PetscSolverGlobalMatrix.cc 25.7 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 25 26 27
  {
    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();
28 29 30
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
    int nRankRows = meshDistributor->getNumberRankDofs(feSpaces);
    int nOverallRows = meshDistributor->getNumberOverallDofs(feSpaces);
Thomas Witkowski's avatar
Thomas Witkowski committed
31

32
    // === Create PETSc vector (solution and a temporary vector). ===
Thomas Witkowski's avatar
Thomas Witkowski committed
33

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

37 38 39 40 41 42 43 44
    int testddd = 1;
    Parameters::get("block size", testddd);
    if (testddd > 1) {
      VecSetBlockSize(petscSolVec, testddd);
      VecSetBlockSize(petscTmpVec, testddd);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
45
    int recvAllValues = 0;
46 47 48 49
    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
50

51 52 53
    recvAllValues = 1;

    if (!d_nnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
54 55 56 57 58

      // 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
59 60 61 62 63 64 65 66 67 68 69 70 71 72
      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. ===

73
    MatCreateMPIAIJ(PETSC_COMM_WORLD, nRankRows, nRankRows, 
74
 		    nOverallRows, nOverallRows,
75
		    0, d_nnz, 0, o_nnz, &petscMatrix);
76

77 78 79 80 81
    if (testddd > 1) {
      MatSetBlockSize(petscMatrix, testddd);
      MSG("MAT SET BLOCK SIZE: %d\n", testddd);
    }

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

111 112 113 114 115 116
    // === 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);
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()");
132
   
133 134
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
    TEST_EXIT_DBG(meshDistributor)("No mesh distributor defined!\n");
135

136 137 138
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(vec);
    int nRankRows = meshDistributor->getNumberRankDofs(feSpaces);
    int nOverallRows = meshDistributor->getNumberOverallDofs(feSpaces);
139 140

    VecCreateMPI(PETSC_COMM_WORLD, nRankRows, nOverallRows, &petscRhsVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
141

142 143 144 145 146 147
    int testddd = 1;
    Parameters::get("block size", testddd);
    if (testddd > 1)
      VecSetBlockSize(petscRhsVec, testddd);


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

    VecAssemblyBegin(petscRhsVec);
    VecAssemblyEnd(petscRhsVec);
154 155 156 157 158 159 160

    if (removeRhsNullSpace) {
      MatNullSpace sp;
      MatNullSpaceCreate(PETSC_COMM_WORLD, PETSC_TRUE, 0, PETSC_NULL, &sp);
      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));
196 197
      const FiniteElemSpace *feSpace = dv.getFeSpace();
      int nRankDofs = meshDistributor->getNumberRankDofs(feSpace);
198

Thomas Witkowski's avatar
Thomas Witkowski committed
199
      for (int j = 0; j < nRankDofs; j++)
200
	dv[meshDistributor->mapLocalToDof(feSpace, j)] = vecPointer[c++]; 
Thomas Witkowski's avatar
Thomas Witkowski committed
201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216
    }

    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. ===

217
    VecDestroy(&petscRhsVec);
218 219 220 221 222 223 224 225 226
  }


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

    MatDestroy(&petscMatrix);
    KSPDestroy(&solver);
227 228
    VecDestroy(&petscSolVec);
    VecDestroy(&petscTmpVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
229 230 231
  }


232 233
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* mat,
					     int nRowMat, int nColMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
234 235 236 237 238 239
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

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

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
240
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
241 242 243 244 245 246 247 248 249 250 251 252 253 254 255
    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;

256 257 258
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();

Thomas Witkowski's avatar
Thomas Witkowski committed
259 260 261 262 263 264
    // === 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) {

265 266 267
      const FiniteElemSpace *rowFe = mat->getRowFeSpace();
      const FiniteElemSpace *colFe = mat->getColFeSpace();

Thomas Witkowski's avatar
Thomas Witkowski committed
268
      // Global index of the current row DOF.
269
      int globalRowDof = 
270
	meshDistributor->mapDofToGlobal(rowFe, *cursor);
Thomas Witkowski's avatar
Thomas Witkowski committed
271
      // Test if the current row DOF is a periodic DOF.
272
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
273

Thomas Witkowski's avatar
Thomas Witkowski committed
274 275 276
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

277
	// Get PETSc's mat row index.
278
	int rowIndex = dofToMatIndex.get(nRowMat, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
279 280 281 282 283 284 285 286

