PetscSolverGlobalMatrix.cc 23.2 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 {

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

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
24 25 26 27 28 29
    TEST_EXIT_DBG(meshDistributor)("No mesh distributor object defined!\n");
    TEST_EXIT_DBG(interiorMap)("No parallel mapping object defined!\n");
    TEST_EXIT_DBG(seqMat)("No DOF matrix defined!\n");
    
    double wtime = MPI::Wtime();

30 31 32
    petscData.init(interiorMap, coarseSpaceMap, 
		   subdomainLevel, mpiCommLocal, mpiCommGlobal,
		   meshDistributor);
Thomas Witkowski's avatar
Thomas Witkowski committed
33
    petscData.create(*seqMat);
34

Thomas Witkowski's avatar
Thomas Witkowski committed
35
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
36
      fillPetscMatrixWithCoarseSpace(seqMat);
37 38 39
      return;
    }

40 41
    // === Create PETSc vector (solution and a temporary vector). ===

Thomas Witkowski's avatar
Thomas Witkowski committed
42 43 44 45 46 47
#if (DEBUG != 0)
    MSG("Fill petsc matrix 1 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

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

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
48
    int nComponents = seqMat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
49 50
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
51 52
	if ((*seqMat)[i][j])
	  setDofMatrix((*seqMat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
53 54 55 56 57

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

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
58
    petscData.matAssembly();
59 60 61
    
    if (printMatInfo) {
      MatInfo matInfo;
62
      MatGetInfo(petscData.getInteriorMat(), MAT_GLOBAL_SUM, &matInfo);
63 64 65 66 67 68 69
      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));
    }
70 71 72

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

73
    //    removeDirichletBcDofs(mat);
74 75
    

76
    // === Init PETSc solver. ===
77

78 79
    KSPCreate(mpiCommGlobal, &kspInterior);
    KSPGetPC(kspInterior, &pcInterior);
80 81 82 83
    KSPSetOperators(kspInterior, 
		    petscData.getInteriorMat(), 
		    petscData.getInteriorMat(), 
		    SAME_NONZERO_PATTERN); 
84 85 86 87
    KSPSetTolerances(kspInterior, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(kspInterior, KSPBCGS);
    KSPSetOptionsPrefix(kspInterior, kspPrefix.c_str());
    KSPSetFromOptions(kspInterior);
88

89
    initPreconditioner(pcInterior);
90

91 92
    // Do not delete the solution vector, use it for the initial guess.
    if (!zeroStartVector)
93
      KSPSetInitialGuessNonzero(kspInterior, PETSC_TRUE);
94

Thomas Witkowski's avatar
Thomas Witkowski committed
95 96 97
#if (DEBUG != 0)
    MSG("Fill petsc matrix 3 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif
98 99 100
  }


101 102 103 104 105 106 107 108
  void PetscSolverGlobalMatrix::fillPetscMatrix(DOFMatrix *mat)
  {
    Matrix<DOFMatrix*> m(1, 1);
    m[0][0] = mat;
    fillPetscMatrix(&m);
  }


Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
109
  void PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace(Matrix<DOFMatrix*> *seqMat)
110 111
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace()");
112 113

    TEST_EXIT_DBG(interiorMap)("Should not happen!\n");
114 115
    TEST_EXIT_DBG(coarseSpaceMap.size() == seqMat->getSize())
      ("Wrong sizes %d %d\n", coarseSpaceMap.size(), seqMat->getSize());
116

Thomas Witkowski's avatar
Thomas Witkowski committed
117
    vector<const FiniteElemSpace*> feSpaces = AMDiS::getFeSpaces(*seqMat);
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
118

119 120
    int nRowsRankInterior = interiorMap->getRankDofs();
    int nRowsOverallInterior = interiorMap->getOverallDofs();
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
121
    int rStartInterior = petscData.getStartInterior();
122

123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141
    // === 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.                                       ===

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
142
    int nComponents = seqMat->getSize();
143 144
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
145
	if (!(*seqMat)[i][j])
146 147
	  continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
148 149 150
	ParallelDofMapping *rowCoarseSpace = coarseSpaceMap[i];
	ParallelDofMapping *colCoarseSpace = coarseSpaceMap[j];

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
151 152
	traits::col<Matrix>::type col((*seqMat)[i][j]->getBaseMatrix());
	traits::const_value<Matrix>::type value((*seqMat)[i][j]->getBaseMatrix());
153 154
	
