ParallelDomainBase.cc

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

#include "parallel/ParallelDomainBase.h"
#include "parallel/ParallelDomainDbg.h"
#include "parallel/StdMpi.h"
#include "ParMetisPartitioner.h"
#include "Mesh.h"
#include "Traverse.h"
#include "ElInfo.h"
#include "Element.h"
#include "MacroElement.h"
#include "PartitionElementData.h"
#include "DOFMatrix.h"
#include "DOFVector.h"
#include "SystemVector.h"
#include "VtkWriter.h"
#include "ElementDofIterator.h"
#include "ProblemStatBase.h"
#include "StandardProblemIteration.h"
#include "ElementFileWriter.h"
#include "VertexVector.h"
#include "MeshStructure.h"
#include "ProblemVec.h"
#include "ProblemInstat.h"
#include "Debug.h"

namespace AMDiS {

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

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


  MeshDistributor::MeshDistributor(std::string str)
    : probStat(0),
      name(str),
      feSpace(NULL),
      mesh(NULL),
      refineManager(NULL),
      info(10),
      partitioner(NULL),
      initialPartitionMesh(true),
      nRankDofs(0),
      nOverallDofs(0),
      rstart(0),
      deserialized(false),
      writeSerializationFile(false),
      lastMeshChangeIndex(0),
      macroElementStructureConsisten(false)
  {
    FUNCNAME("MeshDistributor::ParalleDomainBase()");

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


  void MeshDistributor::initParallelization(AdaptInfo *adaptInfo)
  {
    FUNCNAME("MeshDistributor::initParallelization()");

    TEST_EXIT(mpiSize > 1)
      ("Parallelization does not work with only one process!\n");

    TEST_EXIT(mesh)("No mesh has been defined for mesh distribution!\n");

    // If the problem has been already read from a file, we do not need to do anything.
    if (deserialized)
      return;
    

    // 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();


    // create an initial partitioning of the mesh
    partitioner->createPartitionData();
    // set the element weights, which are 1 at the very first begin
    setElemWeights(adaptInfo);
    // and now partition the mesh
    partitionMesh(adaptInfo);   


#if (DEBUG != 0)
    debug::ElementIdxToDofs elMap;
    debug::createSortedDofs(mesh, elMap);
    if (mpiRank == 0) {
      int writePartMesh = 1;
      GET_PARAMETER(0, "dbg->write part mesh", "%d", &writePartMesh);

      if (writePartMesh > 0)
	writePartitioningMesh("part.vtu");
      else 
	MSG("Skip write part mesh!\n");
    }

    ParallelDomainDbg::testAllElements(*this);
#endif


    // === Create interior boundary information. ===

    createInteriorBoundaryInfo();

#if (DEBUG != 0)
    ParallelDomainDbg::printBoundaryInfo(*this);
#endif


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

    createLocalGlobalNumbering();


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

    removeMacroElements();
    macroElementStructureConsisten = true;


    // === Reset all DOFAdmins of the mesh. ===

    updateDofAdmins();


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

#if (DEBUG != 0)
    MSG("AMDiS runs in debug mode, so make some test ...\n");
    debug::testSortedDofs(mesh, elMap);
    ParallelDomainDbg::testInteriorBoundary(*this);
    ParallelDomainDbg::testCommonDofs(*this, true);
    MSG("Debug mode tests finished!\n");

    debug::writeMesh(feSpace, -1, "macro_mesh");   
#endif


    // === Create periodic dof mapping, if there are periodic boundaries. ===

    createPeriodicMap();


    // === Global refinements. ===

    int globalRefinement = 0;
    GET_PARAMETER(0, mesh->getName() + "->global refinements", "%d", &globalRefinement);

    if (globalRefinement > 0) {
      refineManager->globalRefine(mesh, globalRefinement);

#if (DEBUG != 0)
      debug::writeMesh(feSpace, -1, "gr_mesh");
#endif

      updateLocalGlobalNumbering();
      
