DistributedTetrahedralMesh.cpp

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*/
 
#include "DistributedTetrahedralMesh.hpp"
 
#include <cassert>
#include <sstream>
#include <string>
#include <iterator>
#include <algorithm>
#include <boost/scoped_array.hpp>
 
#include "Exception.hpp"
#include "Element.hpp"
#include "BoundaryElement.hpp"
 
#include "PetscTools.hpp"
#include "PetscMatTools.hpp"
#include "DistributedVectorFactory.hpp"
#include "OutputFileHandler.hpp"
#include "NodePartitioner.hpp"
 
#include "RandomNumberGenerator.hpp"
 
#include "Timer.hpp"
#include "TetrahedralMesh.hpp"
#include "Warnings.hpp"
 
#include "petscao.h"
 
//   IMPLEMENTATION
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::DistributedTetrahedralMesh(DistributedTetrahedralMeshPartitionType::type partitioningMethod)
    :
      mTotalNumElements(0u),
      mTotalNumBoundaryElements(0u),
      mTotalNumNodes(0u),
      mpSpaceRegion(nullptr),
      mPartitioning(partitioningMethod)
{
    if (ELEMENT_DIM == 1 && (partitioningMethod != DistributedTetrahedralMeshPartitionType::GEOMETRIC))
    {
        //No partition is possible - revert to DUMB
        mPartitioning = DistributedTetrahedralMeshPartitionType::DUMB;
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::~DistributedTetrahedralMesh()
{
    for (unsigned i=0; i<this->mHaloNodes.size(); i++)
    {
        delete this->mHaloNodes[i];
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::SetDistributedVectorFactory(DistributedVectorFactory* pFactory)
{
    AbstractMesh<ELEMENT_DIM,SPACE_DIM>::SetDistributedVectorFactory(pFactory);
    mPartitioning = DistributedTetrahedralMeshPartitionType::DUMB;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ComputeMeshPartitioning(
    AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
    std::set<unsigned>& rNodesOwned,
    std::set<unsigned>& rHaloNodesOwned,
    std::set<unsigned>& rElementsOwned,
    std::vector<unsigned>& rProcessorsOffset)
{
    if (mPartitioning == DistributedTetrahedralMeshPartitionType::METIS_LIBRARY)
    {
        EXCEPTION("METIS partitioning is deprecated.  Please use PARMETIS_LIBRARY for parMETIS (or the parMETIS interface to PT-Scotch).");
    }
    if (mPartitioning == DistributedTetrahedralMeshPartitionType::PETSC_MAT_PARTITION && !PetscTools::HasParMetis())
    {
        // The following warning can only be reproduced on machines which do not have the PETSc/parMETIS interface.
// LCOV_EXCL_START
        WARNING("PETSc/parMETIS partitioning requires PETSc to be configured with parMETIS as an option.  Current install has PETSc and parMETIS installed independently.  Switching to parMETIS");
        mPartitioning = DistributedTetrahedralMeshPartitionType::PARMETIS_LIBRARY;
// LCOV_EXCL_STOP
    }
    if (mPartitioning==DistributedTetrahedralMeshPartitionType::PARMETIS_LIBRARY && PetscTools::IsParallel())
    {
        /*
         *  With ParMetisLibraryNodeAndElementPartitioning we compute the element partition first
         *  and then we work out the node ownership.
         */
        ParMetisLibraryNodeAndElementPartitioning(rMeshReader, rElementsOwned, rNodesOwned, rHaloNodesOwned, rProcessorsOffset);
    }
    else
    {
        /*
         *  Otherwise we compute the node partition and then we work out element distribution
         */
        if (mPartitioning==DistributedTetrahedralMeshPartitionType::PETSC_MAT_PARTITION && PetscTools::IsParallel())
        {
            NodePartitioner<ELEMENT_DIM, SPACE_DIM>::PetscMatrixPartitioning(rMeshReader, this->mNodePermutation, rNodesOwned, rProcessorsOffset);
        }
        else if (mPartitioning==DistributedTetrahedralMeshPartitionType::GEOMETRIC && PetscTools::IsParallel())
        {
            if (!mpSpaceRegion)
            {
                EXCEPTION("Using GEOMETRIC partition for DistributedTetrahedralMesh with local regions not set. Call SetProcessRegion(ChasteCuboid)");
            }
            NodePartitioner<ELEMENT_DIM, SPACE_DIM>::GeometricPartitioning(rMeshReader, this->mNodePermutation, rNodesOwned, rProcessorsOffset, mpSpaceRegion);
        }
        else
        {
            NodePartitioner<ELEMENT_DIM, SPACE_DIM>::DumbPartitioning(*this, rNodesOwned);
        }
 
        if (rMeshReader.HasNclFile())
        {
            // Form a set of all the element indices we are going to own
            // (union of the sets from the lines in the NCL file)
            for (std::set<unsigned>::iterator iter = rNodesOwned.begin();
                 iter != rNodesOwned.end();
                 ++iter)
            {
                std::vector<unsigned> containing_elements = rMeshReader.GetContainingElementIndices( *iter );
                rElementsOwned.insert( containing_elements.begin(), containing_elements.end() );
            }
 
            // Iterate through that set rather than mTotalNumElements (knowing that we own a least one node in each line)
            // Then read all the data into a node_index set
            std::set<unsigned> node_index_set;
 
            for (std::set<unsigned>::iterator iter = rElementsOwned.begin();
                 iter != rElementsOwned.end();
                 ++iter)
            {
                ElementData element_data = rMeshReader.GetElementData(*iter);
                node_index_set.insert( element_data.NodeIndices.begin(), element_data.NodeIndices.end() );
            }
 
            // Subtract off the rNodesOwned set to produce rHaloNodesOwned.
            // Note that rNodesOwned is a subset of node_index_set.
            std::set_difference(node_index_set.begin(), node_index_set.end(),
                                rNodesOwned.begin(), rNodesOwned.end(),
                                std::inserter(rHaloNodesOwned, rHaloNodesOwned.begin()));
        }
        else
        {
            for (unsigned element_number = 0; element_number < mTotalNumElements; element_number++)
            {
                ElementData element_data = rMeshReader.GetNextElementData();
 
                bool element_owned = false;
                std::set<unsigned> temp_halo_nodes;
 
                for (std::vector<unsigned>::const_iterator it = element_data.NodeIndices.begin();
                     it != element_data.NodeIndices.end();
                     ++it)
                {
                    if (rNodesOwned.find(*it) != rNodesOwned.end())
                    {
                        element_owned = true;
                        rElementsOwned.insert(element_number);
                    }
                    else
                    {
                        temp_halo_nodes.insert(*it);
                    }
                }
 
                if (element_owned)
                {
                    rHaloNodesOwned.insert(temp_halo_nodes.begin(), temp_halo_nodes.end());
                }
            }
        }
 
        if (mPartitioning==DistributedTetrahedralMeshPartitionType::PETSC_MAT_PARTITION && PetscTools::IsParallel())
        {
            PetscTools::Barrier();
            if (PetscTools::AmMaster())
            {
                Timer::PrintAndReset("Element and halo node assignation");
            }
        }
    }
    rMeshReader.Reset();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ConstructFromMeshReader(
    AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader)
{
    std::set<unsigned> nodes_owned;
    std::set<unsigned> halo_nodes_owned;
    std::set<unsigned> elements_owned;
    std::vector<unsigned> proc_offsets;//(PetscTools::GetNumProcs());
 
    this->mMeshFileBaseName = rMeshReader.GetMeshFileBaseName();
    mTotalNumElements = rMeshReader.GetNumElements();
    mTotalNumBoundaryElements = rMeshReader.GetNumFaces();
    mTotalNumNodes = rMeshReader.GetNumNodes();
 
