src/ParaMEDMEM/ParaUMesh.cxx

   1 //
   2 // Copyright (C) 2020  CEA/DEN, EDF R&D
   3 //
   4 // This library is free software; you can redistribute it and/or
   5 // modify it under the terms of the GNU Lesser General Public
   6 // License as published by the Free Software Foundation; either
   7 // version 2.1 of the License, or (at your option) any later version.
   8 //
   9 // This library is distributed in the hope that it will be useful,
  10 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  11 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  12 // Lesser General Public License for more details.
  13 //
  14 // You should have received a copy of the GNU Lesser General Public
  15 // License along with this library; if not, write to the Free Software
  16 // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
  17 //
  18 // See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com
  19 //
  20 // Author : Anthony Geay (EDF R&D)
  21
  22 #include "ParaUMesh.hxx"
  23 #include "ProcessorGroup.hxx"
  24 #include "MPIProcessorGroup.hxx"
  25 #include "Topology.hxx"
  26 #include "BlockTopology.hxx"
  27 #include "CommInterface.hxx"
  28 #include "MEDCouplingMemArray.hxx"
  29
  30 #include "mpi.h"
  31
  32 #include <fstream>
  33 #include <sstream>
  34 #include <numeric>
  35 #include <memory>
  36 #include <vector>
  37
  38 using namespace MEDCoupling;
  39
  40 ParaUMesh *ParaUMesh::New(MEDCouplingUMesh *mesh, DataArrayIdType *globalCellIds, DataArrayIdType *globalNodeIds)
  41 {
  42   return new ParaUMesh(mesh,globalCellIds,globalNodeIds);
  43 }
  44
  45 ParaUMesh::ParaUMesh(MEDCouplingUMesh *mesh, DataArrayIdType *globalCellIds, DataArrayIdType *globalNodeIds)
  46 {
  47   _mesh.takeRef(mesh);
  48   _cell_global.takeRef(globalCellIds);
  49   _node_global.takeRef(globalNodeIds);
  50   _mesh.checkNotNull();
  51   _cell_global.checkNotNull();
  52   _node_global.checkNotNull();
  53   _mesh->checkConsistencyLight();
  54   if(_mesh->getNumberOfNodes() != _node_global->getNumberOfTuples())
  55     throw INTERP_KERNEL::Exception("ParaUMesh constructor : mismatch between # nodes and len of global # nodes.");
  56   if(_mesh->getNumberOfCells() != _cell_global->getNumberOfTuples())
  57     throw INTERP_KERNEL::Exception("ParaUMesh constructor : mismatch between # cells and len of global # cells.");
  58 }
  59
  60 std::size_t ParaUMesh::getHeapMemorySizeWithoutChildren() const
  61 {
  62   return 0;
  63 }
  64
  65 std::vector<const BigMemoryObject *> ParaUMesh::getDirectChildrenWithNull() const
  66 {
  67   return {_mesh,_cell_global,_node_global};
  68 }
  69
  70 /*!
  71 * This method computes the cells part of distributed mesh lying on \a globalNodeIds nodes.
  72 * The input \a globalNodeIds are not supposed to reside on the current process.
  73 */
  74 MCAuto<DataArrayIdType> ParaUMesh::getCellIdsLyingOnNodes(const DataArrayIdType *globalNodeIds, bool fullyIn) const
  75 {
  76   if(fullyIn)
  77     throw INTERP_KERNEL::Exception("ParaUMesh::getCellIdsLyingOnNodes : not implemented yet for fullyIn == True !");
  78   MPI_Comm comm(MPI_COMM_WORLD);
  79   CommInterface ci;
  80   int size;
  81   ci.commSize(comm,&size);
  82   std::unique_ptr<mcIdType[]> nbOfElems(new mcIdType[size]),nbOfElems2(new mcIdType[size]),nbOfElems3(new mcIdType[size]);
  83   mcIdType nbOfNodeIdsLoc(globalNodeIds->getNumberOfTuples());
  84   ci.allGather(&nbOfNodeIdsLoc,1,MPI_ID_TYPE,nbOfElems.get(),1,MPI_ID_TYPE,comm);
  85   std::vector< MCAuto<DataArrayIdType> > tabs(size);
  86   // loop to avoid to all procs to have all the nodes per proc
  87   for(int subDiv = 0 ; subDiv < size ; ++subDiv)
  88   {
  89     std::unique_ptr<mcIdType[]> nbOfElemsSp(CommInterface::SplitArrayOfLength(nbOfElems,size,subDiv,size));
