PetscSolverGlobalMatrix.cc 34.5 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
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrix()");

24
    if (coarseSpaceMap != NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
25
      updateSubdomainData();
26 27 28 29
      fillPetscMatrixWithCoarseSpace(mat);
      return;
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
30
    TEST_EXIT_DBG(meshDistributor)("No mesh distributor object defined!\n");
31
    TEST_EXIT_DBG(interiorMap)("No parallel mapping object defined!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
32
    TEST_EXIT_DBG(mat)("No DOF matrix defined!\n");
33
    
Thomas Witkowski's avatar
Thomas Witkowski committed
34
    double wtime = MPI::Wtime();
35

36 37 38
    
    // === Check if mesh was changed and, in this case, recompute matrix ===
    // === nnz structure and matrix indices.                             ===
39

Thomas Witkowski's avatar
Thomas Witkowski committed
40
    int recvAllValues = 0;
41 42
    int sendValue = 
      static_cast<int>(meshDistributor->getLastMeshChangeIndex() != lastMeshNnz);
43
    mpiCommGlobal.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
Thomas Witkowski's avatar
Thomas Witkowski committed
44

45
    if (!d_nnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
46
      vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
47 48
      interiorMap->setComputeMatIndex(true, true);
      interiorMap->update(feSpaces);
49

Thomas Witkowski's avatar
Thomas Witkowski committed
50 51 52 53 54 55 56
      if (d_nnz) {
	delete [] d_nnz;
	d_nnz = NULL;
	delete [] o_nnz;
	o_nnz = NULL;
      }

Thomas Witkowski's avatar
Thomas Witkowski committed
57
      updateSubdomainData();
Thomas Witkowski's avatar
Thomas Witkowski committed
58 59 60 61 62
      createPetscNnzStructure(mat);
      lastMeshNnz = meshDistributor->getLastMeshChangeIndex();
    }


63 64
    // === Create PETSc vector (solution and a temporary vector). ===

65 66
    int nRankRows = interiorMap->getRankDofs();
    int nOverallRows = interiorMap->getOverallDofs();
67

68
    VecCreateMPI(mpiCommGlobal, nRankRows, nOverallRows, &petscSolVec);
69 70


Thomas Witkowski's avatar
Thomas Witkowski committed
71 72
    // === Create PETSc matrix with the computed nnz data structure. ===

73
    MatCreateMPIAIJ(mpiCommGlobal, nRankRows, nRankRows, 
74
 		    nOverallRows, nOverallRows,
75
		    0, d_nnz, 0, o_nnz, &matIntInt);
76

Thomas Witkowski's avatar
Thomas Witkowski committed
77 78 79 80 81 82
#if (DEBUG != 0)
    MSG("Fill petsc matrix 1 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

#if (DEBUG != 0)
    int a, b;
83 84 85
    MatGetOwnershipRange(matIntInt, &a, &b);
    TEST_EXIT(a == interiorMap->getStartDofs())("Wrong matrix ownership range!\n");
    TEST_EXIT(b == interiorMap->getStartDofs() + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
86 87 88 89 90 91
      ("Wrong matrix ownership range!\n");
#endif


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

92
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
93 94 95
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
	if ((*mat)[i][j])
96
	  setDofMatrix((*mat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
97 98 99 100 101

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

102 103
    MatAssemblyBegin(matIntInt, MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(matIntInt, MAT_FINAL_ASSEMBLY);
Thomas Witkowski's avatar
Thomas Witkowski committed
104

105 106 107

    // === Remove Dirichlet BC DOFs. ===

108
    //    removeDirichletBcDofs(mat);
109 110
    

111
    // === Init PETSc solver. ===
112

113 114 115 116 117 118 119 120
    KSPCreate(mpiCommGlobal, &kspInterior);
    KSPGetPC(kspInterior, &pcInterior);
    KSPSetOperators(kspInterior, matIntInt, matIntInt, SAME_NONZERO_PATTERN); 
    KSPSetTolerances(kspInterior, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(kspInterior, KSPBCGS);
    KSPSetOptionsPrefix(kspInterior, kspPrefix.c_str());
    KSPSetFromOptions(kspInterior);
    PCSetFromOptions(pcInterior);
121 122 123

    // Do not delete the solution vector, use it for the initial guess.
    if (!zeroStartVector)
124
      KSPSetInitialGuessNonzero(kspInterior, PETSC_TRUE);
125

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


130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305
  void PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace(Matrix<DOFMatrix*> *mat)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace()");
    