 
    PetscTools::Barrier();
    Timer::Reset();
    ComputeMeshPartitioning(rMeshReader, nodes_owned, halo_nodes_owned, elements_owned, proc_offsets);
    PetscTools::Barrier();
    //Timer::Print("partitioning");
 
    // Reserve memory
    this->mElements.reserve(elements_owned.size());
    this->mNodes.reserve(nodes_owned.size());
 
    if (rMeshReader.IsFileFormatBinary())
    {
        std::vector<double> coords;
        // Binary : load only the nodes which are needed
        for (typename AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_it = rMeshReader.GetNodeIteratorBegin(nodes_owned);
                      node_it != rMeshReader.GetNodeIteratorEnd();
                      ++node_it)
        {
            // Loop over wholly-owned nodes
            unsigned global_node_index = node_it.GetIndex();
            coords = *node_it;
            RegisterNode(global_node_index);
            Node<SPACE_DIM>* p_node = new Node<SPACE_DIM>(global_node_index, coords, false);
 
// Node attributes in binary format are not yet supported, see #1730
//            for (unsigned i = 0; i < rMeshReader.GetNodeAttributes().size(); i++)
//            {
//                double attribute = rMeshReader.GetNodeAttributes()[i];
//                p_node->AddNodeAttribute(attribute);
//            }
 
            this->mNodes.push_back(p_node);
        }
        for (typename AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_it = rMeshReader.GetNodeIteratorBegin(halo_nodes_owned);
             node_it != rMeshReader.GetNodeIteratorEnd();
             ++node_it)
        {
            // Loop over halo-owned nodes
            unsigned global_node_index = node_it.GetIndex();
            coords = *node_it;
            RegisterHaloNode(global_node_index);
            mHaloNodes.push_back(new Node<SPACE_DIM>(global_node_index, coords, false));
        }
    }
    else
    {
        // Ascii : Sequentially load all the nodes and store those owned (or halo-owned) by the process
        for (unsigned node_index=0; node_index < mTotalNumNodes; node_index++)
        {
            std::vector<double> coords;
            coords = rMeshReader.GetNextNode();
 
            // The node is owned by the processor
            if (nodes_owned.find(node_index) != nodes_owned.end())
            {
                RegisterNode(node_index);
                Node<SPACE_DIM>* p_node =  new Node<SPACE_DIM>(node_index, coords, false);
 
                for (unsigned i = 0; i < rMeshReader.GetNodeAttributes().size(); i++)
                {
                    double attribute = rMeshReader.GetNodeAttributes()[i];
                    p_node->AddNodeAttribute(attribute);
                }
 
                this->mNodes.push_back(p_node);
            }
 
            // The node is a halo node in this processor
            if (halo_nodes_owned.find(node_index) != halo_nodes_owned.end())
            {
                RegisterHaloNode(node_index);
                mHaloNodes.push_back(new Node<SPACE_DIM>(node_index, coords, false));
            }
        }
    }
 
    for (typename AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>::ElementIterator elem_it
             = rMeshReader.GetElementIteratorBegin(elements_owned);
         elem_it != rMeshReader.GetElementIteratorEnd();
         ++elem_it)
    {
        ElementData element_data = *elem_it;
        unsigned global_element_index = elem_it.GetIndex();
 
        std::vector<Node<SPACE_DIM>*> nodes;
        for (unsigned j=0; j<ELEMENT_DIM+1; j++)
        {
            // Because we have populated mNodes and mHaloNodes above, we can now use this method, which should never throw
            nodes.push_back(this->GetNodeOrHaloNode(element_data.NodeIndices[j]));
        }
 
        RegisterElement(global_element_index);
        Element<ELEMENT_DIM,SPACE_DIM>* p_element = new Element<ELEMENT_DIM,SPACE_DIM>(global_element_index, nodes);
        this->mElements.push_back(p_element);
 
        if (rMeshReader.GetNumElementAttributes() > 0)
        {
            assert(rMeshReader.GetNumElementAttributes() == 1);
            double attribute_value = element_data.AttributeValue;
            p_element->SetAttribute(attribute_value);
        }
    }
 
    // Boundary nodes and elements
    try
    {
        for (unsigned face_index=0; face_index<mTotalNumBoundaryElements; face_index++)
        {
            ElementData face_data = rMeshReader.GetNextFaceData();
            std::vector<unsigned> node_indices = face_data.NodeIndices;
 
            bool own = false;
 
            for (unsigned node_index=0; node_index<node_indices.size(); node_index++)
            {
                // if I own this node
                if (mNodesMapping.find(node_indices[node_index]) != mNodesMapping.end())
                {
                    own = true;
                    break;
                }
            }
 
            if (!own)
            {
                continue;
            }
 
            // Determine if this is a boundary face
            //std::set<unsigned> containing_element_indices; // Elements that contain this face
            std::vector<Node<SPACE_DIM>*> nodes;
 
            for (unsigned node_index=0; node_index<node_indices.size(); node_index++)
            {
                //because we have populated mNodes and mHaloNodes above, we can now use this method,
                //which SHOULD never throw (but it does).
                try
                {
                    nodes.push_back(this->GetNodeOrHaloNode(node_indices[node_index]));
                }
                catch (Exception &)
                {
                    EXCEPTION("Face does not appear in element file (Face " << face_index << " in "<<this->mMeshFileBaseName<< ")");
                }
            }
 
            // This is a boundary face
            // Ensure all its nodes are marked as boundary nodes
            for (unsigned j=0; j<nodes.size(); j++)
            {
                if (!nodes[j]->IsBoundaryNode())
                {
                    nodes[j]->SetAsBoundaryNode();
                    this->mBoundaryNodes.push_back(nodes[j]);
                }
                // Register the index that this boundary element will have with the node
                nodes[j]->AddBoundaryElement(face_index);
            }
 
            RegisterBoundaryElement(face_index);
            BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>* p_boundary_element = new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(face_index, nodes);
            this->mBoundaryElements.push_back(p_boundary_element);
 
            if (rMeshReader.GetNumFaceAttributes() > 0)
            {
                assert(rMeshReader.GetNumFaceAttributes() == 1);
                p_boundary_element->SetAttribute(face_data.AttributeValue);
            }
        }
    }
    catch (Exception &e)
    {
        PetscTools::ReplicateException(true); //Bad face exception
        throw e;
    }
    PetscTools::ReplicateException(false);
 
    if (mPartitioning != DistributedTetrahedralMeshPartitionType::DUMB && PetscTools::IsParallel())
    {
        assert(this->mNodePermutation.size() != 0);
        // If we are partitioning (and permuting) a mesh, we need to be certain that we aren't doing it twice
        assert(rMeshReader.HasNodePermutation() == false);
 
