ParallelDomainProblem.cc 15.8 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
#include "ParallelDomainProblem.h"
#include "ProblemScal.h"
#include "ProblemInstat.h"
#include "ParMetisPartitioner.h"
#include "Mesh.h"
#include "Traverse.h"
#include "ElInfo.h"
#include "Element.h"
#include "MacroElement.h"
#include "PartitionElementData.h"
11
12
#include "DOFMatrix.h"
#include "DOFVector.h"
13
14
15
#include "VtkWriter.h"

#include "petscksp.h"
16
17
18
19

namespace AMDiS {

  ParallelDomainProblemBase::ParallelDomainProblemBase(const std::string& name,
20
21
						       ProblemIterationInterface *iIF,
						       ProblemTimeInterface *tIF,
22
						       FiniteElemSpace *fe)
23
24
    : iterationIF(iIF),
      timeIF(tIF),
25
26
      feSpace(fe),
      mesh(fe->getMesh()),
27
      initialPartitionMesh(true),
28
      nRankDOFs(0)
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
  {
    mpiRank = MPI::COMM_WORLD.Get_rank();
    mpiSize = MPI::COMM_WORLD.Get_size();
    mpiComm = MPI::COMM_WORLD;
    partitioner = new ParMetisPartitioner(mesh, &mpiComm);
  }

  void ParallelDomainProblemBase::initParallelization(AdaptInfo *adaptInfo)
  {
    if (mpiSize <= 1)
      return;

    // create an initial partitioning of the mesh
    partitioner->createPartitionData();
    // set the element weights, which are 1 at the very first begin
    setElemWeights(adaptInfo);
    // and now partition the mesh
    partitionMesh(adaptInfo);   


Thomas Witkowski's avatar
Thomas Witkowski committed
49
50
51
    /// === Determine to each dof the set of partitions the dof belongs to. ===

    std::map<const DegreeOfFreedom*, std::set<int> > partitionDofs;
52
53
54
55
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
    while (elInfo) {
      Element *element = elInfo->getElement();
56
57
58

      // Determine to each dof the partition(s) it corresponds to.
      for (int i = 0; i < 3; i++) 
Thomas Witkowski's avatar
Thomas Witkowski committed
59
	partitionDofs[element->getDOF(i)].insert(partitionVec[element->getIndex()]);
60
          
61
62
63
      elInfo = stack.traverseNext(elInfo);
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
64
65
66
67
    /// === Determine the set of ranks dofs and the dofs ownership at the boundary. ===

    std::vector<const DegreeOfFreedom*> rankDofs;
    for (std::map<const DegreeOfFreedom*, std::set<int> >::iterator it = partitionDofs.begin();
68
69
70
71
72
73
74
75
76
	 it != partitionDofs.end();
	 ++it) {
      for (std::set<int>::iterator itpart1 = it->second.begin();
	   itpart1 != it->second.end();
	   ++itpart1) {
	if (*itpart1 == mpiRank) {
	  if (it->second.size() == 1) {
	    rankDofs.push_back(it->first);
	  } else {	    
Thomas Witkowski's avatar
Thomas Witkowski committed
77
78
79
	    // This dof is at the ranks boundary. It is owned by the rank only if
	    // the rank number is the highest of all ranks containing this dof.

80
	    bool insert = true;
Thomas Witkowski's avatar
Thomas Witkowski committed
81
	    int highestRank = mpiRank;
82
83
84
	    for (std::set<int>::iterator itpart2 = it->second.begin();
		 itpart2 != it->second.end();
		 ++itpart2) {
Thomas Witkowski's avatar
Thomas Witkowski committed
85
	      if (*itpart2 > mpiRank)
86
		insert = false;
Thomas Witkowski's avatar
Thomas Witkowski committed
87
88
89

	      if (*itpart2 > highestRank)
		highestRank = *itpart2;
90
	    }
Thomas Witkowski's avatar
Thomas Witkowski committed
91
92

	    if (insert)
93
	      rankDofs.push_back(it->first);
Thomas Witkowski's avatar
Thomas Witkowski committed
94
95

	    boundaryDofs[it->first] = highestRank;
96
97
98
99
100
	  }
	}
      }
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131

    // === Create interior boundary information ===

    elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL | Mesh::FILL_NEIGH);
    while (elInfo) {
      Element *element = elInfo->getElement();

