MeshDistributor.cc

//
// Software License for AMDiS
//
// Copyright (c) 2010 Dresden University of Technology 
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
// This file is part of AMDiS
//
// See also license.opensource.txt in the distribution.


#include <algorithm>
#include <iostream>
#include <fstream>
#include <limits>
#include <stdint.h>
#include <boost/lexical_cast.hpp>
#include <boost/filesystem.hpp>

#include "parallel/MeshDistributor.h"
#include "parallel/MeshManipulation.h"
#include "parallel/ParallelDebug.h"
#include "parallel/StdMpi.h"
#include "parallel/MeshPartitioner.h"
#include "parallel/ParMetisPartitioner.h"
#include "parallel/ZoltanPartitioner.h"
#include "parallel/SimplePartitioner.h"
#include "parallel/CheckerPartitioner.h"
#include "parallel/MpiHelper.h"
#include "parallel/DofComm.h"
#include "parallel/ParallelProblemStatBase.h"
#include "io/ElementFileWriter.h"
#include "io/MacroInfo.h"
#include "io/MacroWriter.h"
#include "io/VtkWriter.h"
#include "io/ArhReader.h"
#include "Mesh.h"
#include "Traverse.h"
#include "ElInfo.h"
#include "Element.h"
#include "MacroElement.h"
#include "DOFMatrix.h"
#include "DOFVector.h"
#include "SystemVector.h"
#include "ElementDofIterator.h"
#include "ProblemStatBase.h"
#include "StandardProblemIteration.h"
#include "VertexVector.h"
#include "MeshStructure.h"
#include "ProblemStat.h"
#include "ProblemInstat.h"
#include "RefinementManager3d.h"
#include "Debug.h"

namespace AMDiS {

  using boost::lexical_cast;
  using namespace boost::filesystem;
  using namespace std;

  MeshDistributor* MeshDistributor::globalMeshDistributor = NULL;

  const Flag MeshDistributor::BOUNDARY_SUBOBJ_SORTED              = 0X01L;
  const Flag MeshDistributor::BOUNDARY_FILL_INFO_SEND_DOFS        = 0X02L;
  const Flag MeshDistributor::BOUNDARY_FILL_INFO_RECV_DOFS        = 0X04L;

  inline bool cmpDofsByValue(const DegreeOfFreedom* dof1, const DegreeOfFreedom* dof2)
  {
    return (*dof1 < *dof2);
  }

  MeshDistributor::MeshDistributor()
    : problemStat(0),
      initialized(false),
      name("parallel"),
      mesh(NULL),
      refineManager(NULL),
      partitioner(NULL),
      deserialized(false),
      writeSerializationFile(false),
      repartitioningAllowed(false),
      repartitionIthChange(20),
      repartitioningWaitAfterFail(20),
      nMeshChangesAfterLastRepartitioning(0),
      repartitioningCounter(0),
      repartitioningFailed(0),

      debugOutputDir(""),
      lastMeshChangeIndex(0),
      createBoundaryDofFlag(0),
      boundaryDofInfo(1),
      meshAdaptivity(true),
      hasPeriodicBoundary(false),
      printTimings(false)
  {
    FUNCNAME("MeshDistributor::ParalleDomainBase()");

    mpiComm = MPI::COMM_WORLD;
    mpiRank = mpiComm.Get_rank();
    mpiSize = mpiComm.Get_size();

    Parameters::get(name + "->repartitioning", repartitioningAllowed);
    Parameters::get(name + "->debug output dir", debugOutputDir);
    Parameters::get(name + "->repartition ith change", repartitionIthChange);
    Parameters::get(name + "->repartition wait after fail", repartitioningWaitAfterFail);
    Parameters::get(name + "->mesh adaptivity", meshAdaptivity);
    
    string partStr = "parmetis";
    Parameters::get(name + "->partitioner", partStr);

    if (partStr == "parmetis") 
      partitioner = new ParMetisPartitioner(&mpiComm);

    if (partStr == "zoltan") {
#ifdef HAVE_ZOLTAN
      partitioner = new ZoltanPartitioner(&mpiComm);
#else
      ERROR_EXIT("AMDiS was compiled without Zoltan support. Therefore you cannot make use of it!\n");
#endif
    }

    if (partStr == "checker")
      partitioner = new CheckerPartitioner(&mpiComm);

    if (partStr == "simple")
      partitioner = new SimplePartitioner(&mpiComm);

    int tmp = 0;
    Parameters::get(name + "->box partitioning", tmp);
    partitioner->setBoxPartitioning(static_cast<bool>(tmp));

