PetscSolverGlobalMatrix.cc 27.3 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()");

Thomas Witkowski's avatar
Thomas Witkowski committed
24
    if (coarseSpaceMap.size()) {
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))
Thomas Witkowski's avatar
Thomas Witkowski committed
39
      nnzInterior.create(mat, mpiCommGlobal, *interiorMap, 
40 41
			 &(meshDistributor->getPeriodicMap()),
			 meshDistributor->getElementObjectDb());
Thomas Witkowski's avatar
Thomas Witkowski committed
42

43 44
    // === Create PETSc vector (solution and a temporary vector). ===

45 46
    int nRankRows = interiorMap->getRankDofs();
    int nOverallRows = interiorMap->getOverallDofs();
47

48
    VecCreateMPI(mpiCommGlobal, nRankRows, nOverallRows, &petscSolVec);
49 50


Thomas Witkowski's avatar
Thomas Witkowski committed
51 52
    // === Create PETSc matrix with the computed nnz data structure. ===

53
    MatCreateAIJ(mpiCommGlobal, nRankRows, nRankRows, 
54
		 nOverallRows, nOverallRows,
55 56 57
		 0, nnzInterior.dnnz, 
		 0, nnzInterior.onnz, 
		 &matIntInt);
58 59

    MatSetOption(matIntInt, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
60

Thomas Witkowski's avatar
Thomas Witkowski committed
61 62 63 64 65 66
#if (DEBUG != 0)
    MSG("Fill petsc matrix 1 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

#if (DEBUG != 0)
    int a, b;
67 68 69
    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
70 71 72 73 74 75
      ("Wrong matrix ownership range!\n");
#endif


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

76
    int nComponents = mat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
77 78 79
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
	if ((*mat)[i][j])
80
	  setDofMatrix((*mat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
81 82 83 84 85

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

86 87
    MatAssemblyBegin(matIntInt, MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(matIntInt, MAT_FINAL_ASSEMBLY);
Thomas Witkowski's avatar
Thomas Witkowski committed
88

89 90 91 92 93 94 95 96 97 98 99
    
    if (printMatInfo) {
      MatInfo matInfo;
      MatGetInfo(matIntInt, MAT_GLOBAL_SUM, &matInfo);
      MSG("Matrix info:\n");
      MSG("  memory usage: %e MB\n", matInfo.memory / (1024.0 * 1024.0));
      MSG("  mallocs: %d\n", static_cast<int>(matInfo.mallocs));
      MSG("  nz allocated: %d\n", static_cast<int>(matInfo.nz_allocated));
      MSG("  nz used: %d\n", static_cast<int>(matInfo.nz_used));
      MSG("  nz unneeded: %d\n", static_cast<int>(matInfo.nz_unneeded));
    }
100 101 102

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

103
    //    removeDirichletBcDofs(mat);
104 105
    

106
    // === Init PETSc solver. ===
107

108 109 110 111 112 113 114
    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);
115

116
    initPreconditioner(pcInterior);
117

118 119
    // Do not delete the solution vector, use it for the initial guess.
    if (!zeroStartVector)
120
      KSPSetInitialGuessNonzero(kspInterior, PETSC_TRUE);
121

Thomas Witkowski's avatar
Thomas Witkowski committed
122 123 124
#if (DEBUG != 0)
    MSG("Fill petsc matrix 3 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif
125 126 127
  }


128 129 130 131 132 133 134 135
  void PetscSolverGlobalMatrix::fillPetscMatrix(DOFMatrix *mat)
  {
    Matrix<DOFMatrix*> m(1, 1);
    m[0][0] = mat;
    fillPetscMatrix(&m);
  }


136 137 138
  void PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace(Matrix<DOFMatrix*> *mat)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace()");
139 140

    TEST_EXIT_DBG(interiorMap)("Should not happen!\n");
141

142 143 144 145 146
    vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);

