PetscSolverGlobalMatrix.cc 26.8 KB
Newer Older
Thomas Witkowski's avatar
Thomas Witkowski committed
1 2 3 4 5 6 7 8 9 10 11
//
// 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.

12 13
#include <mpi.h>
#include "DirichletBC.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 21 22 23 24 25 26 27 28 29 30

  PetscSolverGlobalMatrix::PetscSolverGlobalMatrix(string name)
    : PetscSolver(name),
      zeroStartVector(false),
      printMatInfo(false)
  {
    Parameters::get("parallel->use zero start vector", zeroStartVector);
    Parameters::get("parallel->print matrix info", printMatInfo);
  }


Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
31
  void PetscSolverGlobalMatrix::fillPetscMatrix(Matrix<DOFMatrix*> *seqMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
32 33 34
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrix()");

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
35 36 37 38 39 40
    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();

41
    createMatVec(*seqMat);
42

Thomas Witkowski's avatar
Thomas Witkowski committed
43
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
44
      fillPetscMatrixWithCoarseSpace(seqMat);
45 46 47
      return;
    }

48 49
    // === Create PETSc vector (solution and a temporary vector). ===

Thomas Witkowski's avatar
Thomas Witkowski committed
50 51 52 53 54 55
#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
56
    int nComponents = seqMat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
57 58
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
59 60
	if ((*seqMat)[i][j])
	  setDofMatrix((*seqMat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
61 62 63 64 65

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

66
    matAssembly();
67

68 69
    if (printMatInfo) {
      MatInfo matInfo;
70
      MatGetInfo(getMatInterior(), MAT_GLOBAL_SUM, &matInfo);
71 72 73 74 75 76 77
      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));
    }
78 79


80
    // === Init PETSc solver and preconditioner objects. ===
81

82 83
    initSolver(kspInterior);
    KSPGetPC(kspInterior, &pcInterior);
84
    initPreconditioner(pcInterior);
85

86

Thomas Witkowski's avatar
Thomas Witkowski committed
87 88 89
#if (DEBUG != 0)
    MSG("Fill petsc matrix 3 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif
90 91


92 93 94 95 96 97 98 99 100 101 102
    // === 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);
    }
103 104 105
  }


Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
106
  void PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace(Matrix<DOFMatrix*> *seqMat)
107 108
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace()");
109 110

    TEST_EXIT_DBG(interiorMap)("Should not happen!\n");
111 112
    TEST_EXIT_DBG(coarseSpaceMap.size() == seqMat->getSize())
      ("Wrong sizes %d %d\n", coarseSpaceMap.size(), seqMat->getSize());
113

114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132
    // === 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
133
    int nComponents = seqMat->getSize();
Thomas Witkowski's avatar
Thomas Witkowski committed
134 135 136 137 138
    for (int rowComponent = 0; rowComponent < nComponents; rowComponent++) {
      for (int colComponent = 0; colComponent < nComponents; colComponent++) {
	DOFMatrix* dofMat = (*seqMat)[rowComponent][colComponent];

	if (!dofMat)
139 140
	  continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
141 142
	ParallelDofMapping *rowCoarseSpace = coarseSpaceMap[rowComponent];
	ParallelDofMapping *colCoarseSpace = coarseSpaceMap[colComponent];
Thomas Witkowski's avatar
Thomas Witkowski committed
143

Thomas Witkowski's avatar
Thomas Witkowski committed
144 145
	std::set<DegreeOfFreedom> &dirichletRows = dofMat->getDirichletRows();

Thomas Witkowski's avatar
Thomas Witkowski committed
146 147
	traits::col<Matrix>::type col(dofMat->getBaseMatrix());
	traits::const_value<Matrix>::type value(dofMat->getBaseMatrix());
148 149
	