    Parameters::get(name + "->print timings", printTimings);

    TEST_EXIT(partitioner)("Could not create partitioner \"%s\"!\n", partStr.c_str());
  }


  MeshDistributor::~MeshDistributor()
  {
    if (partitioner)
      delete partitioner;
  }


  void MeshDistributor::initParallelization()
  {
    FUNCNAME("MeshDistributor::initParallelization()");

    if (initialized)
      return;

    double first = MPI::Wtime();
    MSG("Initialization phase 1 needed %.5f seconds\n", 
	first - ParallelProblemStatBase::initTimeStamp);

    TEST_EXIT(mpiSize > 1)
      ("Parallelization does not work with only one process!\n");
    TEST_EXIT(feSpaces.size() > 0)
      ("No FE space has been defined for the mesh distributor!\n");
    TEST_EXIT(mesh)("No mesh has been defined for the mesh distributor!\n");

    // === Sort FE spaces with respect to the degree of the basis ===
    // === functions. Use stuiped bubble sort for this.           ===

    bool doNext = false;
    do {
      doNext = false;
      for (unsigned int i = 0; i < feSpaces.size() - 1; i++) {
	if (feSpaces[i]->getBasisFcts()->getDegree() >
	    feSpaces[i + 1]->getBasisFcts()->getDegree()) {
	  const FiniteElemSpace *tmp = feSpaces[i + 1];
	  feSpaces[i + 1] = feSpaces[i];
	  feSpaces[i] = tmp;
	  doNext = true;
	}
      }
    } while (doNext);

    elObjDb.setFeSpace(feSpaces[0]);

    // If required, create hierarchical mesh level structure.
    createMeshLevelStructure();

    // If the problem has been already read from a file, we need only to set
    // isRankDofs to all matrices and rhs vector and to remove periodic 
    // boundary conditions (if there are some).
    if (deserialized) {
      createMeshLevelStructure();
      
      updateMacroElementInfo();

      removePeriodicBoundaryConditions();

      elObjDb.createMacroElementInfo(allMacroElements);

      updateLocalGlobalNumbering();

      elObjDb.setData(partitionMap, levelData);

#if (DEBUG != 0)
      TEST_EXIT_DBG(dofMaps.size())("No DOF mapping defined!\n");
      ParallelDebug::writeDebugFile(feSpaces[feSpaces.size() - 1], 
				    *(dofMaps[0]), 
				    debugOutputDir + "mpi-dbg", "dat");
#endif    

      initialized = true;
      return;
    }


    // Create a very first pariitioning of the mesh.
    createInitialPartitioning();


#if (DEBUG != 0)    
    debug::ElementIdxToDofs elMap;
    debug::createSortedDofs(mesh, elMap);
#endif

    if (mpiRank == 0) {
#if (DEBUG != 0)    
      int writePartMesh = 1;
#else
      int writePartMesh = 0;
#endif
      Parameters::get("parallel->debug->write mesh partitioning", writePartMesh);

      if (writePartMesh > 0) {
	debug::writeElementIndexMesh(mesh , debugOutputDir + "elementIndex");
	ParallelDebug::writePartitioning(*this, debugOutputDir + "part.vtu");
      }
    }

    // Create interior boundary information.
    createInteriorBoundary(true);

