MeshDistributor.cc 66 KB
Newer Older
Thomas Witkowski's avatar
Thomas Witkowski committed
1
#include <algorithm>
2
3
#include <iostream>
#include <fstream>
4
5
#include <limits>
#include <stdint.h>
Thomas Witkowski's avatar
Thomas Witkowski committed
6
#include <boost/lexical_cast.hpp>
7
8
#include <boost/filesystem.hpp>

9
#include "parallel/MeshDistributor.h"
10
#include "parallel/MeshManipulation.h"
11
#include "parallel/ParallelDebug.h"
12
#include "parallel/StdMpi.h"
13
#include "parallel/ParMetisPartitioner.h"
14
15
16
#include "io/ElementFileWriter.h"
#include "io/MacroInfo.h"
#include "io/VtkWriter.h"
17
18
19
20
21
#include "Mesh.h"
#include "Traverse.h"
#include "ElInfo.h"
#include "Element.h"
#include "MacroElement.h"
22
23
#include "DOFMatrix.h"
#include "DOFVector.h"
24
#include "SystemVector.h"
25
#include "ElementDofIterator.h"
26
27
#include "ProblemStatBase.h"
#include "StandardProblemIteration.h"
28
#include "VertexVector.h"
29
#include "MeshStructure.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
30
31
#include "ProblemVec.h"
#include "ProblemInstat.h"
32
#include "Debug.h"
33

34
35
namespace AMDiS {

Thomas Witkowski's avatar
Thomas Witkowski committed
36
  using boost::lexical_cast;
37
  using namespace boost::filesystem;
Thomas Witkowski's avatar
Thomas Witkowski committed
38

39
40
41
42
43
  inline bool cmpDofsByValue(const DegreeOfFreedom* dof1, const DegreeOfFreedom* dof2)
  {
    return (*dof1 < *dof2);
  }

44
45
46
47
48
  bool cmpElement(MacroElement* lhs, MacroElement* rhs)
  {
    return lhs->getIndex() < rhs->getIndex();
  }
  
49

50
51
52
53
54
55
56
57
  MeshDistributor::MeshDistributor(std::string str)
    : probStat(0),
      name(str),
      feSpace(NULL),
      mesh(NULL),
      refineManager(NULL),
      info(10),
      partitioner(NULL),
58
      nRankDofs(0),
59
      nOverallDofs(0),
60
      rstart(0),
61
      deserialized(false),
62
      writeSerializationFile(false),
63
      repartitioningAllowed(false),
64
      nTimestepsAfterLastRepartitioning(0),
65
      repartCounter(0),
66
      lastMeshChangeIndex(0)
67
  {
68
    FUNCNAME("MeshDistributor::ParalleDomainBase()");
Thomas Witkowski's avatar
Thomas Witkowski committed
69

70
71
72
    mpiRank = MPI::COMM_WORLD.Get_rank();
    mpiSize = MPI::COMM_WORLD.Get_size();
    mpiComm = MPI::COMM_WORLD;
73
74
75
76

    int tmp = 0;
    GET_PARAMETER(0, name + "->repartitioning", "%d", &tmp);
    repartitioningAllowed = (tmp > 0);
77
78
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
79

80
  void MeshDistributor::initParallelization()
81
  {
82
    FUNCNAME("MeshDistributor::initParallelization()");
83
84
85
86

    TEST_EXIT(mpiSize > 1)
      ("Parallelization does not work with only one process!\n");

87
88
    TEST_EXIT(feSpace)("No FE space has been defined for the mesh distributor!\n");
    TEST_EXIT(mesh)("No mesh has been defined for the mesh distributor!\n");
89

90
91
92
    // If the problem has been already read from a file, we need only to set
    // isRankDofs to all matrices and rhs vector and to remove periodic 
    // boundary conditions (if there are some).
93
    if (deserialized) {
94
95
      updateMacroElementInfo();

96
      setRankDofs();
97

98
      removePeriodicBoundaryConditions();
99

100
101
      macroElIndexMap.clear();
      macroElIndexTypeMap.clear();
102
103
104
105
106

      std::map<int, bool>& elementInRank = partitioner->getElementInRank();
      for (std::vector<MacroElement*>::iterator it = allMacroElements.begin();
	   it != allMacroElements.end(); ++it) {
	elementInRank[(*it)->getIndex()] = false;
107
108
109
110
	macroElIndexMap[(*it)->getIndex()] = (*it)->getElement();
	macroElIndexTypeMap[(*it)->getIndex()] = (*it)->getElType();
      }

