DistributedTetrahedralMesh.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef DISTRIBUTEDTETRAHEDRALMESH_HPP_
#define DISTRIBUTEDTETRAHEDRALMESH_HPP_

#include <map>
#include <vector>
#include <set>

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>

#include "AbstractTetrahedralMesh.hpp"
#include "Node.hpp"
#include "AbstractMeshReader.hpp"
#include "DistributedTetrahedralMeshPartitionType.hpp"

#define UNASSIGNED_NODE UINT_MAX

/*
 * The following definition fixes an odd incompatibility of METIS 4.0 and Chaste. Since
 * the library was compiled with a plain-C compiler, it fails to link using a C++ compiler.
 * Note that METIS 4.0 fails to compile with g++ or icpc, so a C compiler should be used.
 *
 * Somebody had this problem before: http://www-users.cs.umn.edu/~karypis/.discus/messages/15/113.html?1119486445
 *
 * Note that it is necessary to define the function header before the #include statement.
*/
extern "C" {
extern void METIS_PartMeshNodal(int*, int*, int*, int*, int*, int*, int*, int*, int*);
}
#include <parmetis.h>

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class DistributedTetrahedralMesh : public AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM>
{
    friend class TestDistributedTetrahedralMesh;
private:

    unsigned mTotalNumElements;

    unsigned mTotalNumBoundaryElements;

    unsigned mTotalNumNodes;

    std::vector<Node<SPACE_DIM>* > mHaloNodes;

    std::map<unsigned, unsigned> mNodesMapping;

    std::map<unsigned, unsigned> mHaloNodesMapping;

    std::map<unsigned, unsigned> mElementsMapping;

    std::map<unsigned, unsigned> mBoundaryElementsMapping;

    DistributedTetrahedralMeshPartitionType::type mMetisPartitioning;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> >(*this);
    }


    void SetElementOwnerships();


public:

    DistributedTetrahedralMesh(DistributedTetrahedralMeshPartitionType::type partitioningMethod=DistributedTetrahedralMeshPartitionType::METIS_LIBRARY);

    virtual ~DistributedTetrahedralMesh();

    void SetDistributedVectorFactory(DistributedVectorFactory* pFactory);

    void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM,SPACE_DIM>& rMeshReader);

    unsigned GetNumLocalNodes() const;
    
    unsigned GetNumHaloNodes() const;

    unsigned GetNumLocalElements() const;

    unsigned GetNumLocalBoundaryElements() const;

    unsigned GetNumNodes() const;

    unsigned GetNumAllNodes() const;

    unsigned GetNumElements() const;

    DistributedTetrahedralMeshPartitionType::type GetPartitionType() const;

    unsigned GetNumBoundaryElements() const;

    void GetHaloNodeIndices(std::vector<unsigned>& rHaloIndices) const;


    bool CalculateDesignatedOwnershipOfElement( unsigned elementIndex );

    bool CalculateDesignatedOwnershipOfBoundaryElement( unsigned faceIndex );

     void ConstructLinearMesh(unsigned width);

    void ConstructRectangularMesh(unsigned width, unsigned height, bool stagger=true);

    void ConstructCuboid(unsigned width, unsigned height, unsigned depth);
    virtual void Scale(const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0);

    Node<SPACE_DIM>* GetNodeOrHaloNode(unsigned index) const;
    
    virtual ChasteCuboid<SPACE_DIM> CalculateBoundingBox() const;
  
protected:
    unsigned SolveNodeMapping(unsigned index) const;

    unsigned SolveElementMapping(unsigned index) const;

    unsigned SolveBoundaryElementMapping(unsigned index) const;
private:

    void RegisterNode(unsigned index);

    void RegisterHaloNode(unsigned index);

    void RegisterElement(unsigned index);

    void RegisterBoundaryElement(unsigned index);


    void ComputeMeshPartitioning(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                 std::set<unsigned>& rNodesOwned,
                                 std::set<unsigned>& rHaloNodesOwned,
                                 std::set<unsigned>& rElementsOwned,
                                 std::vector<unsigned>& rProcessorsOffset);

    void DumbNodePartitioning(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                              std::set<unsigned>& rNodesOwned);


    void MetisLibraryNodePartitioning(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                      std::set<unsigned>& rNodesOwned,
                                      std::vector<unsigned>& rProcessorsOffset);

    void PetscMatrixPartitioning(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                 std::set<unsigned>& rNodesOwned,
                                 std::vector<unsigned>& rProcessorsOffset);
     void ParMetisLibraryNodePartitioning(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                          std::set<unsigned>& rElementsOwned,
                                          std::set<unsigned>& rNodesOwned,
                                          std::set<unsigned>& rHaloNodesOwned,
                                          std::vector<unsigned>& rProcessorsOffset);

    void ReorderNodes();
    
    //                            Iterators                             //

public:
    // The other iterators aren't (so only need to be dereferenced once). Consistency would be good...

    typedef typename std::vector<Node<SPACE_DIM> *>::const_iterator HaloNodeIterator;
    
    HaloNodeIterator GetHaloNodeIteratorBegin() const;

    HaloNodeIterator GetHaloNodeIteratorEnd() const;
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(DistributedTetrahedralMesh)

namespace boost
{
namespace serialization
{
template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
inline void save_construct_data(
    Archive & ar, const DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> * t, const BOOST_PFTO unsigned int file_version)
{
    unsigned num_procs = PetscTools::GetNumProcs();
    const DistributedTetrahedralMeshPartitionType::type partition_type = t->GetPartitionType();
    ar << num_procs;
    ar << partition_type;
}

template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
inline void load_construct_data(
    Archive & ar, DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> * t, const unsigned int file_version)
{
    unsigned num_procs;
    DistributedTetrahedralMeshPartitionType::type partition_type;

    ar >> num_procs;
    ar >> partition_type;

    // Invoke inplace constructor to initialise instance
    //::new(t)DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>(partition_type);
    ::new(t)DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>(DistributedTetrahedralMeshPartitionType::DUMB);

    /*
     * The exception needs to be thrown after the call to ::new(t), or Boost will try
     * to free non-allocated memory when the exception is thrown.
     */
    if (DistributedVectorFactory::CheckNumberOfProcessesOnLoad() &&
        num_procs != PetscTools::GetNumProcs())
    {
        EXCEPTION("This archive was written for a different number of processors");
    }

}
}
} // namespace ...

#endif /*DISTRIBUTEDTETRAHEDRALMESH_HPP_*/

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