	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.
287
	  int globalColDof = 
288
	    meshDistributor->mapDofToGlobal(colFe, col(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
289
	  // Test if the current col dof is a periodic dof.
290
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
291
	  // Get PETSc's mat col index.
292
	  int colIndex = dofToMatIndex.get(nColMat, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
293 294 295 296 297 298 299 300 301 302 303 304 305 306

	  // 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;
307
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331
	    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++) {
332
 		TEST_EXIT_DBG(perMap.isPeriodic(colFe, *it, newCols[i]))
Thomas Witkowski's avatar
Thomas Witkowski committed
333 334 335
 		  ("Wrong periodic DOF associations at boundary %d with DOF %d!\n",
		   *it, newCols[i]);

336
		newCols.push_back(perMap.map(colFe, *it, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
337 338 339 340
	      }
	    }

	    for (unsigned int i = 0; i < newCols.size(); i++) {
341
	      cols.push_back(dofToMatIndex.get(nColMat, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362
	      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.
363
	  int globalColDof = 
364
	    meshDistributor->mapDofToGlobal(colFe, col(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
365 366 367 368 369 370 371 372 373 374 375

	  // 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;

376 377
	  if (perMap.isPeriodic(colFe, globalColDof)) {
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
378 379 380 381 382 383
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
	      if (*it >= -3)
		perAsc.insert(*it);
	  }

384
	  std::set<int>& perRowAsc = perMap.getAssociations(rowFe, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402
	  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));

403 404
	  // Then, traverse the periodic associations of the row and column
	  // indices and create the corresponding entries.
Thomas Witkowski's avatar
Thomas Witkowski committed
405 406 407 408
	  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;
409

410 411
	      if (perMap.isPeriodic(rowFe, *it, entry[i].first))
		perRowDof = perMap.map(rowFe, *it, entry[i].first);
Thomas Witkowski's avatar
Thomas Witkowski committed
412 413 414 415
	      else
		perRowDof = entry[i].first;

	      int perColDof;
416 417
	      if (perMap.isPeriodic(colFe, *it, entry[i].second))
		perColDof = perMap.map(colFe, *it, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
418 419 420 421 422 423 424 425 426 427 428
	      else
		perColDof = entry[i].second;	      	      
	      

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


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

429
	  for (unsigned int i = 0; i < entry.size(); i++) {
430 431
	    int rowIdx = dofToMatIndex.get(nRowMat, entry[i].first);
	    int colIdx = dofToMatIndex.get(nColMat, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
432

433 434
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
435 436 437 438 439 440 441 442 443 444 445 446
	  }
	}


	// === 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;
447

Thomas Witkowski's avatar
Thomas Witkowski committed
448 449 450 451 452 453 454 455
	  MatSetValues(petscMatrix, 1, &rowIndex, rowIt->second.size(),
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


456 457
  void PetscSolverGlobalMatrix::setDofVector(Vec& petscVec, 
					     DOFVector<double>* vec, 
458
					     int nRowVec, 
459
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
460 461 462
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

463
    const FiniteElemSpace *feSpace = vec->getFeSpace();
464
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
465

Thomas Witkowski's avatar
Thomas Witkowski committed
466 467 468
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
469
      if (rankOnly && !meshDistributor->getIsRankDof(feSpace, dofIt.getDOFIndex()))
Thomas Witkowski's avatar
Thomas Witkowski committed
470 471 472 473
	continue;

      // Calculate global row index of the DOF.
      DegreeOfFreedom globalRowDof = 
474
	meshDistributor->mapDofToGlobal(feSpace, dofIt.getDOFIndex());
475
      // Get PETSc's mat index of the row DOF.
476
      int index = dofToMatIndex.get(nRowVec, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
477

478 479
      if (perMap.isPeriodic(feSpace, globalRowDof)) {
	std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
480 481 482
	double value = *dofIt / (perAsc.size() + 1.0);
	VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);

483 484 485
	for (std::set<int>::iterator perIt = perAsc.begin(); 
	     perIt != perAsc.end(); ++perIt) {
	  int mappedDof = perMap.map(feSpace, *perIt, globalRowDof);
486
	  int mappedIndex = dofToMatIndex.get(nRowVec, mappedDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504
	  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");

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

532 533 534 535 536 537 538 539 540 541
    // 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
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;
546 547 548 549 550 551 552
    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
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
565 566 567 568 569 570 571 572 573 574 575
	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) {

