MeshDistributor.h 21.9 KB
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/******************************************************************************
 *
 * AMDiS - Adaptive multidimensional simulations
 *
 * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
 * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
 *
 * Authors: 
 * Simon Vey, Thomas Witkowski, Andreas Naumann, Simon Praetorius, et al.
 *
 * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
 * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
 *
 *
 * This file is part of AMDiS
 *
 * See also license.opensource.txt in the distribution.
 * 
 ******************************************************************************/
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/** \file MeshDistributor.h */
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#ifndef AMDIS_MESHDISTRIBUTOR_H
#define AMDIS_MESHDISTRIBUTOR_H
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#include <mpi.h>
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#include "parallel/DofComm.h"
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#include "parallel/ElementObjectDatabase.h"
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#include "parallel/ParallelTypes.h"
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#include "parallel/MeshLevelData.h"
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#include "parallel/MeshPartitioner.h"
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#include "parallel/InteriorBoundary.h"
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#include "parallel/ParallelDofMapping.h"
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#include "parallel/PeriodicMap.h"
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#include "parallel/StdMpi.h"
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#include "AMDiS_fwd.h"
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#include "Containers.h"
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#include "Global.h"
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#include "ProblemTimeInterface.h"
#include "ProblemIterationInterface.h"
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#include "FiniteElemSpace.h"
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#include "Serializer.h"
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#include "BoundaryManager.h"
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#include <string>

#include "operations/functors.hpp"
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namespace AMDiS { namespace Parallel {
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  struct BoundaryDofInfo
  {
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    std::map<GeoIndex, DofContainerSet> geoDofs;
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  };

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  class MeshDistributor
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  {
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  private:
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    MeshDistributor();
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  public:
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    ~MeshDistributor();

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    /// Initialization of mesh distributor.
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    void initParallelization();
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    /// Clean up procedure for the mesh distributor and attached objects.
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    void exitParallelization();
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    /** \brief
     * Register a parallel DOF mapping. This DOF mapping object will than 
     * automatically updated by the mesh distributer after mesh changes.
     *
     * \param[in]  dofMap   Parallel DOF mapping object.
     */
    void registerDofMap(ParallelDofMapping &dofMap);

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    /** \brief
     * Removes a registered DOF mapping from the mesh distributor.
     *
     * \param[in] dofMap   Parallel DOF mapping object to be removed.
     */
    void removeDofMap(ParallelDofMapping &dofMap);

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    /// Adds a DOFVector to the set of \ref interchangeVecs. Thus, this vector 
    /// will be automatically interchanged between ranks when mesh is 
    /// repartitioned.
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    void addInterchangeVector(DOFVector<double> *vec)
    {
      interchangeVectors.push_back(vec);
    }

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    /// Adds all DOFVectors of a SystemVector to \ref interchangeVecs.
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    void addInterchangeVector(SystemVector *vec);
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    /** \brief
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     * This function checks if the mesh has changed on at least on rank. In 
     * this case, the interior boundaries are adapted on all ranks such that 
     * they fit together on all ranks. Furthermore the function 
     * \ref updateLocalGlobalNumbering() is called to update the DOF numberings 
     * and mappings on all rank due to the new mesh structure.
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     *
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     * \param[in]  tryRepartition   If this parameter is true, repartitioning 
     *                              may be done. This depends on several other 
     *                              parameters. If the parameter is false, the 
     *                              mesh is only checked and adapted but never 
     *                              repartitioned.
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     */
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    void checkMeshChange(bool tryRepartition = true);
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    /// Checks if is required to repartition the mesh. If this is the case, a new
    /// partition will be created and the mesh will be redistributed between the
    /// ranks.
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    bool repartitionMesh();
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    void quickRepartition();
    
    void fullRepartition();
    
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    void getImbalanceFactor(double &imbalance, 
			    int &minDofs, 
			    int &maxDofs,
			    int &sumDofs);

    double getImbalanceFactor();

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    /// Calculates the imbalancing factor and prints it to screen.
    void printImbalanceFactor();

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    /// Test, if the mesh consists of macro elements only. The mesh partitioning 
    /// of the parallelization works for macro meshes only and would fail, if the 
    /// mesh is already refined in some way. Therefore, this function will exit
    /// the program if it finds a non macro element in the mesh.
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    void testForMacroMesh();
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    inline std::string getName() 
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    { 
      return name; 
    }
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    inline Mesh* getMesh()
    {
      return mesh;
    }