	// Traverse all rows.
Thomas Witkowski's avatar
Thomas Witkowski committed
150 151
	for (cursor_type cursor = begin<row>(dofMat->getBaseMatrix()), 
	       cend = end<row>(dofMat->getBaseMatrix()); cursor != cend; ++cursor) {
152

Thomas Witkowski's avatar
Thomas Witkowski committed
153
	  bool isRowCoarse = isCoarseSpace(rowComponent, *cursor);
Thomas Witkowski's avatar
Thomas Witkowski committed
154 155 156 157 158 159

	  // For the case, this is a dirichlet row we have to check whether the 
	  // rank is also owner of this row DOF.
	  if (dirichletRows.count(*cursor)) {
	    if ((!isRowCoarse && !(*interiorMap)[rowComponent].isRankDof(*cursor)) ||
		(isRowCoarse && !(*rowCoarseSpace)[rowComponent].isRankDof(*cursor)))
160
	      continue;    
Thomas Witkowski's avatar
Thomas Witkowski committed
161
	  }
162 163 164 165 166 167 168 169 170 171
  
	  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
172
	    bool isColCoarse = isCoarseSpace(colComponent, col(*icursor));
173

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
174
	    if (isColCoarse == false)
175
	      if ((*interiorMap)[colComponent].isSet(col(*icursor)) == false)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
176 177
		continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
178 179 180
	    if (isColCoarse == isRowCoarse) {
	      cols.push_back(col(*icursor));
	      values.push_back(value(*icursor));
181
	    } else {
Thomas Witkowski's avatar
Thomas Witkowski committed
182 183
	      colsOther.push_back(col(*icursor));
	      valuesOther.push_back(value(*icursor));
184 185 186 187 188 189
	    }
	  }  // for each nnz in row


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

Thomas Witkowski's avatar
Thomas Witkowski committed
190
	  if (isRowCoarse) {
Thomas Witkowski's avatar
Thomas Witkowski committed
191 192
	    for (unsigned int i = 0; i < cols.size(); i++)
	      cols[i] = colCoarseSpace->getMatIndex(colComponent, cols[i]);
193

Thomas Witkowski's avatar
Thomas Witkowski committed
194
	    int rowIndex = rowCoarseSpace->getMatIndex(rowComponent, *cursor);
Thomas Witkowski's avatar
Thomas Witkowski committed
195
	    MatSetValues(getMatCoarseByComponent(rowComponent, colComponent),
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
196
			 1, &rowIndex, cols.size(),
197 198 199
			 &(cols[0]), &(values[0]), ADD_VALUES);

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

Thomas Witkowski's avatar
Thomas Witkowski committed
205
	      MatSetValues(getMatCoarseInteriorByComponent(rowComponent), 
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
206
			   1, &rowIndex, colsOther.size(),
207 208 209
 			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
	    }
	  } else {
210
	    if ((*interiorMap)[rowComponent].isSet(*cursor) == false)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
211 212
	      continue;

213
	    int localRowIndex = 
Thomas Witkowski's avatar
Thomas Witkowski committed
214 215 216
	      (subdomainLevel == 0 ? 
	       interiorMap->getLocalMatIndex(rowComponent, *cursor) :
	       interiorMap->getMatIndex(rowComponent, *cursor));
217

Thomas Witkowski's avatar
Thomas Witkowski committed
218
	    for (unsigned int i = 0; i < cols.size(); i++) {
219
	      if (subdomainLevel == 0)
Thomas Witkowski's avatar
Thomas Witkowski committed
220
		cols[i] = interiorMap->getLocalMatIndex(colComponent, cols[i]);
221
	      else
Thomas Witkowski's avatar
Thomas Witkowski committed
222
		cols[i] = interiorMap->getMatIndex(colComponent, cols[i]);
223 224
	    }
	    
225
  	    MatSetValues(getMatInterior(), 1, &localRowIndex, cols.size(),
226
  			 &(cols[0]), &(values[0]), ADD_VALUES);
Thomas Witkowski's avatar
Thomas Witkowski committed
227
	    
