refineable_mesh.template.cc

Go to the documentation of this file.

// LIC// ====================================================================
// LIC// This file forms part of oomph-lib, the object-oriented,
// LIC// multi-physics finite-element library, available
// LIC// at http://www.oomph-lib.org.
// LIC//
// LIC// Copyright (C) 2006-2024 Matthias Heil and Andrew Hazel
// LIC//
// LIC// This library is free software; you can redistribute it and/or
// LIC// modify it under the terms of the GNU Lesser General Public
// LIC// License as published by the Free Software Foundation; either
// LIC// version 2.1 of the License, or (at your option) any later version.
// LIC//
// LIC// This library is distributed in the hope that it will be useful,
// LIC// but WITHOUT ANY WARRANTY; without even the implied warranty of
// LIC// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
// LIC// Lesser General Public License for more details.
// LIC//
// LIC// You should have received a copy of the GNU Lesser General Public
// LIC// License along with this library; if not, write to the Free Software
// LIC// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
// LIC// 02110-1301  USA.
// LIC//
// LIC// The authors may be contacted at oomph-lib@maths.man.ac.uk.
// LIC//
// LIC//====================================================================
// Templated refineable mesh functions
 
// Include guards to prevent multiple inclusion of the header
#ifndef OOMPH_REFINEABLE_MESH_TEMPLATE_CC
#define OOMPH_REFINEABLE_MESH_TEMPLATE_CC
 
// Config header generated by autoconfig
#ifdef HAVE_CONFIG_H
#include <oomph-lib-config.h>
#endif
 
// oomph-lib headers
#include "refineable_mesh.h"
#include "missing_masters.h"
#include "missing_masters.template.cc"
 
namespace oomph
{
#ifdef OOMPH_HAS_MPI
 
  //========================================================================
  /// Additional actions required to synchronise halo nodes where master
  /// nodes could not be found during synchronise_hanging_nodes().
  /// Overloaded from Mesh class to take care of master nodes on
  /// the outer edge of the halo layer which do not exist on that
  /// processor. This fixes problems with the synchronisation of
  /// hanging nodes for elements with non-uniformly spaced nodes.
  //========================================================================
  template<class ELEMENT>
  void TreeBasedRefineableMesh<ELEMENT>::additional_synchronise_hanging_nodes(
    const unsigned& ncont_interpolated_values)
  {
    // Check if additional synchronisation of hanging nodes is disabled
    if (is_additional_synchronisation_of_hanging_nodes_disabled() == true)
    {
      return;
    }
 
    // This provides all the node-adding helper functions required to
    // reconstruct the missing halo master nodes on this processor
    using namespace Missing_masters_functions;
 
 
    double t_start = 0.0;
    double t_end = 0.0;
    if (Global_timings::Doc_comprehensive_timings)
    {
      t_start = TimingHelpers::timer();
    }
 
    // Store number of processors and current process
    MPI_Status status;
    int n_proc = Comm_pt->nproc();
    int my_rank = Comm_pt->my_rank();
 
 
#ifdef PARANOID
    // Paranoid check to make sure nothing else is using the
    // external storage. This will need to be changed at some
    // point if we are to use non-uniformly spaced nodes in
    // multi-domain problems.
    bool err = false;
    // Print out external storage
    for (int d = 0; d < n_proc; d++)
    {
      if (d != my_rank)
      {
        // Check to see if external storage is being used by anybody else
        if (nexternal_haloed_node(d) != 0)
        {
          err = true;
          oomph_info << "Processor " << my_rank
                     << "'s external haloed nodes with processor " << d
                     << " are:" << std::endl;
          for (unsigned i = 0; i < nexternal_haloed_node(d); i++)
          {
            oomph_info << "external_haloed_node_pt(" << d << "," << i
                       << ") = " << external_haloed_node_pt(d, i) << std::endl;
            oomph_info << "x = ( " << external_haloed_node_pt(d, i)->x(0)
                       << " , " << external_haloed_node_pt(d, i)->x(1) << " )"
                       << std::endl;
          }
        }
      }
    }
    for (int d = 0; d < n_proc; d++)
    {
      if (d != my_rank)
      {
        // Check to see if external storage is being used by anybody else
        if (nexternal_halo_node(d) != 0)
        {
          err = true;
          oomph_info << "Processor " << my_rank
                     << "'s external halo nodes with processor " << d
                     << " are:" << std::endl;
          for (unsigned i = 0; i < nexternal_halo_node(d); i++)
          {
            oomph_info << "external_halo_node_pt(" << d << "," << i
                       << ") = " << external_halo_node_pt(d, i) << std::endl;
            oomph_info << "x = ( " << external_halo_node_pt(d, i)->x(0) << " , "
                       << external_halo_node_pt(d, i)->x(1) << " )"
                       << std::endl;
          }
        }
      }
    }
    if (err)
    {
      std::ostringstream err_stream;
      err_stream << "There are already some nodes in the external storage"
                 << std::endl
                 << "for this mesh. This bit assumes that nothing else"
                 << std::endl
                 << "uses this storage (for now).";
      throw OomphLibError(
        err_stream.str(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
    }
#endif
 