    // === Remove neighbourhood relations due to periodic bounday conditions. ===

    for (deque<MacroElement*>::iterator it = mesh->firstMacroElement();
	 it != mesh->endOfMacroElements(); ++it) {
      for (int i = 0; i < mesh->getGeo(NEIGH); i++) {
	if ((*it)->getNeighbour(i) && 
	    mesh->isPeriodicAssociation((*it)->getBoundary(i))) {

	  int neighIndex = (*it)->getNeighbour(i)->getIndex();

	  (*it)->getNeighbour(i)->setNeighbour((*it)->getOppVertex(i), NULL);
	  (*it)->setNeighbour(i, NULL);
	  (*it)->setBoundary(i, 0);

	  macroElementNeighbours[(*it)->getIndex()][i] = -1;
	  macroElementNeighbours[neighIndex][(*it)->getOppVertex(i)] = -1;
	}
      }
    }

    for (vector<MacroElement*>::iterator it = allMacroElements.begin();
	 it != allMacroElements.end(); ++it) {
      for (int i = 0; i < mesh->getGeo(NEIGH); i++) {
	if ((*it)->getNeighbour(i) && 
	    mesh->isPeriodicAssociation((*it)->getBoundary(i))) {

	  int neighIndex = (*it)->getNeighbour(i)->getIndex();

	  (*it)->getNeighbour(i)->setNeighbour((*it)->getOppVertex(i), NULL);
	  (*it)->setNeighbour(i, NULL);
	  (*it)->setBoundary(i, 0);

	  macroElementNeighbours[(*it)->getIndex()][i] = -1;
	  macroElementNeighbours[neighIndex][(*it)->getOppVertex(i)] = -1;

	}
      }
    }

    // === Remove all macro elements that are not part of the rank partition. ===

    removeMacroElements();

    // === Create new global and local DOF numbering. ===


    // We have to remove the VertexVectors, which contain periodic assoiciations, 
    // because they are not valid anymore after some macro elements have been
    // removed and the corresponding DOFs were deleted.
    for (map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
	 it != mesh->getPeriodicAssociations().end(); ++it)
      const_cast<DOFAdmin&>(mesh->getDofAdmin(0)).removeDOFContainer(dynamic_cast<DOFContainer*>(it->second));

    updateLocalGlobalNumbering();


    // === In 3D we have to fix the mesh to allow local refinements. ===

    fix3dMeshRefinement();


    // === If in debug mode, make some tests. ===

#if (DEBUG != 0)
    MSG("AMDiS runs in debug mode, so make some test ...\n");

    ParallelDebug::testAllElements(*this);
    debug::testSortedDofs(mesh, elMap);
    ParallelDebug::testInteriorBoundary(*this);
    ParallelDebug::followBoundary(*this);

    debug::writeMesh(feSpaces[0], -1, debugOutputDir + "macro_mesh");   

    MSG("Debug mode tests finished!\n");
#endif

    // Remove periodic boundary conditions in sequential problem definition. 
    removePeriodicBoundaryConditions();

#if (DEBUG != 0)
    ParallelDebug::testPeriodicBoundary(*this);
#endif

    // === Global refinements. ===
    
    int globalRefinement = 0;
    Parameters::get(mesh->getName() + "->global refinements", globalRefinement);
    
    if (globalRefinement > 0) {
      refineManager->globalRefine(mesh, globalRefinement);
     
      updateLocalGlobalNumbering();

#if (DEBUG != 0)
    ParallelDebug::testPeriodicBoundary(*this);
#endif
    }

    // And delete some data, we there is no mesh adaptivty.
    if (!meshAdaptivity)
      elObjDb.clear();

    initialized = true;
    MSG("Init parallelization needed %.5f seconds\n", MPI::Wtime() - first);
  }


  void MeshDistributor::createInitialPartitioning()
  {
    FUNCNAME("MeshDistributor::createInitialPartitioning()");

    // Test, if the mesh is the macro mesh only! Paritioning of the mesh is
    // supported only for macro meshes, so it will not work yet if the mesh is
    // already refined in some way.
    testForMacroMesh();

