PetscSolverGlobalMatrix.cc 30.3 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
    // === If required, recompute non zero structure of the matrix. ===
Thomas Witkowski's avatar
Thomas Witkowski committed
37

38
    if (checkMeshChange(mat))
39
      nnzInterior.create(mat, mpiCommGlobal, *interiorMap);
Thomas Witkowski's avatar
Thomas Witkowski committed
40

41 42
    // === Create PETSc vector (solution and a temporary vector). ===

43 44
    int nRankRows = interiorMap->getRankDofs();
    int nOverallRows = interiorMap->getOverallDofs();
45

46
    VecCreateMPI(mpiCommGlobal, nRankRows, nOverallRows, &petscSolVec);
47 48


Thomas Witkowski's avatar
Thomas Witkowski committed
49 50
    // === Create PETSc matrix with the computed nnz data structure. ===

51
    MatCreateAIJ(mpiCommGlobal, nRankRows, nRankRows, 
52
		 nOverallRows, nOverallRows,
53 54 55
		 0, nnzInterior.dnnz, 
		 0, nnzInterior.onnz, 
		 &matIntInt);
56 57

    MatSetOption(matIntInt, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
58

Thomas Witkowski's avatar
Thomas Witkowski committed
59 60 61 62 63 64
#if (DEBUG != 0)
    MSG("Fill petsc matrix 1 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

#if (DEBUG != 0)
    int a, b;
65 66 67
    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
68 69 70 71 72 73
      ("Wrong matrix ownership range!\n");
#endif


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

74
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
75 76 77
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
	if ((*mat)[i][j])
78
	  setDofMatrix((*mat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
79 80 81 82 83

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

84 85
    MatAssemblyBegin(matIntInt, MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(matIntInt, MAT_FINAL_ASSEMBLY);
Thomas Witkowski's avatar
Thomas Witkowski committed
86

87 88 89

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

90
    //    removeDirichletBcDofs(mat);
91 92
    

93
    // === Init PETSc solver. ===
94

95 96 97 98 99 100 101
    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);
102

103
    initPreconditioner(pcInterior);
104

105 106
    // Do not delete the solution vector, use it for the initial guess.
    if (!zeroStartVector)
107
      KSPSetInitialGuessNonzero(kspInterior, PETSC_TRUE);
108

Thomas Witkowski's avatar
Thomas Witkowski committed
109 110 111
#if (DEBUG != 0)
    MSG("Fill petsc matrix 3 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif
112 113 114
  }


115 116 117 118 119 120 121 122
  void PetscSolverGlobalMatrix::fillPetscMatrix(DOFMatrix *mat)
  {
    Matrix<DOFMatrix*> m(1, 1);
    m[0][0] = mat;
    fillPetscMatrix(&m);
  }


123 124 125 126 127 128 129 130 131
  void PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace(Matrix<DOFMatrix*> *mat)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace()");
    
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);

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

132 133 134 135
    // === If required, recompute non zero structure of the matrix. ===

    bool localMatrix = (subdomainLevel == 0);
    if (checkMeshChange(mat, localMatrix)) {
136
      nnzInterior.create(mat, mpiCommGlobal, *interiorMap, localMatrix);
137 138

      if (coarseSpaceMap) {
139 140 141
	nnzCoarse.create(mat, mpiCommGlobal, *coarseSpaceMap);
	nnzCoarseInt.create(mat, mpiCommGlobal, *coarseSpaceMap, *interiorMap);
	nnzIntCoarse.create(mat, mpiCommGlobal, *interiorMap, *coarseSpaceMap);
142
      }
143 144 145
    }

    if (localMatrix) {
146
      MatCreateSeqAIJ(mpiCommLocal, nRowsRankInterior, nRowsRankInterior,
147 148
		      0, nnzInterior.dnnz, 
		      &matIntInt);
149
    } else {
150 151 152
      MatCreateAIJ(mpiCommLocal, 
		   nRowsRankInterior, nRowsRankInterior,
		   nRowsOverallInterior, nRowsOverallInterior,
153
		   0, nnzInterior.dnnz, 0, nnzInterior.onnz, 
154
		   &matIntInt);
155
    }
156
    
