PetscSolverGlobalMatrix.cc 24.9 KB
Newer Older
Thomas Witkowski's avatar
Thomas Witkowski committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
//
// Software License for AMDiS
//
// Copyright (c) 2010 Dresden University of Technology 
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
// This file is part of AMDiS
//
// See also license.opensource.txt in the distribution.


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

namespace AMDiS {

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

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

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

31
    // === Create PETSc vector (solution and a temporary vector). ===
Thomas Witkowski's avatar
Thomas Witkowski committed
32

33 34
    VecCreateMPI(PETSC_COMM_WORLD, nRankRows, nOverallRows, &petscSolVec);
    VecCreateMPI(PETSC_COMM_WORLD, nRankRows, nOverallRows, &petscTmpVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
35 36

    int recvAllValues = 0;
37 38 39 40
    int sendValue = 
      static_cast<int>(meshDistributor->getLastMeshChangeIndex() != lastMeshNnz);
    meshDistributor->getMpiComm().Allreduce(&sendValue, &recvAllValues, 
					    1, MPI_INT, MPI_SUM);
Thomas Witkowski's avatar
Thomas Witkowski committed
41

42 43 44
    recvAllValues = 1;

    if (!d_nnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
45 46 47 48 49

      // Global DOF mapping must only be recomputed, if the NNZ structure has
      // changed (thus, also the mesh has changed).
      createGlobalDofMapping(feSpaces);

Thomas Witkowski's avatar
Thomas Witkowski committed
50 51 52 53 54 55 56 57 58 59 60 61 62 63
      if (d_nnz) {
	delete [] d_nnz;
	d_nnz = NULL;
	delete [] o_nnz;
	o_nnz = NULL;
      }

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


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

64
    MatCreateMPIAIJ(PETSC_COMM_WORLD, nRankRows, nRankRows, 
65
 		    nOverallRows, nOverallRows,
66
		    0, d_nnz, 0, o_nnz, &petscMatrix);
67

Thomas Witkowski's avatar
Thomas Witkowski committed
68 69 70 71 72 73 74
#if (DEBUG != 0)
    MSG("Fill petsc matrix 1 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

#if (DEBUG != 0)
    int a, b;
    MatGetOwnershipRange(petscMatrix, &a, &b);
75
    TEST_EXIT(a == meshDistributor->getStartDofs(feSpaces))
Thomas Witkowski's avatar
Thomas Witkowski committed
76
      ("Wrong matrix ownership range!\n");
77
    TEST_EXIT(b == meshDistributor->getStartDofs(feSpaces) + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
78 79 80 81 82 83
      ("Wrong matrix ownership range!\n");
#endif


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

84
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
85 86 87
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
	if ((*mat)[i][j])
88
	  setDofMatrix((*mat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
89 90 91 92 93 94 95 96

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

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

97 98 99 100 101 102 103 104 105 106 107 108 109
    // === Init PETSc solver. ===
    KSPCreate(PETSC_COMM_WORLD, &solver);
    KSPGetPC(solver, &pc);
    KSPSetOperators(solver, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN); 
    KSPSetTolerances(solver, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(solver, KSPBCGS);
    KSPSetFromOptions(solver);
    PCSetFromOptions(pc);

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

110 111 112 113 114 115 116
    MSG("Fill petsc matrix needed %.5f seconds\n", MPI::Wtime() - wtime);
  }


  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
117
   
118 119
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
    TEST_EXIT_DBG(meshDistributor)("No mesh distributor defined!\n");
120

121 122 123
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(vec);
    int nRankRows = meshDistributor->getNumberRankDofs(feSpaces);
    int nOverallRows = meshDistributor->getNumberOverallDofs(feSpaces);
124 125

    VecCreateMPI(PETSC_COMM_WORLD, nRankRows, nOverallRows, &petscRhsVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
126 127

    // === Transfer values from DOF vector to the PETSc vector. === 
128
    for (int i = 0; i < vec->getSize(); i++)
129
      setDofVector(petscRhsVec, vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
130 131 132 133 134 135

    VecAssemblyBegin(petscRhsVec);
    VecAssemblyEnd(petscRhsVec);
  }


136 137
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
138 139 140 141 142 143 144 145 146 147
  {
    FUNCNAME("PetscSolverGlobalMatrix::solvePetscMatrix()");

    int nComponents = vec.getSize();

