static PetscErrorCode PCSetUp_LU(PC pc) { PetscErrorCode ierr; PC_LU *dir = (PC_LU*)pc->data; PetscFunctionBegin; if (dir->reusefill && pc->setupcalled) ((PC_Factor*)dir)->info.fill = dir->actualfill; if (dir->inplace) { if (dir->row && dir->col && dir->row != dir->col) {ierr = ISDestroy(dir->row);CHKERRQ(ierr);} if (dir->col) {ierr = ISDestroy(dir->col);CHKERRQ(ierr);} ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);CHKERRQ(ierr); if (dir->row) { ierr = PetscLogObjectParent(pc,dir->row);CHKERRQ(ierr); ierr = PetscLogObjectParent(pc,dir->col);CHKERRQ(ierr); } ierr = MatLUFactor(pc->pmat,dir->row,dir->col,&((PC_Factor*)dir)->info);CHKERRQ(ierr); ((PC_Factor*)dir)->fact = pc->pmat; } else { MatInfo info; if (!pc->setupcalled) { ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);CHKERRQ(ierr); if (dir->nonzerosalongdiagonal) { ierr = MatReorderForNonzeroDiagonal(pc->pmat,dir->nonzerosalongdiagonaltol,dir->row,dir->col);CHKERRQ(ierr); } if (dir->row) { ierr = PetscLogObjectParent(pc,dir->row);CHKERRQ(ierr); ierr = PetscLogObjectParent(pc,dir->col);CHKERRQ(ierr); } ierr = MatGetFactor(pc->pmat,((PC_Factor*)dir)->solvertype,MAT_FACTOR_LU,&((PC_Factor*)dir)->fact);CHKERRQ(ierr); ierr = MatLUFactorSymbolic(((PC_Factor*)dir)->fact,pc->pmat,dir->row,dir->col,&((PC_Factor*)dir)->info);CHKERRQ(ierr); ierr = MatGetInfo(((PC_Factor*)dir)->fact,MAT_LOCAL,&info);CHKERRQ(ierr); dir->actualfill = info.fill_ratio_needed; ierr = PetscLogObjectParent(pc,((PC_Factor*)dir)->fact);CHKERRQ(ierr); } else if (pc->flag != SAME_NONZERO_PATTERN) { if (!dir->reuseordering) { if (dir->row && dir->col && dir->row != dir->col) {ierr = ISDestroy(dir->row);CHKERRQ(ierr);} if (dir->col) {ierr = ISDestroy(dir->col);CHKERRQ(ierr);} ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);CHKERRQ(ierr); if (dir->nonzerosalongdiagonal) { ierr = MatReorderForNonzeroDiagonal(pc->pmat,dir->nonzerosalongdiagonaltol,dir->row,dir->col);CHKERRQ(ierr); } if (dir->row) { ierr = PetscLogObjectParent(pc,dir->row);CHKERRQ(ierr); ierr = PetscLogObjectParent(pc,dir->col);CHKERRQ(ierr); } } ierr = MatDestroy(((PC_Factor*)dir)->fact);CHKERRQ(ierr); ierr = MatGetFactor(pc->pmat,((PC_Factor*)dir)->solvertype,MAT_FACTOR_LU,&((PC_Factor*)dir)->fact);CHKERRQ(ierr); ierr = MatLUFactorSymbolic(((PC_Factor*)dir)->fact,pc->pmat,dir->row,dir->col,&((PC_Factor*)dir)->info);CHKERRQ(ierr); ierr = MatGetInfo(((PC_Factor*)dir)->fact,MAT_LOCAL,&info);CHKERRQ(ierr); dir->actualfill = info.fill_ratio_needed; ierr = PetscLogObjectParent(pc,((PC_Factor*)dir)->fact);CHKERRQ(ierr); } ierr = MatLUFactorNumeric(((PC_Factor*)dir)->fact,pc->pmat,&((PC_Factor*)dir)->info);CHKERRQ(ierr); } PetscFunctionReturn(0); }
void MultigridSolver_RestrictMatrix( MultigridSolver* self, MultigridSolver_Level* level, Mat* dstMatrix ) { Mat srcMat; PetscInt nSrcRows, nSrcCols; PetscInt nRRows, nRCols; #if( PETSC_VERSION_MAJOR > 2 ) PetscInt dummy; #endif PetscScalar fillRatio; MatInfo mInfo; PetscScalar nRowsA, nRowsC; PetscScalar nzA, nzP, nzC; assert( self ); assert( level ); assert( dstMatrix ); srcMat = level->downSolver->matrix; MatGetSize( srcMat, &nSrcRows, &nSrcCols ); MatGetSize( level->R, &nRRows, &nRCols ); if( nRCols == nSrcRows ) { //Matrix_PAPt( srcMat, level->R, (void**)dstMatrix ); /* this function implementation was commented out in the PETScMatrix function - not sure if it should * be implemented here?? */ MatGetInfo( srcMat, MAT_GLOBAL_SUM, &mInfo ); #if( PETSC_VERSION_MAJOR <= 2 ) nRowsA = mInfo.rows_global; #else MatGetSize( srcMat, &nRowsA, &dummy ); #endif nzA = mInfo.nz_used; MatGetInfo( level->R, MAT_GLOBAL_SUM, &mInfo ); #if( PETSC_VERSION_MAJOR <= 2 ) nRowsC = mInfo.columns_global; #else MatGetSize( level->R, &dummy, &nRowsC ); #endif nzP = mInfo.nz_used; nzC = ( nRowsC / nRowsA ) * nzA; fillRatio = nzC / ( nzA + nzP ); /* this function doesn't exist! */ //MatPAPt( srcMat, level->R, MAT_REUSE_MATRIX, fillRatio, dstMatrix ); } else { //Matrix_PtAP( srcMat, level->R, (void**)dstMatrix ); if( dstMatrix ) MatPtAP( srcMat, level->R, MAT_REUSE_MATRIX, 1.0, dstMatrix ); else MatPtAP( srcMat, level->R, MAT_INITIAL_MATRIX, 1.0, dstMatrix ); } }
PetscErrorCode printMatInfo(const char *label, Mat m){ PetscErrorCode err; MatInfo info; err = MatGetInfo(m, MAT_GLOBAL_SUM, &info); CHKERRQ(err); err = PetscPrintf(PETSC_COMM_WORLD, "%s nnz: %f\n", label, info.nz_used); CHKERRQ(err); return err; }
PetscErrorCode PCView_Factor(PC pc,PetscViewer viewer) { PC_Factor *factor = (PC_Factor*)pc->data; PetscErrorCode ierr; PetscBool isstring,iascii; PetscFunctionBegin; ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSTRING,&isstring);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); if (iascii) { if (factor->factortype == MAT_FACTOR_ILU || factor->factortype == MAT_FACTOR_ICC) { if (factor->info.dt > 0) { ierr = PetscViewerASCIIPrintf(viewer," drop tolerance %G\n",factor->info.dt);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer," max nonzeros per row %D\n",factor->info.dtcount);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer," column permutation tolerance %G\n",(PetscInt)factor->info.dtcol);CHKERRQ(ierr); } else if (factor->info.levels == 1) { ierr = PetscViewerASCIIPrintf(viewer," %D level of fill\n",(PetscInt)factor->info.levels);CHKERRQ(ierr); } else { ierr = PetscViewerASCIIPrintf(viewer," %D levels of fill\n",(PetscInt)factor->info.levels);CHKERRQ(ierr); } } ierr = PetscViewerASCIIPrintf(viewer," tolerance for zero pivot %G\n",factor->info.zeropivot);CHKERRQ(ierr); if (factor->info.shifttype==(PetscReal)MAT_SHIFT_POSITIVE_DEFINITE) { ierr = PetscViewerASCIIPrintf(viewer," using Manteuffel shift\n");CHKERRQ(ierr); } if (factor->info.shifttype==(PetscReal)MAT_SHIFT_NONZERO) { ierr = PetscViewerASCIIPrintf(viewer," using diagonal shift to prevent zero pivot\n");CHKERRQ(ierr); } if (factor->info.shifttype==(PetscReal)MAT_SHIFT_INBLOCKS) { ierr = PetscViewerASCIIPrintf(viewer," using diagonal shift on blocks to prevent zero pivot\n");CHKERRQ(ierr); } ierr = PetscViewerASCIIPrintf(viewer," matrix ordering: %s\n",factor->ordering);CHKERRQ(ierr); if (factor->fact) { MatInfo info; ierr = MatGetInfo(factor->fact,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer," factor fill ratio given %G, needed %G\n",info.fill_ratio_given,info.fill_ratio_needed);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer," Factored matrix follows:\n");CHKERRQ(ierr); ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr); ierr = MatView(factor->fact,viewer);CHKERRQ(ierr); ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); } } else if (isstring) { MatFactorType t; ierr = MatGetFactorType(factor->fact,&t);CHKERRQ(ierr); if (t == MAT_FACTOR_ILU || t == MAT_FACTOR_ICC) { ierr = PetscViewerStringSPrintf(viewer," lvls=%D,order=%s",(PetscInt)factor->info.levels,factor->ordering);CHKERRQ(ierr);CHKERRQ(ierr); } } PetscFunctionReturn(0); }