    // For later mesh repartitioning, we need to store some information about
    // the macro mesh.
    createMacroElementInfo();

    // create an initial partitioning of the mesh
    bool useInitialPartitioning = partitioner->createInitialPartitioning();

    // set the element weights, which are 1 at the very first begin
    setInitialElementWeights();

    if (!useInitialPartitioning) {
      // and now partition the mesh    
      bool partitioningSucceed = partitioner->partition(elemWeights, INITIAL);
      TEST_EXIT(partitioningSucceed)("Initial partitioning does not work!\n");
    }

    partitioner->createPartitionMap(partitionMap);
  }


  void MeshDistributor::setInitialElementWeights() 
  {
    FUNCNAME("MeshDistributor::setInitialElementWeights()");

    elemWeights.clear();
      
    string filename = "";
    Parameters::get(mesh->getName() + "->macro weights", filename);
    if (filename != "") {
      MSG("Read macro weights from %s\n", filename.c_str());

      ifstream infile;
      infile.open(filename.c_str(), ifstream::in);
      while (!infile.eof()) {
	int elNum, elWeight;
	infile >> elNum;
	if (infile.eof())
	  break;
	infile >> elWeight;

	elemWeights[elNum] = elWeight;
      }

      infile.close();

      return;
    }

    filename = "";
    Parameters::get("parallel->partitioner->read meta arh", filename);
    if (filename != "") {
      map<int, int> arhElInRank;
      map<int, int> arhElCodeSize;

      int nProc = ArhReader::readMetaData(filename, arhElInRank, arhElCodeSize);
      for (map<int, int>::iterator it = arhElCodeSize.begin(); 
	   it != arhElCodeSize.end(); ++it)
	elemWeights[it->first] = it->second;

      return;
    }

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
    while (elInfo) {
      elemWeights[elInfo->getElement()->getIndex()] = 1.0;
      elInfo = stack.traverseNext(elInfo);    
    }
  }


  void MeshDistributor::addProblemStat(ProblemStatSeq *probStat)
  {
    FUNCNAME("MeshDistributor::addProblemStat()");

    TEST_EXIT_DBG(probStat->getFeSpaces().size())
      ("No FE spaces in stationary problem!\n");


    // === Add all FE spaces from stationary problem. ===

    vector<const FiniteElemSpace*> newFeSpaces = probStat->getFeSpaces();
    for (int i = 0; i < static_cast<int>(newFeSpaces.size()); i++)
      if (find(feSpaces.begin(), feSpaces.end(), newFeSpaces[i]) == 
	  feSpaces.end())
	feSpaces.push_back(newFeSpaces[i]);
    

    // === Add mesh of stationary problem and create a corresponding  ===
    // === refinement manager object.                                 ===
    
    if (mesh != NULL) {
      TEST_EXIT(mesh == probStat->getMesh())
	("Does not yet support for different meshes!\n");
    } else {
      mesh = probStat->getMesh();
    }
    
    switch (mesh->getDim()) {
    case 2:
      refineManager = new RefinementManager2d();
      break;
    case 3:
      refineManager = new RefinementManager3d();
      break;
    default:
      ERROR_EXIT("This should not happen for dim = %d!\n", mesh->getDim());
    }
    
    partitioner->setMesh(mesh);
    

    // === Check whether the stationary problem should be serialized. ===


    // Create parallel serialization file writer, if needed.
    int writeSerialization = 0;
    Parameters::get(probStat->getName() + "->output->write serialization",  
		    writeSerialization);
    if (writeSerialization && !writeSerializationFile) {
      string filename = "";
      Parameters::get(name + "->output->serialization filename", filename);
      
      TEST_EXIT(filename != "")
	("No filename defined for parallel serialization file!\n");

      int tsModulo = -1;
      Parameters::get(probStat->getName() + "->output->write every i-th timestep", 
		      tsModulo);
      
      probStat->getFileWriterList().push_back(new Serializer<MeshDistributor>(this, filename, tsModulo));
      writeSerializationFile = true;
    }    


