index_set.cc

// ---------------------------------------------------------------------
//
// Copyright (C) 2005 - 2015 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 at
// the top level of the deal.II distribution.
//
// ---------------------------------------------------------------------

#include <deal.II/base/memory_consumption.h>
#include <deal.II/base/index_set.h>
#include <list>

#ifdef DEAL_II_WITH_TRILINOS
#  ifdef DEAL_II_WITH_MPI
#    include <Epetra_MpiComm.h>
#  endif
#  include <Epetra_SerialComm.h>
#  include <Epetra_Map.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_Map &map)
  :
  is_compressed (true),
  index_space_size (map.NumGlobalElements64()),
  largest_range (numbers::invalid_unsigned_int)
{
  // 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 = (size_type *)map.MyGlobalElements64();
      add_indices(indices, indices+n_indices);
    }
  compress();
}

#else

// this is the standard 32-bit implementation

IndexSet::IndexSet (const Epetra_Map &map)
  :
  is_compressed (true),
  index_space_size (map.NumGlobalElements()),
  largest_range (numbers::invalid_unsigned_int)
{
  // 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 = (unsigned int *)map.MyGlobalElements();
      add_indices(indices, indices+n_indices);
    }
  compress();
}

#endif

#endif // ifdef DEAL_II_WITH_TRILINOS



void
IndexSet::add_range (const size_type begin,
                     const size_type end)
{
  Assert ((begin < index_space_size)
          ||
          ((begin == index_space_size) && (end == index_space_size)),
          ExcIndexRangeType<size_type> (begin, 0, index_space_size));
  Assert (end <= index_space_size,
          ExcIndexRangeType<size_type> (end, 0, index_space_size+1));
  Assert (begin <= end,
          ExcIndexRangeType<size_type> (begin, 0, end));

  if (begin != end)
    {
      const Range new_range(begin,end);

      // the new index might be larger than the last index present in the
      // ranges. Then we can skip the binary search
      if (ranges.size() == 0 || begin > ranges.back().end)
        ranges.push_back(new_range);
      else
        ranges.insert (Utilities::lower_bound (ranges.begin(),
                                               ranges.end(),
                                               new_range),
                       new_range);
      is_compressed = false;
    }
}



void
IndexSet::do_compress () const
{
  // 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());
}



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;
}



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;
}



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 list and
  // add all of them in one go at the end. This is necessary because a growing
  // ranges vector invalidates iterators.
  std::list<Range> temp_list;

  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
          temp_list.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
  for (std::list<Range>::iterator it = temp_list.begin();
       it != temp_list.end();
       ++it)
    add_range(it->begin, it->end);

  compress();
}



void
IndexSet::add_indices(const IndexSet &other,
                      const unsigned int offset)
{
  if ((this == &other) && (offset == 0))
    return;

  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.push_back(Range(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)
{
  size_type s;
  unsigned int numranges;

  in >> s >> numranges;
  ranges.clear();
  set_size(s);
  for (unsigned int i=0; i<numranges; ++i)
    {
      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));
  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;
  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 (std::vector<Range>::iterator it = ranges.begin();
       it != ranges.end();
       ++it)
    for (size_type i=it->begin; i<it->end; ++i)
      indices.push_back (i);

  Assert (indices.size() == n_elements(), ExcInternalError());
}





#ifdef DEAL_II_WITH_TRILINOS

Epetra_Map
IndexSet::make_trilinos_map (const MPI_Comm &communicator,
                             const bool overlapping) const
{
  compress ();

#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 "
                          + Utilities::to_string (n_global_elements) +
                          " whereas the total size of the object to be "
                          "allocated is "
                          + Utilities::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

  if ((is_contiguous() == true) && (!overlapping))
    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[0])
                          :
                          0),
                         0,
#ifdef DEAL_II_WITH_MPI
                         Epetra_MpiComm(communicator));
#else
                         Epetra_SerialComm());
      (void)communicator;
#endif
    }
}


#endif


std::size_t
IndexSet::memory_consumption () const
{
  return (MemoryConsumption::memory_consumption (ranges) +
          MemoryConsumption::memory_consumption (is_compressed) +
          MemoryConsumption::memory_consumption (index_space_size));
}



DEAL_II_NAMESPACE_CLOSE