228
	    if (colsOther.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
229 230 231
	      int globalRowIndex = 
		interiorMap->getMatIndex(rowComponent, *cursor) + rStartInterior;
      
Thomas Witkowski's avatar
Thomas Witkowski committed
232 233 234
	      for (unsigned int i = 0; i < colsOther.size(); i++)
		colsOther[i] = 
		  colCoarseSpace->getMatIndex(colComponent, colsOther[i]);
235

Thomas Witkowski's avatar
Thomas Witkowski committed
236
  	      MatSetValues(getMatInteriorCoarseByComponent(colComponent), 
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
237
			   1, &globalRowIndex, colsOther.size(),
238 239 240 241 242 243 244
  			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
	    }
	  }
	} 
      }
    }

245
    matAssembly();
246

247 248 249
    // === Create solver for the non primal (thus local) variables. ===

    KSPCreate(mpiCommLocal, &kspInterior);
250
    KSPSetOperators(kspInterior, getMatInterior(), getMatInterior(),
251
		    SAME_NONZERO_PATTERN);
252 253 254
    KSPSetOptionsPrefix(kspInterior, "interior_");
    KSPSetType(kspInterior, KSPPREONLY);
    KSPGetPC(kspInterior, &pcInterior);
255 256
    if (isSymmetric) {
      PCSetType(pcInterior, PCCHOLESKY);
257
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
258 259 260 261 262 263 264
    } else {
      PCSetType(pcInterior, PCLU);
      if (subdomainLevel == 0)
	PCFactorSetMatSolverPackage(pcInterior, MATSOLVERUMFPACK);
      else
	PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
    }
265
    KSPSetFromOptions(kspInterior);
266 267 268
  }


269 270 271
  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
Thomas Witkowski's avatar
Thomas Witkowski committed
272

273
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
274
    TEST_EXIT_DBG(interiorMap)("No parallel DOF map defined!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
275
    
Thomas Witkowski's avatar
Thomas Witkowski committed
276
    // === Transfer values from DOF vector to the PETSc vector. === 
Thomas Witkowski's avatar
Thomas Witkowski committed
277
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
278
      for (int i = 0; i < vec->getSize(); i++)
279
	setDofVector(getVecRhsInterior(), 
Thomas Witkowski's avatar
Thomas Witkowski committed
280
		     getVecRhsCoarseByComponent(i), vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
281 282
    } else {
      for (int i = 0; i < vec->getSize(); i++)
283
	setDofVector(getVecRhsInterior(), vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
284 285
    }

286
    vecRhsAssembly();
287 288 289 290 291 292 293 294 295 296 297 298

    // === 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
299 300 301
  }


302 303
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
304 305 306 307 308 309 310
  {
    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
311 312
      TEST_EXIT(coarseSpaceMap.size() == 0)("Not yet supported!\n");

313
      VecSet(getVecSolInterior(), 0.0);
Thomas Witkowski's avatar
Thomas Witkowski committed
314 315
      
      for (int i = 0; i < nComponents; i++)
316
	setDofVector(getVecSolInterior(), vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
317

318
      vecSolAssembly();
Thomas Witkowski's avatar
Thomas Witkowski committed
319 320
    }

321

Thomas Witkowski's avatar
Thomas Witkowski committed
322 323
    MatNullSpace matNullspace;
    Vec nullspaceBasis;
324 325 326
    if (nullspace.size() > 0 || 
	hasConstantNullspace ||
	constNullspaceComponent.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
327
      TEST_EXIT_DBG(nullspace.size() <= 1)("Not yet implemented!\n");
328

329 330 331 332 333 334 335 336 337 338
      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
339
      if (nullspace.size() > 0) {
340
	VecDuplicate(getVecSolInterior(), &nullspaceBasis);
341
	setDofVector(nullspaceBasis, *(nullspace[0]), true);
Thomas Witkowski's avatar
Thomas Witkowski committed
342 343 344
	
