MeshDistributor.cc 66.1 KB
Newer Older
1
//
2
3
4
5
6
7
8
9
10
11
12
// Software License for AMDiS
//
// Copyright (c) 2010 Dresden University of Technology 
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
// This file is part of AMDiS
//
// See also license.opensource.txt in the distribution.


Thomas Witkowski's avatar
Thomas Witkowski committed
13
#include <algorithm>
14
15
#include <iostream>
#include <fstream>
16
17
#include <limits>
#include <stdint.h>
Thomas Witkowski's avatar
Thomas Witkowski committed
18
#include <boost/lexical_cast.hpp>
19
20
#include <boost/filesystem.hpp>

21
#include "parallel/MeshDistributor.h"
22
#include "parallel/MeshManipulation.h"
23
#include "parallel/ParallelDebug.h"
24
#include "parallel/StdMpi.h"
25
#include "parallel/ParMetisPartitioner.h"
26
27
28
#include "io/ElementFileWriter.h"
#include "io/MacroInfo.h"
#include "io/VtkWriter.h"
29
30
31
32
33
#include "Mesh.h"
#include "Traverse.h"
#include "ElInfo.h"
#include "Element.h"
#include "MacroElement.h"
34
35
#include "DOFMatrix.h"
#include "DOFVector.h"
36
#include "SystemVector.h"
37
#include "ElementDofIterator.h"
38
39
#include "ProblemStatBase.h"
#include "StandardProblemIteration.h"
40
#include "VertexVector.h"
41
#include "MeshStructure.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
42
43
#include "ProblemVec.h"
#include "ProblemInstat.h"
44
#include "Debug.h"
45

46
47
namespace AMDiS {

Thomas Witkowski's avatar
Thomas Witkowski committed
48
  using boost::lexical_cast;
49
  using namespace boost::filesystem;
Thomas Witkowski's avatar
Thomas Witkowski committed
50

51
52
53
54
55
  inline bool cmpDofsByValue(const DegreeOfFreedom* dof1, const DegreeOfFreedom* dof2)
  {
    return (*dof1 < *dof2);
  }

56

57
58
59
60
61
62
63
64
  MeshDistributor::MeshDistributor(std::string str)
    : probStat(0),
      name(str),
      feSpace(NULL),
      mesh(NULL),
      refineManager(NULL),
      info(10),
      partitioner(NULL),
65
      nRankDofs(0),
66
      nOverallDofs(0),
67
      rstart(0),
68
      deserialized(false),
69
      writeSerializationFile(false),
70
      repartitioningAllowed(false),
71
      repartitionIthChange(20),
72
      nTimestepsAfterLastRepartitioning(0),
73
      repartCounter(0),
74
      debugOutputDir(""),
75
      lastMeshChangeIndex(0)
76
  {
77
    FUNCNAME("MeshDistributor::ParalleDomainBase()");
Thomas Witkowski's avatar
Thomas Witkowski committed
78

79
80
81
    mpiRank = MPI::COMM_WORLD.Get_rank();
    mpiSize = MPI::COMM_WORLD.Get_size();
    mpiComm = MPI::COMM_WORLD;
82
83
84
85

    int tmp = 0;
    GET_PARAMETER(0, name + "->repartitioning", "%d", &tmp);
    repartitioningAllowed = (tmp > 0);
86

87
88
89
    GET_PARAMETER(0, name + "->debug output dir", &debugOutputDir);

    GET_PARAMETER(0, name + "->repartition ith change", "%d", &repartitionIthChange);
90
91
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
92

93
  void MeshDistributor::initParallelization()
94
  {
95
    FUNCNAME("MeshDistributor::initParallelization()");
96
97
98
99

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

100
101
    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");
102

103
104
105
    // 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).
106
    if (deserialized) {
107
108
      updateMacroElementInfo();