      // Hidde elements which are not part of ranks partition.
      PartitionElementData *partitionData = 
	dynamic_cast<PartitionElementData*>(element->getElementData(PARTITION_ED));   
      if (partitionData->getPartitionStatus() == IN) {
	for (int i = 0; i < 3; i++) {
	  if (!elInfo->getNeighbour(i))
	    continue;

	  PartitionElementData *neighbourPartitionData =
	    dynamic_cast<PartitionElementData*>(elInfo->getNeighbour(i)->getElementData(PARTITION_ED));
 	  if (neighbourPartitionData->getPartitionStatus() == OUT) {
 	    AtomicBoundary& bound = interiorBoundary.
	      getNewAtomicBoundary(partitionVec[elInfo->getNeighbour(i)->getIndex()]);
 	    bound.rankObject.el = element;
 	    bound.rankObject.subObjAtBoundary = EDGE;
 	    bound.rankObject.ithObjAtBoundary = i;
 	    bound.neighbourObject.el = elInfo->getNeighbour(i);
 	    bound.neighbourObject.subObjAtBoundary = EDGE;
 	    bound.neighbourObject.ithObjAtBoundary = -1;
 	  }
	}
      }

      elInfo = stack.traverseNext(elInfo);
Thomas Witkowski's avatar
Thomas Witkowski committed
132
133
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
134

135
136
    // === Remove all macro elements that are not part of the rank partition. ===

137
138
139
140
141
142
143
    std::vector<MacroElement*> macrosToRemove;
    for (std::deque<MacroElement*>::iterator it = mesh->firstMacroElement();
	 it != mesh->endOfMacroElements();
	 ++it) {
      PartitionElementData *partitionData = 
	dynamic_cast<PartitionElementData*>
	((*it)->getElement()->getElementData(PARTITION_ED));
144
      if (partitionData->getPartitionStatus() != IN)
145
146
147
148
149
	macrosToRemove.push_back(*it);
    }

    mesh->removeMacroElements(macrosToRemove);

150
151
    // === Create local and global dofs ordering. ===

152
153
154
    int *gOrder = (int*)(malloc(sizeof(int) * rankDofs.size()));
    int *lOrder = (int*)(malloc(sizeof(int) * rankDofs.size()));

Thomas Witkowski's avatar
Thomas Witkowski committed
155
    for (std::vector<const DegreeOfFreedom*>::iterator it = rankDofs.begin();
156
	 it != rankDofs.end(); ++it)
Thomas Witkowski's avatar
Thomas Witkowski committed
157
      gOrder[nRankDOFs++] = (*it)[0];
158
159
160

    int rstart = 0;
    MPI_Scan(&nRankDOFs, &rstart, 1, MPI_INT, MPI_SUM, PETSC_COMM_WORLD);
161
    rstart -= nRankDOFs;
Thomas Witkowski's avatar
Thomas Witkowski committed
162
   
163
    for (int i = 0; i < nRankDOFs; i++)
164
      lOrder[i] = rstart + i;
165
166

    AOCreateBasic(PETSC_COMM_WORLD, nRankDOFs, gOrder, lOrder, &applicationOrdering);
Thomas Witkowski's avatar
Thomas Witkowski committed
167
    
168
169
    free(gOrder);
    free(lOrder);
Thomas Witkowski's avatar
Thomas Witkowski committed
170
171
172
173
174
175
176
177
178

    /// === Create information which dof indices must be send and which must be received. ===

    std::map<int, std::map<DegreeOfFreedom, DegreeOfFreedom> > sendNewDofs;
    std::map<int, std::vector<DegreeOfFreedom> > recvNewDofs;

    for (std::map<const DegreeOfFreedom*, int>::iterator it = boundaryDofs.begin();
	 it != boundaryDofs.end();
	 ++it) {
179

Thomas Witkowski's avatar
Thomas Witkowski committed
180
      if (it->second == mpiRank) {
181
182
183
	// If the boundary dof is a rank dof, it must be send to other ranks.