	VecAssemblyBegin(nullspaceBasis);
	VecAssemblyEnd(nullspaceBasis);
345 346

	VecNormalize(nullspaceBasis, PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
347 348 349 350
	
	MatNullSpaceCreate(mpiCommGlobal, (hasConstantNullspace ? PETSC_TRUE : PETSC_FALSE), 
			   1, &nullspaceBasis, &matNullspace);

351
	MatMult(getMatInterior(), nullspaceBasis, getVecSolInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
352
	PetscReal n;
353
	VecNorm(getVecSolInterior(), NORM_2, &n);
Thomas Witkowski's avatar
Thomas Witkowski committed
354 355 356 357
	MSG("NORM IS: %e\n", n);
      } else {
	MatNullSpaceCreate(mpiCommGlobal, PETSC_TRUE, 0, PETSC_NULL, &matNullspace);
      }
358

Thomas Witkowski's avatar
Thomas Witkowski committed
359 360 361
      MSG("NULLSPACE IS NOT REMOVED!\n");
      // MatSetNullSpace(getMatInterior(), matNullspace);
      // KSPSetNullSpace(kspInterior, matNullspace);
362

Thomas Witkowski's avatar
Thomas Witkowski committed
363
      // === Remove null space, if requested. ===
364

Thomas Witkowski's avatar
Thomas Witkowski committed
365
      if (removeRhsNullspace) {
Thomas Witkowski's avatar
Thomas Witkowski committed
366
	TEST_EXIT_DBG(coarseSpaceMap.empty())("Not supported!\n");
367 368

	MSG("Remove nullspace from rhs vector.\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
369
	
370
	MatNullSpaceRemove(matNullspace, getVecRhsInterior(), PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
371 372 373 374
      }
    } else {
      TEST_EXIT(removeRhsNullspace == false)
	("No nullspace provided that should be removed from rhs!\n");
375 376
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
377
    // PETSc.
378
    solve(getVecRhsInterior(), getVecSolInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
379

380 381

    if (nullspace.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
382
      MatNullSpaceDestroy(&matNullspace);
383 384 385 386
      VecDestroy(&nullspaceBasis);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
387 388
    // === Transfere values from PETSc's solution vectors to the DOF vectors. ===
    PetscScalar *vecPointer;
389
    VecGetArray(getVecSolInterior(), &vecPointer);    
Thomas Witkowski's avatar
Thomas Witkowski committed
390

391
    int c = 0;
392 393
    for (int component = 0; component < nComponents; component++) {
      DOFVector<double> &dv = *(vec.getDOFVector(component));
394

395
      DofMap& d = (*interiorMap)[component].getMap();
396 397 398
      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
399 400
    }

401
    VecRestoreArray(getVecSolInterior(), &vecPointer);
Thomas Witkowski's avatar
Thomas Witkowski committed
402 403 404 405

    // === Synchronize DOFs at common DOFs, i.e., DOFs that correspond to ===  
    // === more than one partition.                                       ===  
    meshDistributor->synchVector(vec);
406 407 408
  }


409 410 411 412
  void PetscSolverGlobalMatrix::solveGlobal(Vec &rhs, Vec &sol)
  {
    FUNCNAME("PetscSolverGlobalMatrix::solveGlobal()");

413 414 415
    double wtime = MPI::Wtime();
    double t0 = 0.0, t1 = 0.0;

416 417
    Vec tmp;
    if (mpiCommLocal.Get_size() == 1)
Thomas Witkowski's avatar
Thomas Witkowski committed
418
      interiorMap->createLocalVec(tmp);
419
    else
Thomas Witkowski's avatar
Thomas Witkowski committed
420
      interiorMap->createVec(tmp);
421 422 423 424 425 426 427 428 429 430 431

    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);