    // === Set old solution to be initiual guess for PETSc solver. ===
    if (!zeroStartVector) {
      VecSet(petscSolVec, 0.0);
      
      for (int i = 0; i < nComponents; i++)
148
	setDofVector(petscSolVec, vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Thomas Witkowski committed
149 150 151 152 153 154 155 156 157 158 159 160
      
      VecAssemblyBegin(petscSolVec);
      VecAssemblyEnd(petscSolVec);
    }

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

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

161
    int c = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
162
    for (int i = 0; i < nComponents; i++) {
163
      DOFVector<double> &dv = *(vec.getDOFVector(i));
164 165
      const FiniteElemSpace *feSpace = dv.getFeSpace();
      int nRankDofs = meshDistributor->getNumberRankDofs(feSpace);
166

Thomas Witkowski's avatar
Thomas Witkowski committed
167
      for (int j = 0; j < nRankDofs; j++)
168
	dv[meshDistributor->mapLocalToDof(feSpace, j)] = vecPointer[c++]; 
Thomas Witkowski's avatar
Thomas Witkowski committed
169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184
    }

    VecRestoreArray(petscSolVec, &vecPointer);


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


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


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

185
    VecDestroy(&petscRhsVec);
186 187 188 189 190 191 192 193 194
  }


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

    MatDestroy(&petscMatrix);
    KSPDestroy(&solver);
195 196
    VecDestroy(&petscSolVec);
    VecDestroy(&petscTmpVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
197 198 199
  }


200 201
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* mat,
					     int nRowMat, int nColMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
202 203 204 205 206 207
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

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

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

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

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

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

224 225 226
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();

Thomas Witkowski's avatar
Thomas Witkowski committed
227 228 229 230 231 232
    // === Traverse all rows of the dof matrix and insert row wise the values ===
    // === to the PETSc matrix.                                               ===

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

233 234 235
      const FiniteElemSpace *rowFe = mat->getRowFeSpace();
      const FiniteElemSpace *colFe = mat->getColFeSpace();

Thomas Witkowski's avatar
Thomas Witkowski committed
236
      // Global index of the current row DOF.
237
      int globalRowDof = 
238
	meshDistributor->mapDofToGlobal(rowFe, *cursor);
Thomas Witkowski's avatar
Thomas Witkowski committed
239
      // Test if the current row DOF is a periodic DOF.
240
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
241

Thomas Witkowski's avatar
Thomas Witkowski committed
242 243 244
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

245
	// Get PETSc's mat row index.
246
	int rowIndex = dofToMatIndex.get(nRowMat, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
247 248 249 250 251 252 253 254

	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.
255
	  int globalColDof = 
256
	    meshDistributor->mapDofToGlobal(colFe, col(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
257
	  // Test if the current col dof is a periodic dof.
258
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
259
	  // Get PETSc's mat col index.
260
	  int colIndex = dofToMatIndex.get(nColMat, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
261 262 263 264 265 266 267 268 269 270 271 272 273 274

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

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

	    // Create set of all periodic associations of the column index.
	    std::set<int> perAsc;
275
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
	      if (*it >= -3)
		perAsc.insert(*it);
    
	    // Scale value to the number of periodic associations of the column index.
	    double scaledValue = 
	      value(*icursor) * pow(0.5, static_cast<double>(perAsc.size()));

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

	    vector<int> newCols;

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

	      for (int i = 0; i < nCols; i++) {
300
 		TEST_EXIT_DBG(perMap.isPeriodic(colFe, *it, newCols[i]))
Thomas Witkowski's avatar
Thomas Witkowski committed
301 302 303
 		  ("Wrong periodic DOF associations at boundary %d with DOF %d!\n",
		   *it, newCols[i]);

304
		newCols.push_back(perMap.map(colFe, *it, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
305 306 307 308
	      }
	    }

	    for (unsigned int i = 0; i < newCols.size(); i++) {
309
	      cols.push_back(dofToMatIndex.get(nColMat, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330
	      values.push_back(scaledValue);	      
	    }
	  }
	}

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

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

	// Traverse all column entries.
	for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); 
	     icursor != icend; ++icursor) {
	  // Global index of the current column index.
331
	  int globalColDof = 
332
	    meshDistributor->mapDofToGlobal(colFe, col(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
333 334 335 336 337 338 339 340 341 342 343

	  // 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;

344 345
	  if (perMap.isPeriodic(colFe, globalColDof)) {
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
346 347 348 349 350 351
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
	      if (*it >= -3)
		perAsc.insert(*it);
	  }