        // We reorder so that each process owns a contiguous set of the indices and we can then build a distributed vector factory.
        ReorderNodes();
 
        unsigned num_owned;
        unsigned rank = PetscTools::GetMyRank();
        if (!PetscTools::AmTopMost())
        {
            num_owned =  proc_offsets[rank+1]-proc_offsets[rank];
        }
        else
        {
            num_owned = mTotalNumNodes - proc_offsets[rank];
        }
 
        assert(!this->mpDistributedVectorFactory);
        this->mpDistributedVectorFactory = new DistributedVectorFactory(this->GetNumNodes(), num_owned);
    }
    else
    {
        // Dumb or sequential partition
        assert(this->mpDistributedVectorFactory);
 
        if (rMeshReader.HasNodePermutation())
        {
            // This is probably an unarchiving operation where the original run applied a permutation to the mesh
            // We need to re-record that the permutation has happened (so that we can archive it correctly later).
            this->mNodePermutation = rMeshReader.rGetNodePermutation();
        }
    }
    rMeshReader.Reset();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumLocalNodes() const
{
    return this->mNodes.size();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumHaloNodes() const
{
    return this->mHaloNodes.size();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumLocalElements() const
{
    return this->mElements.size();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumLocalBoundaryElements() const
{
    return this->mBoundaryElements.size();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumNodes() const
{
    return mTotalNumNodes;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumAllNodes() const
{
    return mTotalNumNodes;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumElements() const
{
    return mTotalNumElements;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
DistributedTetrahedralMeshPartitionType::type DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetPartitionType() const
{
    return mPartitioning;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumBoundaryElements() const
{
    return mTotalNumBoundaryElements;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetHaloNodeIndices(std::vector<unsigned>& rHaloIndices) const
{
    //Make sure the output vector is empty
    rHaloIndices.clear();
    for (unsigned i=0; i<mHaloNodes.size(); i++)
    {
        rHaloIndices.push_back(mHaloNodes[i]->GetIndex());
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ChasteCuboid<SPACE_DIM>*  DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetProcessRegion()
{
    if (mpSpaceRegion == nullptr)
    {
        EXCEPTION("Trying to get unset mpSpaceRegion");
    }
    return mpSpaceRegion;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::SetElementOwnerships()
{
    // All the local elements are owned by the processor (obviously...)
    //Does nothing - unlike the non-distributed version
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::SetProcessRegion(ChasteCuboid<SPACE_DIM>* pRegion)
{
    mpSpaceRegion = pRegion;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateDesignatedOwnershipOfElement( unsigned elementIndex )
{
    try
    {
        return(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateDesignatedOwnershipOfElement(elementIndex));
    }
    catch(Exception&)      // we don't own the element
    {
        return false;
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateDesignatedOwnershipOfBoundaryElement( unsigned faceIndex )
{
    try
    {
        return(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateDesignatedOwnershipOfBoundaryElement(faceIndex));
    }
    catch(Exception&)      //  we don't own the face
    {
        return false;
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::RegisterNode(unsigned index)
{
    mNodesMapping[index] = this->mNodes.size();
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::RegisterHaloNode(unsigned index)
{
    mHaloNodesMapping[index] = mHaloNodes.size();
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::RegisterElement(unsigned index)
{
    mElementsMapping[index] = this->mElements.size();
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::RegisterBoundaryElement(unsigned index)
{
    mBoundaryElementsMapping[index] = this->mBoundaryElements.size();
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::SolveNodeMapping(unsigned index) const
{
    std::map<unsigned, unsigned>::const_iterator node_position = mNodesMapping.find(index);
 
    if (node_position == mNodesMapping.end())
    {
        EXCEPTION("Requested node " << index << " does not belong to processor " << PetscTools::GetMyRank());
    }
    return node_position->second;
}
 
//template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
//unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::SolveHaloNodeMapping(unsigned index)
//{
//    assert(mHaloNodesMapping.find(index) != mHaloNodesMapping.end());
//    return mHaloNodesMapping[index];
//}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::SolveElementMapping(unsigned index) const
{
    std::map<unsigned, unsigned>::const_iterator element_position = mElementsMapping.find(index);
 
    if (element_position == mElementsMapping.end())
    {
        EXCEPTION("Requested element " << index << " does not belong to processor " << PetscTools::GetMyRank());
    }
 
    return element_position->second;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::SolveBoundaryElementMapping(unsigned index) const
{
    std::map<unsigned, unsigned>::const_iterator boundary_element_position = mBoundaryElementsMapping.find(index);
 
    if (boundary_element_position == mBoundaryElementsMapping.end())
    {
        EXCEPTION("Requested boundary element " << index << " does not belong to processor " << PetscTools::GetMyRank());
    }
 
    return boundary_element_position->second;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Node<SPACE_DIM> * DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNodeOrHaloNode(unsigned index) const
{
    std::map<unsigned, unsigned>::const_iterator node_position;
    // First search the halo (expected to be a smaller map so quicker)
    if ((node_position=mHaloNodesMapping.find(index)) != mHaloNodesMapping.end())
    {
        return mHaloNodes[node_position->second];
    }
    // Next search the owned node
    if ((node_position=mNodesMapping.find(index)) != mNodesMapping.end())
    {
        //Found an owned node
        return this->mNodes[node_position->second];
    }
    // Not here
    EXCEPTION("Requested node/halo " << index << " does not belong to processor " << PetscTools::GetMyRank());
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ReorderNodes()
{
    assert(PetscTools::IsParallel());
 
    // Need to rebuild global-local maps
    mNodesMapping.clear();
    mHaloNodesMapping.clear();
 
    // Update indices
    for (unsigned index=0; index<this->mNodes.size(); index++)
    {
        unsigned old_index = this->mNodes[index]->GetIndex();
        unsigned new_index = this->mNodePermutation[old_index];
 
        this->mNodes[index]->SetIndex(new_index);
        mNodesMapping[new_index] = index;
    }
 
    for (unsigned index=0; index<mHaloNodes.size(); index++)
    {
        unsigned old_index = mHaloNodes[index]->GetIndex();
        unsigned new_index = this->mNodePermutation[old_index];
 
        mHaloNodes[index]->SetIndex(new_index);
        mHaloNodesMapping[new_index] = index;
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ConstructLinearMesh(unsigned width)
{
    assert(ELEMENT_DIM == 1);     // LCOV_EXCL_LINE
 
     //Check that there are enough nodes to make the parallelisation worthwhile
    if (width==0)
    {
        EXCEPTION("There aren't enough nodes to make parallelisation worthwhile");
    }
 
    // Hook to pick up when we are using a geometric partition.
    if (mPartitioning == DistributedTetrahedralMeshPartitionType::GEOMETRIC)
    {
        if (!mpSpaceRegion)
        {
            EXCEPTION("Space region not set for GEOMETRIC partition of DistributedTetrahedralMesh");
        }
 
        // Write a serial file, the load on distributed processors.
        {
            TrianglesMeshWriter<ELEMENT_DIM,SPACE_DIM> mesh_writer("", "temp_linear_mesh");
            TetrahedralMesh<ELEMENT_DIM,SPACE_DIM> base_mesh;
            base_mesh.ConstructLinearMesh(width);
            mesh_writer.WriteFilesUsingMesh(base_mesh);
        }
        PetscTools::Barrier();
 
        OutputFileHandler output_handler("", false);
 
        std::string output_dir = output_handler.GetOutputDirectoryFullPath();
        TrianglesMeshReader<ELEMENT_DIM,SPACE_DIM> mesh_reader(output_dir+"temp_linear_mesh");
 
        this->ConstructFromMeshReader(mesh_reader);
    }
    else    // use a default partition.
    {
        //Use dumb partition so that archiving doesn't permute anything
        mPartitioning=DistributedTetrahedralMeshPartitionType::DUMB;
        mTotalNumNodes=width+1;
        mTotalNumBoundaryElements=2u;
        mTotalNumElements=width;
 
        //Use DistributedVectorFactory to make a dumb partition of the nodes
        assert(!this->mpDistributedVectorFactory);
        this->mpDistributedVectorFactory = new DistributedVectorFactory(mTotalNumNodes);
        if (this->mpDistributedVectorFactory->GetLocalOwnership() == 0)
        {
            // It's a short mesh and this process owns no nodes.
            // This return cannot be covered by regular testing, but is covered by the Nightly -np 3 builder
            return;  //LCOV_EXCL_LINE
        }
 