109
      setRankDofs();
110

111
      removePeriodicBoundaryConditions();
112

113
114
      macroElIndexMap.clear();
      macroElIndexTypeMap.clear();
115
116
117
118
119

      std::map<int, bool>& elementInRank = partitioner->getElementInRank();
      for (std::vector<MacroElement*>::iterator it = allMacroElements.begin();
	   it != allMacroElements.end(); ++it) {
	elementInRank[(*it)->getIndex()] = false;
120
121
122
123
	macroElIndexMap[(*it)->getIndex()] = (*it)->getElement();
	macroElIndexTypeMap[(*it)->getIndex()] = (*it)->getElType();
      }

124
125
126
127
      for (std::deque<MacroElement*>::iterator it = mesh->getMacroElements().begin();
	   it != mesh->getMacroElements().end(); ++it)
	elementInRank[(*it)->getIndex()] = true;      

128
      return;
129
    }
130

131
   
132
133
134
135
136
    // 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();

137
138
139
140
    // For later mesh repartitioning, we need to store some information about the
    // macro mesh.
    createMacroElementInfo();

141
142
    // create an initial partitioning of the mesh
    partitioner->createPartitionData();
143

144
    // set the element weights, which are 1 at the very first begin
145
    setInitialElementWeights();
146
147
148
149
150
151

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

152

Thomas Witkowski's avatar
Thomas Witkowski committed
153
#if (DEBUG != 0)
154
155
    debug::ElementIdxToDofs elMap;
    debug::createSortedDofs(mesh, elMap);
156
157
158
    if (mpiRank == 0) {
      int writePartMesh = 1;
      GET_PARAMETER(0, "dbg->write part mesh", "%d", &writePartMesh);
159

160
      if (writePartMesh > 0) {
161
162
	debug::writeElementIndexMesh(mesh, debugOutputDir + "elementIndex.vtu");
	writePartitioningMesh(debugOutputDir + "part.vtu");
163
      } else {
164
	MSG("Skip write part mesh!\n");
165
      }
166
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
167
#endif
168

169

170
    // === Create interior boundary information. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
171

172
    createInteriorBoundaryInfo();
Thomas Witkowski's avatar
Thomas Witkowski committed
173

174
#if (DEBUG != 0)
175
    ParallelDebug::printBoundaryInfo(*this);
176
177
#endif

178

Thomas Witkowski's avatar
n  
Thomas Witkowski committed
179
180
181
    // === Remove all macro elements that are not part of the rank partition. ===

    removeMacroElements();
182

Thomas Witkowski's avatar
n  
Thomas Witkowski committed
183

184
185
    // === Create new global and local DOF numbering. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
186

187
188
189
190
191
192
    // 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));
193

194
    updateLocalGlobalNumbering();
195

196

197
198
    // === If in debug mode, make some tests. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
199
#if (DEBUG != 0)
200
    MSG("AMDiS runs in debug mode, so make some test ...\n");
201

202
    ParallelDebug::testAllElements(*this);
203
    debug::testSortedDofs(mesh, elMap);
204
205
    ParallelDebug::testInteriorBoundary(*this);
    ParallelDebug::testCommonDofs(*this, true);
206
    ParallelDebug::testGlobalIndexByCoords(*this);
Thomas Witkowski's avatar
Thomas Witkowski committed
207

208
    debug::writeMesh(feSpace, -1, debugOutputDir + "macro_mesh");   
209
210

    MSG("Debug mode tests finished!\n");
211
#endif
212

213

214
215
    // === Create periodic dof mapping, if there are periodic boundaries. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
216
    createPeriodicMap();    
217

218
    // === Global refinements. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
219

Thomas Witkowski's avatar
Thomas Witkowski committed
220
    int globalRefinement = 0;
221
    GET_PARAMETER(0, mesh->getName() + "->global refinements", "%d", &globalRefinement);
Thomas Witkowski's avatar
Thomas Witkowski committed
222

Thomas Witkowski's avatar
Thomas Witkowski committed
223
    if (globalRefinement > 0) {
224
      refineManager->globalRefine(mesh, globalRefinement);
225

226
      updateLocalGlobalNumbering();
227
228

     
229
230
      // === Update periodic mapping, if there are periodic boundaries. ===     

231
      createPeriodicMap();
Thomas Witkowski's avatar
Thomas Witkowski committed
232
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
233

234

Thomas Witkowski's avatar
Thomas Witkowski committed
235
236
    /// === Set DOF rank information to all matrices and vectors. ===