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

147 148 149 150
    // === If required, recompute non zero structure of the matrix. ===

    bool localMatrix = (subdomainLevel == 0);
    if (checkMeshChange(mat, localMatrix)) {
151 152 153
      nnzInterior.create(mat, mpiCommGlobal, *interiorMap, NULL, 
			 meshDistributor->getElementObjectDb(),
			 localMatrix);
154

Thomas Witkowski's avatar
Thomas Witkowski committed
155
      if (coarseSpaceMap.size()) {
156 157 158
	nnzCoarse.create(mat, mpiCommGlobal, *coarseSpaceMap, NULL, meshDistributor->getElementObjectDb());
	nnzCoarseInt.create(mat, mpiCommGlobal, *coarseSpaceMap, *interiorMap, NULL, meshDistributor->getElementObjectDb());
	nnzIntCoarse.create(mat, mpiCommGlobal, *interiorMap, *coarseSpaceMap, NULL, meshDistributor->getElementObjectDb());
159
      }
160 161 162
    }

    if (localMatrix) {
163
      MatCreateSeqAIJ(mpiCommLocal, nRowsRankInterior, nRowsRankInterior,
164 165
		      0, nnzInterior.dnnz, 
		      &matIntInt);
166
    } else {
167 168 169
      MatCreateAIJ(mpiCommLocal, 
		   nRowsRankInterior, nRowsRankInterior,
		   nRowsOverallInterior, nRowsOverallInterior,
170
		   0, nnzInterior.dnnz, 0, nnzInterior.onnz, 
171
		   &matIntInt);
172
    }
173 174

   
Thomas Witkowski's avatar
Thomas Witkowski committed
175
    if (coarseSpaceMap.size()) {
176 177 178
      int nRowsRankCoarse = coarseSpaceMap->getRankDofs();
      int nRowsOverallCoarse = coarseSpaceMap->getOverallDofs();

179 180 181
      MatCreateAIJ(mpiCommGlobal,
		   nRowsRankCoarse, nRowsRankCoarse,
		   nRowsOverallCoarse, nRowsOverallCoarse,
182
		   0, nnzCoarse.dnnz, 0, nnzCoarse.onnz, 
183 184
		   &matCoarseCoarse);

185 186 187
      MatCreateAIJ(mpiCommGlobal,
		   nRowsRankCoarse, nRowsRankInterior,
		   nRowsOverallCoarse, nGlobalOverallInterior,
188
		   0, nnzCoarseInt.dnnz, 0, nnzCoarseInt.onnz,
189 190
		   &matCoarseInt);

191 192 193
      MatCreateAIJ(mpiCommGlobal,
		   nRowsRankInterior, nRowsRankCoarse,
		   nGlobalOverallInterior, nRowsOverallCoarse,
194
		   0, nnzIntCoarse.dnnz, 0, nnzIntCoarse.onnz,
195
		   &matIntCoarse);
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
    // === 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;

Thomas Witkowski's avatar
Thomas Witkowski committed
224 225 226
	ParallelDofMapping *rowCoarseSpace = coarseSpaceMap[i];
	ParallelDofMapping *colCoarseSpace = coarseSpaceMap[j];

227 228 229 230 231 232 233
	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) {

Thomas Witkowski's avatar
Thomas Witkowski committed
234
	  bool isRowCoarse = isCoarseSpace(i, feSpaces[i], *cursor);
235 236 237 238 239 240 241 242 243 244
  
	  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) {

Thomas Witkowski's avatar
Thomas Witkowski committed
245
	    bool isColCoarse = isCoarseSpace(j, feSpaces[j], col(*icursor));
246