      // === Update periodic mapping, if there are periodic boundaries. ===
      
      createPeriodicMap();
    }


    /// === Set DOF rank information to all matrices and vectors. ===

    for (unsigned int i = 0; i < probStat.size(); i++) {
      int nComponents = probStat[i]->getNumComponents();
      for (int j = 0; j < nComponents; j++) {
	for (int k = 0; k < nComponents; k++)
	  if (probStat[i]->getSystemMatrix(j, k))
	    probStat[i]->getSystemMatrix(j, k)->setRankDofs(isRankDof);

	TEST_EXIT_DBG(probStat[i]->getRhs()->getDOFVector(j))("No RHS vector!\n");
	TEST_EXIT_DBG(probStat[i]->getSolution()->getDOFVector(j))("No solution vector!\n");
	
	probStat[i]->getRhs()->getDOFVector(j)->setRankDofs(isRankDof);
	probStat[i]->getSolution()->getDOFVector(j)->setRankDofs(isRankDof);
      }
    }


    // === Remove periodic boundary conditions in sequential problem definition. ===

    // Remove periodic boundaries in boundary manager on matrices and vectors.
    for (unsigned int i = 0; i < probStat.size(); i++) {
      int nComponents = probStat[i]->getNumComponents();

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

    // 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);
    }    
  }


  void MeshDistributor::addProblemStat(ProblemVec *probVec)
  {
    FUNCNAME("MeshDistributor::addProblemVec()");

    if (feSpace != NULL) {
      std::vector<FiniteElemSpace*> feSpaces = probVec->getFeSpaces();
      for (unsigned int i = 0; i < feSpaces.size(); i++) {
	TEST_EXIT(feSpace == feSpaces[i])
	  ("Parallelizaton is not supported for multiple FE spaces!\n");
      }
    } else {
      feSpace = probVec->getFeSpace(0);
      mesh = feSpace->getMesh();
      info = probVec->getInfo();
      
      TEST_EXIT(mesh->getNumberOfDOFAdmin() == 1)
	("Only meshes with one DOFAdmin are supported!\n");
      TEST_EXIT(mesh->getDOFAdmin(0).getNumberOfPreDOFs(0) == 0)
	("Wrong pre dof number for DOFAdmin!\n");
      
      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 = new ParMetisPartitioner(mesh, &mpiComm);
    }

    // Create parallel serialization file writer, if needed.
    int writeSerialization = 0;
    GET_PARAMETER(0, probVec->getName() + "->output->write serialization", "%d", 
		  &writeSerialization);
    if (writeSerialization && !writeSerializationFile) {
      std::string f = "";
      GET_PARAMETER(0, probVec->getName() + "->output->serialization filename", &f);
      path myPath(f);
      std::string meshFilename = 
	myPath.parent_path().directory_string() + "/meshDistributor.ser";


      int tsModulo = -1;
      GET_PARAMETER(0, probVec->getName() + "->output->write every i-th timestep", 
		    "%d", &tsModulo);
      
      probVec->getFileWriterList().push_back(new Serializer<MeshDistributor>(this, meshFilename, tsModulo));
      writeSerializationFile = true;
    }    

    int readSerialization = 0;
    GET_PARAMETER(0, probVec->getName() + "->input->read serialization", "%d", 
		  &readSerialization);
    if (readSerialization) {
      std::string filename = "";
      GET_PARAMETER(0, probVec->getName() + "->input->serialization filename", &filename);
      filename += ".p" + lexical_cast<std::string>(mpiRank);
      MSG("Start deserialization with %s\n", filename.c_str());
      std::ifstream in(filename.c_str());
      probVec->deserialize(in);
      in.close();
      MSG("Deserialization from file: %s\n", filename.c_str());

      if (!deserialized) {
	GET_PARAMETER(0, probVec->getName() + "->input->serialization filename", &filename);
	path myPath(filename);
	std::string meshFilename = 
	  myPath.parent_path().directory_string() + "/meshDistributor.ser.p" + 
	  lexical_cast<std::string>(mpiRank);
	std::ifstream in(meshFilename.c_str());
	deserialize(in);
	in.close();
	MSG("Deserializtion of mesh distributor from file: %s\n", meshFilename.c_str());
	deserialized = true;
      }
    }

    probStat.push_back(probVec);
  }


  void MeshDistributor::exitParallelization(AdaptInfo *adaptInfo)
  {}

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

    for (int i = 0; i < mesh->getNumberOfDOFAdmin(); i++) {
      DOFAdmin& admin = const_cast<DOFAdmin&>(mesh->getDOFAdmin(i));