111
112
113
114
      for (std::deque<MacroElement*>::iterator it = mesh->getMacroElements().begin();
	   it != mesh->getMacroElements().end(); ++it)
	elementInRank[(*it)->getIndex()] = true;      

115
      return;
116
    }
117

118
   
119
120
121
122
123
    // Test, if the mesh is the macro mesh only! Paritioning of the mesh is supported
    // only for macro meshes, so it will not work yet if the mesh is already refined
    // in some way.
    testForMacroMesh();

124
125
126
127
    // For later mesh repartitioning, we need to store some information about the
    // macro mesh.
    createMacroElementInfo();

128
129
    // create an initial partitioning of the mesh
    partitioner->createPartitionData();
130

131
    // set the element weights, which are 1 at the very first begin
132
    setInitialElementWeights();
133
134
135
136
137
138

    // and now partition the mesh    
    partitioner->fillCoarsePartitionVec(&oldPartitionVec);
    partitioner->partition(&elemWeights, INITIAL);
    partitioner->fillCoarsePartitionVec(&partitionVec);

139

Thomas Witkowski's avatar
Thomas Witkowski committed
140
#if (DEBUG != 0)
141
142
    debug::ElementIdxToDofs elMap;
    debug::createSortedDofs(mesh, elMap);
143
144
145
    if (mpiRank == 0) {
      int writePartMesh = 1;
      GET_PARAMETER(0, "dbg->write part mesh", "%d", &writePartMesh);
146

147
148
      if (writePartMesh > 0) {
	debug::writeElementIndexMesh(mesh, "elementIndex.vtu");
149
	writePartitioningMesh("part.vtu");
150
      } else {
151
	MSG("Skip write part mesh!\n");
152
      }
153
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
154
#endif
155

156

157
    // === Create interior boundary information. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
158

159
    createInteriorBoundaryInfo();
Thomas Witkowski's avatar
Thomas Witkowski committed
160

161
#if (DEBUG != 0)
162
    ParallelDebug::printBoundaryInfo(*this);
163
164
#endif

165

Thomas Witkowski's avatar
n  
Thomas Witkowski committed
166
167
168
    // === Remove all macro elements that are not part of the rank partition. ===

    removeMacroElements();
169

Thomas Witkowski's avatar
n  
Thomas Witkowski committed
170

171
172
    // === Create new global and local DOF numbering. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
173

174
175
176
177
178
179
    // We have to remove the VertexVectors, which contain periodic assoiciations, 
    // because they are not valid anymore after some macro elements have been removed
    // and the corresponding DOFs were deleted.
    for (std::map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
	 it != mesh->getPeriodicAssociations().end(); ++it)
      const_cast<DOFAdmin&>(mesh->getDofAdmin(0)).removeDOFContainer(dynamic_cast<DOFContainer*>(it->second));
180

181
    updateLocalGlobalNumbering();
182

183

184
185
    // === If in debug mode, make some tests. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
186
#if (DEBUG != 0)
187
    MSG("AMDiS runs in debug mode, so make some test ...\n");
188

189
    ParallelDebug::testAllElements(*this);
190
    debug::testSortedDofs(mesh, elMap);
191
192
    ParallelDebug::testInteriorBoundary(*this);
    ParallelDebug::testCommonDofs(*this, true);
193
    ParallelDebug::testGlobalIndexByCoords(*this);
Thomas Witkowski's avatar
Thomas Witkowski committed
194

195
    debug::writeMesh(feSpace, -1, "macro_mesh");   
196
197

    MSG("Debug mode tests finished!\n");
198
#endif
199

200

201
202
    // === Create periodic dof mapping, if there are periodic boundaries. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
203
    createPeriodicMap();    
204

205
    // === Global refinements. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
206

Thomas Witkowski's avatar
Thomas Witkowski committed
207
    int globalRefinement = 0;
208
    GET_PARAMETER(0, mesh->getName() + "->global refinements", "%d", &globalRefinement);
Thomas Witkowski's avatar
Thomas Witkowski committed
209