static PetscErrorCode PCSetup_ICC(PC pc) { PC_ICC *icc = (PC_ICC*)pc->data; IS perm,cperm; PetscErrorCode ierr; MatInfo info; PetscFunctionBegin; ierr = MatGetOrdering(pc->pmat, ((PC_Factor*)icc)->ordering,&perm,&cperm);CHKERRQ(ierr); if (!pc->setupcalled) { if (!((PC_Factor*)icc)->fact) { ierr = MatGetFactor(pc->pmat,((PC_Factor*)icc)->solvertype,MAT_FACTOR_ICC,&((PC_Factor*)icc)->fact);CHKERRQ(ierr); } ierr = MatICCFactorSymbolic(((PC_Factor*)icc)->fact,pc->pmat,perm,&((PC_Factor*)icc)->info);CHKERRQ(ierr); } else if (pc->flag != SAME_NONZERO_PATTERN) { ierr = MatDestroy(&((PC_Factor*)icc)->fact);CHKERRQ(ierr); ierr = MatGetFactor(pc->pmat,((PC_Factor*)icc)->solvertype,MAT_FACTOR_ICC,&((PC_Factor*)icc)->fact);CHKERRQ(ierr); ierr = MatICCFactorSymbolic(((PC_Factor*)icc)->fact,pc->pmat,perm,&((PC_Factor*)icc)->info);CHKERRQ(ierr); } ierr = MatGetInfo(((PC_Factor*)icc)->fact,MAT_LOCAL,&info);CHKERRQ(ierr); icc->actualfill = info.fill_ratio_needed; ierr = ISDestroy(&cperm);CHKERRQ(ierr); ierr = ISDestroy(&perm);CHKERRQ(ierr); ierr = MatCholeskyFactorNumeric(((PC_Factor*)icc)->fact,pc->pmat,&((PC_Factor*)icc)->info);CHKERRQ(ierr); PetscFunctionReturn(0); }
/*@ MatSchurComplementComputeExplicitOperator - Compute the Schur complement matrix explicitly Collective on Mat Input Parameter: . M - the matrix obtained with MatCreateSchurComplement() Output Parameter: . S - the Schur complement matrix Note: This can be expensive, so it is mainly for testing Level: advanced .seealso: MatCreateSchurComplement(), MatSchurComplementUpdate() @*/ PetscErrorCode MatSchurComplementComputeExplicitOperator(Mat M, Mat *S) { Mat B, C, D; KSP ksp; PC pc; PetscBool isLU, isILU; PetscReal fill = 2.0; PetscErrorCode ierr; PetscFunctionBegin; ierr = MatSchurComplementGetSubMatrices(M, NULL, NULL, &B, &C, &D);CHKERRQ(ierr); ierr = MatSchurComplementGetKSP(M, &ksp);CHKERRQ(ierr); ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject) pc, PCLU, &isLU);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject) pc, PCILU, &isILU);CHKERRQ(ierr); if (isLU || isILU) { Mat fact, Bd, AinvB, AinvBd; PetscReal eps = 1.0e-10; /* This can be sped up for banded LU */ ierr = KSPSetUp(ksp);CHKERRQ(ierr); ierr = PCFactorGetMatrix(pc, &fact);CHKERRQ(ierr); ierr = MatConvert(B, MATDENSE, MAT_INITIAL_MATRIX, &Bd);CHKERRQ(ierr); ierr = MatDuplicate(Bd, MAT_DO_NOT_COPY_VALUES, &AinvBd);CHKERRQ(ierr); ierr = MatMatSolve(fact, Bd, AinvBd);CHKERRQ(ierr); ierr = MatDestroy(&Bd);CHKERRQ(ierr); ierr = MatChop(AinvBd, eps);CHKERRQ(ierr); ierr = MatConvert(AinvBd, MATAIJ, MAT_INITIAL_MATRIX, &AinvB);CHKERRQ(ierr); ierr = MatDestroy(&AinvBd);CHKERRQ(ierr); ierr = MatMatMult(C, AinvB, MAT_INITIAL_MATRIX, fill, S);CHKERRQ(ierr); ierr = MatDestroy(&AinvB);CHKERRQ(ierr); } else { Mat Ainvd, Ainv; ierr = PCComputeExplicitOperator(pc, &Ainvd);CHKERRQ(ierr); ierr = MatConvert(Ainvd, MATAIJ, MAT_INITIAL_MATRIX, &Ainv);CHKERRQ(ierr); ierr = MatDestroy(&Ainvd);CHKERRQ(ierr); #if 0 /* Symmetric version */ ierr = MatPtAP(Ainv, B, MAT_INITIAL_MATRIX, fill, S);CHKERRQ(ierr); #else /* Nonsymmetric version */ ierr = MatMatMatMult(C, Ainv, B, MAT_INITIAL_MATRIX, fill, S);CHKERRQ(ierr); #endif ierr = MatDestroy(&Ainv);CHKERRQ(ierr); } ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr); ierr = MatView(*S, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); if (D) { MatInfo info; ierr = MatGetInfo(D, MAT_GLOBAL_SUM, &info);CHKERRQ(ierr); if (info.nz_used) SETERRQ(PetscObjectComm((PetscObject) M), PETSC_ERR_SUP, "Not yet implemented"); } PetscFunctionReturn(0); }
void BSSCR_get_number_nonzeros_AIJ( Mat A, PetscInt *nnz ) { MatInfo info; MatGetInfo( A, MAT_GLOBAL_SUM, &info ); *nnz = info.nz_used; }
double SparseGp_percentNonzero (SparseGp *gp) { MatInfo info; MatGetInfo (gp->_K, MAT_GLOBAL_SUM, &info); PetscLogDouble nzUsed = info.nz_used; PetscInt N = gp->trainLabels->size; return (nzUsed / (N*N)) * 100; }
PetscErrorCode PCView_Factor(PC pc,PetscViewer viewer) { PC_Factor *factor = (PC_Factor*)pc->data; PetscErrorCode ierr; PetscBool isstring,iascii; PetscFunctionBegin; ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSTRING,&isstring);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); if (iascii) { if (factor->factortype == MAT_FACTOR_ILU || factor->factortype == MAT_FACTOR_ICC) { if (factor->info.dt > 0) { ierr = PetscViewerASCIIPrintf(viewer," drop tolerance %G\n",factor->info.dt);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer," max nonzeros per row %D\n",factor->info.dtcount);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer," column permutation tolerance %G\n",(PetscInt)factor->info.dtcol);CHKERRQ(ierr); } else if (factor->info.levels == 1) { ierr = PetscViewerASCIIPrintf(viewer," %D level of fill\n",(PetscInt)factor->info.levels);CHKERRQ(ierr); } else { ierr = PetscViewerASCIIPrintf(viewer," %D levels of fill\n",(PetscInt)factor->info.levels);CHKERRQ(ierr); } } ierr = PetscViewerASCIIPrintf(viewer," tolerance for zero pivot %G\n",factor->info.zeropivot);CHKERRQ(ierr); if (MatFactorShiftTypesDetail[(int)factor->info.shifttype]) { /* Only print when using