PetscSolverGlobalMatrix.cc 25.4 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 37 38 39 40 41 42 43
    int testddd = 1;
    Parameters::get("block size", testddd);
    if (testddd > 1) {
      VecSetBlockSize(petscSolVec, testddd);
      VecSetBlockSize(petscTmpVec, testddd);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
44
    int recvAllValues = 0;
45 46 47 48
    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
49

50 51 52
    recvAllValues = 1;

    if (!d_nnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
53 54 55 56 57

      // 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
58 59 60 61 62 63 64 65 66 67 68 69 70 71
      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. ===

72
    MatCreateMPIAIJ(PETSC_COMM_WORLD, nRankRows, nRankRows, 
73
 		    nOverallRows, nOverallRows,
74
		    0, d_nnz, 0, o_nnz, &petscMatrix);
75

76 77 78 79 80
    if (testddd > 1) {
      MatSetBlockSize(petscMatrix, testddd);
      MSG("MAT SET BLOCK SIZE: %d\n", testddd);
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
81 82 83 84 85 86 87
#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);
88
    TEST_EXIT(a == meshDistributor->getStartDofs(feSpaces))
Thomas Witkowski's avatar
Thomas Witkowski committed
89
      ("Wrong matrix ownership range!\n");
90
    TEST_EXIT(b == meshDistributor->getStartDofs(feSpaces) + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
91 92 93 94 95 96
      ("Wrong matrix ownership range!\n");
#endif


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

97
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
98 99 100
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
	if ((*mat)[i][j])
101
	  setDofMatrix((*mat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
102 103 104 105 106 107 108 109

#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);

110 111 112 113 114 115 116 117 118 119 120 121 122
    // === 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);

123 124 125 126 127 128 129
    MSG("Fill petsc matrix needed %.5f seconds\n", MPI::Wtime() - wtime);
  }


  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
130
   
131 132
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
    TEST_EXIT_DBG(meshDistributor)("No mesh distributor defined!\n");
133

134 135 136
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(vec);
    int nRankRows = meshDistributor->getNumberRankDofs(feSpaces);
    int nOverallRows = meshDistributor->getNumberOverallDofs(feSpaces);
137 138

    VecCreateMPI(PETSC_COMM_WORLD, nRankRows, nOverallRows, &petscRhsVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
139

140 141 142 143 144 145
    int testddd = 1;
    Parameters::get("block size", testddd);
    if (testddd > 1)
      VecSetBlockSize(petscRhsVec, testddd);


Thomas Witkowski's avatar
Thomas Witkowski committed
146
    // === Transfer values from DOF vector to the PETSc vector. === 
147
    for (int i = 0; i < vec->getSize(); i++)
148
      setDofVector(petscRhsVec, vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
149 150 151 152 153 154

    VecAssemblyBegin(petscRhsVec);
    VecAssemblyEnd(petscRhsVec);
  }


155 156
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
157 158 159 160 161 162 163 164 165 166
  {
    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++)
167
	setDofVector(petscSolVec, vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Thomas Witkowski committed
168 169 170 171 172 173 174 175 176 177 178 179
      
      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);

180
    int c = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
181
    for (int i = 0; i < nComponents; i++) {
182
      DOFVector<double> &dv = *(vec.getDOFVector(i));
183 184
      const FiniteElemSpace *feSpace = dv.getFeSpace();
      int nRankDofs = meshDistributor->getNumberRankDofs(feSpace);
185

Thomas Witkowski's avatar
Thomas Witkowski committed
186
      for (int j = 0; j < nRankDofs; j++)
187
	dv[meshDistributor->mapLocalToDof(feSpace, j)] = vecPointer[c++]; 
Thomas Witkowski's avatar
Thomas Witkowski committed
188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203
    }

    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. ===

204
    VecDestroy(&petscRhsVec);
205 206 207 208 209 210 211 212 213
  }


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

    MatDestroy(&petscMatrix);
    KSPDestroy(&solver);
214 215
    VecDestroy(&petscSolVec);
    VecDestroy(&petscTmpVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
216 217 218
  }


219 220
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* mat,
					     int nRowMat, int nColMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
221 222 223 224 225 226
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

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

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
227
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
228 229 230 231 232 233 234 235 236 237 238 239 240 241 242
    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;

243 244 245
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();

Thomas Witkowski's avatar
Thomas Witkowski committed
246 247 248 249 250 251
    // === 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) {

252 253 254
      const FiniteElemSpace *rowFe = mat->getRowFeSpace();
      const FiniteElemSpace *colFe = mat->getColFeSpace();

Thomas Witkowski's avatar
Thomas Witkowski committed
255
      // Global index of the current row DOF.
256
      int globalRowDof = 
257
	meshDistributor->mapDofToGlobal(rowFe, *cursor);
Thomas Witkowski's avatar
Thomas Witkowski committed
258
      // Test if the current row DOF is a periodic DOF.
259
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
260

Thomas Witkowski's avatar
Thomas Witkowski committed
261 262 263
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