432 433 434
    t0 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
435
    KSPSolve(kspInterior, tmp, tmp);
436 437 438
    t1 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
439 440 441 442 443 444 445 446 447 448 449

    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);
450 451
    t0 += MPI::Wtime() - wtime;

452
    //    MSG("TIMEING: %.5f %.5f\n", t0, t1);
453 454 455
  }


456 457 458 459
  void PetscSolverGlobalMatrix::destroyMatrixData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyMatrixData()");

460
    matDestroy();
Thomas Witkowski's avatar
Thomas Witkowski committed
461

462 463 464
    exitPreconditioner(pcInterior);

    exitSolver(kspInterior);
Thomas Witkowski's avatar
Thomas Witkowski committed
465 466 467
  }


468 469 470 471
  void PetscSolverGlobalMatrix::destroyVectorData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyVectorData()");

472
    vecDestroy();
473 474 475
  }


476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494
  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());

495
      TEST_EXIT(nComponents > 0)("No IS block for block %d defined!\n", i);
496 497 498 499 500 501 502 503

      // 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());
      }

504
      createFieldSplit(pc, isNames[i].c_str(), blockComponents);
505 506 507 508
    }
  }


509
  void PetscSolverGlobalMatrix::createFieldSplit(PC pc, 
510
						 const char* splitName, 
511 512 513 514 515 516
						 vector<int> &components)
  {
    FUNCNAME("PetscSolverGlobalMatrix::createFieldSplit()");

    IS is;
    interiorMap->createIndexSet(is, components[0], components.size());
517
    PCFieldSplitSetIS(pc, splitName, is);
518 519 520 521
    ISDestroy(&is);
  }


522
  void PetscSolverGlobalMatrix::initSolver(KSP &ksp)
523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547
  {
    FUNCNAME("PetscSolverGlobalMatrix::initSolver()");

    KSPCreate(mpiCommGlobal, &ksp);
    KSPSetOperators(ksp, getMatInterior(), getMatInterior(), 
		    SAME_NONZERO_PATTERN); 
    KSPSetTolerances(ksp, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(ksp, KSPBCGS);
    KSPSetOptionsPrefix(ksp, kspPrefix.c_str());
    KSPSetFromOptions(ksp);

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


  void PetscSolverGlobalMatrix::exitSolver(KSP ksp)
  {
    FUNCNAME("PetscSolverGlobalMatrix::exitSolver()");

    KSPDestroy(&ksp);
  }  


548 549 550 551 552 553 554 555 556 557 558 559 560 561 562
  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
563
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* seqMat,
Thomas Witkowski's avatar
Thomas Witkowski committed
564
					     int rowComp, int colComp)
Thomas Witkowski's avatar
Thomas Witkowski committed
565 566 567
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
568
    TEST_EXIT(seqMat)("No DOFMatrix!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
569 570

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
571
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
572 573
    typedef DOFMatrix::base_matrix_type Matrix;

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
574 575
    traits::col<Matrix>::type col(seqMat->getBaseMatrix());
    traits::const_value<Matrix>::type value(seqMat->getBaseMatrix());
Thomas Witkowski's avatar
Thomas Witkowski committed
576 577 578 579 580 581 582 583 584 585 586

    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;

587 588
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
Thomas Witkowski's avatar
Thomas Witkowski committed
589 590
    std::set<DegreeOfFreedom> &dirichletRows = seqMat->getDirichletRows();
      
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
591 592
    const FiniteElemSpace *rowFe = seqMat->getRowFeSpace();
    const FiniteElemSpace *colFe = seqMat->getColFeSpace();
Thomas Witkowski's avatar
Thomas Witkowski committed
593 594

    // === Traverse all rows of the DOF matrix and insert row wise the values ===
Thomas Witkowski's avatar
Thomas Witkowski committed
595 596
    // === to the PETSc matrix.                                               ===