Thomas Witkowski's avatar
Thomas Witkowski committed
247 248
	    if (isColCoarse) {
	      if (isRowCoarse) {
249 250 251 252 253 254 255
		cols.push_back(col(*icursor));
		values.push_back(value(*icursor));
	      } else {
		colsOther.push_back(col(*icursor));
		valuesOther.push_back(value(*icursor));
	      }
	    } else {
Thomas Witkowski's avatar
Thomas Witkowski committed
256
	      if (isRowCoarse) {
257 258 259 260 261 262 263 264 265 266 267 268
		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. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
269 270
	  if (isRowCoarse) {
	    int rowIndex = rowCoarseSpace->getMatIndex(i, *cursor);
271
	    for (unsigned int k = 0; k < cols.size(); k++)
Thomas Witkowski's avatar
Thomas Witkowski committed
272
	      cols[k] = colCoarseSpace->getMatIndex(j, cols[k]);
273 274 275 276 277 278

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

	    if (colsOther.size()) {
	      if (subdomainLevel == 0) {
279
		for (unsigned int k = 0; k < colsOther.size(); k++)
280 281 282 283 284 285
		  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;
	      }
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
	      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++)
Thomas Witkowski's avatar
Thomas Witkowski committed
312
		colsOther[k] = colCoarseSpace->getMatIndex(j, colsOther[k]);
313 314 315 316 317 318 319 320 321

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

322

323 324 325 326 327
    // === Start global assembly procedure. ===

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

328

Thomas Witkowski's avatar
Thomas Witkowski committed
329
    if (coarseSpaceMap.size()) {
330 331 332 333 334 335 336 337 338 339
      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);
    }

340

341 342
    // === Remove Dirichlet BC DOFs. ===

343
    //    removeDirichletBcDofs(mat);
344

345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360
    // === 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);  
  }


361 362 363
  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
Thomas Witkowski's avatar
Thomas Witkowski committed
364

Thomas Witkowski's avatar
Thomas Witkowski committed
365 366 367 368
    VecCreateMPI(mpiCommGlobal, 
		 interiorMap->getRankDofs(), 
		 nGlobalOverallInterior,
		 &rhsInterior);
369

Thomas Witkowski's avatar
Thomas Witkowski committed
370
    if (coarseSpaceMap.size()) 
Thomas Witkowski's avatar
Thomas Witkowski committed
371 372 373 374 375
      VecCreateMPI(mpiCommGlobal, 
		   coarseSpaceMap->getRankDofs(), 
		   coarseSpaceMap->getOverallDofs(),
		   &rhsCoarseSpace);
    
376
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
377
    TEST_EXIT_DBG(interiorMap)("No parallel DOF map defined!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
378
    
379

Thomas Witkowski's avatar
Thomas Witkowski committed
380
    // === Transfer values from DOF vector to the PETSc vector. === 
Thomas Witkowski's avatar
Thomas Witkowski committed
381
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
382 383
      for (int i = 0; i < vec->getSize(); i++)
	setDofVector(rhsInterior, rhsCoarseSpace, vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
384 385 386 387
    } else {
      for (int i = 0; i < vec->getSize(); i++)
	setDofVector(rhsInterior, vec->getDOFVector(i), i);
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
388

389 390
    VecAssemblyBegin(rhsInterior);
    VecAssemblyEnd(rhsInterior);
391

Thomas Witkowski's avatar
Thomas Witkowski committed
392
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
393 394 395 396
      VecAssemblyBegin(rhsCoarseSpace);
      VecAssemblyEnd(rhsCoarseSpace);
    }

397 398 399

    // === Remove Dirichlet BC DOFs. ===
    //    removeDirichletBcDofs(vec);
Thomas Witkowski's avatar
Thomas Witkowski committed
400
 
Thomas Witkowski's avatar
Thomas Witkowski committed
401 402 403
  }


404 405
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
406 407 408 409 410 411 412 413 414 415
  {
    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++)
416
	setDofVector(petscSolVec, vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Thomas Witkowski committed
417 418 419 420 421
      