	// old global index
Thomas Witkowski's avatar
Thomas Witkowski committed
184
	int oldDofIndex = (it->first)[0];
185
	// search for new dof index in ranks partition for this boundary dof
Thomas Witkowski's avatar
Thomas Witkowski committed
186
187
188
189
190
191
192
193
	int newDofIndex = 0;
	for (int i = 0; i < static_cast<int>(rankDofs.size()); i++) {
	  if (rankDofs[i] == it->first) {
	    newDofIndex = rstart + i;
	    break;
	  }
	}

194
	// Search for all ranks that have this dof too.
Thomas Witkowski's avatar
Thomas Witkowski committed
195
196
197
	for (std::set<int>::iterator itRanks = partitionDofs[it->first].begin();
	     itRanks != partitionDofs[it->first].end();
	     ++itRanks) {
198
	  if (*itRanks != mpiRank) {
Thomas Witkowski's avatar
Thomas Witkowski committed
199
	    sendNewDofs[*itRanks][oldDofIndex] = newDofIndex;
200
201
	    sendDofs[*itRanks].push_back(newDofIndex);
	  }
Thomas Witkowski's avatar
Thomas Witkowski committed
202
203
	}
      } else {
204
205
	// If the boundary dof is not a rank dof, its new dof index, and later
	// also the dof values, must be received from another rank.
Thomas Witkowski's avatar
Thomas Witkowski committed
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
	recvNewDofs[it->second].push_back((it->first)[0]);
      }
    }

    /// === Send and receive the dof indices at boundary. ===

    std::vector<int*> sendBuffers(sendNewDofs.size());
    std::vector<int*> recvBuffers(recvNewDofs.size());
    
    int i = 0;
    for (std::map<int, std::map<DegreeOfFreedom, DegreeOfFreedom> >::iterator sendIt = sendNewDofs.begin();
	 sendIt != sendNewDofs.end();
	 ++sendIt, i++) {
      sendBuffers[i] = new int[sendIt->second.size() * 2];
      int c = 0;
      for (std::map<DegreeOfFreedom, DegreeOfFreedom>::iterator dofIt = sendIt->second.begin();
	   dofIt != sendIt->second.end();
	   ++dofIt, c += 2) {
	sendBuffers[i][c] = dofIt->first;
	sendBuffers[i][c + 1] = dofIt->second;
      }

      mpiComm.Isend(sendBuffers[i], sendIt->second.size() * 2, MPI_INT, sendIt->first, 0);
    }

    i = 0;
    for (std::map<int, std::vector<DegreeOfFreedom> >::iterator recvIt = recvNewDofs.begin();
	 recvIt != recvNewDofs.end();
	 ++recvIt, i++) {
      recvBuffers[i] = new int[recvIt->second.size() * 2];
      
      mpiComm.Irecv(recvBuffers[i], recvIt->second.size() * 2, MPI_INT, recvIt->first, 0);
    }


    mpiComm.Barrier();

243
244
245
246
247
248
249
250
251

    /// === Reset all DOFAdmins of the mesh. ===

    int nAdmins = mesh->getNumberOfDOFAdmin();
    for (int i = 0; i < nAdmins; i++) 
      for (int j = 0; j < mesh->getDOFAdmin(i).getSize(); j++)
	const_cast<DOFAdmin&>(mesh->getDOFAdmin(i)).setDOFFree(j, true);
    

Thomas Witkowski's avatar
Thomas Witkowski committed
252
253
254
255
256
257
258
259
260
261
262
263
    /// === Change dof indices at boundary from other ranks. ===

    i = 0;
    for (std::map<int, std::vector<DegreeOfFreedom> >::iterator recvIt = recvNewDofs.begin();
	 recvIt != recvNewDofs.end();
	 ++recvIt, i++) {

      for (int j = 0; j < static_cast<int>(recvIt->second.size()); j++) {
	for (std::map<const DegreeOfFreedom*, int>::iterator dofIt = boundaryDofs.begin();
	     dofIt != boundaryDofs.end();
	     ++dofIt) {
	  if ((dofIt->first)[0] == recvBuffers[i][j * 2]) {
264
265
266
267
268
269
270
271
272
	    int newDof = recvBuffers[i][j * 2 + 1];

	    recvDofs[recvIt->first].push_back(newDof);

	    const_cast<DegreeOfFreedom*>(dofIt->first)[0] = newDof;

	    for (int k = 0; k < nAdmins; k++) 
	      const_cast<DOFAdmin&>(mesh->getDOFAdmin(k)).setDOFFree(newDof, false);

Thomas Witkowski's avatar
Thomas Witkowski committed
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
	    break;
	  }
	}
      }

      delete [] recvBuffers[i];
    }

    i = 0;
    for (std::map<int, std::map<DegreeOfFreedom, DegreeOfFreedom> >::iterator sendIt = sendNewDofs.begin();
	 sendIt != sendNewDofs.end();
	 ++sendIt, i++) {
      delete [] sendBuffers[i];
    }