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);

    int nRowsRankInterior = interiorMap->getRankDofs();
    int nRowsOverallInterior = interiorMap->getOverallDofs();

    if (subdomainLevel == 0) {
      MatCreateSeqAIJ(mpiCommLocal, nRowsRankInterior, nRowsRankInterior,
		      60, PETSC_NULL, &matIntInt);
    } else {
      MatCreateMPIAIJ(mpiCommLocal, 
		      nRowsRankInterior, nRowsRankInterior,
		      nRowsOverallInterior, nRowsOverallInterior,
		      60, PETSC_NULL, 60, PETSC_NULL, &matIntInt);
    }

    if (coarseSpaceMap) {
      int nRowsRankCoarse = coarseSpaceMap->getRankDofs();
      int nRowsOverallCoarse = coarseSpaceMap->getOverallDofs();

      MatCreateMPIAIJ(mpiCommGlobal,
		      nRowsRankCoarse, nRowsRankCoarse,
		      nRowsOverallCoarse, nRowsOverallCoarse,
		      60, PETSC_NULL, 60, PETSC_NULL, &matCoarseCoarse);
      
      MatCreateMPIAIJ(mpiCommGlobal,
		      nRowsRankCoarse, nRowsRankInterior,
		      nRowsOverallCoarse, nGlobalOverallInterior,
		      60, PETSC_NULL, 60, PETSC_NULL, &matCoarseInt);
      
      MatCreateMPIAIJ(mpiCommGlobal,
		      nRowsRankInterior, nRowsRankCoarse,
		      nGlobalOverallInterior, nRowsOverallCoarse,
		      60, PETSC_NULL, 60, PETSC_NULL, &matIntCoarse);
    }

    // === Prepare traverse of sequentially created matrices. ===

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
    namespace traits = mtl::traits;
    typedef DOFMatrix::base_matrix_type Matrix;

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

    vector<int> cols, colsOther;
    vector<double> values, valuesOther;
    cols.reserve(300);
    colsOther.reserve(300);
    values.reserve(300);
    valuesOther.reserve(300);

    // === Traverse all sequentially created matrices and add the values to ===
    // === the global PETSc matrices.                                       ===

    int nComponents = mat->getSize();
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
	if (!(*mat)[i][j])
	  continue;

	traits::col<Matrix>::type col((*mat)[i][j]->getBaseMatrix());
	traits::const_value<Matrix>::type value((*mat)[i][j]->getBaseMatrix());
	
	// Traverse all rows.
	for (cursor_type cursor = begin<row>((*mat)[i][j]->getBaseMatrix()), 
	       cend = end<row>((*mat)[i][j]->getBaseMatrix()); cursor != cend; ++cursor) {

	  bool rowPrimal = isCoarseSpace(feSpaces[i], *cursor);
  
	  cols.clear();
	  colsOther.clear();
	  values.clear();	  
	  valuesOther.clear();

	  // Traverse all columns.
	  for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); 
	       icursor != icend; ++icursor) {

	    bool colPrimal = isCoarseSpace(feSpaces[j], col(*icursor));

	    if (colPrimal) {
	      if (rowPrimal) {
		cols.push_back(col(*icursor));
		values.push_back(value(*icursor));
	      } else {
		colsOther.push_back(col(*icursor));
		valuesOther.push_back(value(*icursor));
	      }
	    } else {
	      if (rowPrimal) {
		colsOther.push_back(col(*icursor));
		valuesOther.push_back(value(*icursor));
	      } else {
		cols.push_back(col(*icursor));
		values.push_back(value(*icursor));
	      }
	    }
	  }  // for each nnz in row


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

	  if (rowPrimal) {
	    int rowIndex = coarseSpaceMap->getMatIndex(i, *cursor);
	    for (unsigned int k = 0; k < cols.size(); k++)
	      cols[k] = coarseSpaceMap->getMatIndex(j, cols[k]);

	    MatSetValues(matCoarseCoarse, 1, &rowIndex, cols.size(),
			 &(cols[0]), &(values[0]), ADD_VALUES);

	    if (colsOther.size()) {
	      if (subdomainLevel == 0) {
		for (unsigned int k = 0; k < colsOther.size(); k++)
		  colsOther[k] = interiorMap->getMatIndex(j, colsOther[k]);
	      } else {
		for (unsigned int k = 0; k < colsOther.size(); k++)
		  colsOther[k] = 
		    interiorMap->getMatIndex(j, colsOther[k]) + rStartInterior;
	      }
 	      