237
    setRankDofs();
Thomas Witkowski's avatar
Thomas Witkowski committed
238

239

Thomas Witkowski's avatar
Thomas Witkowski committed
240
241
    // === Remove periodic boundary conditions in sequential problem definition. ===

242
    removePeriodicBoundaryConditions();
243
244
  }

245

246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
  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");
263
      TEST_EXIT(mesh->getDofAdmin(0).getNumberOfPreDofs(VERTEX) == 0)
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
	("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;
282
283
284
    GET_PARAMETER(0, probVec->getName() + "->output->write serialization", "%d", 
		  &writeSerialization);
    if (writeSerialization && !writeSerializationFile) {
285
286
287
288
289
      std::string filename = "";
      GET_PARAMETER(0, name + "->output->serialization filename", &filename);
      
      TEST_EXIT(filename != "")
	("No filename defined for parallel serialization file!\n");
290
291
292
293
294

      int tsModulo = -1;
      GET_PARAMETER(0, probVec->getName() + "->output->write every i-th timestep", 
		    "%d", &tsModulo);
      
295
      probVec->getFileWriterList().push_back(new Serializer<MeshDistributor>(this, filename, tsModulo));
296
297
      writeSerializationFile = true;
    }    
298
299

    int readSerialization = 0;
300
301
    GET_PARAMETER(0, probVec->getName() + "->input->read serialization", "%d", 
		  &readSerialization);
302
303
304
305
    if (readSerialization) {
      std::string filename = "";
      GET_PARAMETER(0, probVec->getName() + "->input->serialization filename", &filename);
      filename += ".p" + lexical_cast<std::string>(mpiRank);
306
      MSG("Start deserialization with %s\n", filename.c_str());
307
      std::ifstream in(filename.c_str());
308
309
310
311

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

312
      probVec->deserialize(in);
313
      in.close();
314
315
      MSG("Deserialization from file: %s\n", filename.c_str());

316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
      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;
332
333
334
335
336
337
    }

    probStat.push_back(probVec);
  }


338
  void MeshDistributor::exitParallelization()
339
  {}
340

341
  
342
  void MeshDistributor::testForMacroMesh()
343
  {
344
    FUNCNAME("MeshDistributor::testForMacroMesh()");
345
346
347
348
349
350
351

    int nMacroElements = 0;

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
    while (elInfo) {
      TEST_EXIT(elInfo->getLevel() == 0)
352
	("Mesh is already refined! This does not work with parallelization!\n");
353
354
355

      TEST_EXIT(elInfo->getType() == 0)
	("Only macro elements with level 0 are supported!\n");
356
357
358
359
360
361
362
363
364
365
      
      nMacroElements++;

      elInfo = stack.traverseNext(elInfo);
    }

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

366

367
  void MeshDistributor::synchVector(DOFVector<double> &vec)
368
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
369
    StdMpi<std::vector<double> > stdMpi(mpiComm);
370
371

    for (RankToDofContainer::iterator sendIt = sendDofs.begin();
Thomas Witkowski's avatar
Thomas Witkowski committed
372
	 sendIt != sendDofs.end(); ++sendIt) {
373
      std::vector<double> dofs;
Thomas Witkowski's avatar
Thomas Witkowski committed
374
375
      int nSendDofs = sendIt->second.size();
      dofs.reserve(nSendDofs);
376
      
Thomas Witkowski's avatar
Thomas Witkowski committed
377
378
      for (int i = 0; i < nSendDofs; i++)
	dofs.push_back(vec[*((sendIt->second)[i])]);
379
380
381
382

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

Thomas Witkowski's avatar
Thomas Witkowski committed
383
384
385
    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
	 recvIt != recvDofs.end(); ++recvIt)
      stdMpi.recv(recvIt->first, recvIt->second.size());
386

Thomas Witkowski's avatar
Thomas Witkowski committed
387
    stdMpi.startCommunication<double>(MPI_DOUBLE);
388

Thomas Witkowski's avatar
Thomas Witkowski committed
389
390
391
392
393
    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];
  }
394
395


