PetscSolverGlobalMatrix.cc 23.9 KB
Newer Older
Thomas Witkowski's avatar
Thomas Witkowski committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
//
// 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.


#include "parallel/PetscSolverGlobalMatrix.h"
#include "parallel/StdMpi.h"
#include "parallel/MpiHelper.h"

namespace AMDiS {

19
  void PetscSolverGlobalMatrix::fillPetscMatrix(Matrix<DOFMatrix*> *mat)
Thomas Witkowski's avatar
Thomas Witkowski committed
20
21
22
23
24
25
26
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrix()");

    TEST_EXIT_DBG(meshDistributor)("No mesh distributor object defined!\n");
    TEST_EXIT_DBG(mat)("No DOF matrix defined!\n");

    double wtime = MPI::Wtime();
27
28
29
30
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
    createGlobalDofMapping(feSpaces);
    int nRankRows = meshDistributor->getNumberRankDofs(feSpaces);
    int nOverallRows = meshDistributor->getNumberOverallDofs(feSpaces);
Thomas Witkowski's avatar
Thomas Witkowski committed
31

32
    // === Create PETSc vector (solution and a temporary vector). ===
Thomas Witkowski's avatar
Thomas Witkowski committed
33

34
35
    VecCreateMPI(PETSC_COMM_WORLD, nRankRows, nOverallRows, &petscSolVec);
    VecCreateMPI(PETSC_COMM_WORLD, nRankRows, nOverallRows, &petscTmpVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
36
37

    int recvAllValues = 0;
38
39
40
41
    int sendValue = 
      static_cast<int>(meshDistributor->getLastMeshChangeIndex() != lastMeshNnz);
    meshDistributor->getMpiComm().Allreduce(&sendValue, &recvAllValues, 
					    1, MPI_INT, MPI_SUM);
Thomas Witkowski's avatar
Thomas Witkowski committed
42

43
44
45
    recvAllValues = 1;

    if (!d_nnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
Thomas Witkowski's avatar
Thomas Witkowski committed
46
47
48
49
50
51
52
53
54
55
56
57
58
59
      if (d_nnz) {
	delete [] d_nnz;
	d_nnz = NULL;
	delete [] o_nnz;
	o_nnz = NULL;
      }

      createPetscNnzStructure(mat);
      lastMeshNnz = meshDistributor->getLastMeshChangeIndex();
    }


    // === Create PETSc matrix with the computed nnz data structure. ===

60
61
62
     MatCreateMPIAIJ(PETSC_COMM_WORLD, nRankRows, nRankRows, 
		     nOverallRows, nOverallRows,
		     0, d_nnz, 0, o_nnz, &petscMatrix);
63

Thomas Witkowski's avatar
Thomas Witkowski committed
64
65
66
67
68
69
70
#if (DEBUG != 0)
    MSG("Fill petsc matrix 1 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

#if (DEBUG != 0)
    int a, b;
    MatGetOwnershipRange(petscMatrix, &a, &b);
71
    TEST_EXIT(a == meshDistributor->getStartDofs(feSpaces))
Thomas Witkowski's avatar
Thomas Witkowski committed
72
      ("Wrong matrix ownership range!\n");
73
    TEST_EXIT(b == meshDistributor->getStartDofs(feSpaces) + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
74
75
76
77
78
79
      ("Wrong matrix ownership range!\n");
#endif


    // === Transfer values from DOF matrices to the PETSc matrix. === 

80
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
81
82
83
84
85
86
87
88
89
90
91
92
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
	if ((*mat)[i][j])
	  setDofMatrix((*mat)[i][j], nComponents, i, j);

#if (DEBUG != 0)
    MSG("Fill petsc matrix 2 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

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

93
94
95
96
97
98
99
100
101
102
103
104
105
    // === Init PETSc solver. ===
    KSPCreate(PETSC_COMM_WORLD, &solver);
    KSPGetPC(solver, &pc);
    KSPSetOperators(solver, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN); 
    KSPSetTolerances(solver, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(solver, KSPBCGS);
    KSPSetFromOptions(solver);
    PCSetFromOptions(pc);

    // Do not delete the solution vector, use it for the initial guess.
    if (!zeroStartVector)
      KSPSetInitialGuessNonzero(solver, PETSC_TRUE);

