parallel_dual_graph_impl.hpp

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/*
 * Copyright (c) 2013-2015:  G-CSC, Goethe University Frankfurt
 * Author: Sebastian Reiter
 * 
 * This file is part of UG4.
 * 
 * UG4 is free software: you can redistribute it and/or modify it under the
 * terms of the GNU Lesser General Public License version 3 (as published by the
 * Free Software Foundation) with the following additional attribution
 * requirements (according to LGPL/GPL v3 §7):
 * 
 * (1) The following notice must be displayed in the Appropriate Legal Notices
 * of covered and combined works: "Based on UG4 (www.ug4.org/license)".
 * 
 * (2) The following notice must be displayed at a prominent place in the
 * terminal output of covered works: "Based on UG4 (www.ug4.org/license)".
 * 
 * (3) The following bibliography is recommended for citation and must be
 * preserved in all covered files:
 * "Reiter, S., Vogel, A., Heppner, I., Rupp, M., and Wittum, G. A massively
 *   parallel geometric multigrid solver on hierarchically distributed grids.
 *   Computing and visualization in science 16, 4 (2013), 151-164"
 * "Vogel, A., Reiter, S., Rupp, M., Nägel, A., and Wittum, G. UG4 -- a novel
 *   flexible software system for simulating pde based models on high performance
 *   computers. Computing and visualization in science 16, 4 (2013), 165-179"
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU Lesser General Public License for more details.
 */
 
#ifndef __H__UG__parallel_dual_graph_impl__
#define __H__UG__parallel_dual_graph_impl__
 
#include "parallel_dual_graph.h"
#include "compol_gather_vec_attachment.h"
#include "compol_copy_attachment.h"
#include "../distributed_grid.h"
 
namespace ug{
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
ParallelDualGraph(MultiGrid* pmg) :
  m_procCom(pcl::PCD_EMPTY),
  m_pMG(NULL)
{
  if(pmg)
    set_grid(pmg);
}
ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
~ParallelDualGraph()
{
  if(m_pMG)
    detach_data();
}
ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
void ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
set_grid(MultiGrid* pmg)
{
  if(m_pMG == pmg)
    return;
 
  if(m_pMG)
    detach_data();
 
  m_pMG = pmg;
  if(m_pMG)
    attach_data();
}
void ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
TIndexType ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
num_graph_vertices()
{
  if(m_adjacencyMapStructure.empty())
    return 0;
 
  return (TIndexType)m_adjacencyMapStructure.size() - 1;
}
TIndexType ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
TIndexType ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
num_graph_edges()
{
  return (TIndexType)m_adjacencyMap.size();
}
TIndexType ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
TIndexType* ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
adjacency_map_structure()
{
  UG_ASSERT(!m_adjacencyMapStructure.empty(),
        "Call generate graph before calling this method!");
  return &m_adjacencyMapStructure.front();
}
TIndexType* ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
TIndexType* ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
adjacency_map()
{
  UG_ASSERT(!m_adjacencyMap.empty(),
        "Call generate graph before calling this method!");
  return &m_adjacencyMap.front();
}
TIndexType* ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
TIndexType* ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
parallel_offset_map()
{
  UG_ASSERT(!m_nodeOffsetMap.empty(),
        "Call generate graph before calling this method!");
  return &m_nodeOffsetMap.front();
}
TIndexType* ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
bool ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
was_considered(TGeomBaseObj* o)
{
  UG_ASSERT(m_pMG, "A MultiGrid has to be set!");
  return m_aaElemIndex[o] != -1;
}
bool ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
void ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
attach_data()
{
  assert(m_pMG);
  m_pMG->attach_to<TGeomBaseObj>(m_aElemIndex);
  m_pMG->attach_to<TConnectingObj>(m_aElemIndices);
  m_aaElemIndex.access(*m_pMG, m_aElemIndex);
  m_aaElemIndices.access(*m_pMG, m_aElemIndices);
}
void ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
void ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
detach_data()
{
  assert(m_pMG);
  m_pMG->detach_from<TGeomBaseObj>(m_aElemIndex);
  m_pMG->detach_from<TConnectingObj>(m_aElemIndices);
  m_aaElemIndex.invalidate();
  m_aaElemIndices.invalidate();
}
void ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
 
template <class TGeomBaseObj, class TIndexType, class TConnectingObj>
void ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>::
generate_graph(int level, pcl::ProcessCommunicator procCom)
{
  GDIST_PROFILE_FUNC();
  UG_DLOG(LIB_GRID, 1, "ParallelDualGraph-start generate_graph\n");
  UG_ASSERT(m_pMG, "A MultiGrid has to be set!");
 
  using namespace std;
  typedef TGeomBaseObj Elem;
  typedef TConnectingObj ConElem;
  typedef typename geometry_traits<Elem>::iterator ElemIterator;
  typedef typename geometry_traits<ConElem>::iterator ConElemIterator;
 
  MultiGrid& mg = *m_pMG;
  Grid::AttachmentAccessor<TGeomBaseObj, AElemIndex>& aaInd = m_aaElemIndex;
  Grid::AttachmentAccessor<TConnectingObj, AElemIndices>& aaConInds = m_aaElemIndices;
 
  DistributedGridManager& distGridMgr = *mg.distributed_grid_manager();
  GridLayoutMap& glm = distGridMgr.grid_layout_map();
 
//  init the indices and count ghosts and normal elements on the fly
  size_t numElems = 0;
  m_elems.clear();
  {
    for(ElemIterator iter = mg.begin<Elem>(level);
      iter != mg.end<Elem>(level); ++iter)
    {
      if(distGridMgr.is_ghost(*iter))
        aaInd[*iter] = -1;
      else{
        aaInd[*iter] = numElems++;
        m_elems.push_back(*iter);
      }
    }
  }
 