396
  void MeshDistributor::synchVector(SystemVector &vec)
Thomas Witkowski's avatar
Thomas Witkowski committed
397
  {
398
    int nComponents = vec.getSize();
Thomas Witkowski's avatar
Thomas Witkowski committed
399
400
401
402
403
404
405
406
407
408
409
410
    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])]);
411
412
      }

Thomas Witkowski's avatar
Thomas Witkowski committed
413
      stdMpi.send(sendIt->first, dofs);
414
415
416
    }

    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
Thomas Witkowski's avatar
Thomas Witkowski committed
417
418
	 recvIt != recvDofs.end(); ++recvIt)
      stdMpi.recv(recvIt->first, recvIt->second.size() * nComponents);
419

Thomas Witkowski's avatar
Thomas Witkowski committed
420
    stdMpi.startCommunication<double>(MPI_DOUBLE);
421
422

    for (RankToDofContainer::iterator recvIt = recvDofs.begin();
Thomas Witkowski's avatar
Thomas Witkowski committed
423
424
	 recvIt != recvDofs.end(); ++recvIt) {
      int nRecvDofs = recvIt->second.size();
425
426

      int counter = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
427
428
429
430
431
      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++];
432
433
434
435
      }
    }
  }

436

437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
  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);
      }
    }
  }


456
457
  void MeshDistributor::removePeriodicBoundaryConditions()
  {
458
459
    FUNCNAME("MeshDistributor::removePeriodicBoundaryConditions()");

460
461
462
463
464
465
466
467
    // 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())
468
	    removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(mat->getBoundaryManager()->getBoundaryConditionMap()));
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
	}
	
	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);
    }    
486
487
488

    // Remove periodic vertex associations
    mesh->getPeriodicAssociations().clear();
489
490
491
492
  }


  void MeshDistributor::removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap)
Thomas Witkowski's avatar
Thomas Witkowski committed
493
494
495
496
497
498
499
500
501
502
503
  {
    BoundaryIndexMap::iterator it = boundaryMap.begin();
    while (it != boundaryMap.end()) {
      if (it->second->isPeriodic())
	boundaryMap.erase(it++);
      else
	++it;      
    }    
  }


504
  void MeshDistributor::checkMeshChange()
505
  {
506
    FUNCNAME("MeshDistributor::checkMeshChange()");    
507

508
#if (DEBUG != 0)
509
    debug::writeMesh(feSpace, -1, debugOutputDir + "before_check_mesh");
510
511
#endif

512
513
514
515
516
    // === 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);
517

518
    if (recvAllValues == 0)
519
520
      return;

521
522
    // === At least one rank mesh has been changed, so the boundaries must be ===
    // === adapted to the new mesh structure.                                 ===
523

524
525
526
527
528
    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.
529
      RankToBoundMap allBound;
Thomas Witkowski's avatar
Thomas Witkowski committed
530
531

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

      for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it)
537
538
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
539
	  allBound[it.getRank()].push_back(*it);
Thomas Witkowski's avatar
Thomas Witkowski committed
540

541
      for (InteriorBoundary::iterator it(periodicBoundary); !it.end(); ++it)
542
543
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
544
 	  allBound[it.getRank()].push_back(*it);	
545

546

547
      // === Check the boundaries and adapt mesh if necessary. ===
548
549
550
551
#if (DEBUG != 0)
      MSG("Run checkAndAdaptBoundary ...\n");
#endif

552
553
554
555
556
557
558
      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);
559
560
561
562

#if (DEBUG != 0)
      MSG("Mesh changed on %d ranks!\n", recvAllValues);
#endif
563
    } while (recvAllValues != 0);
564

565
#if (DEBUG != 0)
566
    debug::writeMesh(feSpace, -1, debugOutputDir + "mesh");
567
568
569
570
571
572
#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. ===
573

574
575
    updateLocalGlobalNumbering();

576
577
578
579

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

    createPeriodicMap();
580
581
582
583


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

584
585
586
    nTimestepsAfterLastRepartitioning++;

    if (repartitioningAllowed) {
587
      if (nTimestepsAfterLastRepartitioning >= repartitionIthChange) {
588
589
	repartitionMesh();
	nTimestepsAfterLastRepartitioning = 0;
590
      }
591
    }
592
593
594
  }