576
	  int globalRowDof =
577
	    meshDistributor->mapDofToGlobal(feSpaces[i], *cursor);
578

579
	  // The corresponding global matrix row index of the current row DOF.
580
	  int petscRowIdx = dofToMatIndex.get(i, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
581
	  
582
	  if (meshDistributor->getIsRankDof(feSpaces[i], *cursor)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
583
	    	    
584 585
	    // === 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
586 587
	    
	    // This is the local row index of the local PETSc matrix.
588
	    int localPetscRowIdx = petscRowIdx - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
589 590 591 592
	    
	    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, 
593
	       meshDistributor->mapDofToGlobal(feSpaces[i], *cursor), 
Thomas Witkowski's avatar
Thomas Witkowski committed
594 595
	       petscRowIdx, 
	       localPetscRowIdx, 
596
	       rankStartIndex,
Thomas Witkowski's avatar
Thomas Witkowski committed
597 598 599 600 601 602 603
	       nComponents, 
	       nRankRows);
	    
	    
	    // Traverse all non zero entries in this row.
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
604
	      int globalColDof =
605
		meshDistributor->mapDofToGlobal(feSpaces[j], col(*icursor));
606
	      int petscColIdx = dofToMatIndex.get(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
607 608 609
	      
	      if (value(*icursor) != 0.0 || petscRowIdx == petscColIdx) {
		// The row DOF is a rank DOF, if also the column is a rank DOF, 
610 611 612 613
		// 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
614 615 616 617 618 619
		  d_nnz[localPetscRowIdx]++;
		else
		  o_nnz[localPetscRowIdx]++;
	      }    
	    }
	  } else {
620 621 622 623 624
	    // === 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
625 626
	    
	    // Send all non zero entries to the member of the row DOF.
627
	    int sendToRank = sendDofToRank[make_pair(*cursor, i)];
Thomas Witkowski's avatar
Thomas Witkowski committed
628 629 630 631
	    
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
	      if (value(*icursor) != 0.0) {
632
		int globalColDof =
633
		  meshDistributor->mapDofToGlobal(feSpaces[j], col(*icursor));
634
		int petscColIdx = dofToMatIndex.get(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655
		
		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();


656 657
    // === 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
658 659 660 661 662 663 664 665

    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;

666
	  int localRowIdx = r - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
667 668 669 670 671

	  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);
	  
672
	  if (c < rankStartIndex || c >= rankStartIndex + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690
	    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);
  }

691 692 693 694 695 696 697 698

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

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

699
    dofToMatIndex.clear();
700
  
701 702 703 704 705 706 707 708
    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)) {
709
	  int globalIndex = 
710
	    meshDistributor->mapDofToGlobal(feSpaces[i], **it);
711 712 713 714

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

715
	  dofToMatIndex.add(i, globalIndex, globalMatIndex);
716 717 718
	}
	  

719
      // === Communicate interior boundary DOFs between domains. ===
720 721 722 723 724 725 726 727

      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()) {
728
	  int globalIndex = 
729
	    meshDistributor->mapDofToGlobal(feSpaces[i], it.getDofIndex());
730
	  int globalMatIndex = dofToMatIndex.get(i, globalIndex);
731
	  sendGlobalDofs.push_back(globalMatIndex);
732 733 734 735 736 737 738 739 740 741 742 743 744 745
	}

	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()) {
746 747 748 749
	  int globalIndex = 
	    meshDistributor->mapDofToGlobal(feSpaces[i], it.getDofIndex());
	  int globalMatIndex = 
	    stdMpi.getRecvData(it.getRank())[it.getDofCounter()];
750

751
	  dofToMatIndex.add(i, globalIndex, globalMatIndex);
752 753 754 755 756 757 758 759 760 761 762 763
	}


      // === 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()) {
764 765
	  int ind0 = 
	    meshDistributor->mapDofToGlobal(feSpaces[i], it.getDofIndex());
766
	  int ind1 = dofToMatIndex.get(i, ind0);
767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783

	  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];

784
	  dofToMatIndex.add(i, ind0, ind1);
785 786 787 788 789 790 791
	}
      
      // === Update offset. ===

      offset += meshDistributor->getNumberRankDofs(feSpaces[i]);
    }
  }
Thomas Witkowski's avatar
Thomas Witkowski committed
792
}