 
    // Compare the halo and haloed nodes for discrepancies in hanging status
 
    // Storage for the hanging status of halo/haloed nodes on elements
    Vector<Vector<int>> haloed_hanging(n_proc);
    Vector<Vector<int>> halo_hanging(n_proc);
 
    // Storage for the haloed nodes with discrepancies in their hanging status
    // with each processor
    Vector<std::map<Node*, unsigned>> haloed_hanging_node_with_discrepancy_pt(
      n_proc);
 
    if (Global_timings::Doc_comprehensive_timings)
    {
      t_start = TimingHelpers::timer();
    }
 
    // Store number of continuosly interpolated values as int
    int ncont_inter_values = ncont_interpolated_values;
 
    // Loop over processes: Each processor checks that is haloed nodes
    // with proc d have consistent hanging stats with halo counterparts.
    for (int d = 0; d < n_proc; d++)
    {
      // No halo with self: Setup hang info for my haloed nodes with proc d
      // then get ready to receive halo info from processor d.
      if (d != my_rank)
      {
        // Loop over haloed nodes
        unsigned nh = nhaloed_node(d);
        for (unsigned j = 0; j < nh; j++)
        {
          // Get node
          Node* nod_pt = haloed_node_pt(d, j);
 
          // Loop over the hanging status for each interpolated variable
          // (and the geometry)
          for (int icont = -1; icont < ncont_inter_values; icont++)
          {
            // Store the hanging status of this haloed node
            if (nod_pt->is_hanging(icont))
            {
              unsigned n_master = nod_pt->hanging_pt(icont)->nmaster();
              haloed_hanging[d].push_back(n_master);
            }
            else
            {
              haloed_hanging[d].push_back(0);
            }
          }
        }
 
        // Receive the hanging status information from the corresponding process
        unsigned count_haloed = haloed_hanging[d].size();
 
#ifdef PARANOID
        // Check that number of halo and haloed data match
        unsigned tmp = 0;
        MPI_Recv(&tmp, 1, MPI_UNSIGNED, d, 0, Comm_pt->mpi_comm(), &status);
        if (tmp != count_haloed)
        {
          std::ostringstream error_stream;
          error_stream << "Number of halo data, " << tmp
                       << ", does not match number of haloed data, "
                       << count_haloed << std::endl;
          throw OomphLibError(error_stream.str(),
                              OOMPH_CURRENT_FUNCTION,
                              OOMPH_EXCEPTION_LOCATION);
        }
#endif
 
        // Get the data (if any)
        if (count_haloed != 0)
        {
          halo_hanging[d].resize(count_haloed);
          MPI_Recv(&halo_hanging[d][0],
                   count_haloed,
                   MPI_INT,
                   d,
                   0,
                   Comm_pt->mpi_comm(),
                   &status);
        }
      }
      else // d==my_rank, i.e. current process: Send halo hanging status
           // to process dd where it's received (see above) and compared
           // and compared against the hang status of the haloed nodes
      {
        for (int dd = 0; dd < n_proc; dd++)
        {
          // No halo with yourself
          if (dd != d)
          {
            // Storage for halo hanging status and counter
            Vector<int> local_halo_hanging;
 
            // Loop over halo nodes
            unsigned nh = nhalo_node(dd);
            for (unsigned j = 0; j < nh; j++)
            {
              // Get node
              Node* nod_pt = halo_node_pt(dd, j);
 
