PetscSolverGlobalMatrix.cc 28.5 KB
Newer Older
1 2 3 4 5 6 7
/******************************************************************************
 *
 * AMDiS - Adaptive multidimensional simulations
 *
 * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
 * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
 *
8
 * Authors:
9 10 11 12 13 14 15 16 17
 * Simon Vey, Thomas Witkowski, Andreas Naumann, Simon Praetorius, et al.
 *
 * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
 * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
 *
 *
 * This file is part of AMDiS
 *
 * See also license.opensource.txt in the distribution.
18
 *
19
 ******************************************************************************/
Thomas Witkowski's avatar
Thomas Witkowski committed
20

21
#include <mpi.h>
22
// #include "DirichletBC.h"
23
#include "DOFVector.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
24 25 26
#include "parallel/PetscSolverGlobalMatrix.h"
#include "parallel/StdMpi.h"
#include "parallel/MpiHelper.h"
27
#include "solver/PetscTypes.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
28

29 30
using namespace std;

31
namespace AMDiS { namespace Parallel {
32

33
  PetscSolverGlobalMatrix::PetscSolverGlobalMatrix(string name, bool setOptions)
34 35 36
    : PetscSolver(name),
      zeroStartVector(false),
      printMatInfo(false)
37
  { FUNCNAME_DBG("PetscSolverGlobalMatrix()");
38

39
    bool matSolverPackage = false;
40 41
    if (setOptions) {
      PetscParameters params;
42

43 44 45
      // set the solver
      std::string solverName = "petsc";
      Parameters::get(name, solverName);
46
      if (solverName == "petsc")
47
	Parameters::get(name + "->ksp_type", solverName);
48

49
      std::string kspSolver = params.solverMap[solverName];
50

51 52
      if (params.matSolverPackage.find(kspSolver) != params.matSolverPackage.end()) {
	// direct solvers
53 54 55
	petsc::options_insert_string(("-" + kspPrefix + "ksp_type preonly").c_str());
	petsc::options_insert_string(("-" + kspPrefix + "pc_type lu").c_str());
	petsc::options_insert_string(("-" + kspPrefix + "pc_factor_mat_solver_package " + kspSolver).c_str());
56 57 58
	setMaxIterations(1);
	zeroStartVector = true;
	matSolverPackage = true;
59
      } else if (params.emptyParam.find(kspSolver) == params.emptyParam.end() && solverName != "petsc") {
60
	// other solvers
61
	petsc::options_insert_string(("-" + kspPrefix + "ksp_type " + kspSolver).c_str());
62
      }
63

64 65 66 67 68
      // set the preconditioner
      string precon = "";
      Parameters::get(name + "->pc_type", precon);
      if (!precon.size())
	Parameters::get(name + "->left precon", precon);
69 70
      if (!precon.size())
	Parameters::get(name + "->right precon", precon);
71 72
      if (!matSolverPackage && params.emptyParam.find(precon) == params.emptyParam.end()) {
	precon = (params.preconMap.find(precon) != params.preconMap.end() ? params.preconMap[precon] : precon);
73
	petsc::options_insert_string(("-" + kspPrefix + "pc_type " + precon).c_str());
74
      }
75

76 77 78
      petsc::options_insert_string(("-" + kspPrefix + "ksp_max_it " + boost::lexical_cast<std::string>(getMaxIterations())).c_str());
      petsc::options_insert_string(("-" + kspPrefix + "ksp_rtol " + boost::lexical_cast<std::string>(getRelative())).c_str());
      petsc::options_insert_string(("-" + kspPrefix + "ksp_atol " + boost::lexical_cast<std::string>(getTolerance())).c_str());
79

80
      if (getInfo() >= 20)
81
	petsc::options_insert_string(("-" + kspPrefix + "ksp_monitor_true_residual").c_str());
82
      else if (getInfo() >= 10)
83
	petsc::options_insert_string(("-" + kspPrefix + "ksp_monitor").c_str());
84 85
    }
    if (!matSolverPackage) {
86
      Parameters::get(name + "->use zero start vector", zeroStartVector);
87
    }
88
    Parameters::get("parallel->print matrix info", printMatInfo);
89