      // There must be always more allocated DOFs than used DOFs in DOFAdmin. Otherwise,
      // it is not possible to define a first DOF hole.
      if (static_cast<unsigned int>(admin.getSize()) == mapLocalGlobalDofs.size())
	admin.enlargeDOFLists();
      
      for (int j = 0; j < admin.getSize(); j++)
	admin.setDOFFree(j, true);
      for (unsigned int j = 0; j < mapLocalGlobalDofs.size(); j++)
 	admin.setDOFFree(j, false);

      admin.setUsedSize(mapLocalGlobalDofs.size());
      admin.setUsedCount(mapLocalGlobalDofs.size());
      admin.setFirstHole(mapLocalGlobalDofs.size());
    }
  }


  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");
      
      nMacroElements++;

      elInfo = stack.traverseNext(elInfo);
    }

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


  void MeshDistributor::synchVector(DOFVector<double> &vec)
  {
    StdMpi<std::vector<double> > stdMpi(mpiComm);

    for (RankToDofContainer::iterator sendIt = sendDofs.begin();
	 sendIt != sendDofs.end(); ++sendIt) {
      std::vector<double> dofs;
      int nSendDofs = sendIt->second.size();
      dofs.reserve(nSendDofs);
      
      for (int i = 0; i < nSendDofs; i++)
	dofs.push_back(vec[*((sendIt->second)[i])]);

      stdMpi.send(sendIt->first, dofs);
    }

    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
	 recvIt != recvDofs.end(); ++recvIt)
      stdMpi.recv(recvIt->first, recvIt->second.size());

    stdMpi.startCommunication<double>(MPI_DOUBLE);

    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
	 recvIt != recvDofs.end(); ++recvIt)
      for (unsigned int i = 0; i < recvIt->second.size(); i++)
	vec[*(recvIt->second)[i]] = stdMpi.getRecvData(recvIt->first)[i];
  }


  void MeshDistributor::synchVector(SystemVector &vec)
  {
    int nComponents = vec.getSize();
    StdMpi<std::vector<double> > stdMpi(mpiComm);

    for (RankToDofContainer::iterator sendIt = sendDofs.begin();
	 sendIt != sendDofs.end(); ++sendIt) {
      std::vector<double> dofs;
      int nSendDofs = sendIt->second.size();
      dofs.reserve(nComponents * nSendDofs);
      
      for (int i = 0; i < nComponents; i++) {
	DOFVector<double> *dofvec = vec.getDOFVector(i);
	for (int j = 0; j < nSendDofs; j++)
	  dofs.push_back((*dofvec)[*((sendIt->second)[j])]);
      }

      stdMpi.send(sendIt->first, dofs);
    }

    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
	 recvIt != recvDofs.end(); ++recvIt)
      stdMpi.recv(recvIt->first, recvIt->second.size() * nComponents);

    stdMpi.startCommunication<double>(MPI_DOUBLE);

    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
	 recvIt != recvDofs.end(); ++recvIt) {
      int nRecvDofs = recvIt->second.size();

      int counter = 0;
      for (int i = 0; i < nComponents; i++) {
	DOFVector<double> *dofvec = vec.getDOFVector(i);
 	for (int j = 0; j < nRecvDofs; j++)
	  (*dofvec)[*(recvIt->second)[j]] = 
	    stdMpi.getRecvData(recvIt->first)[counter++];
      }
    }
  }


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


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

#if (DEBUG != 0)
    debug::writeMesh(feSpace, -1, "before_check_mesh");
#endif

    // === If mesh has not been changed on all ranks, return. ===

    int recvAllValues = 0;
    int sendValue = static_cast<int>(mesh->getChangeIndex() != lastMeshChangeIndex);
    mpiComm.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);

    if (recvAllValues == 0)
      return;