    // === Check whether the stationary problem should be deserialized. ===

    int readSerialization = 0;
    Parameters::get(probStat->getName() + "->input->read serialization", 
		    readSerialization);
    if (readSerialization) {
      string filename = "";
      Parameters::get(probStat->getName() + "->input->serialization filename", 
		      filename);
      filename += ".p" + lexical_cast<string>(mpiRank);
      MSG("Start deserialization with %s\n", filename.c_str());
      ifstream in(filename.c_str());

      TEST_EXIT(!in.fail())("Could not open deserialization file: %s\n",
			    filename.c_str());

      // Read the revision number of the AMDiS version which was used to create 
      // the serialization file.
      int revNumber = -1;
      SerUtil::deserialize(in, revNumber);

      probStat->deserialize(in);
      in.close();
      MSG("Deserialization from file: %s\n", filename.c_str());

      filename = "";
      Parameters::get(name + "->input->serialization filename", filename);
      
      TEST_EXIT(filename != "")
	("No filename defined for parallel deserialization file!\n");
      
      string rankFilename = filename + ".p" + lexical_cast<string>(mpiRank);
      in.open(rankFilename.c_str());
      
      TEST_EXIT(!in.fail())("Could not open parallel deserialization file: %s\n",
			    filename.c_str());

      // Read the revision number of the AMDiS version which was used to create 
      // the serialization file.
      revNumber = -1;
      SerUtil::deserialize(in, revNumber);
      
      deserialize(in);
      in.close();
      MSG("Deserializtion of mesh distributor from file: %s\n", rankFilename.c_str());
      deserialized = true;
    }

    problemStat.push_back(probStat);


    // === If the mesh distributor is already initialized, don't forget to  ===
    // === remove the periodic boundary conditions on these objects.        ===

    if (initialized)
      removePeriodicBoundaryConditions(probStat);
  }


  void MeshDistributor::addProblemStatGlobal(ProblemStatSeq *probStat)
  {
    FUNCNAME("MeshDistributor::addProblemStatGlobal()");

    if (globalMeshDistributor == NULL)
      globalMeshDistributor = new MeshDistributor();

    globalMeshDistributor->addProblemStat(probStat);
  }


  void MeshDistributor::exitParallelization()
  {}


  void MeshDistributor::registerDofMap(ParallelDofMapping &dofMap)
  {
    FUNCNAME("MeshDistributor::registerDofMap()");

    TEST_EXIT(find(dofMaps.begin(), dofMaps.end(), &dofMap) ==
	      dofMaps.end())
      ("Parallel DOF mapping already registerd in mesh distributor object!\n");

    dofMaps.push_back(&dofMap);
  }


  void MeshDistributor::removeDofMap(ParallelDofMapping &dofMap)
  {
    FUNCNAME("MeshDistributor::removeDofMap()");

    vector<ParallelDofMapping*>::iterator it = 
      find(dofMaps.begin(), dofMaps.end(), &dofMap);

    TEST_EXIT(it != dofMaps.end())
      ("Cannot find Parallel DOF mapping object which should be removed!\n");

    dofMaps.erase(it);
  }


  void MeshDistributor::testForMacroMesh()
  {
    FUNCNAME("MeshDistributor::testForMacroMesh()");

    int nMacroElements = 0;

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
    while (elInfo) {
      TEST_EXIT(elInfo->getLevel() == 0)
	("Mesh is already refined! This does not work with parallelization!\n");

      TEST_EXIT(elInfo->getType() == 0)
	("Only macro elements with level 0 are supported!\n");
      
      nMacroElements++;

      elInfo = stack.traverseNext(elInfo);
    }

    TEST_EXIT(nMacroElements >= mpiSize)
      ("The mesh has less macro elements than number of mpi processes!\n");
  }


  void MeshDistributor::synchVector(SystemVector &vec, int level)
  {
    FUNCNAME("MeshDistributor::synchVector()");

    TEST_EXIT_DBG(level >= 0 && level <= 1)("Wrong level number!\n");