90
#ifndef NDEBUG
91 92 93 94 95 96 97
    bool printOptionsInfo = false;
    Parameters::get("parallel->debug->print options info", printOptionsInfo);
    if (printOptionsInfo) {
    MSG("PetscOptionsView:\n");
    PetscViewer viewer;
    PetscViewerCreate(PETSC_COMM_WORLD, &viewer);
    PetscViewerSetType(viewer, PETSCVIEWERASCII);
98
    petsc::options_view(viewer);
99
    PetscViewerDestroy(&viewer);
100

101 102
    }
#endif
103 104 105
  }


Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
106
  void PetscSolverGlobalMatrix::fillPetscMatrix(Matrix<DOFMatrix*> *seqMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
107 108 109
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrix()");

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
110 111 112
    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");
113

114
#ifndef NDEBUG
115
    Timer t;
116
#endif
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
117

118
    createMatVec(*seqMat);
119

Thomas Witkowski's avatar
Thomas Witkowski committed
120
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
121
      fillPetscMatrixWithCoarseSpace(seqMat);
122 123
      return;
    }
124

125 126
    // === Create PETSc vector (solution and a temporary vector). ===

127
#ifndef NDEBUG
128 129
    MSG("Fill petsc matrix 1 needed %.5f seconds\n", t.elapsed());
    t.reset();
Thomas Witkowski's avatar
Thomas Witkowski committed
130 131
#endif

132
    // === Transfer values from DOF matrices to the PETSc matrix. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
133

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
134
    int nComponents = seqMat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
135 136
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
137 138
	if ((*seqMat)[i][j])
	  setDofMatrix((*seqMat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
139

140
#ifndef NDEBUG
141 142
    MSG("Fill petsc matrix 2 needed %.5f seconds\n", t.elapsed());
    t.reset();
Thomas Witkowski's avatar
Thomas Witkowski committed
143 144
#endif

145
    matAssembly();
146

147 148
    if (printMatInfo) {
      MatInfo matInfo;
149
      MatGetInfo(getMatInterior(), MAT_GLOBAL_SUM, &matInfo);
150 151 152 153 154 155 156
      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));
    }
157 158


159
    // === Init PETSc solver and preconditioner objects. ===
160

161 162
    initSolver(kspInterior);
    KSPGetPC(kspInterior, &pcInterior);
Praetorius, Simon's avatar
Praetorius, Simon committed
163
    initPreconditioner(*seqMat, mat[0][0]);
164

165

166
#ifndef NDEBUG
167
    MSG("Fill petsc matrix 3 needed %.5f seconds\n", t.elapsed());
Thomas Witkowski's avatar
Thomas Witkowski committed
168
#endif
169 170


171 172 173 174 175 176 177 178 179 180 181
    // === For debugging allow to write the matrix to a file. ===

    bool dbgWriteMatrix = false;
    Parameters::get("parallel->debug->write matrix", dbgWriteMatrix);
    if (dbgWriteMatrix) {
      PetscViewer matView;
      PetscViewerBinaryOpen(PETSC_COMM_WORLD, "mpi.mat",
			    FILE_MODE_WRITE, &matView);
      MatView(getMatInterior(), matView);
      PetscViewerDestroy(&matView);
    }
182 183 184
  }


Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
185
  void PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace(Matrix<DOFMatrix*> *seqMat)
186
  {
187
    FUNCNAME_DBG("PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace()");
188

189
    TEST_EXIT_DBG(interiorMap)("No interiorMap! Should not happen!\n");
190
    TEST_EXIT_DBG(coarseSpaceMap.size() == (size_t)seqMat->getSize())
191
      ("Wrong sizes %d %d\n", coarseSpaceMap.size(), seqMat->getSize());
192

193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208
    // === 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);

209
    bool localMatrix =
210 211
      (meshDistributor->getMeshLevelData().getMpiComm(meshLevel) == MPI::COMM_SELF);

212 213 214
    // === Traverse all sequentially created matrices and add the values to ===
    // === the global PETSc matrices.                                       ===