    // === At least one rank mesh has been changed, so the boundaries must be ===
    // === adapted to the new mesh structure.                                 ===

    clock_t first = clock();
    
    do {
      // To check the interior boundaries, the ownership of the boundaries is not 
      // important. Therefore, we add all boundaries to one boundary container.
      RankToBoundMap allBound;

      for (InteriorBoundary::iterator it(myIntBoundary); !it.end(); ++it)
	if (it->rankObj.subObj == EDGE || it->rankObj.subObj == FACE)
	  allBound[it.getRank()].push_back(*it);

      for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it)
	if (it->rankObj.subObj == EDGE || it->rankObj.subObj == FACE)
	  allBound[it.getRank()].push_back(*it);


      // === Check the boundaries and adapt mesh if necessary. ===

#if (DEBUG != 0)
      MSG("Run checkAndAdaptBoundary ...\n");
#endif

      bool meshChanged = checkAndAdaptBoundary(allBound);

      // === Check on all ranks if at least one rank's mesh has changed. ===

      int sendValue = static_cast<int>(!meshChanged);
      recvAllValues = 0;
      mpiComm.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);

#if (DEBUG != 0)
      MSG("Mesh changed on %d ranks!\n", recvAllValues);
#endif
    } while (recvAllValues != 0);


#if (DEBUG != 0)
    debug::writeMesh(feSpace, -1, "mesh");
#endif

    INFO(info, 8)("Parallel mesh adaption needed %.5f seconds\n", 
		  TIME_USED(first, clock()));

    // === Because the mesh has been changed, update the DOF numbering and mappings. ===

    mesh->dofCompress();
    updateLocalGlobalNumbering();

    // === Update periodic mapping, if there are periodic boundaries. ===

    createPeriodicMap();
  }

  
  bool MeshDistributor::checkAndAdaptBoundary(RankToBoundMap &allBound)
  {
    FUNCNAME("MeshDistributor::checkAndAdaptBoundary()");

    // === Create mesh structure codes for all ranks boundary elements. ===
       
    std::map<int, MeshCodeVec> sendCodes;
   
    for (RankToBoundMap::iterator it = allBound.begin(); it != allBound.end(); ++it) {
      for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt) {
	MeshStructure elCode;
	elCode.init(boundIt->rankObj);
	sendCodes[it->first].push_back(elCode);
      }
    }

    StdMpi<MeshCodeVec> stdMpi(mpiComm, true);
    stdMpi.send(sendCodes);
    stdMpi.recv(allBound);
    stdMpi.startCommunication<unsigned long int>(MPI_UNSIGNED_LONG);
 
    // === Compare received mesh structure codes. ===
    
    bool meshFitTogether = true;

    for (RankToBoundMap::iterator it = allBound.begin(); it != allBound.end(); ++it) {
      
      MeshCodeVec &recvCodes = stdMpi.getRecvData()[it->first];
      int i = 0;
      
      for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt) {

	MeshStructure elCode;	
	elCode.init(boundIt->rankObj);
	
	if (elCode.getCode() != recvCodes[i].getCode()) {
	  TEST_EXIT_DBG(refineManager)("Refinement manager is not set correctly!\n");

	  bool b = fitElementToMeshCode(recvCodes[i], 
					boundIt->rankObj.el,
					boundIt->rankObj.subObj,
					boundIt->rankObj.ithObj, 
					boundIt->rankObj.elType,
					boundIt->rankObj.reverseMode);  

	  if (b)
	    meshFitTogether = false;
	}
	
	i++;
      }
    }

    return meshFitTogether;
  }


  bool MeshDistributor::fitElementToMeshCode(MeshStructure &code, 
					     Element *el, 
					     GeoIndex subObj,
					     int ithObj, 
					     int elType,
					     bool reverseMode)
  {
    FUNCNAME("MeshDistributor::fitElementToMeshCode()");

