MeshDistributor.cc 63.3 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
49
50
51
52
  MeshDistributor::MeshDistributor(std::string str)
    : probStat(0),
      name(str),
      feSpace(NULL),
      mesh(NULL),
      refineManager(NULL),
      info(10),
      partitioner(NULL),
53
      nRankDofs(0),
54
      nOverallDofs(0),
55
      rstart(0),
56
      deserialized(false),
57
      writeSerializationFile(false),
58
      repartitioningAllowed(false),
59
      nTimestepsAfterLastRepartitioning(0),
60
      repartCounter(0),
61
      lastMeshChangeIndex(0)
62
  {
63
    FUNCNAME("MeshDistributor::ParalleDomainBase()");
Thomas Witkowski's avatar
Thomas Witkowski committed
64

65
66
67
    mpiRank = MPI::COMM_WORLD.Get_rank();
    mpiSize = MPI::COMM_WORLD.Get_size();
    mpiComm = MPI::COMM_WORLD;
68
69
70
71

    int tmp = 0;
    GET_PARAMETER(0, name + "->repartitioning", "%d", &tmp);
    repartitioningAllowed = (tmp > 0);
72
73
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
74

75
  void MeshDistributor::initParallelization()
76
  {
77
    FUNCNAME("MeshDistributor::initParallelization()");
78
79
80
81

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

82
83
    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");
84

85
86
87
    // 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).
88
    if (deserialized) {
89
      setRankDofs();
90
      removePeriodicBoundaryConditions();
91

92
93
94
95
96
97
98
99
100
      macroElIndexMap.clear();
      macroElIndexTypeMap.clear();
      std::deque<MacroElement*>& macros = mesh->getMacroElements();
      for (std::deque<MacroElement*>::iterator it = macros.begin();
	   it != macros.end(); ++it) {
	macroElIndexMap[(*it)->getIndex()] = (*it)->getElement();
	macroElIndexTypeMap[(*it)->getIndex()] = (*it)->getElType();
      }

101
      return;
102
    }
103

104
   
105
106
107
108
109
    // 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();

110
111
112
113
    // For later mesh repartitioning, we need to store some information about the
    // macro mesh.
    createMacroElementInfo();

114
115
    // create an initial partitioning of the mesh
    partitioner->createPartitionData();
116

117
    // set the element weights, which are 1 at the very first begin
118
    setInitialElementWeights();
119
120
121
122
123
124

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

125

Thomas Witkowski's avatar
Thomas Witkowski committed
126
#if (DEBUG != 0)
127
128
    debug::ElementIdxToDofs elMap;
    debug::createSortedDofs(mesh, elMap);
129
130
131
    if (mpiRank == 0) {
      int writePartMesh = 1;
      GET_PARAMETER(0, "dbg->write part mesh", "%d", &writePartMesh);
132

133
134
      if (writePartMesh > 0) {
	debug::writeElementIndexMesh(mesh, "elementIndex.vtu");
135
	writePartitioningMesh("part.vtu");
136
      } else {
137
	MSG("Skip write part mesh!\n");
138
      }
139
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
140
#endif
141

142

143
    // === Create interior boundary information. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
144

145
    createInteriorBoundaryInfo();
Thomas Witkowski's avatar
Thomas Witkowski committed
146

147
#if (DEBUG != 0)
148
    ParallelDebug::printBoundaryInfo(*this);
149
150
#endif

151

Thomas Witkowski's avatar
n  
Thomas Witkowski committed
152
153
154
    // === Remove all macro elements that are not part of the rank partition. ===

    removeMacroElements();
155

Thomas Witkowski's avatar
n  
Thomas Witkowski committed
156

157
158
    // === Create new global and local DOF numbering. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
159

160
161
162
163
164
165
    // 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));
166

167
    updateLocalGlobalNumbering();
168

169

170
171
    // === If in debug mode, make some tests. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
172
#if (DEBUG != 0)
173
    MSG("AMDiS runs in debug mode, so make some test ...\n");
174

175
    ParallelDebug::testAllElements(*this);
176
    debug::testSortedDofs(mesh, elMap);
177
178
    ParallelDebug::testInteriorBoundary(*this);
    ParallelDebug::testCommonDofs(*this, true);
179
    ParallelDebug::testGlobalIndexByCoords(*this);
Thomas Witkowski's avatar
Thomas Witkowski committed
180

181
    debug::writeMesh(feSpace, -1, "macro_mesh");   
182
183

    MSG("Debug mode tests finished!\n");
184
#endif
185

186

187
188
    // === Create periodic dof mapping, if there are periodic boundaries. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
189
    createPeriodicMap();    
190