    /// === Change dof indices for rank partition. ===

290
291
292
293
294
295
296
    for (int i = 0; i < static_cast<int>(rankDofs.size()); i++) {
      const_cast<DegreeOfFreedom*>(rankDofs[i])[0] = rstart + i; 

      for (int k = 0; k < nAdmins; k++) 
	const_cast<DOFAdmin&>(mesh->getDOFAdmin(k)).setDOFFree(rstart + i, false);

    }
297
298
299
300
301
302
303
304
305
306
307

    /// === Create petsc matrix. ===
    int ierr;
    ierr = MatCreate(PETSC_COMM_WORLD, &petscMatrix);
    ierr = MatSetSizes(petscMatrix, rankDofs.size(), rankDofs.size(),
		       partitionDofs.size(), partitionDofs.size());
    ierr = MatSetType(petscMatrix, MATAIJ);

    ierr = VecCreate(PETSC_COMM_WORLD, &petscRhsVec);
    ierr = VecSetSizes(petscRhsVec, rankDofs.size(), partitionDofs.size());    
    ierr = VecSetType(petscRhsVec, VECMPI);
308
309
310
311

    ierr = VecCreate(PETSC_COMM_WORLD, &petscSolVec);
    ierr = VecSetSizes(petscSolVec, rankDofs.size(), partitionDofs.size());    
    ierr = VecSetType(petscSolVec, VECMPI);
312
313
314
315
  }

  void ParallelDomainProblemBase::exitParallelization(AdaptInfo *adaptInfo)
  {
316
    AODestroy(applicationOrdering);
317
318
  }

319
320
321
  void ParallelDomainProblemBase::fillPetscMatrix(DOFMatrix *mat, 
						  DOFVector<double> *vec)
  {
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
    using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
    namespace traits= mtl::traits;
    typedef DOFMatrix::base_matrix_type Matrix;

    traits::row<Matrix>::type row(mat->getBaseMatrix());
    traits::col<Matrix>::type col(mat->getBaseMatrix());
    traits::const_value<Matrix>::type value(mat->getBaseMatrix());

    typedef traits::range_generator<major, Matrix>::type cursor_type;
    typedef traits::range_generator<nz, cursor_type>::type icursor_type;

    std::cout.precision(10);
    for (cursor_type cursor = begin<major>(mat->getBaseMatrix()), cend = end<major>(mat->getBaseMatrix()); cursor != cend; ++cursor)
      for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); icursor != icend; ++icursor)
	if (value(*icursor) != 0.0) {
	  int r = row(*icursor);
	  int c = col(*icursor);
	  double v = value(*icursor);
	  MatSetValues(petscMatrix, 1, &r, 1, &c, &v, ADD_VALUES);
341
	}
342

343
344
345
346
347
348
349
350
351
352

    MatAssemblyBegin(petscMatrix, MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(petscMatrix, MAT_FINAL_ASSEMBLY);

    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
      int index = dofIt.getDOFIndex();
      double value = *dofIt;

      VecSetValues(petscRhsVec, 1, &index, &value, ADD_VALUES);
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
    }
  }

  void ParallelDomainProblemBase::solvePetscMatrix(DOFVector<double> *vec)
  {
    KSP ksp;
    PC pc;

    KSPCreate(PETSC_COMM_WORLD, &ksp);
    KSPSetOperators(ksp, petscMatrix, petscMatrix, DIFFERENT_NONZERO_PATTERN);
    KSPGetPC(ksp, &pc);
    PCSetType(pc, PCJACOBI);
    KSPSetTolerances(ksp, 1.e-7, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(ksp, KSPBCGS);
    KSPMonitorSet(ksp, KSPMonitorDefault, PETSC_NULL, 0);
    KSPSolve(ksp, petscRhsVec, petscSolVec);

    PetscScalar *vecPointer;
    VecGetArray(petscSolVec, &vecPointer);

    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    int counter = 0;
    for (dofIt.reset(); !dofIt.end(); ++dofIt)
376
      *dofIt = vecPointer[counter++];
377
378
379

    VecRestoreArray(petscSolVec, &vecPointer);