264
	// Get PETSc's mat row index.
265
	int rowIndex = dofToMatIndex.get(nRowMat, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
266 267 268 269 270 271 272 273

	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.
274
	  int globalColDof = 
275
	    meshDistributor->mapDofToGlobal(colFe, col(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
276
	  // Test if the current col dof is a periodic dof.
277
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
278
	  // Get PETSc's mat col index.
279
	  int colIndex = dofToMatIndex.get(nColMat, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
280 281 282 283 284 285 286 287 288 289 290 291 292 293

	  // 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;
294
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318
	    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++) {
319
 		TEST_EXIT_DBG(perMap.isPeriodic(colFe, *it, newCols[i]))
Thomas Witkowski's avatar
Thomas Witkowski committed
320 321 322
 		  ("Wrong periodic DOF associations at boundary %d with DOF %d!\n",
		   *it, newCols[i]);

323
		newCols.push_back(perMap.map(colFe, *it, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
324 325 326 327
	      }
	    }

	    for (unsigned int i = 0; i < newCols.size(); i++) {
328
	      cols.push_back(dofToMatIndex.get(nColMat, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349
	      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.
350
	  int globalColDof = 
351
	    meshDistributor->mapDofToGlobal(colFe, col(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
352 353 354 355 356 357 358 359 360 361 362

	  // 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;

363 364
	  if (perMap.isPeriodic(colFe, globalColDof)) {
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
365 366 367 368 369 370
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
	      if (*it >= -3)
		perAsc.insert(*it);
	  }

371
	  std::set<int>& perRowAsc = perMap.getAssociations(rowFe, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389
	  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));

390 391
	  // Then, traverse the periodic associations of the row and column
	  // indices and create the corresponding entries.
Thomas Witkowski's avatar
Thomas Witkowski committed
392 393 394 395
	  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;
396

397 398
	      if (perMap.isPeriodic(rowFe, *it, entry[i].first))
		perRowDof = perMap.map(rowFe, *it, entry[i].first);
Thomas Witkowski's avatar
Thomas Witkowski committed
399 400 401 402
	      else
		perRowDof = entry[i].first;

	      int perColDof;
403 404
	      if (perMap.isPeriodic(colFe, *it, entry[i].second))
		perColDof = perMap.map(colFe, *it, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
405 406 407 408 409 410 411 412 413 414 415
	      else
		perColDof = entry[i].second;	      	      
	      

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


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

416
	  for (unsigned int i = 0; i < entry.size(); i++) {
417 418
	    int rowIdx = dofToMatIndex.get(nRowMat, entry[i].first);
	    int colIdx = dofToMatIndex.get(nColMat, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
419

420 421
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
422 423 424 425 426 427 428 429 430 431 432 433
	  }
	}


	// === 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;
434

Thomas Witkowski's avatar
Thomas Witkowski committed
435 436 437 438 439 440 441 442
	  MatSetValues(petscMatrix, 1, &rowIndex, rowIt->second.size(),
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


443 444
  void PetscSolverGlobalMatrix::setDofVector(Vec& petscVec, 
					     DOFVector<double>* vec, 
445
					     int nRowVec, 
446
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
447 448 449
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

450
    const FiniteElemSpace *feSpace = vec->getFeSpace();
451
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
452

Thomas Witkowski's avatar
Thomas Witkowski committed
453 454 455
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
456
      if (rankOnly && !meshDistributor->getIsRankDof(feSpace, dofIt.getDOFIndex()))
Thomas Witkowski's avatar
Thomas Witkowski committed
457 458 459 460
	continue;

      // Calculate global row index of the DOF.
      DegreeOfFreedom globalRowDof = 
461
	meshDistributor->mapDofToGlobal(feSpace, dofIt.getDOFIndex());
462
      // Get PETSc's mat index of the row DOF.
463
      int index = dofToMatIndex.get(nRowVec, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
464

465 466
      if (perMap.isPeriodic(feSpace, globalRowDof)) {
	std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
467 468 469
	double value = *dofIt / (perAsc.size() + 1.0);
	VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);

470 471 472
	for (std::set<int>::iterator perIt = perAsc.begin(); 
	     perIt != perAsc.end(); ++perIt) {
	  int mappedDof = perMap.map(feSpace, *perIt, globalRowDof);
473
	  int mappedIndex = dofToMatIndex.get(nRowVec, mappedDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491
	  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");

492 493 494
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
    int nRankRows = meshDistributor->getNumberRankDofs(feSpaces);
    int rankStartIndex = meshDistributor->getStartDofs(feSpaces);
Thomas Witkowski's avatar
Thomas Witkowski committed
495 496 497 498 499 500 501 502 503 504 505 506 507
    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;

508 509 510 511
    // 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
512 513 514 515
    map<int, MatrixNnzEntry> sendMatrixEntry;

    // Maps to each DOF that must be send to another rank the rank number of the
    // receiving rank.
516
    map<pair<DegreeOfFreedom, int>, int> sendDofToRank;
Thomas Witkowski's avatar
Thomas Witkowski committed
517

