PetscSolverGlobalMatrix.cc 46.2 KB
Newer Older
Thomas Witkowski's avatar
Thomas Witkowski committed
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.


13
#include "AMDiS.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
14
15
16
17
18
19
#include "parallel/PetscSolverGlobalMatrix.h"
#include "parallel/StdMpi.h"
#include "parallel/MpiHelper.h"

namespace AMDiS {

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

24
    if (coarseSpaceMap != NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
25
      updateSubdomainData();
26
27
28
29
      fillPetscMatrixWithCoarseSpace(mat);
      return;
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
30
    TEST_EXIT_DBG(meshDistributor)("No mesh distributor object defined!\n");
31
    TEST_EXIT_DBG(interiorMap)("No parallel mapping object defined!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
32
    TEST_EXIT_DBG(mat)("No DOF matrix defined!\n");
33
    
Thomas Witkowski's avatar
Thomas Witkowski committed
34
    double wtime = MPI::Wtime();
35

36
    // === If required, recompute non zero structure of the matrix. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
37

38
    if (checkMeshChange(mat))
Thomas Witkowski's avatar
Thomas Witkowski committed
39
40
41
      createPetscNnzStructure(mat);


42
43
    // === Create PETSc vector (solution and a temporary vector). ===

44
45
    int nRankRows = interiorMap->getRankDofs();
    int nOverallRows = interiorMap->getOverallDofs();
46

47
    VecCreateMPI(mpiCommGlobal, nRankRows, nOverallRows, &petscSolVec);
48
49


Thomas Witkowski's avatar
Thomas Witkowski committed
50
51
    // === Create PETSc matrix with the computed nnz data structure. ===

52
    MatCreateAIJ(mpiCommGlobal, nRankRows, nRankRows, 
53
		 nOverallRows, nOverallRows,
54
		 0, matInteriorDiagNnz, 0, matInteriorOffdiagNnz, &matIntInt);
55
56

    MatSetOption(matIntInt, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
57

Thomas Witkowski's avatar
Thomas Witkowski committed
58
59
60
61
62
63
#if (DEBUG != 0)
    MSG("Fill petsc matrix 1 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

#if (DEBUG != 0)
    int a, b;
64
65
66
    MatGetOwnershipRange(matIntInt, &a, &b);
    TEST_EXIT(a == interiorMap->getStartDofs())("Wrong matrix ownership range!\n");
    TEST_EXIT(b == interiorMap->getStartDofs() + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
67
68
69
70
71
72
      ("Wrong matrix ownership range!\n");
#endif


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

73
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
74
75
76
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
	if ((*mat)[i][j])
77
	  setDofMatrix((*mat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
78
79
80
81
82

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

83
84
    MatAssemblyBegin(matIntInt, MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(matIntInt, MAT_FINAL_ASSEMBLY);
Thomas Witkowski's avatar
Thomas Witkowski committed
85

86
87
88

    // === Remove Dirichlet BC DOFs. ===

89
    //    removeDirichletBcDofs(mat);
90
91
    

92
    // === Init PETSc solver. ===
93

94
95
96
97
98
99
100
    KSPCreate(mpiCommGlobal, &kspInterior);
    KSPGetPC(kspInterior, &pcInterior);
    KSPSetOperators(kspInterior, matIntInt, matIntInt, SAME_NONZERO_PATTERN); 
    KSPSetTolerances(kspInterior, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(kspInterior, KSPBCGS);
    KSPSetOptionsPrefix(kspInterior, kspPrefix.c_str());
    KSPSetFromOptions(kspInterior);
101

102
    initPreconditioner(pcInterior);
103

104
105
    // Do not delete the solution vector, use it for the initial guess.
    if (!zeroStartVector)
106
      KSPSetInitialGuessNonzero(kspInterior, PETSC_TRUE);
107

Thomas Witkowski's avatar
Thomas Witkowski committed
108
109
110
#if (DEBUG != 0)
    MSG("Fill petsc matrix 3 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif
111
112
113
  }


114
115
116
117
118
119
120
121
  void PetscSolverGlobalMatrix::fillPetscMatrix(DOFMatrix *mat)
  {
    Matrix<DOFMatrix*> m(1, 1);
    m[0][0] = mat;
    fillPetscMatrix(&m);
  }


122
123
124
125
126
127
128
129
130
  void PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace(Matrix<DOFMatrix*> *mat)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace()");
    
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);

    int nRowsRankInterior = interiorMap->getRankDofs();
    int nRowsOverallInterior = interiorMap->getOverallDofs();

131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
    // === If required, recompute non zero structure of the matrix. ===

    bool localMatrix = (subdomainLevel == 0);
    if (checkMeshChange(mat, localMatrix)) {
      createPetscNnzStructureWithCoarseSpace(mat, 
					     *interiorMap, 
					     matInteriorDiagNnz,
					     matInteriorOffdiagNnz,
					     localMatrix);

      if (coarseSpaceMap)
	createPetscNnzStructureWithCoarseSpace(mat, 
					       *coarseSpaceMap, 
					       matCoarseDiagNnz,
					       matCoarseOffdiagNnz);	
    }

    if (localMatrix) {
149
      MatCreateSeqAIJ(mpiCommLocal, nRowsRankInterior, nRowsRankInterior,
150
		      0, matInteriorDiagNnz, &matIntInt);
151
    } else {
152
153
154
      MatCreateAIJ(mpiCommLocal, 
		   nRowsRankInterior, nRowsRankInterior,
		   nRowsOverallInterior, nRowsOverallInterior,
155
156
		   0, matInteriorDiagNnz, 0, matInteriorOffdiagNnz, 
		   &matIntInt);
157
    }
158
    
