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 "io/ElementFileWriter.h"
#include "io/MacroInfo.h"
#include "io/MacroWriter.h"
#include "io/VtkWriter.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"),
      feSpaces(0),
      mesh(NULL),
      refineManager(NULL),
      info(10),
      partitioner(NULL),
      deserialized(false),
      writeSerializationFile(false),
      repartitioningAllowed(false),
      repartitionIthChange(20),
      nMeshChangesAfterLastRepartitioning(0),
      repartitioningCounter(0),
      debugOutputDir(""),
      lastMeshChangeIndex(0),
      createBoundaryDofFlag(0),
      sebastianMode(false)
  {
    FUNCNAME("MeshDistributor::ParalleDomainBase()");

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

    Parameters::get(name + "->repartitioning", repartitioningAllowed);
    Parameters::get(name + "->debug output dir", debugOutputDir);
    Parameters::get(name + "->repartition ith change", repartitionIthChange);
    Parameters::get(name + "->log main rank", Msg::outputMainRank);

    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));

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


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

    if (initialized)
      return;

    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 {
      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.setMesh(feSpaces[0]->getMesh());

    // 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) {
      updateMacroElementInfo();

      setRankDofs();

      removePeriodicBoundaryConditions();

      macroElIndexMap.clear();
      macroElIndexTypeMap.clear();

      for (vector<MacroElement*>::iterator it = allMacroElements.begin();
	   it != allMacroElements.end(); ++it) {
	macroElIndexMap.insert(make_pair((*it)->getIndex(), (*it)->getElement()));
	macroElIndexTypeMap.insert(make_pair((*it)->getIndex(), (*it)->getElType()));
      }

      createBoundaryDofs();

#if (DEBUG != 0)
      ParallelDebug::writeDebugFile(*this, debugOutputDir + "mpi-dbg", "dat");
#endif    

      initialized = true;
      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();

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

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

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

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


#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("dbg->write part mesh", writePartMesh);

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


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

    createInteriorBoundaryInfo();

#if (DEBUG != 0)    
    ParallelDebug::printBoundaryInfo(*this);
#endif
    
    // === 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 make some test, if the resulting mesh is valid.  ===
    // === If it is not valid, there is no possiblity yet to fix this        ===
    // === problem, just exit with an error message.                         ===
    
    check3dValidMesh();

    // === 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

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

    createPeriodicMap();

#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();
     
      // === Update periodic mapping, if there are periodic boundaries. ===     

      createPeriodicMap();

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

    // Set DOF rank information to all matrices and vectors.
    setRankDofs();

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

    initialized = true;
  }


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

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

    // === Add FE spaces from stationary problem to mesh distributor. ===

    for (unsigned int i = 0; i < probStat->getFeSpaces().size(); i++) {
      bool foundFeSpace = false;
      for (unsigned int j = 0; j < feSpaces.size(); j++) {
	if (feSpaces[j] == probStat->getFeSpaces()[i])
	  foundFeSpace = true;

	TEST_EXIT(feSpaces[j]->getMesh() == probStat->getFeSpaces()[i]->getMesh())
	  ("MeshDistributor does not yet support usage of different meshes!\n");
      }

      if (!foundFeSpace)
	feSpaces.push_back(probStat->getFeSpaces()[i]);
    }

    TEST_EXIT(feSpaces.size() > 0)("Should not happen!\n");

    mesh = feSpaces[0]->getMesh();
    info = probStat->getInfo();
    
    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);
    

    // 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;
    }    

    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 set rank
    // DOFs object to the matrices and vectors of the added stationary problem,
    // and to remove the periodic boundary conditions on these objects.

    if (initialized) {
      setRankDofs(probStat);
      removePeriodicBoundaryConditions(probStat);
    }
  }


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

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

    globalMeshDistributor->addProblemStat(probStat);
  }


  void MeshDistributor::exitParallelization()
  {}

  
  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)
  {
    FUNCNAME("MeshDistributor::synchVector()");