Thomas Witkowski's avatar
Thomas Witkowski committed
210
    if (globalRefinement > 0) {
211
      refineManager->globalRefine(mesh, globalRefinement);
212

213
#if (DEBUG != 0)
214
      debug::writeMesh(feSpace, -1, "gr_mesh");
215
216
#endif

217
      updateLocalGlobalNumbering();
218
219

     
220
      // === Update periodic mapping, if there are periodic boundaries. ===
221
      
222
      createPeriodicMap();
Thomas Witkowski's avatar
Thomas Witkowski committed
223
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
224

225

Thomas Witkowski's avatar
Thomas Witkowski committed
226
227
    /// === Set DOF rank information to all matrices and vectors. ===

228
    setRankDofs();
Thomas Witkowski's avatar
Thomas Witkowski committed
229

230

Thomas Witkowski's avatar
Thomas Witkowski committed
231
232
    // === Remove periodic boundary conditions in sequential problem definition. ===

233
    removePeriodicBoundaryConditions();
234
235
  }

236

237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
  void MeshDistributor::addProblemStat(ProblemVec *probVec)
  {
    FUNCNAME("MeshDistributor::addProblemVec()");

    if (feSpace != NULL) {
      std::vector<FiniteElemSpace*> feSpaces = probVec->getFeSpaces();
      for (unsigned int i = 0; i < feSpaces.size(); i++) {
	TEST_EXIT(feSpace == feSpaces[i])
	  ("Parallelizaton is not supported for multiple FE spaces!\n");
      }
    } else {
      feSpace = probVec->getFeSpace(0);
      mesh = feSpace->getMesh();
      info = probVec->getInfo();
      
      TEST_EXIT(mesh->getNumberOfDOFAdmin() == 1)
	("Only meshes with one DOFAdmin are supported!\n");
254
      TEST_EXIT(mesh->getDofAdmin(0).getNumberOfPreDOFs(0) == 0)
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
	("Wrong pre dof number for DOFAdmin!\n");
      
      switch (mesh->getDim()) {
      case 2:
	refineManager = new RefinementManager2d();
	break;
      case 3:
	refineManager = new RefinementManager3d();
	break;
      default:
	ERROR_EXIT("This should not happen for dim = %d!\n", mesh->getDim());
      }

      partitioner = new ParMetisPartitioner(mesh, &mpiComm);
    }

    // Create parallel serialization file writer, if needed.
    int writeSerialization = 0;
273
274
275
    GET_PARAMETER(0, probVec->getName() + "->output->write serialization", "%d", 
		  &writeSerialization);
    if (writeSerialization && !writeSerializationFile) {
276
277
278
279
280
      std::string filename = "";
      GET_PARAMETER(0, name + "->output->serialization filename", &filename);
      
      TEST_EXIT(filename != "")
	("No filename defined for parallel serialization file!\n");
281
282
283
284
285

      int tsModulo = -1;
      GET_PARAMETER(0, probVec->getName() + "->output->write every i-th timestep", 
		    "%d", &tsModulo);
      
286
      probVec->getFileWriterList().push_back(new Serializer<MeshDistributor>(this, filename, tsModulo));
287
288
      writeSerializationFile = true;
    }    
289
290

    int readSerialization = 0;
291
292
    GET_PARAMETER(0, probVec->getName() + "->input->read serialization", "%d", 
		  &readSerialization);
293
294
295
296
    if (readSerialization) {
      std::string filename = "";
      GET_PARAMETER(0, probVec->getName() + "->input->serialization filename", &filename);
      filename += ".p" + lexical_cast<std::string>(mpiRank);
297
      MSG("Start deserialization with %s\n", filename.c_str());
298
      std::ifstream in(filename.c_str());
299
300
301
302

      TEST_EXIT(!in.fail())("Could not open deserialization file: %s\n",
			    filename.c_str());

303
      probVec->deserialize(in);
304
      in.close();
305
306
      MSG("Deserialization from file: %s\n", filename.c_str());

307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
      filename = "";
      GET_PARAMETER(0, name + "->input->serialization filename", &filename);
      
      TEST_EXIT(filename != "")
	("No filename defined for parallel deserialization file!\n");
      
      std::string rankFilename = filename + ".p" + lexical_cast<std::string>(mpiRank);
      in.open(rankFilename.c_str());
      