106
107
108
109
110
111
112
    MSG("Fill petsc matrix needed %.5f seconds\n", MPI::Wtime() - wtime);
  }


  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
113
   
114
115
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
    TEST_EXIT_DBG(meshDistributor)("No mesh distributor defined!\n");
116

117
118
119
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(vec);
    int nRankRows = meshDistributor->getNumberRankDofs(feSpaces);
    int nOverallRows = meshDistributor->getNumberOverallDofs(feSpaces);
120
121

    VecCreateMPI(PETSC_COMM_WORLD, nRankRows, nOverallRows, &petscRhsVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
122
123

    // === Transfer values from DOF vector to the PETSc vector. === 
124
125
    for (int i = 0; i < vec->getSize(); i++)
      setDofVector(petscRhsVec, vec->getDOFVector(i), vec->getSize(), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
126
127
128
129
130
131

    VecAssemblyBegin(petscRhsVec);
    VecAssemblyEnd(petscRhsVec);
  }


132
133
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
  {
    FUNCNAME("PetscSolverGlobalMatrix::solvePetscMatrix()");

    int nComponents = vec.getSize();

    // === Set old solution to be initiual guess for PETSc solver. ===
    if (!zeroStartVector) {
      VecSet(petscSolVec, 0.0);
      
      for (int i = 0; i < nComponents; i++)
	setDofVector(petscSolVec, vec.getDOFVector(i), nComponents, i, true);
      
      VecAssemblyBegin(petscSolVec);
      VecAssemblyEnd(petscSolVec);
    }

    // PETSc.
    KSPSolve(solver, petscRhsVec, petscSolVec);

    // === Transfere values from PETSc's solution vectors to the DOF vectors. ===
    PetscScalar *vecPointer;
    VecGetArray(petscSolVec, &vecPointer);

157
    int c = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
158
    for (int i = 0; i < nComponents; i++) {
159
      DOFVector<double> &dv = *(vec.getDOFVector(i));
160
161
      const FiniteElemSpace *feSpace = dv.getFeSpace();
      int nRankDofs = meshDistributor->getNumberRankDofs(feSpace);
162

Thomas Witkowski's avatar
Thomas Witkowski committed
163
      for (int j = 0; j < nRankDofs; j++)
164
	dv[meshDistributor->mapLocalToDofIndex(feSpace, j)] = vecPointer[c++]; 
Thomas Witkowski's avatar
Thomas Witkowski committed
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
    }

    VecRestoreArray(petscSolVec, &vecPointer);


    // === Synchronize DOFs at common DOFs, i.e., DOFs that correspond to ===
    // === more than one partition.                                       ===
    meshDistributor->synchVector(vec);


    // Print iteration counter and residual norm of the solution.
    printSolutionInfo(adaptInfo);


    // === Destroy PETSc's variables. ===

181
    VecDestroy(&petscRhsVec);
182
183
184
185
186
187
188
189
190
  }


  void PetscSolverGlobalMatrix::destroyMatrixData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyMatrixData()");

    MatDestroy(&petscMatrix);
    KSPDestroy(&solver);
191
192
    VecDestroy(&petscSolVec);
    VecDestroy(&petscTmpVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
193
194
195
196
  }


  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* mat, int dispMult, 
197
					     int dispAddRow, int dispAddCol)
Thomas Witkowski's avatar
Thomas Witkowski committed
198
199
200
201
202
203
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

    TEST_EXIT(mat)("No DOFMatrix!\n");

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
204
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
    typedef DOFMatrix::base_matrix_type Matrix;

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

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

    vector<int> cols;
    vector<double> values;
    cols.reserve(300);
    values.reserve(300);
    
    vector<int> globalCols;


    // === Traverse all rows of the dof matrix and insert row wise the values ===
    // === to the PETSc matrix.                                               ===

    for (cursor_type cursor = begin<row>(mat->getBaseMatrix()), 
	   cend = end<row>(mat->getBaseMatrix()); cursor != cend; ++cursor) {

      // Global index of the current row DOF.
228
229
      int globalRowDof = 
	meshDistributor->mapLocalToGlobal(mat->getRowFeSpace(), *cursor);
Thomas Witkowski's avatar
Thomas Witkowski committed
230
231
232
233
234
235
236
      // Test if the current row DOF is a periodic DOF.
      bool periodicRow = meshDistributor->isPeriodicDof(globalRowDof);