              // Loop over the hanging status for each interpolated variable
              // (and the geometry)
              for (int icont = -1; icont < ncont_inter_values; icont++)
              {
                // Store hanging status of halo node
                if (nod_pt->is_hanging(icont))
                {
                  unsigned n_master = nod_pt->hanging_pt(icont)->nmaster();
                  local_halo_hanging.push_back(n_master);
                }
                else
                {
                  local_halo_hanging.push_back(0);
                }
              }
            }
 
 
            // Send the information to the relevant process
            unsigned count_halo = local_halo_hanging.size();
 
#ifdef PARANOID
            // Check that number of halo and haloed data match
            MPI_Send(&count_halo, 1, MPI_UNSIGNED, dd, 0, Comm_pt->mpi_comm());
#endif
 
            // Send data (if any)
            if (count_halo != 0)
            {
              MPI_Send(&local_halo_hanging[0],
                       count_halo,
                       MPI_INT,
                       dd,
                       0,
                       Comm_pt->mpi_comm());
            }
          }
        }
      }
    }
 
    if (Global_timings::Doc_comprehensive_timings)
    {
      t_end = TimingHelpers::timer();
      oomph_info << "Time for first all-to-all in "
                    "additional_synchronise_hanging_nodes(): "
                 << t_end - t_start << std::endl;
      t_start = TimingHelpers::timer();
    }
 
 
    // Now compare equivalent halo and haloed vectors to find discrepancies.
    // It is possible that a master node may not be on either process involved
    // in the halo-haloed scheme; to work round this, we use the shared_node
    // storage scheme, which stores all nodes that are on each pair of
    // processors in the same order on each of the two processors
 
 
    // Loop over domains: Each processor checks consistency of hang status
    // of its haloed nodes with proc d against the halo counterpart. Haloed
    // wins if there are any discrepancies.
    for (int d = 0; d < n_proc; d++)
    {
      // No halo with yourself
      if (d != my_rank)
      {
        // Counter for traversing haloed data
        unsigned count = 0;
 
        // Loop over haloed nodes
        unsigned nh = nhaloed_node(d);
        for (unsigned j = 0; j < nh; j++)
        {
          // Get node
          Node* nod_pt = haloed_node_pt(d, j);
 
          // Loop over the hanging status for each interpolated variable
          // (and the geometry)
          for (int icont = -1; icont < ncont_inter_values; icont++)
          {
            // Compare hanging status of halo/haloed counterpart structure
 
            // Haloed is is hanging and haloed has different number
            // of master nodes (which includes none in which case it isn't
            // hanging)
            if ((haloed_hanging[d][count] > 0) &&
                (haloed_hanging[d][count] != halo_hanging[d][count]))
            {
              // Store this node so it can be synchronised later
              haloed_hanging_node_with_discrepancy_pt[d].insert(
                std::pair<Node*, unsigned>(nod_pt, d));
            }
            // Increment counter for number of haloed data
            count++;
          } // end of loop over icont
        } // end of loop over haloed nodes
      }
    } // end loop over all processors
 
 
    // Populate external halo(ed) node storage with master nodes of halo(ed)
    // nodes
 
    // Loop over domains: Each processor checks consistency of hang status
    // of its haloed nodes with proc d against the halo counterpart. Haloed
    // wins if there are any discrepancies.
    for (int d = 0; d < n_proc; d++)
    {
      // No halo with yourself
      if (d != my_rank)
      {
        // Now add haloed master nodes to external storage
        //===============================================
 
        // Storage for data to be sent
        Vector<unsigned> send_unsigneds(0);
        Vector<double> send_doubles(0);
 
        // Count number of haloed nonmaster nodes for halo process
        unsigned nhaloed_nonmaster_nodes_processed = 0;
        Vector<unsigned> haloed_nonmaster_node_index(0);
 