	// Traverse all rows.
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
155 156
	for (cursor_type cursor = begin<row>((*seqMat)[i][j]->getBaseMatrix()), 
	       cend = end<row>((*seqMat)[i][j]->getBaseMatrix()); cursor != cend; ++cursor) {
157

Thomas Witkowski's avatar
Thomas Witkowski committed
158
	  bool isRowCoarse = isCoarseSpace(i, feSpaces[i], *cursor);
159 160 161 162 163 164 165 166 167 168
  
	  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
169
	    bool isColCoarse = isCoarseSpace(j, feSpaces[j], col(*icursor));
170

Thomas Witkowski's avatar
Thomas Witkowski committed
171 172
	    if (isColCoarse) {
	      if (isRowCoarse) {
173 174 175 176 177 178 179
		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
180
	      if (isRowCoarse) {
181 182 183 184 185 186 187 188 189 190 191 192
		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
193 194
	  if (isRowCoarse) {
	    int rowIndex = rowCoarseSpace->getMatIndex(i, *cursor);
195
	    for (unsigned int k = 0; k < cols.size(); k++)
Thomas Witkowski's avatar
Thomas Witkowski committed
196
	      cols[k] = colCoarseSpace->getMatIndex(j, cols[k]);
197

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
198
	    // matCoarseCoarse
199
	    MatSetValues(petscData.getCoarseMatComp(i),
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
200
			 1, &rowIndex, cols.size(),
201 202 203 204
			 &(cols[0]), &(values[0]), ADD_VALUES);

	    if (colsOther.size()) {
	      if (subdomainLevel == 0) {
205
		for (unsigned int k = 0; k < colsOther.size(); k++)
206 207 208 209 210 211
		  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;
	      }
212

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
213
	      // matCoarseInt
214
	      MatSetValues(petscData.getCoarseIntMatComp(i), 
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
215
			   1, &rowIndex, colsOther.size(),
216 217 218 219 220 221 222 223 224 225 226 227 228 229
 			   &(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]);
	    }
	    
230
  	    MatSetValues(petscData.getInteriorMat(), 1, &localRowIndex, cols.size(),
231 232 233 234 235 236 237 238 239
  			 &(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
240
		colsOther[k] = colCoarseSpace->getMatIndex(j, colsOther[k]);
241

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
242
	      // matIntCoarse
243
  	      MatSetValues(petscData.getIntCoarseMatComp(i), 
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
244
			   1, &globalRowIndex, colsOther.size(),
245 246 247 248 249 250 251
  			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
	    }
	  }
	} 
      }
    }

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
252
    petscData.matAssembly();
253

254 255 256
    // === Create solver for the non primal (thus local) variables. ===

    KSPCreate(mpiCommLocal, &kspInterior);
257 258 259 260
    KSPSetOperators(kspInterior, 
		    petscData.getInteriorMat(),
		    petscData.getInteriorMat(),
		    SAME_NONZERO_PATTERN);
261 262 263 264 265 266 267 268 269 270 271 272
    KSPSetOptionsPrefix(kspInterior, "interior_");
    KSPSetType(kspInterior, KSPPREONLY);
    KSPGetPC(kspInterior, &pcInterior);
    PCSetType(pcInterior, PCLU);
    if (subdomainLevel == 0)
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERUMFPACK);
    else
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
    KSPSetFromOptions(kspInterior);  
  }


273 274 275
  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
Thomas Witkowski's avatar
Thomas Witkowski committed
276

277
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
278
    TEST_EXIT_DBG(interiorMap)("No parallel DOF map defined!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
279
    
Thomas Witkowski's avatar
Thomas Witkowski committed
280
    // === Transfer values from DOF vector to the PETSc vector. === 
Thomas Witkowski's avatar
Thomas Witkowski committed
281
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
282
      for (int i = 0; i < vec->getSize(); i++)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
283
	setDofVector(getRhsInterior(), getRhsCoarseSpace(), vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
284 285
    } else {
      for (int i = 0; i < vec->getSize(); i++)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
286
	setDofVector(getRhsInterior(), vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
287 288
    }

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
289
    petscData.vecRhsAssembly();
Thomas Witkowski's avatar
Thomas Witkowski committed
290 291 292
  }


293 294
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
295 296 297 298 299 300 301
  {
    FUNCNAME("PetscSolverGlobalMatrix::solvePetscMatrix()");

    int nComponents = vec.getSize();