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
215
    int nComponents = seqMat->getSize();
Thomas Witkowski's avatar
Thomas Witkowski committed
216 217 218 219 220
    for (int rowComponent = 0; rowComponent < nComponents; rowComponent++) {
      for (int colComponent = 0; colComponent < nComponents; colComponent++) {
	DOFMatrix* dofMat = (*seqMat)[rowComponent][colComponent];

	if (!dofMat)
221 222
	  continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
223 224
	ParallelDofMapping *rowCoarseSpace = coarseSpaceMap[rowComponent];
	ParallelDofMapping *colCoarseSpace = coarseSpaceMap[colComponent];
Thomas Witkowski's avatar
Thomas Witkowski committed
225

Thomas Witkowski's avatar
Thomas Witkowski committed
226 227
	std::set<DegreeOfFreedom> &dirichletRows = dofMat->getDirichletRows();

Thomas Witkowski's avatar
Thomas Witkowski committed
228 229
	traits::col<Matrix>::type col(dofMat->getBaseMatrix());
	traits::const_value<Matrix>::type value(dofMat->getBaseMatrix());
230

231
	// Traverse all rows.
232
	for (cursor_type cursor = begin<row>(dofMat->getBaseMatrix()),
Thomas Witkowski's avatar
Thomas Witkowski committed
233
	       cend = end<row>(dofMat->getBaseMatrix()); cursor != cend; ++cursor) {
234

235
	  bool isRowCoarse = isCoarseSpace(rowComponent, cursor.value());
Thomas Witkowski's avatar
Thomas Witkowski committed
236

237
	  // For the case, this is a dirichlet row we have to check whether the
Thomas Witkowski's avatar
Thomas Witkowski committed
238
	  // rank is also owner of this row DOF.
239 240 241
	  if (dirichletRows.count(cursor.value())) {
	    if ((!isRowCoarse && !(*interiorMap)[rowComponent].isRankDof(cursor.value())) ||
		(isRowCoarse && !(*rowCoarseSpace)[rowComponent].isRankDof(cursor.value())))
242
	      continue;
Thomas Witkowski's avatar
Thomas Witkowski committed
243
	  }
244

245 246
	  cols.clear();
	  colsOther.clear();
247
	  values.clear();
248 249 250
	  valuesOther.clear();

	  // Traverse all columns.
251
	  for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor);
252 253
	       icursor != icend; ++icursor) {

Thomas Witkowski's avatar
Thomas Witkowski committed
254
	    bool isColCoarse = isCoarseSpace(colComponent, col(*icursor));
255

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
256
	    if (isColCoarse == false)
257
	      if ((*interiorMap)[colComponent].isSet(col(*icursor)) == false)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
258 259
		continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
260 261 262
	    if (isColCoarse == isRowCoarse) {
	      cols.push_back(col(*icursor));
	      values.push_back(value(*icursor));
263
	    } else {
Thomas Witkowski's avatar
Thomas Witkowski committed
264 265
	      colsOther.push_back(col(*icursor));
	      valuesOther.push_back(value(*icursor));
266 267 268 269 270 271
	    }
	  }  // for each nnz in row


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

Thomas Witkowski's avatar
Thomas Witkowski committed
272
	  if (isRowCoarse) {
Thomas Witkowski's avatar
Thomas Witkowski committed
273 274
	    for (unsigned int i = 0; i < cols.size(); i++)
	      cols[i] = colCoarseSpace->getMatIndex(colComponent, cols[i]);
275

276
	    int rowIndex = rowCoarseSpace->getMatIndex(rowComponent, cursor.value());
Thomas Witkowski's avatar
Thomas Witkowski committed
277
	    MatSetValues(getMatCoarseByComponent(rowComponent, colComponent),
278 279
	    		 1, &rowIndex, cols.size(),
	    		 &(cols[0]), &(values[0]), ADD_VALUES);
280 281

	    if (colsOther.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
282
	      for (unsigned int i = 0; i < colsOther.size(); i++)
283 284 285
		colsOther[i] =
		  interiorMap->getMatIndex(colComponent, colsOther[i]) +
		  rStartInterior;
286

287
	      MatSetValues(getMatCoarseInteriorByComponent(rowComponent),
288 289
	       		   1, &rowIndex, colsOther.size(),
 	       		   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
290 291
	    }
	  } else {
292
	    if ((*interiorMap)[rowComponent].isSet(cursor.value()) == false)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
293 294
	      continue;