        // Loop over hanging halo nodes with discrepancies
        std::map<Node*, unsigned>::iterator j;
        for (j = haloed_hanging_node_with_discrepancy_pt[d].begin();
             j != haloed_hanging_node_with_discrepancy_pt[d].end();
             j++)
        {
          Node* nod_pt = (*j).first;
          // Find index of this haloed node in the halo storage of processor d
          //(But find in shared node storage in case it is actually haloed on
          // another processor which we don't know about)
          std::vector<Node*>::iterator it = std::find(
            Shared_node_pt[d].begin(), Shared_node_pt[d].end(), nod_pt);
          if (it != Shared_node_pt[d].end())
          {
            // Tell other processor to create this node
            // send_unsigneds.push_back(1);
            nhaloed_nonmaster_nodes_processed++;
 
            // Tell the other processor where to find this node in its halo node
            // storage
            unsigned index = it - Shared_node_pt[d].begin();
            haloed_nonmaster_node_index.push_back(index);
 
            // Tell this processor that this node is really a haloed node
            // This also packages up the data which needs to be sent to the
            // processor on which the halo equivalent node lives
            recursively_add_masters_of_external_haloed_node(d,
                                                            nod_pt,
                                                            this,
                                                            ncont_inter_values,
                                                            send_unsigneds,
                                                            send_doubles);
          }
          else
          {
            throw OomphLibError("Haloed node not found in haloed node storage",
                                OOMPH_CURRENT_FUNCTION,
                                OOMPH_EXCEPTION_LOCATION);
          }
        }
 
        // How much data needs to be sent?
        unsigned send_unsigneds_count = send_unsigneds.size();
        unsigned send_doubles_count = send_doubles.size();
 
        // Send ammount of data
        MPI_Send(
          &send_unsigneds_count, 1, MPI_UNSIGNED, d, 0, Comm_pt->mpi_comm());
        MPI_Send(
          &send_doubles_count, 1, MPI_UNSIGNED, d, 1, Comm_pt->mpi_comm());
 
        // Send to halo process the number of haloed nodes we processed
        MPI_Send(&nhaloed_nonmaster_nodes_processed,
                 1,
                 MPI_UNSIGNED,
                 d,
                 2,
                 Comm_pt->mpi_comm());
        if (nhaloed_nonmaster_nodes_processed > 0)
        {
          MPI_Send(&haloed_nonmaster_node_index[0],
                   nhaloed_nonmaster_nodes_processed,
                   MPI_UNSIGNED,
                   d,
                   3,
                   Comm_pt->mpi_comm());
        }
 
        // Send data about external halo nodes
        if (send_unsigneds_count > 0)
        {
          // Only send if there is anything to send
          MPI_Send(&send_unsigneds[0],
                   send_unsigneds_count,
                   MPI_UNSIGNED,
                   d,
                   4,
                   Comm_pt->mpi_comm());
        }
        if (send_doubles_count > 0)
        {
          // Only send if there is anything to send
          MPI_Send(&send_doubles[0],
                   send_doubles_count,
                   MPI_DOUBLE,
                   d,
                   5,
                   Comm_pt->mpi_comm());
        }
      }
      else // (d==my_rank), current process
      {
        // Now construct and add halo versions of master nodes to external
        // storage
        //=======================================================================
 
        // Loop over processors to get data
        for (int dd = 0; dd < n_proc; dd++)
        {
          // Don't talk to yourself
          if (dd != d)
          {
            // How much data to be received
            unsigned nrecv_unsigneds = 0;
            unsigned nrecv_doubles = 0;
            MPI_Recv(&nrecv_unsigneds,
                     1,
                     MPI_UNSIGNED,
                     dd,
                     0,
                     Comm_pt->mpi_comm(),
                     &status);
            MPI_Recv(&nrecv_doubles,
                     1,
                     MPI_UNSIGNED,
                     dd,
                     1,
                     Comm_pt->mpi_comm(),
                     &status);
 
            // Get from haloed process the number of halo nodes we need to
            // process
            unsigned nhalo_nonmaster_nodes_to_process = 0;
            MPI_Recv(&nhalo_nonmaster_nodes_to_process,
                     1,
                     MPI_UNSIGNED,
                     dd,
                     2,
                     Comm_pt->mpi_comm(),
                     &status);
            Vector<unsigned> halo_nonmaster_node_index(
              nhalo_nonmaster_nodes_to_process);
            if (nhalo_nonmaster_nodes_to_process != 0)
            {
              MPI_Recv(&halo_nonmaster_node_index[0],
                       nhalo_nonmaster_nodes_to_process,
                       MPI_UNSIGNED,
                       dd,
                       3,
                       Comm_pt->mpi_comm(),
                       &status);
            }
 