  
595
  bool MeshDistributor::checkAndAdaptBoundary(RankToBoundMap &allBound)
596
  {
597
    FUNCNAME("MeshDistributor::checkAndAdaptBoundary()");
598
599
600
601
602
603

    // === Create mesh structure codes for all ranks boundary elements. ===
       
    std::map<int, MeshCodeVec> sendCodes;
   
    for (RankToBoundMap::iterator it = allBound.begin(); it != allBound.end(); ++it) {
604

605
606
607
      for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt) {
	MeshStructure elCode;
608
	elCode.init(boundIt->rankObj);
609
610
611
612
	sendCodes[it->first].push_back(elCode);
      }
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
613
    StdMpi<MeshCodeVec> stdMpi(mpiComm, true);
614
    stdMpi.send(sendCodes);
615
    stdMpi.recv(allBound);
616
    stdMpi.startCommunication<uint64_t>(MPI_UNSIGNED_LONG);
617
 
618
    // === Compare received mesh structure codes. ===
619
    
620
621
    bool meshFitTogether = true;

622
    for (RankToBoundMap::iterator it = allBound.begin(); it != allBound.end(); ++it) {
623
     
624
625
      MeshCodeVec &recvCodes = stdMpi.getRecvData()[it->first];
      int i = 0;
626
      
627
628
      for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt) {
629

630
631
	MeshStructure elCode;	
	elCode.init(boundIt->rankObj);
632

633
634
	if (elCode.getCode() != recvCodes[i].getCode()) {
	  TEST_EXIT_DBG(refineManager)("Refinement manager is not set correctly!\n");
635

636
637
638
639
640
641
	  bool b = startFitElementToMeshCode(recvCodes[i], 
					     boundIt->rankObj.el,
					     boundIt->rankObj.subObj,
					     boundIt->rankObj.ithObj, 
					     boundIt->rankObj.elType,
					     boundIt->rankObj.reverseMode);
642

643
	  if (b)
644
	    meshFitTogether = false;	  
645
 	}
646

647
	i++;
648
649
650
      }
    }

651
    return meshFitTogether;
652
  }
653
654


655
656
657
658
659
660
  bool MeshDistributor::startFitElementToMeshCode(MeshStructure &code, 
						  Element *el, 
						  GeoIndex subObj,
						  int ithObj, 
						  int elType,
						  bool reverseMode)
661
  {
662
    FUNCNAME("MeshDistributor::startFitElementToMeshCode()");
663

664
665
    TEST_EXIT_DBG(el)("No element given!\n");

666
667
    // If the code is empty, the element does not matter and the function can
    // return without chaning the mesh.
668
669
    if (code.empty())
      return false;
670

671
672
673
674
675
    // 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);
676

677
    TEST_EXIT_DBG(s0 != -1 || s1 != -1)("This should not happen!\n");
678

679
    bool meshChanged = false;
680
681
682
    Flag traverseFlag = 
      Mesh::CALL_EVERY_EL_PREORDER | Mesh::FILL_NEIGH | Mesh::FILL_BOUND;

683
684
685
686
687
    // Test for reverse mode, in which the left and right children of elements
    // are flipped.
    if (reverseMode)
      traverseFlag |= Mesh::CALL_REVERSE_MODE;    

688

689
690
691
692
693
    // === 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.
694
      TraverseStack stack;
695
      ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);
696
697
      while (elInfo && elInfo->getElement() != el)
	elInfo = stack.traverseNext(elInfo);      
698

699
700
      TEST_EXIT_DBG(elInfo->getElement() == el)("This should not happen!\n");

701
      meshChanged = fitElementToMeshCode(code, stack, subObj, ithObj, reverseMode);
702
703
      return meshChanged;
    }
704

705
706
707

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

708
    if (el->isLeaf()) {
709
710

      // If element is leaf and code contains only one leaf element, we are finished.
711
712
713
      if (code.getNumElements() == 1 && code.isLeafElement())
	return false;     