      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

	// Calculate PETSc row index.
237
238
239
	TEST_EXIT_DBG(dofToGlobalIndex.count(make_pair(*cursor, dispAddRow)))
	  ("Should not happen!\n");
	int rowIndex = dofToGlobalIndex[make_pair(*cursor, dispAddRow)];
Thomas Witkowski's avatar
Thomas Witkowski committed
240
241
242
243
244
245
246
247

	cols.clear();
	values.clear();

	for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); 
	     icursor != icend; ++icursor) {

	  // Global index of the current column index.
248
	  int globalColDof = 
249
	    meshDistributor->mapLocalToGlobal(mat->getColFeSpace(), col(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
250
251
252
	  // Test if the current col dof is a periodic dof.
	  bool periodicCol = meshDistributor->isPeriodicDof(globalColDof);
	  // Calculate PETSc col index.
253
254
255
	  TEST_EXIT_DBG(dofToGlobalIndex.count(make_pair(col(*icursor), dispAddCol)))
	    ("Should not happen!\n");
	  int colIndex = dofToGlobalIndex[make_pair(col(*icursor), dispAddCol)];
Thomas Witkowski's avatar
Thomas Witkowski committed
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327

	  // Ignore all zero entries, expect it is a diagonal entry.
 	  if (value(*icursor) == 0.0 && rowIndex != colIndex)
 	    continue;

	  if (!periodicCol) {
	    // Calculate the exact position of the column index in the PETSc matrix.
	    cols.push_back(colIndex);
	    values.push_back(value(*icursor));
	  } else {
	    // === Row index is not periodic, but column index is. ===

	    // Create set of all periodic associations of the column index.
	    std::set<int> perAsc;
	    std::set<int>& perColAsc = 
	      meshDistributor->getPerDofAssociations(globalColDof);
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
	      if (*it >= -3)
		perAsc.insert(*it);
    
	    // Scale value to the number of periodic associations of the column index.
	    double scaledValue = 
	      value(*icursor) * pow(0.5, static_cast<double>(perAsc.size()));

	    
	    // === Create set of all matrix column indices due to the periodic ===
	    // === associations of the column DOF index.                       ===

	    vector<int> newCols;

	    // First, add the original matrix index.
	    newCols.push_back(globalColDof);
	    
	    // And add all periodic matrix indices.
	    for (std::set<int>::iterator it = perAsc.begin(); 
		 it != perAsc.end(); ++it) {
	      int nCols = static_cast<int>(newCols.size());

	      for (int i = 0; i < nCols; i++) {
 		TEST_EXIT_DBG(meshDistributor->isPeriodicDof(newCols[i], *it))
 		  ("Wrong periodic DOF associations at boundary %d with DOF %d!\n",
		   *it, newCols[i]);

		newCols.push_back(meshDistributor->getPeriodicMapping(newCols[i], *it));
	      }
	    }

	    for (unsigned int i = 0; i < newCols.size(); i++) {
	      cols.push_back(newCols[i] * dispMult + dispAddCol);
	      values.push_back(scaledValue);	      
	    }
	  }
	}

	MatSetValues(petscMatrix, 1, &rowIndex, cols.size(), 
		     &(cols[0]), &(values[0]), ADD_VALUES);	
      } else {
	// === Row DOF index is periodic. ===

	// Because this row is periodic, we will have to add the entries of this 
	// matrix row to multiple rows. The following maps store to each row an
	// array of column indices and values of the entries that must be added to
	// the PETSc matrix.
	map<int, vector<int> > colsMap;
	map<int, vector<double> > valsMap;

	// Traverse all column entries.
	for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); 
	     icursor != icend; ++icursor) {

	  // Global index of the current column index.
328
329
	  int globalColDof = 
	    meshDistributor->mapLocalToGlobal(mat->getColFeSpace(), col(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
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

	  // Ignore all zero entries, expect it is a diagonal entry.
 	  if (value(*icursor) == 0.0 && globalRowDof != globalColDof)
 	    continue;