191
    // === Global refinements. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
192

Thomas Witkowski's avatar
Thomas Witkowski committed
193
    int globalRefinement = 0;
194
    GET_PARAMETER(0, mesh->getName() + "->global refinements", "%d", &globalRefinement);
Thomas Witkowski's avatar
Thomas Witkowski committed
195

Thomas Witkowski's avatar
Thomas Witkowski committed
196
    if (globalRefinement > 0) {
197
      refineManager->globalRefine(mesh, globalRefinement);
198

199
#if (DEBUG != 0)
200
      debug::writeMesh(feSpace, -1, "gr_mesh");
201
202
#endif

203
      updateLocalGlobalNumbering();
204
205

     
206
      // === Update periodic mapping, if there are periodic boundaries. ===
207
      
208
      createPeriodicMap();
Thomas Witkowski's avatar
Thomas Witkowski committed
209
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
210

211

Thomas Witkowski's avatar
Thomas Witkowski committed
212
213
    /// === Set DOF rank information to all matrices and vectors. ===

214
    setRankDofs();
Thomas Witkowski's avatar
Thomas Witkowski committed
215

216

Thomas Witkowski's avatar
Thomas Witkowski committed
217
218
    // === Remove periodic boundary conditions in sequential problem definition. ===

219
    removePeriodicBoundaryConditions();
220
221
  }

222

223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
  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");
240
      TEST_EXIT(mesh->getDofAdmin(0).getNumberOfPreDOFs(0) == 0)
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
	("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;
259
260
261
    GET_PARAMETER(0, probVec->getName() + "->output->write serialization", "%d", 
		  &writeSerialization);
    if (writeSerialization && !writeSerializationFile) {
262
263
264
265
266
      std::string filename = "";
      GET_PARAMETER(0, name + "->output->serialization filename", &filename);
      
      TEST_EXIT(filename != "")
	("No filename defined for parallel serialization file!\n");
267
268
269
270
271

      int tsModulo = -1;
      GET_PARAMETER(0, probVec->getName() + "->output->write every i-th timestep", 
		    "%d", &tsModulo);
      
272
      probVec->getFileWriterList().push_back(new Serializer<MeshDistributor>(this, filename, tsModulo));
273
274
      writeSerializationFile = true;
    }    
275
276

    int readSerialization = 0;
277
278
    GET_PARAMETER(0, probVec->getName() + "->input->read serialization", "%d", 
		  &readSerialization);
279
280
281
282
    if (readSerialization) {
      std::string filename = "";
      GET_PARAMETER(0, probVec->getName() + "->input->serialization filename", &filename);
      filename += ".p" + lexical_cast<std::string>(mpiRank);
283
      MSG("Start deserialization with %s\n", filename.c_str());
284
      std::ifstream in(filename.c_str());
285
286
287
288

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

289
      probVec->deserialize(in);
290
      in.close();
291
292
      MSG("Deserialization from file: %s\n", filename.c_str());

293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
      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;
309
310
311
312
313
314
    }

    probStat.push_back(probVec);
  }


315
  void MeshDistributor::exitParallelization()
316
  {}
317

318
  
319
  void MeshDistributor::testForMacroMesh()
320
  {
321
    FUNCNAME("MeshDistributor::testForMacroMesh()");
322
323
324
325
326
327
328

    int nMacroElements = 0;

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
    while (elInfo) {
      TEST_EXIT(elInfo->getLevel() == 0)
329
	("Mesh is already refined! This does not work with parallelization!\n");
330
331
332

      TEST_EXIT(elInfo->getType() == 0)
	("Only macro elements with level 0 are supported!\n");
333
334
335
336
337
338
339
340
341
342
      
      nMacroElements++;

      elInfo = stack.traverseNext(elInfo);
    }

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

343

344
  void MeshDistributor::synchVector(DOFVector<double> &vec)
345
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
346
    StdMpi<std::vector<double> > stdMpi(mpiComm);
347
348

    for (RankToDofContainer::iterator sendIt = sendDofs.begin();
Thomas Witkowski's avatar
Thomas Witkowski committed
349
	 sendIt != sendDofs.end(); ++sendIt) {
350
      std::vector<double> dofs;
Thomas Witkowski's avatar
Thomas Witkowski committed
351
352
      int nSendDofs = sendIt->second.size();
      dofs.reserve(nSendDofs);
353
      
Thomas Witkowski's avatar
Thomas Witkowski committed
354
355
      for (int i = 0; i < nSendDofs; i++)
	dofs.push_back(vec[*((sendIt->second)[i])]);
356
357
358
359