	      MatSetValues(matCoarseInt, 1, &rowIndex, colsOther.size(),
 			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
	    }
	  } else {
	    int localRowIndex = 
	      (subdomainLevel == 0 ? interiorMap->getLocalMatIndex(i, *cursor) :
	       interiorMap->getMatIndex(i, *cursor));

	    for (unsigned int k = 0; k < cols.size(); k++) {
	      if (subdomainLevel == 0)
		cols[k] = interiorMap->getLocalMatIndex(j, cols[k]);
	      else
		cols[k] = interiorMap->getMatIndex(j, cols[k]);
	    }
	    
  	    MatSetValues(matIntInt, 1, &localRowIndex, cols.size(),
  			 &(cols[0]), &(values[0]), ADD_VALUES);

	    if (colsOther.size()) {
	      int globalRowIndex = interiorMap->getMatIndex(i, *cursor);

	      if (subdomainLevel != 0)
		globalRowIndex += rStartInterior;

	      for (unsigned int k = 0; k < colsOther.size(); k++)
		colsOther[k] = coarseSpaceMap->getMatIndex(j, colsOther[k]);

  	      MatSetValues(matIntCoarse, 1, &globalRowIndex, colsOther.size(),
  			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
	    }
	  }
	} 
      }
    }

    // === Start global assembly procedure. ===

    MatAssemblyBegin(matIntInt, MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(matIntInt, MAT_FINAL_ASSEMBLY);

    if (coarseSpaceMap) {
      MatAssemblyBegin(matCoarseCoarse, MAT_FINAL_ASSEMBLY);
      MatAssemblyEnd(matCoarseCoarse, MAT_FINAL_ASSEMBLY);
      
      MatAssemblyBegin(matIntCoarse, MAT_FINAL_ASSEMBLY);
      MatAssemblyEnd(matIntCoarse, MAT_FINAL_ASSEMBLY);
      
      MatAssemblyBegin(matCoarseInt, MAT_FINAL_ASSEMBLY);
      MatAssemblyEnd(matCoarseInt, MAT_FINAL_ASSEMBLY);
    }


306 307
    // === Remove Dirichlet BC DOFs. ===

308
    //    removeDirichletBcDofs(mat);
309

310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326
    // === Create solver for the non primal (thus local) variables. ===

    KSPCreate(mpiCommLocal, &kspInterior);
    KSPSetOperators(kspInterior, matIntInt, matIntInt, SAME_NONZERO_PATTERN);
    KSPSetOptionsPrefix(kspInterior, "interior_");
    KSPSetType(kspInterior, KSPPREONLY);
    PC pcInterior;
    KSPGetPC(kspInterior, &pcInterior);
    PCSetType(pcInterior, PCLU);
    if (subdomainLevel == 0)
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERUMFPACK);
    else
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
    KSPSetFromOptions(kspInterior);  
  }


327 328 329
  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
Thomas Witkowski's avatar
Thomas Witkowski committed
330

Thomas Witkowski's avatar
Thomas Witkowski committed
331 332 333 334
    VecCreateMPI(mpiCommGlobal, 
		 interiorMap->getRankDofs(), 
		 nGlobalOverallInterior,
		 &rhsInterior);
335

Thomas Witkowski's avatar
Thomas Witkowski committed
336 337 338 339 340 341
    if (coarseSpaceMap) 
      VecCreateMPI(mpiCommGlobal, 
		   coarseSpaceMap->getRankDofs(), 
		   coarseSpaceMap->getOverallDofs(),
		   &rhsCoarseSpace);
    
342
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
343
    TEST_EXIT_DBG(interiorMap)("No parallel DOF map defined!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
344
    
345

Thomas Witkowski's avatar
Thomas Witkowski committed
346
    // === Transfer values from DOF vector to the PETSc vector. === 
Thomas Witkowski's avatar
Thomas Witkowski committed
347
    if (coarseSpaceMap) {
Thomas Witkowski's avatar
Thomas Witkowski committed
348 349
      for (int i = 0; i < vec->getSize(); i++)
	setDofVector(rhsInterior, rhsCoarseSpace, vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
350 351 352 353
    } else {
      for (int i = 0; i < vec->getSize(); i++)
	setDofVector(rhsInterior, vec->getDOFVector(i), i);
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
354

355 356
    VecAssemblyBegin(rhsInterior);
    VecAssemblyEnd(rhsInterior);
357

Thomas Witkowski's avatar
Thomas Witkowski committed
358 359 360 361 362
    if (coarseSpaceMap) {
      VecAssemblyBegin(rhsCoarseSpace);
      VecAssemblyEnd(rhsCoarseSpace);
    }

