index_set.cc

Go to the documentation of this file.

// ---------------------------------------------------------------------
//
// Copyright (C) 2005 - 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/base/index_set.h>
#include <deal.II/base/memory_consumption.h>
#include <deal.II/base/mpi.h>
 
#include <vector>
 
#ifdef DEAL_II_WITH_TRILINOS
#  ifdef DEAL_II_WITH_MPI
#    include <Epetra_MpiComm.h>
#  endif
#  include <Epetra_Map.h>
#  include <Epetra_SerialComm.h>
#endif
 
DEAL_II_NAMESPACE_OPEN
 
 
 
#ifdef DEAL_II_WITH_TRILINOS
 
// the 64-bit path uses a few different names, so put that into a separate
// implementation
 
#  ifdef DEAL_II_WITH_64BIT_INDICES
 
IndexSet::IndexSet(const Epetra_BlockMap &map)
  : is_compressed(true)
  , index_space_size(1 + map.MaxAllGID64())
  , largest_range(numbers::invalid_unsigned_int)
{
  Assert(map.MinAllGID64() == 0,
         ExcMessage(
           "The Epetra_BlockMap does not contain the global index 0, "
           "which means some entries are not present on any processor."));
 
  // For a contiguous map, we do not need to go through the whole data...
  if (map.LinearMap())
    add_range(size_type(map.MinMyGID64()), size_type(map.MaxMyGID64() + 1));
  else
    {
      const size_type n_indices = map.NumMyElements();
      size_type *     indices =
        reinterpret_cast<size_type *>(map.MyGlobalElements64());
      add_indices(indices, indices + n_indices);
    }
  compress();
}
 
#  else
 
// this is the standard 32-bit implementation
 
IndexSet::IndexSet(const Epetra_BlockMap &map)
  : is_compressed(true)
  , index_space_size(1 + map.MaxAllGID())
  , largest_range(numbers::invalid_unsigned_int)
{
  Assert(map.MinAllGID() == 0,
         ExcMessage(
           "The Epetra_BlockMap does not contain the global index 0, "
           "which means some entries are not present on any processor."));
 
  // For a contiguous map, we do not need to go through the whole data...
  if (map.LinearMap())
    add_range(size_type(map.MinMyGID()), size_type(map.MaxMyGID() + 1));
  else
    {
      const size_type n_indices = map.NumMyElements();
      unsigned int *  indices =
        reinterpret_cast<unsigned int *>(map.MyGlobalElements());
      add_indices(indices, indices + n_indices);
    }
  compress();
}
 
#  endif
 
#endif // ifdef DEAL_II_WITH_TRILINOS
 
 
 
void
IndexSet::do_compress() const
{
  // we will, in the following, modify mutable variables. this can only
  // work in multithreaded applications if we lock the data structures
  // via a mutex, so that users can call 'const' functions from threads
  // in parallel (and these 'const' functions can then call compress()
  // which itself calls the current function)
  std::lock_guard<std::mutex> lock(compress_mutex);
 
  // see if any of the contiguous ranges can be merged. do not use
  // std::vector::erase in-place as it is quadratic in the number of
  // ranges. since the ranges are sorted by their first index, determining
  // overlap isn't all that hard
  std::vector<Range>::iterator store = ranges.begin();
  for (std::vector<Range>::iterator i = ranges.begin(); i != ranges.end();)
    {
      std::vector<Range>::iterator next = i;
      ++next;
 
      size_type first_index = i->begin;
      size_type last_index  = i->end;
 
      // see if we can merge any of the following ranges
      while (next != ranges.end() && (next->begin <= last_index))
        {
          last_index = std::max(last_index, next->end);
          ++next;
        }
      i = next;
 
      // store the new range in the slot we last occupied
      *store = Range(first_index, last_index);
      ++store;
    }
  // use a compact array with exactly the right amount of storage
  if (store != ranges.end())
    {
      std::vector<Range> new_ranges(ranges.begin(), store);
      ranges.swap(new_ranges);
    }
 
  // now compute indices within set and the range with most elements
  size_type next_index = 0, largest_range_size = 0;
  for (std::vector<Range>::iterator i = ranges.begin(); i != ranges.end(); ++i)
    {
      Assert(i->begin < i->end, ExcInternalError());
 
      i->nth_index_in_set = next_index;
      next_index += (i->end - i->begin);
      if (i->end - i->begin > largest_range_size)
        {
          largest_range_size = i->end - i->begin;
          largest_range      = i - ranges.begin();
        }
    }
  is_compressed = true;
 