	  // === Add all periodic associations of both, the row and the column ===
	  // === indices to the set perAsc.                                    ===

	  std::set<int> perAsc;

	  if (meshDistributor->isPeriodicDof(globalColDof)) {
	    std::set<int>& perColAsc = 
	      meshDistributor->getPerDofAssociations(globalColDof);
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
	      if (*it >= -3)
		perAsc.insert(*it);
	  }

	  std::set<int>& perRowAsc = 
	    meshDistributor->getPerDofAssociations(globalRowDof);
	  for (std::set<int>::iterator it = perRowAsc.begin(); 
	       it != perRowAsc.end(); ++it)
	    if (*it >= -3)
	      perAsc.insert(*it);

	  // Scale the value with respect to the number of periodic associations.
	  double scaledValue = 
	    value(*icursor) * pow(0.5, static_cast<double>(perAsc.size()));


	  // === Create all matrix entries with respect to the periodic  ===
	  // === associations of the row and column indices.             ===

	  vector<pair<int, int> > entry;
	  
	  // First, add the original entry.
	  entry.push_back(make_pair(globalRowDof, globalColDof));

	  // Then, traverse the periodic associations of the row and column indices
	  // and create the corresponding entries.
	  for (std::set<int>::iterator it = perAsc.begin(); it != perAsc.end(); ++it) {
	    int nEntry = static_cast<int>(entry.size());
	    for (int i = 0; i < nEntry; i++) {
	      int perRowDof = 0;
	      if (meshDistributor->getPeriodicMapping()[*it].count(entry[i].first))
		perRowDof = meshDistributor->getPeriodicMapping(entry[i].first, *it);
	      else
		perRowDof = entry[i].first;

	      int perColDof;
	      if (meshDistributor->getPeriodicMapping()[*it].count(entry[i].second))
		perColDof = meshDistributor->getPeriodicMapping(entry[i].second, *it);
	      else
		perColDof = entry[i].second;	      	      
	      

	      entry.push_back(make_pair(perRowDof, perColDof));
	    }
	  }


	  // === Translate the matrix entries to PETSc's matrix.

	  for (vector<pair<int, int> >::iterator eIt = entry.begin(); 
	       eIt != entry.end(); ++eIt) {
	    // Calculate row and column indices of the PETSc matrix.
	    int rowIndex = eIt->first * dispMult + dispAddRow;
	    int colIndex = eIt->second * dispMult + dispAddCol;

	    colsMap[rowIndex].push_back(colIndex);
	    valsMap[rowIndex].push_back(scaledValue);
	  }
	}


	// === Finally, add all periodic rows to the PETSc matrix. ===

	for (map<int, vector<int> >::iterator rowIt = colsMap.begin();
	     rowIt != colsMap.end(); ++rowIt) {
	  TEST_EXIT_DBG(rowIt->second.size() == valsMap[rowIt->first].size())
	    ("Should not happen!\n");

	  int rowIndex = rowIt->first;
	  MatSetValues(petscMatrix, 1, &rowIndex, rowIt->second.size(),
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


423
424
425
426
427
  void PetscSolverGlobalMatrix::setDofVector(Vec& petscVec, 
					     DOFVector<double>* vec, 
					     int dispMult, 
					     int dispAdd, 
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
428
429
430
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

431
    const FiniteElemSpace *feSpace = vec->getFeSpace();
432

Thomas Witkowski's avatar
Thomas Witkowski committed
433
434
435
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
436
      if (rankOnly && !meshDistributor->getIsRankDof(feSpace, dofIt.getDOFIndex()))
Thomas Witkowski's avatar
Thomas Witkowski committed
437
438
439
440
	continue;

      // Calculate global row index of the DOF.
      DegreeOfFreedom globalRowDof = 
441
	meshDistributor->mapLocalToGlobal(feSpace, dofIt.getDOFIndex());
Thomas Witkowski's avatar
Thomas Witkowski committed
442
      // Calculate PETSc index of the row DOF.
443
444
445
      TEST_EXIT_DBG(dofToGlobalIndex.count(make_pair(dofIt.getDOFIndex(), dispAdd)))
	("Should not happen!\n");
      int index = dofToGlobalIndex[make_pair(dofIt.getDOFIndex(), dispAdd)];
Thomas Witkowski's avatar
Thomas Witkowski committed
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