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

    for (DofComm::Iterator it(sendDofs); !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()]);
      }

      stdMpi.send(it.getRank(), dofs);
    }
	   
    for (DofComm::Iterator it(recvDofs); !it.end(); it.nextRank())
      stdMpi.recv(it.getRank());

    stdMpi.startCommunication();

    for (DofComm::Iterator it(recvDofs); !it.end(); it.nextRank()) {
      int counter = 0;

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

	for (it.beginDofIter(vec.getFeSpace(i)); !it.endDofIter(); it.nextDof())
	  dofVec[it.getDofIndex()] = stdMpi.getRecvData(it.getRank())[counter++];
      }
    }
  }


  void MeshDistributor::check3dValidMesh()
  {
    FUNCNAME("MeshDistributor::check3dValidMesh()");

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

    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 < 4; i++) {
	ElementObjectData elData(elInfo->getElement()->getIndex(), i);
	allEdges.insert(elObjDb.getEdgeLocalMap(elData));
      }

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

      elInfo = stack.traverseNext(elInfo);
    }


    FixRefinementPatch::connectedEdges.clear();
    bool valid3dMesh = true;

    for (std::set<DofEdge>::iterator it = allEdges.begin(); it != allEdges.end(); ++it) {
      vector<ElementObjectData>& edgeEls = elObjDb.getElements(*it);

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

      std::set<int> el0, el1;
      map<int, int> edgeNoInEl;

      for (unsigned int i = 0; i < edgeEls.size(); i++) {
	if (rankMacroEls.count(edgeEls[i].elIndex)) {
	  if (el0.empty())
	    el0.insert(edgeEls[i].elIndex);
	  else
	    el1.insert(edgeEls[i].elIndex);

	  edgeNoInEl[edgeEls[i].elIndex] = edgeEls[i].ithObject;
	}
      }
            
      TEST_EXIT_DBG(!el0.empty())("Should not happen!\n");

      if (el1.empty())
	continue;
      
      bool found = false;      
      do {
	found = false;
	for (std::set<int>::iterator elIt = el0.begin(); elIt != el0.end(); ++elIt) {
	  for (int i = 0; i < 4; i++) {
	    int neighEl = macroElementNeighbours[*elIt][i];
	    if (neighEl != -1 && el1.count(neighEl)) {
	      el0.insert(neighEl);
	      el1.erase(neighEl);
	      found = true;
	    }
	  }
	  
	  if (found)
	    break;
	}
      } while (found);
      
      if (!el1.empty()) {
	valid3dMesh = false;

	MSG_DBG("Unvalid 3D mesh with %d (%d - %d) elements on this edge!\n", 
		edgeEls.size(), el0.size(), el1.size());

	for (std::set<int>::iterator elIt0 = el0.begin(); elIt0 != el0.end(); ++elIt0) {
	  for (std::set<int>::iterator elIt1 = el1.begin(); elIt1 != el1.end(); ++elIt1) {
	    pair<Element*, int> edge0 = 
	      make_pair(macroElIndexMap[*elIt0], edgeNoInEl[*elIt0]);
	    pair<Element*, int> edge1 = 
	      make_pair(macroElIndexMap[*elIt1], edgeNoInEl[*elIt1]);

	    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_DBG("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");

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

    MSG_DBG("Mesh is 3d valid mesh: %d\n", valid3dMesh);
  }


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

    DofContainerSet dofSet;
    for (DofComm::Iterator it(sendDofs, feSpace); !it.end(); it.nextRank())
      dofSet.insert(it.getDofs().begin(), it.getDofs().end());
    for (DofComm::Iterator it(recvDofs, 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::setRankDofs(ProblemStatSeq *probStat)
  {
    FUNCNAME("MeshDistributor::setRankDofs()");

    int nComponents = probStat->getNumComponents();
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++)
	if (probStat->getSystemMatrix(i, j)) {
	  const FiniteElemSpace *rowFeSpace = 
	    probStat->getSystemMatrix(i, j)->getRowFeSpace();