    TEST_EXIT_DBG(el)("No element given!\n");

    if (code.empty())
      return false;

    int s1 = el->getSubObjOfChild(0, subObj, ithObj, elType);
    int s2 = el->getSubObjOfChild(1, subObj, ithObj, elType);

    TEST_EXIT_DBG(s1 != -1 || s2 != -1)("This should not happen!\n");

    bool meshChanged = false;
    Flag traverseFlag = 
      Mesh::CALL_EVERY_EL_PREORDER | Mesh::FILL_NEIGH | Mesh::FILL_BOUND;

    if (reverseMode) {
      std::swap(s1, s2);
      traverseFlag |= Mesh::CALL_REVERSE_MODE;
    }

    if (s1 != -1 && s2 != -1) {
      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);
      while (elInfo && elInfo->getElement() != el) {
	elInfo = stack.traverseNext(elInfo);
      }

      meshChanged = fitElementToMeshCode2(code, stack, subObj, ithObj, elType, reverseMode);
      return meshChanged;
    }

    if (el->isLeaf()) {
      if (code.getNumElements() == 1 && code.isLeafElement())
	return false;     

      meshChanged = true;

      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);

      while (elInfo && elInfo->getElement() != el) {
	elInfo = stack.traverseNext(elInfo);
      }

      TEST_EXIT_DBG(elInfo)("This should not happen!\n");

      el->setMark(1);
      refineManager->setMesh(el->getMesh());
      refineManager->setStack(&stack);
      refineManager->refineFunction(elInfo);
    }

    Element *child0 = el->getFirstChild();
    Element *child1 = el->getSecondChild();
    if (reverseMode)
      std::swap(child0, child1);

    if (s1 != -1) {
      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);

      while (elInfo && elInfo->getElement() != child0) {
	elInfo = stack.traverseNext(elInfo);
      }

      meshChanged |= 
	fitElementToMeshCode2(code, stack, subObj, s1, el->getChildType(elType), reverseMode);
    } else {
      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);

      while (elInfo && elInfo->getElement() != child1) {
	elInfo = stack.traverseNext(elInfo);
      }

      meshChanged |= 
	fitElementToMeshCode2(code, stack, subObj, s2, el->getChildType(elType), reverseMode);
    }

    return meshChanged;
  }


  bool MeshDistributor::fitElementToMeshCode2(MeshStructure &code, 
					      TraverseStack &stack,
					      GeoIndex subObj,
					      int ithObj, 
					      int elType,
					      bool reverseMode)
  {
    FUNCNAME("MeshDistributor::fitElementToMeshCode2()");

    ElInfo *elInfo = stack.getElInfo();

    bool value = false;
    if (!elInfo)
      return value;

    Element *el = elInfo->getElement();

    if (code.isLeafElement()) {
      int level = elInfo->getLevel();

      do {
	elInfo = stack.traverseNext(elInfo);
      } while (elInfo && elInfo->getLevel() > level);
     
      return value;
    }

    if (!elInfo)
      return value;

    if (el->isLeaf()) {
      el->setMark(1);
      refineManager->setMesh(el->getMesh());
      refineManager->setStack(&stack);
      refineManager->refineFunction(elInfo);
      value = true;
    }

    int s1 = el->getSubObjOfChild(0, subObj, ithObj, elType);
    int s2 = el->getSubObjOfChild(1, subObj, ithObj, elType);
    Element *child0 = el->getFirstChild();
    Element *child1 = el->getSecondChild();
    if (reverseMode) {
      std::swap(s1, s2);
      std::swap(child0, child1);
    }

    if (s1 != -1) {
      stack.traverseNext(elInfo);
      code.nextElement();
      value |= fitElementToMeshCode2(code, stack, subObj, s1, el->getChildType(elType), reverseMode);
      elInfo = stack.getElInfo();
    } else {
      do {
	elInfo = stack.traverseNext(elInfo);
      } while (elInfo && elInfo->getElement() != child1);      
    }  