159
160
161
162
    if (coarseSpaceMap) {
      int nRowsRankCoarse = coarseSpaceMap->getRankDofs();
      int nRowsOverallCoarse = coarseSpaceMap->getOverallDofs();

163
164
165
      MatCreateAIJ(mpiCommGlobal,
		   nRowsRankCoarse, nRowsRankCoarse,
		   nRowsOverallCoarse, nRowsOverallCoarse,
166
167
168
		   0, matCoarseDiagNnz, 0, matCoarseOffdiagNnz, 
		   &matCoarseCoarse);

169
170
171
      MatCreateAIJ(mpiCommGlobal,
		   nRowsRankCoarse, nRowsRankInterior,
		   nRowsOverallCoarse, nGlobalOverallInterior,
172
173
174
175
		   100, PETSC_NULL, 100, PETSC_NULL,
		   &matCoarseInt);
      MatSetOption(matCoarseInt, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);

176
177
178
      MatCreateAIJ(mpiCommGlobal,
		   nRowsRankInterior, nRowsRankCoarse,
		   nGlobalOverallInterior, nRowsOverallCoarse,
179
180
181
182
		   100, PETSC_NULL, 100, PETSC_NULL,
		   //	   0, matInteriorDiagNnz, 0, matCoarseOffdiagNnz,
		   &matIntCoarse);
      MatSetOption(matIntCoarse, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
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
243
244
245
246
247
248
249
250
251
252
253
254
255
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
    }

    // === Prepare traverse of sequentially created matrices. ===

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

    vector<int> cols, colsOther;
    vector<double> values, valuesOther;
    cols.reserve(300);
    colsOther.reserve(300);
    values.reserve(300);
    valuesOther.reserve(300);

    // === Traverse all sequentially created matrices and add the values to ===
    // === the global PETSc matrices.                                       ===

    int nComponents = mat->getSize();
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
	if (!(*mat)[i][j])
	  continue;

	traits::col<Matrix>::type col((*mat)[i][j]->getBaseMatrix());
	traits::const_value<Matrix>::type value((*mat)[i][j]->getBaseMatrix());
	
	// Traverse all rows.
	for (cursor_type cursor = begin<row>((*mat)[i][j]->getBaseMatrix()), 
	       cend = end<row>((*mat)[i][j]->getBaseMatrix()); cursor != cend; ++cursor) {

	  bool rowPrimal = isCoarseSpace(feSpaces[i], *cursor);
  
	  cols.clear();
	  colsOther.clear();
	  values.clear();	  
	  valuesOther.clear();

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

	    bool colPrimal = isCoarseSpace(feSpaces[j], col(*icursor));

	    if (colPrimal) {
	      if (rowPrimal) {
		cols.push_back(col(*icursor));
		values.push_back(value(*icursor));
	      } else {
		colsOther.push_back(col(*icursor));
		valuesOther.push_back(value(*icursor));
	      }
	    } else {
	      if (rowPrimal) {
		colsOther.push_back(col(*icursor));
		valuesOther.push_back(value(*icursor));
	      } else {
		cols.push_back(col(*icursor));
		values.push_back(value(*icursor));
	      }
	    }
	  }  // for each nnz in row


	  // === Set matrix values. ===

	  if (rowPrimal) {
	    int rowIndex = coarseSpaceMap->getMatIndex(i, *cursor);
	    for (unsigned int k = 0; k < cols.size(); k++)
	      cols[k] = coarseSpaceMap->getMatIndex(j, cols[k]);

	    MatSetValues(matCoarseCoarse, 1, &rowIndex, cols.size(),
			 &(cols[0]), &(values[0]), ADD_VALUES);

	    if (colsOther.size()) {
	      if (subdomainLevel == 0) {
		for (unsigned int k = 0; k < colsOther.size(); k++)
		  colsOther[k] = interiorMap->getMatIndex(j, colsOther[k]);
	      } else {
		for (unsigned int k = 0; k < colsOther.size(); k++)
		  colsOther[k] = 
		    interiorMap->getMatIndex(j, colsOther[k]) + rStartInterior;
	      }
 	      
	      MatSetValues(matCoarseInt, 1, &rowIndex, colsOther.size(),
 			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
	    }
	  } else {
	    int localRowIndex = 
	      (subdomainLevel == 0 ? interiorMap->getLocalMatIndex(i, *cursor) :
	       interiorMap->getMatIndex(i, *cursor));

	    for (unsigned int k = 0; k < cols.size(); k++) {
	      if (subdomainLevel == 0)
		cols[k] = interiorMap->getLocalMatIndex(j, cols[k]);
	      else
		cols[k] = interiorMap->getMatIndex(j, cols[k]);
	    }
	    
  	    MatSetValues(matIntInt, 1, &localRowIndex, cols.size(),
  			 &(cols[0]), &(values[0]), ADD_VALUES);

	    if (colsOther.size()) {
	      int globalRowIndex = interiorMap->getMatIndex(i, *cursor);

	      if (subdomainLevel != 0)
		globalRowIndex += rStartInterior;

	      for (unsigned int k = 0; k < colsOther.size(); k++)
		colsOther[k] = coarseSpaceMap->getMatIndex(j, colsOther[k]);

