GlobalMatrixSolver.cc 16.2 KB
Newer Older
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488
#include "GlobalMatrixSolver.h"
#include "DOFVector.h"
#include "Debug.h"
#include "SystemVector.h"
#include "parallel/StdMpi.h"

#include "petscksp.h"

namespace AMDiS {

  PetscErrorCode myKSPMonitor(KSP ksp, PetscInt iter, PetscReal rnorm, void *)
  {    
    if (iter % 10 == 0 && MPI::COMM_WORLD.Get_rank() == 0)
      std::cout << "[0]  Petsc-Iteration " << iter << ": " << rnorm << std::endl;

    return 0;
  }
 
  void GlobalMatrixSolver::solve()
  {
    FUNCNAME("GlobalMatrixSolver::solve()");

#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif
    clock_t first = clock();

    fillPetscMatrix(probStat->getSystemMatrix(), probStat->getRHS());
    solvePetscMatrix(*(probStat->getSolution()));

#ifdef _OPENMP
    INFO(info, 8)("solution of discrete system needed %.5f seconds system time / %.5f seconds wallclock time\n",
		   TIME_USED(first, clock()),
		   omp_get_wtime() - wtime);
#else
    INFO(info, 8)("solution of discrete system needed %.5f seconds\n",
		   TIME_USED(first, clock()));
#endif    
  }


  void GlobalMatrixSolver::setDofMatrix(DOFMatrix* mat, int dispMult, 
					int dispAddRow, int dispAddCol)
  {
    FUNCNAME("GlobalMatrixSolver::setDofMatrix()");

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

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
    namespace traits= mtl::traits;
    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;

    std::vector<int> cols;
    std::vector<double> values;
    cols.reserve(300);
    values.reserve(300);

    // === Traverse all rows of the dof matrix and insert row wise the values ===
    // === to the petsc matrix.                                               ===

    for (cursor_type cursor = begin<row>(mat->getBaseMatrix()), 
	   cend = end<row>(mat->getBaseMatrix()); cursor != cend; ++cursor) {

      cols.clear();
      values.clear();

      // Global index of the current row dof.
      int globalRowDof = mapLocalGlobalDofs[*cursor];
      // Test if the current row dof is a periodic dof.
      bool periodicRow = (periodicDof.count(globalRowDof) > 0);


      // === Traverse all non zero entries of the row and produce vector cols ===
      // === with the column indices of all row entries and vector values     ===
      // === with the corresponding values.                                   ===

      for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); 
	   icursor != icend; ++icursor) {

	// Set only non null values.
	if (value(*icursor) != 0.0) {
	  // Global index of the current column index.
	  int globalColDof = mapLocalGlobalDofs[col(*icursor)];
	  // Calculate the exact position of the column index in the petsc matrix.
	  int colIndex = globalColDof * dispMult + dispAddCol;

	  // If the current row is not periodic, but the current dof index is periodic,
	  // we have to duplicate the value to the other corresponding periodic columns.
 	  if (periodicRow == false && periodicDof.count(globalColDof) > 0) {
	    // The value is assign to n matrix entries, therefore, every entry 
	    // has only 1/n value of the original entry.
	    double scalFactor = 1.0 / (periodicDof[globalColDof].size() + 1.0);

	    // Insert original entry.
 	    cols.push_back(colIndex);
 	    values.push_back(value(*icursor) * scalFactor);

	    // Insert the periodic entries.
 	    for (std::set<DegreeOfFreedom>::iterator it = 
		   periodicDof[globalColDof].begin();
 		 it != periodicDof[globalColDof].end(); ++it) {
 	      cols.push_back(*it * dispMult + dispAddCol);
 	      values.push_back(value(*icursor) * scalFactor);
	    }
 	  } else {
	    // Neigher row nor column dof index is periodic, simple add entry.
	    cols.push_back(colIndex);
	    values.push_back(value(*icursor));
	  }
	}
      }


      // === Up to now we have assembled on row. Now, the row must be send to the ===
      // === corresponding rows to the petsc matrix.                              ===

      // Calculate petsc row index.
      int rowIndex = globalRowDof * dispMult + dispAddRow;
      
      if (periodicRow) {
	// The row dof is periodic, so send dof to all the corresponding rows.

	double scalFactor = 1.0 / (periodicDof[globalRowDof].size() + 1.0);
	
	int diagIndex = -1;
	for (int i = 0; i < static_cast<int>(values.size()); i++) {
	  // Change only the non diagonal values in the col. For the diagonal test
	  // we compare the global dof indices of the dof matrix (not of the petsc
	  // matrix!).
	  if ((cols[i] - dispAddCol) / dispMult != globalRowDof)
	    values[i] *= scalFactor;
	  else
	    diagIndex = i;
	}
	