    // === Set old solution to be initiual guess for PETSc solver. ===
    if (!zeroStartVector) {
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
302 303 304
      TEST_EXIT(coarseSpaceMap.size() == 0)("Not yet supported!\n");

      VecSet(getSolInterior(), 0.0);
Thomas Witkowski's avatar
Thomas Witkowski committed
305 306
      
      for (int i = 0; i < nComponents; i++)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
307 308 309
	setDofVector(getSolInterior(), vec.getDOFVector(i), i, true);

      petscData.vecSolAssembly();
Thomas Witkowski's avatar
Thomas Witkowski committed
310 311
    }

312

Thomas Witkowski's avatar
Thomas Witkowski committed
313 314
    MatNullSpace matNullspace;
    Vec nullspaceBasis;
315 316 317
    if (nullspace.size() > 0 || 
	hasConstantNullspace ||
	constNullspaceComponent.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
318
      TEST_EXIT_DBG(nullspace.size() <= 1)("Not yet implemented!\n");
319

320 321 322 323 324 325 326 327 328 329
      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
330
      if (nullspace.size() > 0) {
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
331
	VecDuplicate(getSolInterior(), &nullspaceBasis);
Thomas Witkowski's avatar
Thomas Witkowski committed
332 333 334 335 336
	for (int i = 0; i < nComponents; i++)
	  setDofVector(nullspaceBasis, nullspace[0]->getDOFVector(i), i, true);
	
	VecAssemblyBegin(nullspaceBasis);
	VecAssemblyEnd(nullspaceBasis);
337 338

	VecNormalize(nullspaceBasis, PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
339 340 341 342
	
	MatNullSpaceCreate(mpiCommGlobal, (hasConstantNullspace ? PETSC_TRUE : PETSC_FALSE), 
			   1, &nullspaceBasis, &matNullspace);

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
343
	MatMult(petscData.getInteriorMat(), nullspaceBasis, getSolInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
344
	PetscReal n;
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
345
	VecNorm(getSolInterior(), NORM_2, &n);
Thomas Witkowski's avatar
Thomas Witkowski committed
346 347 348 349
	MSG("NORM IS: %e\n", n);
      } else {
	MatNullSpaceCreate(mpiCommGlobal, PETSC_TRUE, 0, PETSC_NULL, &matNullspace);
      }
350

351
      MatSetNullSpace(petscData.getInteriorMat(), matNullspace);
Thomas Witkowski's avatar
Thomas Witkowski committed
352
      KSPSetNullSpace(kspInterior, matNullspace);
353

Thomas Witkowski's avatar
Thomas Witkowski committed
354
      // === Remove null space, if requested. ===
355

Thomas Witkowski's avatar
Thomas Witkowski committed
356
      if (removeRhsNullspace) {
Thomas Witkowski's avatar
Thomas Witkowski committed
357
	TEST_EXIT_DBG(coarseSpaceMap.empty())("Not supported!\n");
358 359

	MSG("Remove nullspace from rhs vector.\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
360
	
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
361
	MatNullSpaceRemove(matNullspace, getRhsInterior(), PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
362 363 364 365
      }
    } else {
      TEST_EXIT(removeRhsNullspace == false)
	("No nullspace provided that should be removed from rhs!\n");
366 367
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
368
    // PETSc.
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
369
    solve(getRhsInterior(), getSolInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
370

371 372

    if (nullspace.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
373
      MatNullSpaceDestroy(&matNullspace);
374 375 376 377
      VecDestroy(&nullspaceBasis);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
378 379
    // === Transfere values from PETSc's solution vectors to the DOF vectors. ===
    PetscScalar *vecPointer;
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
380
    VecGetArray(getSolInterior(), &vecPointer);    
Thomas Witkowski's avatar
Thomas Witkowski committed
381

382
    int c = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
383
    for (int i = 0; i < nComponents; i++) {
384
      DOFVector<double> &dv = *(vec.getDOFVector(i));
385

386
      DofMap& d = (*interiorMap)[dv.getFeSpace()].getMap();
387 388 389
      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
390 391
    }

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
392
    VecRestoreArray(getSolInterior(), &vecPointer);
Thomas Witkowski's avatar
Thomas Witkowski committed
393 394 395 396

    // === Synchronize DOFs at common DOFs, i.e., DOFs that correspond to ===  
    // === more than one partition.                                       ===  
    meshDistributor->synchVector(vec);
397 398 399
  }


