PetscSolverGlobalMatrix.cc 22.5 KB
Newer Older
Thomas Witkowski's avatar
Thomas Witkowski committed
1 2 3 4 5 6 7 8 9 10 11 12
//
// Software License for AMDiS
//
// Copyright (c) 2010 Dresden University of Technology 
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
// This file is part of AMDiS
//
// See also license.opensource.txt in the distribution.


13
#include "AMDiS.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
14 15 16 17 18 19
#include "parallel/PetscSolverGlobalMatrix.h"
#include "parallel/StdMpi.h"
#include "parallel/MpiHelper.h"

namespace AMDiS {

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

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

30 31 32
    
    // === Check if mesh was changed and, in this case, recompute matrix ===
    // === nnz structure and matrix indices.                             ===
33

Thomas Witkowski's avatar
Thomas Witkowski committed
34
    int recvAllValues = 0;
35 36
    int sendValue = 
      static_cast<int>(meshDistributor->getLastMeshChangeIndex() != lastMeshNnz);
Thomas Witkowski's avatar
Thomas Witkowski committed
37
    mpiComm.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
Thomas Witkowski's avatar
Thomas Witkowski committed
38

39
    if (!d_nnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
40 41 42
      vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
      dofMap->setComputeMatIndex(true, true);
      dofMap->update(feSpaces);
43

Thomas Witkowski's avatar
Thomas Witkowski committed
44 45 46 47 48 49 50 51 52 53 54 55
      if (d_nnz) {
	delete [] d_nnz;
	d_nnz = NULL;
	delete [] o_nnz;
	o_nnz = NULL;
      }

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


56 57
    // === Create PETSc vector (solution and a temporary vector). ===

58 59
    int nRankRows = dofMap->getRankDofs();
    int nOverallRows = dofMap->getOverallDofs();
60 61 62 63 64 65 66 67 68 69 70 71

    VecCreateMPI(mpiComm, nRankRows, nOverallRows, &petscSolVec);
    VecCreateMPI(mpiComm, nRankRows, nOverallRows, &petscTmpVec);

    int testddd = 1;
    Parameters::get("block size", testddd);
    if (testddd > 1) {
      VecSetBlockSize(petscSolVec, testddd);
      VecSetBlockSize(petscTmpVec, testddd);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
72 73
    // === Create PETSc matrix with the computed nnz data structure. ===

74
    MatCreateMPIAIJ(mpiComm, nRankRows, nRankRows, 
75
 		    nOverallRows, nOverallRows,
76
		    0, d_nnz, 0, o_nnz, &petscMatrix);
77

78 79 80 81 82
    if (testddd > 1) {
      MatSetBlockSize(petscMatrix, testddd);
      MSG("MAT SET BLOCK SIZE: %d\n", testddd);
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
83 84 85 86 87 88 89
#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);
90 91
    TEST_EXIT(a == dofMap->getStartDofs())("Wrong matrix ownership range!\n");
    TEST_EXIT(b == dofMap->getStartDofs() + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
92 93 94 95 96 97
      ("Wrong matrix ownership range!\n");
#endif


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

98
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
99 100 101
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
	if ((*mat)[i][j])
102
	  setDofMatrix((*mat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
103 104 105 106 107 108 109 110

#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);

111
    // === Init PETSc solver. ===
112
    KSPCreate(mpiComm, &solver);
113 114 115 116
    KSPGetPC(solver, &pc);
    KSPSetOperators(solver, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN); 
    KSPSetTolerances(solver, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(solver, KSPBCGS);
117
    KSPSetOptionsPrefix(solver, kspPrefix.c_str());
118 119 120 121 122 123 124
    KSPSetFromOptions(solver);
    PCSetFromOptions(pc);

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

125 126 127 128 129 130 131
    MSG("Fill petsc matrix needed %.5f seconds\n", MPI::Wtime() - wtime);
  }


  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
Thomas Witkowski's avatar
Thomas Witkowski committed
132

133
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
134
    TEST_EXIT_DBG(dofMap)("No parallel DOF map defined!\n");
135