714
      // Create traverse stack and traverse the mesh to the element.
715
      TraverseStack stack;
716
      ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);
717
718
      while (elInfo && elInfo->getElement() != el)
	elInfo = stack.traverseNext(elInfo);      
719
720
721

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

722
      // Code is not leaf, therefore refine the element.
723
      el->setMark(1);
724
725
      refineManager->setMesh(el->getMesh());
      refineManager->setStack(&stack);
726
      refineManager->refineFunction(elInfo);
727
      meshChanged = true;
728
    }
729

730
731
    Element *child0 = el->getFirstChild();
    Element *child1 = el->getSecondChild();
732
733
734
735
    if (reverseMode) {
      std::swap(s0, s1);
      std::swap(child0, child1);    
    }
736

737
738
739
    // === 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.                                          ===
740

741
742
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(el->getMesh(), -1, traverseFlag);
743

744
745
746
    if (s0 != -1) {
      while (elInfo && elInfo->getElement() != child0)
	elInfo = stack.traverseNext(elInfo);     
747

748
749
750
751
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s0, reverseMode);
    } else {
      while (elInfo && elInfo->getElement() != child1) 
	elInfo = stack.traverseNext(elInfo);      
752

753
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s1, reverseMode);
754
755
    }

756

757
    return meshChanged;
758
759
  }

760

761
762
763
764
765
  bool MeshDistributor::fitElementToMeshCode(MeshStructure &code, 
					     TraverseStack &stack,
					     GeoIndex subObj,
					     int ithObj, 
					     bool reverseMode)
766
  {
767
768
769
770
    FUNCNAME("MeshDistributor::fitElementToMeshCode()");


    // === Test if there are more elements in stack to check with the code. ===
771

772
773
    ElInfo *elInfo = stack.getElInfo();
    if (!elInfo)
774
      return false;
775

776
777
778
779

    // === 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.                                               ===
780
781
782
783
784
785
786

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

      do {
	elInfo = stack.traverseNext(elInfo);
      } while (elInfo && elInfo->getLevel() > level);
787

788
      return false;
789
    }
790

791
792
793
794
795
796

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


    // === If element is leaf (and the code is not), refine the element. ===
797

798
    if (el->isLeaf()) {
799
800
      TEST_EXIT_DBG(elInfo->getLevel() < 255)("This should not happen!\n");

801
      el->setMark(1);
802
803
      refineManager->setMesh(el->getMesh());
      refineManager->setStack(&stack);
804
      refineManager->refineFunction(elInfo);
805
      meshChanged = true;
806
807
    }

808
809
810
811
812
813

    // === 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());
814
815
816
    Element *child0 = el->getFirstChild();
    Element *child1 = el->getSecondChild();
    if (reverseMode) {
817
      std::swap(s0, s1);
818
819
      std::swap(child0, child1);
    }
820

821
822
823
824
825
826
827
    
    // === Traverse left child. ===

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

828
      stack.traverseNext(elInfo);
829
      code.nextElement();
830
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s0, reverseMode);
831
832
      elInfo = stack.getElInfo();
    } else {
833
834
835
836
      // 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.

837
838
      do {
	elInfo = stack.traverseNext(elInfo);
839
840
841
      } while (elInfo && elInfo->getElement() != child1); 

      TEST_EXIT_DBG(elInfo != NULL)("This should not happen!\n");
842
843
    }  

844
845
846
847
848
849
850
851
852
853
    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.
854
855

      code.nextElement();
856
      meshChanged |= fitElementToMeshCode(code, stack, subObj, s1, reverseMode);
857
    } else {
858
859
860
861
      // 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.

862
      int level = elInfo->getLevel();
863

864
865
866
867
      do {
	elInfo = stack.traverseNext(elInfo);
      } while (elInfo && elInfo->getLevel() > level);
    }
868

869
870

    return meshChanged;
871
872
  }

873
  
874
  void MeshDistributor::serialize(std::ostream &out, DofContainer &data)
Thomas Witkowski's avatar
Thomas Witkowski committed
875
  {    
876
    int vecSize = data.size();
877
    SerUtil::serialize(out, vecSize);