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    /// Returns the periodic mapping handler, \ref periodicMap.
    inline PeriodicMap& getPeriodicMap()
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    {
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      return periodicMap;
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    }
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    DofComm& getDofComm(int level)
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    {
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      return dofComm[level];
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    }

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    InteriorBoundary& getIntBoundary(int level)
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    {
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      return intBoundary[level];
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    }

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    inline long getLastMeshChangeIndex()
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    {
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      return lastMeshChangeIndex;
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    }
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    inline int getMpiRank()
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    {
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      return mpiRank;
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    }
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    inline int getMpiSize(int level)
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    {
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      return levelData.getMpiComm(level).Get_size();
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    }

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    inline MPI::Intracomm& getMpiComm(int level)
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    {
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      return levelData.getMpiComm(level);
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    }

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    inline bool isInitialized()
    {
      return initialized;
    }

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    // Writes all data of this object to an output stream.
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    void serialize(std::ostream &out);
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    // Reads the object data from an input stream.
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    void deserialize(std::istream &in);
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    /// Works quite similar to the function \ref synchVector, but instead the 
    /// values of subdomain vectors are combined along the boundaries, by a
    /// binary functor. 
    template<typename T, typename Operator>
    void synchVector(DOFVector<T> &vec, Operator op)
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    {
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      const FiniteElemSpace *fe = vec.getFeSpace();

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      int nLevels = levelData.getNumberOfLevels();
      for (int level = nLevels - 1; level >= 0; level--) {
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	StdMpi<std::vector<T> > stdMpi(levelData.getMpiComm(level));
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	for (DofComm::Iterator it(dofComm[level].getRecvDofs(), fe);
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	     !it.end(); it.nextRank()) {
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	  std::vector<T> dofs;
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	  dofs.reserve(it.getDofs().size());
	  
	  for (; !it.endDofIter(); it.nextDof())
	    dofs.push_back(vec[it.getDofIndex()]);
	  
	  stdMpi.send(it.getRank(), dofs);
	}
	
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	for (DofComm::Iterator it(dofComm[level].getSendDofs()); 
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	     !it.end(); it.nextRank())
	  stdMpi.recv(it.getRank());
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	stdMpi.startCommunication();
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	for (DofComm::Iterator it(dofComm[level].getSendDofs(), fe); 
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	     !it.end(); it.nextRank())
	  for (; !it.endDofIter(); it.nextDof())
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	    op(vec[it.getDofIndex()],
	       stdMpi.getRecvData(it.getRank())[it.getDofCounter()]);
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      }
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      if (!boost::is_same<Operator, functors::assign<T> >::value)
	synchVector(vec);
    }
    
    /** \brief
     * This function must be used if the values of a DOFVector must be 
     * synchronised over all ranks. That means, that each rank sends the 
     * values of the DOFs, which are owned by the rank and lie on an interior 
     * boundary, to all other ranks also having these DOFs.
     *
     * This function must be used, for example, after the linear system is
     * solved, or after the DOFVector is set by some user defined functions, 
     * e.g., initial solution functions.
     */    
    template<typename T>
    void synchVector(DOFVector<T> &vec) 
    {
      synchVector(vec, functors::assign<T>());
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    }
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    /// Works in the same way as the function above defined for DOFVectors. Due
    /// to performance, this function does not call \ref synchVector for each 
    /// DOFVector, but instead sends all values of all DOFVectors all at once.
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    void synchVector(SystemVector &vec);
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    template<typename T>
    void synchAddVector(DOFVector<T> &vec)
    {
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      synchVector(vec, functors::add_assign<T>());
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    }

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    /// In 3D, a subdomain may not be a valid AMDiS mesh if it contains two
    /// parts which are only connected by an edge. In this case, the standard
    /// refinement algorithm does not work correctly, as two elements connected
    /// only on one edge are not neighours by definition. This functions checks
    /// for this situation and fix the problem. For this, the mesh is search for
    /// all edges connecting two elements that are otherwise not connected.
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    void fix3dMeshRefinement();

    /** \brief Is used only within \ref fix3dMeshRefinement.
     * 
     * \param[in]  elems            Set of macro element indices.
     * \param[in]  edgeNoInEl       Maps from each element index in elems to a
     *                              local edge number.
     * \param[out] disconnectedEls  On output, this vector contains sets of
     *                              element indices. The union is equal to elems.
     *                              Each set contains all element indices, which
     *                              are reachable among each other by neighbour
     *                              relations. Elements within two different sets
     *                              cannot be reached via neigbourhood relation.
     */
    void helpToFix(std::set<int> &elems, 
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		   std::map<int, int> &edgeNoInEl,
		   std::vector<std::set<int> > &disconnectedEls);
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    void setBoundaryDofRequirement(Flag flag)
    {
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      createBoundaryDofFlag |= flag;
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    }