352
	  std::set<int>& perRowAsc = perMap.getAssociations(rowFe, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370
	  for (std::set<int>::iterator it = perRowAsc.begin(); 
	       it != perRowAsc.end(); ++it)
	    if (*it >= -3)
	      perAsc.insert(*it);

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


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

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

371 372
	  // Then, traverse the periodic associations of the row and column
	  // indices and create the corresponding entries.
Thomas Witkowski's avatar
Thomas Witkowski committed
373 374 375 376
	  for (std::set<int>::iterator it = perAsc.begin(); it != perAsc.end(); ++it) {
	    int nEntry = static_cast<int>(entry.size());
	    for (int i = 0; i < nEntry; i++) {
	      int perRowDof = 0;
377

378 379
	      if (perMap.isPeriodic(rowFe, *it, entry[i].first))
		perRowDof = perMap.map(rowFe, *it, entry[i].first);
Thomas Witkowski's avatar
Thomas Witkowski committed
380 381 382 383
	      else
		perRowDof = entry[i].first;

	      int perColDof;
384 385
	      if (perMap.isPeriodic(colFe, *it, entry[i].second))
		perColDof = perMap.map(colFe, *it, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
386 387 388 389 390 391 392 393 394 395 396
	      else
		perColDof = entry[i].second;	      	      
	      

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


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

397
	  for (unsigned int i = 0; i < entry.size(); i++) {
398 399
	    int rowIdx = dofToMatIndex.get(nRowMat, entry[i].first);
	    int colIdx = dofToMatIndex.get(nColMat, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
400

401 402
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422
	  }
	}


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

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

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


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

430
    const FiniteElemSpace *feSpace = vec->getFeSpace();
431
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
432

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

      // Calculate global row index of the DOF.
      DegreeOfFreedom globalRowDof = 
441
	meshDistributor->mapDofToGlobal(feSpace, dofIt.getDOFIndex());
442
      // Get PETSc's mat index of the row DOF.
443
      int index = dofToMatIndex.get(nRowVec, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
444

445 446
      if (perMap.isPeriodic(feSpace, globalRowDof)) {
	std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
447 448 449
	double value = *dofIt / (perAsc.size() + 1.0);
	VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);

450 451 452
	for (std::set<int>::iterator perIt = perAsc.begin(); 
	     perIt != perAsc.end(); ++perIt) {
	  int mappedDof = perMap.map(feSpace, *perIt, globalRowDof);
453
	  int mappedIndex = dofToMatIndex.get(nRowVec, mappedDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471
	  VecSetValues(petscVec, 1, &mappedIndex, &value, ADD_VALUES);
	}
      } else {
	// The DOF index is not periodic.
	double value = *dofIt;
	VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);
      }
    }
  }


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

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

472 473 474
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
    int nRankRows = meshDistributor->getNumberRankDofs(feSpaces);
    int rankStartIndex = meshDistributor->getStartDofs(feSpaces);
Thomas Witkowski's avatar
Thomas Witkowski committed
475 476 477 478 479 480 481 482 483 484 485 486 487
    d_nnz = new int[nRankRows];
    o_nnz = new int[nRankRows];
    for (int i = 0; i < nRankRows; i++) {
      d_nnz[i] = 0;
      o_nnz[i] = 0;
    }

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

488 489 490 491
    // Stores to each rank a list of nnz entries (i.e. pairs of row and column
    // index) that this rank will send to. These nnz entries will be assembled
    // on this rank, but because the row DOFs are not DOFs of this rank they 
    // will be send to the owner of the row DOFs.
Thomas Witkowski's avatar
Thomas Witkowski committed
492 493 494 495
    map<int, MatrixNnzEntry> sendMatrixEntry;

    // Maps to each DOF that must be send to another rank the rank number of the
    // receiving rank.
496
    map<pair<DegreeOfFreedom, int>, int> sendDofToRank;
Thomas Witkowski's avatar
Thomas Witkowski committed
497

498

499 500 501 502 503 504 505 506 507 508
    // First, create for all ranks, to which we send data to, MatrixNnzEntry 
    // object with 0 entries.
    for (unsigned int i = 0; i < feSpaces.size(); i++) {
      for (DofComm::Iterator it(meshDistributor->getRecvDofs(), feSpaces[i]);
	   !it.end(); it.nextRank()) {
	sendMatrixEntry[it.getRank()].resize(0);
	
	for (; !it.endDofIter(); it.nextDof())
	  sendDofToRank[make_pair(it.getDofIndex(), i)] = it.getRank();
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
509 510
    }