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

Thomas Witkowski's avatar
Thomas Witkowski committed
360
361
362
    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
	 recvIt != recvDofs.end(); ++recvIt)
      stdMpi.recv(recvIt->first, recvIt->second.size());
363

Thomas Witkowski's avatar
Thomas Witkowski committed
364
    stdMpi.startCommunication<double>(MPI_DOUBLE);
365

Thomas Witkowski's avatar
Thomas Witkowski committed
366
367
368
369
370
    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];
  }
371
372


373
  void MeshDistributor::synchVector(SystemVector &vec)
Thomas Witkowski's avatar
Thomas Witkowski committed
374
  {
375
    int nComponents = vec.getSize();
Thomas Witkowski's avatar
Thomas Witkowski committed
376
377
378
379
380
381
382
383
384
385
386
387
    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])]);
388
389
      }

Thomas Witkowski's avatar
Thomas Witkowski committed
390
      stdMpi.send(sendIt->first, dofs);
391
392
393
    }

    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
Thomas Witkowski's avatar
Thomas Witkowski committed
394
395
	 recvIt != recvDofs.end(); ++recvIt)
      stdMpi.recv(recvIt->first, recvIt->second.size() * nComponents);
396

Thomas Witkowski's avatar
Thomas Witkowski committed
397
    stdMpi.startCommunication<double>(MPI_DOUBLE);
398
399

    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
Thomas Witkowski's avatar
Thomas Witkowski committed
400
401
	 recvIt != recvDofs.end(); ++recvIt) {
      int nRecvDofs = recvIt->second.size();
402
403

      int counter = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
404
405
406
407
408
      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++];
409
410
411
412
      }
    }
  }

413

414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
  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);
      }
    }
  }


433
434
  void MeshDistributor::removePeriodicBoundaryConditions()
  {
435
436
    FUNCNAME("MeshDistributor::removePeriodicBoundaryConditions()");

437
438
439
440
441
442
443
444
    // 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())
445
	    removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(mat->getBoundaryManager()->getBoundaryConditionMap()));
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
	}
	
	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);
    }    
463
464
465

    // Remove periodic vertex associations
    mesh->getPeriodicAssociations().clear();
466
467
468
469
  }


  void MeshDistributor::removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap)
Thomas Witkowski's avatar
Thomas Witkowski committed
470
471
472
473
474
475
476
477
478
479
480
  {
    BoundaryIndexMap::iterator it = boundaryMap.begin();
    while (it != boundaryMap.end()) {
      if (it->second->isPeriodic())
	boundaryMap.erase(it++);
      else
	++it;      
    }    
  }


481
  void MeshDistributor::checkMeshChange()
482
  {
483
    FUNCNAME("MeshDistributor::checkMeshChange()");    
484

485
486
487
488
#if (DEBUG != 0)
    debug::writeMesh(feSpace, -1, "before_check_mesh");
#endif

489
490
491
492
493
    // === 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);
494

495
    if (recvAllValues == 0)
496
497
      return;

498
499
    // === At least one rank mesh has been changed, so the boundaries must be ===
    // === adapted to the new mesh structure.                                 ===
500

501
502
503
504
505
    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.
506
      RankToBoundMap allBound;
Thomas Witkowski's avatar
Thomas Witkowski committed
507
508

      for (InteriorBoundary::iterator it(myIntBoundary); !it.end(); ++it)
509
510
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
511
 	  allBound[it.getRank()].push_back(*it);
Thomas Witkowski's avatar
Thomas Witkowski committed
512
513

      for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it)
514
515
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
516
	  allBound[it.getRank()].push_back(*it);
Thomas Witkowski's avatar
Thomas Witkowski committed
517

518
      for (InteriorBoundary::iterator it(periodicBoundary); !it.end(); ++it)
519
520
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
521
 	  allBound[it.getRank()].push_back(*it);	
522

523

524
      // === Check the boundaries and adapt mesh if necessary. ===
525
526
527
528
#if (DEBUG != 0)
      MSG("Run checkAndAdaptBoundary ...\n");
#endif

529
530
531
532
533
534
535
      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);
536
537
538
539

#if (DEBUG != 0)
      MSG("Mesh changed on %d ranks!\n", recvAllValues);
#endif
540
    } while (recvAllValues != 0);
541

542
#if (DEBUG != 0)
543
    debug::writeMesh(feSpace, -1, "mesh");
544
545
546
547
548
549
#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. ===
550