  // check that next_index is correct. needs to be after the previous
  // statement because we otherwise will get into an endless loop
  Assert(next_index == n_elements(), ExcInternalError());
}
 
 
 
#ifndef DOXYGEN
IndexSet IndexSet::operator&(const IndexSet &is) const
{
  Assert(size() == is.size(), ExcDimensionMismatch(size(), is.size()));
 
  compress();
  is.compress();
 
  std::vector<Range>::const_iterator r1 = ranges.begin(),
                                     r2 = is.ranges.begin();
  IndexSet result(size());
 
  while ((r1 != ranges.end()) && (r2 != is.ranges.end()))
    {
      // if r1 and r2 do not overlap at all, then move the pointer that sits
      // to the left of the other up by one
      if (r1->end <= r2->begin)
        ++r1;
      else if (r2->end <= r1->begin)
        ++r2;
      else
        {
          // the ranges must overlap somehow
          Assert(((r1->begin <= r2->begin) && (r1->end > r2->begin)) ||
                   ((r2->begin <= r1->begin) && (r2->end > r1->begin)),
                 ExcInternalError());
 
          // add the overlapping range to the result
          result.add_range(std::max(r1->begin, r2->begin),
                           std::min(r1->end, r2->end));
 
          // now move that iterator that ends earlier one up. note that it has
          // to be this one because a subsequent range may still have a chance
          // of overlapping with the range that ends later
          if (r1->end <= r2->end)
            ++r1;
          else
            ++r2;
        }
    }
 
  result.compress();
  return result;
}
#endif
 
 
 
IndexSet
IndexSet::get_view(const size_type begin, const size_type end) const
{
  Assert(begin <= end,
         ExcMessage("End index needs to be larger or equal to begin index!"));
  Assert(end <= size(), ExcMessage("Given range exceeds index set dimension"));
 
  IndexSet                           result(end - begin);
  std::vector<Range>::const_iterator r1 = ranges.begin();
 
  while (r1 != ranges.end())
    {
      if ((r1->end > begin) && (r1->begin < end))
        {
          result.add_range(std::max(r1->begin, begin) - begin,
                           std::min(r1->end, end) - begin);
        }
      else if (r1->begin >= end)
        break;
 
      ++r1;
    }
 
  result.compress();
  return result;
}
 
std::vector<IndexSet>
IndexSet::split_by_block(
  const std::vector<types::global_dof_index> &n_indices_per_block) const
{
  std::vector<IndexSet> partitioned;
  const unsigned int    n_blocks = n_indices_per_block.size();
 
  partitioned.reserve(n_blocks);
  types::global_dof_index start = 0;
  types::global_dof_index sum   = 0;
  for (const auto n_block_indices : n_indices_per_block)
    {
      partitioned.push_back(this->get_view(start, start + n_block_indices));
      start += n_block_indices;
      sum += partitioned.back().size();
    }
  AssertDimension(sum, this->size());
  return partitioned;
}
 
void
IndexSet::subtract_set(const IndexSet &other)
{
  compress();
  other.compress();
  is_compressed = false;
 
 
  // we save new ranges to be added to our IndexSet in an temporary vector and
  // add all of them in one go at the end.
  std::vector<Range> new_ranges;
 
  std::vector<Range>::iterator own_it   = ranges.begin();
  std::vector<Range>::iterator other_it = other.ranges.begin();
 
  while (own_it != ranges.end() && other_it != other.ranges.end())
    {
      // advance own iterator until we get an overlap
      if (own_it->end <= other_it->begin)
        {
          ++own_it;
          continue;
        }
      // we are done with other_it, so advance
      if (own_it->begin >= other_it->end)
        {
          ++other_it;
          continue;
        }
 
      // Now own_it and other_it overlap.  First save the part of own_it that
      // is before other_it (if not empty).
      if (own_it->begin < other_it->begin)
        {
          Range r(own_it->begin, other_it->begin);
          r.nth_index_in_set = 0; // fix warning of unused variable
          new_ranges.push_back(r);
        }
      // change own_it to the sub range behind other_it. Do not delete own_it
      // in any case. As removal would invalidate iterators, we just shrink
      // the range to an empty one.
      own_it->begin = other_it->end;
      if (own_it->begin > own_it->end)
        {
          own_it->begin = own_it->end;
          ++own_it;
        }
 
