PetscSolverGlobalMatrix.cc 22.7 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 {

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

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
24
25
26
27
28
29
    TEST_EXIT_DBG(meshDistributor)("No mesh distributor object defined!\n");
    TEST_EXIT_DBG(interiorMap)("No parallel mapping object defined!\n");
    TEST_EXIT_DBG(seqMat)("No DOF matrix defined!\n");
    
    double wtime = MPI::Wtime();

30
    createMatVec(*seqMat);
31

Thomas Witkowski's avatar
Thomas Witkowski committed
32
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
33
      fillPetscMatrixWithCoarseSpace(seqMat);
34
35
36
      return;
    }

37
38
    // === Create PETSc vector (solution and a temporary vector). ===

Thomas Witkowski's avatar
Thomas Witkowski committed
39
40
41
42
43
44
#if (DEBUG != 0)
    MSG("Fill petsc matrix 1 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

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

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
45
    int nComponents = seqMat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
46
47
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
48
49
	if ((*seqMat)[i][j])
	  setDofMatrix((*seqMat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
50
51
52
53
54

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

55
    matAssembly();
56
57
58
    
    if (printMatInfo) {
      MatInfo matInfo;
59
      MatGetInfo(getMatInterior(), MAT_GLOBAL_SUM, &matInfo);
60
61
62
63
64
65
66
      MSG("Matrix info:\n");
      MSG("  memory usage: %e MB\n", matInfo.memory / (1024.0 * 1024.0));
      MSG("  mallocs: %d\n", static_cast<int>(matInfo.mallocs));
      MSG("  nz allocated: %d\n", static_cast<int>(matInfo.nz_allocated));
      MSG("  nz used: %d\n", static_cast<int>(matInfo.nz_used));
      MSG("  nz unneeded: %d\n", static_cast<int>(matInfo.nz_unneeded));
    }
67

68
    // === Init PETSc solver. ===
69

70
71
    KSPCreate(mpiCommGlobal, &kspInterior);
    KSPGetPC(kspInterior, &pcInterior);
72
    KSPSetOperators(kspInterior, getMatInterior(), getMatInterior(), 
73
		    SAME_NONZERO_PATTERN); 
74
75
76
77
    KSPSetTolerances(kspInterior, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(kspInterior, KSPBCGS);
    KSPSetOptionsPrefix(kspInterior, kspPrefix.c_str());
    KSPSetFromOptions(kspInterior);
78

79
    initPreconditioner(pcInterior);
80

81
82
    // Do not delete the solution vector, use it for the initial guess.
    if (!zeroStartVector)
83
      KSPSetInitialGuessNonzero(kspInterior, PETSC_TRUE);
84

Thomas Witkowski's avatar
Thomas Witkowski committed
85
86
87
#if (DEBUG != 0)
    MSG("Fill petsc matrix 3 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif
88
89
90
  }


91
92
93
94
95
96
97
98
  void PetscSolverGlobalMatrix::fillPetscMatrix(DOFMatrix *mat)
  {
    Matrix<DOFMatrix*> m(1, 1);
    m[0][0] = mat;
    fillPetscMatrix(&m);
  }


Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
99
  void PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace(Matrix<DOFMatrix*> *seqMat)
100
101
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace()");
102
103

    TEST_EXIT_DBG(interiorMap)("Should not happen!\n");
104
105
    TEST_EXIT_DBG(coarseSpaceMap.size() == seqMat->getSize())
      ("Wrong sizes %d %d\n", coarseSpaceMap.size(), seqMat->getSize());
106

107
    vector<const FiniteElemSpace*> feSpaces = AMDiS::getComponentFeSpaces(*seqMat);
Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
108

109
110
    int nRowsRankInterior = interiorMap->getRankDofs();
    int nRowsOverallInterior = interiorMap->getOverallDofs();
111

112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
    // === 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.                                       ===