363 364 365

    // === Remove Dirichlet BC DOFs. ===
    //    removeDirichletBcDofs(vec);
Thomas Witkowski's avatar
Thomas Witkowski committed
366
 
Thomas Witkowski's avatar
Thomas Witkowski committed
367 368 369
  }


370 371
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
372 373 374 375 376 377 378 379 380 381
  {
    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++)
382
	setDofVector(petscSolVec, vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Thomas Witkowski committed
383 384 385 386 387
      
      VecAssemblyBegin(petscSolVec);
      VecAssemblyEnd(petscSolVec);
    }

388

Thomas Witkowski's avatar
Thomas Witkowski committed
389 390
    MatNullSpace matNullspace;
    Vec nullspaceBasis;
391

Thomas Witkowski's avatar
Thomas Witkowski committed
392 393
    if (nullspace.size() > 0 || hasConstantNullspace) {
      TEST_EXIT_DBG(nullspace.size() <= 1)("Not yet implemented!\n");
394

Thomas Witkowski's avatar
Thomas Witkowski committed
395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412
      if (nullspace.size() > 0) {
	VecDuplicate(petscSolVec, &nullspaceBasis);
	for (int i = 0; i < nComponents; i++)
	  setDofVector(nullspaceBasis, nullspace[0]->getDOFVector(i), i, true);
	
	VecAssemblyBegin(nullspaceBasis);
	VecAssemblyEnd(nullspaceBasis);
	
	MatNullSpaceCreate(mpiCommGlobal, (hasConstantNullspace ? PETSC_TRUE : PETSC_FALSE), 
			   1, &nullspaceBasis, &matNullspace);

	MatMult(matIntInt, nullspaceBasis, petscSolVec);
	PetscReal n;
	VecNorm(petscSolVec, NORM_2, &n);
	MSG("NORM IS: %e\n", n);
      } else {
	MatNullSpaceCreate(mpiCommGlobal, PETSC_TRUE, 0, PETSC_NULL, &matNullspace);
      }
413

Thomas Witkowski's avatar
Thomas Witkowski committed
414
      KSPSetNullSpace(kspInterior, matNullspace);
415

Thomas Witkowski's avatar
Thomas Witkowski committed
416
      // === Remove null space, if requested. ===
417

Thomas Witkowski's avatar
Thomas Witkowski committed
418 419 420 421 422 423 424 425
      if (removeRhsNullspace) {
	TEST_EXIT_DBG(coarseSpaceMap == NULL)("Not supported!\n");
	
	MatNullSpaceRemove(matNullspace, rhsInterior, PETSC_NULL);
      }
    } else {
      TEST_EXIT(removeRhsNullspace == false)
	("No nullspace provided that should be removed from rhs!\n");
426 427
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
428

Thomas Witkowski's avatar
Thomas Witkowski committed
429
    // PETSc.
430
    solve(rhsInterior, petscSolVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
431

432 433

    if (nullspace.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
434
      MatNullSpaceDestroy(&matNullspace);
435 436 437 438
      VecDestroy(&nullspaceBasis);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
439 440
    // === Transfere values from PETSc's solution vectors to the DOF vectors. ===
    PetscScalar *vecPointer;
441
    VecGetArray(petscSolVec, &vecPointer);    
Thomas Witkowski's avatar
Thomas Witkowski committed
442

443
    int c = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
444
    for (int i = 0; i < nComponents; i++) {
445
      DOFVector<double> &dv = *(vec.getDOFVector(i));
446

447
      DofMap& d = (*interiorMap)[dv.getFeSpace()].getMap();
448 449 450
      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
451 452 453 454 455 456 457 458
    }

    VecRestoreArray(petscSolVec, &vecPointer);


    // === Synchronize DOFs at common DOFs, i.e., DOFs that correspond to ===
    // === more than one partition.                                       ===
    meshDistributor->synchVector(vec);
459 460 461
  }


462 463 464 465
  void PetscSolverGlobalMatrix::solveGlobal(Vec &rhs, Vec &sol)
  {
    FUNCNAME("PetscSolverGlobalMatrix::solveGlobal()");

466 467 468
    double wtime = MPI::Wtime();
    double t0 = 0.0, t1 = 0.0;

469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487
    Vec tmp;
    if (mpiCommLocal.Get_size() == 1)
      VecCreateSeq(mpiCommLocal, interiorMap->getRankDofs(), &tmp);
    else
      VecCreateMPI(mpiCommLocal,
		   interiorMap->getRankDofs(),
		   interiorMap->getOverallDofs(),
		   &tmp);