  	      MatSetValues(matIntCoarse, 1, &globalRowIndex, colsOther.size(),
  			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
	    }
	  }
	} 
      }
    }

    // === Start global assembly procedure. ===

    MatAssemblyBegin(matIntInt, MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(matIntInt, MAT_FINAL_ASSEMBLY);

    if (coarseSpaceMap) {
      MatAssemblyBegin(matCoarseCoarse, MAT_FINAL_ASSEMBLY);
      MatAssemblyEnd(matCoarseCoarse, MAT_FINAL_ASSEMBLY);
      
      MatAssemblyBegin(matIntCoarse, MAT_FINAL_ASSEMBLY);
      MatAssemblyEnd(matIntCoarse, MAT_FINAL_ASSEMBLY);
      
      MatAssemblyBegin(matCoarseInt, MAT_FINAL_ASSEMBLY);
      MatAssemblyEnd(matCoarseInt, MAT_FINAL_ASSEMBLY);
    }


322
323
    // === Remove Dirichlet BC DOFs. ===

324
    //    removeDirichletBcDofs(mat);
325

326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
    // === Create solver for the non primal (thus local) variables. ===

    KSPCreate(mpiCommLocal, &kspInterior);
    KSPSetOperators(kspInterior, matIntInt, matIntInt, SAME_NONZERO_PATTERN);
    KSPSetOptionsPrefix(kspInterior, "interior_");
    KSPSetType(kspInterior, KSPPREONLY);
    KSPGetPC(kspInterior, &pcInterior);
    PCSetType(pcInterior, PCLU);
    if (subdomainLevel == 0)
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERUMFPACK);
    else
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
    KSPSetFromOptions(kspInterior);  
  }


342
343
344
  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
Thomas Witkowski's avatar
Thomas Witkowski committed
345

Thomas Witkowski's avatar
Thomas Witkowski committed
346
347
348
349
    VecCreateMPI(mpiCommGlobal, 
		 interiorMap->getRankDofs(), 
		 nGlobalOverallInterior,
		 &rhsInterior);
350

Thomas Witkowski's avatar
Thomas Witkowski committed
351
352
353
354
355
356
    if (coarseSpaceMap) 
      VecCreateMPI(mpiCommGlobal, 
		   coarseSpaceMap->getRankDofs(), 
		   coarseSpaceMap->getOverallDofs(),
		   &rhsCoarseSpace);
    
357
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
358
    TEST_EXIT_DBG(interiorMap)("No parallel DOF map defined!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
359
    
360

Thomas Witkowski's avatar
Thomas Witkowski committed
361
    // === Transfer values from DOF vector to the PETSc vector. === 
Thomas Witkowski's avatar
Thomas Witkowski committed
362
    if (coarseSpaceMap) {
Thomas Witkowski's avatar
Thomas Witkowski committed
363
364
      for (int i = 0; i < vec->getSize(); i++)
	setDofVector(rhsInterior, rhsCoarseSpace, vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
365
366
367
368
    } else {
      for (int i = 0; i < vec->getSize(); i++)
	setDofVector(rhsInterior, vec->getDOFVector(i), i);
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
369

370
371
    VecAssemblyBegin(rhsInterior);
    VecAssemblyEnd(rhsInterior);
372

Thomas Witkowski's avatar
Thomas Witkowski committed
373
374
375
376
377
    if (coarseSpaceMap) {
      VecAssemblyBegin(rhsCoarseSpace);
      VecAssemblyEnd(rhsCoarseSpace);
    }

378
379
380

    // === Remove Dirichlet BC DOFs. ===
    //    removeDirichletBcDofs(vec);
Thomas Witkowski's avatar
Thomas Witkowski committed
381
 
Thomas Witkowski's avatar
Thomas Witkowski committed
382
383
384
  }


385
386
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
387
388
389
390
391
392
393
394
395
396
  {
    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++)
397
	setDofVector(petscSolVec, vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Thomas Witkowski committed
398
399
400
401
402
      
      VecAssemblyBegin(petscSolVec);
      VecAssemblyEnd(petscSolVec);
    }

403

Thomas Witkowski's avatar
Thomas Witkowski committed
404
405
    MatNullSpace matNullspace;
    Vec nullspaceBasis;
406

407
408
409
    if (nullspace.size() > 0 || 
	hasConstantNullspace ||
	constNullspaceComponent.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
410
      TEST_EXIT_DBG(nullspace.size() <= 1)("Not yet implemented!\n");
411

412
413
414
415
416
417
418
419
420
421
      if (constNullspaceComponent.size() > 0) {
	nullspace.clear();
	SystemVector *basisVec = new SystemVector(vec);
	basisVec->set(0.0);
	for (unsigned int i = 0; i < constNullspaceComponent.size(); i++)
	  basisVec->getDOFVector(constNullspaceComponent[i])->set(1.0);

	nullspace.push_back(basisVec);
      } 

Thomas Witkowski's avatar
Thomas Witkowski committed
422
423
424
425
426
427
428
      if (nullspace.size() > 0) {
	VecDuplicate(petscSolVec, &nullspaceBasis);
	for (int i = 0; i < nComponents; i++)
	  setDofVector(nullspaceBasis, nullspace[0]->getDOFVector(i), i, true);
	