157 158 159 160
    if (coarseSpaceMap) {
      int nRowsRankCoarse = coarseSpaceMap->getRankDofs();
      int nRowsOverallCoarse = coarseSpaceMap->getOverallDofs();

161 162 163
      MatCreateAIJ(mpiCommGlobal,
		   nRowsRankCoarse, nRowsRankCoarse,
		   nRowsOverallCoarse, nRowsOverallCoarse,
164
		   0, nnzCoarse.dnnz, 0, nnzCoarse.onnz, 
165 166
		   &matCoarseCoarse);

167 168 169
      MatCreateAIJ(mpiCommGlobal,
		   nRowsRankCoarse, nRowsRankInterior,
		   nRowsOverallCoarse, nGlobalOverallInterior,
170
		   0, nnzCoarseInt.dnnz, 0, nnzCoarseInt.onnz,
171 172
		   &matCoarseInt);

173 174 175
      MatCreateAIJ(mpiCommGlobal,
		   nRowsRankInterior, nRowsRankCoarse,
		   nGlobalOverallInterior, nRowsOverallCoarse,
176
		   0, nnzIntCoarse.dnnz, 0, nnzIntCoarse.onnz,
177
		   &matIntCoarse);
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
    }

    // === 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) {
257 258 259 260 261
		for (unsigned int k = 0; k < colsOther.size(); k++) {
		  int local = interiorMap->getMatIndex(j, colsOther[k]) - interiorMap->getStartDofs();
		  if (rowIndex == 0 && local == 9297)
		    MSG("FOUND: %d %d %d\n", colsOther[k], j, interiorMap->getMatIndex(j, colsOther[k]));

262
		  colsOther[k] = interiorMap->getMatIndex(j, colsOther[k]);
263
		}
264 265 266 267 268
	      } else {
		for (unsigned int k = 0; k < colsOther.size(); k++)
		  colsOther[k] = 
		    interiorMap->getMatIndex(j, colsOther[k]) + rStartInterior;
	      }
269

270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320
	      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);
    }

321 322
    // === Remove Dirichlet BC DOFs. ===

323
    //    removeDirichletBcDofs(mat);
324

325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340
    // === 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);
    KSPGetPC(kspInterior, &pcInterior);
    PCSetType(pcInterior, PCLU);
    if (subdomainLevel == 0)
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERUMFPACK);
    else
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
    KSPSetFromOptions(kspInterior);  
  }


341 342 343
  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
Thomas Witkowski's avatar
Thomas Witkowski committed
344

Thomas Witkowski's avatar
Thomas Witkowski committed
345 346 347 348
    VecCreateMPI(mpiCommGlobal, 
		 interiorMap->getRankDofs(), 
		 nGlobalOverallInterior,
		 &rhsInterior);
349

Thomas Witkowski's avatar
Thomas Witkowski committed
350 351 352 353 354 355
    if (coarseSpaceMap) 
      VecCreateMPI(mpiCommGlobal, 
		   coarseSpaceMap->getRankDofs(), 
		   coarseSpaceMap->getOverallDofs(),
		   &rhsCoarseSpace);
    
356
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
357
    TEST_EXIT_DBG(interiorMap)("No parallel DOF map defined!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
358
    
359

Thomas Witkowski's avatar
Thomas Witkowski committed
360
    // === Transfer values from DOF vector to the PETSc vector. === 
Thomas Witkowski's avatar
Thomas Witkowski committed
361
    if (coarseSpaceMap) {
Thomas Witkowski's avatar
Thomas Witkowski committed
362 363
      for (int i = 0; i < vec->getSize(); i++)
	setDofVector(rhsInterior, rhsCoarseSpace, vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
364 365 366 367
    } else {
      for (int i = 0; i < vec->getSize(); i++)
	setDofVector(rhsInterior, vec->getDOFVector(i), i);
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
368

369 370
    VecAssemblyBegin(rhsInterior);
    VecAssemblyEnd(rhsInterior);
371

Thomas Witkowski's avatar
Thomas Witkowski committed
372 373 374 375 376
    if (coarseSpaceMap) {
      VecAssemblyBegin(rhsCoarseSpace);
      VecAssemblyEnd(rhsCoarseSpace);
    }