        /* am_top_most is like PetscTools::AmTopMost() but accounts for the fact that a
         * higher numbered process may have dropped out of this construction altogether
         * (because is has no local ownership)
         */
        bool am_top_most = (this->mpDistributedVectorFactory->GetHigh() == mTotalNumNodes);
 
        unsigned lo_node=this->mpDistributedVectorFactory->GetLow();
        unsigned hi_node=this->mpDistributedVectorFactory->GetHigh();
        if (!PetscTools::AmMaster())
        {
            //Allow for a halo node
            lo_node--;
        }
        if (!am_top_most)
        {
            //Allow for a halo node
            hi_node++;
        }
        Node<SPACE_DIM>* p_old_node=nullptr;
        for (unsigned node_index=lo_node; node_index<hi_node; node_index++)
        {
            // create node or halo-node
            Node<SPACE_DIM>* p_node = new Node<SPACE_DIM>(node_index, node_index==0 || node_index==width, node_index);
            if (node_index<this->mpDistributedVectorFactory->GetLow() ||
                node_index==this->mpDistributedVectorFactory->GetHigh() )
            {
                //Beyond left or right it's a halo node
                RegisterHaloNode(node_index);
                mHaloNodes.push_back(p_node);
            }
            else
            {
                RegisterNode(node_index);
                this->mNodes.push_back(p_node); // create node
 
                //A boundary face has to be wholely owned by the process
                //Since, when ELEMENT_DIM>1 we have *at least* boundary node as a non-halo
                if (node_index==0) // create left boundary node and boundary element
                {
                    this->mBoundaryNodes.push_back(p_node);
                    RegisterBoundaryElement(0);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(0, p_node) );
                }
                if (node_index==width) // create right boundary node and boundary element
                {
                    this->mBoundaryNodes.push_back(p_node);
                    RegisterBoundaryElement(1);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(1, p_node) );
                }
                }
            if (node_index>lo_node) // create element
            {
                std::vector<Node<SPACE_DIM>*> nodes;
                nodes.push_back(p_old_node);
                nodes.push_back(p_node);
                RegisterElement(node_index-1);
                this->mElements.push_back(new Element<ELEMENT_DIM,SPACE_DIM>(node_index-1, nodes) );
            }
            //Keep track of the node which we've just created
            p_old_node=p_node;
        }
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ConstructRectangularMesh(unsigned width, unsigned height, bool stagger)
{
    assert(SPACE_DIM == 2);     // LCOV_EXCL_LINE
    assert(ELEMENT_DIM == 2);     // LCOV_EXCL_LINE
    //Check that there are enough nodes to make the parallelisation worthwhile
    if (height==0)
    {
        EXCEPTION("There aren't enough nodes to make parallelisation worthwhile");
    }
 
    // Hook to pick up when we are using a geometric partition.
    if (mPartitioning == DistributedTetrahedralMeshPartitionType::GEOMETRIC)
    {
        if (!mpSpaceRegion)
        {
            EXCEPTION("Space region not set for GEOMETRIC partition of DistributedTetrahedralMesh");
        }
 
        // Write a serial file, the load on distributed processors.
        {
            TrianglesMeshWriter<ELEMENT_DIM,SPACE_DIM> mesh_writer("", "temp_rectangular_mesh");
            TetrahedralMesh<ELEMENT_DIM,SPACE_DIM> base_mesh;
            base_mesh.ConstructRectangularMesh(width, height);
            mesh_writer.WriteFilesUsingMesh(base_mesh);
        }
        PetscTools::Barrier();
 
        OutputFileHandler output_handler("", false);
 
        std::string output_dir = output_handler.GetOutputDirectoryFullPath();
        TrianglesMeshReader<ELEMENT_DIM,SPACE_DIM> mesh_reader(output_dir+"temp_rectangular_mesh");
 
        this->ConstructFromMeshReader(mesh_reader);
    }
    else
    {
        //Use dumb partition so that archiving doesn't permute anything
        mPartitioning=DistributedTetrahedralMeshPartitionType::DUMB;
 
        mTotalNumNodes=(width+1)*(height+1);
        mTotalNumBoundaryElements=(width+height)*2;
        mTotalNumElements=width*height*2;
 
        //Use DistributedVectorFactory to make a dumb partition of space
        DistributedVectorFactory y_partition(height+1);
        unsigned lo_y = y_partition.GetLow();
        unsigned hi_y = y_partition.GetHigh();
        //Dumb partition of nodes has to be such that each process gets complete slices
        assert(!this->mpDistributedVectorFactory);
        this->mpDistributedVectorFactory = new DistributedVectorFactory(mTotalNumNodes, (width+1)*y_partition.GetLocalOwnership());
        if (this->mpDistributedVectorFactory->GetLocalOwnership() == 0)
        {
            // It's a short mesh and this process owns no nodes.
            // This return cannot be covered by regular testing, but is covered by the Nightly -np 3 builder
            return;  //LCOV_EXCL_LINE
        }
 
        /* am_top_most is like PetscTools::AmTopMost() but accounts for the fact that a
         * higher numbered process may have dropped out of this construction altogether
         * (because is has no local ownership)
         */
        bool am_top_most = (this->mpDistributedVectorFactory->GetHigh() == mTotalNumNodes);
 
 
        if (!PetscTools::AmMaster())
        {
            //Allow for a halo node
            lo_y--;
        }
        if (!am_top_most)
        {
            //Allow for a halo node
            hi_y++;
        }
 
        //Construct the nodes
        for (unsigned j=lo_y; j<hi_y; j++)
        {
            for (unsigned i=0; i<width+1; i++)
            {
                bool is_boundary=false;
                if (i==0 || j==0 || i==width || j==height)
                {
                    is_boundary=true;
                }
                unsigned global_node_index=((width+1)*(j) + i); //Verified from sequential
                Node<SPACE_DIM>* p_node = new Node<SPACE_DIM>(global_node_index, is_boundary, i, j);
                if (j<y_partition.GetLow() || j==y_partition.GetHigh() )
                {
                    //Beyond left or right it's a halo node
                    RegisterHaloNode(global_node_index);
                    mHaloNodes.push_back(p_node);
                }
                else
                {
                    RegisterNode(global_node_index);
                    this->mNodes.push_back(p_node);
                }
                if (is_boundary)
                {
                    this->mBoundaryNodes.push_back(p_node);
                }
            }
        }
 
        //Construct the boundary elements
        unsigned belem_index;
        //Top
        if (am_top_most)
        {
           for (unsigned i=0; i<width; i++)
           {
                std::vector<Node<SPACE_DIM>*> nodes;
                nodes.push_back(GetNodeOrHaloNode( height*(width+1)+i+1 ));
                nodes.push_back(GetNodeOrHaloNode( height*(width+1)+i ));
                belem_index=i;
                RegisterBoundaryElement(belem_index);
                this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index,nodes));
            }
        }
 
        //Right
        for (unsigned j=lo_y+1; j<hi_y; j++)
        {
            std::vector<Node<SPACE_DIM>*> nodes;
            nodes.push_back(GetNodeOrHaloNode( (width+1)*j-1 ));
            nodes.push_back(GetNodeOrHaloNode( (width+1)*(j+1)-1 ));
            belem_index=width+j-1;
            RegisterBoundaryElement(belem_index);
            this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index,nodes));
        }
 