511
    // Create list of ranks from which we receive data from.
Thomas Witkowski's avatar
Thomas Witkowski committed
512
    std::set<int> recvFromRank;
513 514 515 516 517 518 519
    for (unsigned int i = 0; i < feSpaces.size(); i++) 
      for (DofComm::Iterator it(meshDistributor->getSendDofs(), feSpaces[i]);
	   !it.end(); it.nextRank())
	recvFromRank.insert(it.getRank());


    // === Traverse matrices to create nnz data. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
520

521
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
522 523 524 525 526
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
 	if (!(*mat)[i][j])
	  continue;

527 528 529 530 531
	TEST_EXIT_DBG((*mat)[i][j]->getRowFeSpace() == feSpaces[i])
	  ("Should not happen!\n");
	TEST_EXIT_DBG((*mat)[i][j]->getColFeSpace() == feSpaces[j])
	  ("Should not happen!\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
532 533 534 535 536 537 538 539 540 541 542
	Matrix bmat = (*mat)[i][j]->getBaseMatrix();

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

543
	  int globalRowDof =
544
	    meshDistributor->mapDofToGlobal(feSpaces[i], *cursor);
545

546
	  // The corresponding global matrix row index of the current row DOF.
547
	  int petscRowIdx = dofToMatIndex.get(i, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
548
	  
549
	  if (meshDistributor->getIsRankDof(feSpaces[i], *cursor)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
550
	    	    
551 552
	    // === The current row DOF is a rank DOF, so create the       ===
	    // === corresponding nnz values directly on rank's nnz data.  ===
Thomas Witkowski's avatar
Thomas Witkowski committed
553 554
	    
	    // This is the local row index of the local PETSc matrix.
555
	    int localPetscRowIdx = petscRowIdx - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
556 557 558 559
	    
	    TEST_EXIT_DBG(localPetscRowIdx >= 0 && localPetscRowIdx < nRankRows)
	      ("Should not happen! \n Debug info: localRowIdx = %d   globalRowIndx = %d   petscRowIdx = %d   localPetscRowIdx = %d   rStart = %d   nCompontens = %d   nRankRows = %d\n",
	       *cursor, 
560
	       meshDistributor->mapDofToGlobal(feSpaces[i], *cursor), 
Thomas Witkowski's avatar
Thomas Witkowski committed
561 562
	       petscRowIdx, 
	       localPetscRowIdx, 
563
	       rankStartIndex,
Thomas Witkowski's avatar
Thomas Witkowski committed
564 565 566 567 568 569 570
	       nComponents, 
	       nRankRows);
	    
	    
	    // Traverse all non zero entries in this row.
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
571
	      int globalColDof =
572
		meshDistributor->mapDofToGlobal(feSpaces[j], col(*icursor));
573
	      int petscColIdx = dofToMatIndex.get(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
574 575 576
	      
	      if (value(*icursor) != 0.0 || petscRowIdx == petscColIdx) {
		// The row DOF is a rank DOF, if also the column is a rank DOF, 
577 578 579 580
		// increment the d_nnz values for this row, otherwise the 
		// o_nnz value.
		if (petscColIdx >= rankStartIndex && 
		    petscColIdx < rankStartIndex + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
581 582 583 584 585 586
		  d_nnz[localPetscRowIdx]++;
		else
		  o_nnz[localPetscRowIdx]++;
	      }    
	    }
	  } else {
587 588 589 590 591
	    // === The current row DOF is not a rank DOF, i.e., its values   ===
	    // === are also created on this rank, but afterthere they will   ===
	    // === be send to another rank. So we need to send also the      ===
	    // === corresponding nnz structure of this row to the corres-    ===
	    // === ponding rank.                                             ===
Thomas Witkowski's avatar
Thomas Witkowski committed
592 593
	    
	    // Send all non zero entries to the member of the row DOF.
594
	    int sendToRank = sendDofToRank[make_pair(*cursor, i)];
Thomas Witkowski's avatar
Thomas Witkowski committed
595 596 597 598
	    
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
	      if (value(*icursor) != 0.0) {
599
		int globalColDof =
600
		  meshDistributor->mapDofToGlobal(feSpaces[j], col(*icursor));
601
		int petscColIdx = dofToMatIndex.get(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622
		
		sendMatrixEntry[sendToRank].
		  push_back(make_pair(petscRowIdx, petscColIdx));
	      }
	    }
	    
	  } // if (isRankDof[*cursor]) ... else ...
	} // for each row in mat[i][j]
      } 
    }