a nontrivial shift */ ierr = PetscViewerASCIIPrintf(viewer," using %s [%s]\n",MatFactorShiftTypesDetail[(int)factor->info.shifttype],MatFactorShiftTypes[(int)factor->info.shifttype]);CHKERRQ(ierr); } ierr = PetscViewerASCIIPrintf(viewer," matrix ordering: %s\n",factor->ordering);CHKERRQ(ierr); if (factor->fact) { MatInfo info; ierr = MatGetInfo(factor->fact,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer," factor fill ratio given %G, needed %G\n",info.fill_ratio_given,info.fill_ratio_needed);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(viewer," Factored matrix follows:\n");CHKERRQ(ierr); ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr); ierr = MatView(factor->fact,viewer);CHKERRQ(ierr); ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); } } else if (isstring) { MatFactorType t; ierr = MatGetFactorType(factor->fact,&t);CHKERRQ(ierr); if (t == MAT_FACTOR_ILU || t == MAT_FACTOR_ICC) { ierr = PetscViewerStringSPrintf(viewer," lvls=%D,order=%s",(PetscInt)factor->info.levels,factor->ordering);CHKERRQ(ierr);CHKERRQ(ierr); } } PetscFunctionReturn(0); }
/* Displays basic information for a matrix (PETSc) */ void Display_matrix_info(Mat A, const char *name) { MatInfo info; MatGetInfo(A, MAT_GLOBAL_SUM, &info); int mal = (int) info.mallocs; int memory = (int) info.memory; int nz_allocated = (int) info.nz_allocated; int nz_used = (int) info.nz_allocated; int nz_unneeded = (int) info.nz_unneeded; PetscPrintf(PCW, "Display.c/ printing information for the %s matrix. \n", name); PetscPrintf(PCW, "Display.c/ allocated non-zeros:%d used non-zeros:%d unneeded non-zeros:%d\n", nz_allocated, nz_used, nz_unneeded); PetscPrintf(PCW, "Display.c/ memory (bytes):%d number of extra mallocs:%d \n", memory, mal); }
/* name[] is operator name */ PetscErrorCode BSSCR_MatInfoLog(PetscViewer v,Mat A,const char name[]) { MatInfo i; PetscReal nrm_1,nrm_f,nrm_inf; MatType mtype; PetscInt M,N; PetscViewerType vtype; PetscTruth isascii; PetscViewerGetType( v, &vtype ); Stg_PetscObjectTypeCompare( (PetscObject)v,PETSC_VIEWER_ASCII,&isascii ); if (!isascii) { PetscFunctionReturn(0); } MatGetSize( A, &M,&N ); MatGetInfo(A,MAT_GLOBAL_SUM,&i); MatGetType( A, &mtype ); MatNorm( A, NORM_1, &nrm_1 ); MatNorm( A, NORM_FROBENIUS, &nrm_f ); MatNorm( A, NORM_INFINITY, &nrm_inf ); PetscViewerASCIIPrintf( v, "MatInfo: %s \n", name ); PetscViewerASCIIPushTab(v); PetscViewerASCIIPrintf( v, "type=%s \n", mtype ); PetscViewerASCIIPrintf( v, "dimension=%Dx%D \n", M,N ); PetscViewerASCIIPrintf( v, "nnz=%D (total)\n", (PetscInt)i.nz_used ); PetscViewerASCIIPrintf( v, "nnz=%D (allocated)\n", (PetscInt)i.nz_allocated ); PetscViewerASCIIPrintf( v, "|A|_1 = %1.12e\n", nrm_1 ); PetscViewerASCIIPrintf( v, "|A|_frobenius = %1.12e\n", nrm_f ); PetscViewerASCIIPrintf( v, "|A|_inf = %1.12e\n", nrm_inf ); PetscViewerASCIIPopTab(v); PetscFunctionReturn(0); }
/* PEPBuildDiagonalScaling - compute two diagonal matrices to be applied for balancing in polynomial eigenproblems. */ PetscErrorCode PEPBuildDiagonalScaling(PEP pep) { PetscErrorCode ierr; PetscInt it,i,j,k,nmat,nr,e,nz,lst,lend,nc=0,*cols,emax,emin,emaxl,eminl; const PetscInt *cidx,*ridx; Mat M,*T,A; PetscMPIInt n; PetscBool cont=PETSC_TRUE,flg=PETSC_FALSE; PetscScalar *array,*Dr,*Dl,t; PetscReal l2,d,*rsum,*aux,*csum,w=1.0; MatStructure str; MatInfo info; PetscFunctionBegin; l2 = 2*PetscLogReal(2.0); nmat = pep->nmat; ierr = PetscMPIIntCast(pep->n,&n); ierr = STGetMatStructure(pep->st,&str);CHKERRQ(ierr); ierr = PetscMalloc1(nmat,&T);CHKERRQ(ierr); for (k=0;k<nmat;k++) { ierr = STGetTOperators(pep->st,k,&T[k]);CHKERRQ(ierr); } /* Form local auxiliar matrix M */ ierr = PetscObjectTypeCompareAny((PetscObject)T[0],&cont,MATMPIAIJ,MATSEQAIJ);CHKERRQ(ierr); if (!cont) SETERRQ(PetscObjectComm((PetscObject)T[0]),PETSC_ERR_SUP,"Only for MPIAIJ or SEQAIJ matrix types"); ierr = PetscObjectTypeCompare((PetscObject)T[0],MATMPIAIJ,&cont);CHKERRQ(ierr); if (cont) { ierr = MatMPIAIJGetLocalMat(T[0],MAT_INITIAL_MATRIX,&M);CHKERRQ(ierr); flg = PETSC_TRUE; } else { ierr = MatDuplicate(T[0],MAT_COPY_VALUES,&M);CHKERRQ(ierr); } ierr = MatGetInfo(M,MAT_LOCAL,&info);CHKERRQ(ierr); nz = info.nz_used; ierr = MatSeqAIJGetArray(M,&array);CHKERRQ(ierr); for (i=0;i<nz;i++) { t = PetscAbsScalar(array[i]); array[i] = t*t; } ierr = MatSeqAIJRestoreArray(M,&array);CHKERRQ(ierr); for (k=1;k<nmat;k++) { if (flg) { ierr = MatMPIAIJGetLocalMat(T[k],MAT_INITIAL_MATRIX,&A);CHKERRQ(ierr); } else { if (str==SAME_NONZERO_PATTERN) { ierr = MatCopy(T[k],A,SAME_NONZERO_PATTERN);CHKERRQ(ierr); } else { ierr = MatDuplicate(T[k],MAT_COPY_VALUES,&A);CHKERRQ(ierr); } } ierr = MatGetInfo(A,MAT_LOCAL,&info);CHKERRQ(ierr); nz = info.nz_used; ierr = MatSeqAIJGetArray(A,&array);CHKERRQ(ierr); for (i=0;i<nz;i++) { t = PetscAbsScalar(array[i]); array[i] = t*t; } ierr = MatSeqAIJRestoreArray(A,&array);CHKERRQ(ierr); w *= pep->slambda*pep->slambda*pep->sfactor; ierr = MatAXPY(M,w,A,str);CHKERRQ(ierr); if (flg || str!=SAME_NONZERO_PATTERN || k==nmat-2) { ierr = MatDestroy(&A);CHKERRQ(ierr); } } ierr = MatGetRowIJ(M,0,PETSC_FALSE,PETSC_FALSE,&nr,&ridx,&cidx,&cont);CHKERRQ(ierr); if (!cont) SETERRQ(PetscObjectComm((PetscObject)T[0]), PETSC_ERR_SUP,"It is not possible to compute scaling diagonals for these PEP matrices"); ierr = MatGetInfo(M,MAT_LOCAL,&info);CHKERRQ(ierr); nz = info.nz_used; ierr = VecGetOwnershipRange(pep->Dl,&lst,&lend);CHKERRQ(ierr); ierr = PetscMalloc4(nr,&rsum,pep->n,&csum,pep->n,&aux,PetscMin(pep->n-lend+lst,nz),&cols);CHKERRQ(ierr); ierr = VecSet(pep->Dr,1.0);CHKERRQ(ierr); ierr = VecSet(pep->Dl,1.0);CHKERRQ(ierr); ierr = VecGetArray(pep->Dl,&Dl);CHKERRQ(ierr); ierr = VecGetArray(pep->Dr,&Dr);CHKERRQ(ierr); ierr = MatSeqAIJGetArray(M,&array);CHKERRQ(ierr); ierr = PetscMemzero(aux,pep->n*sizeof(PetscReal));CHKERRQ(ierr); for (j=0;j<nz;j++) { /* Search non-zero columns outsize lst-lend */ if (aux[cidx[j]]==0 && (cidx[j]<lst || lend<=cidx[j])) cols[nc++] = cidx[j]; /* Local column sums */ aux[cidx[j]] += PetscAbsScalar(array[j]); } for (it=0;it<pep->sits && cont;it++) { emaxl = 0; eminl = 0; /* Column sum */ if (it>0) { /* it=0 has been already done*/ ierr = MatSeqAIJGetArray(M,&array);CHKERRQ(ierr); ierr = PetscMemzero(aux,pep->n*sizeof(PetscReal));CHKERRQ(ierr); for (j=0;j<nz;j++) aux[cidx[j]] += PetscAbsScalar(array[j]); ierr = MatSeqAIJRestoreArray(M,&array);CHKERRQ(ierr); } ierr = MPI_Allreduce(aux,csum,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)pep->Dr)); /* Update Dr */ for (j=lst;j<lend;j++) { d = PetscLogReal(csum[j])/l2; e = -(PetscInt)((d < 0)?