    PetscScalar *tmpValues, *rhsValues;
    VecGetArray(tmp, &tmpValues);
    VecGetArray(rhs, &rhsValues);

    for (int i = 0; i < interiorMap->getRankDofs(); i++)
      tmpValues[i] = rhsValues[i];

    VecRestoreArray(rhs, &rhsValues);
    VecRestoreArray(tmp, &tmpValues);

488 489 490
    t0 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
491
    KSPSolve(kspInterior, tmp, tmp);
492 493 494
    t1 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
495 496 497 498 499 500 501 502 503 504 505

    VecGetArray(tmp, &tmpValues);
    VecGetArray(sol, &rhsValues);

    for (int i = 0; i < interiorMap->getRankDofs(); i++) 
      rhsValues[i] = tmpValues[i];

    VecRestoreArray(sol, &rhsValues);
    VecRestoreArray(tmp, &tmpValues);

    VecDestroy(&tmp);
506 507
    t0 += MPI::Wtime() - wtime;

508
    //    MSG("TIMEING: %.5f %.5f\n", t0, t1);
509 510 511
  }


512 513 514 515
  void PetscSolverGlobalMatrix::destroyMatrixData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyMatrixData()");

516 517
    MatDestroy(&matIntInt);
    KSPDestroy(&kspInterior);
Thomas Witkowski's avatar
Thomas Witkowski committed
518

519 520 521 522 523 524 525
    if (coarseSpaceMap) {
      MatDestroy(&matCoarseCoarse);
      MatDestroy(&matCoarseInt);
      MatDestroy(&matIntCoarse);
    }

    if (petscSolVec != PETSC_NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
526
      VecDestroy(&petscSolVec);
527 528
      petscSolVec = PETSC_NULL;
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
529 530 531
  }


532 533 534 535
  void PetscSolverGlobalMatrix::destroyVectorData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyVectorData()");

536
    VecDestroy(&rhsInterior);
537 538 539

    if (coarseSpaceMap)
      VecDestroy(&rhsCoarseSpace);
540 541 542
  }


543 544
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* mat,
					     int nRowMat, int nColMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
545 546 547 548 549 550
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

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

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
551
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
552 553 554 555 556 557 558 559 560 561 562 563 564 565 566
    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;

567 568 569
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();

Thomas Witkowski's avatar
Thomas Witkowski committed
570 571 572 573 574 575
    // === 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) {

576 577 578
      const FiniteElemSpace *rowFe = mat->getRowFeSpace();
      const FiniteElemSpace *colFe = mat->getColFeSpace();

Thomas Witkowski's avatar
Thomas Witkowski committed
579
      // Global index of the current row DOF.
580
      int globalRowDof = (*interiorMap)[rowFe][*cursor].global;
581

Thomas Witkowski's avatar
Thomas Witkowski committed
582
      // Test if the current row DOF is a periodic DOF.
583
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
584

Thomas Witkowski's avatar
Thomas Witkowski committed
585 586 587
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

588
	// Get PETSc's mat row index.
589
	int rowIndex = interiorMap->getMatIndex(nRowMat, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
590 591 592 593 594 595 596 597

	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.
598
	  int globalColDof = (*interiorMap)[colFe][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
599
	  // Test if the current col dof is a periodic dof.
600
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
601
	  // Get PETSc's mat col index.
602
	  int colIndex = interiorMap->getMatIndex(nColMat, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
603 604 605 606 607 608 609 610 611 612 613 614 615 616

	  // 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;
617
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
618 619
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
620
	      if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
621 622 623 624 625 626 627 628 629 630 631 632 633 634
		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);
635

Thomas Witkowski's avatar
Thomas Witkowski committed
636 637 638 639 640 641
	    // 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++) {
642
 		TEST_EXIT_DBG(perMap.isPeriodic(colFe, *it, newCols[i]))
Thomas Witkowski's avatar
Thomas Witkowski committed
643 644 645
 		  ("Wrong periodic DOF associations at boundary %d with DOF %d!\n",
		   *it, newCols[i]);

646
		newCols.push_back(perMap.map(colFe, *it, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
647 648 649 650
	      }
	    }

	    for (unsigned int i = 0; i < newCols.size(); i++) {
651
	      cols.push_back(interiorMap->getMatIndex(nColMat, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
652 653 654 655 656
	      values.push_back(scaledValue);	      
	    }
	  }
	}