      if (meshDistributor->isPeriodicDof(globalRowDof)) {
	std::set<int>& perAsc = meshDistributor->getPerDofAssociations(globalRowDof);
	double value = *dofIt / (perAsc.size() + 1.0);
	VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);

	for (std::set<int>::iterator perIt = perAsc.begin(); perIt != perAsc.end(); ++perIt) {
	  int mappedDof = meshDistributor->getPeriodicMapping(globalRowDof, *perIt);
	  int mappedIndex = mappedDof * dispMult + dispAdd;
	  VecSetValues(petscVec, 1, &mappedIndex, &value, ADD_VALUES);
	}
      } else {
	// The DOF index is not periodic.
	double value = *dofIt;
	VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);
      }
    }
  }


  void PetscSolverGlobalMatrix::createPetscNnzStructure(Matrix<DOFMatrix*> *mat)
  {
    FUNCNAME("PetscSolverGlobalMatrix::createPetscNnzStructure()");

    TEST_EXIT_DBG(!d_nnz)("There is something wrong!\n");
    TEST_EXIT_DBG(!o_nnz)("There is something wrong!\n");

473
474
475
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
    int nRankRows = meshDistributor->getNumberRankDofs(feSpaces);
    int rankStartIndex = meshDistributor->getStartDofs(feSpaces);
Thomas Witkowski's avatar
Thomas Witkowski committed
476
477
478
479
480
481
482
483
484
485
486
487
488
    d_nnz = new int[nRankRows];
    o_nnz = new int[nRankRows];
    for (int i = 0; i < nRankRows; i++) {
      d_nnz[i] = 0;
      o_nnz[i] = 0;
    }

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
    namespace traits = mtl::traits;
    typedef DOFMatrix::base_matrix_type Matrix;
    typedef vector<pair<int, int> > MatrixNnzEntry;
    typedef map<int, DofContainer> RankToDofContainer;

489
490
491
492
    // Stores to each rank a list of nnz entries (i.e. pairs of row and column
    // index) that this rank will send to. These nnz entries will be assembled
    // on this rank, but because the row DOFs are not DOFs of this rank they 
    // will be send to the owner of the row DOFs.
Thomas Witkowski's avatar
Thomas Witkowski committed
493
494
495
496
    map<int, MatrixNnzEntry> sendMatrixEntry;

    // Maps to each DOF that must be send to another rank the rank number of the
    // receiving rank.
497
    map<pair<DegreeOfFreedom, int>, int> sendDofToRank;
Thomas Witkowski's avatar
Thomas Witkowski committed
498

499

500
501
502
503
504
505
506
507
508
509
    // First, create for all ranks, to which we send data to, MatrixNnzEntry 
    // object with 0 entries.
    for (unsigned int i = 0; i < feSpaces.size(); i++) {
      for (DofComm::Iterator it(meshDistributor->getRecvDofs(), feSpaces[i]);
	   !it.end(); it.nextRank()) {
	sendMatrixEntry[it.getRank()].resize(0);
	
	for (; !it.endDofIter(); it.nextDof())
	  sendDofToRank[make_pair(it.getDofIndex(), i)] = it.getRank();
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
510
511
    }

512
    // Create list of ranks from which we receive data from.
Thomas Witkowski's avatar
Thomas Witkowski committed
513
    std::set<int> recvFromRank;
514
515
516
517
518
519
520
    for (unsigned int i = 0; i < feSpaces.size(); i++) 
      for (DofComm::Iterator it(meshDistributor->getSendDofs(), feSpaces[i]);
	   !it.end(); it.nextRank())
	recvFromRank.insert(it.getRank());


    // === Traverse matrices to create nnz data. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
521

522
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
523
524
525
526
527
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
 	if (!(*mat)[i][j])
	  continue;

528
529
530
531
532
	TEST_EXIT_DBG((*mat)[i][j]->getRowFeSpace() == feSpaces[i])
	  ("Should not happen!\n");
	TEST_EXIT_DBG((*mat)[i][j]->getColFeSpace() == feSpaces[j])
	  ("Should not happen!\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
533
534
535
536
537
538
539
540
541
542
543
	Matrix bmat = (*mat)[i][j]->getBaseMatrix();

	traits::col<Matrix>::type col(bmat);
	traits::const_value<Matrix>::type value(bmat);
	  
	typedef traits::range_generator<row, Matrix>::type cursor_type;
	typedef traits::range_generator<nz, cursor_type>::type icursor_type;
	
	for (cursor_type cursor = begin<row>(bmat), 
	       cend = end<row>(bmat); cursor != cend; ++cursor) {