      TEST_EXIT(!in.fail())("Could not open parallel deserialization file: %s\n",
			    filename.c_str());
      
      deserialize(in);
      in.close();
      MSG("Deserializtion of mesh distributor from file: %s\n", rankFilename.c_str());
      deserialized = true;
323
324
325
326
327
328
    }

    probStat.push_back(probVec);
  }


329
  void MeshDistributor::exitParallelization()
330
  {}
331

332
  
333
  void MeshDistributor::testForMacroMesh()
334
  {
335
    FUNCNAME("MeshDistributor::testForMacroMesh()");
336
337
338
339
340
341
342

    int nMacroElements = 0;

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
    while (elInfo) {
      TEST_EXIT(elInfo->getLevel() == 0)
343
	("Mesh is already refined! This does not work with parallelization!\n");
344
345
346

      TEST_EXIT(elInfo->getType() == 0)
	("Only macro elements with level 0 are supported!\n");
347
348
349
350
351
352
353
354
355
356
      
      nMacroElements++;

      elInfo = stack.traverseNext(elInfo);
    }

    TEST_EXIT(nMacroElements >= mpiSize)
      ("The mesh has less macro elements than number of mpi processes!\n");
  }

357

358
  void MeshDistributor::synchVector(DOFVector<double> &vec)
359
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
360
    StdMpi<std::vector<double> > stdMpi(mpiComm);
361
362

    for (RankToDofContainer::iterator sendIt = sendDofs.begin();
Thomas Witkowski's avatar
Thomas Witkowski committed
363
	 sendIt != sendDofs.end(); ++sendIt) {
364
      std::vector<double> dofs;
Thomas Witkowski's avatar
Thomas Witkowski committed
365
366
      int nSendDofs = sendIt->second.size();
      dofs.reserve(nSendDofs);
367
      
Thomas Witkowski's avatar
Thomas Witkowski committed
368
369
      for (int i = 0; i < nSendDofs; i++)
	dofs.push_back(vec[*((sendIt->second)[i])]);
370
371
372
373

      stdMpi.send(sendIt->first, dofs);
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
374
375
376
    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
	 recvIt != recvDofs.end(); ++recvIt)
      stdMpi.recv(recvIt->first, recvIt->second.size());
377

Thomas Witkowski's avatar
Thomas Witkowski committed
378
    stdMpi.startCommunication<double>(MPI_DOUBLE);
379

Thomas Witkowski's avatar
Thomas Witkowski committed
380
381
382
383
384
    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
	 recvIt != recvDofs.end(); ++recvIt)
      for (unsigned int i = 0; i < recvIt->second.size(); i++)
	vec[*(recvIt->second)[i]] = stdMpi.getRecvData(recvIt->first)[i];
  }
385
386


387
  void MeshDistributor::synchVector(SystemVector &vec)
Thomas Witkowski's avatar
Thomas Witkowski committed
388
  {
389
    int nComponents = vec.getSize();
Thomas Witkowski's avatar
Thomas Witkowski committed
390
391
392
393
394
395
396
397
398
399
400
401
    StdMpi<std::vector<double> > stdMpi(mpiComm);

    for (RankToDofContainer::iterator sendIt = sendDofs.begin();
	 sendIt != sendDofs.end(); ++sendIt) {
      std::vector<double> dofs;
      int nSendDofs = sendIt->second.size();
      dofs.reserve(nComponents * nSendDofs);
      
      for (int i = 0; i < nComponents; i++) {
	DOFVector<double> *dofvec = vec.getDOFVector(i);
	for (int j = 0; j < nSendDofs; j++)
	  dofs.push_back((*dofvec)[*((sendIt->second)[j])]);
402
403
      }

Thomas Witkowski's avatar
Thomas Witkowski committed
404
      stdMpi.send(sendIt->first, dofs);
405
406
407
    }

    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
Thomas Witkowski's avatar
Thomas Witkowski committed
408
409
	 recvIt != recvDofs.end(); ++recvIt)
      stdMpi.recv(recvIt->first, recvIt->second.size() * nComponents);
410

Thomas Witkowski's avatar
Thomas Witkowski committed
411
    stdMpi.startCommunication<double>(MPI_DOUBLE);
412
413