551
552
    updateLocalGlobalNumbering();

553
554
555
556

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

    createPeriodicMap();
557
558
559
560


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

561
562
563
564
565
566
567
568
    nTimestepsAfterLastRepartitioning++;

    if (repartitioningAllowed) {
      if (nTimestepsAfterLastRepartitioning >= 20) {
	repartitionMesh();
	nTimestepsAfterLastRepartitioning = 0;
      }
    }
569
570
571
  }

  
572
  bool MeshDistributor::checkAndAdaptBoundary(RankToBoundMap &allBound)
573
  {
574
    FUNCNAME("MeshDistributor::checkAndAdaptBoundary()");
575
576
577
578
579
580

    // === Create mesh structure codes for all ranks boundary elements. ===
       
    std::map<int, MeshCodeVec> sendCodes;
   
    for (RankToBoundMap::iterator it = allBound.begin(); it != allBound.end(); ++it) {
581

582
583
584
      for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt) {
	MeshStructure elCode;
585
	elCode.init(boundIt->rankObj);
586
587
588
589
	sendCodes[it->first].push_back(elCode);
      }
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
590
    StdMpi<MeshCodeVec> stdMpi(mpiComm, true);
591
    stdMpi.send(sendCodes);
592
    stdMpi.recv(allBound);
593
    stdMpi.startCommunication<uint64_t>(MPI_UNSIGNED_LONG);
594
 
595
    // === Compare received mesh structure codes. ===
596
    
597
598
    bool meshFitTogether = true;

599
    for (RankToBoundMap::iterator it = allBound.begin(); it != allBound.end(); ++it) {
600
     
601
602
      MeshCodeVec &recvCodes = stdMpi.getRecvData()[it->first];
      int i = 0;
603
      
604
605
      for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt) {
606

607
608
	MeshStructure elCode;	
	elCode.init(boundIt->rankObj);
609

610
611
	if (elCode.getCode() != recvCodes[i].getCode()) {
	  TEST_EXIT_DBG(refineManager)("Refinement manager is not set correctly!\n");
612

613
614
615
616
617
618
	  bool b = startFitElementToMeshCode(recvCodes[i], 
					     boundIt->rankObj.el,
					     boundIt->rankObj.subObj,
					     boundIt->rankObj.ithObj, 
					     boundIt->rankObj.elType,
					     boundIt->rankObj.reverseMode);
619

620
	  if (b)
621
	    meshFitTogether = false;	  
622
 	}
623

624
	i++;
625
626
627
      }
    }

628
    return meshFitTogether;
629
  }
630
631


632
633
634
635
636
637
  bool MeshDistributor::startFitElementToMeshCode(MeshStructure &code, 
						  Element *el, 
						  GeoIndex subObj,
						  int ithObj, 
						  int elType,
						  bool reverseMode)
638
  {
639
    FUNCNAME("MeshDistributor::startFitElementToMeshCode()");
640

641
642
    TEST_EXIT_DBG(el)("No element given!\n");

643
644
    // If the code is empty, the element does not matter and the function can
    // return without chaning the mesh.
645
646
    if (code.empty())
      return false;
647

648
649
650
651
652
    // 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);
653

654
    TEST_EXIT_DBG(s0 != -1 || s1 != -1)("This should not happen!\n");
655

656
    bool meshChanged = false;
657
658
659
    Flag traverseFlag = 
      Mesh::CALL_EVERY_EL_PREORDER | Mesh::FILL_NEIGH | Mesh::FILL_BOUND;

660
661
662
663
664
    // Test for reverse mode, in which the left and right children of elements
    // are flipped.
    if (reverseMode)
      traverseFlag |= Mesh::CALL_REVERSE_MODE;    

665

666
667
668
669
670
    // === 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.
671
      TraverseStack stack;
672
      ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);
673
674
      while (elInfo && elInfo->getElement() != el)
	elInfo = stack.traverseNext(elInfo);      
675

676
677
      TEST_EXIT_DBG(elInfo->getElement() == el)("This should not happen!\n");

678
      meshChanged = fitElementToMeshCode(code, stack, subObj, ithObj, reverseMode);
679
680
      return meshChanged;
    }
681

682
683
684

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

685
    if (el->isLeaf()) {
686
687

      // If element is leaf and code contains only one leaf element, we are finished.
688
689
690
      if (code.getNumElements() == 1 && code.isLeafElement())
	return false;     

691
      // Create traverse stack and traverse the mesh to the element.
692
      TraverseStack stack;
693
      ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);
694
695
      while (elInfo && elInfo->getElement() != el)
	elInfo = stack.traverseNext(elInfo);      
696
697
698