	// Send the main row to the petsc matrix.
	MatSetValues(petscMatrix, 1, &rowIndex, cols.size(), 
		     &(cols[0]), &(values[0]), ADD_VALUES);	
 
	// Set diagonal element to zero, i.e., the diagonal element of the current
	// row is not send to the periodic row indices.
	if (diagIndex != -1)
	  values[diagIndex] = 0.0;

	// Send the row to all periodic row indices.
	for (std::set<DegreeOfFreedom>::iterator it = periodicDof[globalRowDof].begin();
	     it != periodicDof[globalRowDof].end(); ++it) {
	  int perRowIndex = *it * dispMult + dispAddRow;
	  MatSetValues(petscMatrix, 1, &perRowIndex, cols.size(), 
		       &(cols[0]), &(values[0]), ADD_VALUES);
	}

      } else {
	// The row dof is not periodic, simply send the row to the petsc matrix.
	MatSetValues(petscMatrix, 1, &rowIndex, cols.size(), 
		     &(cols[0]), &(values[0]), ADD_VALUES);
      }    
    }
  }


  void GlobalMatrixSolver::setDofVector(Vec& petscVec, DOFVector<double>* vec, 
					int dispMult, int dispAdd)
  {
    // Traverse all used dofs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
      // Calculate global row index of the dof.
      int globalRow = mapLocalGlobalDofs[dofIt.getDOFIndex()];
      // Calculate petsc index of the row dof.
      int index = globalRow * dispMult + dispAdd;

      if (periodicDof.count(globalRow) > 0) {
	// The dof index is periodic, so devide the value to all dof entries.

	double value = *dofIt / (periodicDof[globalRow].size() + 1.0);
	VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);

	for (std::set<DegreeOfFreedom>::iterator it = periodicDof[globalRow].begin();
	     it != periodicDof[globalRow].end(); ++it) {
	  index = *it * dispMult + dispAdd;
	  VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);
	}

      } else {
	// The dof index is not periodic.
	double value = *dofIt;
	VecSetValues(petscVec, 1, &index, &value, ADD_VALUES);
      }
    }    
  }


  void GlobalMatrixSolver::createPetscNnzStructure(Matrix<DOFMatrix*> *mat)
  {
    FUNCNAME("GlobalMatrixSolver::createPetscNnzStructure()");

    TEST_EXIT_DBG(!d_nnz)("There is something wrong!\n");
    TEST_EXIT_DBG(!o_nnz)("There is something wrong!\n");

    d_nnz = new int[nRankRows];
    o_nnz = new int[nRankRows];
    for (int i = 0; i < nRankRows; i++) {
      d_nnz[i] = 0;
      o_nnz[i] = 0;
    }

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
    namespace traits = mtl::traits;
    typedef DOFMatrix::base_matrix_type Matrix;
    typedef std::vector<std::pair<int, int> > MatrixNnzEntry;

    // Stores to each rank a list of nnz entries (i.e. pairs of row and column index)
    // that this rank will send to. This nnz entries will be assembled on this rank,
    // but because the row DOFs are not DOFs of this rank they will be send to the
    // owner of the row DOFs.
    std::map<int, MatrixNnzEntry> sendMatrixEntry;

    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
 	if ((*mat)[i][j]) {
	  Matrix bmat = (*mat)[i][j]->getBaseMatrix();

	  traits::col<Matrix>::type col(bmat);
	  traits::const_value<Matrix>::type value(bmat);
	  
	  typedef traits::range_generator<row, Matrix>::type cursor_type;
	  typedef traits::range_generator<nz, cursor_type>::type icursor_type;
	  
	  for (cursor_type cursor = begin<row>(bmat), 
		 cend = end<row>(bmat); cursor != cend; ++cursor) {

	    // Map the local row number to the global DOF index and create from it
	    // the global PETSc row index of this DOF.
	    int petscRowIdx = mapLocalGlobalDofs[*cursor] * nComponents + i;

	    if (isRankDof[*cursor]) {

	      // === The current row DOF is a rank dof, so create the corresponding ===
	      // === nnz values directly on rank's nnz data.                        ===

	      // This is the local row index of the local PETSc matrix.
	      int localPetscRowIdx = petscRowIdx - rstart * nComponents;