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

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


623 624
    // === Evaluate the nnz structure this rank got from other ranks and add ===
    // === it to the PETSc nnz data structure.                               ===
Thomas Witkowski's avatar
Thomas Witkowski committed
625 626 627 628 629 630 631 632

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

633
	  int localRowIdx = r - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
634 635 636 637 638

	  TEST_EXIT_DBG(localRowIdx >= 0 && localRowIdx < nRankRows)
	    ("Got row index %d/%d (nRankRows = %d) from rank %d. Should not happen!\n",
	     r, localRowIdx, nRankRows, it->first);
	  
639
	  if (c < rankStartIndex || c >= rankStartIndex + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657
	    o_nnz[localRowIdx]++;
	  else
	    d_nnz[localRowIdx]++;
	}
      }
    }

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

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

658 659 660 661 662 663 664 665

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

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

666
    dofToMatIndex.clear();
667
  
668 669 670 671 672 673 674 675
    for (unsigned int i = 0; i < feSpaces.size(); i++) {

      // === Create indices for all DOFs in rank' domain. ===
      std::set<const DegreeOfFreedom*> rankDofSet;
      mesh->getAllDofs(feSpaces[i], rankDofSet);
      for (std::set<const DegreeOfFreedom*>::iterator it = rankDofSet.begin();
	   it != rankDofSet.end(); ++it)
	if (meshDistributor->getIsRankDof(feSpaces[i], **it)) {
676
	  int globalIndex = 
677
	    meshDistributor->mapDofToGlobal(feSpaces[i], **it);
678 679
	  int globalMatIndex =  
	    globalIndex - meshDistributor->getStartDofs(feSpaces[i]) + offset;
680

681
	  dofToMatIndex.add(i, globalIndex, globalMatIndex);
682 683 684
	}
	  

685
      // === Communicate interior boundary DOFs between domains. ===
686 687 688 689 690 691 692 693

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

	for (; !it.endDofIter(); it.nextDof()) {
694
	  int globalIndex = 
695
	    meshDistributor->mapDofToGlobal(feSpaces[i], it.getDofIndex());
696
	  int globalMatIndex = dofToMatIndex.get(i, globalIndex);
697
	  sendGlobalDofs.push_back(globalMatIndex);
698 699 700 701 702 703 704 705 706 707 708 709 710 711
	}

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

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

      stdMpi.startCommunication();

      for (DofComm::Iterator it(meshDistributor->getRecvDofs(), feSpaces[i]);
	   !it.end(); it.nextRank())
	for (; !it.endDofIter(); it.nextDof()) {
712 713 714 715
	  int globalIndex = 
	    meshDistributor->mapDofToGlobal(feSpaces[i], it.getDofIndex());
	  int globalMatIndex = 
	    stdMpi.getRecvData(it.getRank())[it.getDofCounter()];
716

717
	  dofToMatIndex.add(i, globalIndex, globalMatIndex);
718 719 720 721 722 723 724 725 726 727 728 729
	}


      // === Communicate DOFs on periodic boundaries. ===

      stdMpi.clear();

      for (DofComm::Iterator it(meshDistributor->getPeriodicDofs(), feSpaces[i]);
	   !it.end(); it.nextRank()) {
	vector<DegreeOfFreedom> sendGlobalDofs;
	
	for (; !it.endDofIter(); it.nextDof()) {
730 731
	  int ind0 = 
	    meshDistributor->mapDofToGlobal(feSpaces[i], it.getDofIndex());
732
	  int ind1 = dofToMatIndex.get(i, ind0);
733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749

	  sendGlobalDofs.push_back(ind0);
	  sendGlobalDofs.push_back(ind1);
	}

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

      stdMpi.startCommunication();

      for (DofComm::Iterator it(meshDistributor->getPeriodicDofs(), feSpaces[i]);
	   !it.end(); it.nextRank())
	for (; !it.endDofIter(); it.nextDof()) {
	  int ind0 = stdMpi.getRecvData(it.getRank())[it.getDofCounter() * 2];
	  int ind1 = stdMpi.getRecvData(it.getRank())[it.getDofCounter() * 2 + 1];

750
	  dofToMatIndex.add(i, ind0, ind1);
751 752 753 754 755 756 757
	}
      
      // === Update offset. ===

      offset += meshDistributor->getNumberRankDofs(feSpaces[i]);
    }
  }
Thomas Witkowski's avatar
Thomas Witkowski committed
758
}