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    BoundaryDofInfo& getBoundaryDofInfo(const FiniteElemSpace *feSpace,
					int level)
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    {
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      FUNCNAME("MeshDistributor::getBoundaryDofInfo()");

      TEST_EXIT_DBG(level < static_cast<int>(boundaryDofInfo.size()))
	("Wrong level number: %d, whereas array size is %d!\n", 
	 level, boundaryDofInfo.size());

      return boundaryDofInfo[level][feSpace];
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    }

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    void getAllBoundaryDofs(const FiniteElemSpace *feSpace, 
			    int level,
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			    DofContainer& dofs);
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    ElementObjectDatabase& getElementObjectDb() 
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    {
      return elObjDb;
    }
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    /// Adds a stationary problem to the global mesh distributor objects.
    static void addProblemStatGlobal(ProblemStatSeq *probStat);
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    MeshLevelData& getMeshLevelData() 
    {
      return levelData;
    }

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    /// Updates all registered parallel DOF mappings, see \ref dofMaps.
    void updateParallelDofMappings();

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    void updateLocalGlobalNumbering();

    /// Updates the local and global DOF numbering after the mesh has been 
    /// changed.
    void updateLocalGlobalNumbering(ParallelDofMapping &dmap,
				    const FiniteElemSpace *feSpace);
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    /// set variable \ref repartitioningAllowed
    void setRepartitioningAllowed(bool allowed)
    {
      repartitioningAllowed = allowed;
    }
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    void setElementWeights(std::map<int, double>& elWgts)
    {
      elemWeights = elWgts;
    }
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  protected:
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    /// Checks if repartition is needed.
    bool isRepartitionNecessary();
    
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    /// Creates an initial partitioning of the mesh.
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    void createInitialPartitioning();

    /// Set for each element on the partitioning level the number of 
    /// leaf elements.
    void setInitialElementWeights();
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    /// Calculates \ref elemWeights with the gloabl max weight and 
    /// global sum of weight.
    void calculateElemWeights();
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    ///
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    void addProblemStat(ProblemStatSeq *probStat);

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    /// Determines the interior boundaries, i.e. boundaries between ranks, and
    /// stores all information about them in \ref interiorBoundary.
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    void createInteriorBoundary(bool firstCall);
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    ///
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    void createBoundaryDofs();

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    /// Removes all macro elements from the mesh that are not part of ranks 
    /// partition.
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    void removeMacroElements();

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    /// Calls \ref createPeriodicMap(feSpace) for all FE spaces that are
    /// handled by the mesh distributor.
    void createPeriodicMap();

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    /// Creates, for a specific FE space, to all DOFs in rank's partition that 
    /// are on a periodic boundary the mapping from dof index to the other 
    /// periodic dof indices. This information is stored in \ref periodicDofMap.  
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    void createPeriodicMap(const FiniteElemSpace *feSpace);
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    /// This function is called only once during the initialization when the
    /// whole macro mesh is available on all cores. It copies the pointers of all
    /// macro elements to \ref allMacroElements and stores all neighbour 
    /// information based on macro element indices (and not pointer based) in 
    /// \ref macroElementNeighbours. These information are then used to 
    /// reconstruct macro elements during mesh redistribution.
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    void createMacroElementInfo();

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    void updateMacroElementInfo();

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    /** \brief
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     * Checks for all given interior boundaries if the elements fit together on
     * both sides of the boundaries. If this is not the case, the mesh is 
     * adapted. Because refinement of a certain element may forces the 
     * refinement of other elements, it is not guaranteed that all rank's meshes
     * fit together after this function terminates. Hence, it must be called 
     * until a stable mesh refinement is reached.
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     *
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     * \param[in] allBound   Defines a map from rank to interior boundaries 
     *                       which should be checked.
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     *
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     * \return    If the mesh has  been changed by this function, it returns 
     *            true. Otherwise, it returns false, i.e., the given interior 
     *            boundaries fit together on both sides.
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     */
    bool checkAndAdaptBoundary(RankToBoundMap &allBound);
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    /// Removes all periodic boundary condition information from all matrices and
    /// vectors of all stationary problems and from the mesh itself.
    void removePeriodicBoundaryConditions();