        //Bottom
        if (PetscTools::AmMaster())
        {
            for (unsigned i=0; i<width; i++)
            {
                std::vector<Node<SPACE_DIM>*> nodes;
                nodes.push_back(GetNodeOrHaloNode( i ));
                nodes.push_back(GetNodeOrHaloNode( i+1 ));
                belem_index=width+height+i;
                RegisterBoundaryElement(belem_index);
                this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index,nodes));
            }
        }
 
        //Left
        for (unsigned j=lo_y; j<hi_y-1; j++)
        {
            std::vector<Node<SPACE_DIM>*> nodes;
            nodes.push_back(GetNodeOrHaloNode( (width+1)*(j+1) ));
            nodes.push_back(GetNodeOrHaloNode( (width+1)*(j) ));
            belem_index=2*width+height+j;
            RegisterBoundaryElement(belem_index);
            this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index,nodes));
        }
 
 
        //Construct the elements
        unsigned elem_index;
        for (unsigned j=lo_y; j<hi_y-1; j++)
        {
            for (unsigned i=0; i<width; i++)
            {
                unsigned parity=(i+(height-j))%2;//Note that parity is measured from the top-left (not bottom left) for historical reasons
                unsigned nw=(j+1)*(width+1)+i; //ne=nw+1
                unsigned sw=(j)*(width+1)+i;   //se=sw+1
                std::vector<Node<SPACE_DIM>*> upper_nodes;
                upper_nodes.push_back(GetNodeOrHaloNode( nw ));
                upper_nodes.push_back(GetNodeOrHaloNode( nw+1 ));
                if (stagger==false  || parity == 1)
                {
                    upper_nodes.push_back(GetNodeOrHaloNode( sw+1 ));
                }
                else
                {
                    upper_nodes.push_back(GetNodeOrHaloNode( sw ));
                }
                elem_index=2*(j*width+i);
                RegisterElement(elem_index);
                this->mElements.push_back(new Element<ELEMENT_DIM,SPACE_DIM>(elem_index,upper_nodes));
                std::vector<Node<SPACE_DIM>*> lower_nodes;
                lower_nodes.push_back(GetNodeOrHaloNode( sw+1 ));
                lower_nodes.push_back(GetNodeOrHaloNode( sw ));
                if (stagger==false  ||parity == 1)
                {
                    lower_nodes.push_back(GetNodeOrHaloNode( nw ));
                }
                else
                {
                    lower_nodes.push_back(GetNodeOrHaloNode( nw+1 ));
                }
                elem_index++;
                RegisterElement(elem_index);
                this->mElements.push_back(new Element<ELEMENT_DIM,SPACE_DIM>(elem_index,lower_nodes));
            }
        }
    }
}
 
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ConstructCuboid(unsigned width,
        unsigned height,
        unsigned depth)
{
    assert(SPACE_DIM == 3);     // LCOV_EXCL_LINE
    assert(ELEMENT_DIM == 3);     // LCOV_EXCL_LINE
    //Check that there are enough nodes to make the parallelisation worthwhile
    if (depth==0)
    {
        EXCEPTION("There aren't enough nodes to make parallelisation worthwhile");
    }
 
    // Hook to pick up when we are using a geometric partition.
    if (mPartitioning == DistributedTetrahedralMeshPartitionType::GEOMETRIC)
    {
        if (!mpSpaceRegion)
        {
            EXCEPTION("Space region not set for GEOMETRIC partition of DistributedTetrahedralMesh");
        }
 
        // Write a serial file, the load on distributed processors.
        {
            TrianglesMeshWriter<ELEMENT_DIM,SPACE_DIM> mesh_writer("", "temp_cuboid_mesh");
            TetrahedralMesh<ELEMENT_DIM,SPACE_DIM> base_mesh;
            base_mesh.ConstructCuboid(width, height, depth);
            mesh_writer.WriteFilesUsingMesh(base_mesh);
        }
        PetscTools::Barrier();
 
        OutputFileHandler output_handler("", false);
 
        std::string output_dir = output_handler.GetOutputDirectoryFullPath();
        TrianglesMeshReader<ELEMENT_DIM,SPACE_DIM> mesh_reader(output_dir+"temp_cuboid_mesh");
 
        this->ConstructFromMeshReader(mesh_reader);
    }
    else
    {
        //Use dumb partition so that archiving doesn't permute anything
        mPartitioning=DistributedTetrahedralMeshPartitionType::DUMB;
 
        mTotalNumNodes=(width+1)*(height+1)*(depth+1);
        mTotalNumBoundaryElements=((width*height)+(width*depth)+(height*depth))*4;//*2 for top-bottom, *2 for tessellating each unit square
        mTotalNumElements=width*height*depth*6;
 
        //Use DistributedVectorFactory to make a dumb partition of space
        DistributedVectorFactory z_partition(depth+1);
        unsigned lo_z = z_partition.GetLow();
        unsigned hi_z = z_partition.GetHigh();
 
        //Dumb partition of nodes has to be such that each process gets complete slices
        assert(!this->mpDistributedVectorFactory);
        this->mpDistributedVectorFactory = new DistributedVectorFactory(mTotalNumNodes, (width+1)*(height+1)*z_partition.GetLocalOwnership());
        if (this->mpDistributedVectorFactory->GetLocalOwnership() == 0)
        {
            // It's a short mesh and this process owns no nodes.
            // This return cannot be covered by regular testing, but is covered by the Nightly -np 3 builder
            return;  //LCOV_EXCL_LINE
        }
 
        /* am_top_most is like PetscTools::AmTopMost() but accounts for the fact that a
         * higher numbered process may have dropped out of this construction altogether
         * (because is has no local ownership)
         */
        bool am_top_most = (this->mpDistributedVectorFactory->GetHigh() == mTotalNumNodes);
 
        if (!PetscTools::AmMaster())
        {
            //Allow for a halo node
            lo_z--;
        }
        if (!am_top_most)
        {
            //Allow for a halo node
            hi_z++;
        }
 
        //Construct the nodes
        unsigned global_node_index;
        for (unsigned k=lo_z; k<hi_z; k++)
        {
            for (unsigned j=0; j<height+1; j++)
            {
                for (unsigned i=0; i<width+1; i++)
                {
                    bool is_boundary = false;
                    if (i==0 || j==0 || k==0 || i==width || j==height || k==depth)
                    {
                        is_boundary = true;
                    }
                    global_node_index = (k*(height+1)+j)*(width+1)+i;
 
                    Node<SPACE_DIM>* p_node = new Node<SPACE_DIM>(global_node_index, is_boundary, i, j, k);
 
                    if (k<z_partition.GetLow() || k==z_partition.GetHigh() )
                    {
                        //Beyond left or right it's a halo node
                        RegisterHaloNode(global_node_index);
                        mHaloNodes.push_back(p_node);
                    }
                    else
                    {
                        RegisterNode(global_node_index);
                        this->mNodes.push_back(p_node);
                    }
 
                    if (is_boundary)
                    {
                        this->mBoundaryNodes.push_back(p_node);
                    }
                }
            }
        }
 
        // Construct the elements
 
        unsigned element_nodes[6][4] = {{0, 1, 5, 7}, {0, 1, 3, 7},
                                        {0, 2, 3, 7}, {0, 2, 6, 7},
                                        {0, 4, 6, 7}, {0, 4, 5, 7}};
        std::vector<Node<SPACE_DIM>*> tetrahedra_nodes;
 
        for (unsigned k=lo_z; k<hi_z-1; k++)
        {
            unsigned belem_index = 0;
            if (k != 0)
            {
                // height*width squares on upper face, k layers of 2*height+2*width square aroun
                belem_index =   2*(height*width+k*2*(height+width));
            }
 
            for (unsigned j=0; j<height; j++)
            {
                for (unsigned i=0; i<width; i++)
                {
                    // Compute the nodes' index
                    unsigned global_node_indices[8];
                    unsigned local_node_index = 0;
 
                    for (unsigned z = 0; z < 2; z++)
                    {
                        for (unsigned y = 0; y < 2; y++)
                        {
                            for (unsigned x = 0; x < 2; x++)
                            {
                                global_node_indices[local_node_index] = i+x+(width+1)*(j+y+(height+1)*(k+z));
 