    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
Thomas Witkowski's avatar
Thomas Witkowski committed
414
415
	 recvIt != recvDofs.end(); ++recvIt) {
      int nRecvDofs = recvIt->second.size();
416
417

      int counter = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
418
419
420
421
422
      for (int i = 0; i < nComponents; i++) {
	DOFVector<double> *dofvec = vec.getDOFVector(i);
 	for (int j = 0; j < nRecvDofs; j++)
	  (*dofvec)[*(recvIt->second)[j]] = 
	    stdMpi.getRecvData(recvIt->first)[counter++];
423
424
425
426
      }
    }
  }

427

428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
  void MeshDistributor::setRankDofs()
  {
    for (unsigned int i = 0; i < probStat.size(); i++) {
      int nComponents = probStat[i]->getNumComponents();
      for (int j = 0; j < nComponents; j++) {
	for (int k = 0; k < nComponents; k++)
	  if (probStat[i]->getSystemMatrix(j, k))
	    probStat[i]->getSystemMatrix(j, k)->setRankDofs(isRankDof);

	TEST_EXIT_DBG(probStat[i]->getRhs()->getDOFVector(j))("No RHS vector!\n");
	TEST_EXIT_DBG(probStat[i]->getSolution()->getDOFVector(j))("No solution vector!\n");
	
	probStat[i]->getRhs()->getDOFVector(j)->setRankDofs(isRankDof);
	probStat[i]->getSolution()->getDOFVector(j)->setRankDofs(isRankDof);
      }
    }
  }


447
448
  void MeshDistributor::removePeriodicBoundaryConditions()
  {
449
450
    FUNCNAME("MeshDistributor::removePeriodicBoundaryConditions()");

451
452
453
454
455
456
457
458
    // Remove periodic boundaries in boundary manager on matrices and vectors.
    for (unsigned int i = 0; i < probStat.size(); i++) {
      int nComponents = probStat[i]->getNumComponents();

      for (int j = 0; j < nComponents; j++) {
	for (int k = 0; k < nComponents; k++) {
	  DOFMatrix* mat = probStat[i]->getSystemMatrix(j, k);
	  if (mat && mat->getBoundaryManager())
459
	    removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(mat->getBoundaryManager()->getBoundaryConditionMap()));
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
	}
	
	if (probStat[i]->getSolution()->getDOFVector(j)->getBoundaryManager())
	  removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(probStat[i]->getSolution()->getDOFVector(j)->getBoundaryManager()->getBoundaryConditionMap()));
	
	if (probStat[i]->getRhs()->getDOFVector(j)->getBoundaryManager())
	  removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(probStat[i]->getRhs()->getDOFVector(j)->getBoundaryManager()->getBoundaryConditionMap()));
      }
    }

    // Remove periodic boundaries on elements in mesh.
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh,  -1, Mesh::CALL_EVERY_EL_PREORDER);
    while (elInfo) {
      elInfo->getElement()->deleteElementData(PERIODIC);
      elInfo = stack.traverseNext(elInfo);
    }    
477
478
479

    // Remove periodic vertex associations
    mesh->getPeriodicAssociations().clear();
480
481
482
483
  }


  void MeshDistributor::removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap)
Thomas Witkowski's avatar
Thomas Witkowski committed
484
485
486
487
488
489
490
491
492
493
494
  {
    BoundaryIndexMap::iterator it = boundaryMap.begin();
    while (it != boundaryMap.end()) {
      if (it->second->isPeriodic())
	boundaryMap.erase(it++);
      else
	++it;      
    }    
  }


495
  void MeshDistributor::checkMeshChange()
496
  {
497
    FUNCNAME("MeshDistributor::checkMeshChange()");    
498

499
500
501
502
#if (DEBUG != 0)
    debug::writeMesh(feSpace, -1, "before_check_mesh");
#endif

503
504
505
506
507
    // === If mesh has not been changed on all ranks, return. ===

    int recvAllValues = 0;
    int sendValue = static_cast<int>(mesh->getChangeIndex() != lastMeshChangeIndex);
    mpiComm.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
508

509
    if (recvAllValues == 0)
510
511
      return;