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
597 598
    for (cursor_type cursor = begin<row>(seqMat->getBaseMatrix()), 
	   cend = end<row>(seqMat->getBaseMatrix()); cursor != cend; ++cursor) {
Thomas Witkowski's avatar
Thomas Witkowski committed
599
      // Global index of the current row DOF.
600
      MultiIndex rowMultiIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
601
      if ((*interiorMap)[rowComp].find(*cursor, rowMultiIndex) == false)
602 603 604
	continue;

      int globalRowDof = rowMultiIndex.global;
605

Thomas Witkowski's avatar
Thomas Witkowski committed
606
      // Test if the current row DOF is a periodic DOF.
607
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
608

Thomas Witkowski's avatar
Thomas Witkowski committed
609 610 611 612
      // Dirichlet rows can be set only be the owner ranks.
      if (dirichletRows.count(*cursor) && !((*interiorMap)[rowComp].isRankDof(*cursor)))
	continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
613 614 615
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

616
	// Get PETSc's mat row index.
Thomas Witkowski's avatar
Thomas Witkowski committed
617
	int rowIndex = interiorMap->getMatIndex(rowComp, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
618 619 620 621 622 623 624 625

	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.
626
	  MultiIndex colMultiIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
627
	  if ((*interiorMap)[colComp].find(col(*icursor), colMultiIndex) == false)
628 629 630
	    continue;

	  int globalColDof = colMultiIndex.global;
Thomas Witkowski's avatar
Thomas Witkowski committed
631
	  // Test if the current col dof is a periodic dof.
632
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
633
	  // Get PETSc's mat col index.
Thomas Witkowski's avatar
Thomas Witkowski committed
634
	  int colIndex = interiorMap->getMatIndex(colComp, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
635 636 637 638 639 640 641

	  // 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
642 643
 	    cols.push_back(colIndex);
 	    values.push_back(value(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
644 645 646 647 648
	  } else {
	    // === Row index is not periodic, but column index is. ===

	    // Create set of all periodic associations of the column index.
	    std::set<int> perAsc;
649 650 651
	    perMap.fillAssociations(colFe, globalColDof, 
				    meshDistributor->getElementObjectDb(), perAsc);

Thomas Witkowski's avatar
Thomas Witkowski committed
652 653 654 655 656 657 658 659 660
	    // 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;
661
	    perMap.mapDof(colFe, globalColDof, perAsc, newCols);
Thomas Witkowski's avatar
Thomas Witkowski committed
662
	    for (unsigned int i = 0; i < newCols.size(); i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
663
	      cols.push_back(interiorMap->getMatIndex(colComp, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
664 665 666 667 668
	      values.push_back(scaledValue);	      
	    }
	  }
	}

669
  	MatSetValues(getMatInterior(), 1, &rowIndex, cols.size(), 
Thomas Witkowski's avatar
Thomas Witkowski committed
670
  		     &(cols[0]), &(values[0]), ADD_VALUES);	
Thomas Witkowski's avatar
Thomas Witkowski committed
671 672 673 674 675 676 677 678 679 680 681 682 683 684
      } 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.
Thomas Witkowski's avatar
Thomas Witkowski committed
685
	  int globalColDof = (*interiorMap)[colComp][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
686 687 688 689 690 691 692 693 694

	  // 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;
695 696 697 698
	  perMap.fillAssociations(colFe, globalColDof, 
				  meshDistributor->getElementObjectDb(), perAsc);
	  perMap.fillAssociations(rowFe, globalRowDof, 
				  meshDistributor->getElementObjectDb(), perAsc);
Thomas Witkowski's avatar
Thomas Witkowski committed
699 700 701 702 703 704 705 706 707 708

	  // 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
709 710
	  perMap.mapDof(rowFe, colFe, make_pair(globalRowDof, globalColDof),
			perAsc, entry);
Thomas Witkowski's avatar
Thomas Witkowski committed
711 712 713