295 296
	    int localRowIndex =
	      (localMatrix ?
297 298
	       interiorMap->getLocalMatIndex(rowComponent, cursor.value()) :
	       interiorMap->getMatIndex(rowComponent, cursor.value()));
299

Thomas Witkowski's avatar
Thomas Witkowski committed
300
	    for (unsigned int i = 0; i < cols.size(); i++) {
301
	      if (localMatrix)
Thomas Witkowski's avatar
Thomas Witkowski committed
302
		cols[i] = interiorMap->getLocalMatIndex(colComponent, cols[i]);
303
	      else
Thomas Witkowski's avatar
Thomas Witkowski committed
304
		cols[i] = interiorMap->getMatIndex(colComponent, cols[i]);
305
	    }
306

307 308
	    MatSetValues(getMatInterior(), 1, &localRowIndex, cols.size(),
  	     		 &(cols[0]), &(values[0]), ADD_VALUES);
309

310
	    if (colsOther.size()) {
311
	      int globalRowIndex =
312
		interiorMap->getMatIndex(rowComponent, cursor.value()) + rStartInterior;
313

Thomas Witkowski's avatar
Thomas Witkowski committed
314
	      for (unsigned int i = 0; i < colsOther.size(); i++)
315
		colsOther[i] =
Thomas Witkowski's avatar
Thomas Witkowski committed
316
		  colCoarseSpace->getMatIndex(colComponent, colsOther[i]);
317

318
	      MatSetValues(getMatInteriorCoarseByComponent(colComponent),
319 320
			   1, &globalRowIndex, colsOther.size(),
			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
321 322
	    }
	  }
323
	}
324 325 326
      }
    }

327
    matAssembly();
328

329 330
    // === Create solver for the non primal (thus local) variables. ===

331
    KSPCreate(domainComm, &kspInterior);
332
    petsc::ksp_set_operators(kspInterior, getMatInterior(), getMatInterior());
333 334 335
    KSPSetOptionsPrefix(kspInterior, "interior_");
    KSPSetType(kspInterior, KSPPREONLY);
    KSPGetPC(kspInterior, &pcInterior);
336 337
    if (isSymmetric) {
      PCSetType(pcInterior, PCCHOLESKY);
338
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
339 340
    } else {
      PCSetType(pcInterior, PCLU);
341
      if (localMatrix)
342 343 344 345
	PCFactorSetMatSolverPackage(pcInterior, MATSOLVERUMFPACK);
      else
	PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
    }
346
    KSPSetFromOptions(kspInterior);
347 348 349
  }


350 351
  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
352
    FUNCNAME_DBG("PetscSolverGlobalMatrix::fillPetscRhs()");
Thomas Witkowski's avatar
Thomas Witkowski committed
353

354
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
355
    TEST_EXIT_DBG(interiorMap)("No parallel DOF map defined!\n");
356 357

    // === Transfer values from DOF vector to the PETSc vector. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
358
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
359
      for (int i = 0; i < vec->getSize(); i++)
360
	setDofVector(getVecRhsInterior(),
Thomas Witkowski's avatar
Thomas Witkowski committed
361
		     getVecRhsCoarseByComponent(i), vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
362 363
    } else {
      for (int i = 0; i < vec->getSize(); i++)
364
	setDofVector(getVecRhsInterior(), vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
365 366
    }

367
    vecRhsAssembly();
368 369 370 371 372 373 374 375 376 377 378 379

    // === For debugging allow to write the rhs vector to a file. ===

    bool dbgWriteRhs = false;
    Parameters::get("parallel->debug->write rhs", dbgWriteRhs);
    if (dbgWriteRhs) {
      PetscViewer vecView;
      PetscViewerBinaryOpen(PETSC_COMM_WORLD, "mpi.vec",
			    FILE_MODE_WRITE, &vecView);
      VecView(getVecRhsInterior(), vecView);
      PetscViewerDestroy(&vecView);
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
380 381 382
  }


383 384 385 386 387
  /// 1.) set startsolution
  /// 2.) create null-space
  /// 3.) solve Ax=b
  /// 4.) destroy null-space
  /// 5.) transfer solution back to DOFVector
388
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec,
389
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
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) {
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
397 398
      TEST_EXIT(coarseSpaceMap.size() == 0)("Not yet supported!\n");