136 137
    int nRankRows = dofMap->getRankDofs();
    int nOverallRows = dofMap->getOverallDofs();
138

139
    VecCreateMPI(mpiComm, nRankRows, nOverallRows, &petscRhsVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
140

141 142 143 144 145 146
    int testddd = 1;
    Parameters::get("block size", testddd);
    if (testddd > 1)
      VecSetBlockSize(petscRhsVec, testddd);


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

    VecAssemblyBegin(petscRhsVec);
    VecAssemblyEnd(petscRhsVec);
153 154

    if (removeRhsNullSpace) {
155
      MSG("Remove constant null space from the RHS!\n");
156
      MatNullSpace sp;
157
      MatNullSpaceCreate(mpiComm, PETSC_TRUE, 0, PETSC_NULL, &sp);
158 159 160
      MatNullSpaceRemove(sp, petscRhsVec, PETSC_NULL);
      MatNullSpaceDestroy(&sp);
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
161 162 163
  }


164 165
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
166 167 168 169 170 171 172 173 174 175
  {
    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++)
176
	setDofVector(petscSolVec, vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Thomas Witkowski committed
177 178 179 180 181 182
      
      VecAssemblyBegin(petscSolVec);
      VecAssemblyEnd(petscSolVec);
    }

    // PETSc.
183 184 185 186 187
    PetscErrorCode solverError = KSPSolve(solver, petscRhsVec, petscSolVec);
    if (solverError != 0) {
      AMDiS::finalize();
      exit(-1);
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
188 189 190 191 192

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

193
    int c = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
194
    for (int i = 0; i < nComponents; i++) {
195
      DOFVector<double> &dv = *(vec.getDOFVector(i));
196
      DofMap& d = (*dofMap)[dv.getFeSpace()].getMap();
197 198 199
      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
200 201 202 203 204 205 206 207 208 209 210 211
    }

    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);
212 213 214 215 216 217 218 219 220
  }


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

    MatDestroy(&petscMatrix);
    KSPDestroy(&solver);
221 222
    VecDestroy(&petscSolVec);
    VecDestroy(&petscTmpVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
223 224 225
  }


226 227 228 229 230 231 232 233
  void PetscSolverGlobalMatrix::destroyVectorData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyVectorData()");

    VecDestroy(&petscRhsVec);
  }


234 235
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* mat,
					     int nRowMat, int nColMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
236 237 238 239 240 241
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

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

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
242
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
243 244 245 246 247 248 249 250 251 252 253 254 255 256 257
    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;

258 259 260
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();

Thomas Witkowski's avatar
Thomas Witkowski committed
261 262 263 264 265 266
    // === 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) {

267 268 269
      const FiniteElemSpace *rowFe = mat->getRowFeSpace();
      const FiniteElemSpace *colFe = mat->getColFeSpace();

Thomas Witkowski's avatar
Thomas Witkowski committed
270
      // Global index of the current row DOF.
271
      int globalRowDof = (*dofMap)[rowFe][*cursor].global;
272

Thomas Witkowski's avatar
Thomas Witkowski committed
273
      // Test if the current row DOF is a periodic DOF.
274
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
275

Thomas Witkowski's avatar
Thomas Witkowski committed
276 277 278
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

279
	// Get PETSc's mat row index.
280
	int rowIndex = dofMap->getMatIndex(nRowMat, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
281 282 283 284 285 286 287 288

	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.
289
	  int globalColDof = (*dofMap)[colFe][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
290
	  // Test if the current col dof is a periodic dof.
291
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
292
	  // Get PETSc's mat col index.
293
	  int colIndex = dofMap->getMatIndex(nColMat, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
294 295 296 297 298 299 300 301 302 303 304 305 306 307

	  // 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;
308
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
309 310
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
311
	      if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
312 313 314 315 316 317 318 319 320 321 322 323 324 325
		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);
326

Thomas Witkowski's avatar
Thomas Witkowski committed
327 328 329 330 331 332
	    // 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++) {
333
 		TEST_EXIT_DBG(perMap.isPeriodic(colFe, *it, newCols[i]))
Thomas Witkowski's avatar
Thomas Witkowski committed
334 335 336
 		  ("Wrong periodic DOF associations at boundary %d with DOF %d!\n",
		   *it, newCols[i]);