(d-0.5):(d+0.5)); d = PetscPowReal(2.0,e); Dr[j-lst] *= d; aux[j] = d*d; emaxl = PetscMax(emaxl,e); eminl = PetscMin(eminl,e); } for (j=0;j<nc;j++) { d = PetscLogReal(csum[cols[j]])/l2; e = -(PetscInt)((d < 0)?(d-0.5):(d+0.5)); d = PetscPowReal(2.0,e); aux[cols[j]] = d*d; emaxl = PetscMax(emaxl,e); eminl = PetscMin(eminl,e); } /* Scale M */ ierr = MatSeqAIJGetArray(M,&array);CHKERRQ(ierr); for (j=0;j<nz;j++) { array[j] *= aux[cidx[j]]; } ierr = MatSeqAIJRestoreArray(M,&array);CHKERRQ(ierr); /* Row sum */ ierr = PetscMemzero(rsum,nr*sizeof(PetscReal));CHKERRQ(ierr); ierr = MatSeqAIJGetArray(M,&array);CHKERRQ(ierr); for (i=0;i<nr;i++) { for (j=ridx[i];j<ridx[i+1];j++) rsum[i] += PetscAbsScalar(array[j]); /* Update Dl */ d = PetscLogReal(rsum[i])/l2; e = -(PetscInt)((d < 0)?(d-0.5):(d+0.5)); d = PetscPowReal(2.0,e); Dl[i] *= d; /* Scale M */ for (j=ridx[i];j<ridx[i+1];j++) array[j] *= d*d; emaxl = PetscMax(emaxl,e); eminl = PetscMin(eminl,e); } ierr = MatSeqAIJRestoreArray(M,&array);CHKERRQ(ierr); /* Compute global max and min */ ierr = MPI_Allreduce(&emaxl,&emax,1,MPIU_INT,MPIU_MAX,PetscObjectComm((PetscObject)pep->Dl)); ierr = MPI_Allreduce(&eminl,&emin,1,MPIU_INT,MPIU_MIN,PetscObjectComm((PetscObject)pep->Dl)); if (emax<=emin+2) cont = PETSC_FALSE; } ierr = VecRestoreArray(pep->Dr,&Dr);CHKERRQ(ierr); ierr = VecRestoreArray(pep->Dl,&Dl);CHKERRQ(ierr); /* Free memory*/ ierr = MatDestroy(&M);CHKERRQ(ierr); ierr = PetscFree4(rsum,csum,aux,cols);CHKERRQ(ierr); ierr = PetscFree(T);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc, char *argv[]) { GRID *g; DOF *u_h; MAT *A, *A0, *B; MAP *map; INT i; size_t nnz, mem, mem_peak; VEC *x, *y0, *y1, *y2; double t0, t1, dnz, dnz1, mflops, mop; char *fn = "../test/cube.dat"; FLOAT mem_max = 300; INT refine = 0; phgOptionsRegisterFilename("-mesh_file", "Mesh file", (char **)&fn); phgOptionsRegisterInt("-loop_count", "Loop count", &loop_count); phgOptionsRegisterInt("-refine", "Refinement level", &refine); phgOptionsRegisterFloat("-mem_max", "Maximum memory", &mem_max); phgInit(&argc, &argv); g = phgNewGrid(-1); if (!phgImport(g, fn, FALSE)) phgError(1, "can't read file \"%s\".\n", fn); phgRefineAllElements(g, refine); u_h = phgDofNew(g, DOF_DEFAULT, 1, "u_h", DofNoAction); while (TRUE) { phgPrintf("\n"); if (phgBalanceGrid(g, 1.2, 1, NULL, 0.)) phgPrintf("Repartition mesh, %d submeshes, load imbalance: %lg\n", g->nprocs, (double)g->lif); map = phgMapCreate(u_h, NULL); A = phgMapCreateMat(map, map); A->handle_bdry_eqns = TRUE; build_matrix(A, u_h); phgMatAssemble(A); /* Note: A is unsymmetric (A' != A) if boundary entries not removed */ phgMatRemoveBoundaryEntries(A); #if 0 /* test block matrix operation */ A0 = phgMatCreateBlockMatrix(g->comm, 1, 1, &A, NULL); #else A0 = A; #endif phgPrintf("%d DOF, %d elems, %d submeshes, matrix size: %d, LIF: %lg\n", DofGetDataCountGlobal(u_h), g->nleaf_global, g->nprocs, A->rmap->nglobal, (double)g->lif); /* test PHG mat-vec multiply */ x = phgMapCreateVec(A->cmap, 1); y1 = phgMapCreateVec(A->rmap, 1); phgVecRandomize(x, 123); phgMatVec(MAT_OP_N, 1.0, A0, x, 0.0, &y1); phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */ t0 = phgGetTime(NULL); for (i = 0; i < loop_count; i++) { phgMatVec(MAT_OP_N, 1.0, A0, x, 0.0, &y1); } t1 = phgGetTime(NULL); mflops = phgPerfGetMflops(g, NULL, NULL); y0 = phgVecCopy(y1, NULL); nnz = A->nnz_d + A->nnz_o; #if USE_MPI dnz1 = nnz; MPI_Reduce(&dnz1, &dnz, 1, MPI_DOUBLE, MPI_SUM, 0, g->comm); #else dnz = nnz; #endif mop = loop_count * (dnz + dnz - A->rmap->nlocal) * 1e-6; phgPrintf("\n"); t1 -= t0; phgPrintf(" PHG: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF)\n", t1, dnz, mop / (t1 == 0 ? 1. : t1), mflops); /* test trans(A)*x */ phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */ t0 = phgGetTime(NULL); for (i = 0; i < loop_count; i++) { phgMatVec(MAT_OP_T, 1.0, A0, x, 0.0, &y1); } t1 = phgGetTime(NULL); mflops = phgPerfGetMflops(g, NULL, NULL); t1 -= t0; phgPrintf(" A'*x: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF), " "err: %le\n", t1, dnz, mop / (t1 == 0 ? 1. : t1), mflops, (double)phgVecNorm2(phgVecAXPBY(-1.0, y0, 1.0, &y1), 0, NULL)); /* time A * trans(A) */ phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */ t0 = phgGetTime(NULL); B = phgMatMat(MAT_OP_N, MAT_OP_N, 1.0, A, A, 0.0, NULL); t1 = phgGetTime(NULL); mflops = phgPerfGetMflops(g, NULL, NULL); nnz = B->nnz_d + B->nnz_o; #if USE_MPI dnz1 = nnz; MPI_Reduce(&dnz1, &dnz, 1, MPI_DOUBLE, MPI_SUM, 0, g->comm); #else dnz = nnz; #endif /* compare B*x <--> A*A*x */ y2 = phgMatVec(MAT_OP_N, 1.0, B, x, 0.0, NULL); phgMatVec(MAT_OP_N, 1.0, A0, y0, 0.0, &y1); phgMatDestroy(&B); t1 -= t0; phgPrintf(" A*A: time %0.4lf, nnz %0.16lg, %0.2lfMF, err: %le\n", t1, dnz, mflops, (double)phgVecNorm2(phgVecAXPBY(-1.0, y1, 1.0, &y2), 0, NULL)); #if USE_PETSC { Mat ma, mb; MatInfo info; Vec va, vb, vc; PetscScalar *vec; ma = phgPetscCreateMatAIJ(A); MatGetVecs(ma, PETSC_NULL, &va); VecDuplicate(va, &vb); VecGetArray(va, &vec); memcpy(vec, x->data, x->map->nlocal * sizeof(*vec)); VecRestoreArray(va, &vec); MatMult(ma, va, vb); phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */ t0 = phgGetTime(NULL); for (i = 0; i < loop_count; i++) { MatMult(ma, va, vb); } t1 = phgGetTime(NULL); mflops = phgPerfGetMflops(g, NULL, NULL); VecGetArray(vb, &vec); memcpy(y1->data, vec, x->map->nlocal * sizeof(*vec)); VecRestoreArray(vb, &vec); MatGetInfo(ma, MAT_GLOBAL_SUM, &info); /*phgPrintf(" --------------------------------------------" "-------------------------\n");*/ phgPrintf("\n"); t1 -= t0; dnz = info.nz_used; phgPrintf(" PETSc: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF), " "err: %le\n", t1, dnz, mop / (t1==0 ? 