399
      VecSet(getVecSolInterior(), 0.0);
400

Thomas Witkowski's avatar
Thomas Witkowski committed
401
      for (int i = 0; i < nComponents; i++)
402
	setDofVector(getVecSolInterior(), vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
403

404
      vecSolAssembly();
Thomas Witkowski's avatar
Thomas Witkowski committed
405 406
    }

407

Thomas Witkowski's avatar
Thomas Witkowski committed
408 409
    MatNullSpace matNullspace;
    Vec nullspaceBasis;
410
    if (nullspace.size() > 0 ||
411 412
	hasConstantNullspace ||
	constNullspaceComponent.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
413
      TEST_EXIT_DBG(nullspace.size() <= 1)("Not yet implemented!\n");
414

415 416 417 418 419 420 421 422
      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);
423
      }
424

Thomas Witkowski's avatar
Thomas Witkowski committed
425
      if (nullspace.size() > 0) {
426
	VecDuplicate(getVecSolInterior(), &nullspaceBasis);
427
	setDofVector(nullspaceBasis, *(nullspace[0]), true);
428

Thomas Witkowski's avatar
Thomas Witkowski committed
429 430
	VecAssemblyBegin(nullspaceBasis);
	VecAssemblyEnd(nullspaceBasis);
431 432

	VecNormalize(nullspaceBasis, PETSC_NULL);
433 434

	MatNullSpaceCreate(domainComm, (hasConstantNullspace ? PETSC_TRUE : PETSC_FALSE),
Thomas Witkowski's avatar
Thomas Witkowski committed
435 436
			   1, &nullspaceBasis, &matNullspace);

437
	MatMult(getMatInterior(), nullspaceBasis, getVecSolInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
438
	PetscReal n;
439
	VecNorm(getVecSolInterior(), NORM_2, &n);
Thomas Witkowski's avatar
Thomas Witkowski committed
440 441
	MSG("NORM IS: %e\n", n);
      } else {
442
	MatNullSpaceCreate(domainComm, PETSC_TRUE, 0, PETSC_NULL, &matNullspace);
Thomas Witkowski's avatar
Thomas Witkowski committed
443
      }
444

Thomas Witkowski's avatar
Thomas Witkowski committed
445 446 447
      MSG("NULLSPACE IS NOT REMOVED!\n");
      // MatSetNullSpace(getMatInterior(), matNullspace);
      // KSPSetNullSpace(kspInterior, matNullspace);
448

Thomas Witkowski's avatar
Thomas Witkowski committed
449
      // === Remove null space, if requested. ===
450

Thomas Witkowski's avatar
Thomas Witkowski committed
451
      if (removeRhsNullspace) {
Thomas Witkowski's avatar
Thomas Witkowski committed
452
	TEST_EXIT_DBG(coarseSpaceMap.empty())("Not supported!\n");
453 454

	MSG("Remove nullspace from rhs vector.\n");
455
	petsc::mat_nullspace_remove(matNullspace, getVecRhsInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
456 457 458 459
      }
    } else {
      TEST_EXIT(removeRhsNullspace == false)
	("No nullspace provided that should be removed from rhs!\n");
460 461
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
462
    // PETSc.
463
    solve(getVecRhsInterior(), getVecSolInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
464

465 466

    if (nullspace.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
467
      MatNullSpaceDestroy(&matNullspace);
468 469 470 471
      VecDestroy(&nullspaceBasis);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
472 473
    // === Transfere values from PETSc's solution vectors to the DOF vectors. ===
    PetscScalar *vecPointer;
474
    VecGetArray(getVecSolInterior(), &vecPointer);
Thomas Witkowski's avatar
Thomas Witkowski committed
475

476
    int c = 0;
477 478
    for (int component = 0; component < nComponents; component++) {
      DOFVector<double> &dv = *(vec.getDOFVector(component));
479

480
      DofMap& d = (*interiorMap)[component].getMap();
481 482 483
      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
484 485
    }