337
		newCols.push_back(perMap.map(colFe, *it, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
338 339 340 341
	      }
	    }

	    for (unsigned int i = 0; i < newCols.size(); i++) {
342
	      cols.push_back(dofMap->getMatIndex(nColMat, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363
	      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.
364
	  int globalColDof = (*dofMap)[colFe][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
365 366 367 368 369 370 371 372 373 374

	  // 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;

375 376
	  if (perMap.isPeriodic(colFe, globalColDof)) {
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
377 378
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
379
	      if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
380 381 382
		perAsc.insert(*it);
	  }

383
	  std::set<int>& perRowAsc = perMap.getAssociations(rowFe, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
384 385
	  for (std::set<int>::iterator it = perRowAsc.begin(); 
	       it != perRowAsc.end(); ++it)
386
	    if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
387 388 389 390 391 392 393 394 395 396 397 398 399 400 401
	      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));

402 403
	  // Then, traverse the periodic associations of the row and column
	  // indices and create the corresponding entries.
Thomas Witkowski's avatar
Thomas Witkowski committed
404 405 406 407
	  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;
408

409 410
	      if (perMap.isPeriodic(rowFe, *it, entry[i].first))
		perRowDof = perMap.map(rowFe, *it, entry[i].first);
Thomas Witkowski's avatar
Thomas Witkowski committed
411 412 413 414
	      else
		perRowDof = entry[i].first;

	      int perColDof;
415 416
	      if (perMap.isPeriodic(colFe, *it, entry[i].second))
		perColDof = perMap.map(colFe, *it, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
417 418 419 420 421 422 423 424 425 426 427
	      else
		perColDof = entry[i].second;	      	      
	      

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


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

428
	  for (unsigned int i = 0; i < entry.size(); i++) {
429 430
	    int rowIdx = dofMap->getMatIndex(nRowMat, entry[i].first);
	    int colIdx = dofMap->getMatIndex(nColMat, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
431

432 433
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
434 435 436 437 438 439 440 441 442 443 444 445
	  }
	}


	// === 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;
446

Thomas Witkowski's avatar
Thomas Witkowski committed
447 448 449 450 451 452 453 454
	  MatSetValues(petscMatrix, 1, &rowIndex, rowIt->second.size(),
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


455 456
  void PetscSolverGlobalMatrix::setDofVector(Vec& petscVec, 
					     DOFVector<double>* vec, 
457
					     int nRowVec, 
458
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
459 460 461
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

462
    const FiniteElemSpace *feSpace = vec->getFeSpace();
463
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
464

Thomas Witkowski's avatar
Thomas Witkowski committed
465 466 467
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
468
      if (rankOnly && !(*dofMap)[feSpace].isRankDof(dofIt.getDOFIndex()))
Thomas Witkowski's avatar
Thomas Witkowski committed
469 470 471 472
	continue;

      // Calculate global row index of the DOF.
      DegreeOfFreedom globalRowDof = 
473
	(*dofMap)[feSpace][dofIt.getDOFIndex()].global;
474
      // Get PETSc's mat index of the row DOF.
475
      int index = dofMap->getMatIndex(nRowVec, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
476

477 478
      if (perMap.isPeriodic(feSpace, globalRowDof)) {
	std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
479 480 481
	double value = *dofIt / (perAsc.size() + 1.0);
	VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);

482 483 484
	for (std::set<int>::iterator perIt = perAsc.begin(); 
	     perIt != perAsc.end(); ++perIt) {
	  int mappedDof = perMap.map(feSpace, *perIt, globalRowDof);
485
	  int mappedIndex = dofMap->getMatIndex(nRowVec, mappedDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503
	  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");

504
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
505 506
    int nRankRows = dofMap->getRankDofs();
    int rankStartIndex = dofMap->getStartDofs();
507

Thomas Witkowski's avatar
Thomas Witkowski committed
508 509 510 511 512 513 514 515 516 517 518 519 520
    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;

521 522 523 524
    // 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
525 526 527 528
    map<int, MatrixNnzEntry> sendMatrixEntry;