            // Storage for data to be received
            Vector<unsigned> recv_unsigneds(nrecv_unsigneds);
            Vector<double> recv_doubles(nrecv_doubles);
 
            // Receive data about external haloed equivalent nodes
            if (nrecv_unsigneds > 0)
            {
              // Only send if there is anything to send
              MPI_Recv(&recv_unsigneds[0],
                       nrecv_unsigneds,
                       MPI_UNSIGNED,
                       dd,
                       4,
                       Comm_pt->mpi_comm(),
                       &status);
            }
            if (nrecv_doubles > 0)
            {
              // Only send if there is anything to send
              MPI_Recv(&recv_doubles[0],
                       nrecv_doubles,
                       MPI_DOUBLE,
                       dd,
                       5,
                       Comm_pt->mpi_comm(),
                       &status);
            }
 
            // Counters for flat packed data counters
            unsigned recv_unsigneds_count = 0;
            unsigned recv_doubles_count = 0;
 
            // Loop over halo nodes with discrepancies in their hanging status
            for (unsigned j = 0; j < nhalo_nonmaster_nodes_to_process; j++)
            {
              // Get pointer to halo nonmaster node which needs processing
              //(But given index is its index in the shared storage)
              Node* nod_pt = shared_node_pt(dd, halo_nonmaster_node_index[j]);
 
#ifdef PARANOID
              // Check if we have a MacroElementNodeUpdateNode
              if (dynamic_cast<MacroElementNodeUpdateNode*>(nod_pt))
              {
                // BENFLAG: The construction of missing master nodes for
                //         MacroElementNodeUpdateNodes does not work as
                //         expected. They require MacroElementNodeUpdateElements
                //         to be created for the missing halo nodes which will
                //         be added. It behaves as expected until duplicate
                //         nodes are pruned at the problem level.
                std::ostringstream err_stream;
                err_stream
                  << "This currently doesn't work for" << std::endl
                  << "MacroElementNodeUpdateNodes because these require"
                  << std::endl
                  << "MacroElementNodeUpdateElements to be created for"
                  << std::endl
                  << "the missing halo nodes which will be added" << std::endl;
                throw OomphLibError(err_stream.str(),
                                    OOMPH_CURRENT_FUNCTION,
                                    OOMPH_EXCEPTION_LOCATION);
                // OomphLibWarning(err_stream.str(),
                //                OOMPH_CURRENT_FUNCTION,
                //                OOMPH_EXCEPTION_LOCATION);
              }
#endif
 
              // Construct copy of node and add to external halo node storage.
              unsigned loc_p = (unsigned)dd;
              unsigned node_index;
              recursively_add_masters_of_external_halo_node_to_storage<ELEMENT>(
                nod_pt,
                this,
                loc_p,
                node_index,
                ncont_inter_values,
                recv_unsigneds_count,
                recv_unsigneds,
                recv_doubles_count,
                recv_doubles);
            }
 
          } // end of dd!=d
        } // end of second loop over all processors
      }
    } // end loop over all processors
 
 
    if (Global_timings::Doc_comprehensive_timings)
    {
      t_end = TimingHelpers::timer();
      oomph_info << "Time for second all-to-all in "
                    "additional_synchronise_hanging_nodes() "
                 << t_end - t_start << std::endl;
      t_start = TimingHelpers::timer();
    }
 
    // Populate external halo(ed) node storage with master nodes of halo(ed)
    // nodes [end]
 
    // Count how many external halo/haloed nodes are added
    unsigned external_halo_count = 0;
    unsigned external_haloed_count = 0;
 
    // Flag to test whether we attampt to add any duplicate haloed nodes to the
    // shared storage -- if this is the case then we have duplicate halo nodes
    // on another processor but with different pointers and the shared scheme
    // will not be set up correctly
    bool duplicate_haloed_node_exists = false;
 
    // Loop over all the processors and add the shared nodes
    for (int d = 0; d < n_proc; d++)
    {
      // map of bools for whether the (external) node has been shared,
      // initialised to 0 (false) for each domain d
      std::map<Node*, bool> node_shared;
 