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
131
    int nComponents = seqMat->getSize();
Thomas Witkowski's avatar
Thomas Witkowski committed
132
133
134
135
136
    for (int rowComponent = 0; rowComponent < nComponents; rowComponent++) {
      for (int colComponent = 0; colComponent < nComponents; colComponent++) {
	DOFMatrix* dofMat = (*seqMat)[rowComponent][colComponent];

	if (!dofMat)
137
138
	  continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
139
140
	ParallelDofMapping *rowCoarseSpace = coarseSpaceMap[rowComponent];
	ParallelDofMapping *colCoarseSpace = coarseSpaceMap[colComponent];
Thomas Witkowski's avatar
Thomas Witkowski committed
141

Thomas Witkowski's avatar
Thomas Witkowski committed
142
143
	traits::col<Matrix>::type col(dofMat->getBaseMatrix());
	traits::const_value<Matrix>::type value(dofMat->getBaseMatrix());
144
145
	
	// Traverse all rows.
Thomas Witkowski's avatar
Thomas Witkowski committed
146
147
	for (cursor_type cursor = begin<row>(dofMat->getBaseMatrix()), 
	       cend = end<row>(dofMat->getBaseMatrix()); cursor != cend; ++cursor) {
148

Thomas Witkowski's avatar
Thomas Witkowski committed
149
150
	  bool isRowCoarse = 
	    isCoarseSpace(rowComponent, feSpaces[colComponent], *cursor);
151
152
153
154
155
156
157
158
159
160
  
	  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) {

Thomas Witkowski's avatar
Thomas Witkowski committed
161
162
	    bool isColCoarse = 
	      isCoarseSpace(colComponent, feSpaces[colComponent], col(*icursor));
163

Thomas Witkowski's avatar
Thomas Witkowski committed
164
165
	    if (isColCoarse) {
	      if (isRowCoarse) {
166
167
168
169
170
171
172
		cols.push_back(col(*icursor));
		values.push_back(value(*icursor));
	      } else {
		colsOther.push_back(col(*icursor));
		valuesOther.push_back(value(*icursor));
	      }
	    } else {
Thomas Witkowski's avatar
Thomas Witkowski committed
173
	      if (isRowCoarse) {
174
175
176
177
178
179
180
181
182
183
184
185
		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. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
186
	  if (isRowCoarse) {
Thomas Witkowski's avatar
Thomas Witkowski committed
187
188
189
	    int rowIndex = rowCoarseSpace->getMatIndex(rowComponent, *cursor);
	    for (unsigned int i = 0; i < cols.size(); i++)
	      cols[i] = colCoarseSpace->getMatIndex(colComponent, cols[i]);
190

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
191
	    // matCoarseCoarse
Thomas Witkowski's avatar
Thomas Witkowski committed
192
	    MatSetValues(getMatCoarseByComponent(rowComponent),
Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
193
			 1, &rowIndex, cols.size(),
194
195
196
197
			 &(cols[0]), &(values[0]), ADD_VALUES);

	    if (colsOther.size()) {
	      if (subdomainLevel == 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
198
199
200
		for (unsigned int i = 0; i < colsOther.size(); i++)
		  colsOther[i] = 
		    interiorMap->getMatIndex(colComponent, colsOther[i]);
201
	      } else {
Thomas Witkowski's avatar
Thomas Witkowski committed
202
203
204
205
		for (unsigned int i = 0; i < colsOther.size(); i++)
		  colsOther[i] = 
		    interiorMap->getMatIndex(colComponent, colsOther[i]) + 
		    rStartInterior;
206
	      }
207

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
208
	      // matCoarseInt
Thomas Witkowski's avatar
Thomas Witkowski committed
209
	      MatSetValues(getMatCoarseInteriorByComponent(rowComponent), 
Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
210
			   1, &rowIndex, colsOther.size(),
211
212
213
214
 			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
	    }
	  } else {
	    int localRowIndex = 
Thomas Witkowski's avatar
Thomas Witkowski committed
215
216
217
	      (subdomainLevel == 0 ? 
	       interiorMap->getLocalMatIndex(rowComponent, *cursor) :
	       interiorMap->getMatIndex(rowComponent, *cursor));
218