	VecAssemblyBegin(nullspaceBasis);
	VecAssemblyEnd(nullspaceBasis);
429
430

	VecNormalize(nullspaceBasis, PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
431
432
433
434
435
436
437
438
439
440
441
	
	MatNullSpaceCreate(mpiCommGlobal, (hasConstantNullspace ? PETSC_TRUE : PETSC_FALSE), 
			   1, &nullspaceBasis, &matNullspace);

	MatMult(matIntInt, nullspaceBasis, petscSolVec);
	PetscReal n;
	VecNorm(petscSolVec, NORM_2, &n);
	MSG("NORM IS: %e\n", n);
      } else {
	MatNullSpaceCreate(mpiCommGlobal, PETSC_TRUE, 0, PETSC_NULL, &matNullspace);
      }
442

443
      MatSetNullSpace(matIntInt, matNullspace);
Thomas Witkowski's avatar
Thomas Witkowski committed
444
      KSPSetNullSpace(kspInterior, matNullspace);
445

Thomas Witkowski's avatar
Thomas Witkowski committed
446
      // === Remove null space, if requested. ===
447

Thomas Witkowski's avatar
Thomas Witkowski committed
448
449
450
451
452
453
454
455
      if (removeRhsNullspace) {
	TEST_EXIT_DBG(coarseSpaceMap == NULL)("Not supported!\n");
	
	MatNullSpaceRemove(matNullspace, rhsInterior, PETSC_NULL);
      }
    } else {
      TEST_EXIT(removeRhsNullspace == false)
	("No nullspace provided that should be removed from rhs!\n");
456
457
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
458

Thomas Witkowski's avatar
Thomas Witkowski committed
459
    // PETSc.
460
    solve(rhsInterior, petscSolVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
461

462
463

    if (nullspace.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
464
      MatNullSpaceDestroy(&matNullspace);
465
466
467
468
      VecDestroy(&nullspaceBasis);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
469
470
    // === Transfere values from PETSc's solution vectors to the DOF vectors. ===
    PetscScalar *vecPointer;
471
    VecGetArray(petscSolVec, &vecPointer);    
Thomas Witkowski's avatar
Thomas Witkowski committed
472

473
    int c = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
474
    for (int i = 0; i < nComponents; i++) {
475
      DOFVector<double> &dv = *(vec.getDOFVector(i));
476

477
      DofMap& d = (*interiorMap)[dv.getFeSpace()].getMap();
478
479
480
      for (DofMap::iterator it = d.begin(); it != d.end(); ++it)
	if (it->second.local != -1)
	  dv[it->first] = vecPointer[c++];
Thomas Witkowski's avatar
Thomas Witkowski committed
481
482
483
    }

    VecRestoreArray(petscSolVec, &vecPointer);
484
485
486
  }


487
488
489
490
  void PetscSolverGlobalMatrix::solveGlobal(Vec &rhs, Vec &sol)
  {
    FUNCNAME("PetscSolverGlobalMatrix::solveGlobal()");

491
492
493
    double wtime = MPI::Wtime();
    double t0 = 0.0, t1 = 0.0;

494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
    Vec tmp;
    if (mpiCommLocal.Get_size() == 1)
      VecCreateSeq(mpiCommLocal, interiorMap->getRankDofs(), &tmp);
    else
      VecCreateMPI(mpiCommLocal,
		   interiorMap->getRankDofs(),
		   interiorMap->getOverallDofs(),
		   &tmp);

    PetscScalar *tmpValues, *rhsValues;
    VecGetArray(tmp, &tmpValues);
    VecGetArray(rhs, &rhsValues);

    for (int i = 0; i < interiorMap->getRankDofs(); i++)
      tmpValues[i] = rhsValues[i];

    VecRestoreArray(rhs, &rhsValues);
    VecRestoreArray(tmp, &tmpValues);

513
514
515
    t0 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
516
    KSPSolve(kspInterior, tmp, tmp);
517
518
519
    t1 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
520
521
522
523
524
525
526
527
528
529
530

    VecGetArray(tmp, &tmpValues);
    VecGetArray(sol, &rhsValues);

    for (int i = 0; i < interiorMap->getRankDofs(); i++) 
      rhsValues[i] = tmpValues[i];

    VecRestoreArray(sol, &rhsValues);
    VecRestoreArray(tmp, &tmpValues);

    VecDestroy(&tmp);
531
532
    t0 += MPI::Wtime() - wtime;

533
    //    MSG("TIMEING: %.5f %.5f\n", t0, t1);
534
535
536
  }


537
538
539
540
  void PetscSolverGlobalMatrix::destroyMatrixData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyMatrixData()");

541
542
    exitPreconditioner(pcInterior);

543
544
    MatDestroy(&matIntInt);
    KSPDestroy(&kspInterior);
Thomas Witkowski's avatar
Thomas Witkowski committed
545

546
547
548
549
550
551
552
    if (coarseSpaceMap) {
      MatDestroy(&matCoarseCoarse);
      MatDestroy(&matCoarseInt);
      MatDestroy(&matIntCoarse);
    }

    if (petscSolVec != PETSC_NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
553
      VecDestroy(&petscSolVec);
554
555
      petscSolVec = PETSC_NULL;
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
556
557
558
  }