512
513
    // === At least one rank mesh has been changed, so the boundaries must be ===
    // === adapted to the new mesh structure.                                 ===
514

515
516
517
518
519
    clock_t first = clock();
    
    do {
      // To check the interior boundaries, the ownership of the boundaries is not 
      // important. Therefore, we add all boundaries to one boundary container.
520
      RankToBoundMap allBound;
Thomas Witkowski's avatar
Thomas Witkowski committed
521
522

      for (InteriorBoundary::iterator it(myIntBoundary); !it.end(); ++it)
523
524
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
525
 	  allBound[it.getRank()].push_back(*it);
Thomas Witkowski's avatar
Thomas Witkowski committed
526
527

      for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it)
528
529
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
530
	  allBound[it.getRank()].push_back(*it);
Thomas Witkowski's avatar
Thomas Witkowski committed
531

532
      for (InteriorBoundary::iterator it(periodicBoundary); !it.end(); ++it)
533
534
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
535
 	  allBound[it.getRank()].push_back(*it);	
536

537

538
      // === Check the boundaries and adapt mesh if necessary. ===
539
540
541
542
#if (DEBUG != 0)
      MSG("Run checkAndAdaptBoundary ...\n");
#endif

543
544
545
546
547
548
549
      bool meshChanged = checkAndAdaptBoundary(allBound);

      // === Check on all ranks if at least one rank's mesh has changed. ===

      int sendValue = static_cast<int>(!meshChanged);
      recvAllValues = 0;
      mpiComm.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
550
551
552
553

#if (DEBUG != 0)
      MSG("Mesh changed on %d ranks!\n", recvAllValues);
#endif
554
    } while (recvAllValues != 0);
555

556
#if (DEBUG != 0)
557
    debug::writeMesh(feSpace, -1, "mesh");
558
559
560
561
562
563
#endif

    INFO(info, 8)("Parallel mesh adaption needed %.5f seconds\n", 
		  TIME_USED(first, clock()));

    // === Because the mesh has been changed, update the DOF numbering and mappings. ===
564

565
566
    updateLocalGlobalNumbering();

567
568
569
570

    // === Update periodic mapping, if there are periodic boundaries. ===

    createPeriodicMap();
571
572
573
574


    // === The mesh has changed, so check if it is required to repartition the mesh. ===

575
576
577
    nTimestepsAfterLastRepartitioning++;

    if (repartitioningAllowed) {
578
      //      if (nTimestepsAfterLastRepartitioning >= 20) {
579
580
	repartitionMesh();
	nTimestepsAfterLastRepartitioning = 0;
581
	//      }
582
    }
583
584
585
  }

  
586
  bool MeshDistributor::checkAndAdaptBoundary(RankToBoundMap &allBound)
587
  {
588
    FUNCNAME("MeshDistributor::checkAndAdaptBoundary()");
589
590
591
592
593
594

    // === Create mesh structure codes for all ranks boundary elements. ===
       
    std::map<int, MeshCodeVec> sendCodes;
   
    for (RankToBoundMap::iterator it = allBound.begin(); it != allBound.end(); ++it) {
595

596
597
598
      for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt) {
	MeshStructure elCode;
599
	elCode.init(boundIt->rankObj);
600
601
602
603
	sendCodes[it->first].push_back(elCode);
      }
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
604
    StdMpi<MeshCodeVec> stdMpi(mpiComm, true);
605
    stdMpi.send(sendCodes);
606
    stdMpi.recv(allBound);
607
    stdMpi.startCommunication<uint64_t>(MPI_UNSIGNED_LONG);
608
 
609
    // === Compare received mesh structure codes. ===
610
    
611
612
    bool meshFitTogether = true;

613
    for (RankToBoundMap::iterator it = allBound.begin(); it != allBound.end(); ++it) {
614
     
615
616
      MeshCodeVec &recvCodes = stdMpi.getRecvData()[it->first];
      int i = 0;
617
      
618
619
      for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt) {
620

621
622
	MeshStructure elCode;	
	elCode.init(boundIt->rankObj);
623

624
625
	if (elCode.getCode() != recvCodes[i].getCode()) {
	  TEST_EXIT_DBG(refineManager)("Refinement manager is not set correctly!\n");
626