Thomas Witkowski's avatar
Thomas Witkowski committed
219
	    for (unsigned int i = 0; i < cols.size(); i++) {
220
	      if (subdomainLevel == 0)
Thomas Witkowski's avatar
Thomas Witkowski committed
221
		cols[i] = interiorMap->getLocalMatIndex(colComponent, cols[i]);
222
	      else
Thomas Witkowski's avatar
Thomas Witkowski committed
223
		cols[i] = interiorMap->getMatIndex(colComponent, cols[i]);
224
225
	    }
	    
226
  	    MatSetValues(getMatInterior(), 1, &localRowIndex, cols.size(),
227
228
229
  			 &(cols[0]), &(values[0]), ADD_VALUES);

	    if (colsOther.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
230
	      int globalRowIndex = interiorMap->getMatIndex(rowComponent, *cursor);
231
232
233
234

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

Thomas Witkowski's avatar
Thomas Witkowski committed
235
236
237
	      for (unsigned int i = 0; i < colsOther.size(); i++)
		colsOther[i] = 
		  colCoarseSpace->getMatIndex(colComponent, colsOther[i]);
238

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
239
	      // matIntCoarse
Thomas Witkowski's avatar
Thomas Witkowski committed
240
  	      MatSetValues(getMatInteriorCoarseByComponent(rowComponent), 
Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
241
			   1, &globalRowIndex, colsOther.size(),
242
243
244
245
246
247
248
  			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
	    }
	  }
	} 
      }
    }

249
    matAssembly();
250

251
252
253
    // === Create solver for the non primal (thus local) variables. ===

    KSPCreate(mpiCommLocal, &kspInterior);
254
    KSPSetOperators(kspInterior, getMatInterior(), getMatInterior(),
255
		    SAME_NONZERO_PATTERN);
256
257
258
259
260
261
262
263
264
265
266
267
    KSPSetOptionsPrefix(kspInterior, "interior_");
    KSPSetType(kspInterior, KSPPREONLY);
    KSPGetPC(kspInterior, &pcInterior);
    PCSetType(pcInterior, PCLU);
    if (subdomainLevel == 0)
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERUMFPACK);
    else
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
    KSPSetFromOptions(kspInterior);  
  }


268
269
270
  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
Thomas Witkowski's avatar
Thomas Witkowski committed
271

272
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
273
    TEST_EXIT_DBG(interiorMap)("No parallel DOF map defined!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
274
    
Thomas Witkowski's avatar
Thomas Witkowski committed
275
    // === Transfer values from DOF vector to the PETSc vector. === 
Thomas Witkowski's avatar
Thomas Witkowski committed
276
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
277
      for (int i = 0; i < vec->getSize(); i++)
278
	setDofVector(getVecRhsInterior(), getVecRhsCoarse(), vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
279
280
    } else {
      for (int i = 0; i < vec->getSize(); i++)
281
	setDofVector(getVecRhsInterior(), vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
282
283
    }

284
    vecRhsAssembly();
Thomas Witkowski's avatar
Thomas Witkowski committed
285
286
287
  }


288
289
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
290
291
292
293
294
295
296
  {
    FUNCNAME("PetscSolverGlobalMatrix::solvePetscMatrix()");

    int nComponents = vec.getSize();

    // === Set old solution to be initiual guess for PETSc solver. ===
    if (!zeroStartVector) {
Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
297
298
      TEST_EXIT(coarseSpaceMap.size() == 0)("Not yet supported!\n");

299
      VecSet(getVecSolInterior(), 0.0);
Thomas Witkowski's avatar
Thomas Witkowski committed
300
301
      
      for (int i = 0; i < nComponents; i++)
302
	setDofVector(getVecSolInterior(), vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
303

304
      vecSolAssembly();
Thomas Witkowski's avatar
Thomas Witkowski committed
305
306
    }

