MeshDistributor.cc 76.7 KB
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//
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// 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.


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

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

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  using boost::lexical_cast;
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  using namespace boost::filesystem;
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  using namespace std;
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  MeshDistributor* MeshDistributor::globalMeshDistributor = NULL;

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

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  MeshDistributor::MeshDistributor()
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    : problemStat(0),
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      initialized(false),
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      name("parallel"),
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      feSpaces(0),
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      mesh(NULL),
      refineManager(NULL),
      info(10),
      partitioner(NULL),
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      deserialized(false),
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      writeSerializationFile(false),
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      repartitioningAllowed(false),
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      repartitionIthChange(20),
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      nMeshChangesAfterLastRepartitioning(0),
      repartitioningCounter(0),
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      debugOutputDir(""),
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      lastMeshChangeIndex(0),
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      createBoundaryDofFlag(0),
      sebastianMode(false)
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  {
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    FUNCNAME("MeshDistributor::ParalleDomainBase()");
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    mpiComm = MPI::COMM_WORLD;
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    mpiRank = mpiComm.Get_rank();
    mpiSize = mpiComm.Get_size();
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    Parameters::get(name + "->repartitioning", repartitioningAllowed);
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    Parameters::get(name + "->debug output dir", debugOutputDir);
    Parameters::get(name + "->repartition ith change", repartitionIthChange);
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    Parameters::get(name + "->log main rank", Msg::outputMainRank);
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    string partStr = "parmetis";
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    Parameters::get(name + "->partitioner", partStr);
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    if (partStr == "parmetis") 
      partitioner = new ParMetisPartitioner(&mpiComm);

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

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

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

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

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  void MeshDistributor::initParallelization()
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  {
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    FUNCNAME("MeshDistributor::initParallelization()");
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    if (initialized)
      return;

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

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    TEST_EXIT(feSpaces.size() > 0)
      ("No FE space has been defined for the mesh distributor!\n");
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    TEST_EXIT(mesh)("No mesh has been defined for the mesh distributor!\n");
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    // === Sort FE spaces with respect to the degree of the basis ===
    // === functions. Use stuiped bubble sort for this.           ===

    bool doNext = false;
    do {
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      doNext = false;
      for (unsigned int i = 0; i < feSpaces.size() - 1; i++) {
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	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;
	}
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      }
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    } while (doNext);

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    elObjDb.setMesh(feSpaces[0]->getMesh());
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    // 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).
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    if (deserialized) {
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      updateMacroElementInfo();

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

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      createBoundaryDofs();

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

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

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    // create an initial partitioning of the mesh
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    partitioner->createInitialPartitioning();
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    // set the element weights, which are 1 at the very first begin
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    setInitialElementWeights();
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    // and now partition the mesh    
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    bool partitioningSucceed = partitioner->partition(elemWeights, INITIAL);
    TEST_EXIT(partitioningSucceed)("Initial partitioning does not work!\n");
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    partitioner->createPartitionMap(partitionMap);
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#if (DEBUG != 0)    
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    debug::ElementIdxToDofs elMap;
    debug::createSortedDofs(mesh, elMap);
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#endif

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    if (mpiRank == 0) {
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#if (DEBUG != 0)    
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      int writePartMesh = 1;
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#else
      int writePartMesh = 0;
#endif
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      Parameters::get("dbg->write part mesh", writePartMesh);
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      if (writePartMesh > 0) {
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	debug::writeElementIndexMesh(mesh, debugOutputDir + "elementIndex.vtu");
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	ParallelDebug::writePartitioning(*this, debugOutputDir + "part.vtu");
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      }
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    }
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    // === Create interior boundary information. ===
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    createInteriorBoundaryInfo();
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#if (DEBUG != 0)    
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    ParallelDebug::printBoundaryInfo(*this);
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#endif
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    // === Remove neighbourhood relations due to periodic bounday conditions. ===

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

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

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

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

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

	  macroElementNeighbours[(*it)->getIndex()][i] = -1;
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	  macroElementNeighbours[neighIndex][(*it)->getOppVertex(i)] = -1;
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	}
      }
    }
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    // === Remove all macro elements that are not part of the rank partition. ===

    removeMacroElements();
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    // === Create new global and local DOF numbering. ===