486
    VecRestoreArray(getVecSolInterior(), &vecPointer);
Thomas Witkowski's avatar
Thomas Witkowski committed
487

488 489
    // === Synchronize DOFs at common DOFs, i.e., DOFs that correspond to ===
    // === more than one partition.                                       ===
Thomas Witkowski's avatar
Thomas Witkowski committed
490
    meshDistributor->synchVector(vec);
491 492 493
  }


494 495 496
  void PetscSolverGlobalMatrix::solveGlobal(Vec &rhs, Vec &sol)
  {
    Vec tmp;
497
    if (domainComm.Get_size() == 1)
498
      createLocalVec(*interiorMap, tmp);
499
    else
500
      createVec(*interiorMap, tmp);
501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516

    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);

    KSPSolve(kspInterior, tmp, tmp);

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

517
    for (int i = 0; i < interiorMap->getRankDofs(); i++)
518 519 520 521 522 523 524 525 526
      rhsValues[i] = tmpValues[i];

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

    VecDestroy(&tmp);
  }


527 528
  void PetscSolverGlobalMatrix::destroyMatrixData()
  {
529
    matDestroy();
Thomas Witkowski's avatar
Thomas Witkowski committed
530

531 532
    exitPreconditioner(pcInterior);
    exitSolver(kspInterior);
Thomas Witkowski's avatar
Thomas Witkowski committed
533 534 535
  }


536 537
  void PetscSolverGlobalMatrix::destroyVectorData()
  {
538
    vecDestroy();
539 540 541
  }


542 543 544 545 546 547 548 549 550 551 552 553 554 555 556
  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;
557
      Parameters::get("parallel->solver->is block " + boost::lexical_cast<string>(i),
558 559 560
		      blockComponents);
      int nComponents = static_cast<int>(blockComponents.size());

561
      TEST_EXIT(nComponents > 0)("No IS block for block %d defined!\n", i);
562 563 564 565

      // Check if blocks are continous
      for (int j = 0; j < nComponents; j++) {
	TEST_EXIT(blockComponents[j] == blockComponents[0] + j)
566
	  ("Does not yet support not continous IS blocks! Block %s\n",
567 568 569
	   isNames[i].c_str());
      }

570
      createFieldSplit(pc, isNames[i].c_str(), blockComponents);
571 572 573 574
    }
  }


575 576
  void PetscSolverGlobalMatrix::createFieldSplit(PC pc,
						 const char* splitName,
577 578 579 580
						 vector<int> &components)
  {
    IS is;
    interiorMap->createIndexSet(is, components[0], components.size());
581
    PCFieldSplitSetIS(pc, splitName, is);
582 583
    ISDestroy(&is);
  }
584 585


586 587 588 589 590 591 592
  void PetscSolverGlobalMatrix::extractVectorComponent(Vec input, int i, Vec *output, int numberOfComponents)
  {
    IS is;
    interiorMap->createIndexSet(is, i, numberOfComponents);
    VecGetSubVector(input, is, output);
    ISDestroy(&is);
  }
593

594 595 596 597 598 599 600 601 602
  void PetscSolverGlobalMatrix::extractMatrixComponent(Mat input, int startRow, int numberOfRows, int startCol, int numberOfCols, Mat *output)
  {
    IS isrow, iscol;
    interiorMap->createIndexSet(isrow, startRow, numberOfRows);
    interiorMap->createIndexSet(iscol, startCol, numberOfCols);
    MatGetSubMatrix(input, isrow, iscol, MAT_INITIAL_MATRIX, output);
    ISDestroy(&iscol);
    ISDestroy(&isrow);
  }
603

604

605
  void PetscSolverGlobalMatrix::initSolver(KSP &ksp)
606
  {
607
    KSPCreate(domainComm, &ksp);
608
    petsc::ksp_set_operators(ksp, getMatInterior(), getMatInterior());
609 610 611
    KSPSetTolerances(ksp, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(ksp, KSPBCGS);
    KSPSetOptionsPrefix(ksp, kspPrefix.c_str());
612
    MatSetOptionsPrefix(getMatInterior(), kspPrefix.c_str());
613 614 615 616 617
    KSPSetFromOptions(ksp);

    // Do not delete the solution vector, use it for the initial guess.
    if (!zeroStartVector)
      KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);
618
  }
619 620