400 401 402 403
  void PetscSolverGlobalMatrix::solveGlobal(Vec &rhs, Vec &sol)
  {
    FUNCNAME("PetscSolverGlobalMatrix::solveGlobal()");

404 405 406
    double wtime = MPI::Wtime();
    double t0 = 0.0, t1 = 0.0;

407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425
    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);

426 427 428
    t0 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
429
    KSPSolve(kspInterior, tmp, tmp);
430 431 432
    t1 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
433 434 435 436 437 438 439 440 441 442 443

    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);
444 445
    t0 += MPI::Wtime() - wtime;

446
    //    MSG("TIMEING: %.5f %.5f\n", t0, t1);
447 448 449
  }


450 451 452 453
  void PetscSolverGlobalMatrix::destroyMatrixData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyMatrixData()");

454 455
    exitPreconditioner(pcInterior);

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
456
    petscData.matDestroy();
Thomas Witkowski's avatar
Thomas Witkowski committed
457

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
458
    KSPDestroy(&kspInterior);
Thomas Witkowski's avatar
Thomas Witkowski committed
459 460 461
  }


462 463 464 465
  void PetscSolverGlobalMatrix::destroyVectorData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyVectorData()");

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
466
    petscData.vecDestroy();
467 468 469
  }


470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505
  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);
    }
  }


506 507 508 509 510 511 512 513 514 515 516 517 518 519 520
  void PetscSolverGlobalMatrix::initPreconditioner(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::initPreconditioner()");

    PCSetFromOptions(pc);
    createFieldSplit(pc);
  }

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


Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
521
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* seqMat,
522
					     int nRowMat, int nColMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
523 524 525
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
526
    TEST_EXIT(seqMat)("No DOFMatrix!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
527 528

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
529
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
530 531
    typedef DOFMatrix::base_matrix_type Matrix;

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
532 533
    traits::col<Matrix>::type col(seqMat->getBaseMatrix());
    traits::const_value<Matrix>::type value(seqMat->getBaseMatrix());
Thomas Witkowski's avatar
Thomas Witkowski committed
534 535 536 537 538 539 540 541 542 543 544

    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;

545 546 547
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
548 549
    const FiniteElemSpace *rowFe = seqMat->getRowFeSpace();
    const FiniteElemSpace *colFe = seqMat->getColFeSpace();
Thomas Witkowski's avatar
Thomas Witkowski committed
550 551 552 553
    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
554 555
    // === to the PETSc matrix.                                               ===

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
556 557
    for (cursor_type cursor = begin<row>(seqMat->getBaseMatrix()), 
	   cend = end<row>(seqMat->getBaseMatrix()); cursor != cend; ++cursor) {
Thomas Witkowski's avatar
Thomas Witkowski committed
558
      // Global index of the current row DOF.
Thomas Witkowski's avatar
Thomas Witkowski committed
559
      int globalRowDof = rowMap[*cursor].global;
560

Thomas Witkowski's avatar
Thomas Witkowski committed
561
      // Test if the current row DOF is a periodic DOF.
562
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
563

Thomas Witkowski's avatar
Thomas Witkowski committed
564 565 566
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

567
	// Get PETSc's mat row index.
568
	int rowIndex = interiorMap->getMatIndex(nRowMat, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
569 570 571 572 573 574 575 576

	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
577
	  int globalColDof = colMap[col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
578
	  // Test if the current col dof is a periodic dof.
579
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
580
	  // Get PETSc's mat col index.
581
	  int colIndex = interiorMap->getMatIndex(nColMat, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
582 583 584 585 586 587 588

	  // 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
589 590
 	    cols.push_back(colIndex);
 	    values.push_back(value(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
591 592 593 594 595
	  } else {
	    // === Row index is not periodic, but column index is. ===

	    // Create set of all periodic associations of the column index.
	    std::set<int> perAsc;
596 597 598
	    perMap.fillAssociations(colFe, globalColDof, 
				    meshDistributor->getElementObjectDb(), perAsc);

Thomas Witkowski's avatar
Thomas Witkowski committed
599 600 601 602 603 604 605 606 607
	    // 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;
608
	    perMap.mapDof(colFe, globalColDof, perAsc, newCols);
Thomas Witkowski's avatar
Thomas Witkowski committed
609
	    for (unsigned int i = 0; i < newCols.size(); i++) {
610
	      cols.push_back(interiorMap->getMatIndex(nColMat, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
611 612 613 614 615
	      values.push_back(scaledValue);	      
	    }
	  }
	}

