJSetPreallocationCSR(matrix, &i, &i, nullptr);
          AssertThrow(ierr == 0, ExcPETScError(ierr));
        }
      compress(::VectorOperation::insert);
 
      {
        close_matrix(matrix);
        set_keep_zero_rows(matrix);
      }
    }
 
 
    template <typename SparsityPatternType>
    void
    SparseMatrix::do_reinit(
      const SparsityPatternType &   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)
    {
      Assert(local_rows_per_process.size() == local_columns_per_process.size(),
             ExcDimensionMismatch(local_rows_per_process.size(),
                                  local_columns_per_process.size()));
      Assert(this_process < local_rows_per_process.size(), ExcInternalError());
      assert_is_compressed();
 
      // for each row that we own locally, we
      // have to count how many of the
      // entries in the sparsity pattern lie
      // in the column area we have locally,
      // and how many aren't. for this, we
      // first have to know which areas are
      // ours
      size_type local_row_start = 0;
      size_type local_col_start = 0;
      for (unsigned int p = 0; p < this_process; ++p)
        {
          local_row_start += local_rows_per_process[p];
          local_col_start += local_columns_per_process[p];
        }
      const size_type local_row_end =
        local_row_start + local_rows_per_process[this_process];
 
      // create the matrix. We
      // do not set row length but set the
      // correct SparsityPattern later.
      PetscErrorCode ierr = MatCreate(communicator, &matrix);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      ierr = MatSetSizes(matrix,
                         local_rows_per_process[this_process],
                         local_columns_per_process[this_process],
                         sparsity_pattern.n_rows(),
                         sparsity_pattern.n_cols());
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      ierr = MatSetType(matrix, MATMPIAIJ);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      // next preset the exact given matrix
      // entries with zeros, if the user
      // requested so. this doesn't avoid any
      // memory allocations, but it at least
      // avoids some searches later on. the
      // key here is that we can use the
      // matrix set routines that set an
      // entire row at once, not a single
      // entry at a time
      //
      // for the usefulness of this option
      // read the documentation of this
      // class.
      if (preset_nonzero_locations == true)
        {
          // MatMPIAIJSetPreallocationCSR
          // can be used to allocate the sparsity
          // pattern of a matrix if it is already
          // available:
 
          // first set up the column number
          // array for the rows to be stored
          // on the local processor. have one
          // dummy entry at the end to make
          // sure petsc doesn't read past the
          // end
          std::vector<PetscInt>
 
            rowstart_in_window(local_row_end - local_row_start + 1, 0),
            colnums_in_window;
          {
            size_type n_cols = 0;
            for (size_type i = local_row_start; i < local_row_end; ++i)
              {
                const size_type row_length = sparsity_pattern.row_length(i);
                rowstart_in_window[i + 1 - local_row_start] =
                  rowstart_in_window[i - local_row_start] + row_length;
                n_cols += row_length;
              }
            colnums_in_window.resize(n_cols + 1, -1);
          }
 
          // now copy over the information
          // from the sparsity pattern.
          {
            PetscInt *ptr = colnums_in_window.data();
            for (size_type i = local_row_start; i < local_row_end; ++i)
              for (typename SparsityPatternType::iterator p =
                     sparsity_pattern.begin(i);
                   p != sparsity_pattern.end(i);
                   ++p, ++ptr)
                *ptr = p->column();
          }
 
 
          // then call the petsc function
          // that summarily allocates these
          // entries:
          ierr = MatMPIAIJSetPreallocationCSR(matrix,
                                              rowstart_in_window.data(),
                                              colnums_in_window.data(),
                                              nullptr);
          AssertThrow(ierr == 0, ExcPETScError(ierr));
 
          close_matrix(matrix);
          set_keep_zero_rows(matrix);
        }
    }
 
#  ifndef DOXYGEN
    // explicit instantiations
    //
    template SparseMatrix::SparseMatrix(const MPI_Comm &,
                                        const SparsityPattern &,
                                        const std::vector<size_type> &,
                                        const std::vector<size_type> &,
                                        const unsigned int,
                                        const bool);
    template SparseMatrix::SparseMatrix(const MPI_Comm &,
                                        const DynamicSparsityPattern &,
                                        const std::vector<size_type> &,
                                        const std::vector<size_type> &,
                                        const unsigned int,
                                        const bool);
 
