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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,
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11 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
12 // Lesser General Public License for more details.
13 //
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15 // License along with this library; if not, write to the Free Software
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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 DataArrayIdType *ParaUMesh::redistributeCellField(const DataArrayIdType *globalCellIds, const DataArrayIdType *fieldValueToRed) const
135 {
136   return this->redistributeCellFieldT<mcIdType>(globalCellIds,fieldValueToRed);
137 }
138
139 DataArrayDouble *ParaUMesh::redistributeCellField(const DataArrayIdType *globalCellIds, const DataArrayDouble *fieldValueToRed) const
140 {
141   return this->redistributeCellFieldT<double>(globalCellIds,fieldValueToRed);
142 }
143
144 DataArrayIdType *ParaUMesh::redistributeNodeField(const DataArrayIdType *globalCellIds, const DataArrayIdType *fieldValueToRed) const
145 {
146   return this->redistributeNodeFieldT<mcIdType>(globalCellIds,fieldValueToRed);
147 }
148
149 DataArrayDouble *ParaUMesh::redistributeNodeField(const DataArrayIdType *globalCellIds, const DataArrayDouble *fieldValueToRed) const
150 {
151   return this->redistributeNodeFieldT<double>(globalCellIds,fieldValueToRed);
152 }
153
154 /*!
155  * Return part of \a this mesh split over COMM_WORLD. Part is defined by global cell ids array \a globaCellIds.
156  */
157 ParaUMesh *ParaUMesh::redistributeCells(const DataArrayIdType *globalCellIds) const
158 {
159   MPI_Comm comm(MPI_COMM_WORLD);
160   CommInterface ci;
161   std::unique_ptr<mcIdType[]> allGlobalCellIds,allGlobalCellIdsIndex;
162   int size(ci.allGatherArrays(comm,globalCellIds,allGlobalCellIds,allGlobalCellIdsIndex));
163   // Prepare ParaUMesh parts to be sent : compute for each proc the contribution of current rank.
164   std::vector< MCAuto<DataArrayIdType> > globalCellIdsToBeSent(size),globalNodeIdsToBeSent(size);
165   std::vector< MCAuto<MEDCouplingUMesh> > meshPartsToBeSent(size);
166   for(int curRk = 0 ; curRk < size ; ++curRk)
167   {
168     mcIdType offset(allGlobalCellIdsIndex[curRk]);
169     MCAuto<DataArrayIdType> globalCellIdsOfCurProc(DataArrayIdType::New());
170     globalCellIdsOfCurProc->useArray(allGlobalCellIds.get()+offset,false,DeallocType::CPP_DEALLOC,allGlobalCellIdsIndex[curRk+1]-offset,1);
171     // the key call is here : compute for rank curRk the cells to be sent
172     MCAuto<DataArrayIdType> globalCellIdsCaptured(_cell_global->buildIntersection(globalCellIdsOfCurProc));// OK for the global cellIds
173     MCAuto<DataArrayIdType> localCellIdsCaptured(_cell_global->findIdForEach(globalCellIdsCaptured->begin(),globalCellIdsCaptured->end()));
174     MCAuto<MEDCouplingUMesh> meshPart(_mesh->buildPartOfMySelf(localCellIdsCaptured->begin(),localCellIdsCaptured->end(),true));
175     MCAuto<DataArrayIdType> o2n(meshPart->zipCoordsTraducer());// OK for the mesh
176     MCAuto<DataArrayIdType> n2o(o2n->invertArrayO2N2N2O(meshPart->getNumberOfNodes()));
177     MCAuto<DataArrayIdType> globalNodeIdsPart(_node_global->selectByTupleIdSafe(n2o->begin(),n2o->end())); // OK for the global nodeIds
178     meshPartsToBeSent[curRk] = meshPart;
179     globalCellIdsToBeSent[curRk] = globalCellIdsCaptured;
180     globalNodeIdsToBeSent[curRk] = globalNodeIdsPart;
181   }
182   // Receive
183   std::vector< MCAuto<DataArrayIdType> > globalCellIdsReceived,globalNodeIdsReceived;
184   ci.allToAllArrays(comm,globalCellIdsToBeSent,globalCellIdsReceived);
185   ci.allToAllArrays(comm,globalNodeIdsToBeSent,globalNodeIdsReceived);
186   //now exchange the 3 arrays for the umesh : connectivity, connectivityindex and coordinates
187   std::vector<const MEDCouplingUMesh *> meshPartsToBeSent2(FromVecAutoToVecOfConst<MEDCouplingUMesh>(meshPartsToBeSent));
188   //connectivityindex
189   std::vector< MCAuto<DataArrayIdType> > connectivityIndexReceived,connectivityReceived;
190   {
191     std::vector<const DataArrayIdType *> connectivityIndexToBeSent(UMeshConnectivityIndexIterator(0,&meshPartsToBeSent2),UMeshConnectivityIndexIterator(meshPartsToBeSent2.size(),&meshPartsToBeSent2));
192     ci.allToAllArrays(comm,FromVecConstToVecAuto<DataArrayIdType>(connectivityIndexToBeSent),connectivityIndexReceived);
193   }
194   //connectivity
195   {
196     std::vector<const DataArrayIdType *> connectivityToBeSent(UMeshConnectivityIterator(0,&meshPartsToBeSent2),UMeshConnectivityIterator(meshPartsToBeSent2.size(),&meshPartsToBeSent2));
197     ci.allToAllArrays(comm,FromVecConstToVecAuto<DataArrayIdType>(connectivityToBeSent),connectivityReceived);
198   }
199   //coordinates
200   MCAuto<DataArrayDouble> coords;
201   {
202     std::vector<const DataArrayDouble *> coordsToBeSent(UMeshCoordsIterator(0,&meshPartsToBeSent2),UMeshCoordsIterator(meshPartsToBeSent2.size(),&meshPartsToBeSent2));
203     ci.allToAllArrays(comm,FromVecConstToVecAuto<DataArrayDouble>(coordsToBeSent),coords);
204   }
205   /////// Sort it all !