    MPI::Intracomm &levelComm = levelData.getMpiComm(level);
    DofComm &dc = (level == 0 ? dofComm : dofCommSd);

    StdMpi<vector<double> > stdMpi(levelComm);

    for (DofComm::Iterator it(dc.getSendDofs()); 
	 !it.end(); it.nextRank()) {
      vector<double> dofs;

      for (int i = 0; i < vec.getSize(); i++) {
	DOFVector<double> &dofVec = *(vec.getDOFVector(i));
	for (it.beginDofIter(vec.getFeSpace(i)); !it.endDofIter(); it.nextDof())
	  dofs.push_back(dofVec[it.getDofIndex()]);
      }

      int rank = it.getRank();
      if (level > 0)
	rank = levelData.mapRank(rank, 0, level);
      stdMpi.send(rank, dofs);
    }
	   
    for (DofComm::Iterator it(dc.getRecvDofs()); !it.end(); it.nextRank()) {
      int rank = it.getRank();
      if (level > 0)
	rank = levelData.mapRank(rank, 0, level);
      stdMpi.recv(rank);
    }

    stdMpi.startCommunication();

    for (DofComm::Iterator it(dc.getRecvDofs()); !it.end(); it.nextRank()) {
      int rank = it.getRank();
      if (level > 0)
	rank = levelData.mapRank(rank, 0, level);

      int counter = 0;
      vector<double> &recvData =  stdMpi.getRecvData(rank);

      for (int i = 0; i < vec.getSize(); i++) {
	DOFVector<double> &dofVec = *(vec.getDOFVector(i));

	for (it.beginDofIter(vec.getFeSpace(i)); !it.endDofIter(); it.nextDof()) {
	  TEST_EXIT_DBG(counter < recvData.size())
	    ("Recv data from rank %d has only %d entries!\n", rank, recvData.size());
	  dofVec[it.getDofIndex()] = recvData[counter++];
	}
      }
    }
  }


  void MeshDistributor::fix3dMeshRefinement()
  {
    FUNCNAME("MeshDistributor::fix3dMeshRefinement()");

    if (mesh->getDim() != 3)
      return;

    MPI::COMM_WORLD.Barrier();
    double first = MPI::Wtime();


    // === Create set of all edges and all macro element indices in rank's ===
    // === subdomain.                                                      ===

    std::set<DofEdge> allEdges;
    std::set<int> rankMacroEls;

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
    while (elInfo) {
      for (int i = 0; i < mesh->getGeo(EDGE); i++) {
	ElementObjectData elData(elInfo->getElement()->getIndex(), i);
	DofEdge e = elObjDb.getEdgeLocalMap(elData);
	allEdges.insert(e);
      }

      rankMacroEls.insert(elInfo->getElement()->getIndex());

      elInfo = stack.traverseNext(elInfo);
    }


    // === Reset fixed edges, and start new search for edges that must  ===
    // === be fixed.                                                    ===

    FixRefinementPatch::connectedEdges.clear();

    // Traverse all edges
    for (std::set<DofEdge>::iterator it = allEdges.begin(); it != allEdges.end(); ++it) {
      // For each edge get all macro elements that contain this edge.
      vector<ElementObjectData>& edgeEls = elObjDb.getElements(*it);

      TEST_EXIT_DBG(edgeEls.size() > 0)
	("No edge %d/%d in elObjDB!\n", it->first, it->second);


      // We have now to check, if the current edge connects two macro elements,
      // which are otherwise not connected. 