559
560
561
562
  void PetscSolverGlobalMatrix::destroyVectorData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyVectorData()");

563
    VecDestroy(&rhsInterior);
564
565
566

    if (coarseSpaceMap)
      VecDestroy(&rhsCoarseSpace);
567
568
569
  }


570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
  bool PetscSolverGlobalMatrix::checkMeshChange(Matrix<DOFMatrix*> *mat,
						bool localMatrix)
  {
    FUNCNAME("PetscSolverGlobalMatrix::checkMeshChange()");

    int recvAllValues = 0;
    int sendValue = 
      static_cast<int>(meshDistributor->getLastMeshChangeIndex() != lastMeshNnz);
    mpiCommGlobal.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);

    if (!matInteriorDiagNnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
      vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
      
      interiorMap->setComputeMatIndex(true, !localMatrix);
      interiorMap->update(feSpaces);

      if (matInteriorDiagNnz) {
	delete [] matInteriorDiagNnz;
	matInteriorDiagNnz = NULL;
      }
      
      if (matInteriorOffdiagNnz) {
	delete [] matInteriorOffdiagNnz;
	matInteriorOffdiagNnz = NULL;
      }

      if (matCoarseDiagNnz) {
	delete [] matCoarseDiagNnz;
	matCoarseDiagNnz = NULL;
      }
      
      if (matCoarseOffdiagNnz) {
	delete [] matCoarseOffdiagNnz;
	matCoarseOffdiagNnz = NULL;
      }

      updateSubdomainData();
      lastMeshNnz = meshDistributor->getLastMeshChangeIndex();

      return true;
    }

    return false;
  }


616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
  void PetscSolverGlobalMatrix::createFieldSplit(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::createFieldSplit()");

    vector<string> isNames;
    Parameters::get("parallel->solver->is blocks", isNames);

    int nBlocks = isNames.size();
    if (nBlocks == 0)
      return;

    for (int i = 0; i < nBlocks; i++) {
      MSG("Create for block %s\n", isNames[i].c_str());

      vector<int> blockComponents;
      Parameters::get("parallel->solver->is block " + lexical_cast<string>(i),
		      blockComponents);
      int nComponents = static_cast<int>(blockComponents.size());

      TEST_EXIT(nComponents > 0)("No is block for block %d defined!\n", i);

      // Check if blocks are continous
      for (int j = 0; j < nComponents; j++) {
	TEST_EXIT(blockComponents[j] == blockComponents[0] + j)
	  ("Does not yet support not continous IS blocks! Block %s\n", 
	   isNames[i].c_str());
      }

      IS is;
      interiorMap->createIndexSet(is, blockComponents[0], nComponents);
      PCFieldSplitSetIS(pc, isNames[i].c_str(), is);
      ISDestroy(&is);
    }
  }


652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
  void PetscSolverGlobalMatrix::initPreconditioner(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::initPreconditioner()");

    PCSetFromOptions(pc);
    createFieldSplit(pc);
  }

 
  void PetscSolverGlobalMatrix::exitPreconditioner(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::exitPreconditioner()");
  }


667
668
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* mat,
					     int nRowMat, int nColMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
669
670
671
672
673
674
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

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

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
675
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
    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;

691
692
693
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();

Thomas Witkowski's avatar
Thomas Witkowski committed
694
695
696
697
698
699
    const FiniteElemSpace *rowFe = mat->getRowFeSpace();
    const FiniteElemSpace *colFe = mat->getColFeSpace();
    DofMap& rowMap = (*interiorMap)[rowFe].getMap();
    DofMap& colMap = (*interiorMap)[colFe].getMap();

    // === Traverse all rows of the DOF matrix and insert row wise the values ===
Thomas Witkowski's avatar
Thomas Witkowski committed
700
701
702
703
704
    // === 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.
Thomas Witkowski's avatar
Thomas Witkowski committed
705
      int globalRowDof = rowMap[*cursor].global;
706

Thomas Witkowski's avatar
Thomas Witkowski committed
707
      // Test if the current row DOF is a periodic DOF.
708
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
709

Thomas Witkowski's avatar
Thomas Witkowski committed
710
711
712
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

713
	// Get PETSc's mat row index.
714
	int rowIndex = interiorMap->getMatIndex(nRowMat, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
715
716
717
718
719
720
721
722

	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.
Thomas Witkowski's avatar
Thomas Witkowski committed
723
	  int globalColDof = colMap[col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
724
	  // Test if the current col dof is a periodic dof.
725
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
726
	  // Get PETSc's mat col index.
727
	  int colIndex = interiorMap->getMatIndex(nColMat, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
728
729
730
731
732
733
734

	  // 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.
Thomas Witkowski's avatar
Thomas Witkowski committed
735
736
 	    cols.push_back(colIndex);
 	    values.push_back(value(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
737
738
739
740
741
	  } else {
	    // === Row index is not periodic, but column index is. ===

	    // Create set of all periodic associations of the column index.
	    std::set<int> perAsc;
742
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
743
744
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
745
	      if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
746
747
748
749
750
751
752
753
754
755
756
757
758
759
		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);
760