    TEST_EXIT_DBG(elInfo->getElement() == child1)("This should not happen!\n");

    if (s2 != -1) {
      code.nextElement();
      value |= fitElementToMeshCode2(code, stack, subObj, s2, el->getChildType(elType), reverseMode);
    } else {
      int level = elInfo->getLevel();

      do {
	elInfo = stack.traverseNext(elInfo);
      } while (elInfo && elInfo->getLevel() > level);
    }

    return value;
  }

  
  void MeshDistributor::serialize(std::ostream &out, DofContainer &data)
  {    
    int vecSize = data.size();
    SerUtil::serialize(out, vecSize);
    for (int i = 0; i < vecSize; i++) {
      int dofIndex = (*data[i]);
      SerUtil::serialize(out, dofIndex);
    }
  }


  void MeshDistributor::deserialize(std::istream &in, DofContainer &data,
				    std::map<int, const DegreeOfFreedom*> &dofMap)
  {
    FUNCNAME("MeshDistributor::deserialize()");

    int vecSize = 0;
    SerUtil::deserialize(in, vecSize);
    data.resize(vecSize);
    for (int i = 0; i < vecSize; i++) {
      int dofIndex = 0;
      SerUtil::deserialize(in, dofIndex);

      TEST_EXIT_DBG(dofMap.count(dofIndex) != 0)
	("Dof index could not be deserialized correctly!\n");

      data[i] = dofMap[dofIndex];
    }
  }


  void MeshDistributor::serialize(std::ostream &out, RankToDofContainer &data)
  {
    int mapSize = data.size();
    SerUtil::serialize(out, mapSize);
    for (RankToDofContainer::iterator it = data.begin(); it != data.end(); ++it) {
      int rank = it->first;
      SerUtil::serialize(out, rank);
      serialize(out, it->second);
    }
  }

  
  void MeshDistributor::deserialize(std::istream &in, RankToDofContainer &data,
				    std::map<int, const DegreeOfFreedom*> &dofMap)
  {
    int mapSize = 0;
    SerUtil::deserialize(in, mapSize);
    for (int i = 0; i < mapSize; i++) {
      int rank = 0;
      SerUtil::deserialize(in, rank);
      deserialize(in, data[rank], dofMap);      
    }
  }


  double MeshDistributor::setElemWeights(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("MeshDistributor::setElemWeights()");

    double localWeightSum = 0.0;
    elemWeights.clear();
      
    std::string filename = "";
    GET_PARAMETER(0, mesh->getName() + "->macro weights", &filename);
    if (filename != "") {
      MSG("Read macro weights from %s\n", filename.c_str());

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

	elemWeights[elNum] = elWeight;
	localWeightSum += elWeight;
      }

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

	elInfo = stack.traverseNext(elInfo);
      }
    }

    return localWeightSum;
  }


  void MeshDistributor::partitionMesh(AdaptInfo *adaptInfo)
  {
    FUNCNAME("MeshDistributor::partitionMesh()");

    if (initialPartitionMesh) {
      initialPartitionMesh = false;
      partitioner->fillCoarsePartitionVec(&oldPartitionVec);
      partitioner->partition(&elemWeights, INITIAL);
    } else {
      oldPartitionVec = partitionVec;
      partitioner->partition(&elemWeights, ADAPTIVE_REPART, 100.0 /*0.000001*/);
    }    

    partitioner->fillCoarsePartitionVec(&partitionVec);
  }


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

    // === First, create the interior boundaries based on macro element's  ===
    // === neighbour informations.                                         ===

    createMacroElementInteriorBoundaryInfo();

    // === Second, search the whole mesh for interior boundaries that consists of ===
    // === substructures of the macro elements.                                   ===

    createSubstructureInteriorBoundaryInfo();


    // === Once we have this information, we must care about the order of the atomic ===
    // === bounds in the three boundary handling object. Eventually all the bound-   ===
    // === aries have to be in the same order on both ranks that share the bounday.  ===

    StdMpi<std::vector<AtomicBoundary> > stdMpi(mpiComm);
    stdMpi.send(myIntBoundary.boundary);
    stdMpi.recv(otherIntBoundary.boundary);
    stdMpi.startCommunication<int>(MPI_INT);