657
	MatSetValues(matIntInt, 1, &rowIndex, cols.size(), 
Thomas Witkowski's avatar
Thomas Witkowski committed
658 659 660 661 662 663 664 665 666 667 668 669 670 671 672
		     &(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.
673
	  int globalColDof = (*interiorMap)[colFe][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
674 675 676 677 678 679 680 681 682 683

	  // 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;

684 685
	  if (perMap.isPeriodic(colFe, globalColDof)) {
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
686 687
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
688
	      if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
689 690 691
		perAsc.insert(*it);
	  }

692
	  std::set<int>& perRowAsc = perMap.getAssociations(rowFe, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
693 694
	  for (std::set<int>::iterator it = perRowAsc.begin(); 
	       it != perRowAsc.end(); ++it)
695
	    if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
696 697 698 699 700 701 702 703 704 705 706 707 708 709 710
	      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));

711 712
	  // Then, traverse the periodic associations of the row and column
	  // indices and create the corresponding entries.
Thomas Witkowski's avatar
Thomas Witkowski committed
713 714 715 716
	  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;
717

718 719
	      if (perMap.isPeriodic(rowFe, *it, entry[i].first))
		perRowDof = perMap.map(rowFe, *it, entry[i].first);
Thomas Witkowski's avatar
Thomas Witkowski committed
720 721 722 723
	      else
		perRowDof = entry[i].first;

	      int perColDof;
724 725
	      if (perMap.isPeriodic(colFe, *it, entry[i].second))
		perColDof = perMap.map(colFe, *it, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
726 727 728 729 730 731 732 733 734 735 736
	      else
		perColDof = entry[i].second;	      	      
	      

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


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

737
	  for (unsigned int i = 0; i < entry.size(); i++) {
738 739
	    int rowIdx = interiorMap->getMatIndex(nRowMat, entry[i].first);
	    int colIdx = interiorMap->getMatIndex(nColMat, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
740

741 742
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
743 744 745 746 747 748 749 750 751 752 753 754
	  }
	}


	// === 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;
755

756
	  MatSetValues(matIntInt, 1, &rowIndex, rowIt->second.size(),
Thomas Witkowski's avatar
Thomas Witkowski committed
757 758 759 760 761 762 763
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
764 765
  void PetscSolverGlobalMatrix::setDofVector(Vec vecInterior, 
					     Vec vecCoarse,
766
					     DOFVector<double>* vec, 
767
					     int nRowVec, 
768
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
769 770 771
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

772
    const FiniteElemSpace *feSpace = vec->getFeSpace();
773
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
774

Thomas Witkowski's avatar
Thomas Witkowski committed
775 776 777
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
778
      if (rankOnly && !(*interiorMap)[feSpace].isRankDof(dofIt.getDOFIndex()))
Thomas Witkowski's avatar
Thomas Witkowski committed
779 780
	continue;

781
      if (isCoarseSpace(feSpace, dofIt.getDOFIndex())) {
782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800
	TEST_EXIT_DBG(vecCoarse != PETSC_NULL)("Should not happen!\n");

	int index = coarseSpaceMap->getMatIndex(nRowVec, dofIt.getDOFIndex());
	VecSetValue(vecCoarse, index, *dofIt, ADD_VALUES);
      } else {
	// Calculate global row index of the DOF.
	DegreeOfFreedom globalRowDof = 
	  (*interiorMap)[feSpace][dofIt.getDOFIndex()].global;
	
	// Get PETSc's mat index of the row DOF.
	int index = 0;
	if (interiorMap->isMatIndexFromGlobal())
	  index = 
	    interiorMap->getMatIndex(nRowVec, globalRowDof) + rStartInterior;
	else
	  index =
	    interiorMap->getMatIndex(nRowVec, dofIt.getDOFIndex()) + rStartInterior;
	
	if (perMap.isPeriodic(feSpace, globalRowDof)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
801 802 803
	  std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
	  double value = *dofIt / (perAsc.size() + 1.0);
	  VecSetValue(vecInterior, index, value, ADD_VALUES);
804

Thomas Witkowski's avatar
Thomas Witkowski committed
805 806 807 808 809
	  for (std::set<int>::iterator perIt = perAsc.begin(); 
	       perIt != perAsc.end(); ++perIt) {
	    int mappedDof = perMap.map(feSpace, *perIt, globalRowDof);
	    int mappedIndex = interiorMap->getMatIndex(nRowVec, mappedDof);
	    VecSetValue(vecInterior, mappedIndex, value, ADD_VALUES);
810 811 812 813
	  }	  
	} else {	  
	  // The DOF index is not periodic.
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
814 815
	  VecSetValue(vecInterior, index, *dofIt, ADD_VALUES);
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
816 817 818 819 820
      }
    }
  }