Thomas Witkowski's avatar
Thomas Witkowski committed
761
762
763
764
765
766
	    // 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++) {
767
 		TEST_EXIT_DBG(perMap.isPeriodic(colFe, *it, newCols[i]))
Thomas Witkowski's avatar
Thomas Witkowski committed
768
769
770
 		  ("Wrong periodic DOF associations at boundary %d with DOF %d!\n",
		   *it, newCols[i]);

771
		newCols.push_back(perMap.map(colFe, *it, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
772
773
774
775
	      }
	    }

	    for (unsigned int i = 0; i < newCols.size(); i++) {
776
	      cols.push_back(interiorMap->getMatIndex(nColMat, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
777
778
779
780
781
	      values.push_back(scaledValue);	      
	    }
	  }
	}

Thomas Witkowski's avatar
Thomas Witkowski committed
782
783
  	MatSetValues(matIntInt, 1, &rowIndex, cols.size(), 
  		     &(cols[0]), &(values[0]), ADD_VALUES);	
Thomas Witkowski's avatar
Thomas Witkowski committed
784
785
786
787
788
789
790
791
792
793
794
795
796
797
      } 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.
798
	  int globalColDof = (*interiorMap)[colFe][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
799
800
801
802
803
804
805
806
807
808

	  // 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;

809
810
	  if (perMap.isPeriodic(colFe, globalColDof)) {
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
811
812
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
813
	      if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
814
815
816
		perAsc.insert(*it);
	  }

817
	  std::set<int>& perRowAsc = perMap.getAssociations(rowFe, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
818
819
	  for (std::set<int>::iterator it = perRowAsc.begin(); 
	       it != perRowAsc.end(); ++it)
820
	    if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
	      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));

836
837
	  // Then, traverse the periodic associations of the row and column
	  // indices and create the corresponding entries.
Thomas Witkowski's avatar
Thomas Witkowski committed
838
839
840
841
	  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;
842

843
844
	      if (perMap.isPeriodic(rowFe, *it, entry[i].first))
		perRowDof = perMap.map(rowFe, *it, entry[i].first);
Thomas Witkowski's avatar
Thomas Witkowski committed
845
846
847
848
	      else
		perRowDof = entry[i].first;

	      int perColDof;
849
850
	      if (perMap.isPeriodic(colFe, *it, entry[i].second))
		perColDof = perMap.map(colFe, *it, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
851
852
853
854
855
856
857
858
859
860
	      else
		perColDof = entry[i].second;	      	      
	      
	      entry.push_back(make_pair(perRowDof, perColDof));
	    }
	  }


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

861
	  for (unsigned int i = 0; i < entry.size(); i++) {
862
863
	    int rowIdx = interiorMap->getMatIndex(nRowMat, entry[i].first);
	    int colIdx = interiorMap->getMatIndex(nColMat, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
864

865
866
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
867
868
869
870
871
872
873
874
875
876
877
878
	  }
	}


	// === 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;
879

880
	  MatSetValues(matIntInt, 1, &rowIndex, rowIt->second.size(),
Thomas Witkowski's avatar
Thomas Witkowski committed
881
882
883
884
885
886
887
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
888
889
  void PetscSolverGlobalMatrix::setDofVector(Vec vecInterior, 
					     Vec vecCoarse,
890
					     DOFVector<double>* vec, 
891
					     int nRowVec, 
892
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
893
894
895
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

896
    const FiniteElemSpace *feSpace = vec->getFeSpace();
897
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
898

Thomas Witkowski's avatar
Thomas Witkowski committed
899
900
901
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
902

903
      if (rankOnly && !(*interiorMap)[feSpace].isRankDof(dofIt.getDOFIndex()))
Thomas Witkowski's avatar
Thomas Witkowski committed
904
905
	continue;

906
      if (isCoarseSpace(feSpace, dofIt.getDOFIndex())) {
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
	TEST_EXIT_DBG(vecCoarse != PETSC_NULL)("Should not happen!\n");

	int index = coarseSpaceMap->getMatIndex(nRowVec, dofIt.getDOFIndex());
	VecSetValue(vecCoarse, index, *dofIt, ADD_VALUES);
      } else {
	// Calculate global row index of the DOF.
	DegreeOfFreedom globalRowDof = 
	  (*interiorMap)[feSpace][dofIt.getDOFIndex()].global;
	
	// Get PETSc's mat index of the row DOF.
	int index = 0;
	if (interiorMap->isMatIndexFromGlobal())
	  index = 
	    interiorMap->getMatIndex(nRowVec, globalRowDof) + rStartInterior;
	else
	  index =
	    interiorMap->getMatIndex(nRowVec, dofIt.getDOFIndex()) + rStartInterior;
924

925
	if (perMap.isPeriodic(feSpace, globalRowDof)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
926
927
928
	  std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
	  double value = *dofIt / (perAsc.size() + 1.0);
	  VecSetValue(vecInterior, index, value, ADD_VALUES);
929

Thomas Witkowski's avatar
Thomas Witkowski committed
930
931
932
933
	  for (std::set<int>::iterator perIt = perAsc.begin(); 
	       perIt != perAsc.end(); ++perIt) {
	    int mappedDof = perMap.map(feSpace, *perIt, globalRowDof);
	    int mappedIndex = interiorMap->getMatIndex(nRowVec, mappedDof);
934