544
545
	  // The corresponding global matrix row index of the current row DOF.
	  int petscRowIdx = dofToGlobalIndex[make_pair(*cursor, i)];
Thomas Witkowski's avatar
Thomas Witkowski committed
546
	  
547
	  if (meshDistributor->getIsRankDof(feSpaces[i], *cursor)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
548
	    	    
549
550
	    // === The current row DOF is a rank DOF, so create the       ===
	    // === corresponding nnz values directly on rank's nnz data.  ===
Thomas Witkowski's avatar
Thomas Witkowski committed
551
552
	    
	    // This is the local row index of the local PETSc matrix.
553
	    int localPetscRowIdx = petscRowIdx - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
554
555
556
557
	    
	    TEST_EXIT_DBG(localPetscRowIdx >= 0 && localPetscRowIdx < nRankRows)
	      ("Should not happen! \n Debug info: localRowIdx = %d   globalRowIndx = %d   petscRowIdx = %d   localPetscRowIdx = %d   rStart = %d   nCompontens = %d   nRankRows = %d\n",
	       *cursor, 
558
	       meshDistributor->mapLocalToGlobal(feSpaces[i], *cursor), 
Thomas Witkowski's avatar
Thomas Witkowski committed
559
560
	       petscRowIdx, 
	       localPetscRowIdx, 
561
	       rankStartIndex,
Thomas Witkowski's avatar
Thomas Witkowski committed
562
563
564
565
566
567
568
	       nComponents, 
	       nRankRows);
	    
	    
	    // Traverse all non zero entries in this row.
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
569
	      int petscColIdx = dofToGlobalIndex[make_pair(col(*icursor), j)];
Thomas Witkowski's avatar
Thomas Witkowski committed
570
571
572
	      
	      if (value(*icursor) != 0.0 || petscRowIdx == petscColIdx) {
		// The row DOF is a rank DOF, if also the column is a rank DOF, 
573
574
575
576
		// increment the d_nnz values for this row, otherwise the 
		// o_nnz value.
		if (petscColIdx >= rankStartIndex && 
		    petscColIdx < rankStartIndex + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
577
578
579
580
581
582
		  d_nnz[localPetscRowIdx]++;
		else
		  o_nnz[localPetscRowIdx]++;
	      }    
	    }
	  } else {
583
584
585
586
587
	    // === The current row DOF is not a rank DOF, i.e., its values   ===
	    // === are also created on this rank, but afterthere they will   ===
	    // === be send to another rank. So we need to send also the      ===
	    // === corresponding nnz structure of this row to the corres-    ===
	    // === ponding rank.                                             ===
Thomas Witkowski's avatar
Thomas Witkowski committed
588
589
	    
	    // Send all non zero entries to the member of the row DOF.
590
	    int sendToRank = sendDofToRank[make_pair(*cursor, i)];
Thomas Witkowski's avatar
Thomas Witkowski committed
591
592
593
594
	    
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
	      if (value(*icursor) != 0.0) {
595
		int petscColIdx = dofToGlobalIndex[make_pair(col(*icursor), j)];
Thomas Witkowski's avatar
Thomas Witkowski committed
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
		
		sendMatrixEntry[sendToRank].
		  push_back(make_pair(petscRowIdx, petscColIdx));
	      }
	    }
	    
	  } // if (isRankDof[*cursor]) ... else ...
	} // for each row in mat[i][j]
      } 
    }

    // === Send and recv the nnz row structure to/from other ranks. ===

    StdMpi<MatrixNnzEntry> stdMpi(meshDistributor->getMpiComm(), true);
    stdMpi.send(sendMatrixEntry);
    for (std::set<int>::iterator it = recvFromRank.begin(); 
	 it != recvFromRank.end(); ++it)
      stdMpi.recv(*it);
    stdMpi.startCommunication();