627
628
629
630
631
632
	  bool b = startFitElementToMeshCode(recvCodes[i], 
					     boundIt->rankObj.el,
					     boundIt->rankObj.subObj,
					     boundIt->rankObj.ithObj, 
					     boundIt->rankObj.elType,
					     boundIt->rankObj.reverseMode);
633

634
	  if (b)
635
	    meshFitTogether = false;	  
636
 	}
637

638
	i++;
639
640
641
      }
    }

642
    return meshFitTogether;
643
  }
644
645


646
647
648
649
650
651
  bool MeshDistributor::startFitElementToMeshCode(MeshStructure &code, 
						  Element *el, 
						  GeoIndex subObj,
						  int ithObj, 
						  int elType,
						  bool reverseMode)
652
  {
653
    FUNCNAME("MeshDistributor::startFitElementToMeshCode()");
654

655
656
    TEST_EXIT_DBG(el)("No element given!\n");

657
658
    // If the code is empty, the element does not matter and the function can
    // return without chaning the mesh.
659
660
    if (code.empty())
      return false;
661

662
663
664
665
666
    // s0 and s1 are the number of the edge/face in both child of the element,
    // which contain the edge/face the function has to traverse through. If the
    // edge/face is not contained in one of the children, s0 or s1 is -1.
    int s0 = el->getSubObjOfChild(0, subObj, ithObj, elType);
    int s1 = el->getSubObjOfChild(1, subObj, ithObj, elType);
667

668
    TEST_EXIT_DBG(s0 != -1 || s1 != -1)("This should not happen!\n");
669

670
    bool meshChanged = false;
671
672
673
    Flag traverseFlag = 
      Mesh::CALL_EVERY_EL_PREORDER | Mesh::FILL_NEIGH | Mesh::FILL_BOUND;

674
675
676
677
678
    // Test for reverse mode, in which the left and right children of elements
    // are flipped.
    if (reverseMode)
      traverseFlag |= Mesh::CALL_REVERSE_MODE;    

679

680
681
682
683
684
    // === If the edge/face is contained in both children. ===

    if (s0 != -1 && s1 != -1) {
      // Create traverse stack and traverse within the mesh until the element,
      // which should be fitted to the mesh structure code, is reached.
685
      TraverseStack stack;
686
      ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);
687
688
      while (elInfo && elInfo->getElement() != el)
	elInfo = stack.traverseNext(elInfo);      
689

690
691
      TEST_EXIT_DBG(elInfo->getElement() == el)("This should not happen!\n");

692
      meshChanged = fitElementToMeshCode(code, stack, subObj, ithObj, reverseMode);
693
694
      return meshChanged;
    }
695

696
697
698

    // === The edge/face is contained in only on of the both children. ===

699
    if (el->isLeaf()) {
700
701

      // If element is leaf and code contains only one leaf element, we are finished.
702
703
704
      if (code.getNumElements() == 1 && code.isLeafElement())
	return false;     

705
      // Create traverse stack and traverse the mesh to the element.
706
      TraverseStack stack;
707
      ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);
708
709
      while (elInfo && elInfo->getElement() != el)
	elInfo = stack.traverseNext(elInfo);      
710
711
712

      TEST_EXIT_DBG(elInfo)("This should not happen!\n");

713
      // Code is not leaf, therefore refine the element.
714
      el->setMark(1);
715
716
      refineManager->setMesh(el->getMesh());
      refineManager->setStack(&stack);
717
      refineManager->refineFunction(elInfo);
718
      meshChanged = true;
719
    }
720

721
722
    Element *child0 = el->getFirstChild();
    Element *child1 = el->getSecondChild();
723
724
725
726
    if (reverseMode) {
      std::swap(s0, s1);
      std::swap(child0, child1);    
    }
727

728
729
730
    // === We know that the edge/face is contained in only one of the children. ===
    // === Therefore, traverse the mesh to this children and fit this element   ===
    // === To the mesh structure code.                                          ===
731

732
733
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);
734

735
736
737
    if (s0 != -1) {
      while (elInfo && elInfo->getElement() != child0)
	elInfo = stack.traverseNext(elInfo);     
738

739
740
741
742
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s0, reverseMode);
    } else {
      while (elInfo && elInfo->getElement() != child1) 
	elInfo = stack.traverseNext(elInfo);      
743