Thomas Witkowski's avatar
Thomas Witkowski committed
935
	    VecSetValue(vecInterior, mappedIndex, value, ADD_VALUES);
936
937
938
939
	  }	  
	} else {	  
	  // The DOF index is not periodic.
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
940
941
	  VecSetValue(vecInterior, index, *dofIt, ADD_VALUES);
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
942
943
944
945
946
      }
    }
  }


947
948
949
950
  void PetscSolverGlobalMatrix::removeDirichletBcDofs(Matrix<DOFMatrix*> *mat)
  {
    FUNCNAME("PetscSolverGlobalMatrix::removeDirichletBcDofs()");

Thomas Witkowski's avatar
Thomas Witkowski committed
951
#if 0
952
953
954
955
    vector<int> dofsInterior, dofsCoarse;

    int nComponents = mat->getNumRows();
    for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
      for (int j = 0; j < nComponents; j++) {
	if ((*mat)[i][j]) {
	  const FiniteElemSpace *feSpace = (*mat)[i][j]->getRowFeSpace();
	    
	  std::set<DegreeOfFreedom> &dirichletDofs = *((*mat)[i][j]->getApplyDBCs());

	  MSG("DIRICHLET DOFS: %d %d -> %d\n", i, j, dirichletDofs.size());
	  
	  for (std::set<DegreeOfFreedom>::iterator it = dirichletDofs.begin();
	       it != dirichletDofs.end(); ++it) {
	    if (isCoarseSpace(feSpace, *it)) {
	      if ((*coarseSpaceMap)[feSpace].isRankDof(*it)) {
		int globalDof = (*coarseSpaceMap)[feSpace][*it].global;
		dofsCoarse.push_back(coarseSpaceMap->getMatIndex(i, globalDof));
	      }
	    } else {
	      if ((*interiorMap)[feSpace].isRankDof(*it)) {
		int globalDof = (*interiorMap)[feSpace][*it].global;
		dofsInterior.push_back(interiorMap->getMatIndex(i, globalDof));
	      }
976
	    }
977
	  }
Thomas Witkowski's avatar
Thomas Witkowski committed
978
979
	} else {
	  MSG("NO MAT DIAG in %d\n", i);
980
981
982
983
984
985
986
987
988
989
	}
      }
    }

    MatZeroRows(matIntInt, dofsInterior.size(), &(dofsInterior[0]), 1.0, 
		PETSC_NULL, PETSC_NULL);

    if (coarseSpaceMap != NULL)
      MatZeroRows(matCoarseCoarse, dofsCoarse.size(), &(dofsCoarse[0]), 1.0, 
		  PETSC_NULL, PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
990
#endif
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
  }


  void PetscSolverGlobalMatrix::removeDirichletBcDofs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::removeDirichletBcDofs()");

    int nComponents = vec->getSize();
    for (int i = 0; i < nComponents; i++) {
      const FiniteElemSpace *feSpace = vec->getDOFVector(i)->getFeSpace();

      map<DegreeOfFreedom, double> &dirichletValues = 
	vec->getDOFVector(i)->getDirichletValues();

      for (map<DegreeOfFreedom, double>::iterator it = dirichletValues.begin();
	   it != dirichletValues.end(); ++it) {
	if (isCoarseSpace(feSpace, it->first)) {
1008
1009
1010
	  if ((*coarseSpaceMap)[feSpace].isRankDof(it->first)) {
	    int globalDof = (*coarseSpaceMap)[feSpace][it->first].global;
	    VecSetValue(rhsCoarseSpace, coarseSpaceMap->getMatIndex(i, globalDof), 
1011
			it->second, INSERT_VALUES);
1012
	  }
1013
1014
	} else {
	  if ((*interiorMap)[feSpace].isRankDof(it->first)) {
1015
1016
	    int globalDof = (*interiorMap)[feSpace][it->first].global;
	    VecSetValue(rhsInterior, interiorMap->getMatIndex(i, globalDof),
1017
1018
1019
1020
1021
			it->second, INSERT_VALUES);	    
	  }
	}
      }
    }
1022
1023
1024
1025
1026
1027
1028
1029

    VecAssemblyBegin(rhsInterior);
    VecAssemblyEnd(rhsInterior);

    if (coarseSpaceMap) {
      VecAssemblyBegin(rhsCoarseSpace);
      VecAssemblyEnd(rhsCoarseSpace);
    }
1030
1031
1032
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
1033
1034
1035
1036
  void PetscSolverGlobalMatrix::createPetscNnzStructure(Matrix<DOFMatrix*> *mat)
  {
    FUNCNAME("PetscSolverGlobalMatrix::createPetscNnzStructure()");

1037
    TEST_EXIT_DBG(!matInteriorDiagNnz)("There is something wrong!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
1038

1039
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
1040
1041
    int nRankRows = interiorMap->getRankDofs();
    int rankStartIndex = interiorMap->getStartDofs();
1042

1043
1044
    matInteriorDiagNnz = new int[nRankRows];
    matInteriorOffdiagNnz = new int[nRankRows];
Thomas Witkowski's avatar
Thomas Witkowski committed
1045
    for (int i = 0; i < nRankRows; i++) {
1046
1047
      matInteriorDiagNnz[i] = 0;
      matInteriorOffdiagNnz[i] = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
1048
1049
1050
1051
1052
1053
1054
1055
    }

    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;

1056
1057
1058
1059
    // 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
1060
1061
1062
1063
    map<int, MatrixNnzEntry> sendMatrixEntry;