307

Thomas Witkowski's avatar
Thomas Witkowski committed
308
309
    MatNullSpace matNullspace;
    Vec nullspaceBasis;
310
311
312
    if (nullspace.size() > 0 || 
	hasConstantNullspace ||
	constNullspaceComponent.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
313
      TEST_EXIT_DBG(nullspace.size() <= 1)("Not yet implemented!\n");
314

315
316
317
318
319
320
321
322
323
324
      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
325
      if (nullspace.size() > 0) {
326
	VecDuplicate(getVecSolInterior(), &nullspaceBasis);
Thomas Witkowski's avatar
Thomas Witkowski committed
327
328
329
330
331
	for (int i = 0; i < nComponents; i++)
	  setDofVector(nullspaceBasis, nullspace[0]->getDOFVector(i), i, true);
	
	VecAssemblyBegin(nullspaceBasis);
	VecAssemblyEnd(nullspaceBasis);
332
333

	VecNormalize(nullspaceBasis, PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
334
335
336
337
	
	MatNullSpaceCreate(mpiCommGlobal, (hasConstantNullspace ? PETSC_TRUE : PETSC_FALSE), 
			   1, &nullspaceBasis, &matNullspace);

338
	MatMult(getMatInterior(), nullspaceBasis, getVecSolInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
339
	PetscReal n;
340
	VecNorm(getVecSolInterior(), NORM_2, &n);
Thomas Witkowski's avatar
Thomas Witkowski committed
341
342
343
344
	MSG("NORM IS: %e\n", n);
      } else {
	MatNullSpaceCreate(mpiCommGlobal, PETSC_TRUE, 0, PETSC_NULL, &matNullspace);
      }
345

346
      MatSetNullSpace(getMatInterior(), matNullspace);
Thomas Witkowski's avatar
Thomas Witkowski committed
347
      KSPSetNullSpace(kspInterior, matNullspace);
348

Thomas Witkowski's avatar
Thomas Witkowski committed
349
      // === Remove null space, if requested. ===
350

Thomas Witkowski's avatar
Thomas Witkowski committed
351
      if (removeRhsNullspace) {
Thomas Witkowski's avatar
Thomas Witkowski committed
352
	TEST_EXIT_DBG(coarseSpaceMap.empty())("Not supported!\n");
353
354

	MSG("Remove nullspace from rhs vector.\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
355
	
356
	MatNullSpaceRemove(matNullspace, getVecRhsInterior(), PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
357
358
359
360
      }
    } else {
      TEST_EXIT(removeRhsNullspace == false)
	("No nullspace provided that should be removed from rhs!\n");
361
362
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
363
    // PETSc.
364
    solve(getVecRhsInterior(), getVecSolInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
365

366
367

    if (nullspace.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
368
      MatNullSpaceDestroy(&matNullspace);
369
370
371
372
      VecDestroy(&nullspaceBasis);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
373
374
    // === Transfere values from PETSc's solution vectors to the DOF vectors. ===
    PetscScalar *vecPointer;
375
    VecGetArray(getVecSolInterior(), &vecPointer);    
Thomas Witkowski's avatar
Thomas Witkowski committed
376

377
    int c = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
378
    for (int i = 0; i < nComponents; i++) {
379
      DOFVector<double> &dv = *(vec.getDOFVector(i));
380

381
      DofMap& d = (*interiorMap)[dv.getFeSpace()].getMap();
382
383
384
      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
385
386
    }

387
    VecRestoreArray(getVecSolInterior(), &vecPointer);
Thomas Witkowski's avatar
Thomas Witkowski committed
388
389
390
391

    // === Synchronize DOFs at common DOFs, i.e., DOFs that correspond to ===  
    // === more than one partition.                                       ===  
    meshDistributor->synchVector(vec);
392
393
394
  }


395
396
397
398
  void PetscSolverGlobalMatrix::solveGlobal(Vec &rhs, Vec &sol)
  {
    FUNCNAME("PetscSolverGlobalMatrix::solveGlobal()");

399
400
401
    double wtime = MPI::Wtime();
    double t0 = 0.0, t1 = 0.0;

402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
    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);