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

714
	  for (unsigned int i = 0; i < entry.size(); i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
715 716
	    int rowIdx = interiorMap->getMatIndex(rowComp, entry[i].first);
	    int colIdx = interiorMap->getMatIndex(colComp, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
717

718 719
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
720 721 722 723 724 725 726 727 728 729 730 731
	  }
	}


	// === 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;
732

733
	  MatSetValues(getMatInterior(), 1, &rowIndex, rowIt->second.size(),
Thomas Witkowski's avatar
Thomas Witkowski committed
734 735 736 737 738 739 740
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
741 742
  void PetscSolverGlobalMatrix::setDofVector(Vec vecInterior, 
					     Vec vecCoarse,
743
					     DOFVector<double>* vec, 
Thomas Witkowski's avatar
Thomas Witkowski committed
744
					     int rowComp, 
745
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
746 747 748
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

749
    const FiniteElemSpace *feSpace = vec->getFeSpace();
750
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
751

752
    ParallelDofMapping *rowCoarseSpace = 
Thomas Witkowski's avatar
Thomas Witkowski committed
753 754 755
      (coarseSpaceMap.size() ? coarseSpaceMap[rowComp] : NULL);

    map<DegreeOfFreedom, double> &dirichletValues = vec->getDirichletValues();
756

Thomas Witkowski's avatar
Thomas Witkowski committed
757 758 759
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
Thomas Witkowski's avatar
Thomas Witkowski committed
760 761 762 763 764
      
      DegreeOfFreedom dof = dofIt.getDOFIndex();
      
      if (rankOnly && !(*interiorMap)[rowComp].isRankDof(dof))
	continue;
765

766 767
      bool isCoarseDof = isCoarseSpace(rowComp, dof);

Thomas Witkowski's avatar
Thomas Witkowski committed
768
      // Dirichlet rows can be set only be the owner ranks.
769 770 771 772 773
      if (dirichletValues.count(dof)) {
	if ((!isCoarseDof && !((*interiorMap)[rowComp].isRankDof(dof))) ||
	    (isCoarseDof && !((*rowCoarseSpace)[rowComp].isRankDof(dof))))
	  continue;
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
774

775
      if (isCoarseDof) {
776 777
	TEST_EXIT_DBG(vecCoarse != PETSC_NULL)("Should not happen!\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
778
	int index = rowCoarseSpace->getMatIndex(rowComp, dof);
779 780
	VecSetValue(vecCoarse, index, *dofIt, ADD_VALUES);
      } else {
Thomas Witkowski's avatar
Thomas Witkowski committed
781
	if ((*interiorMap)[rowComp].isSet(dof) == false)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
782 783
	  continue;

784
	// Calculate global row index of the DOF.
Thomas Witkowski's avatar
Thomas Witkowski committed
785
	DegreeOfFreedom globalRowDof = (*interiorMap)[rowComp][dof].global;
786 787 788 789 790
	
	// Get PETSc's mat index of the row DOF.
	int index = 0;
	if (interiorMap->isMatIndexFromGlobal())
	  index = 
Thomas Witkowski's avatar
Thomas Witkowski committed
791
	    interiorMap->getMatIndex(rowComp, globalRowDof) + rStartInterior;
792 793
	else
	  index =
Thomas Witkowski's avatar
Thomas Witkowski committed
794
	    interiorMap->getMatIndex(rowComp, dof) + rStartInterior;
795

796
	if (perMap.isPeriodic(feSpace, globalRowDof)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
797 798 799
	  std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
	  double value = *dofIt / (perAsc.size() + 1.0);
	  VecSetValue(vecInterior, index, value, ADD_VALUES);
800

Thomas Witkowski's avatar
Thomas Witkowski committed
801 802 803
	  for (std::set<int>::iterator perIt = perAsc.begin(); 
	       perIt != perAsc.end(); ++perIt) {
	    int mappedDof = perMap.map(feSpace, *perIt, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
804
	    int mappedIndex = interiorMap->getMatIndex(rowComp, mappedDof);
805