821 822 823 824
  void PetscSolverGlobalMatrix::removeDirichletBcDofs(Matrix<DOFMatrix*> *mat)
  {
    FUNCNAME("PetscSolverGlobalMatrix::removeDirichletBcDofs()");

Thomas Witkowski's avatar
Thomas Witkowski committed
825
#if 0
826 827 828 829
    vector<int> dofsInterior, dofsCoarse;

    int nComponents = mat->getNumRows();
    for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849
      for (int j = 0; j < nComponents; j++) {
	if ((*mat)[i][j]) {
	  const FiniteElemSpace *feSpace = (*mat)[i][j]->getRowFeSpace();
	    
	  std::set<DegreeOfFreedom> &dirichletDofs = *((*mat)[i][j]->getApplyDBCs());

	  MSG("DIRICHLET DOFS: %d %d -> %d\n", i, j, dirichletDofs.size());
	  
	  for (std::set<DegreeOfFreedom>::iterator it = dirichletDofs.begin();
	       it != dirichletDofs.end(); ++it) {
	    if (isCoarseSpace(feSpace, *it)) {
	      if ((*coarseSpaceMap)[feSpace].isRankDof(*it)) {
		int globalDof = (*coarseSpaceMap)[feSpace][*it].global;
		dofsCoarse.push_back(coarseSpaceMap->getMatIndex(i, globalDof));
	      }
	    } else {
	      if ((*interiorMap)[feSpace].isRankDof(*it)) {
		int globalDof = (*interiorMap)[feSpace][*it].global;
		dofsInterior.push_back(interiorMap->getMatIndex(i, globalDof));
	      }
850
	    }
851
	  }
Thomas Witkowski's avatar
Thomas Witkowski committed
852 853
	} else {
	  MSG("NO MAT DIAG in %d\n", i);
854 855 856 857 858 859 860 861 862 863
	}
      }
    }

    MatZeroRows(matIntInt, dofsInterior.size(), &(dofsInterior[0]), 1.0, 
		PETSC_NULL, PETSC_NULL);

    if (coarseSpaceMap != NULL)
      MatZeroRows(matCoarseCoarse, dofsCoarse.size(), &(dofsCoarse[0]), 1.0, 
		  PETSC_NULL, PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
864
#endif
865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881
  }


  void PetscSolverGlobalMatrix::removeDirichletBcDofs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::removeDirichletBcDofs()");

    int nComponents = vec->getSize();
    for (int i = 0; i < nComponents; i++) {
      const FiniteElemSpace *feSpace = vec->getDOFVector(i)->getFeSpace();

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

      for (map<DegreeOfFreedom, double>::iterator it = dirichletValues.begin();
	   it != dirichletValues.end(); ++it) {
	if (isCoarseSpace(feSpace, it->first)) {
882 883 884
	  if ((*coarseSpaceMap)[feSpace].isRankDof(it->first)) {
	    int globalDof = (*coarseSpaceMap)[feSpace][it->first].global;
	    VecSetValue(rhsCoarseSpace, coarseSpaceMap->getMatIndex(i, globalDof), 
885
			it->second, INSERT_VALUES);
886
	  }
887 888
	} else {
	  if ((*interiorMap)[feSpace].isRankDof(it->first)) {
889 890
	    int globalDof = (*interiorMap)[feSpace][it->first].global;
	    VecSetValue(rhsInterior, interiorMap->getMatIndex(i, globalDof),
891 892 893 894 895
			it->second, INSERT_VALUES);	    
	  }
	}
      }
    }
896 897 898 899 900 901 902 903

    VecAssemblyBegin(rhsInterior);
    VecAssemblyEnd(rhsInterior);

    if (coarseSpaceMap) {
      VecAssemblyBegin(rhsCoarseSpace);
      VecAssemblyEnd(rhsCoarseSpace);
    }
904 905 906
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
907 908 909 910 911 912 913
  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");

914
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
915 916
    int nRankRows = interiorMap->getRankDofs();
    int rankStartIndex = interiorMap->getStartDofs();
917

Thomas Witkowski's avatar
Thomas Witkowski committed
918 919 920 921 922 923 924 925 926 927 928 929 930
    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;

931 932 933 934
    // 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
935 936 937 938
    map<int, MatrixNnzEntry> sendMatrixEntry;

    // Maps to each DOF that must be send to another rank the rank number of the
    // receiving rank.
939
    map<pair<DegreeOfFreedom, int>, int> sendDofToRank;
Thomas Witkowski's avatar
Thomas Witkowski committed
940