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    // We have to remove the VertexVectors, which contain periodic assoiciations, 
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    // because they are not valid anymore after some macro elements have been
    // removed and the corresponding DOFs were deleted.
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    for (map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
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	 it != mesh->getPeriodicAssociations().end(); ++it)
      const_cast<DOFAdmin&>(mesh->getDofAdmin(0)).removeDOFContainer(dynamic_cast<DOFContainer*>(it->second));
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    updateLocalGlobalNumbering();
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    // === 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.                         ===
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    check3dValidMesh();

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

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#if (DEBUG != 0)
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    MSG("AMDiS runs in debug mode, so make some test ...\n");
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    ParallelDebug::testAllElements(*this);
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    debug::testSortedDofs(mesh, elMap);
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    ParallelDebug::testInteriorBoundary(*this);
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    ParallelDebug::followBoundary(*this);
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    debug::writeMesh(feSpaces[0], -1, debugOutputDir + "macro_mesh");   
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    MSG("Debug mode tests finished!\n");
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#endif
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    // Create periodic DOF mapping, if there are periodic boundaries.
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    createPeriodicMap();
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    // Remove periodic boundary conditions in sequential problem definition. 
    removePeriodicBoundaryConditions();

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#if (DEBUG != 0)
    ParallelDebug::testPeriodicBoundary(*this);
#endif
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    // If required, create hierarchical mesh level structure.
    createMeshLevelStructure();

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

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      createPeriodicMap();
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#if (DEBUG != 0)
    ParallelDebug::testPeriodicBoundary(*this);
#endif
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    }
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    // Set DOF rank information to all matrices and vectors.
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    setRankDofs();
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    initialized = true;
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  }

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  void MeshDistributor::addProblemStat(ProblemStatSeq *probStat)
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  {
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    FUNCNAME("MeshDistributor::addProblemStat()");
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    TEST_EXIT_DBG(probStat->getFeSpaces().size())
      ("No FE spaces in stationary problem!\n");

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    // === 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");
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      }

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      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());
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    }
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    partitioner->setMesh(mesh);
    
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    // Create parallel serialization file writer, if needed.
    int writeSerialization = 0;
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    Parameters::get(probStat->getName() + "->output->write serialization",  
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		    writeSerialization);
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    if (writeSerialization && !writeSerializationFile) {
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      string filename = "";
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      Parameters::get(name + "->output->serialization filename", filename);
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      TEST_EXIT(filename != "")
	("No filename defined for parallel serialization file!\n");
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      int tsModulo = -1;
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      Parameters::get(probStat->getName() + "->output->write every i-th timestep", 
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		      tsModulo);
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      probStat->getFileWriterList().push_back(new Serializer<MeshDistributor>(this, filename, tsModulo));
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      writeSerializationFile = true;
    }    
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    int readSerialization = 0;
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    Parameters::get(probStat->getName() + "->input->read serialization", 
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		    readSerialization);
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    if (readSerialization) {
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      string filename = "";
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      Parameters::get(probStat->getName() + "->input->serialization filename", 
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		      filename);
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      filename += ".p" + lexical_cast<string>(mpiRank);
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      MSG("Start deserialization with %s\n", filename.c_str());
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      ifstream in(filename.c_str());
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      TEST_EXIT(!in.fail())("Could not open deserialization file: %s\n",
			    filename.c_str());

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

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

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      filename = "";
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      Parameters::get(name + "->input->serialization filename", filename);
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      TEST_EXIT(filename != "")
	("No filename defined for parallel deserialization file!\n");
      
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      string rankFilename = filename + ".p" + lexical_cast<string>(mpiRank);
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      in.open(rankFilename.c_str());
      
      TEST_EXIT(!in.fail())("Could not open parallel deserialization file: %s\n",
			    filename.c_str());
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      // Read the revision number of the AMDiS version which was used to create 
      // the serialization file.
      revNumber = -1;
      SerUtil::deserialize(in, revNumber);
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      deserialize(in);
      in.close();
      MSG("Deserializtion of mesh distributor from file: %s\n", rankFilename.c_str());
      deserialized = true;
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    }