617
618
    // === Evaluate the nnz structure this rank got from other ranks and add ===
    // === it to the PETSc nnz data structure.                               ===
Thomas Witkowski's avatar
Thomas Witkowski committed
619
620
621
622
623
624
625
626

    for (map<int, MatrixNnzEntry>::iterator it = stdMpi.getRecvData().begin();
	 it != stdMpi.getRecvData().end(); ++it) {
      if (it->second.size() > 0) {
	for (unsigned int i = 0; i < it->second.size(); i++) {
	  int r = it->second[i].first;
	  int c = it->second[i].second;

627
	  int localRowIdx = r - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
628
629
630
631
632

	  TEST_EXIT_DBG(localRowIdx >= 0 && localRowIdx < nRankRows)
	    ("Got row index %d/%d (nRankRows = %d) from rank %d. Should not happen!\n",
	     r, localRowIdx, nRankRows, it->first);
	  
633
	  if (c < rankStartIndex || c >= rankStartIndex + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
	    o_nnz[localRowIdx]++;
	  else
	    d_nnz[localRowIdx]++;
	}
      }
    }

    // The above algorithm for calculating the number of nnz per row over-
    // approximates the value, i.e., the number is always equal or larger to 
    // the real number of nnz values in the global parallel matrix. For small
    // matrices, the problem may arise, that the result is larger than the
    // number of elements in a row. This is fixed in the following.

    if (nRankRows < 100) 
      for (int i = 0; i < nRankRows; i++)
	d_nnz[i] = std::min(d_nnz[i], nRankRows);
  }

652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713

  void PetscSolverGlobalMatrix::createGlobalDofMapping(vector<const FiniteElemSpace*> &feSpaces)
  {
    FUNCNAME("PetscSolverGlobalMatrix::createGlobalDofMapping()");

    int offset = meshDistributor->getStartDofs(feSpaces);
    Mesh *mesh = meshDistributor->getMesh();

    for (unsigned int i = 0; i < feSpaces.size(); i++) {

      // === Create indices for all DOFs in rank' domain. ===
      std::set<const DegreeOfFreedom*> rankDofSet;
      mesh->getAllDofs(feSpaces[i], rankDofSet);
      for (std::set<const DegreeOfFreedom*>::iterator it = rankDofSet.begin();
	   it != rankDofSet.end(); ++it)
	if (meshDistributor->getIsRankDof(feSpaces[i], **it)) {
	  int localIndex = **it;
	  int globalIndex =  
	    meshDistributor->mapLocalToGlobal(feSpaces[i], localIndex) -
	    meshDistributor->getStartDofs(feSpaces[i]) +
	    offset;

	  dofToGlobalIndex[make_pair(localIndex, i)] = globalIndex;
	}
	  

      // === Communicated interior boundary DOFs between domains. ===

      StdMpi<vector<int> > stdMpi(meshDistributor->getMpiComm());
    
      for (DofComm::Iterator it(meshDistributor->getSendDofs(), feSpaces[i]);
	   !it.end(); it.nextRank()) {
	vector<DegreeOfFreedom> sendGlobalDofs;

	for (; !it.endDofIter(); it.nextDof()) {
	  int globalIndex = dofToGlobalIndex[make_pair(it.getDofIndex(), i)];
	  sendGlobalDofs.push_back(globalIndex);
	}

	stdMpi.send(it.getRank(), sendGlobalDofs);
      }

      for (DofComm::Iterator it(meshDistributor->getRecvDofs(), feSpaces[i]);
	   !it.end(); it.nextRank())
	stdMpi.recv(it.getRank());

      stdMpi.startCommunication();

      for (DofComm::Iterator it(meshDistributor->getRecvDofs(), feSpaces[i]);
	   !it.end(); it.nextRank())
	for (; !it.endDofIter(); it.nextDof()) {
	  DegreeOfFreedom localIndex = it.getDofIndex();
	  int globalIndex = stdMpi.getRecvData(it.getRank())[it.getDofCounter()];
	  dofToGlobalIndex[make_pair(localIndex, i)] = globalIndex;
	}
	 
      
      // === Update offset. ===

      offset += meshDistributor->getNumberRankDofs(feSpaces[i]);
    }
  }
Thomas Witkowski's avatar
Thomas Witkowski committed
714
}