      // All elements on this edge.
      std::set<int> allEls;
      // Maps from each element index to the local edge index of the common edge.
      map<int, int> edgeNoInEl;

      for (unsigned int i = 0; i < edgeEls.size(); i++) {
	if (rankMacroEls.count(edgeEls[i].elIndex)) {
	  allEls.insert(edgeEls[i].elIndex);
	  edgeNoInEl[edgeEls[i].elIndex] = edgeEls[i].ithObject;
	}
      }
           
      TEST_EXIT_DBG(!allEls.empty())("Should not happen!\n");


      // If there is only one element in rank on this edge, there is nothing 
      // to do.
      if (allEls.size() == 1)
	continue;
      
      // Create a set of element index sets. All element within one set are 
      // neighbours of each other, but can not reach any other element of the
      // other index sets by neighbourhood relations.
      vector<std::set<int> > disconnectedEls;
      helpToFix(allEls, edgeNoInEl, disconnectedEls);   
      
      // Fix the edges
      for (int dc0 = 0; dc0 < static_cast<int>(disconnectedEls.size()); dc0++) {
	for (int dc1 = 0; dc1 < static_cast<int>(disconnectedEls.size()); dc1++) {
	  if (dc0 == dc1)
	    continue;   
	  
	  int elIdx = *(disconnectedEls[dc1].begin());
	  pair<Element*, int> edge0 = 
	    make_pair(elObjDb.getElementPtr(elIdx), edgeNoInEl[elIdx]);
	  
	  for (std::set<int>::iterator elIt = disconnectedEls[dc0].begin();
	       elIt != disconnectedEls[dc0].end(); ++elIt) {
	    pair<Element*, int> edge1 = 
	      make_pair(elObjDb.getElementPtr(*elIt), edgeNoInEl[*elIt]);

#if (DEBUG != 0)
	    DofEdge dofEdge0 = edge0.first->getEdge(edge0.second);
	    DofEdge dofEdge1 = edge1.first->getEdge(edge1.second);
	    
	    WorldVector<double> c0, c1;
	    mesh->getDofIndexCoords(dofEdge0.first, feSpaces[0], c0);
	    mesh->getDofIndexCoords(dofEdge0.second, feSpaces[0], c1);
	    
	    // 	      MSG("FOUND EDGE %d/%d <-> %d/%d\n", 
	    // 		  edge0.first->getIndex(), edge0.second,
	    // 		  edge1.first->getIndex(), edge1.second);
	    
	    // 	      MSG("FOUND EDGE: %d %d with coords %f %f %f   %f %f %f\n",
	    // 		  dofEdge0.first, dofEdge0.second, 
	    // 		  c0[0], c0[1], c0[2],
	    // 		  c1[0], c1[1], c1[2]);
	    
	    TEST_EXIT_DBG(dofEdge0 == dofEdge1)("Should noth happen!\n");
#endif

	    FixRefinementPatch::connectedEdges.push_back(make_pair(edge1, edge0));
	  }
	}	  
      }
    }


    MPI::COMM_WORLD.Barrier();
    MSG("Fix 3D mesh refinement needed %.5f seconds\n", MPI::Wtime() - first);
  }


  void MeshDistributor::helpToFix(std::set<int> &elems, 
				  map<int, int> &edgeNoInEl,
				  vector<std::set<int> > &disconnectedEls)
  {
    std::set<int> firstElem;
    firstElem.insert(*(elems.begin()));

    std::set<int> otherElems(++(elems.begin()), elems.end());
    
    bool found = false;      
    do {
      found = false;
      for (std::set<int>::iterator elIt = firstElem.begin(); elIt != firstElem.end(); ++elIt) {
	for (int i = 0; i < mesh->getGeo(NEIGH); i++) {
	  int neighEl = macroElementNeighbours[*elIt][i];
	  if (neighEl != -1 && otherElems.count(neighEl)) {
	    firstElem.insert(neighEl);
	    otherElems.erase(neighEl);
	    found = true;
	  }
	}
	
	if (found)
	  break;
      }
    } while (found);

    disconnectedEls.push_back(firstElem);
    if (otherElems.size())
      helpToFix(otherElems, edgeNoInEl, disconnectedEls);
  }


  void MeshDistributor::getAllBoundaryDofs(const FiniteElemSpace *feSpace,
					   int level,
					   DofContainer& dofs)
  {
    FUNCNAME("MeshDistributor::getAllBoundaryDofs()");