  90     mcIdType nbOfNodeIdsSum(std::accumulate(nbOfElemsSp.get(),nbOfElemsSp.get()+size,0));
  91     std::unique_ptr<mcIdType[]> allGlobalNodeIds(new mcIdType[nbOfNodeIdsSum]);
  92     std::unique_ptr<int[]> nbOfElemsInt( CommInterface::ToIntArray<mcIdType>(nbOfElemsSp,size) );
  93     std::unique_ptr<int[]> offsetsIn( CommInterface::ComputeOffset(nbOfElemsInt,size) );
  94     mcIdType startGlobalNodeIds,endGlobalNodeIds;
  95     DataArray::GetSlice(0,globalNodeIds->getNumberOfTuples(),1,subDiv,size,startGlobalNodeIds,endGlobalNodeIds);
  96     ci.allGatherV(globalNodeIds->begin()+startGlobalNodeIds,endGlobalNodeIds-startGlobalNodeIds,MPI_ID_TYPE,allGlobalNodeIds.get(),nbOfElemsInt.get(),offsetsIn.get(),MPI_ID_TYPE,comm);
  97     mcIdType offset(0);
  98     for(int curRk = 0 ; curRk < size ; ++curRk)
  99     {
 100       MCAuto<DataArrayIdType> globalNodeIdsOfCurProc(DataArrayIdType::New());
 101       globalNodeIdsOfCurProc->useArray(allGlobalNodeIds.get()+offset,false,DeallocType::CPP_DEALLOC,nbOfElemsSp[curRk],1);
 102       offset += nbOfElemsSp[curRk];
 103       MCAuto<DataArrayIdType> globalNodeIdsCaptured(_node_global->buildIntersection(globalNodeIdsOfCurProc));
 104       MCAuto<DataArrayIdType> localNodeIdsToLocate(_node_global->findIdForEach(globalNodeIdsCaptured->begin(),globalNodeIdsCaptured->end()));
 105       MCAuto<DataArrayIdType> localCellCaptured(_mesh->getCellIdsLyingOnNodes(localNodeIdsToLocate->begin(),localNodeIdsToLocate->end(),false));
 106       MCAuto<DataArrayIdType> localCellCapturedGlob(_cell_global->selectByTupleIdSafe(localCellCaptured->begin(),localCellCaptured->end()));
 107       if(tabs[curRk].isNull())
 108         tabs[curRk] = localCellCapturedGlob;
 109       else
 110         tabs[curRk]->insertAtTheEnd(localCellCapturedGlob->begin(),localCellCapturedGlob->end());
 111     }
 112   }
 113   for(int curRk = 0 ; curRk < size ; ++curRk)
 114   {
 115     tabs[curRk] = tabs[curRk]->buildUniqueNotSorted();
 116     nbOfElems3[curRk] = tabs[curRk]->getNumberOfTuples();
 117   }
 118   std::vector<const DataArrayIdType *> tabss(tabs.begin(),tabs.end());
 119   MCAuto<DataArrayIdType> cells(DataArrayIdType::Aggregate(tabss));
 120   ci.allToAll(nbOfElems3.get(),1,MPI_ID_TYPE,nbOfElems2.get(),1,MPI_ID_TYPE,comm);
 121   mcIdType nbOfCellIdsSum(std::accumulate(nbOfElems2.get(),nbOfElems2.get()+size,0));
 122   MCAuto<DataArrayIdType> cellIdsFromProcs(DataArrayIdType::New());
 123   cellIdsFromProcs->alloc(nbOfCellIdsSum,1);
 124   {
 125     std::unique_ptr<int[]> nbOfElemsInt( CommInterface::ToIntArray<mcIdType>(nbOfElems3,size) ),nbOfElemsOutInt( CommInterface::ToIntArray<mcIdType>(nbOfElems2,size) );
 126     std::unique_ptr<int[]> offsetsIn( CommInterface::ComputeOffset(nbOfElemsInt,size) ), offsetsOut( CommInterface::ComputeOffset(nbOfElemsOutInt,size) );
 127     ci.allToAllV(cells->begin(),nbOfElemsInt.get(),offsetsIn.get(),MPI_ID_TYPE,
 128                  cellIdsFromProcs->getPointer(),nbOfElemsOutInt.get(),offsetsOut.get(),MPI_ID_TYPE,comm);
 129   }
 130   cellIdsFromProcs->sort();
 131   return cellIdsFromProcs;
 132 }
 133
 134 /*!
 135  * Return part of \a this mesh split over COMM_WORLD. Part is defined by global cell ids array \a globaCellIds.
 136  */
 137 ParaUMesh *ParaUMesh::redistributeCells(const DataArrayIdType *globalCellIds) const
 138 {
 139   MPI_Comm comm(MPI_COMM_WORLD);
 140   CommInterface ci;
 141   std::unique_ptr<mcIdType[]> allGlobalCellIds,allGlobalCellIdsIndex;
 142   int size(ci.allGatherArrays(comm,globalCellIds,allGlobalCellIds,allGlobalCellIdsIndex));
 143   // Prepare ParaUMesh parts to be sent : compute for each proc the contribution of current rank.