      VecAssemblyBegin(petscSolVec);
      VecAssemblyEnd(petscSolVec);
    }

422

Thomas Witkowski's avatar
Thomas Witkowski committed
423 424
    MatNullSpace matNullspace;
    Vec nullspaceBasis;
425 426 427
    if (nullspace.size() > 0 || 
	hasConstantNullspace ||
	constNullspaceComponent.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
428
      TEST_EXIT_DBG(nullspace.size() <= 1)("Not yet implemented!\n");
429

430 431 432 433 434 435 436 437 438 439
      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
440 441 442 443 444 445 446
      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);
447 448

	VecNormalize(nullspaceBasis, PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
449 450 451 452 453 454 455 456 457 458 459
	
	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);
      }
460

461
      MatSetNullSpace(matIntInt, matNullspace);
Thomas Witkowski's avatar
Thomas Witkowski committed
462
      KSPSetNullSpace(kspInterior, matNullspace);
463

Thomas Witkowski's avatar
Thomas Witkowski committed
464
      // === Remove null space, if requested. ===
465

Thomas Witkowski's avatar
Thomas Witkowski committed
466
      if (removeRhsNullspace) {
Thomas Witkowski's avatar
Thomas Witkowski committed
467
	TEST_EXIT_DBG(coarseSpaceMap.empty())("Not supported!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
468 469 470 471 472 473
	
	MatNullSpaceRemove(matNullspace, rhsInterior, PETSC_NULL);
      }
    } else {
      TEST_EXIT(removeRhsNullspace == false)
	("No nullspace provided that should be removed from rhs!\n");
474 475
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
476
    // PETSc.
477
    solve(rhsInterior, petscSolVec);
Thomas Witkowski's avatar
Thomas Witkowski committed
478

479 480

    if (nullspace.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
481
      MatNullSpaceDestroy(&matNullspace);
482 483 484 485
      VecDestroy(&nullspaceBasis);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
486 487
    // === Transfere values from PETSc's solution vectors to the DOF vectors. ===
    PetscScalar *vecPointer;
488
    VecGetArray(petscSolVec, &vecPointer);    
Thomas Witkowski's avatar
Thomas Witkowski committed
489

490
    int c = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
491
    for (int i = 0; i < nComponents; i++) {
492
      DOFVector<double> &dv = *(vec.getDOFVector(i));
493

494
      DofMap& d = (*interiorMap)[dv.getFeSpace()].getMap();
495 496 497
      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
498 499 500
    }

    VecRestoreArray(petscSolVec, &vecPointer);
Thomas Witkowski's avatar
Thomas Witkowski committed
501 502 503 504

    // === Synchronize DOFs at common DOFs, i.e., DOFs that correspond to ===  
    // === more than one partition.                                       ===  
    meshDistributor->synchVector(vec);
505 506 507
  }


508 509 510 511
  void PetscSolverGlobalMatrix::solveGlobal(Vec &rhs, Vec &sol)
  {
    FUNCNAME("PetscSolverGlobalMatrix::solveGlobal()");

512 513 514
    double wtime = MPI::Wtime();
    double t0 = 0.0, t1 = 0.0;

515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533
    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);

534 535 536
    t0 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
537
    KSPSolve(kspInterior, tmp, tmp);
538 539 540
    t1 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
541 542 543 544 545 546 547 548 549 550 551

    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);
552 553
    t0 += MPI::Wtime() - wtime;

554
    //    MSG("TIMEING: %.5f %.5f\n", t0, t1);
555 556 557
  }


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

562 563
    exitPreconditioner(pcInterior);

564 565
    MatDestroy(&matIntInt);
    KSPDestroy(&kspInterior);
Thomas Witkowski's avatar
Thomas Witkowski committed
566

Thomas Witkowski's avatar
Thomas Witkowski committed
567
    if (coarseSpaceMap.size()) {
568 569 570 571 572 573
      MatDestroy(&matCoarseCoarse);
      MatDestroy(&matCoarseInt);
      MatDestroy(&matIntCoarse);
    }

    if (petscSolVec != PETSC_NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
574
      VecDestroy(&petscSolVec);
575 576
      petscSolVec = PETSC_NULL;
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
577 578 579
  }