377 378 379

    // === Remove Dirichlet BC DOFs. ===
    //    removeDirichletBcDofs(vec);
Thomas Witkowski's avatar
Thomas Witkowski committed
380
 
Thomas Witkowski's avatar
Thomas Witkowski committed
381 382 383
  }


384 385
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
386 387 388 389 390 391 392 393 394 395
  {
    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++)
396
	setDofVector(petscSolVec, vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Thomas Witkowski committed
397 398 399 400 401
      
      VecAssemblyBegin(petscSolVec);
      VecAssemblyEnd(petscSolVec);
    }

402

Thomas Witkowski's avatar
Thomas Witkowski committed
403 404
    MatNullSpace matNullspace;
    Vec nullspaceBasis;
405

406 407 408
    if (nullspace.size() > 0 || 
	hasConstantNullspace ||
	constNullspaceComponent.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
409
      TEST_EXIT_DBG(nullspace.size() <= 1)("Not yet implemented!\n");
410

411 412 413 414 415 416 417 418 419 420
      if (constNullspaceComponent.size() > 0) {
	nullspace.clear();
	SystemVector *basisVec = new SystemVector(vec);
	basisVec->set(0.0);
	for (unsigned int i = 0; i < constNullspaceComponent.size(); i++)
	  basisVec->getDOFVector(constNullspaceComponent[i])->set(1.0);

	nullspace.push_back(basisVec);
      } 

Thomas Witkowski's avatar
Thomas Witkowski committed
421 422 423 424 425 426 427
      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);
428 429

	VecNormalize(nullspaceBasis, PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
430 431 432 433 434 435 436 437 438 439 440
	
	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);
      }
441

442
      MatSetNullSpace(matIntInt, matNullspace);
Thomas Witkowski's avatar
Thomas Witkowski committed
443
      KSPSetNullSpace(kspInterior, matNullspace);
444

Thomas Witkowski's avatar
Thomas Witkowski committed
445
      // === Remove null space, if requested. ===
446

Thomas Witkowski's avatar
Thomas Witkowski committed
447 448 449 450 451 452 453 454
      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");
455 456
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
457

Thomas Witkowski's avatar
Thomas Witkowski committed
458
    // PETSc.
459
    solve(rhsInterior, petscSolVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
460

461 462

    if (nullspace.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
463
      MatNullSpaceDestroy(&matNullspace);
464 465 466 467
      VecDestroy(&nullspaceBasis);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
468 469
    // === Transfere values from PETSc's solution vectors to the DOF vectors. ===
    PetscScalar *vecPointer;
470
    VecGetArray(petscSolVec, &vecPointer);    
Thomas Witkowski's avatar
Thomas Witkowski committed
471

472
    int c = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
473
    for (int i = 0; i < nComponents; i++) {
474
      DOFVector<double> &dv = *(vec.getDOFVector(i));
475

476
      DofMap& d = (*interiorMap)[dv.getFeSpace()].getMap();
477 478 479
      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
480 481 482
    }

    VecRestoreArray(petscSolVec, &vecPointer);
483 484 485
  }


486 487 488 489
  void PetscSolverGlobalMatrix::solveGlobal(Vec &rhs, Vec &sol)
  {
    FUNCNAME("PetscSolverGlobalMatrix::solveGlobal()");

490 491 492
    double wtime = MPI::Wtime();
    double t0 = 0.0, t1 = 0.0;

493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511
    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);

512 513 514
    t0 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
515
    KSPSolve(kspInterior, tmp, tmp);
516 517 518
    t1 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
519 520 521 522 523 524 525 526 527 528 529

    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);
530 531
    t0 += MPI::Wtime() - wtime;

532
    //    MSG("TIMEING: %.5f %.5f\n", t0, t1);
533 534 535
  }


536 537 538 539
  void PetscSolverGlobalMatrix::destroyMatrixData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyMatrixData()");

540 541
    exitPreconditioner(pcInterior);

542 543
    MatDestroy(&matIntInt);
    KSPDestroy(&kspInterior);
Thomas Witkowski's avatar
Thomas Witkowski committed
544