#if (DEBUG != 0)    
	      if (localPetscRowIdx < 0 || localPetscRowIdx >= nRankRows) {
		std::cout << "ERROR in rank: " << mpiRank << std::endl;
		std::cout << "  Wrong r = " << localPetscRowIdx << " " << *cursor 
			  << " " << mapLocalGlobalDofs[*cursor] << " " 
			  << nRankRows << std::endl;
		ERROR_EXIT("Should not happen!\n");
	      }
#endif
	      
	      // Traverse all non zero entries in this row.
	      for (icursor_type icursor = begin<nz>(cursor), 
		     icend = end<nz>(cursor); icursor != icend; ++icursor) {
		if (value(*icursor) != 0.0) {
		  int petscColIdx = mapLocalGlobalDofs[col(*icursor)] * nComponents + j;

		  // The row DOF is a rank DOF, if also the column is a rank DOF, 
		  // increment the d_nnz values for this row, otherwise the o_nnz value.
		  if (petscColIdx >= rstart * nComponents && 
		      petscColIdx < rstart * nComponents + nRankRows)
		    d_nnz[localPetscRowIdx]++;
		  else
		    o_nnz[localPetscRowIdx]++;
		}    
	      }
	    } else {
	      
	      // === The current row DOF is not a rank dof, i.e., it will be created ===
	      // === on this rank, but after this it will be send to another rank    ===
	      // === matrix. So we need to send also the corresponding nnz structure ===
	      // === of this row to the corresponding rank.                          ===

	      // Find out who is the member of this DOF.
	      int sendToRank = -1;
	      for (RankToDofContainer::iterator it = recvDofs.begin();
		   it != recvDofs.end(); ++it) {
		for (DofContainer::iterator dofIt = it->second.begin();
		     dofIt != it->second.end(); ++dofIt) {
		  if (**dofIt == *cursor) {

		    if (petscRowIdx == 6717) {
		      debug::writeDofMesh(mpiRank, *cursor, feSpace);
		      MSG("SEND DOF TO: %d/%d\n", it->first, *cursor);
		    }

		    sendToRank = it->first;
		    break;
		  }
		}

		if (sendToRank != -1)
		  break;
	      }

	      TEST_EXIT_DBG(sendToRank != -1)("Should not happen!\n");

	      // Send all non zero entries to the member of the row DOF.
	      for (icursor_type icursor = begin<nz>(cursor), 
		     icend = end<nz>(cursor); icursor != icend; ++icursor) {
		if (value(*icursor) != 0.0) {
		  int petscColIdx = mapLocalGlobalDofs[col(*icursor)] * nComponents + j;
		  
		  sendMatrixEntry[sendToRank].
		    push_back(std::make_pair(petscRowIdx, petscColIdx));
		}
	      }

	    } // if (isRankDof[*cursor]) ... else ...
	  } // for each row in mat[i][j]
	} // if mat[i][j]
      } 
    }

    // === Send and recv the nnz row structure to/from other ranks. ===

    StdMpi<MatrixNnzEntry> stdMpi(mpiComm, true);
    stdMpi.send(sendMatrixEntry);
    stdMpi.recv(sendDofs);
    stdMpi.startCommunication<int>(MPI_INT);

    // === Evaluate the nnz structure this rank got from other ranks and add it to ===
    // === the PETSc nnz data structure.                                           ===

    for (std::map<int, MatrixNnzEntry>::iterator it = stdMpi.getRecvData().begin();
	 it != stdMpi.getRecvData().end(); ++it) {
      if (it->second.size() > 0) {
	for (unsigned int i = 0; i < it->second.size(); i++) {
	  int r = it->second[i].first;
	  int c = it->second[i].second;

	  int localRowIdx = r - rstart * nComponents;

	  TEST_EXIT_DBG(localRowIdx >= 0 && localRowIdx < nRankRows)
	    ("Got row index %d/%d (nRankRows = %d) from rank %d. Should not happen!\n",
	     r, localRowIdx, nRankRows, it->first);
	  
	  if (c < rstart * nComponents || c >= rstart * nComponents + nRankRows)
	    o_nnz[localRowIdx]++;
	  else
	    d_nnz[localRowIdx]++;
	}
      }
    }  
  }


  void GlobalMatrixSolver::fillPetscMatrix(Matrix<DOFMatrix*> *mat, SystemVector *vec)
  {
    FUNCNAME("GlobalMatrixSolver::fillPetscMatrix()");

    clock_t first = clock();

    // === Create PETSc vector (rhs, solution and a temporary vector). ===

    VecCreate(PETSC_COMM_WORLD, &petscRhsVec);
    VecSetSizes(petscRhsVec, nRankRows, nOverallRows);
    VecSetType(petscRhsVec, VECMPI);