      // continue without advancing iterators, the right one will be advanced
      // next.
    }
 
  // Now delete all empty ranges we might
  // have created.
  for (std::vector<Range>::iterator it = ranges.begin(); it != ranges.end();)
    {
      if (it->begin >= it->end)
        it = ranges.erase(it);
      else
        ++it;
    }
 
  // done, now add the temporary ranges
  const std::vector<Range>::iterator end = new_ranges.end();
  for (std::vector<Range>::iterator it = new_ranges.begin(); it != end; ++it)
    add_range(it->begin, it->end);
 
  compress();
}
 
 
 
IndexSet
IndexSet::tensor_product(const IndexSet &other) const
{
  IndexSet set(this->size() * other.size());
  for (const auto el : *this)
    set.add_indices(other, el * other.size());
  set.compress();
  return set;
}
 
 
 
IndexSet::size_type
IndexSet::pop_back()
{
  Assert(is_empty() == false,
         ExcMessage(
           "pop_back() failed, because this IndexSet contains no entries."));
 
  const size_type index = ranges.back().end - 1;
  --ranges.back().end;
 
  if (ranges.back().begin == ranges.back().end)
    ranges.pop_back();
 
  return index;
}
 
 
 
IndexSet::size_type
IndexSet::pop_front()
{
  Assert(is_empty() == false,
         ExcMessage(
           "pop_front() failed, because this IndexSet contains no entries."));
 
  const size_type index = ranges.front().begin;
  ++ranges.front().begin;
 
  if (ranges.front().begin == ranges.front().end)
    ranges.erase(ranges.begin());
 
  // We have to set this in any case, because nth_index_in_set is no longer
  // up to date for all but the first range
  is_compressed = false;
 
  return index;
}
 
 
 
void
IndexSet::add_indices(const IndexSet &other, const size_type offset)
{
  if ((this == &other) && (offset == 0))
    return;
 
  if (other.ranges.size() != 0)
    {
      AssertIndexRange(other.ranges.back().end - 1, index_space_size);
    }
 
  compress();
  other.compress();
 
  std::vector<Range>::const_iterator r1 = ranges.begin(),
                                     r2 = other.ranges.begin();
 
  std::vector<Range> new_ranges;
  // just get the start and end of the ranges right in this method, everything
  // else will be done in compress()
  while (r1 != ranges.end() || r2 != other.ranges.end())
    {
      // the two ranges do not overlap or we are at the end of one of the
      // ranges
      if (r2 == other.ranges.end() ||
          (r1 != ranges.end() && r1->end < (r2->begin + offset)))
        {
          new_ranges.push_back(*r1);
          ++r1;
        }
      else if (r1 == ranges.end() || (r2->end + offset) < r1->begin)
        {
          new_ranges.emplace_back(r2->begin + offset, r2->end + offset);
          ++r2;
        }
      else
        {
          // ok, we do overlap, so just take the combination of the current
          // range (do not bother to merge with subsequent ranges)
          Range next(std::min(r1->begin, r2->begin + offset),
                     std::max(r1->end, r2->end + offset));
          new_ranges.push_back(next);
          ++r1;
          ++r2;
        }
    }
  ranges.swap(new_ranges);
 
  is_compressed = false;
  compress();
}
 
 
 
void
IndexSet::write(std::ostream &out) const
{
  compress();
  out << size() << " ";
  out << ranges.size() << std::endl;
  std::vector<Range>::const_iterator r = ranges.begin();
  for (; r != ranges.end(); ++r)
    {
      out << r->begin << " " << r->end << std::endl;
    }
}
 