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    problemStat.push_back(probStat);
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    // 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.
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    if (initialized) {
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      setRankDofs(probStat);
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      removePeriodicBoundaryConditions(probStat);
    }
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  }


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

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

    globalMeshDistributor->addProblemStat(probStat);
  }


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  void MeshDistributor::exitParallelization()
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  {}
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  void MeshDistributor::testForMacroMesh()
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  {
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    FUNCNAME("MeshDistributor::testForMacroMesh()");
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    int nMacroElements = 0;

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

      elInfo = stack.traverseNext(elInfo);
    }

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

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

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    StdMpi<vector<double> > stdMpi(mpiComm);
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    for (DofComm::Iterator it(sendDofs); !it.end(); it.nextRank()) {
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      vector<double> dofs;
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      for (int i = 0; i < vec.getSize(); i++) {
	DOFVector<double> &dofVec = *(vec.getDOFVector(i));
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	for (it.beginDofIter(vec.getFeSpace(i)); !it.endDofIter(); it.nextDof())
	  dofs.push_back(dofVec[it.getDofIndex()]);
      }
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      stdMpi.send(it.getRank(), dofs);
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    }
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    for (DofComm::Iterator it(recvDofs); !it.end(); it.nextRank())
      stdMpi.recv(it.getRank());
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    stdMpi.startCommunication();
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    for (DofComm::Iterator it(recvDofs); !it.end(); it.nextRank()) {
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      int counter = 0;
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      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++];
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      }
    }
  }

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  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);
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	allEdges.insert(elObjDb.getEdgeLocalMap(elData));
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      }

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

      elInfo = stack.traverseNext(elInfo);
    }

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    FixRefinementPatch::connectedEdges.clear();
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    bool valid3dMesh = true;
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    for (std::set<DofEdge>::iterator it = allEdges.begin(); it != allEdges.end(); ++it) {
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      vector<ElementObjectData>& edgeEls = elObjDb.getElements(*it);
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      TEST_EXIT_DBG(edgeEls.size() > 0)
	("No edge %d/%d in elObjDB!\n", it->first, it->second);

      std::set<int> el0, el1;
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      map<int, int> edgeNoInEl;
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      for (unsigned int i = 0; i < edgeEls.size(); i++) {
	if (rankMacroEls.count(edgeEls[i].elIndex)) {
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	  if (el0.empty())
	    el0.insert(edgeEls[i].elIndex);
	  else
	    el1.insert(edgeEls[i].elIndex);
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	  edgeNoInEl[edgeEls[i].elIndex] = edgeEls[i].ithObject;
	}
      }
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      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()) {
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	valid3dMesh = false;

	MSG_DBG("Unvalid 3D mesh with %d (%d - %d) elements on this edge!\n", 
		edgeEls.size(), el0.size(), el1.size());
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	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;
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	    mesh->getDofIndexCoords(dofEdge0.first, feSpaces[0], c0);
	    mesh->getDofIndexCoords(dofEdge0.second, feSpaces[0], c1);
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	    /*
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	    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]);
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	    */
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	    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));
	  }
	}
      }
    }
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    MSG_DBG("Mesh is 3d valid mesh: %d\n", valid3dMesh);
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  }


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

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


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

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    int nComponents = probStat->getNumComponents();
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    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++)
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	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);
	}
    
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      TEST_EXIT_DBG(probStat->getRhs()->getDOFVector(i))("No RHS vector!\n");
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      TEST_EXIT_DBG(probStat->getSolution()->getDOFVector(i))
	("No solution vector!\n");
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      TEST_EXIT_DBG(probStat->getRhsVector(i)->getFeSpace() ==
		    probStat->getSolution(i)->getFeSpace())
	("Should not happen!\n");
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      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);
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    }    
  }


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


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

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    // Remove periodic boundaries in boundary manager on matrices and vectors.
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    for (unsigned int i = 0; i < problemStat.size(); i++)
      removePeriodicBoundaryConditions(problemStat[i]);
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    // 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);
    }    
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    // Remove periodic vertex associations
    mesh->getPeriodicAssociations().clear();
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  }


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  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()));
    }
  }