    // Maps to each DOF that must be send to another rank the rank number of the
    // receiving rank.
1064
    map<pair<DegreeOfFreedom, int>, int> sendDofToRank;
Thomas Witkowski's avatar
Thomas Witkowski committed
1065

1066

1067
1068
1069
    // 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++) {
1070
      for (DofComm::Iterator it(meshDistributor->getDofComm().getRecvDofs(), feSpaces[i]);
1071
1072
1073
1074
1075
1076
	   !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
1077
1078
    }

1079
    // Create list of ranks from which we receive data from.
Thomas Witkowski's avatar
Thomas Witkowski committed
1080
    std::set<int> recvFromRank;
1081
    for (unsigned int i = 0; i < feSpaces.size(); i++) 
1082
      for (DofComm::Iterator it(meshDistributor->getDofComm().getSendDofs(), feSpaces[i]);
1083
1084
1085
1086
1087
	   !it.end(); it.nextRank())
	recvFromRank.insert(it.getRank());


    // === Traverse matrices to create nnz data. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
1088

1089
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
1090
1091
1092
1093
1094
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
 	if (!(*mat)[i][j])
	  continue;

1095
1096
1097
1098
1099
	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
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
	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) {
1110
	  int globalRowDof = (*interiorMap)[feSpaces[i]][*cursor].global;
1111

1112
	  // The corresponding global matrix row index of the current row DOF.
1113
1114
	  int petscRowIdx = interiorMap->getMatIndex(i, globalRowDof);
	  if ((*interiorMap)[feSpaces[i]].isRankDof(*cursor)) {
1115
    	    
1116
1117
	    // === 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
1118
1119
	    
	    // This is the local row index of the local PETSc matrix.
1120
	    int localPetscRowIdx = petscRowIdx - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
1121
1122
	    
	    TEST_EXIT_DBG(localPetscRowIdx >= 0 && localPetscRowIdx < nRankRows)
1123
	      ("Should not happen! \n Debug info: DOF = %d   globalRowIndx = %d   petscRowIdx = %d   localPetscRowIdx = %d   rStart = %d   compontens = %d from %d   nRankRows = %d\n",
1124
	       *cursor,
1125
	       (*interiorMap)[feSpaces[i]][*cursor].global,
Thomas Witkowski's avatar
Thomas Witkowski committed
1126
1127
	       petscRowIdx, 
	       localPetscRowIdx, 
1128
	       rankStartIndex,
1129
	       i,
Thomas Witkowski's avatar
Thomas Witkowski committed
1130
1131
1132
1133
1134
1135
1136
	       nComponents, 
	       nRankRows);
	    
	    
	    // Traverse all non zero entries in this row.
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
1137
1138
	      int globalColDof = (*interiorMap)[feSpaces[j]][col(*icursor)].global;
	      int petscColIdx = interiorMap->getMatIndex(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
1139
1140
1141
	      
	      if (value(*icursor) != 0.0 || petscRowIdx == petscColIdx) {
		// The row DOF is a rank DOF, if also the column is a rank DOF, 
1142
1143
		// increment the matInteriorDiagNnz values for this row, 
		// otherwise the matInteriorDiagNnz value.
1144
1145
		if (petscColIdx >= rankStartIndex && 
		    petscColIdx < rankStartIndex + nRankRows)
1146
		  matInteriorDiagNnz[localPetscRowIdx]++;
Thomas Witkowski's avatar
Thomas Witkowski committed
1147
		else
1148
		  matInteriorOffdiagNnz[localPetscRowIdx]++;
Thomas Witkowski's avatar
Thomas Witkowski committed
1149
1150
1151
	      }    
	    }
	  } else {
1152
1153
1154
1155
1156
	    // === 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
1157
1158
	    
	    // Send all non zero entries to the member of the row DOF.
1159
	    int sendToRank = sendDofToRank[make_pair(*cursor, i)];
Thomas Witkowski's avatar
Thomas Witkowski committed
1160
1161
1162
1163
	    
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
	      if (value(*icursor) != 0.0) {
1164
		int globalColDof = 
1165
1166
		  (*interiorMap)[feSpaces[j]][col(*icursor)].global;
		int petscColIdx = interiorMap->getMatIndex(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
		
		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. ===

1180
    StdMpi<MatrixNnzEntry> stdMpi(mpiCommGlobal, true);
Thomas Witkowski's avatar
Thomas Witkowski committed
1181
1182
1183
1184
1185
1186
1187
    stdMpi.send(sendMatrixEntry);
    for (std::set<int>::iterator it = recvFromRank.begin(); 
	 it != recvFromRank.end(); ++it)
      stdMpi.recv(*it);
    stdMpi.startCommunication();


1188
1189
    // === 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
1190
1191
1192
1193
1194
1195
1196
1197

    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;

1198
	  int localRowIdx = r - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
1199
1200
1201
1202
1203

	  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);
	  
1204
	  if (c < rankStartIndex || c >= rankStartIndex + nRankRows)
1205
	    matInteriorOffdiagNnz[localRowIdx]++;
Thomas Witkowski's avatar
Thomas Witkowski committed
1206
	  else
1207
	    matInteriorDiagNnz[localRowIdx]++;
Thomas Witkowski's avatar
Thomas Witkowski committed
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
	}
      }
    }

    // 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