      // For all domains lower than the current domain: Do halos first
      // then haloed, to ensure correct order in lookup scheme from
      // the other side
      if (d < my_rank)
      {
        // Do external halo nodes
        unsigned nexternal_halo_nod = nexternal_halo_node(d);
        for (unsigned j = 0; j < nexternal_halo_nod; j++)
        {
          Node* nod_pt = external_halo_node_pt(d, j);
 
          // Add it as a shared node from current domain
          if (!node_shared[nod_pt])
          {
            this->add_shared_node_pt(d, nod_pt);
            node_shared[nod_pt] = true;
            external_halo_count++;
          }
 
        } // end loop over nodes
 
        // Do external haloed nodes
        unsigned nexternal_haloed_nod = nexternal_haloed_node(d);
        for (unsigned j = 0; j < nexternal_haloed_nod; j++)
        {
          Node* nod_pt = external_haloed_node_pt(d, j);
 
          // Add it as a shared node from current domain
          if (!node_shared[nod_pt])
          {
            this->add_shared_node_pt(d, nod_pt);
            node_shared[nod_pt] = true;
            external_haloed_count++;
          }
          else
          {
            duplicate_haloed_node_exists = true;
          }
 
        } // end loop over nodes
      }
 
      // If the domain is bigger than the current rank: Do haloed first
      // then halo, to ensure correct order in lookup scheme from
      // the other side
      if (d > my_rank)
      {
        // Do external haloed nodes
        unsigned nexternal_haloed_nod = nexternal_haloed_node(d);
        for (unsigned j = 0; j < nexternal_haloed_nod; j++)
        {
          Node* nod_pt = external_haloed_node_pt(d, j);
 
          // Add it as a shared node from current domain
          if (!node_shared[nod_pt])
          {
            this->add_shared_node_pt(d, nod_pt);
            node_shared[nod_pt] = true;
            external_haloed_count++;
          }
          else
          {
            duplicate_haloed_node_exists = true;
          }
 
        } // end loop over nodes
 
        // Do external halo nodes
        unsigned nexternal_halo_nod = nexternal_halo_node(d);
        for (unsigned j = 0; j < nexternal_halo_nod; j++)
        {
          Node* nod_pt = external_halo_node_pt(d, j);
 
          // Add it as a shared node from current domain
          if (!node_shared[nod_pt])
          {
            this->add_shared_node_pt(d, nod_pt);
            node_shared[nod_pt] = true;
            external_halo_count++;
          }
 
        } // end loop over nodes
 
      } // end if (d ...)
 
    } // end loop over processes
 
 
    // Say how many external halo/haloed nodes were added
    oomph_info << "INFO: " << external_halo_count << " external halo nodes and"
               << std::endl;
    oomph_info << "INFO: " << external_haloed_count
               << " external haloed nodes were added to the shared node scheme"
               << std::endl;
 
    // If we added duplicate haloed nodes, throw an error
    if (duplicate_haloed_node_exists)
    {
      // This problem should now be avoided because we are using existing
      // communication methods to locate nodes in this case. The error used
      // to arise as follows:
      /// / Let my_rank==A. If this has happened then it means that
      /// / duplicate haloed nodes exist on another processor (B). This
      /// / problem arises if a master of a haloed node with a discrepancy
      /// / is haloed with a different processor (C). A copy is constructed
      /// / in the external halo storage on processor (B) because that node
      /// / is not found in the (internal) haloed storage on (A) with (B)
      /// / but that node already exists on processor (B) in the (internal)
      /// / halo storage with processor (C). Thus two copies of this master
      /// / node now exist on processor (B).
 
      std::ostringstream err_stream;
      err_stream << "Duplicate halo nodes exist on another processor!"
                 << std::endl
                 << "(See source code for more detailed explanation)"
                 << std::endl;
 
      throw OomphLibError(
        err_stream.str(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
    }
 
 
    if (Global_timings::Doc_comprehensive_timings)
    {
      t_end = TimingHelpers::timer();
      oomph_info << "Time for identification of shared nodes in "
                    "additional_synchronise_hanging_nodes(): "
                 << t_end - t_start << std::endl;
    }
  }
 
#endif
 
} // namespace oomph
 
#endif