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

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


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

    if (mpiSize != 16)
      return;

    std::set<int> neighbours;
    for (InteriorBoundary::iterator it(rankIntBoundary); !it.end(); ++it)
      neighbours.insert(it.getRank());

    for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it)
      neighbours.insert(it.getRank());

    levelData.init(neighbours);

    bool multiLevelTest = false;
    Parameters::get("parallel->multi level test", multiLevelTest);
    if (multiLevelTest) {
      switch (mpiRank) {
      case 0: case 1: case 4: case 5:
	{
	  std::set<int> m;
	  m.insert(0); m.insert(1); m.insert(4); m.insert(5);
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	  levelData.addLevel(m, 0);
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	}
	break;
      case 2: case 3: case 6: case 7:
	{
	  std::set<int> m;
	  m.insert(2); m.insert(3); m.insert(6); m.insert(7);
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	  levelData.addLevel(m, 1);
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	}
	break;
      case 8: case 9: case 12: case 13:
	{
	  std::set<int> m;
	  m.insert(8); m.insert(9); m.insert(12); m.insert(13);
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	  levelData.addLevel(m, 2);
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	}
	break;
      case 10: case 11: case 14: case 15:
	{
	  std::set<int> m;
	  m.insert(10); m.insert(11); m.insert(14); m.insert(15);
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	  levelData.addLevel(m, 3);
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	}
	break;
      }
    }
  }


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  void MeshDistributor::checkMeshChange(bool tryRepartition)
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  {
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    FUNCNAME("MeshDistributor::checkMeshChange()");
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    double first = MPI::Wtime();

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

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    // === 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);
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    if (recvAllValues == 0)
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      return;

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    // === At least one rank mesh has been changed, so the boundaries must be ===
    // === adapted to the new mesh structure.                                 ===
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    if (skip == 0)
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    do {
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      bool meshChanged = false;

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      // To check the interior boundaries, the ownership of the boundaries is not 
      // important. Therefore, we add all boundaries to one boundary container.
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      RankToBoundMap allBound;
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      for (InteriorBoundary::iterator it(rankIntBoundary); !it.end(); ++it)
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	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
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 	  allBound[it.getRank()].push_back(*it);
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      for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it)
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	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
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	  allBound[it.getRank()].push_back(*it);
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      for (InteriorBoundary::iterator it(periodicBoundary); !it.end(); ++it) {
	if (it.getRank() == mpiRank) {
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	  if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	      (mesh->getDim() == 3 && it->rankObj.subObj == FACE)) {
	    MeshStructure elCode;
	    elCode.init(it->rankObj);
	    
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	    MeshManipulation mm(mesh);
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	    meshChanged |= mm.fitElementToMeshCode(elCode, it->neighObj);
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	  }
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	} else {
	  if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	      (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
	    allBound[it.getRank()].push_back(*it);	
	}
      }
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      // === Check the boundaries and adapt mesh if necessary. ===
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      MSG_DBG("Run checkAndAdaptBoundary ...\n");
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      meshChanged |= checkAndAdaptBoundary(allBound);
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      // === Check on all ranks if at least one rank's mesh has changed. ===

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      int sendValue = static_cast<int>(meshChanged);
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      recvAllValues = 0;
      mpiComm.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
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      MSG("Mesh changed on %d ranks!\n", recvAllValues);
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    } while (recvAllValues != 0);
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#if (DEBUG != 0)
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    debug::writeMesh(feSpaces[0], -1, debugOutputDir + "mesh");
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#endif

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

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    // Update periodic mapping, if there are periodic boundaries.
    createPeriodicMap();
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#if (DEBUG != 0)
    ParallelDebug::testPeriodicBoundary(*this);
#endif
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    // === The mesh has changed, so check if it is required to repartition ===
    // === the mesh.                                                       ===
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    nMeshChangesAfterLastRepartitioning++;
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    INFO(info, 8)("Parallel mesh adaption needed %.5f seconds\n", 
		  MPI::Wtime() - first);

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    if (tryRepartition &&
	repartitioningAllowed && 
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	nMeshChangesAfterLastRepartitioning >= repartitionIthChange) {
      repartitionMesh();
      nMeshChangesAfterLastRepartitioning = 0;