//  generate a local procCom, which only contains processes which actually contain elements.
  m_procCom = procCom.create_sub_communicator(numElems > 0);
 
//  generate the nodeOffsetMap and determine the localNodeOffset
  UG_DLOG(LIB_GRID, 2, "ParallelDualGraph-generate_graph: gathering element numbers\n");
  m_nodeOffsetMap.clear();
  int localNodeOffset = 0;
 
  if(!m_procCom.empty()){
    int numElemsTmp = (int)numElems;
    vector<int> elemCounts(m_procCom.size());
      m_procCom.allgather(&numElemsTmp, 1, PCL_DT_INT,
                &elemCounts.front(), 1, PCL_DT_INT);
 
    m_nodeOffsetMap.resize(m_procCom.size() + 1);
    int numElemsTotal = 0;
    for(size_t i = 0; i < elemCounts.size(); ++i){
      m_nodeOffsetMap[i] = numElemsTotal;
      numElemsTotal += elemCounts[i];
    }
    m_nodeOffsetMap[elemCounts.size()] = numElemsTotal;
    localNodeOffset = m_nodeOffsetMap[m_procCom.get_local_proc_id()];
 
    UG_DLOG(LIB_GRID, 2, "ParallelDualGraph-generate_graph: gathering indices of connected elements\n");
  //  we have to gather indices of connected elements in connecting elements.
  //  This is required since we have to communicate those indices between distributed
  //  connecting elements.
    typename Grid::traits<Elem>::secure_container elems;
    for(ConElemIterator iter = mg.begin<ConElem>(level);
      iter != mg.end<ConElem>(level); ++iter)
    {
      ConElem* ce = *iter;
      aaConInds[ce].clear();
      mg.associated_elements(elems, ce);
      for(size_t i = 0; i < elems.size(); ++i){
        if(aaInd[elems[i]] != -1)
          aaConInds[ce].push_back(localNodeOffset + aaInd[elems[i]]);
      }
    }
  }
 
//  communicate connected elements between horizontal interfaces on this level
  typedef typename GridLayoutMap::Types<ConElem>::Layout::LevelLayout Layout;
  pcl::InterfaceCommunicator<Layout> com;
 
  ComPol_GatherVecAttachment<Layout, AElemIndices> compolGather(mg, m_aElemIndices);
  if(glm.has_layout<ConElem>(INT_H_SLAVE)){
    com.send_data(glm.get_layout<ConElem>(INT_H_SLAVE).layout_on_level(level),
            compolGather);
  }
  if(glm.has_layout<ConElem>(INT_H_MASTER)){
    com.receive_data(glm.get_layout<ConElem>(INT_H_MASTER).layout_on_level(level),
             compolGather);
  }
  com.communicate();
 
  ComPol_CopyAttachment<Layout, AElemIndices> compolCopy(mg, m_aElemIndices);
  if(glm.has_layout<ConElem>(INT_H_MASTER)){
    com.send_data(glm.get_layout<ConElem>(INT_H_MASTER).layout_on_level(level),
            compolCopy);
  }
  if(glm.has_layout<ConElem>(INT_H_SLAVE)){
    com.receive_data(glm.get_layout<ConElem>(INT_H_SLAVE).layout_on_level(level),
             compolCopy);
  }
  com.communicate();
 
  UG_DLOG(LIB_GRID, 2, "ParallelDualGraph-generate_graph: building adjacency structure\n");
//  init the adjacencyMapStructure
  m_adjacencyMapStructure.resize(numElems + 1);
  m_adjacencyMapStructure[0] = 0;
  m_adjacencyMap.clear();
  m_connections.clear();
 
//  generate adjacency structure.
  typename Grid::traits<ConElem>::secure_container conElems;
  if(ConElem::dim == Elem::dim - 1){
    int ind = 0;
    for(ElemIterator iter = mg.begin<Elem>(level); iter != mg.end<Elem>(level); ++iter)
    {
      Elem* elem = *iter;
      int eInd = aaInd[elem];
      if(eInd == -1)
        continue;
      eInd += localNodeOffset;
 
    //  store first entry at which the connections will be written to the map
      assert(ind < (int)m_adjacencyMapStructure.size());
      m_adjacencyMapStructure[ind] = m_adjacencyMap.size();
 
      mg.associated_elements(conElems, elem);
    //  iterate over the neighbors and push adjacent indices to the adjacencyMap
      for(size_t i_con = 0; i_con < conElems.size(); ++i_con){
        std::vector<int>& conInds = aaConInds[conElems[i_con]];
        for(size_t i = 0; i < conInds.size(); ++i){
          UG_ASSERT(conInds[i] != -1, "ghosts should be ignored when assigning conInds.");
          if(conInds[i] != eInd){
            m_adjacencyMap.push_back(conInds[i]);
            m_connections.push_back(conElems[i_con]);
          }
        }
      }
      ++ind;
    }
    assert(ind == (int)m_adjacencyMapStructure.size() - 1);
  }
  else{
  //  if ConElem::dim < Elem::dim - 1 then we have to check whether indices have
  //  already been added...
    UG_THROW("Currently a dual graph can only be created if elements are"
        " connected via their sides. Since nearly everything is prepared,"
        " implementing this step for arbitrary connecting elements shouldn't"
        " be much work.");
  }
 
//  add the final element
  m_adjacencyMapStructure[m_adjacencyMapStructure.size() - 1] = m_adjacencyMap.size();
  UG_DLOG(LIB_GRID, 1, "ParallelDualGraph-stop generate_graph\n");
}
void ParallelDualGraph<TGeomBaseObj, TIndexType, TConnectingObj>:: {…}
 
}// end of namespace
 
#endif