    VecCreate(PETSC_COMM_WORLD, &petscSolVec);
    VecSetSizes(petscSolVec, nRankRows, nOverallRows);
    VecSetType(petscSolVec, VECMPI);

    VecCreate(PETSC_COMM_WORLD, &petscTmpVec);
    VecSetSizes(petscTmpVec, nRankRows, nOverallRows);
    VecSetType(petscTmpVec, VECMPI);

    if (!d_nnz)
      createPetscNnzStructure(mat);

    // === Create PETSc matrix with the computed nnz data structure. ===

    MatCreateMPIAIJ(PETSC_COMM_WORLD, nRankRows, nRankRows, nOverallRows, nOverallRows,
		    0, d_nnz, 0, o_nnz, &petscMatrix);

    INFO(info, 8)("Fill petsc matrix 1 needed %.5f seconds\n", TIME_USED(first, clock()));

#if (DEBUG != 0)
    int a, b;
    MatGetOwnershipRange(petscMatrix, &a, &b);
    TEST_EXIT(a == rstart * nComponents)("Wrong matrix ownership range!\n");
    TEST_EXIT(b == rstart * nComponents + nRankRows)("Wrong matrix ownership range!\n");
#endif

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

    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
	if ((*mat)[i][j])
	  setDofMatrix((*mat)[i][j], nComponents, i, j);

    INFO(info, 8)("Fill petsc matrix 2 needed %.5f seconds\n", TIME_USED(first, clock()));

    MatAssemblyBegin(petscMatrix, MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(petscMatrix, MAT_FINAL_ASSEMBLY);

    // === Transfer values from DOF vector to the PETSc vector. === 

    for (int i = 0; i < nComponents; i++)
      setDofVector(petscRhsVec, vec->getDOFVector(i), nComponents, i);

    VecAssemblyBegin(petscRhsVec);
    VecAssemblyEnd(petscRhsVec);

    INFO(info, 8)("Fill petsc matrix needed %.5f seconds\n", TIME_USED(first, clock()));
  }


  void GlobalMatrixSolver::solvePetscMatrix(SystemVector &vec)
  {
    FUNCNAME("GlobalMatrixSolver::solvePetscMatrix()");

#if 0
    // Set old solution to be initiual guess for petsc solver.
    for (int i = 0; i < nComponents; i++)
      setDofVector(petscSolVec, vec->getDOFVector(i), nComponents, i);

    VecAssemblyBegin(petscSolVec);
    VecAssemblyEnd(petscSolVec);
#endif

    // === Init Petsc solver. ===

    KSP solver;
    KSPCreate(PETSC_COMM_WORLD, &solver);
    KSPSetOperators(solver, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN); 
    KSPSetTolerances(solver, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(solver, KSPBCGS);
    KSPMonitorSet(solver, myKSPMonitor, PETSC_NULL, 0);
    KSPSetFromOptions(solver);
    // Do not delete the solution vector, use it for the initial guess.
    //    KSPSetInitialGuessNonzero(solver, PETSC_TRUE);


    // === Run Petsc. ===

    KSPSolve(solver, petscRhsVec, petscSolVec);

    // === Transfere values from Petsc's solution vectors to the dof vectors.
    PetscScalar *vecPointer;
    VecGetArray(petscSolVec, &vecPointer);

    for (int i = 0; i < nComponents; i++) {
      DOFVector<double> *dofvec = vec.getDOFVector(i);
      for (int j = 0; j < nRankDofs; j++)
	(*dofvec)[mapLocalToDofIndex[j]] = vecPointer[j * nComponents + i];      
    }

    VecRestoreArray(petscSolVec, &vecPointer);


    // === Synchronize dofs at common dofs, i.e., dofs that correspond to more ===
    // === than one partition.                                                 ===
    synchVector(vec);


    // === Print information about solution process. ===

    int iterations = 0;
    KSPGetIterationNumber(solver, &iterations);
    MSG("  Number of iterations: %d\n", iterations);
    
    double norm = 0.0;
    MatMult(petscMatrix, petscSolVec, petscTmpVec);
    VecAXPY(petscTmpVec, -1.0, petscRhsVec);
    VecNorm(petscTmpVec, NORM_2, &norm);
    MSG("  Residual norm: %e\n", norm);


    // === Destroy Petsc's variables. ===

    MatDestroy(petscMatrix);
    VecDestroy(petscRhsVec);
    VecDestroy(petscSolVec);
    VecDestroy(petscTmpVec);
    KSPDestroy(solver);
  }

}