621
  void PetscSolverGlobalMatrix::exitSolver(KSP &ksp)
622 623
  {
    KSPDestroy(&ksp);
624
  }
625 626


627 628 629 630 631 632
  void PetscSolverGlobalMatrix::initPreconditioner(PC pc)
  {
    PCSetFromOptions(pc);
    createFieldSplit(pc);
  }

633

634
  void PetscSolverGlobalMatrix::exitPreconditioner(PC pc)
635
  { }
636 637


638
  /// called by \ref fillPetscMatrix
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
639
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* seqMat,
Thomas Witkowski's avatar
Thomas Witkowski committed
640
					     int rowComp, int colComp)
Thomas Witkowski's avatar
Thomas Witkowski committed
641 642 643
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
644
    TEST_EXIT(seqMat)("No DOFMatrix!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
645 646

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
647
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
648 649
    typedef DOFMatrix::base_matrix_type Matrix;

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
650 651
    traits::col<Matrix>::type col(seqMat->getBaseMatrix());
    traits::const_value<Matrix>::type value(seqMat->getBaseMatrix());
Thomas Witkowski's avatar
Thomas Witkowski committed
652 653 654 655 656 657 658 659

    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);
660

661 662
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
663
    std::map<int, int> associatedRows;
Thomas Witkowski's avatar
Thomas Witkowski committed
664
    std::set<DegreeOfFreedom> &dirichletRows = seqMat->getDirichletRows();
665

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
666 667
    const FiniteElemSpace *rowFe = seqMat->getRowFeSpace();
    const FiniteElemSpace *colFe = seqMat->getColFeSpace();
Thomas Witkowski's avatar
Thomas Witkowski committed
668

669
    for (cursor_type cursor = begin<row>(seqMat->getBaseMatrix()),
670
         cend = end<row>(seqMat->getBaseMatrix()); cursor != cend; ++cursor) {
671
      MultiIndex rowMultiIndex;
672
      if ((*interiorMap)[rowComp].find(cursor.value(), rowMultiIndex) == false)
673
        continue;
674 675

      int globalRowDof = rowMultiIndex.global;
676

Thomas Witkowski's avatar
Thomas Witkowski committed
677
      // Test if the current row DOF is a periodic DOF.
678
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
679

Thomas Witkowski's avatar
Thomas Witkowski committed
680
      // Dirichlet rows can be set only be the owner ranks.
681
      if (dirichletRows.count(cursor.value()) && !((*interiorMap)[rowComp].isRankDof(cursor.value())))
682
        continue;
Thomas Witkowski's avatar
Thomas Witkowski committed
683

684 685
      int rowIndex = interiorMap->getMatIndex(rowComp, globalRowDof);
      int assRowIndex = -1;
Thomas Witkowski's avatar
Thomas Witkowski committed
686

687 688 689 690
      if (periodicRow) {
        std::set<int> perAsc;
        perMap.fillAssociations(rowFe, globalRowDof,
                          meshDistributor->getElementObjectDb(), perAsc);
691

692 693
        vector<int> newRows;
        perMap.mapDof(rowFe, globalRowDof, perAsc, newRows);
Thomas Witkowski's avatar
Thomas Witkowski committed
694

695 696 697
        assRowIndex = interiorMap->getMatIndex(rowComp,
                                *std::max_element(newRows.begin(),newRows.end()));
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
698

699 700
      cols.clear();
      values.clear();
Thomas Witkowski's avatar
Thomas Witkowski committed
701

702 703
      for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor);
           icursor != icend; ++icursor) {
Thomas Witkowski's avatar
Thomas Witkowski committed
704

705 706 707 708
        // Global index of the current column index.
        MultiIndex colMultiIndex;
        if ((*interiorMap)[colComp].find(col(*icursor), colMultiIndex) == false)
          continue;
Thomas Witkowski's avatar
Thomas Witkowski committed
709

710 711 712
        int globalColDof = colMultiIndex.global;
        // Get PETSc's mat col index.
        int colIndex = interiorMap->getMatIndex(colComp, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
713

714 715 716
        cols.push_back(colIndex);
        values.push_back(value(*icursor));
          }
Thomas Witkowski's avatar
Thomas Witkowski committed
717