421
422
423
    t0 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
424
    KSPSolve(kspInterior, tmp, tmp);
425
426
427
    t1 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
428
429
430
431
432
433
434
435
436
437
438

    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);
439
440
    t0 += MPI::Wtime() - wtime;

441
    //    MSG("TIMEING: %.5f %.5f\n", t0, t1);
442
443
444
  }


445
446
447
448
  void PetscSolverGlobalMatrix::destroyMatrixData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyMatrixData()");

449
450
    exitPreconditioner(pcInterior);

451
    matDestroy();
Thomas Witkowski's avatar
Thomas Witkowski committed
452

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
453
    KSPDestroy(&kspInterior);
Thomas Witkowski's avatar
Thomas Witkowski committed
454
455
456
  }


457
458
459
460
  void PetscSolverGlobalMatrix::destroyVectorData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyVectorData()");

461
    vecDestroy();
462
463
464
  }


465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
  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);
    }
  }


501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
  void PetscSolverGlobalMatrix::initPreconditioner(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::initPreconditioner()");

    PCSetFromOptions(pc);
    createFieldSplit(pc);
  }

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


Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
516
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* seqMat,
517
					     int nRowMat, int nColMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
518
519
520
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
521
    TEST_EXIT(seqMat)("No DOFMatrix!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
522
523

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
524
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
525
526
    typedef DOFMatrix::base_matrix_type Matrix;

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
527
528
    traits::col<Matrix>::type col(seqMat->getBaseMatrix());
    traits::const_value<Matrix>::type value(seqMat->getBaseMatrix());
Thomas Witkowski's avatar
Thomas Witkowski committed
529
530
531
532
533
534
535
536
537
538
539

    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;

540
541
542
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
543
544
    const FiniteElemSpace *rowFe = seqMat->getRowFeSpace();
    const FiniteElemSpace *colFe = seqMat->getColFeSpace();
Thomas Witkowski's avatar
Thomas Witkowski committed
545
546
547
548
    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
549
550
    // === to the PETSc matrix.                                               ===

Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
551
552
    for (cursor_type cursor = begin<row>(seqMat->getBaseMatrix()), 
	   cend = end<row>(seqMat->getBaseMatrix()); cursor != cend; ++cursor) {
Thomas Witkowski's avatar
Thomas Witkowski committed
553
      // Global index of the current row DOF.
Thomas Witkowski's avatar
Thomas Witkowski committed
554
      int globalRowDof = rowMap[*cursor].global;
555

Thomas Witkowski's avatar
Thomas Witkowski committed
556
      // Test if the current row DOF is a periodic DOF.
557
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
558

Thomas Witkowski's avatar
Thomas Witkowski committed
559
560
561
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

562
	// Get PETSc's mat row index.
563
	int rowIndex = interiorMap->getMatIndex(nRowMat, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
564
565
566
567
568
569
570
571

	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
572
	  int globalColDof = colMap[col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
573
	  // Test if the current col dof is a periodic dof.
574
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
575
	  // Get PETSc's mat col index.
576
	  int colIndex = interiorMap->getMatIndex(nColMat, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
577
578
579
580
581
582
583

	  // 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
584
585
 	    cols.push_back(colIndex);
 	    values.push_back(value(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
586
587
588
589
590
	  } else {
	    // === Row index is not periodic, but column index is. ===

	    // Create set of all periodic associations of the column index.
	    std::set<int> perAsc;
591
592
593
	    perMap.fillAssociations(colFe, globalColDof, 
				    meshDistributor->getElementObjectDb(), perAsc);

Thomas Witkowski's avatar
Thomas Witkowski committed
594
595
596
597
598
599
600
601
602
	    // 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;
603
	    perMap.mapDof(colFe, globalColDof, perAsc, newCols);
Thomas Witkowski's avatar
Thomas Witkowski committed
604
	    for (unsigned int i = 0; i < newCols.size(); i++) {
605
	      cols.push_back(interiorMap->getMatIndex(nColMat, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
606
607
608
609
610
	      values.push_back(scaledValue);	      
	    }
	  }
	}