 144   std::vector< MCAuto<DataArrayIdType> > globalCellIdsToBeSent(size),globalNodeIdsToBeSent(size);
 145   std::vector< MCAuto<MEDCouplingUMesh> > meshPartsToBeSent(size);
 146   for(int curRk = 0 ; curRk < size ; ++curRk)
 147   {
 148     mcIdType offset(allGlobalCellIdsIndex[curRk]);
 149     MCAuto<DataArrayIdType> globalCellIdsOfCurProc(DataArrayIdType::New());
 150     globalCellIdsOfCurProc->useArray(allGlobalCellIds.get()+offset,false,DeallocType::CPP_DEALLOC,allGlobalCellIdsIndex[curRk+1]-offset,1);
 151     // the key call is here : compute for rank curRk the cells to be sent
 152     MCAuto<DataArrayIdType> globalCellIdsCaptured(_cell_global->buildIntersection(globalCellIdsOfCurProc));// OK for the global cellIds
 153     MCAuto<DataArrayIdType> localCellIdsCaptured(_cell_global->findIdForEach(globalCellIdsCaptured->begin(),globalCellIdsCaptured->end()));
 154     MCAuto<MEDCouplingUMesh> meshPart(_mesh->buildPartOfMySelf(localCellIdsCaptured->begin(),localCellIdsCaptured->end(),true));
 155     MCAuto<DataArrayIdType> o2n(meshPart->zipCoordsTraducer());// OK for the mesh
 156     MCAuto<DataArrayIdType> n2o(o2n->invertArrayO2N2N2O(meshPart->getNumberOfNodes()));
 157     MCAuto<DataArrayIdType> globalNodeIdsPart(_node_global->selectByTupleIdSafe(n2o->begin(),n2o->end())); // OK for the global nodeIds
 158     meshPartsToBeSent[curRk] = meshPart;
 159     globalCellIdsToBeSent[curRk] = globalCellIdsCaptured;
 160     globalNodeIdsToBeSent[curRk] = globalNodeIdsPart;
 161   }
 162   // Receive
 163   std::vector< MCAuto<DataArrayIdType> > globalCellIdsReceived,globalNodeIdsReceived;
 164   ci.allToAllArrays(comm,globalCellIdsToBeSent,globalCellIdsReceived);
 165   ci.allToAllArrays(comm,globalNodeIdsToBeSent,globalNodeIdsReceived);
 166   //now exchange the 3 arrays for the umesh : connectivity, connectivityindex and coordinates
 167   std::vector<const MEDCouplingUMesh *> meshPartsToBeSent2(FromVecAutoToVecOfConst<MEDCouplingUMesh>(meshPartsToBeSent));
 168   //connectivityindex
 169   std::vector< MCAuto<DataArrayIdType> > connectivityIndexReceived,connectivityReceived;
 170   {
 171     std::vector<const DataArrayIdType *> connectivityIndexToBeSent(UMeshConnectivityIndexIterator(0,&meshPartsToBeSent2),UMeshConnectivityIndexIterator(meshPartsToBeSent2.size(),&meshPartsToBeSent2));
 172     ci.allToAllArrays(comm,FromVecConstToVecAuto<DataArrayIdType>(connectivityIndexToBeSent),connectivityIndexReceived);
 173   }
 174   //connectivity
 175   {
 176     std::vector<const DataArrayIdType *> connectivityToBeSent(UMeshConnectivityIterator(0,&meshPartsToBeSent2),UMeshConnectivityIterator(meshPartsToBeSent2.size(),&meshPartsToBeSent2));
 177     ci.allToAllArrays(comm,FromVecConstToVecAuto<DataArrayIdType>(connectivityToBeSent),connectivityReceived);
 178   }
 179   //coordinates
 180   MCAuto<DataArrayDouble> coords;
 181   {
 182     std::vector<const DataArrayDouble *> coordsToBeSent(UMeshCoordsIterator(0,&meshPartsToBeSent2),UMeshCoordsIterator(meshPartsToBeSent2.size(),&meshPartsToBeSent2));
 183     ci.allToAllArrays(comm,FromVecConstToVecAuto<DataArrayDouble>(coordsToBeSent),coords);
 184   }
 185   /////// Sort it all !
 186   // firstly deal with nodes.