 
 
void
IndexSet::read(std::istream &in)
{
  AssertThrow(in, ExcIO());
 
  size_type    s;
  unsigned int n_ranges;
 
  in >> s >> n_ranges;
  ranges.clear();
  set_size(s);
  for (unsigned int i = 0; i < n_ranges; ++i)
    {
      AssertThrow(in, ExcIO());
 
      size_type b, e;
      in >> b >> e;
      add_range(b, e);
    }
}
 
 
void
IndexSet::block_write(std::ostream &out) const
{
  AssertThrow(out, ExcIO());
  out.write(reinterpret_cast<const char *>(&index_space_size),
            sizeof(index_space_size));
  std::size_t n_ranges = ranges.size();
  out.write(reinterpret_cast<const char *>(&n_ranges), sizeof(n_ranges));
  if (ranges.empty() == false)
    out.write(reinterpret_cast<const char *>(&*ranges.begin()),
              ranges.size() * sizeof(Range));
  AssertThrow(out, ExcIO());
}
 
void
IndexSet::block_read(std::istream &in)
{
  size_type   size;
  std::size_t n_ranges;
  in.read(reinterpret_cast<char *>(&size), sizeof(size));
  in.read(reinterpret_cast<char *>(&n_ranges), sizeof(n_ranges));
  // we have to clear ranges first
  ranges.clear();
  set_size(size);
  ranges.resize(n_ranges, Range(0, 0));
  if (n_ranges)
    in.read(reinterpret_cast<char *>(&*ranges.begin()),
            ranges.size() * sizeof(Range));
 
  do_compress(); // needed so that largest_range can be recomputed
}
 
 
 
void
IndexSet::fill_index_vector(std::vector<size_type> &indices) const
{
  compress();
 
  indices.clear();
  indices.reserve(n_elements());
 
  for (const auto &range : ranges)
    for (size_type entry = range.begin; entry < range.end; ++entry)
      indices.push_back(entry);
 
  Assert(indices.size() == n_elements(), ExcInternalError());
}
 
 
 
#ifdef DEAL_II_WITH_TRILINOS
#  ifdef DEAL_II_TRILINOS_WITH_TPETRA
 
Tpetra::Map<int, types::global_dof_index>
IndexSet::make_tpetra_map(const MPI_Comm &communicator,
                          const bool      overlapping) const
{
  compress();
  (void)communicator;
 
#    ifdef DEBUG
  if (!overlapping)
    {
      const size_type n_global_elements =
        Utilities::MPI::sum(n_elements(), communicator);
      Assert(n_global_elements == size(),
             ExcMessage("You are trying to create an Tpetra::Map object "
                        "that partitions elements of an index set "
                        "between processors. However, the union of the "
                        "index sets on different processors does not "
                        "contain all indices exactly once: the sum of "
                        "the number of entries the various processors "
                        "want to store locally is " +
                        std::to_string(n_global_elements) +
                        " whereas the total size of the object to be "
                        "allocated is " +
                        std::to_string(size()) +
                        ". In other words, there are "
                        "either indices that are not spoken for "
                        "by any processor, or there are indices that are "
                        "claimed by multiple processors."));
    }
#    endif
 
  // Find out if the IndexSet is ascending and 1:1. This corresponds to a
  // linear Tpetra::Map. Overlapping IndexSets are never 1:1.
  const bool linear =
    overlapping ? false : is_ascending_and_one_to_one(communicator);
  if (linear)
    return Tpetra::Map<int, types::global_dof_index>(
      size(),
      n_elements(),
      0,
#    ifdef DEAL_II_WITH_MPI
      Teuchos::rcp(new Teuchos::MpiComm<int>(communicator))
#    else
      Teuchos::rcp(new Teuchos::Comm<int>())
#    endif
    );
  else
    {
      std::vector<size_type> indices;
      fill_index_vector(indices);
      std::vector<types::global_dof_index> int_indices(indices.size());
      std::copy(indices.begin(), indices.end(), int_indices.begin());
      const Teuchos::ArrayView<types::global_dof_index> arr_view(int_indices);
      return Tpetra::Map<int, types::global_dof_index>(
        size(),
        arr_view,
        0,
#    ifdef DEAL_II_WITH_MPI
        Teuchos::rcp(new Teuchos::MpiComm<int>(communicator))
#    else
        Teuchos::rcp(new Teuchos::Comm<int>())
#    endif
      );
    }
}
#  endif
 
 
 
Epetra_Map
IndexSet::make_trilinos_map(const MPI_Comm &communicator,
                            const bool      overlapping) const
{
  compress();
  (void)communicator;
 