    // === The information about all neighbouring boundaries has been received. So ===
    // === the rank tests if its own atomic boundaries are in the same order. If   ===
    // === not, the atomic boundaries are swaped to the correct order.             ===

    for (RankToBoundMap::iterator rankIt = otherIntBoundary.boundary.begin();
	 rankIt != otherIntBoundary.boundary.end(); ++rankIt) {

      // === We have received from rank "rankIt->first" the ordered list of element ===
      // === indices. Now, we have to sort the corresponding list in this rank to   ===
      // === get the same order.                                                    ===
     
      for (int j = 0; j < static_cast<int>(rankIt->second.size()); j++) {

	// If the expected object is not at place, search for it.

	BoundaryObject &recvedBound = stdMpi.getRecvData()[rankIt->first][j].rankObj;

	if ((rankIt->second)[j].neighObj != recvedBound) {
	  int k = j + 1;
	  for (; k < static_cast<int>(rankIt->second.size()); k++)
 	    if ((rankIt->second)[k].neighObj == recvedBound)
	      break;

	  // The element must always be found, because the list is just in another order.
	  TEST_EXIT_DBG(k < static_cast<int>(rankIt->second.size()))
	    ("Should never happen!\n");

	  // Swap the current with the found element.
	  AtomicBoundary tmpBound = (rankIt->second)[k];
	  (rankIt->second)[k] = (rankIt->second)[j];
	  (rankIt->second)[j] = tmpBound;	
	}
      }
    }

    // === Do the same for the periodic boundaries. ===

    if (periodicBoundary.boundary.size() > 0) {
      stdMpi.clear();

      InteriorBoundary sendBounds, recvBounds;     
      for (RankToBoundMap::iterator rankIt = periodicBoundary.boundary.begin();
	   rankIt != periodicBoundary.boundary.end(); ++rankIt) {

	TEST_EXIT_DBG(rankIt->first != mpiRank)
	  ("It is no possible to have an interior boundary within a rank partition!\n");

	if (rankIt->first < mpiRank)
	  sendBounds.boundary[rankIt->first] = rankIt->second;
	else
	  recvBounds.boundary[rankIt->first] = rankIt->second;
      }

      stdMpi.send(sendBounds.boundary);
      stdMpi.recv(recvBounds.boundary);
      stdMpi.startCommunication<int>(MPI_INT);

      for (RankToBoundMap::iterator rankIt = periodicBoundary.boundary.begin();
	   rankIt != periodicBoundary.boundary.end(); ++rankIt) {
	if (rankIt->first <= mpiRank)
	  continue;
	  
	for (int j = 0; j < static_cast<int>(rankIt->second.size()); j++) {
	  
	  BoundaryObject &recvedBound = stdMpi.getRecvData()[rankIt->first][j].rankObj;
	  
	  if (periodicBoundary.boundary[rankIt->first][j].neighObj != recvedBound) {    
	    int k = j + 1;	    
	    for (; k < static_cast<int>(rankIt->second.size()); k++)
	      if (periodicBoundary.boundary[rankIt->first][k].neighObj == recvedBound)
		break;
	    
	    // The element must always be found, because the list is just in 
	    // another order.
	    TEST_EXIT_DBG(k < static_cast<int>(rankIt->second.size()))
	      ("Should never happen!\n");
	    
	    // Swap the current with the found element.
	    AtomicBoundary tmpBound = (rankIt->second)[k];
	    (rankIt->second)[k] = (rankIt->second)[j];
	    (rankIt->second)[j] = tmpBound;	
	  }  	  
	}
      }     
    } // periodicBoundary.boundary.size() > 0
  }


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

    int nNeighbours = mesh->getGeo(NEIGH);
    int dim = mesh->getDim();
    GeoIndex subObj = INDEX_OF_DIM(dim - 1, dim);

    // === First, traverse the mesh and search for all elements that have an  ===
    // === boundary with an element within another partition.                 ===

    TraverseStack stack;