744
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s1, reverseMode);
745
746
    }

747

748
    return meshChanged;
749
750
  }

751

752
753
754
755
756
  bool MeshDistributor::fitElementToMeshCode(MeshStructure &code, 
					     TraverseStack &stack,
					     GeoIndex subObj,
					     int ithObj, 
					     bool reverseMode)
757
  {
758
759
760
761
    FUNCNAME("MeshDistributor::fitElementToMeshCode()");


    // === Test if there are more elements in stack to check with the code. ===
762

763
764
    ElInfo *elInfo = stack.getElInfo();
    if (!elInfo)
765
      return false;
766

767
768
769
770

    // === Test if code contains a leaf element. If this is the case, the ===
    // === current element is finished. Traverse the mesh to the next     ===
    // === coarser element.                                               ===
771
772
773
774
775
776
777

    if (code.isLeafElement()) {
      int level = elInfo->getLevel();

      do {
	elInfo = stack.traverseNext(elInfo);
      } while (elInfo && elInfo->getLevel() > level);
778

779
      return false;
780
    }
781

782
783
784
785
786
787

    bool meshChanged = false;
    Element *el = elInfo->getElement();


    // === If element is leaf (and the code is not), refine the element. ===
788

789
    if (el->isLeaf()) {
790
791
      TEST_EXIT_DBG(elInfo->getLevel() < 255)("This should not happen!\n");

792
      el->setMark(1);
793
794
      refineManager->setMesh(el->getMesh());
      refineManager->setStack(&stack);
795
      refineManager->refineFunction(elInfo);
796
      meshChanged = true;
797
798
    }

799
800
801
802
803
804

    // === Continue fitting the mesh structure code to the children of the ===
    // === current element.                                                ===

    int s0 = el->getSubObjOfChild(0, subObj, ithObj, elInfo->getType());
    int s1 = el->getSubObjOfChild(1, subObj, ithObj, elInfo->getType());
805
806
807
    Element *child0 = el->getFirstChild();
    Element *child1 = el->getSecondChild();
    if (reverseMode) {
808
      std::swap(s0, s1);
809
810
      std::swap(child0, child1);
    }
811

812
813
814
815
816
817
818
    
    // === Traverse left child. ===

    if (s0 != -1) {
      // The edge/face is contained in the left child, therefore fit this
      // child to the mesh structure code.

819
      stack.traverseNext(elInfo);
820
      code.nextElement();
821
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s0, reverseMode);
822
823
      elInfo = stack.getElInfo();
    } else {
824
825
826
827
      // The edge/face is not contained in the left child. Hence we need
      // to traverse through all subelements of the left child until we get
      // the second child of the current element.

828
829
      do {
	elInfo = stack.traverseNext(elInfo);
830
831
832
      } while (elInfo && elInfo->getElement() != child1); 

      TEST_EXIT_DBG(elInfo != NULL)("This should not happen!\n");
833
834
    }  

835
836
837
838
839
840
841
842
843
844
    TEST_EXIT_DBG(elInfo->getElement() == child1)
      ("Got wrong child with idx = %d! Searched for child idx = %d\n",
       elInfo->getElement()->getIndex(), child1->getIndex());


    // === Traverse right child. ===

    if (s1 != -1) {
      // The edge/face is contained in the right child, therefore fit this
      // child to the mesh structure code.
845
846

      code.nextElement();
847
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s1, reverseMode);
848
    } else {
849
850
851
852
      // The edge/face is not contained in the right child. Hence we need
      // to traverse through all subelements of the right child until we have
      // finished traversing the current element with all its subelements.

853
      int level = elInfo->getLevel();
854

855
856
857
858
      do {
	elInfo = stack.traverseNext(elInfo);
      } while (elInfo && elInfo->getLevel() > level);
    }
859

860
861

    return meshChanged;
862
863
  }

864
  
865
  void MeshDistributor::serialize(std::ostream &out, DofContainer &data)
Thomas Witkowski's avatar
Thomas Witkowski committed
866
  {    
867
    int vecSize = data.size();
868
    SerUtil::serialize(out, vecSize);
869
    for (int i = 0; i < vecSize; i++) {
870
      int dofIndex = *(data[i]);
871
      SerUtil::serialize(out, dofIndex);
Thomas Witkowski's avatar