                                local_node_index++;
                            }
                        }
                    }
 
                    for (unsigned m = 0; m < 6; m++)
                    {
                        // Tetrahedra #m
 
                        tetrahedra_nodes.clear();
 
                        for (unsigned n = 0; n < 4; n++)
                        {
                            tetrahedra_nodes.push_back(GetNodeOrHaloNode( global_node_indices[element_nodes[m][n]] ));
                        }
                        unsigned elem_index = 6 * ((k*height+j)*width+i)+m;
                        RegisterElement(elem_index);
                        this->mElements.push_back(new Element<ELEMENT_DIM,SPACE_DIM>(elem_index, tetrahedra_nodes));
                    }
 
                    //Are we at a boundary?
                    std::vector<Node<SPACE_DIM>*> triangle_nodes;
 
                    if (i == 0) //low face at x==0
                    {
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[0] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[2] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[6] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[0] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[6] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[4] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    }
                    if (i == width-1) //high face at x=width
                    {
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[1] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[5] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[7] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[1] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[7] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[3] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    }
                    if (j == 0) //low face at y==0
                    {
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[0] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[5] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[1] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[0] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[4] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[5] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    }
                    if (j == height-1) //high face at y=height
                    {
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[2] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[3] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[7] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[2] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[7] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[6] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    }
                    if (k == 0) //low face at z==0
                    {
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[0] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[3] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[2] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[0] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[1] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[3] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    }
                    if (k == depth-1) //high face at z=depth
                    {
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[4] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[7] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[5] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                        triangle_nodes.clear();
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[4] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[6] ));
                        triangle_nodes.push_back(GetNodeOrHaloNode( global_node_indices[7] ));
                        RegisterBoundaryElement(belem_index);
                        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    }
                }//i
            }//j
        }//k
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::Scale(const double xFactor, const double yFactor, const double zFactor)
{
    //Base class scale (scales node positions)
    AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::Scale(xFactor, yFactor, zFactor);
    //Scales halos
    for (unsigned i=0; i<mHaloNodes.size(); i++)
    {
        c_vector<double, SPACE_DIM>& r_location = mHaloNodes[i]->rGetModifiableLocation();
        if (SPACE_DIM>=3)
        {
            r_location[2] *= zFactor;
        }
        if (SPACE_DIM>=2)
        {
            r_location[1] *= yFactor;
        }
        r_location[0] *= xFactor;
    }
 
}
 
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ParMetisLibraryNodeAndElementPartitioning(
        AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
        std::set<unsigned>& rElementsOwned,
        std::set<unsigned>& rNodesOwned,
        std::set<unsigned>& rHaloNodesOwned,
        std::vector<unsigned>& rProcessorsOffset)
{
    assert(PetscTools::IsParallel());
    assert(ELEMENT_DIM==2 || ELEMENT_DIM==3); // LCOV_EXCL_LINE // Partitioning works with triangles and tetras
 
    const unsigned num_elements = rMeshReader.GetNumElements();
    const unsigned num_nodes = rMeshReader.GetNumNodes();
    const unsigned num_procs = PetscTools::GetNumProcs();
    const unsigned local_proc_index = PetscTools::GetMyRank();
 
    /*
     *  Work out initial element distribution
     */
    boost::scoped_array<idx_t> element_distribution(new idx_t[num_procs+1]);
    boost::scoped_array<int> element_counts(new int[num_procs]);
 
    element_distribution[0] = 0;
 
    for (unsigned proc_index=1; proc_index<num_procs; proc_index++)
    {
        element_distribution[proc_index] = element_distribution[proc_index-1] + num_elements/num_procs;
        element_counts[proc_index-1] = element_distribution[proc_index] - element_distribution[proc_index-1];
    }
 
    element_distribution[num_procs] = num_elements;
    element_counts[num_procs-1] = element_distribution[num_procs] - element_distribution[num_procs-1];
 
    /*
     *  Create distributed mesh data structure
     */
    idx_t first_local_element = element_distribution[local_proc_index];
    idx_t last_plus_one_element = element_distribution[local_proc_index+1];
    idx_t num_local_elements = last_plus_one_element - first_local_element;
 
    boost::scoped_array<idx_t> eind(new idx_t[num_local_elements*(ELEMENT_DIM+1)]);
    boost::scoped_array<idx_t> eptr(new idx_t[num_local_elements+1]);
 
    if (rMeshReader.IsFileFormatBinary() && first_local_element > 0)
    {
        // Advance the file pointer to the first element before the ones I own.
        rMeshReader.GetElementData(first_local_element - 1);
    }
    else
    {
        // Advance the file pointer to the first element before the ones I own.
        for (idx_t element_index = 0; element_index < first_local_element; element_index++)
        {
            rMeshReader.GetNextElementData();
        }
    }
 
#ifdef CHASTE_HOMEMADE_MESH_TO_DUAL
    // element_node_matrix is an encoding of the .ele file.  Each row is an element with the 
    // 3 or 4 adjacent nodes indicated by a 1 in the approciate column
    Mat element_node_matrix;
    PetscTools::SetupMat(element_node_matrix, num_elements, num_nodes, ELEMENT_DIM+1, num_local_elements);
#endif
    
    unsigned counter = 0;
    for (idx_t element_index = 0; element_index < num_local_elements; element_index++)
    {
        ElementData element_data;
 
        element_data = rMeshReader.GetNextElementData();
 
        eptr[element_index] = counter;
        for (unsigned i=0; i<ELEMENT_DIM+1; i++)
        {
#ifdef CHASTE_HOMEMADE_MESH_TO_DUAL
            PetscMatTools::SetElement(element_node_matrix, element_index+first_local_element, element_data.NodeIndices[i], 1.0);
#else
            eind[counter++] = element_data.NodeIndices[i];
#endif
        }
    }
    eptr[num_local_elements] = counter;
 
    rMeshReader.Reset();
    idx_t numflag = 0; // ParMETIS speak for C-style numbering
 
    MPI_Comm communicator = PETSC_COMM_WORLD;
 
    idx_t* xadj;
    idx_t* adjncy;
 
    Timer::Reset();
#ifdef CHASTE_HOMEMADE_MESH_TO_DUAL
    PetscMatTools::Finalise(element_node_matrix);
    std::vector<idx_t> my_xadj;
    std::vector<idx_t> my_adjncy;
    /* The goal is for my_adjncy to contain, for each local element, a list of the
     * elements that it is adjacent to. These are contiguous but my_xadj will contain the
     * start index for the data of each local element.
     * The element_node_matrix contains data on which nodes support each element.
     * The dot-product of two rows of this matrix is an indication of how many nodes two elements share:
     * ELEMENT_DIM+1 if they are the same row and ELEMENT_DIM if they are neighbours.
     * These dot-products are achieved (slowly) with
     * element_element_matrix = element_node_matrix * transpose(element_node_matrix)
     * 
     * Each entry of element_element_matrix shows how many nodes a pair of elements share.
     */
 