1.:t1), mflops, (double)phgVecNorm2(phgVecAXPBY(-1.0, y0, 1.0, &y1), 0, NULL)); phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */ t0 = phgGetTime(NULL); for (i = 0; i < loop_count; i++) { MatMultTranspose(ma, va, vb); } t1 = phgGetTime(NULL); mflops = phgPerfGetMflops(g, NULL, NULL); VecGetArray(vb, &vec); memcpy(y1->data, vec, x->map->nlocal * sizeof(*vec)); VecRestoreArray(vb, &vec); t1 -= t0; phgPrintf(" A'*x: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF), " "err: %le\n", t1, dnz, mop / (t1==0 ? 1.:t1), mflops, (double)phgVecNorm2(phgVecAXPBY(-1.0, y0, 1.0, &y1), 0, NULL)); phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */ t0 = phgGetTime(NULL); MatMatMult(ma, ma, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &mb); t1 = phgGetTime(NULL); mflops = phgPerfGetMflops(g, NULL, NULL); t1 -= t0; MatGetInfo(mb, MAT_GLOBAL_SUM, &info); dnz = info.nz_used; VecDuplicate(va, &vc); /* compare B*x <--> A*A*x */ MatMult(ma, vb, vc); MatMult(mb, va, vb); VecGetArray(vb, &vec); memcpy(y1->data, vec, x->map->nlocal * sizeof(*vec)); VecRestoreArray(vb, &vec); VecGetArray(vc, &vec); memcpy(y2->data, vec, x->map->nlocal * sizeof(*vec)); VecRestoreArray(vc, &vec); phgPrintf(" A*A: time %0.4lf, nnz %0.16lg, %0.2lfMF, err: %le\n", t1, dnz, mflops, (double)phgVecNorm2(phgVecAXPBY(-1.0, y1, 1.0, &y2), 0, NULL)); phgPetscMatDestroy(&mb); phgPetscMatDestroy(&ma); phgPetscVecDestroy(&va); phgPetscVecDestroy(&vb); phgPetscVecDestroy(&vc); } #endif /* USE_PETSC */ #if USE_HYPRE { HYPRE_IJMatrix ma; HYPRE_IJVector va, vb, vc; HYPRE_ParCSRMatrix par_ma; hypre_ParCSRMatrix *par_mb; HYPRE_ParVector par_va, par_vb, par_vc; HYPRE_Int offset, *ni, start, end; assert(sizeof(INT)==sizeof(int) && sizeof(FLOAT)==sizeof(double)); setup_hypre_mat(A, &ma); ni = phgAlloc(2 * A->rmap->nlocal * sizeof(*ni)); offset = A->cmap->partition[A->cmap->rank]; for (i = 0; i < A->rmap->nlocal; i++) ni[i] = i + offset; HYPRE_IJVectorCreate(g->comm, offset, offset + A->rmap->nlocal - 1, &va); HYPRE_IJVectorCreate(g->comm, offset, offset + A->rmap->nlocal - 1, &vb); HYPRE_IJVectorCreate(g->comm, offset, offset + A->rmap->nlocal - 1, &vc); HYPRE_IJVectorSetObjectType(va, HYPRE_PARCSR); HYPRE_IJVectorSetObjectType(vb, HYPRE_PARCSR); HYPRE_IJVectorSetObjectType(vc, HYPRE_PARCSR); HYPRE_IJVectorSetMaxOffProcElmts(va, 0); HYPRE_IJVectorSetMaxOffProcElmts(vb, 0); HYPRE_IJVectorSetMaxOffProcElmts(vc, 0); HYPRE_IJVectorInitialize(va); HYPRE_IJVectorInitialize(vb); HYPRE_IJVectorInitialize(vc); HYPRE_IJMatrixGetObject(ma, (void **)(void *)&par_ma); HYPRE_IJVectorGetObject(va, (void **)(void *)&par_va); HYPRE_IJVectorGetObject(vb, (void **)(void *)&par_vb); HYPRE_IJVectorGetObject(vc, (void **)(void *)&par_vc); HYPRE_IJVectorSetValues(va, A->cmap->nlocal, ni, (double *)x->data); HYPRE_IJVectorAssemble(va); HYPRE_IJVectorAssemble(vb); HYPRE_IJVectorAssemble(vc); HYPRE_IJMatrixGetRowCounts(ma, A->cmap->nlocal, ni, ni + A->rmap->nlocal); for (i = 0, nnz = 0; i < A->rmap->nlocal; i++) nnz += ni[A->rmap->nlocal + i]; #if USE_MPI dnz1 = nnz; MPI_Reduce(&dnz1, &dnz, 1, MPI_DOUBLE, MPI_SUM, 0, g->comm); #else dnz = nnz; #endif HYPRE_ParCSRMatrixMatvec(1.0, par_ma, par_va, 0.0, par_vb); phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */ t0 = phgGetTime(NULL); for (i = 0; i < loop_count; i++) { HYPRE_ParCSRMatrixMatvec(1.0, par_ma, par_va, 0.0, par_vb); } t1 = phgGetTime(NULL); mflops = phgPerfGetMflops(g, NULL, NULL); HYPRE_IJVectorGetValues(vb, A->rmap->nlocal, ni, (double*)y1->data); /*phgPrintf(" --------------------------------------------" "-------------------------\n");*/ phgPrintf("\n"); t1 -= t0; phgPrintf(" HYPRE: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF), " "err: %le\n", t1, dnz, mop / (t1==0 ? 1.:t1), mflops, (double)phgVecNorm2(phgVecAXPBY(-1.0, y0, 1.0, &y1), 0, NULL)); phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */ t0 = phgGetTime(NULL); for (i = 0; i < loop_count; i++) { HYPRE_ParCSRMatrixMatvecT(1.0, par_ma, par_va, 0.0, par_vb); } t1 = phgGetTime(NULL); mflops = phgPerfGetMflops(g, NULL, NULL); HYPRE_IJVectorGetValues(vb, A->rmap->nlocal, ni, (double*)y1->data); t1 -= t0; phgPrintf(" A'*x: time %0.4lf, nnz %0.16lg, %0.2lfMF (%0.2lfMF), " "err: %le\n", t1, dnz, mop / (t1==0 ? 1.:t1), mflops, (double)phgVecNorm2(phgVecAXPBY(-1.0, y0, 1.0, &y1), 0, NULL)); phgPerfGetMflops(g, NULL, NULL); /* reset flops counter */ t0 = phgGetTime(NULL); /* Note: 'HYPRE_ParCSRMatrix' is currently typedef'ed to * 'hypre_ParCSRMatrix *' */ par_mb = hypre_ParMatmul((hypre_ParCSRMatrix *)par_ma, (hypre_ParCSRMatrix *)par_ma); t1 = phgGetTime(NULL); mflops = phgPerfGetMflops(g, NULL, NULL); start = hypre_ParCSRMatrixFirstRowIndex(par_mb); end = hypre_ParCSRMatrixLastRowIndex(par_mb) + 1; for (i = start, nnz = 0; i < end; i++) { HYPRE_Int ncols; hypre_ParCSRMatrixGetRow(par_mb, i, &ncols, NULL, NULL); hypre_ParCSRMatrixRestoreRow(par_mb, i, &ncols, NULL, NULL); nnz += ncols; } #if USE_MPI dnz1 = nnz; MPI_Reduce(&dnz1, &dnz, 1, MPI_DOUBLE, MPI_SUM, 0, g->comm); #else dnz = nnz; #endif /* compare B*x <--> A*A*x */ HYPRE_ParCSRMatrixMatvec(1.0, par_ma, par_vb, 0.0, par_vc); HYPRE_ParCSRMatrixMatvec(1.0, (void *)par_mb, par_va, 0.0, par_vb); HYPRE_IJVectorGetValues(vb, A->rmap->nlocal, ni, (double*)y1->data); HYPRE_IJVectorGetValues(vc, A->rmap->nlocal, ni, (double*)y2->data); hypre_ParCSRMatrixDestroy((par_mb)); t1 -= t0; phgPrintf(" A*A: time %0.4lf, nnz %0.16lg, %0.2lfMF, err: %le\n", t1, dnz, mflops, (double)phgVecNorm2(phgVecAXPBY(-1.0, y1, 1.0, &y2), 0, NULL)); phgFree(ni); HYPRE_IJMatrixDestroy(ma); HYPRE_IJVectorDestroy(va); HYPRE_IJVectorDestroy(vb); HYPRE_IJVectorDestroy(vc); } #endif /* USE_HYPRE */ if (A0 != A) phgMatDestroy(&A0); #if 0 