580 581 582 583
  void PetscSolverGlobalMatrix::destroyVectorData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyVectorData()");

584
    VecDestroy(&rhsInterior);
585

Thomas Witkowski's avatar
Thomas Witkowski committed
586
    if (coarseSpaceMap.size())
587
      VecDestroy(&rhsCoarseSpace);
588 589 590
  }


591 592 593 594 595 596 597 598 599 600
  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);

601
    if (!nnzInterior.dnnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
602 603
      vector<const FiniteElemSpace*> feSpaces = getFeSpaces(mat);
      
604
      interiorMap->setComputeMatIndex(!localMatrix);
605 606
      interiorMap->update(feSpaces);

607
      nnzInterior.clear();
608

Thomas Witkowski's avatar
Thomas Witkowski committed
609
      if (coarseSpaceMap.size()) {
610 611 612
	nnzCoarse.clear();
	nnzCoarseInt.clear();
	nnzIntCoarse.clear();
613 614 615 616 617 618 619 620 621 622 623 624
      }

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

      return true;
    }

    return false;
  }


625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660
  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);
    }
  }


661 662 663 664 665 666 667 668 669 670 671 672 673 674 675
  void PetscSolverGlobalMatrix::initPreconditioner(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::initPreconditioner()");

    PCSetFromOptions(pc);
    createFieldSplit(pc);
  }

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


676 677
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* mat,
					     int nRowMat, int nColMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
678 679 680 681 682 683
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

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

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
684
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
685 686 687 688 689 690 691 692 693 694 695 696 697 698 699
    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;

700 701 702
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();

Thomas Witkowski's avatar
Thomas Witkowski committed
703 704 705 706 707 708
    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
709 710 711 712 713
    // === 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
714
      int globalRowDof = rowMap[*cursor].global;
715

Thomas Witkowski's avatar
Thomas Witkowski committed
716
      // Test if the current row DOF is a periodic DOF.
717
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
718

Thomas Witkowski's avatar
Thomas Witkowski committed
719 720 721
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

722
	// Get PETSc's mat row index.
723
	int rowIndex = interiorMap->getMatIndex(nRowMat, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
724 725 726 727 728 729 730 731

	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
732
	  int globalColDof = colMap[col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
733
	  // Test if the current col dof is a periodic dof.
734
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
735
	  // Get PETSc's mat col index.
736
	  int colIndex = interiorMap->getMatIndex(nColMat, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
737 738 739 740 741 742 743

	  // 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
744 745
 	    cols.push_back(colIndex);
 	    values.push_back(value(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
746 747 748 749 750
	  } else {
	    // === Row index is not periodic, but column index is. ===

	    // Create set of all periodic associations of the column index.
	    std::set<int> perAsc;
751 752 753
	    perMap.fillAssociations(colFe, globalColDof, 
				    meshDistributor->getElementObjectDb(), perAsc);

Thomas Witkowski's avatar
Thomas Witkowski committed
754 755 756 757 758 759 760 761 762
	    // 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;
763
	    perMap.mapDof(colFe, globalColDof, perAsc, newCols);
Thomas Witkowski's avatar
Thomas Witkowski committed
764
	    for (unsigned int i = 0; i < newCols.size(); i++) {
765
	      cols.push_back(interiorMap->getMatIndex(nColMat, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
766 767 768 769 770
	      values.push_back(scaledValue);	      
	    }
	  }
	}

Thomas Witkowski's avatar
Thomas Witkowski committed
771 772
  	MatSetValues(matIntInt, 1, &rowIndex, cols.size(), 
  		     &(cols[0]), &(values[0]), ADD_VALUES);	
Thomas Witkowski's avatar
Thomas Witkowski committed
773 774 775 776 777 778 779 780 781 782 783 784 785 786
      } 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.
787
	  int globalColDof = (*interiorMap)[colFe][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
788 789 790 791 792 793 794 795 796