    Mat node_element_matrix;
    MatTranspose(element_node_matrix, MAT_INITIAL_MATRIX,  &node_element_matrix);
    Mat element_element_matrix;
    MatMatMult(element_node_matrix, node_element_matrix, MAT_INITIAL_MATRIX,  PETSC_DETERMINE, &element_element_matrix);
    my_xadj.push_back(0);
    PetscInt ncols;
    const PetscInt *cols;
    const PetscScalar *vals;
    for (PetscInt el_index=first_local_element; el_index<last_plus_one_element; el_index++)
    {
         MatGetRow(element_element_matrix, el_index, &ncols, &cols, &vals);
         for (PetscInt i=0;i<ncols;i++)
         {
            if (std::lround(vals[i])==ELEMENT_DIM)
            {
                // Shared edge/face between two elements
                my_adjncy.push_back(cols[i]);
            }
        }
        MatRestoreRow(element_element_matrix, el_index, &ncols, &cols, NULL);
        // Mark where next local element starts
        my_xadj.push_back(my_adjncy.size());
    }
    MatDestroy(&element_node_matrix);
    MatDestroy(&node_element_matrix);
    MatDestroy(&element_element_matrix);
    xadj = &my_xadj[0];
    adjncy = &my_adjncy[0];
 
#else
    // The default behaviour is to use a ParMETIS (or possible Scotch) function to get the dual
    /* Connectivity degree.
     * GRAPH EDGE is placed between any two elements if and only if they share at least this many nodes.
     */
    idx_t ncommonnodes = 3; //Linear tetrahedra
    if (ELEMENT_DIM == 2)
    {
        ncommonnodes = 2;
    }
    ParMETIS_V3_Mesh2Dual(element_distribution.get(), eptr.get(), eind.get(),
                          &numflag, &ncommonnodes, &xadj, &adjncy, &communicator);
#endif
    //Timer::Print("ParMETIS Mesh2Dual");
    // Be more memory efficient, and get rid of (maybe large) arrays as soon as they're no longer needed, rather than at end of scope
    eind.reset();
    eptr.reset();
 
    idx_t weight_flag = 0; // unweighted graph
    idx_t n_constraints = 1; // number of weights that each vertex has (number of balance constraints)
    idx_t n_subdomains = PetscTools::GetNumProcs();
    idx_t options[3]; // extra options
    options[0] = 0; // ignore extra options
    idx_t edgecut;
    boost::scoped_array<real_t> tpwgts(new real_t[n_subdomains]);
    real_t ubvec_value = (real_t)1.05;
    for (unsigned proc=0; proc<PetscTools::GetNumProcs(); proc++)
    {
        tpwgts[proc] = ((real_t)1.0)/n_subdomains;
    }
    boost::scoped_array<idx_t> local_partition(new idx_t[num_local_elements]);
 
/*
 *  In order to use ParMETIS_V3_PartGeomKway, we need to sort out how to compute the coordinates of the
 *  centers of each element efficiently.
 *
 *  In the meantime use ParMETIS_V3_PartKway.
 */
//    int n_dimensions = ELEMENT_DIM;
//    float node_coordinates[num_local_elements*SPACE_DIM];
//
//    ParMETIS_V3_PartGeomKway(element_distribution, xadj, adjncy, NULL, NULL, &weight_flag, &numflag,
//                             &n_dimensions, node_coordinates, &n_constraints, &n_subdomains, NULL, NULL,
//                             options, &edgecut, local_partition, &communicator);
 
    Timer::Reset();
    ParMETIS_V3_PartKway(element_distribution.get(), xadj, adjncy, nullptr, nullptr, &weight_flag, &numflag,
                         &n_constraints, &n_subdomains, tpwgts.get(), &ubvec_value,
                         options, &edgecut, local_partition.get(), &communicator);
    //Timer::Print("ParMETIS PartKway");
    tpwgts.reset();
 
    boost::scoped_array<idx_t> global_element_partition(new idx_t[num_elements]);
 
    //idx_t is normally int (see metis-4.0/Lib/struct.h 17-22) but is 64bit on Windows
    MPI_Datatype mpi_idx_t = MPI_LONG_LONG_INT;
    if (sizeof(idx_t) == sizeof(int))
    {
        mpi_idx_t = MPI_INT;
    }
    boost::scoped_array<int> int_element_distribution(new int[num_procs+1]);
    for (unsigned i=0; i<num_procs+1; ++i)
    {
        int_element_distribution[i] = element_distribution[i];
    }
    MPI_Allgatherv(local_partition.get(), num_local_elements, mpi_idx_t,
                   global_element_partition.get(), element_counts.get(), int_element_distribution.get(), mpi_idx_t, PETSC_COMM_WORLD);
 
    local_partition.reset();
 
    for (unsigned elem_index=0; elem_index<num_elements; elem_index++)
    {
        if ((unsigned) global_element_partition[elem_index] == local_proc_index)
        {
            rElementsOwned.insert(elem_index);
        }
    }
 
    rMeshReader.Reset();
#ifdef CHASTE_HOMEMADE_MESH_TO_DUAL
    // These are contained in std::vectors that are automatically freed
    xadj = NULL;
    adjncy = NULL;
#endif
    free(xadj);
    free(adjncy);
    //unsigned num_nodes = rMeshReader.GetNumNodes();
 
    // Initialise with no nodes known
    std::vector<unsigned> global_node_partition(num_nodes, UNASSIGNED_NODE);
 
    assert(rProcessorsOffset.size() == 0); // Making sure the vector is empty. After calling resize() only newly created memory will be initialised to 0.
    rProcessorsOffset.resize(PetscTools::GetNumProcs(), 0);
 
    /*
     *  Work out node distribution based on initial element distribution returned by ParMETIS
     *
     *  In this loop we handle 4 different data structures:
     *      global_node_partition and rProcessorsOffset are global,
     *      rNodesOwned and rHaloNodesOwned are local.
     */
 
    /*
     * Note that at this point each process has to read the entire element file in order to compute
     * the node partition form the initial element distribution.
     *  * Previously we randomly permuted the BIN file element access order on each process so that the processes
     *    weren't reading the same file sectors at the same time
     *  * We noted that with large files (above about 0.5 GigaByte) on HECToR the random access file reader
     *    was spending all its time in fseekg.  This is presumably because each fseekg from the start of the file
     *    involves multiple levels of indirect file block pointers.
     *  * Hence the use of random element reading is only useful for the niche of moderately large meshes with
     *    process counts in the thousands.
     *  Hence BIN file element permuting is deprecated - we just read the file in order.
     *  See
     *  https://github.com/Chaste/Old-Chaste-svn-mirror/blob/554dbbf5cb7e95105aa8a6f48ee57551edea2a8a/mesh/src/common/DistributedTetrahedralMesh.cpp#L1459
     */
 
    for (unsigned element_number = 0; element_number < mTotalNumElements; element_number++)
    {
        unsigned element_owner = global_element_partition[element_number];
 
        ElementData element_data;
 
        element_data = rMeshReader.GetNextElementData();
 
        for (std::vector<unsigned>::const_iterator node_it = element_data.NodeIndices.begin();
             node_it != element_data.NodeIndices.end();
             ++node_it)
        {
            /*
             * For each node in this element, check whether it hasn't been assigned to another processor yet.
             * If so, assign it to the owner of the element. Otherwise, consider it halo.
             */
            if (global_node_partition[*node_it] == UNASSIGNED_NODE)
            {
                if (element_owner == local_proc_index)
                {
                    rNodesOwned.insert(*node_it);
                }
 
                global_node_partition[*node_it] = element_owner;
 