545 546 547 548 549 550 551
    if (coarseSpaceMap) {
      MatDestroy(&matCoarseCoarse);
      MatDestroy(&matCoarseInt);
      MatDestroy(&matIntCoarse);
    }

    if (petscSolVec != PETSC_NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
552
      VecDestroy(&petscSolVec);
553 554
      petscSolVec = PETSC_NULL;
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
555 556 557
  }


558 559 560 561
  void PetscSolverGlobalMatrix::destroyVectorData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyVectorData()");

562
    VecDestroy(&rhsInterior);
563 564 565

    if (coarseSpaceMap)
      VecDestroy(&rhsCoarseSpace);
566 567 568
  }


569 570 571 572 573 574 575 576 577 578
  bool PetscSolverGlobalMatrix::checkMeshChange(Matrix<DOFMatrix*> *mat,
						bool localMatrix)
  {
    FUNCNAME("PetscSolverGlobalMatrix::checkMeshChange()");

    int recvAllValues = 0;
    int sendValue = 
      static_cast<int>(meshDistributor->getLastMeshChangeIndex() != lastMeshNnz);
    mpiCommGlobal.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);

579
    if (!nnzInterior.dnnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
580 581 582 583 584
      vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
      
      interiorMap->setComputeMatIndex(true, !localMatrix);
      interiorMap->update(feSpaces);

585
      nnzInterior.clear();
586

587 588 589 590
      if (coarseSpaceMap) {
	nnzCoarse.clear();
	nnzCoarseInt.clear();
	nnzIntCoarse.clear();
591 592 593 594 595 596 597 598 599 600 601 602
      }

      updateSubdomainData();
      lastMeshNnz = meshDistributor->getLastMeshChangeIndex();

      return true;
    }

    return false;
  }


603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638
  void PetscSolverGlobalMatrix::createFieldSplit(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::createFieldSplit()");

    vector<string> isNames;
    Parameters::get("parallel->solver->is blocks", isNames);

    int nBlocks = isNames.size();
    if (nBlocks == 0)
      return;

    for (int i = 0; i < nBlocks; i++) {
      MSG("Create for block %s\n", isNames[i].c_str());

      vector<int> blockComponents;
      Parameters::get("parallel->solver->is block " + lexical_cast<string>(i),
		      blockComponents);
      int nComponents = static_cast<int>(blockComponents.size());

      TEST_EXIT(nComponents > 0)("No is block for block %d defined!\n", i);

      // Check if blocks are continous
      for (int j = 0; j < nComponents; j++) {
	TEST_EXIT(blockComponents[j] == blockComponents[0] + j)
	  ("Does not yet support not continous IS blocks! Block %s\n", 
	   isNames[i].c_str());
      }

      IS is;
      interiorMap->createIndexSet(is, blockComponents[0], nComponents);
      PCFieldSplitSetIS(pc, isNames[i].c_str(), is);
      ISDestroy(&is);
    }
  }


639 640 641 642 643 644 645 646 647 648 649 650 651 652 653
  void PetscSolverGlobalMatrix::initPreconditioner(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::initPreconditioner()");

    PCSetFromOptions(pc);
    createFieldSplit(pc);
  }

 
  void PetscSolverGlobalMatrix::exitPreconditioner(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::exitPreconditioner()");
  }


654 655
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* mat,
					     int nRowMat, int nColMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
656 657 658 659 660 661
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

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

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
662
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
663 664 665 666 667 668 669 670 671 672 673 674 675 676 677
    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;

678 679 680
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();

Thomas Witkowski's avatar
Thomas Witkowski committed
681 682 683 684 685 686
    const FiniteElemSpace *rowFe = mat->getRowFeSpace();
    const FiniteElemSpace *colFe = mat->getColFeSpace();
    DofMap& rowMap = (*interiorMap)[rowFe].getMap();
    DofMap& colMap = (*interiorMap)[colFe].getMap();

    // === Traverse all rows of the DOF matrix and insert row wise the values ===
Thomas Witkowski's avatar
Thomas Witkowski committed
687 688 689 690 691
    // === to the PETSc matrix.                                               ===

    for (cursor_type cursor = begin<row>(mat->getBaseMatrix()), 
	   cend = end<row>(mat->getBaseMatrix()); cursor != cend; ++cursor) {
      // Global index of the current row DOF.
Thomas Witkowski's avatar
Thomas Witkowski committed
692
      int globalRowDof = rowMap[*cursor].global;
693