616
  	MatSetValues(petscData.getInteriorMat(), 1, &rowIndex, cols.size(), 
Thomas Witkowski's avatar
Thomas Witkowski committed
617
  		     &(cols[0]), &(values[0]), ADD_VALUES);	
Thomas Witkowski's avatar
Thomas Witkowski committed
618 619 620 621 622 623 624 625 626 627 628 629 630 631
      } 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.
632
	  int globalColDof = (*interiorMap)[colFe][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
633 634 635 636 637 638 639 640 641

	  // 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;
642 643 644 645
	  perMap.fillAssociations(colFe, globalColDof, 
				  meshDistributor->getElementObjectDb(), perAsc);
	  perMap.fillAssociations(rowFe, globalRowDof, 
				  meshDistributor->getElementObjectDb(), perAsc);
Thomas Witkowski's avatar
Thomas Witkowski committed
646 647 648 649 650 651 652 653 654 655

	  // 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
656 657
	  perMap.mapDof(rowFe, colFe, make_pair(globalRowDof, globalColDof),
			perAsc, entry);
Thomas Witkowski's avatar
Thomas Witkowski committed
658 659 660

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

661
	  for (unsigned int i = 0; i < entry.size(); i++) {
662 663
	    int rowIdx = interiorMap->getMatIndex(nRowMat, entry[i].first);
	    int colIdx = interiorMap->getMatIndex(nColMat, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
664

665 666
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
667 668 669 670 671 672 673 674 675 676 677 678
	  }
	}


	// === 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;
679

680
	  MatSetValues(petscData.getInteriorMat(), 1, &rowIndex, rowIt->second.size(),
Thomas Witkowski's avatar
Thomas Witkowski committed
681 682 683 684 685 686 687
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
688 689
  void PetscSolverGlobalMatrix::setDofVector(Vec vecInterior, 
					     Vec vecCoarse,
690
					     DOFVector<double>* vec, 
691
					     int nRowVec, 
692
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
693 694 695
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

696
    const FiniteElemSpace *feSpace = vec->getFeSpace();
697
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
698 699
    int rStartInterior = petscData.getStartInterior();

Thomas Witkowski's avatar
Thomas Witkowski committed
700 701 702
    ParallelDofMapping *rowCoarseSpace = NULL;
    if (coarseSpaceMap.size())
      rowCoarseSpace = coarseSpaceMap[nRowVec];
703

Thomas Witkowski's avatar
Thomas Witkowski committed
704 705 706
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
707

708
      if (rankOnly && !(*interiorMap)[feSpace].isRankDof(dofIt.getDOFIndex()))
Thomas Witkowski's avatar
Thomas Witkowski committed
709 710
	continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
711
      if (isCoarseSpace(nRowVec, feSpace, dofIt.getDOFIndex())) {
712 713
	TEST_EXIT_DBG(vecCoarse != PETSC_NULL)("Should not happen!\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
714
	int index = rowCoarseSpace->getMatIndex(nRowVec, dofIt.getDOFIndex());
715 716 717 718 719 720 721 722 723 724 725 726 727 728
	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;
729

730
	if (perMap.isPeriodic(feSpace, globalRowDof)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
731 732 733
	  std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
	  double value = *dofIt / (perAsc.size() + 1.0);
	  VecSetValue(vecInterior, index, value, ADD_VALUES);
734

Thomas Witkowski's avatar
Thomas Witkowski committed
735 736 737 738
	  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);
739

Thomas Witkowski's avatar
Thomas Witkowski committed
740
	    VecSetValue(vecInterior, mappedIndex, value, ADD_VALUES);
741 742 743 744
	  }	  
	} else {	  
	  // The DOF index is not periodic.
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
745 746
	  VecSetValue(vecInterior, index, *dofIt, ADD_VALUES);
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
747 748 749 750 751
      }
    }
  }


752 753
  void PetscSolverGlobalMatrix::removeDirichletBcDofs(Matrix<DOFMatrix*> *mat)
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
754
    FUNCNAME("PetscSolverGlobalMatrix::removeDirichletBcDofs()");    
755 756 757 758 759 760
  }


  void PetscSolverGlobalMatrix::removeDirichletBcDofs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::removeDirichletBcDofs()");
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
761
  } 
762

Thomas Witkowski's avatar
Thomas Witkowski committed
763
}