380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
    std::vector<double*> sendBuffers(sendDofs.size());
    std::vector<double*> recvBuffers(recvDofs.size());
    
    int i = 0;
    for (std::map<int, std::vector<DegreeOfFreedom> >::iterator sendIt = sendDofs.begin();
	 sendIt != sendDofs.end();
	 ++sendIt, i++) {
      sendBuffers[i] = new double[sendIt->second.size()];

      for (int j = 0; j < sendIt->second.size(); j++)
	sendBuffers[i][j] = (*vec)[(sendIt->second)[j]];

      mpiComm.Isend(sendBuffers[i], sendIt->second.size(), MPI_DOUBLE, sendIt->first, 0);
    }

    i = 0;
    for (std::map<int, std::vector<DegreeOfFreedom> >::iterator recvIt = recvDofs.begin();
	 recvIt != recvDofs.end();
	 ++recvIt, i++) {
      recvBuffers[i] = new double[recvIt->second.size()];

      mpiComm.Irecv(recvBuffers[i], recvIt->second.size(), MPI_DOUBLE, recvIt->first, 0);
    }

    
    mpiComm.Barrier();
    
    i = 0;
    for (std::map<int, std::vector<DegreeOfFreedom> >::iterator recvIt = recvDofs.begin();
	 recvIt != recvDofs.end();
	 ++recvIt, i++) {
      for (int j = 0; j < recvIt->second.size(); j++) {
	if (MPI::COMM_WORLD.Get_rank() == 0)
	  std::cout << (recvIt->second)[j] << " = " << recvBuffers[i][j] << std::endl;      

	(*vec)[(recvIt->second)[j]] = recvBuffers[i][j];
      }

      delete [] recvBuffers[i];
    }
    
    for (int i = 0; i < sendBuffers.size(); i++)
      delete [] sendBuffers[i];    
423

424
425
426
427
428
429
430
431
    std::cout << "TEST" << std::endl;
    
    if (MPI::COMM_WORLD.Get_rank() == 0) {
      DOFVector<double>::Iterator it(vec, USED_DOFS);
      for (it.reset(); !it.end(); ++it) {
	std::cout << it.getDOFIndex() << " = " << *it << std::endl;
      }
    }
432
433
  }

434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
  double ParallelDomainProblemBase::setElemWeights(AdaptInfo *adaptInfo) 
  {
    double localWeightSum = 0.0;
    int elNum = -1;

    elemWeights.clear();

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1,
					 Mesh::CALL_EVERY_EL_PREORDER);
    while (elInfo) {
      Element *element = elInfo->getElement();

      // get partition data
      PartitionElementData *partitionData = dynamic_cast<PartitionElementData*>
	(element->getElementData(PARTITION_ED));

      if (partitionData && partitionData->getPartitionStatus() == IN) {
	if (partitionData->getLevel() == 0) {
	  elNum = element->getIndex();
	}
	TEST_EXIT(elNum != -1)("invalid element number\n");
	if (element->isLeaf()) {
	  elemWeights[elNum] += 1.0;
	  localWeightSum += 1.0;
	}
      }

      elInfo = stack.traverseNext(elInfo);
    }

    return localWeightSum;
  }

  void ParallelDomainProblemBase::partitionMesh(AdaptInfo *adaptInfo)
  {
    if (initialPartitionMesh) {
      initialPartitionMesh = false;
      partitioner->fillCoarsePartitionVec(&oldPartitionVec);
      partitioner->partition(&elemWeights, INITIAL);
    } else {
      oldPartitionVec = partitionVec;
      partitioner->partition(&elemWeights, ADAPTIVE_REPART, 100.0 /*0.000001*/);
    }    

    partitioner->fillCoarsePartitionVec(&partitionVec);
  }

  ParallelDomainProblemScal::ParallelDomainProblemScal(const std::string& name,
						       ProblemScal *problem,
						       ProblemInstatScal *problemInstat)
485
486
    : ParallelDomainProblemBase(name, problem, problemInstat, problem->getFESpace()),
      probScal(problem)
487
488
489
  {
  }

490
491
492
493
494
495
496
497
  Flag ParallelDomainProblemScal::oneIteration(AdaptInfo *adaptInfo, Flag toDo)
  {
    //    return iterationIF->oneIteration(adaptInfo, toDo);

    Flag flag = dynamic_cast<StandardProblemIteration*>(iterationIF)->buildAndAdapt(adaptInfo, toDo);

    fillPetscMatrix(probScal->getSystemMatrix(), probScal->getRHS());

498
499
    solvePetscMatrix(probScal->getSolution());

500
501
502
503
504
505
506
507
508
509
510
511
//     if (toDo.isSet(SOLVE))
//       iterationIF->getProblem()->solve(adaptInfo, false);

//     if (toDo.isSet(SOLVE_RHS))
//       iterationIF->getProblem()->solve(adaptInfo, true);

//     if (toDo.isSet(ESTIMATE)) 
//       iterationIF->getProblem()->estimate(adaptInfo);

    return flag;

  }
512
513

}