 187   MCAuto<DataArrayIdType> aggregatedNodeIds( DataArrayIdType::Aggregate(FromVecAutoToVecOfConst<DataArrayIdType>(globalNodeIdsReceived)) );
 188   MCAuto<DataArrayIdType> aggregatedNodeIdsSorted(aggregatedNodeIds->copySorted());
 189   MCAuto<DataArrayIdType> nodeIdsIntoAggregatedIds(DataArrayIdType::FindPermutationFromFirstToSecondDuplicate(aggregatedNodeIdsSorted,aggregatedNodeIds));
 190   MCAuto<DataArrayIdType> idxOfSameNodeIds(aggregatedNodeIdsSorted->indexOfSameConsecutiveValueGroups());
 191   MCAuto<DataArrayIdType> n2o_nodes(nodeIdsIntoAggregatedIds->selectByTupleIdSafe(idxOfSameNodeIds->begin(),idxOfSameNodeIds->end()-1));//new == new ordering so that global node ids are sorted . old == coarse ordering implied by the aggregation
 192   MCAuto<DataArrayIdType> finalGlobalNodeIds(aggregatedNodeIdsSorted->selectByTupleIdSafe(idxOfSameNodeIds->begin(),idxOfSameNodeIds->end()-1));
 193   MCAuto<DataArrayDouble> finalCoords(coords->selectByTupleIdSafe(n2o_nodes->begin(),n2o_nodes->end()));
 194   finalCoords->copyStringInfoFrom(*_mesh->getCoords());
 195   // secondly renumbering of node ids in connectivityReceived
 196   for(int curRk = 0 ; curRk < size ; ++curRk)
 197   {
 198     auto current(globalNodeIdsReceived[curRk]);
 199     MCAuto<DataArrayIdType> aa(finalGlobalNodeIds->findIdForEach(current->begin(),current->end()));
 200     // work on connectivityReceived[curRk] with transformWithIndArr but do not forget type of cells that should be excluded !
 201     auto connectivityToModify(connectivityReceived[curRk]);
 202     auto connectivityIndex(connectivityIndexReceived[curRk]);
 203     MCAuto<DataArrayIdType> types(connectivityToModify->selectByTupleIdSafe(connectivityIndex->begin(),connectivityIndex->end()-1));
 204     connectivityToModify->setPartOfValuesSimple3(0,connectivityIndex->begin(),connectivityIndex->end()-1,0,1,1);
 205     connectivityToModify->transformWithIndArr(aa->begin(),aa->end());
 206     connectivityToModify->setPartOfValues3(types,connectivityIndex->begin(),connectivityIndex->end()-1,0,1,1,true);
 207   }
 208   // thirdly renumber cells
 209   MCAuto<DataArrayIdType> aggregatedCellIds( DataArrayIdType::Aggregate(FromVecAutoToVecOfConst<DataArrayIdType>(globalCellIdsReceived)) );
 210   MCAuto<DataArrayIdType> aggregatedCellIdsSorted(aggregatedCellIds->copySorted());
 211   MCAuto<DataArrayIdType> idsIntoAggregatedIds(DataArrayIdType::FindPermutationFromFirstToSecondDuplicate(aggregatedCellIdsSorted,aggregatedCellIds));
 212   MCAuto<DataArrayIdType> cellIdsOfSameNodeIds(aggregatedCellIdsSorted->indexOfSameConsecutiveValueGroups());
 213   MCAuto<DataArrayIdType> n2o_cells(idsIntoAggregatedIds->selectByTupleIdSafe(cellIdsOfSameNodeIds->begin(),cellIdsOfSameNodeIds->end()-1));//new == new ordering so that global cell ids are sorted . old == coarse ordering implied by the aggregation
 214   // TODO : check coordsReceived==globalCellIds
 215   MCAuto<DataArrayIdType> connSorted,indicesSorted;
 216   {
 217     MCAuto<DataArrayIdType> conn(DataArrayIdType::Aggregate(FromVecAutoToVecOfConst<DataArrayIdType>(connectivityReceived)));
 218     MCAuto<DataArrayIdType> connIndex(DataArrayIdType::AggregateIndexes(FromVecAutoToVecOfConst<DataArrayIdType>(connectivityIndexReceived)));
 219     {
 220       DataArrayIdType *indicesSortedTmp(nullptr),*valuesSortedTmp(nullptr);
 221       DataArrayIdType::ExtractFromIndexedArrays(n2o_cells->begin(),n2o_cells->end(),conn,connIndex,valuesSortedTmp,indicesSortedTmp);
 222       indicesSorted = indicesSortedTmp; connSorted=valuesSortedTmp;
 223     }
 224   }
 225   // finalize all
 226   MCAuto<MEDCouplingUMesh> mesh(MEDCouplingUMesh::New(_mesh->getName(),_mesh->getMeshDimension()));
 227   mesh->setConnectivity(connSorted,indicesSorted,true);
 228   mesh->setCoords(finalCoords);
 229   mesh->setDescription(_mesh->getDescription());
 230   MCAuto<ParaUMesh> ret(ParaUMesh::New(mesh,aggregatedCellIdsSorted,finalGlobalNodeIds));
 231   return ret.retn();
 232 }