518

519 520 521 522 523 524 525 526 527 528
    // 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
529 530
    }

531
    // Create list of ranks from which we receive data from.
Thomas Witkowski's avatar
Thomas Witkowski committed
532
    std::set<int> recvFromRank;
533 534 535 536 537 538 539
    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
540

541
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
542 543 544 545 546
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
 	if (!(*mat)[i][j])
	  continue;

547 548 549 550 551
	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
552 553 554 555 556 557 558 559 560 561 562
	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) {

563
	  int globalRowDof =
564
	    meshDistributor->mapDofToGlobal(feSpaces[i], *cursor);
565

566
	  // The corresponding global matrix row index of the current row DOF.
567
	  int petscRowIdx = dofToMatIndex.get(i, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
568
	  
569
	  if (meshDistributor->getIsRankDof(feSpaces[i], *cursor)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
570
	    	    
571 572
	    // === 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
573 574
	    
	    // This is the local row index of the local PETSc matrix.
575
	    int localPetscRowIdx = petscRowIdx - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
576 577 578 579
	    
	    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, 
580
	       meshDistributor->mapDofToGlobal(feSpaces[i], *cursor), 
Thomas Witkowski's avatar
Thomas Witkowski committed
581 582
	       petscRowIdx, 
	       localPetscRowIdx, 
583
	       rankStartIndex,
Thomas Witkowski's avatar
Thomas Witkowski committed
584 585 586 587 588 589 590
	       nComponents, 
	       nRankRows);
	    
	    
	    // Traverse all non zero entries in this row.
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
591
	      int globalColDof =
592
		meshDistributor->mapDofToGlobal(feSpaces[j], col(*icursor));
593
	      int petscColIdx = dofToMatIndex.get(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
594 595 596
	      
	      if (value(*icursor) != 0.0 || petscRowIdx == petscColIdx) {
		// The row DOF is a rank DOF, if also the column is a rank DOF, 
597 598 599 600
		// 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
601 602 603 604 605 606
		  d_nnz[localPetscRowIdx]++;
		else
		  o_nnz[localPetscRowIdx]++;
	      }    
	    }
	  } else {
607 608 609 610 611
	    // === 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
612 613
	    
	    // Send all non zero entries to the member of the row DOF.
614
	    int sendToRank = sendDofToRank[make_pair(*cursor, i)];
Thomas Witkowski's avatar
Thomas Witkowski committed
615 616 617 618
	    
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
	      if (value(*icursor) != 0.0) {
619
		int globalColDof =
620
		  meshDistributor->mapDofToGlobal(feSpaces[j], col(*icursor));
621
		int petscColIdx = dofToMatIndex.get(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642
		
		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();


643 644
    // === 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
645 646 647 648 649 650 651 652

    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;

653
	  int localRowIdx = r - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
654 655 656 657 658

	  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);
	  
659
	  if (c < rankStartIndex || c >= rankStartIndex + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677
	    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);
  }

678 679 680 681 682 683 684 685

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

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

686
    dofToMatIndex.clear();
687
  
688 689 690 691 692 693 694 695
    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)) {
696
	  int globalIndex = 
697
	    meshDistributor->mapDofToGlobal(feSpaces[i], **it);
698 699 700 701 702 703

 	  int globalMatIndex =  
 	    globalIndex - meshDistributor->getStartDofs(feSpaces[i]) + offset;

// 	  int globalMatIndex = 
// 	    globalIndex * feSpaces.size() + i;
704

705
	  dofToMatIndex.add(i, globalIndex, globalMatIndex);
706 707 708
	}
	  

709
      // === Communicate interior boundary DOFs between domains. ===
710 711 712 713 714 715 716 717

      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()) {
718
	  int globalIndex = 
719
	    meshDistributor->mapDofToGlobal(feSpaces[i], it.getDofIndex());
720
	  int globalMatIndex = dofToMatIndex.get(i, globalIndex);
721
	  sendGlobalDofs.push_back(globalMatIndex);
722 723 724 725 726 727 728 729 730 731 732 733 734 735
	}

	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()) {
736 737 738 739
	  int globalIndex = 
	    meshDistributor->mapDofToGlobal(feSpaces[i], it.getDofIndex());
	  int globalMatIndex = 
	    stdMpi.getRecvData(it.getRank())[it.getDofCounter()];
740

741
	  dofToMatIndex.add(i, globalIndex, globalMatIndex);
742 743 744 745 746 747 748 749 750 751 752 753
	}


      // === 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()) {
754 755
	  int ind0 = 
	    meshDistributor->mapDofToGlobal(feSpaces[i], it.getDofIndex());
756
	  int ind1 = dofToMatIndex.get(i, ind0);
757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773

	  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];

774
	  dofToMatIndex.add(i, ind0, ind1);
775 776 777 778 779 780 781
	}
      
      // === Update offset. ===

      offset += meshDistributor->getNumberRankDofs(feSpaces[i]);
    }
  }
Thomas Witkowski's avatar
Thomas Witkowski committed
782
}