Thomas Witkowski's avatar
Thomas Witkowski committed
694
      // Test if the current row DOF is a periodic DOF.
695
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
696

Thomas Witkowski's avatar
Thomas Witkowski committed
697 698 699
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

700
	// Get PETSc's mat row index.
701
	int rowIndex = interiorMap->getMatIndex(nRowMat, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
702 703 704 705 706 707 708 709

	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.
Thomas Witkowski's avatar
Thomas Witkowski committed
710
	  int globalColDof = colMap[col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
711
	  // Test if the current col dof is a periodic dof.
712
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
713
	  // Get PETSc's mat col index.
714
	  int colIndex = interiorMap->getMatIndex(nColMat, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
715 716 717 718 719 720 721

	  // 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.
Thomas Witkowski's avatar
Thomas Witkowski committed
722 723
 	    cols.push_back(colIndex);
 	    values.push_back(value(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
724 725 726 727 728
	  } else {
	    // === Row index is not periodic, but column index is. ===

	    // Create set of all periodic associations of the column index.
	    std::set<int> perAsc;
729
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
730 731
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
732
	      if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
733 734 735 736 737 738 739 740 741 742 743 744 745 746
		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);
747

Thomas Witkowski's avatar
Thomas Witkowski committed
748 749 750 751 752 753
	    // 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++) {
754
 		TEST_EXIT_DBG(perMap.isPeriodic(colFe, *it, newCols[i]))
Thomas Witkowski's avatar
Thomas Witkowski committed
755 756 757
 		  ("Wrong periodic DOF associations at boundary %d with DOF %d!\n",
		   *it, newCols[i]);

758
		newCols.push_back(perMap.map(colFe, *it, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
759 760 761 762
	      }
	    }

	    for (unsigned int i = 0; i < newCols.size(); i++) {
763
	      cols.push_back(interiorMap->getMatIndex(nColMat, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
764 765 766 767 768
	      values.push_back(scaledValue);	      
	    }
	  }
	}

Thomas Witkowski's avatar
Thomas Witkowski committed
769 770
  	MatSetValues(matIntInt, 1, &rowIndex, cols.size(), 
  		     &(cols[0]), &(values[0]), ADD_VALUES);	
Thomas Witkowski's avatar
Thomas Witkowski committed
771 772 773 774 775 776 777 778 779 780 781 782 783 784
      } 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.
785
	  int globalColDof = (*interiorMap)[colFe][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
786 787 788 789 790 791 792 793 794 795

	  // 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;

796 797
	  if (perMap.isPeriodic(colFe, globalColDof)) {
	    std::set<int>& perColAsc = perMap.getAssociations(colFe, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
798 799
	    for (std::set<int>::iterator it = perColAsc.begin(); 
		 it != perColAsc.end(); ++it)
800
	      if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
801 802 803
		perAsc.insert(*it);
	  }

804
	  std::set<int>& perRowAsc = perMap.getAssociations(rowFe, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
805 806
	  for (std::set<int>::iterator it = perRowAsc.begin(); 
	       it != perRowAsc.end(); ++it)
807
	    if (meshDistributor->getElementObjectDb().isValidPeriodicType(*it))
Thomas Witkowski's avatar
Thomas Witkowski committed
808 809 810 811 812 813 814 815 816 817 818 819 820 821 822
	      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));

823 824
	  // Then, traverse the periodic associations of the row and column
	  // indices and create the corresponding entries.
Thomas Witkowski's avatar
Thomas Witkowski committed
825 826 827 828
	  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;
829