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    /// Removes all periodic boundary condition information from all matrices and
    /// vector of a given stationary problem.
    void removePeriodicBoundaryConditions(ProblemStatSeq *probStat);

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    // Removes all periodic boundaries from a given boundary map.
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    void removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap);
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    void createMeshLevelStructure();

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    /// Writes a vector of dof pointers to an output stream.
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    void serialize(std::ostream &out, DofContainer &data);
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    /// Writes a \ref RankToDofContainer to an output stream.
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    void serialize(std::ostream &out, 
		   std::map<int, std::map<const FiniteElemSpace*, DofContainer> > &data);
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    /// Reads a vector of dof pointers from an input stream.
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    void deserialize(std::istream &in, DofContainer &data,
		     std::map<int, const DegreeOfFreedom*> &dofIndexMap);
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    /// Reads a \ref RankToDofContainer from an input stream.
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    void deserialize(std::istream &in, 
		     std::map<int, std::map<const FiniteElemSpace*, DofContainer> > &data,
		     std::map<const FiniteElemSpace*, std::map<int, const DegreeOfFreedom*> > &dofIndexMap);
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    /// Writes a mapping from dof pointers to some values to an output stream.
    template<typename T>
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    void serialize(std::ostream &out, std::map<const DegreeOfFreedom*, T> &data)
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    {
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      FUNCNAME("ParallelDomainBase::serialize()");

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      int mapSize = data.size();
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      SerUtil::serialize(out, mapSize);
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      for (typename std::map<const DegreeOfFreedom*, T>::iterator it = data.begin();
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	   it != data.end(); ++it) {
	int v1 = (*(it->first));
	T v2 = it->second;
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	SerUtil::serialize(out, v1);
	SerUtil::serialize(out, v2);
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      }
    }

    /// Reads a mapping from dof pointer to some values from an input stream.
    template<typename T>
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    void deserialize(std::istream &in, std::map<const DegreeOfFreedom*, T> &data,
		     std::map<int, const DegreeOfFreedom*> &dofIndexMap)
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    {
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      FUNCNAME("ParallelDomainBase::deserialize()");

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      int mapSize = 0;
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      SerUtil::deserialize(in, mapSize);
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      for (int i = 0; i < mapSize; i++) {
	int v1 = 0;
	T v2;
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	SerUtil::deserialize(in, v1);
	SerUtil::deserialize(in, v2);
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	TEST_EXIT_DBG(dofIndexMap.count(v1) != 0)
	  ("Cannot find DOF %d in map!\n", v1);
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	data[dofIndexMap[v1]] = v2;
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      }
    }
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  protected:
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    /// List of all stationary problems that are managed by this mesh 
    /// distributor.
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    std::vector<ProblemStatSeq*> problemStat;
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    /// If true, the mesh distributor is already initialized;
    bool initialized;

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    /// The rank of the current process.
    int mpiRank;

    /// Name of the problem (as used in the init files)
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    std::string name;
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    /// Set of all different FE spaces.
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    std::vector<const FiniteElemSpace*> feSpaces;
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    /// Pointer to the only mesh. Note that we do not yet support multi mesh
    /// method, thus even if we consider coupled problems, all problems must
    /// be defined on the same mesh.
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    Mesh *mesh;

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    /// A refinement manager that should be used on the mesh. It is used to 
    /// refine elements at interior boundaries in order to fit together with 
    /// elements on the other side of the interior boundary.    
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    RefinementManager *refineManager;

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    /// Pointer to a mesh partitioner that is used to partition the mesh to 
    /// the ranks.
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    MeshPartitioner *partitioner;
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    /// Pointer to a mesh partitioner that is used for the very first 
    /// partitioning of the mesh. In most cases, this pointer points to the
    /// same object as \ref partitioner, but this must not be the case in
    /// general.
    MeshPartitioner *initialPartitioner;