	  TEST_EXIT(find(feSpaces.begin(), feSpaces.end(), rowFeSpace) != feSpaces.end())
	    ("Should not happen!\n");

	  probStat->getSystemMatrix(i, j)->setRankDofs(dofFeData[rowFeSpace].isRankDof);
	}
    

      TEST_EXIT_DBG(probStat->getRhs()->getDOFVector(i))("No RHS vector!\n");
      TEST_EXIT_DBG(probStat->getSolution()->getDOFVector(i))
	("No solution vector!\n");
      TEST_EXIT_DBG(probStat->getRhsVector(i)->getFeSpace() ==
		    probStat->getSolution(i)->getFeSpace())
	("Should not happen!\n");
      
      const FiniteElemSpace *feSpace = probStat->getRhsVector(i)->getFeSpace();
      TEST_EXIT(find(feSpaces.begin(), feSpaces.end(), feSpace) != feSpaces.end())
	("Should not happen!\n");

      probStat->getRhsVector(i)->setRankDofs(dofFeData[feSpace].isRankDof);
      probStat->getSolution(i)->setRankDofs(dofFeData[feSpace].isRankDof);
    }    
  }


  void MeshDistributor::setRankDofs()
  {
    for (unsigned int i = 0; i < problemStat.size(); i++) 
      setRankDofs(problemStat[i]);
  }


  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::checkMeshChange(bool tryRepartition)
  {
    FUNCNAME("MeshDistributor::checkMeshChange()");

    double first = MPI::Wtime();

    int skip = 0;
    Parameters::get("parallel->debug->skip check mesh change", skip);

    // === 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.                                 ===

    if (skip == 0)
    do {
      bool meshChanged = false;

      // 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(rankIntBoundary); !it.end(); ++it)
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
 	  allBound[it.getRank()].push_back(*it);

      for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it)
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
	  allBound[it.getRank()].push_back(*it);

      for (InteriorBoundary::iterator it(periodicBoundary); !it.end(); ++it) {
	if (it.getRank() == mpiRank) {
	  if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	      (mesh->getDim() == 3 && it->rankObj.subObj == FACE)) {
	    MeshStructure elCode;
	    elCode.init(it->rankObj);
	    
	    MeshManipulation mm(mesh);
	    meshChanged |= mm.fitElementToMeshCode(elCode, it->neighObj);
	  }
	} else {
	  if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	      (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
	    allBound[it.getRank()].push_back(*it);	
	}
      }


      // === Check the boundaries and adapt mesh if necessary. ===
      MSG_DBG("Run checkAndAdaptBoundary ...\n");

      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);

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

#if (DEBUG != 0)
    debug::writeMesh(feSpaces[0], -1, debugOutputDir + "mesh");
#endif


    // Because the mesh has been changed, update the DOF numbering and mappings.
    updateLocalGlobalNumbering();

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


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


    // === The mesh has changed, so check if it is required to repartition ===
    // === the mesh.                                                       ===

    nMeshChangesAfterLastRepartitioning++;


    INFO(info, 8)("Parallel mesh adaption needed %.5f seconds\n", 
		  MPI::Wtime() - first);

    if (tryRepartition &&
	repartitioningAllowed && 
	nMeshChangesAfterLastRepartitioning >= repartitionIthChange) {
      repartitionMesh();
      nMeshChangesAfterLastRepartitioning = 0;
    } else {
      MSG_DBG("Repartitioning not tried because tryRepartitioning = %d   repartitioningAllowed = %d   nMeshChange = %d   repartitionIthChange = %d\n",
	      tryRepartition, repartitioningAllowed, 
	      nMeshChangesAfterLastRepartitioning, repartitionIthChange);
    }

    // === Print imbalance factor. ===

    printImbalanceFactor();
  }

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