    DofContainerSet dofSet;
    for (DofComm::Iterator it(dofComm.getSendDofs(), level, feSpace); 
	 !it.end(); it.nextRank())
      dofSet.insert(it.getDofs().begin(), it.getDofs().end());
    for (DofComm::Iterator it(dofComm.getRecvDofs(), level, feSpace); 
	 !it.end(); it.nextRank())
      dofSet.insert(it.getDofs().begin(), it.getDofs().end());

    dofs.clear();
    dofs.insert(dofs.begin(), dofSet.begin(), dofSet.end());
  }


  void MeshDistributor::removePeriodicBoundaryConditions()
  {
    FUNCNAME("MeshDistributor::removePeriodicBoundaryConditions()");

    // Remove periodic boundaries in boundary manager on matrices and vectors.
    for (unsigned int i = 0; i < problemStat.size(); i++)
      removePeriodicBoundaryConditions(problemStat[i]);

    // Remove periodic boundaries on elements in mesh.
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
    while (elInfo) {
      elInfo->getElement()->deleteElementData(PERIODIC);
      elInfo = stack.traverseNext(elInfo);
    }    

    // Remove periodic vertex associations
    mesh->getPeriodicAssociations().clear();
  }


  void MeshDistributor::removePeriodicBoundaryConditions(ProblemStatSeq *probStat)
  {
    FUNCNAME("MeshDistributor::removePeriodicBoundaryConditions()");

    int nComponents = probStat->getNumComponents();

    for (int j = 0; j < nComponents; j++) {
      for (int k = 0; k < nComponents; k++) {
	DOFMatrix* mat = probStat->getSystemMatrix(j, k);
	if (mat && mat->getBoundaryManager())
	  removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(mat->getBoundaryManager()->getBoundaryConditionMap()));
      }
      
      if (probStat->getSolution()->getDOFVector(j)->getBoundaryManager())
	removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(probStat->getSolution()->getDOFVector(j)->getBoundaryManager()->getBoundaryConditionMap()));
      
      if (probStat->getRhs()->getDOFVector(j)->getBoundaryManager())
	removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(probStat->getRhs()->getDOFVector(j)->getBoundaryManager()->getBoundaryConditionMap()));
    }
  }


  void MeshDistributor::removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap)
  {
    FUNCNAME("MeshDistributor::removePeriodicBoundaryConditions()");

    BoundaryIndexMap::iterator it = boundaryMap.begin();
    while (it != boundaryMap.end()) {
      if (it->second->isPeriodic())
	boundaryMap.erase(it++);
      else
	++it;      
    }    
  }


  void MeshDistributor::createMeshLevelStructure()
  {
    FUNCNAME("MeshDistributor::createMeshLevelStructure()");

    if (mpiSize != 16)
      return;

    std::set<int> neighbours;
    switch (mpiRank) {
    case 0:
      neighbours.insert(1); neighbours.insert(2); neighbours.insert(3);
      break;
    case 1:
      neighbours.insert(0); neighbours.insert(4); neighbours.insert(2); neighbours.insert(3); neighbours.insert(6);
      break;
    case 2:
      neighbours.insert(0); neighbours.insert(1); neighbours.insert(3); neighbours.insert(8); neighbours.insert(9);
      break;
    case 3:
      neighbours.insert(0); neighbours.insert(1); neighbours.insert(4); 
      neighbours.insert(2); neighbours.insert(6);
      neighbours.insert(8); neighbours.insert(9); neighbours.insert(12); 
      break;
    case 4:
      neighbours.insert(1); neighbours.insert(3); neighbours.insert(6); neighbours.insert(7); neighbours.insert(5);
      break;
    case 5:
      neighbours.insert(4); neighbours.insert(6); neighbours.insert(7);
      break;
    case 6:
      neighbours.insert(1); neighbours.insert(4); neighbours.insert(5); 
      neighbours.insert(3); neighbours.insert(7);
      neighbours.insert(9); neighbours.insert(12); neighbours.insert(13);