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

699
      // Code is not leaf, therefore refine the element.
700
      el->setMark(1);
701
702
      refineManager->setMesh(el->getMesh());
      refineManager->setStack(&stack);
703
      refineManager->refineFunction(elInfo);
704
      meshChanged = true;
705
    }
706

707
708
    Element *child0 = el->getFirstChild();
    Element *child1 = el->getSecondChild();
709
710
711
712
    if (reverseMode) {
      std::swap(s0, s1);
      std::swap(child0, child1);    
    }
713

714
715
716
    // === 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.                                          ===
717

718
719
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);
720

721
722
723
    if (s0 != -1) {
      while (elInfo && elInfo->getElement() != child0)
	elInfo = stack.traverseNext(elInfo);     
724

725
726
727
728
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s0, reverseMode);
    } else {
      while (elInfo && elInfo->getElement() != child1) 
	elInfo = stack.traverseNext(elInfo);      
729

730
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s1, reverseMode);
731
732
    }

733

734
    return meshChanged;
735
736
  }

737

738
739
740
741
742
  bool MeshDistributor::fitElementToMeshCode(MeshStructure &code, 
					     TraverseStack &stack,
					     GeoIndex subObj,
					     int ithObj, 
					     bool reverseMode)
743
  {
744
745
746
747
    FUNCNAME("MeshDistributor::fitElementToMeshCode()");


    // === Test if there are more elements in stack to check with the code. ===
748

749
750
    ElInfo *elInfo = stack.getElInfo();
    if (!elInfo)
751
      return false;
752

753
754
755
756

    // === 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.                                               ===
757
758
759
760
761
762
763

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

      do {
	elInfo = stack.traverseNext(elInfo);
      } while (elInfo && elInfo->getLevel() > level);
764

765
      return false;
766
    }
767

768
769
770
771
772
773

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


    // === If element is leaf (and the code is not), refine the element. ===
774

775
    if (el->isLeaf()) {
776
777
      TEST_EXIT_DBG(elInfo->getLevel() < 255)("This should not happen!\n");

778
      el->setMark(1);
779
780
      refineManager->setMesh(el->getMesh());
      refineManager->setStack(&stack);
781
      refineManager->refineFunction(elInfo);
782
      meshChanged = true;
783
784
    }

785
786
787
788
789
790

    // === 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());
791
792
793
    Element *child0 = el->getFirstChild();
    Element *child1 = el->getSecondChild();
    if (reverseMode) {
794
      std::swap(s0, s1);
795
796
      std::swap(child0, child1);
    }
797

798
799
800
801
802
803
804
    
    // === Traverse left child. ===

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

805
      stack.traverseNext(elInfo);
806
      code.nextElement();
807
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s0, reverseMode);
808
809
      elInfo = stack.getElInfo();
    } else {
810
811
812
813
      // 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.

814
815
      do {
	elInfo = stack.traverseNext(elInfo);
816
817
818
      } while (elInfo && elInfo->getElement() != child1); 

      TEST_EXIT_DBG(elInfo != NULL)("This should not happen!\n");
819
820
    }  

821
822
823
824
825
826
827
828
829
830
    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.
831
832

      code.nextElement();
833
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s1, reverseMode);
834
    } else {
835
836
837
838
      // 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.

839
      int level = elInfo->getLevel();
840

841
842
843
844
      do {
	elInfo = stack.traverseNext(elInfo);
      } while (elInfo && elInfo->getLevel() > level);
    }
845

846
847

    return meshChanged;
848
849
  }

850
  
851
  void MeshDistributor::serialize(std::ostream &out, DofContainer &data)
Thomas Witkowski's avatar
Thomas Witkowski committed
852
  {    
853
    int vecSize = data.size();
854
    SerUtil::serialize(out, vecSize);
855
856
    for (int i = 0; i < vecSize; i++) {
      int dofIndex = (*data[i]);
857
      SerUtil::serialize(out, dofIndex);
858
859
860
861
    }
  }


862
  void MeshDistributor::deserialize(std::istream &in, DofContainer &data,
863
				    std::map<int, const DegreeOfFreedom*> &dofMap)
864
  {
865
    FUNCNAME("MeshDistributor::deserialize()");
866
867

    int vecSize = 0;
868
    SerUtil::deserialize(in, vecSize);
869
    data.clear();
870
871
872
    data.resize(vecSize);
    for (int i = 0; i < vecSize; i++) {
      int dofIndex = 0;
873
      SerUtil::deserialize(in, dofIndex);
874
8