#  ifdef DEBUG
  if (!overlapping)
    {
      const size_type n_global_elements =
        Utilities::MPI::sum(n_elements(), communicator);
      Assert(n_global_elements == size(),
             ExcMessage("You are trying to create an Epetra_Map object "
                        "that partitions elements of an index set "
                        "between processors. However, the union of the "
                        "index sets on different processors does not "
                        "contain all indices exactly once: the sum of "
                        "the number of entries the various processors "
                        "want to store locally is " +
                        std::to_string(n_global_elements) +
                        " whereas the total size of the object to be "
                        "allocated is " +
                        std::to_string(size()) +
                        ". In other words, there are "
                        "either indices that are not spoken for "
                        "by any processor, or there are indices that are "
                        "claimed by multiple processors."));
    }
#  endif
 
  // Find out if the IndexSet is ascending and 1:1. This corresponds to a
  // linear EpetraMap. Overlapping IndexSets are never 1:1.
  const bool linear =
    overlapping ? false : is_ascending_and_one_to_one(communicator);
 
  if (linear)
    return Epetra_Map(TrilinosWrappers::types::int_type(size()),
                      TrilinosWrappers::types::int_type(n_elements()),
                      0,
#  ifdef DEAL_II_WITH_MPI
                      Epetra_MpiComm(communicator)
#  else
                      Epetra_SerialComm()
#  endif
    );
  else
    {
      std::vector<size_type> indices;
      fill_index_vector(indices);
      return Epetra_Map(
        TrilinosWrappers::types::int_type(-1),
        TrilinosWrappers::types::int_type(n_elements()),
        (n_elements() > 0 ?
           reinterpret_cast<TrilinosWrappers::types::int_type *>(
             indices.data()) :
           nullptr),
        0,
#  ifdef DEAL_II_WITH_MPI
        Epetra_MpiComm(communicator)
#  else
        Epetra_SerialComm()
#  endif
      );
    }
}
#endif
 
 
 
bool
IndexSet::is_ascending_and_one_to_one(const MPI_Comm &communicator) const
{
  // If the sum of local elements does not add up to the total size,
  // the IndexSet can't be complete.
  const size_type n_global_elements =
    Utilities::MPI::sum(n_elements(), communicator);
  if (n_global_elements != size())
    return false;
 
  if (n_global_elements == 0)
    return true;
 
#ifdef DEAL_II_WITH_MPI
  // Non-contiguous IndexSets can't be linear.
  const bool all_contiguous =
    (Utilities::MPI::min(is_contiguous() ? 1 : 0, communicator) == 1);
  if (!all_contiguous)
    return false;
 
  bool is_globally_ascending = true;
  // we know that there is only one interval
  types::global_dof_index first_local_dof = (n_elements() > 0) ?
                                              *(begin_intervals()->begin()) :
                                              numbers::invalid_dof_index;
 
  const unsigned int my_rank = Utilities::MPI::this_mpi_process(communicator);
  const std::vector<types::global_dof_index> global_dofs =
    Utilities::MPI::gather(communicator, first_local_dof, 0);
 
  if (my_rank == 0)
    {
      // find out if the received std::vector is ascending
      types::global_dof_index index = 0;
      while (global_dofs[index] == numbers::invalid_dof_index)
        ++index;
      types::global_dof_index old_dof = global_dofs[index++];
      for (; index < global_dofs.size(); ++index)
        {
          const types::global_dof_index new_dof = global_dofs[index];
          if (new_dof != numbers::invalid_dof_index)
            {
              if (new_dof <= old_dof)
                {
                  is_globally_ascending = false;
                  break;
                }
              else
                old_dof = new_dof;
            }
        }
    }
 
  // now broadcast the result
  int is_ascending = is_globally_ascending ? 1 : 0;
  int ierr         = MPI_Bcast(&is_ascending, 1, MPI_INT, 0, communicator);
  AssertThrowMPI(ierr);
 
  return (is_ascending == 1);
#else
  return true;
#endif // DEAL_II_WITH_MPI
}
 
 
 
std::size_t
IndexSet::memory_consumption() const
{
  return (MemoryConsumption::memory_consumption(ranges) +
          MemoryConsumption::memory_consumption(is_compressed) +
          MemoryConsumption::memory_consumption(index_space_size) +
          sizeof(compress_mutex));
}
 
 
 
DEAL_II_NAMESPACE_CLOSE