    // Maps to each DOF that must be send to another rank the rank number of the
    // receiving rank.
529
    map<pair<DegreeOfFreedom, int>, int> sendDofToRank;
Thomas Witkowski's avatar
Thomas Witkowski committed
530

531

532 533 534
    // 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++) {
535
      for (DofComm::Iterator it(meshDistributor->getDofComm().getRecvDofs(), feSpaces[i]);
536 537 538 539 540 541
	   !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
542 543
    }

544
    // Create list of ranks from which we receive data from.
Thomas Witkowski's avatar
Thomas Witkowski committed
545
    std::set<int> recvFromRank;
546
    for (unsigned int i = 0; i < feSpaces.size(); i++) 
547
      for (DofComm::Iterator it(meshDistributor->getDofComm().getSendDofs(), feSpaces[i]);
548 549 550 551 552
	   !it.end(); it.nextRank())
	recvFromRank.insert(it.getRank());


    // === Traverse matrices to create nnz data. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
553

554
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
555 556 557 558 559
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
 	if (!(*mat)[i][j])
	  continue;

560 561 562 563 564
	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
565 566 567 568 569 570 571 572 573 574
	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) {
575
	  int globalRowDof = (*dofMap)[feSpaces[i]][*cursor].global;
576

577
	  // The corresponding global matrix row index of the current row DOF.
578 579
	  int petscRowIdx = dofMap->getMatIndex(i, globalRowDof);
	  if ((*dofMap)[feSpaces[i]].isRankDof(*cursor)) {
580
    	    
581 582
	    // === 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
583 584
	    
	    // This is the local row index of the local PETSc matrix.
585
	    int localPetscRowIdx = petscRowIdx - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
586 587 588
	    
	    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",
589
	       *cursor,
590
	       (*dofMap)[feSpaces[i]][*cursor].global,
Thomas Witkowski's avatar
Thomas Witkowski committed
591 592
	       petscRowIdx, 
	       localPetscRowIdx, 
593
	       rankStartIndex,
Thomas Witkowski's avatar
Thomas Witkowski committed
594 595 596 597 598 599 600
	       nComponents, 
	       nRankRows);
	    
	    
	    // Traverse all non zero entries in this row.
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
601 602
	      int globalColDof = (*dofMap)[feSpaces[j]][col(*icursor)].global;
	      int petscColIdx = dofMap->getMatIndex(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
603 604 605
	      
	      if (value(*icursor) != 0.0 || petscRowIdx == petscColIdx) {
		// The row DOF is a rank DOF, if also the column is a rank DOF, 
606 607 608 609
		// 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
610 611 612 613 614 615
		  d_nnz[localPetscRowIdx]++;
		else
		  o_nnz[localPetscRowIdx]++;
	      }    
	    }
	  } else {
616 617 618 619 620
	    // === 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
621 622
	    
	    // Send all non zero entries to the member of the row DOF.
623
	    int sendToRank = sendDofToRank[make_pair(*cursor, i)];
Thomas Witkowski's avatar
Thomas Witkowski committed
624 625 626 627
	    
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
	      if (value(*icursor) != 0.0) {
628
		int globalColDof = 
629 630
		  (*dofMap)[feSpaces[j]][col(*icursor)].global;
		int petscColIdx = dofMap->getMatIndex(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
631 632 633 634 635 636 637 638 639 640 641 642 643
		
		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. ===

644
    StdMpi<MatrixNnzEntry> stdMpi(mpiComm, true);
Thomas Witkowski's avatar
Thomas Witkowski committed
645 646 647 648 649 650 651
    stdMpi.send(sendMatrixEntry);
    for (std::set<int>::iterator it = recvFromRank.begin(); 
	 it != recvFromRank.end(); ++it)
      stdMpi.recv(*it);
    stdMpi.startCommunication();


652 653
    // === 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
654 655 656 657 658 659 660 661

    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;

662
	  int localRowIdx = r - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
663 664 665 666 667

	  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);
	  
668
	  if (c < rankStartIndex || c >= rankStartIndex + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687
	    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);
  }

}