                // Offset is defined as the first node owned by a processor. We compute it incrementally.
                // i.e. if node_index belongs to proc 3 (of 6) we have to shift the processors 4, 5, and 6
                // offset a position.
                for (unsigned proc=element_owner+1; proc<PetscTools::GetNumProcs(); proc++)
                {
                    rProcessorsOffset[proc]++;
                }
            }
            else
            {
                if (element_owner == local_proc_index)
                {
                    //if (rNodesOwned.find(*node_it) == rNodesOwned.end())
                    if (global_node_partition[*node_it] != local_proc_index)
                    {
                        rHaloNodesOwned.insert(*node_it);
                    }
                }
            }
        }
    }
 
 
    /*
     * Refine element distribution. Add extra elements that parMETIS didn't consider initially but
     * include any node owned by the processor. This ensures that all the system matrix rows are
     * assembled locally.
     * It may be that some of these elements are in the set of owned nodes erroneously.
     * The original set of owned elements (from the k-way partition) informed a
     * node partition.  It may be that an element near the edge of this new node
     * partition may no longer be needed.
     *
     * Note that rather than clearing the set we could remove elements to the original element partition set
     * with erase(), if (!element_owned) below.
     */
    rElementsOwned.clear();
    rMeshReader.Reset();
    for (unsigned element_number = 0; element_number < mTotalNumElements; element_number++)
    {
        ElementData element_data = rMeshReader.GetNextElementData();
 
        bool element_owned = false;
        std::set<unsigned> temp_halo_nodes;
 
        for (std::vector<unsigned>::const_iterator node_it = element_data.NodeIndices.begin();
             node_it != element_data.NodeIndices.end();
             ++node_it)
        {
            if (rNodesOwned.find(*node_it) != rNodesOwned.end())
            {
                element_owned = true;
                rElementsOwned.insert(element_number);
            }
            else
            {
                temp_halo_nodes.insert(*node_it);
            }
        }
 
        if (element_owned)
        {
            rHaloNodesOwned.insert(temp_halo_nodes.begin(), temp_halo_nodes.end());
        }
    }
 
    rMeshReader.Reset();
 
    /*
     *  Once we know the offsets we can compute the permutation vector
     */
    std::vector<unsigned> local_index(PetscTools::GetNumProcs(), 0);
 
    this->mNodePermutation.resize(this->GetNumNodes());
 
    for (unsigned node_index=0; node_index<this->GetNumNodes(); node_index++)
    {
        unsigned partition = global_node_partition[node_index];
        assert(partition != UNASSIGNED_NODE);
 
        this->mNodePermutation[node_index] = rProcessorsOffset[partition] + local_index[partition];
 
        local_index[partition]++;
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ChasteCuboid<SPACE_DIM> DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateBoundingBox() const
{
    ChastePoint<SPACE_DIM> my_minimum_point {};
    ChastePoint<SPACE_DIM> my_maximum_point {};
 
    try
    {
        ChasteCuboid<SPACE_DIM> my_box=AbstractMesh<ELEMENT_DIM, SPACE_DIM>::CalculateBoundingBox();
        my_minimum_point=my_box.rGetLowerCorner();
        my_maximum_point=my_box.rGetUpperCorner();
    }
    // LCOV_EXCL_START
    catch (Exception& e)
    {
        PetscTools::ReplicateException(true);
        throw e;
 
    }
    // LCOV_EXCL_STOP
 
    PetscTools::ReplicateException(false);
 
    c_vector<double, SPACE_DIM> global_minimum_point;
    c_vector<double, SPACE_DIM> global_maximum_point;
    MPI_Allreduce(&my_minimum_point.rGetLocation()[0], &global_minimum_point[0], SPACE_DIM, MPI_DOUBLE, MPI_MIN, PETSC_COMM_WORLD);
    MPI_Allreduce(&my_maximum_point.rGetLocation()[0], &global_maximum_point[0], SPACE_DIM, MPI_DOUBLE, MPI_MAX, PETSC_COMM_WORLD);
 
    ChastePoint<SPACE_DIM> min(global_minimum_point);
    ChastePoint<SPACE_DIM> max(global_maximum_point);
 
    return ChasteCuboid<SPACE_DIM>(min, max);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNearestNodeIndex(const ChastePoint<SPACE_DIM>& rTestPoint)
{
    // Call base method to find closest on local processor
    unsigned best_node_index = AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNearestNodeIndex(rTestPoint);
 
    // Recalculate the distance to the best node (if this process has one)
    double best_node_point_distance = DBL_MAX;
    if (best_node_index != UINT_MAX)
    {
        best_node_point_distance = norm_2(this->GetNode(best_node_index)->rGetLocation() - rTestPoint.rGetLocation());
    }
 
 
    // This is a handy data structure that will work with MPI_DOUBLE_INT data type.
    // There is no MPI_DOUBLE_UNSIGNED
    struct
    {
        double distance;
        int node_index;
    } value, minval;
 
    value.node_index = best_node_index;
    value.distance = best_node_point_distance;
 
    MPI_Allreduce( &value, &minval, 1, MPI_DOUBLE_INT, MPI_MINLOC, MPI_COMM_WORLD );
 
    return minval.node_index;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double, 2> DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateMinMaxEdgeLengths()
{
    c_vector<double, 2> local_min_max =  AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateMinMaxEdgeLengths();
    c_vector<double, 2> global_min_max;
 
    MPI_Allreduce(&local_min_max[0], &global_min_max[0], 1, MPI_DOUBLE, MPI_MIN, PETSC_COMM_WORLD);
    MPI_Allreduce(&local_min_max[1], &global_min_max[1], 1, MPI_DOUBLE, MPI_MAX, PETSC_COMM_WORLD);
 
    return global_min_max;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::HaloNodeIterator DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetHaloNodeIteratorBegin() const
{
    return mHaloNodes.begin();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::Rotate(c_matrix<double, SPACE_DIM, SPACE_DIM> rotationMatrix)
{
    // First do the extras
    for (unsigned i=0; i<this->mHaloNodes.size(); i++)
    {
        c_vector<double, SPACE_DIM>& r_location = this->mHaloNodes[i]->rGetModifiableLocation();
        r_location = prod(rotationMatrix, r_location);
    }
    // Now a copy of the base class implementation
    for (unsigned i=0; i<this->mNodes.size(); i++)
    {
        c_vector<double, SPACE_DIM>& r_location = this->mNodes[i]->rGetModifiableLocation();
        r_location = prod(rotationMatrix, r_location);
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::Translate(const c_vector<double, SPACE_DIM>& rDisplacement)
{
    // First do the extras
    for (unsigned i=0; i<this->mHaloNodes.size(); i++)
    {
        c_vector<double, SPACE_DIM>& r_location = this->mHaloNodes[i]->rGetModifiableLocation();
        r_location += rDisplacement;
    }
    // Now a copy of the base class implementation
    for (unsigned i=0; i<this->mNodes.size(); i++)
    {
        c_vector<double, SPACE_DIM>& r_location = this->mNodes[i]->rGetModifiableLocation();
        r_location += rDisplacement;
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::HaloNodeIterator DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetHaloNodeIteratorEnd() const
{
    return mHaloNodes.end();
}
 
// Explicit instantiation
template class DistributedTetrahedralMesh<1,1>;
template class DistributedTetrahedralMesh<1,2>;
template class DistributedTetrahedralMesh<1,3>;
template class DistributedTetrahedralMesh<2,2>;
template class DistributedTetrahedralMesh<2,3>;
template class DistributedTetrahedralMesh<3,3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(DistributedTetrahedralMesh)