if (A->rmap->nglobal > 1000) { VEC *v = phgMapCreateVec(A->rmap, 3); for (i = 0; i < v->map->nlocal; i++) { v->data[i + 0 * v->map->nlocal] = 1 * (i + v->map->partition[g->rank]); v->data[i + 1 * v->map->nlocal] = 2 * (i + v->map->partition[g->rank]); v->data[i + 2 * v->map->nlocal] = 3 * (i + v->map->partition[g->rank]); } phgMatDumpMATLAB(A, "A", "A.m"); phgVecDumpMATLAB(v, "v", "v.m"); phgFinalize(); exit(0); } #endif phgMatDestroy(&A); phgVecDestroy(&x); phgVecDestroy(&y0); phgVecDestroy(&y1); phgVecDestroy(&y2); phgMapDestroy(&map); mem = phgMemoryUsage(g, &mem_peak); dnz = mem / (1024.0 * 1024.0); dnz1 = mem_peak / (1024.0 * 1024.0); /*phgPrintf(" --------------------------------------------" "-------------------------\n");*/ phgPrintf("\n"); phgPrintf(" Memory: current %0.4lgMB, peak %0.4lgMB\n", dnz, dnz1); #if 0 { static int loop_count = 0; if (++loop_count == 4) break; } #endif if (mem_peak > 1024 * (size_t)1024 * mem_max) break; phgRefineAllElements(g, 1); } phgDofFree(&u_h); phgFreeGrid(&g); phgFinalize(); return 0; }
int main(int argc,char **args) { Mat C,Credundant; MatInfo info; PetscMPIInt rank,size,subsize; PetscInt i,j,m = 3,n = 2,low,high,iglobal; PetscInt Ii,J,ldim,nsubcomms; PetscErrorCode ierr; PetscBool flg_info,flg_mat; PetscScalar v,one = 1.0; Vec x,y; MPI_Comm subcomm; ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr; ierr = PetscOptionsGetInt(NULL,NULL,"-m",&m,NULL);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); n = 2*size; ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr); ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,m*n,m*n);CHKERRQ(ierr); ierr = MatSetFromOptions(C);CHKERRQ(ierr); ierr = MatSetUp(C);CHKERRQ(ierr); /* Create the matrix for the five point stencil, YET AGAIN */ for (i=0; i<m; i++) { for (j=2*rank; j<2*rank+2; j++) { v = -1.0; Ii = j + n*i; if (i>0) {J = Ii - n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);} if (i<m-1) {J = Ii + n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);} if (j>0) {J = Ii - 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);} if (j<n-1) {J = Ii + 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);} v = 4.0; ierr = MatSetValues(C,1,&Ii,1,&Ii,&v,INSERT_VALUES);CHKERRQ(ierr); } } /* Add extra elements (to illustrate variants of MatGetInfo) */ Ii = n; J = n-2; v = 100.0; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr); Ii = n-2; J = n; v = 100.0; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr); ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* Form vectors */ ierr = MatCreateVecs(C,&x,&y);CHKERRQ(ierr); ierr = VecGetLocalSize(x,&ldim);CHKERRQ(ierr); ierr = VecGetOwnershipRange(x,&low,&high);CHKERRQ(ierr); for (i=0; i<ldim; i++) { iglobal = i + low; v = one*((PetscReal)i) + 100.0*rank; ierr = VecSetValues(x,1,&iglobal,&v,INSERT_VALUES);CHKERRQ(ierr); } ierr = VecAssemblyBegin(x);CHKERRQ(ierr); ierr = VecAssemblyEnd(x);CHKERRQ(ierr); ierr = MatMult(C,x,y);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,NULL,"-view_info",&flg_info);CHKERRQ(ierr); if (flg_info) { ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr); ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = MatGetInfo(C,MAT_GLOBAL_SUM,&info);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_WORLD,"matrix information (global sums):\nnonzeros = %D, allocated nonzeros = %D\n",(PetscInt)info.nz_used,(PetscInt)info.nz_allocated);CHKERRQ(ierr); ierr = MatGetInfo (C,MAT_GLOBAL_MAX,&info);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_WORLD,"matrix information (global max):\nnonzeros = %D, allocated nonzeros = %D\n",(PetscInt)info.nz_used,(PetscInt)info.nz_allocated);CHKERRQ(ierr); } ierr = PetscOptionsHasName(NULL,NULL,"-view_mat",&flg_mat);CHKERRQ(ierr); if (flg_mat) { ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } /* Test MatCreateRedundantMatrix() */ nsubcomms = size; ierr = PetscOptionsGetInt(NULL,NULL,"-nsubcomms",&nsubcomms,NULL);CHKERRQ(ierr); ierr = MatCreateRedundantMatrix(C,nsubcomms,MPI_COMM_NULL,MAT_INITIAL_MATRIX,&Credundant);CHKERRQ(ierr); ierr = MatCreateRedundantMatrix(C,nsubcomms,MPI_COMM_NULL,MAT_REUSE_MATRIX,&Credundant);CHKERRQ(ierr); ierr = PetscObjectGetComm((PetscObject)Credundant,&subcomm);CHKERRQ(ierr); ierr = MPI_Comm_size(subcomm,&subsize);CHKERRQ(ierr); if (subsize==2 && flg_mat) { ierr = PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_(subcomm),"\n[%d] Credundant:\n",rank);CHKERRQ(ierr); ierr = MatView(Credundant,PETSC_VIEWER_STDOUT_(subcomm));CHKERRQ(ierr); } ierr = MatDestroy(&Credundant);CHKERRQ(ierr); /* Test MatCreateRedundantMatrix() with user-provided subcomm */ { PetscSubcomm psubcomm; ierr = PetscSubcommCreate(PETSC_COMM_WORLD,&psubcomm);CHKERRQ(ierr); ierr = PetscSubcommSetNumber(psubcomm,nsubcomms);CHKERRQ(ierr); ierr = PetscSubcommSetType(psubcomm,PETSC_SUBCOMM_CONTIGUOUS);CHKERRQ(ierr); /* enable runtime switch of psubcomm type, e.g., '-psubcomm_type interlaced */ ierr = PetscSubcommSetFromOptions(psubcomm);CHKERRQ(ierr); ierr = MatCreateRedundantMatrix(C,nsubcomms,PetscSubcommChild(psubcomm),MAT_INITIAL_MATRIX,&Credundant);CHKERRQ(ierr); ierr = MatCreateRedundantMatrix(C,nsubcomms,PetscSubcommChild(psubcomm),MAT_REUSE_MATRIX,&Credundant);CHKERRQ(ierr); ierr = PetscSubcommDestroy(&psubcomm);CHKERRQ(ierr); ierr = MatDestroy(&Credundant);CHKERRQ(ierr); } ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&y);CHKERRQ(ierr); ierr = MatDestroy(&C);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