Thomas Witkowski's avatar
Thomas Witkowski committed
806
	    VecSetValue(vecInterior, mappedIndex, value, ADD_VALUES);
807 808 809
	  }	  
	} else {	  
	  // The DOF index is not periodic.
Thomas Witkowski's avatar
Thomas Witkowski committed
810 811
	  VecSetValue(vecInterior, index, *dofIt, ADD_VALUES);
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
812 813 814 815
      }
    }
  }

816 817 818 819 820 821 822 823 824 825

  PetscSolver* PetscSolverGlobalMatrix::createSubSolver(int component,
							string kspPrefix)
  {
    FUNCNAME("PetscSolverGlobalMatrix::createSubSolver()");

    vector<const FiniteElemSpace*> fe;
    fe.push_back(componentSpaces[component]);

    PetscSolver* subSolver = new PetscSolverGlobalMatrix("");
826
    subSolver->setKspPrefix(kspPrefix);
827 828 829 830 831 832 833 834 835 836 837 838
    subSolver->setMeshDistributor(meshDistributor,
				  mpiCommGlobal,
				  mpiCommLocal);
    subSolver->init(fe, fe);

    ParallelDofMapping &subDofMap = subSolver->getDofMap();
    subDofMap[0] = dofMap[component];
    subDofMap.update();

    return subSolver;
  }

839 840 841 842

  void PetscSolverGlobalMatrix::setConstantNullSpace(KSP ksp,
						     int constFeSpace,
						     bool test)
Thomas Witkowski's avatar
blub  
Thomas Witkowski committed
843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865
  {
    FUNCNAME("PetscSolverGlobalMatrix::setConstantNullSpace()");

    Vec nullSpaceBasis;
    VecDuplicate(getVecSolInterior(), &nullSpaceBasis);
    
    SystemVector basisVec("tmp", componentSpaces, componentSpaces.size(), true);
    basisVec.set(0.0);
    basisVec.getDOFVector(constFeSpace)->set(1.0);
    
    setDofVector(nullSpaceBasis, basisVec, true);
    VecAssemblyBegin(nullSpaceBasis);
    VecAssemblyEnd(nullSpaceBasis);
    VecNormalize(nullSpaceBasis, PETSC_NULL);
    
    if (test) {
      Vec tmp;
      MatGetVecs(getMatInterior(), &tmp, PETSC_NULL);
      MatMult(getMatInterior(), nullSpaceBasis, tmp);
      PetscReal n;
      VecNorm(tmp, NORM_2, &n);
      MSG("NORM IS: %e\n", n);
      VecDestroy(&tmp);
866
    }
Thomas Witkowski's avatar
blub  
Thomas Witkowski committed
867 868 869 870 871 872 873 874
    
    
    MatNullSpace matNullSpace;
    MatNullSpaceCreate(mpiCommGlobal, PETSC_FALSE, 1, &nullSpaceBasis, &matNullSpace);
    KSPSetNullSpace(ksp, matNullSpace);
    MatNullSpaceDestroy(&matNullSpace);
  }

875

Thomas Witkowski's avatar
blub  
Thomas Witkowski committed
876 877 878 879 880 881 882 883 884
  void PetscSolverGlobalMatrix::setConstantNullSpace(KSP ksp)
  {
    FUNCNAME("PetscSolverGlobalMatrix::setConstantNullSpace()");

    MatNullSpace matNullSpace;
    MatNullSpaceCreate(mpiCommGlobal, PETSC_TRUE, 0, PETSC_NULL, &matNullSpace);
    KSPSetNullSpace(ksp, matNullSpace);
    MatNullSpaceDestroy(&matNullSpace);
  }
885

Thomas Witkowski's avatar
Thomas Witkowski committed
886
}