830 831
	      if (perMap.isPeriodic(rowFe, *it, entry[i].first))
		perRowDof = perMap.map(rowFe, *it, entry[i].first);
Thomas Witkowski's avatar
Thomas Witkowski committed
832 833 834 835
	      else
		perRowDof = entry[i].first;

	      int perColDof;
836 837
	      if (perMap.isPeriodic(colFe, *it, entry[i].second))
		perColDof = perMap.map(colFe, *it, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
838 839 840 841 842 843 844 845 846 847
	      else
		perColDof = entry[i].second;	      	      
	      
	      entry.push_back(make_pair(perRowDof, perColDof));
	    }
	  }


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

848
	  for (unsigned int i = 0; i < entry.size(); i++) {
849 850
	    int rowIdx = interiorMap->getMatIndex(nRowMat, entry[i].first);
	    int colIdx = interiorMap->getMatIndex(nColMat, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
851

852 853
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
854 855 856 857 858 859 860 861 862 863 864 865
	  }
	}


	// === 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;
866

867
	  MatSetValues(matIntInt, 1, &rowIndex, rowIt->second.size(),
Thomas Witkowski's avatar
Thomas Witkowski committed
868 869 870 871 872 873 874
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
875 876
  void PetscSolverGlobalMatrix::setDofVector(Vec vecInterior, 
					     Vec vecCoarse,
877
					     DOFVector<double>* vec, 
878
					     int nRowVec, 
879
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
880 881 882
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

883
    const FiniteElemSpace *feSpace = vec->getFeSpace();
884
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
885

Thomas Witkowski's avatar
Thomas Witkowski committed
886 887 888
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
889

890
      if (rankOnly && !(*interiorMap)[feSpace].isRankDof(dofIt.getDOFIndex()))
Thomas Witkowski's avatar
Thomas Witkowski committed
891 892
	continue;

893
      if (isCoarseSpace(feSpace, dofIt.getDOFIndex())) {
894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910
	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;
911

912
	if (perMap.isPeriodic(feSpace, globalRowDof)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
913 914 915
	  std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
	  double value = *dofIt / (perAsc.size() + 1.0);
	  VecSetValue(vecInterior, index, value, ADD_VALUES);
916

Thomas Witkowski's avatar
Thomas Witkowski committed
917 918 919 920
	  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);
921

Thomas Witkowski's avatar
Thomas Witkowski committed
922
	    VecSetValue(vecInterior, mappedIndex, value, ADD_VALUES);
923 924 925 926
	  }	  
	} else {	  
	  // The DOF index is not periodic.
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
927 928
	  VecSetValue(vecInterior, index, *dofIt, ADD_VALUES);
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
929 930 931 932 933
      }
    }
  }


934 935 936 937
  void PetscSolverGlobalMatrix::removeDirichletBcDofs(Matrix<DOFMatrix*> *mat)
  {
    FUNCNAME("PetscSolverGlobalMatrix::removeDirichletBcDofs()");

Thomas Witkowski's avatar
Thomas Witkowski committed
938
#if 0
939 940 941 942
    vector<int> dofsInterior, dofsCoarse;

    int nComponents = mat->getNumRows();
    for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962
      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));
	      }
963
	    }
964
	  }
Thomas Witkowski's avatar
Thomas Witkowski committed
965 966
	} else {
	  MSG("NO MAT DIAG in %d\n", i);
967 968 969 970 971 972 973 974 975 976
	}
      }
    }

    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
977
#endif
978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994
  }


  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)) {
995 996 997
	  if ((*coarseSpaceMap)[feSpace].isRankDof(it->first)) {
	    int globalDof = (*coarseSpaceMap)[feSpace][it->first].global;
	    VecSetValue(rhsCoarseSpace, coarseSpaceMap->getMatIndex(i, globalDof), 
998
			it->second, INSERT_VALUES);
999
	  }
1000 1001
	} else {
	  if ((*interiorMap)[feSpace].isRankDof(it->first)) {
1002 1003
	    int globalDof = (*interiorMap)[feSpace][it->first].global;
	    VecSetValue(rhsInterior, interiorMap->getMatIndex(i, globalDof),
1004 1005 1006 1007 1008
			it->second, INSERT_VALUES);	    
	  }
	}
      }
    }
1009 1010 1011 1012 1013 1014 1015 1016

    VecAssemblyBegin(rhsInterior);
    VecAssemblyEnd(rhsInterior);

    if (coarseSpaceMap) {
      VecAssemblyBegin(rhsCoarseSpace);
      VecAssemblyEnd(rhsCoarseSpace);
    }
1017 1018
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
1019
}