//============================================================================== Epetra_PETScAIJMatrix::Epetra_PETScAIJMatrix(Mat Amat) : Epetra_Object("Epetra::PETScAIJMatrix"), Amat_(Amat), Values_(0), Indices_(0), MaxNumEntries_(-1), ImportVector_(0), NormInf_(-1.0), NormOne_(-1.0) { #ifdef HAVE_MPI MPI_Comm comm; PetscObjectGetComm( (PetscObject)Amat, &comm); Comm_ = new Epetra_MpiComm(comm); #else Comm_ = new Epetra_SerialComm(); #endif int ierr; char errMsg[80]; MatGetType(Amat, &MatType_); if ( strcmp(MatType_,MATSEQAIJ) != 0 && strcmp(MatType_,MATMPIAIJ) != 0 ) { sprintf(errMsg,"PETSc matrix must be either seqaij or mpiaij (but it is %s)",MatType_); throw Comm_->ReportError(errMsg,-1); } petscMatrixType mt; Mat_MPIAIJ* aij=0; if (strcmp(MatType_,MATMPIAIJ) == 0) { mt = PETSC_MPI_AIJ; aij = (Mat_MPIAIJ*)Amat->data; } else if (strcmp(MatType_,MATSEQAIJ) == 0) { mt = PETSC_SEQ_AIJ; } int numLocalRows, numLocalCols; ierr = MatGetLocalSize(Amat,&numLocalRows,&numLocalCols); if (ierr) { sprintf(errMsg,"EpetraExt_PETScAIJMatrix.cpp, line %d, MatGetLocalSize() returned error code %d",__LINE__,ierr); throw Comm_->ReportError(errMsg,-1); } NumMyRows_ = numLocalRows; NumMyCols_ = numLocalCols; //numLocalCols is the total # of unique columns in the local matrix (the diagonal block) //TODO what happens if some columns are empty? if (mt == PETSC_MPI_AIJ) NumMyCols_ += aij->B->cmap->n; MatInfo info; ierr = MatGetInfo(Amat,MAT_LOCAL,&info); if (ierr) { sprintf(errMsg,"EpetraExt_PETScAIJMatrix.cpp, line %d, MatGetInfo() returned error code %d",__LINE__,ierr); throw Comm_->ReportError(errMsg,-1); } NumMyNonzeros_ = (int) info.nz_used; //PETSc stores nnz as double Comm_->SumAll(&(info.nz_used), &NumGlobalNonzeros_, 1); //The PETSc documentation warns that this may not be robust. //In particular, this will break if the ordering is not contiguous! int rowStart, rowEnd; ierr = MatGetOwnershipRange(Amat,&rowStart,&rowEnd); if (ierr) { sprintf(errMsg,"EpetraExt_PETScAIJMatrix.cpp, line %d, MatGetOwnershipRange() returned error code %d",__LINE__,ierr); throw Comm_->ReportError(errMsg,-1); } PetscRowStart_ = rowStart; PetscRowEnd_ = rowEnd; int* MyGlobalElements = new int[rowEnd-rowStart]; for (int i=0; i<rowEnd-rowStart; i++) MyGlobalElements[i] = rowStart+i; ierr = MatGetInfo(Amat,MAT_GLOBAL_SUM,&info); if (ierr) { sprintf(errMsg,"EpetraExt_PETScAIJMatrix.cpp, line %d, MatGetInfo() returned error code %d",__LINE__,ierr); throw Comm_->ReportError(errMsg,-1); } int tmp; ierr = MatGetSize(Amat,&NumGlobalRows_,&tmp); DomainMap_ = new Epetra_Map(NumGlobalRows_, NumMyRows_, MyGlobalElements, 0, *Comm_); // get the GIDs of the non-local columns //FIXME what if the matrix is sequential? int * ColGIDs = new int[NumMyCols_]; for (int i=0; i<numLocalCols; i++) ColGIDs[i] = MyGlobalElements[i]; for (int i=numLocalCols; i<NumMyCols_; i++) ColGIDs[i] = aij->garray[i-numLocalCols]; ColMap_ = new Epetra_Map(-1, NumMyCols_, ColGIDs, 0, *Comm_); Importer_ = new Epetra_Import(*ColMap_, *DomainMap_); delete [] MyGlobalElements; delete [] ColGIDs; } //Epetra_PETScAIJMatrix(Mat Amat)
int main(int argc,char **args) { Mat A,Asp; PetscViewer fd; /* viewer */ char file[PETSC_MAX_PATH_LEN]; /* input file name */ PetscErrorCode ierr; PetscInt m,n,rstart,rend; PetscBool flg; PetscInt row,ncols,j,nrows,nnzA=0,nnzAsp=0; const PetscInt *cols; const PetscScalar *vals; PetscReal norm,percent,val,dtol=1.e-16; PetscMPIInt rank; MatInfo matinfo; PetscInt Dnnz,Onnz; PetscInitialize(&argc,&args,(char *)0,help); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); /* Determine files from which we read the linear systems. */ ierr = PetscOptionsGetString(PETSC_NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option"); /* Open binary file. Note that we use FILE_MODE_READ to indicate reading from this file. */ ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr); /* Load the matrix; then destroy the viewer. */ ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(A,"a_");CHKERRQ(ierr); ierr = MatSetFromOptions(A);CHKERRQ(ierr); ierr = MatLoad(A,fd);CHKERRQ(ierr); ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr); ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); ierr = MatGetInfo(A,MAT_LOCAL,&matinfo);CHKERRQ(ierr); //printf("matinfo.nz_used %g\n",matinfo.nz_used); /* Get a sparse matrix Asp by dumping zero entries of A */ ierr = MatCreate(PETSC_COMM_WORLD,&Asp);CHKERRQ(ierr); ierr = MatSetSizes(Asp,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(Asp,"asp_");CHKERRQ(ierr); ierr = MatSetFromOptions(Asp);CHKERRQ(ierr); Dnnz = (PetscInt)matinfo.nz_used/m + 1; Onnz = Dnnz/2; printf("Dnnz %d %d\n",Dnnz,Onnz); ierr = MatSeqAIJSetPreallocation(Asp,Dnnz,PETSC_NULL);CHKERRQ(ierr); ierr = MatMPIAIJSetPreallocation(Asp,Dnnz,PETSC_NULL,Onnz,PETSC_NULL);CHKERRQ(ierr); /* Check zero rows */ ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr); nrows = 0; for (row=rstart; row<rend; row++){ ierr = MatGetRow(A,row,&ncols,&cols,&vals);CHKERRQ(ierr); nnzA += ncols; norm = 0.0; for (j=0; j<ncols; j++){ val = PetscAbsScalar(vals[j]); if (norm < val) norm = norm; if (val > dtol){ ierr = MatSetValues(Asp,1,&row,1,&cols[j],&vals[j],INSERT_VALUES);CHKERRQ(ierr); nnzAsp++; } } if (!norm) nrows++; ierr = MatRestoreRow(A,row,&ncols,&cols,&vals);CHKERRQ(ierr); } ierr = MatAssemblyBegin(Asp,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(Asp,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); percent=(PetscReal)nnzA*100/(m*n); ierr = PetscPrintf(PETSC_COMM_SELF," [%d] Matrix A local size %d,%d; nnzA %d, %g percent; No. of zero rows: %d\n",rank,m,n,nnzA,percent,nrows); percent=(PetscReal)nnzAsp*100/(m*n); ierr = PetscPrintf(PETSC_COMM_SELF," [%d] Matrix Asp nnzAsp %d, %g percent\n",rank,nnzAsp,percent); /* investigate matcoloring for Asp */ PetscBool Asp_coloring = PETSC_FALSE; ierr = PetscOptionsHasName(PETSC_NULL,"-Asp_color",&Asp_coloring);CHKERRQ(ierr); if (Asp_coloring){ ISColoring iscoloring; MatFDColoring matfdcoloring; ierr = PetscPrintf(PETSC_COMM_WORLD," Create coloring of Asp...\n"); ierr = MatGetColoring(Asp,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringCreate(Asp,iscoloring,&matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr); //ierr = MatFDColoringView(matfdcoloring,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr); } /* Write Asp in binary for study - see ~petsc/src/mat/examples/tests/ex124.c */ PetscBool Asp_write = PETSC_FALSE; ierr = PetscOptionsHasName(PETSC_NULL,"-Asp_write",&Asp_write);CHKERRQ(ierr); if (Asp_write){ PetscViewer viewer; ierr = PetscPrintf(PETSC_COMM_SELF,"Write Asp into file Asp.dat ...\n"); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Asp.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); ierr = MatView(Asp,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&Asp);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