206   // firstly deal with nodes.
207   MCAuto<DataArrayIdType> aggregatedNodeIds( DataArrayIdType::Aggregate(FromVecAutoToVecOfConst<DataArrayIdType>(globalNodeIdsReceived)) );
208   MCAuto<DataArrayIdType> aggregatedNodeIdsSorted(aggregatedNodeIds->copySorted());
209   MCAuto<DataArrayIdType> nodeIdsIntoAggregatedIds(DataArrayIdType::FindPermutationFromFirstToSecondDuplicate(aggregatedNodeIdsSorted,aggregatedNodeIds));
210   MCAuto<DataArrayIdType> idxOfSameNodeIds(aggregatedNodeIdsSorted->indexOfSameConsecutiveValueGroups());
211   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
212   MCAuto<DataArrayIdType> finalGlobalNodeIds(aggregatedNodeIdsSorted->selectByTupleIdSafe(idxOfSameNodeIds->begin(),idxOfSameNodeIds->end()-1));
213   MCAuto<DataArrayDouble> finalCoords(coords->selectByTupleIdSafe(n2o_nodes->begin(),n2o_nodes->end()));
214   finalCoords->copyStringInfoFrom(*_mesh->getCoords());
215   // secondly renumbering of node ids in connectivityReceived
216   for(int curRk = 0 ; curRk < size ; ++curRk)
217   {
218     auto current(globalNodeIdsReceived[curRk]);
219     MCAuto<DataArrayIdType> aa(finalGlobalNodeIds->findIdForEach(current->begin(),current->end()));
220     // work on connectivityReceived[curRk] with transformWithIndArr but do not forget type of cells that should be excluded !
221     auto connectivityToModify(connectivityReceived[curRk]);
222     auto connectivityIndex(connectivityIndexReceived[curRk]);
223     MCAuto<DataArrayIdType> types(connectivityToModify->selectByTupleIdSafe(connectivityIndex->begin(),connectivityIndex->end()-1));
224     connectivityToModify->setPartOfValuesSimple3(0,connectivityIndex->begin(),connectivityIndex->end()-1,0,1,1);
225     connectivityToModify->transformWithIndArr(aa->begin(),aa->end());
226     connectivityToModify->setPartOfValues3(types,connectivityIndex->begin(),connectivityIndex->end()-1,0,1,1,true);
227   }
228   // thirdly renumber cells
229   MCAuto<DataArrayIdType> aggregatedCellIds( DataArrayIdType::Aggregate(FromVecAutoToVecOfConst<DataArrayIdType>(globalCellIdsReceived)) );
230   MCAuto<DataArrayIdType> aggregatedCellIdsSorted(aggregatedCellIds->copySorted());
231   MCAuto<DataArrayIdType> idsIntoAggregatedIds(DataArrayIdType::FindPermutationFromFirstToSecondDuplicate(aggregatedCellIdsSorted,aggregatedCellIds));
232   MCAuto<DataArrayIdType> cellIdsOfSameNodeIds(aggregatedCellIdsSorted->indexOfSameConsecutiveValueGroups());
233   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
234   // TODO : check coordsReceived==globalCellIds
235   MCAuto<DataArrayIdType> connSorted,indicesSorted;
236   {
237     MCAuto<DataArrayIdType> conn(DataArrayIdType::Aggregate(FromVecAutoToVecOfConst<DataArrayIdType>(connectivityReceived)));
238     MCAuto<DataArrayIdType> connIndex(DataArrayIdType::AggregateIndexes(FromVecAutoToVecOfConst<DataArrayIdType>(connectivityIndexReceived))); 
239     {
240       DataArrayIdType *indicesSortedTmp(nullptr),*valuesSortedTmp(nullptr);
241       DataArrayIdType::ExtractFromIndexedArrays(n2o_cells->begin(),n2o_cells->end(),conn,connIndex,valuesSortedTmp,indicesSortedTmp);
242       indicesSorted = indicesSortedTmp; connSorted=valuesSortedTmp;
243     }
244   }
245   // finalize all
246   MCAuto<MEDCouplingUMesh> mesh(MEDCouplingUMesh::New(_mesh->getName(),_mesh->getMeshDimension()));
247   mesh->setConnectivity(connSorted,indicesSorted,true);
248   mesh->setCoords(finalCoords);
249   mesh->setDescription(_mesh->getDescription());
250   MCAuto<ParaUMesh> ret(ParaUMesh::New(mesh,aggregatedCellIdsSorted,finalGlobalNodeIds));
251   return ret.retn();
252 }