	  // 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;
797 798 799 800
	  perMap.fillAssociations(colFe, globalColDof, 
				  meshDistributor->getElementObjectDb(), perAsc);
	  perMap.fillAssociations(rowFe, globalRowDof, 
				  meshDistributor->getElementObjectDb(), perAsc);
Thomas Witkowski's avatar
Thomas Witkowski committed
801 802 803 804 805 806 807 808 809 810

	  // 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;
Thomas Witkowski's avatar
Blbu  
Thomas Witkowski committed
811 812
	  perMap.mapDof(rowFe, colFe, make_pair(globalRowDof, globalColDof),
			perAsc, entry);
Thomas Witkowski's avatar
Thomas Witkowski committed
813 814 815

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

816
	  for (unsigned int i = 0; i < entry.size(); i++) {
817 818
	    int rowIdx = interiorMap->getMatIndex(nRowMat, entry[i].first);
	    int colIdx = interiorMap->getMatIndex(nColMat, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
819

820 821
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
822 823 824 825 826 827 828 829 830 831 832 833
	  }
	}


	// === 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;
834

835
	  MatSetValues(matIntInt, 1, &rowIndex, rowIt->second.size(),
Thomas Witkowski's avatar
Thomas Witkowski committed
836 837 838 839 840 841 842
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
843 844
  void PetscSolverGlobalMatrix::setDofVector(Vec vecInterior, 
					     Vec vecCoarse,
845
					     DOFVector<double>* vec, 
846
					     int nRowVec, 
847
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
848 849 850
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

851
    const FiniteElemSpace *feSpace = vec->getFeSpace();
852
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
Thomas Witkowski's avatar
Thomas Witkowski committed
853 854 855 856
    
    ParallelDofMapping *rowCoarseSpace = NULL;
    if (coarseSpaceMap.size())
      rowCoarseSpace = coarseSpaceMap[nRowVec];
857

Thomas Witkowski's avatar
Thomas Witkowski committed
858 859 860
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
861

862
      if (rankOnly && !(*interiorMap)[feSpace].isRankDof(dofIt.getDOFIndex()))
Thomas Witkowski's avatar
Thomas Witkowski committed
863 864
	continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
865
      if (isCoarseSpace(nRowVec, feSpace, dofIt.getDOFIndex())) {
866 867
	TEST_EXIT_DBG(vecCoarse != PETSC_NULL)("Should not happen!\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
868
	int index = rowCoarseSpace->getMatIndex(nRowVec, dofIt.getDOFIndex());
869 870 871 872 873 874 875 876 877 878 879 880 881 882
	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;
883

884
	if (perMap.isPeriodic(feSpace, globalRowDof)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
885 886 887
	  std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
	  double value = *dofIt / (perAsc.size() + 1.0);
	  VecSetValue(vecInterior, index, value, ADD_VALUES);
888

Thomas Witkowski's avatar
Thomas Witkowski committed
889 890 891 892
	  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);
893

Thomas Witkowski's avatar
Thomas Witkowski committed
894
	    VecSetValue(vecInterior, mappedIndex, value, ADD_VALUES);
895 896 897 898
	  }	  
	} else {	  
	  // The DOF index is not periodic.
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
899 900
	  VecSetValue(vecInterior, index, *dofIt, ADD_VALUES);
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
901 902 903 904 905
      }
    }
  }


906 907
  void PetscSolverGlobalMatrix::removeDirichletBcDofs(Matrix<DOFMatrix*> *mat)
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
908
    FUNCNAME("PetscSolverGlobalMatrix::removeDirichletBcDofs()");    
909 910 911 912 913 914 915 916
  }


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

Thomas Witkowski's avatar
Thomas Witkowski committed
917
}