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    /// Weights for the elements, i.e., the number of leaf elements within 
    /// this element.
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    std::map<int, double> elemWeights;
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    /// Stores to every macro element index the number of the rank that owns this
    /// macro element.
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    std::map<int, int> partitionMap;
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    /// Database to store and query all sub-objects of all elements of the 
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    /// macro mesh.
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    ElementObjectDatabase elObjDb;
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    /// Defines the interior boundaries of the domain that result from 
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    /// partitioning the whole mesh. 
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    MultiLevelInteriorBoundary intBoundary;
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    /// Dof communicator object
    MultiLevelDofComm dofComm;
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    PeriodicMap periodicMap;
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    /// This set of values must be interchanged between ranks when the mesh is 
    /// repartitioned.
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    std::vector<DOFVector<double>*> interchangeVectors;
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    /// If the problem definition has been read from a serialization file, this 
    /// variable is true, otherwise it is false. This variable is used to stop the
    /// initialization function, if the problem definition has already been read
    /// from a serialization file.
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    bool deserialized;
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    /// Denotes whether there exists a filewriter for this object.
    bool writeSerializationFile;

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    /// If true, it is possible to repartition the mesh during computations.
    bool repartitioningAllowed;
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    /// repartition the mesh (only) the first time repartitionMesh() is called
    bool repartitionOnlyOnce;
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    /// Stores the number of mesh changes that must lie in between two 
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    /// repartitionings.
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    int repartitionIthChange;

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    ///
    int repartitioningWaitAfterFail;

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    /// Counts the number of mesh changes after the last mesh repartitioning 
    /// was done.
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    int nMeshChangesAfterLastRepartitioning;
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    /// Countes the number of mesh repartitions that were done. Till now, this 
    /// variable is used only for debug outputs.
    int repartitioningCounter;
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    /// If repartitioning of the mesh fail, this variable has a positive value
    /// that gives the number of mesh changes the mesh distributer will wait
    /// before trying new mesh repartitioning.
    int repartitioningFailed;

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    /// Directory name where all debug output files should be written to.
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    std::string debugOutputDir;
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    /// Stores the mesh change index. This is used to recognize changes in the
    /// mesh structure (e.g. through refinement or coarsening managers).
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    long lastMeshChangeIndex;
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    /// Stores for all macro elements of the original macro mesh the
    /// neighbourhood information based on element indices. Thus, each macro
    /// element index is mapped to a vector containing all indices of 
    /// neighbouring macro elements.
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    std::map<int, std::vector<int> > macroElementNeighbours;
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    /// Store all macro elements of the overall mesh, i.e., before the
    /// mesh is redistributed for the first time.
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    std::vector<MacroElement*> allMacroElements;
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    Flag createBoundaryDofFlag;

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    /// Stores on each mesh level for all FE spaces the information about
    /// all boundary DOFs.
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    std::vector<std::map<const FiniteElemSpace*, BoundaryDofInfo> > boundaryDofInfo;
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    /// Stores information about hierarchical decomposition of the mesh levels.
    /// Is used to specify multi level solver methods.
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    MeshLevelData levelData;

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    /// If there is no mesh adaptivity, the mesh distributor can remove some
    /// data structures which are only used if mesh changes or it must be
    /// redistributed due to some local adaptivity. By default, this variable
    /// is set to true, and thus no special assumption are made.
    bool meshAdaptivity;

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    /// Specifies whether the global domain has periodic boundaries. Thus, this
    /// variable is not related to rank's subdomain but to the global problem
    /// and therefore the value if the same on all ranks.
    bool hasPeriodicBoundary;

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    /// Set of all parallel DOF mapping object that are registered by parallel
    /// solver objects and must be updated automatically after mesh change.
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    std::vector<ParallelDofMapping*> dofMaps;
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    /// If true, detailed timings for benchmarking are printed.
    bool printTimings;

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    /// If true, detailed information about memory usage are printed.
    bool printMemoryUsage;

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  public:
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    /// The boundary DOFs are sorted by subobject entities, i.e., first all
    /// face DOFs, edge DOFs and to the last vertex DOFs will be set to
    /// communication structure vectors, \ref sendDofs and \ref recvDofs.
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    static const Flag BOUNDARY_SUBOBJ_SORTED;

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    /// When boundary DOFs are created, \ref boundaryDofInfo is filled for
    /// all DOFs that this rank will send to other ranks (thus, rank 
    /// owned DOFs.
    static const Flag BOUNDARY_FILL_INFO_SEND_DOFS;

    /// When boundary DOFs are created, \ref boundaryDofInfo is filled for
    /// all DOFs that this rank will receive from other ranks (thus, DOFs
    /// that are owned by another rank).
    static const Flag BOUNDARY_FILL_INFO_RECV_DOFS;
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    static MeshDistributor *globalMeshDistributor;

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    friend class ParallelDebug;
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  };
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} }
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#endif // AMDIS_MESHDISTRIBUTOR_H