    template void
    SparseMatrix::reinit(const MPI_Comm &,
                         const SparsityPattern &,
                         const std::vector<size_type> &,
                         const std::vector<size_type> &,
                         const unsigned int,
                         const bool);
    template void
    SparseMatrix::reinit(const MPI_Comm &,
                         const DynamicSparsityPattern &,
                         const std::vector<size_type> &,
                         const std::vector<size_type> &,
                         const unsigned int,
                         const bool);
 
    template void
    SparseMatrix::reinit(const IndexSet &,
                         const IndexSet &,
                         const SparsityPattern &,
                         const MPI_Comm &);
 
    template void
    SparseMatrix::reinit(const IndexSet &,
                         const IndexSet &,
                         const DynamicSparsityPattern &,
                         const MPI_Comm &);
 
    template void
    SparseMatrix::do_reinit(const SparsityPattern &,
                            const std::vector<size_type> &,
                            const std::vector<size_type> &,
                            const unsigned int,
                            const bool);
    template void
    SparseMatrix::do_reinit(const DynamicSparsityPattern &,
                            const std::vector<size_type> &,
                            const std::vector<size_type> &,
                            const unsigned int,
                            const bool);
 
    template void
    SparseMatrix::do_reinit(const IndexSet &,
                            const IndexSet &,
                            const SparsityPattern &);
 
    template void
    SparseMatrix::do_reinit(const IndexSet &,
                            const IndexSet &,
                            const DynamicSparsityPattern &);
#  endif
 
 
    PetscScalar
    SparseMatrix::matrix_norm_square(const Vector &v) const
    {
      Vector tmp(v);
      vmult(tmp, v);
      // note, that v*tmp returns  sum_i conjugate(v)_i * tmp_i
      return v * tmp;
    }
 
    PetscScalar
    SparseMatrix::matrix_scalar_product(const Vector &u, const Vector &v) const
    {
      Vector tmp(v);
      vmult(tmp, v);
      // note, that v*tmp returns  sum_i conjugate(v)_i * tmp_i
      return u * tmp;
    }
 
    IndexSet
    SparseMatrix::locally_owned_domain_indices() const
    {
      PetscInt       n_rows, n_cols, n_loc_rows, n_loc_cols, min, max;
      PetscErrorCode ierr;
 
      ierr = MatGetSize(matrix, &n_rows, &n_cols);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      ierr = MatGetLocalSize(matrix, &n_loc_rows, &n_loc_cols);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      ierr = MatGetOwnershipRangeColumn(matrix, &min, &max);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      Assert(n_loc_cols == max - min,
             ExcMessage(
               "PETSc is requiring non contiguous memory allocation."));
 
      IndexSet indices(n_cols);
      indices.add_range(min, max);
      indices.compress();
 
      return indices;
    }
 
    IndexSet
    SparseMatrix::locally_owned_range_indices() const
    {
      PetscInt       n_rows, n_cols, n_loc_rows, n_loc_cols, min, max;
      PetscErrorCode ierr;
 
      ierr = MatGetSize(matrix, &n_rows, &n_cols);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      ierr = MatGetLocalSize(matrix, &n_loc_rows, &n_loc_cols);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      ierr = MatGetOwnershipRange(matrix, &min, &max);
      AssertThrow(ierr == 0, ExcPETScError(ierr));
 
      Assert(n_loc_rows == max - min,
             ExcMessage(
               "PETSc is requiring non contiguous memory allocation."));
 
      IndexSet indices(n_rows);
      indices.add_range(min, max);
      indices.compress();
 
      return indices;
    }
 
    void
    SparseMatrix::mmult(SparseMatrix &      C,
                        const SparseMatrix &B,
                        const MPI::Vector & V) const
    {
      // Simply forward to the protected member function of the base class
      // that takes abstract matrix and vector arguments (to which the compiler
      // automatically casts the arguments).
      MatrixBase::mmult(C, B, V);
    }
 
    void
    SparseMatrix::Tmmult(SparseMatrix &      C,
                         const SparseMatrix &B,
                         const MPI::Vector & V) const
    {
      // Simply forward to the protected member function of the base class
      // that takes abstract matrix and vector arguments (to which the compiler
      // automatically casts the arguments).
      MatrixBase::Tmmult(C, B, V);
    }
 
  } // namespace MPI
} // namespace PETScWrappers
 
 
DEAL_II_NAMESPACE_CLOSE
 
#endif // DEAL_II_WITH_PETSC