611
  	MatSetValues(getMatInterior(), 1, &rowIndex, cols.size(), 
Thomas Witkowski's avatar
Thomas Witkowski committed
612
  		     &(cols[0]), &(values[0]), ADD_VALUES);	
Thomas Witkowski's avatar
Thomas Witkowski committed
613
614
615
616
617
618
619
620
621
622
623
624
625
626
      } 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.
627
	  int globalColDof = (*interiorMap)[colFe][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
628
629
630
631
632
633
634
635
636

	  // 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;
637
638
639
640
	  perMap.fillAssociations(colFe, globalColDof, 
				  meshDistributor->getElementObjectDb(), perAsc);
	  perMap.fillAssociations(rowFe, globalRowDof, 
				  meshDistributor->getElementObjectDb(), perAsc);
Thomas Witkowski's avatar
Thomas Witkowski committed
641
642
643
644
645
646
647
648
649
650

	  // 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;
Thomas Witkowski's avatar
Blbu    
Thomas Witkowski committed
651
652
	  perMap.mapDof(rowFe, colFe, make_pair(globalRowDof, globalColDof),
			perAsc, entry);
Thomas Witkowski's avatar
Thomas Witkowski committed
653
654
655

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

656
	  for (unsigned int i = 0; i < entry.size(); i++) {
657
658
	    int rowIdx = interiorMap->getMatIndex(nRowMat, entry[i].first);
	    int colIdx = interiorMap->getMatIndex(nColMat, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
659

660
661
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
662
663
664
665
666
667
668
669
670
671
672
673
	  }
	}


	// === 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;
674

675
	  MatSetValues(getMatInterior(), 1, &rowIndex, rowIt->second.size(),
Thomas Witkowski's avatar
Thomas Witkowski committed
676
677
678
679
680
681
682
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
683
684
  void PetscSolverGlobalMatrix::setDofVector(Vec vecInterior, 
					     Vec vecCoarse,
685
					     DOFVector<double>* vec, 
686
					     int nRowVec, 
687
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
688
689
690
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

691
    const FiniteElemSpace *feSpace = vec->getFeSpace();
692
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
Thomas Witkowski's avatar
Blub    
Thomas Witkowski committed
693

Thomas Witkowski's avatar
Thomas Witkowski committed
694
695
696
    ParallelDofMapping *rowCoarseSpace = NULL;
    if (coarseSpaceMap.size())
      rowCoarseSpace = coarseSpaceMap[nRowVec];
697

Thomas Witkowski's avatar
Thomas Witkowski committed
698
699
700
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
701

702
      if (rankOnly && !(*interiorMap)[feSpace].isRankDof(dofIt.getDOFIndex()))
Thomas Witkowski's avatar
Thomas Witkowski committed
703
704
	continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
705
      if (isCoarseSpace(nRowVec, feSpace, dofIt.getDOFIndex())) {
706
707
	TEST_EXIT_DBG(vecCoarse != PETSC_NULL)("Should not happen!\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
708
	int index = rowCoarseSpace->getMatIndex(nRowVec, dofIt.getDOFIndex());
709
710
711
712
713
714
715
716
717
718
719
720
721
722
	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;
723

724
	if (perMap.isPeriodic(feSpace, globalRowDof)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
725
726
727
	  std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
	  double value = *dofIt / (perAsc.size() + 1.0);
	  VecSetValue(vecInterior, index, value, ADD_VALUES);
728

Thomas Witkowski's avatar
Thomas Witkowski committed
729
730
731
732
	  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);
733

Thomas Witkowski's avatar
Thomas Witkowski committed
734
	    VecSetValue(vecInterior, mappedIndex, value, ADD_VALUES);
735
736
737
738
	  }	  
	} else {	  
	  // The DOF index is not periodic.
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
739
740
	  VecSetValue(vecInterior, index, *dofIt, ADD_VALUES);
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
741
742
743
744
745
      }
    }
  }

}