718 719 720 721 722 723
          if (!periodicRow || assRowIndex == rowIndex)
        MatSetValues(getMatInterior(), 1, &rowIndex, cols.size(),
                &(cols[0]), &(values[0]), ADD_VALUES);
          else {
        MatSetValues(getMatInterior(), 1, &assRowIndex, cols.size(),
                &(cols[0]), &(values[0]), ADD_VALUES);
Thomas Witkowski's avatar
Thomas Witkowski committed
724

725 726 727
        associatedRows.insert(std::make_pair(rowIndex, assRowIndex));
          }
        }
Thomas Witkowski's avatar
Thomas Witkowski committed
728

729 730
        int globalPeriodic = associatedRows.size();
        Parallel::mpi::globalAdd(globalPeriodic);
Thomas Witkowski's avatar
Thomas Witkowski committed
731

732
        if (globalPeriodic) {
Thomas Witkowski's avatar
Thomas Witkowski committed
733

734 735
          MatAssemblyBegin(getMatInterior(), MAT_FLUSH_ASSEMBLY);
          MatAssemblyEnd(getMatInterior(), MAT_FLUSH_ASSEMBLY);
Thomas Witkowski's avatar
Thomas Witkowski committed
736

737
          int c[2]; double v[2] = {1.0, -1.0};
Thomas Witkowski's avatar
Thomas Witkowski committed
738

739 740 741 742
          std::map<int, int>::iterator mapIt = associatedRows.begin();
          for (;mapIt != associatedRows.end(); mapIt++) {
        c[0] = mapIt->first;
        c[1] = mapIt->second;
Thomas Witkowski's avatar
Thomas Witkowski committed
743

744
        MatSetValues(getMatInterior(), 1, &c[0], 2, c, v, INSERT_VALUES);
Thomas Witkowski's avatar
Thomas Witkowski committed
745
      }
746 747 748

      MatAssemblyBegin(getMatInterior(), MAT_FLUSH_ASSEMBLY);
      MatAssemblyEnd(getMatInterior(), MAT_FLUSH_ASSEMBLY);
Thomas Witkowski's avatar
Thomas Witkowski committed
749 750 751 752
    }
  }


753
  /// called by \ref fillPetscRhs
754
  void PetscSolverGlobalMatrix::setDofVector(Vec vecInterior,
Thomas Witkowski's avatar
Thomas Witkowski committed
755
					     Vec vecCoarse,
756 757
					     DOFVector<double>* vec,
					     int rowComp,
758
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
759
  {
760
    FUNCNAME_DBG("PetscSolverGlobalMatrix::setDofVector()");
Thomas Witkowski's avatar
Thomas Witkowski committed
761

762
    const FiniteElemSpace *feSpace = vec->getFeSpace();
763
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
764

765 766
    std::set<int> associatedRows;

767
    ParallelDofMapping *rowCoarseSpace =
768
      (coarseSpaceMap.size() ? coarseSpaceMap[rowComp] : NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
769 770

    map<DegreeOfFreedom, double> &dirichletValues = vec->getDirichletValues();
771

Thomas Witkowski's avatar
Thomas Witkowski committed
772 773 774
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
775

Thomas Witkowski's avatar
Thomas Witkowski committed
776
      DegreeOfFreedom dof = dofIt.getDOFIndex();
777

Thomas Witkowski's avatar
Thomas Witkowski committed
778
      if (rankOnly && !(*interiorMap)[rowComp].isRankDof(dof))
779
        continue;
780

781 782
      bool isCoarseDof = isCoarseSpace(rowComp, dof);

Thomas Witkowski's avatar
Thomas Witkowski committed
783
      // Dirichlet rows can be set only be the owner ranks.
784
      if (dirichletValues.count(dof)) {
785 786 787
        if ((!isCoarseDof && !((*interiorMap)[rowComp].isRankDof(dof))) ||
            (isCoarseDof && !((*rowCoarseSpace)[rowComp].isRankDof(dof))))
          continue;
788
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
789

790
      if (isCoarseDof) {
791
        TEST_EXIT_DBG(vecCoarse != PETSC_NULL)("vecCoarse not set! Should not happen!\n");
792