941

942 943 944
    // 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++) {
945
      for (DofComm::Iterator it(meshDistributor->getDofComm().getRecvDofs(), feSpaces[i]);
946 947 948 949 950 951
	   !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
952 953
    }

954
    // Create list of ranks from which we receive data from.
Thomas Witkowski's avatar
Thomas Witkowski committed
955
    std::set<int> recvFromRank;
956
    for (unsigned int i = 0; i < feSpaces.size(); i++) 
957
      for (DofComm::Iterator it(meshDistributor->getDofComm().getSendDofs(), feSpaces[i]);
958 959 960 961 962
	   !it.end(); it.nextRank())
	recvFromRank.insert(it.getRank());


    // === Traverse matrices to create nnz data. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
963

964
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
965 966 967 968 969
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
 	if (!(*mat)[i][j])
	  continue;

970 971 972 973 974
	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
975 976 977 978 979 980 981 982 983 984
	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) {
985
	  int globalRowDof = (*interiorMap)[feSpaces[i]][*cursor].global;
986

987
	  // The corresponding global matrix row index of the current row DOF.
988 989
	  int petscRowIdx = interiorMap->getMatIndex(i, globalRowDof);
	  if ((*interiorMap)[feSpaces[i]].isRankDof(*cursor)) {
990
    	    
991 992
	    // === 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
993 994
	    
	    // This is the local row index of the local PETSc matrix.
995
	    int localPetscRowIdx = petscRowIdx - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
996 997
	    
	    TEST_EXIT_DBG(localPetscRowIdx >= 0 && localPetscRowIdx < nRankRows)
998
	      ("Should not happen! \n Debug info: DOF = %d   globalRowIndx = %d   petscRowIdx = %d   localPetscRowIdx = %d   rStart = %d   compontens = %d from %d   nRankRows = %d\n",
999
	       *cursor,
1000
	       (*interiorMap)[feSpaces[i]][*cursor].global,
Thomas Witkowski's avatar
Thomas Witkowski committed
1001 1002
	       petscRowIdx, 
	       localPetscRowIdx, 
1003
	       rankStartIndex,
1004
	       i,
Thomas Witkowski's avatar
Thomas Witkowski committed
1005 1006 1007 1008 1009 1010 1011
	       nComponents, 
	       nRankRows);
	    
	    
	    // Traverse all non zero entries in this row.
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
1012 1013
	      int globalColDof = (*interiorMap)[feSpaces[j]][col(*icursor)].global;
	      int petscColIdx = interiorMap->getMatIndex(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
1014 1015 1016
	      
	      if (value(*icursor) != 0.0 || petscRowIdx == petscColIdx) {
		// The row DOF is a rank DOF, if also the column is a rank DOF, 
1017 1018 1019 1020
		// 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
1021 1022 1023 1024 1025 1026
		  d_nnz[localPetscRowIdx]++;
		else
		  o_nnz[localPetscRowIdx]++;
	      }    
	    }
	  } else {
1027 1028 1029 1030 1031
	    // === 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
1032 1033
	    
	    // Send all non zero entries to the member of the row DOF.
1034
	    int sendToRank = sendDofToRank[make_pair(*cursor, i)];
Thomas Witkowski's avatar
Thomas Witkowski committed
1035 1036 1037 1038
	    
	    for (icursor_type icursor = begin<nz>(cursor), 
		   icend = end<nz>(cursor); icursor != icend; ++icursor) {
	      if (value(*icursor) != 0.0) {
1039
		int globalColDof = 
1040 1041
		  (*interiorMap)[feSpaces[j]][col(*icursor)].global;
		int petscColIdx = interiorMap->getMatIndex(j, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054
		
		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. ===

1055
    StdMpi<MatrixNnzEntry> stdMpi(mpiCommGlobal, true);
Thomas Witkowski's avatar
Thomas Witkowski committed
1056 1057 1058 1059 1060 1061 1062
    stdMpi.send(sendMatrixEntry);
    for (std::set<int>::iterator it = recvFromRank.begin(); 
	 it != recvFromRank.end(); ++it)
      stdMpi.recv(*it);
    stdMpi.startCommunication();


1063 1064
    // === 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
1065 1066 1067 1068 1069 1070 1071 1072

    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;

1073
	  int localRowIdx = r - rankStartIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
1074 1075 1076 1077 1078

	  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);
	  
1079
	  if (c < rankStartIndex || c >= rankStartIndex + nRankRows)
Thomas Witkowski's avatar
Thomas Witkowski committed
1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098
	    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);
  }

}