static PetscErrorCode PCSetUp_PARMS(PC pc) { Mat pmat; PC_PARMS *parms = (PC_PARMS*)pc->data; const PetscInt *mapptr0; PetscInt n, lsize, low, high, i, pos, ncols, length; int *maptmp, *mapptr, *ia, *ja, *ja1, *im; PetscScalar *aa, *aa1; const PetscInt *cols; PetscInt meth[8]; const PetscScalar *values; PetscErrorCode ierr; MatInfo matinfo; PetscMPIInt rank, npro; PetscFunctionBegin; /* Get preconditioner matrix from PETSc and setup pARMS structs */ ierr = PCGetOperators(pc,PETSC_NULL,&pmat,PETSC_NULL);CHKERRQ(ierr); MPI_Comm_size(((PetscObject)pmat)->comm,&npro); MPI_Comm_rank(((PetscObject)pmat)->comm,&rank); ierr = MatGetSize(pmat,&n,PETSC_NULL);CHKERRQ(ierr); ierr = PetscMalloc((npro+1)*sizeof(int),&mapptr);CHKERRQ(ierr); ierr = PetscMalloc(n*sizeof(int),&maptmp);CHKERRQ(ierr); ierr = MatGetOwnershipRanges(pmat,&mapptr0);CHKERRQ(ierr); low = mapptr0[rank]; high = mapptr0[rank+1]; lsize = high - low; for (i=0; i<npro+1; i++) mapptr[i] = mapptr0[i]+1; for (i = 0; i<n; i++) maptmp[i] = i+1; /* if created, destroy the previous map */ if (parms->map) { parms_MapFree(&parms->map); parms->map = PETSC_NULL; } /* create pARMS map object */ parms_MapCreateFromPtr(&parms->map,(int)n,maptmp,mapptr,((PetscObject)pmat)->comm,1,NONINTERLACED); /* if created, destroy the previous pARMS matrix */ if (parms->A) { parms_MatFree(&parms->A); parms->A = PETSC_NULL; } /* create pARMS mat object */ parms_MatCreate(&parms->A,parms->map); /* setup and copy csr data structure for pARMS */ ierr = PetscMalloc((lsize+1)*sizeof(int),&ia);CHKERRQ(ierr); ia[0] = 1; ierr = MatGetInfo(pmat,MAT_LOCAL,&matinfo);CHKERRQ(ierr); length = matinfo.nz_used; ierr = PetscMalloc(length*sizeof(int),&ja);CHKERRQ(ierr); ierr = PetscMalloc(length*sizeof(PetscScalar),&aa);CHKERRQ(ierr); for (i = low; i<high; i++) { pos = ia[i-low]-1; ierr = MatGetRow(pmat,i,&ncols,&cols,&values);CHKERRQ(ierr); ia[i-low+1] = ia[i-low] + ncols; if (ia[i-low+1] >= length) { length += ncols; ierr = PetscMalloc(length*sizeof(int),&ja1);CHKERRQ(ierr); ierr = PetscMemcpy(ja1,ja,(ia[i-low]-1)*sizeof(int));CHKERRQ(ierr); ierr = PetscFree(ja);CHKERRQ(ierr); ja = ja1; ierr = PetscMalloc(length*sizeof(PetscScalar),&aa1);CHKERRQ(ierr); ierr = PetscMemcpy(aa1,aa,(ia[i-low]-1)*sizeof(PetscScalar));CHKERRQ(ierr); ierr = PetscFree(aa);CHKERRQ(ierr); aa = aa1; } ierr = PetscMemcpy(&ja[pos],cols,ncols*sizeof(int));CHKERRQ(ierr); ierr = PetscMemcpy(&aa[pos],values,ncols*sizeof(PetscScalar));CHKERRQ(ierr); ierr = MatRestoreRow(pmat,i,&ncols,&cols,&values);CHKERRQ(ierr); } /* csr info is for local matrix so initialize im[] locally */ ierr = PetscMalloc(lsize*sizeof(int),&im);CHKERRQ(ierr); ierr = PetscMemcpy(im,&maptmp[mapptr[rank]-1],lsize*sizeof(int));CHKERRQ(ierr); /* 1-based indexing */ for (i=0; i<ia[lsize]-1; i++) ja[i] = ja[i]+1; /* Now copy csr matrix to parms_mat object */ parms_MatSetValues(parms->A,(int)lsize,im,ia,ja,aa,INSERT); /* free memory */ ierr = PetscFree(maptmp);CHKERRQ(ierr); ierr = PetscFree(mapptr);CHKERRQ(ierr); ierr = PetscFree(aa);CHKERRQ(ierr); ierr = PetscFree(ja);CHKERRQ(ierr); ierr = PetscFree(ia);CHKERRQ(ierr); ierr = PetscFree(im);CHKERRQ(ierr); /* setup parms matrix */ parms_MatSetup(parms->A); /* if created, destroy the previous pARMS pc */ if (parms->pc) { parms_PCFree(&parms->pc); parms->pc = PETSC_NULL; } /* Now create pARMS preconditioner object based on A */ parms_PCCreate(&parms->pc,parms->A); /* Transfer options from PC to pARMS */ switch(parms->global) { case 0: parms_PCSetType(parms->pc, PCRAS); break; case 1: parms_PCSetType(parms->pc, PCSCHUR); break; case 2: parms_PCSetType(parms->pc, PCBJ); break; } switch(parms->local) { case 0: parms_PCSetILUType(parms->pc, PCILU0); break; case 1: parms_PCSetILUType(parms->pc, PCILUK); break; case 2: parms_PCSetILUType(parms->pc, PCILUT); break; case 3: parms_PCSetILUType(parms->pc, PCARMS); break; } parms_PCSetInnerEps(parms->pc, parms->solvetol); parms_PCSetNlevels(parms->pc, parms->levels); parms_PCSetPermType(parms->pc, parms->nonsymperm?1:0); parms_PCSetBsize(parms->pc, parms->blocksize); parms_PCSetTolInd(parms->pc, parms->indtol); parms_PCSetInnerKSize(parms->pc, parms->maxdim); parms_PCSetInnerMaxits(parms->pc, parms->maxits); for (i=0; i<8; i++) meth[i] = parms->meth[i]?1:0; parms_PCSetPermScalOptions(parms->pc, &meth[0], 1); parms_PCSetPermScalOptions(parms->pc, &meth[4], 0); parms_PCSetFill(parms->pc, parms->lfil); parms_PCSetTol(parms->pc, parms->droptol); parms_PCSetup(parms->pc); /* Allocate two auxiliary vector of length lsize */ if (parms->lvec0) { ierr = PetscFree(parms->lvec0);CHKERRQ(ierr); } ierr = PetscMalloc(lsize*sizeof(PetscScalar), &parms->lvec0);CHKERRQ(ierr); if (parms->lvec1) { ierr = PetscFree(parms->lvec1);CHKERRQ(ierr); } ierr = PetscMalloc(lsize*sizeof(PetscScalar), &parms->lvec1);CHKERRQ(ierr); PetscFunctionReturn(0); }
For MATSEQDENSE matrix, the factorization is just a thin wrapper to LAPACK \n\n"; #include <petscmat.h> #undef __FUNCT__ #define __FUNCT__ "main" int main(int argc,char **argv) { Mat mat,F,RHS,SOLU; MatInfo info; PetscErrorCode ierr; PetscInt m = 10,n = 10,i,j,rstart,rend,nrhs=2; PetscScalar value = 1.0; Vec x,y,b,ytmp; PetscReal norm,tol=1.e-15; PetscMPIInt size; PetscScalar *rhs_array,*solu_array; PetscRandom rand; PetscScalar *array,rval; PetscInitialize(&argc,&argv,(char*) 0,help); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a uniprocessor example only!"); /* create single vectors */ ierr = VecCreate(PETSC_COMM_WORLD,&y);CHKERRQ(ierr); ierr = VecSetSizes(y,PETSC_DECIDE,m);CHKERRQ(ierr); ierr = VecSetFromOptions(y);CHKERRQ(ierr); ierr = VecDuplicate(y,&x);CHKERRQ(ierr); ierr = VecDuplicate(y,&ytmp);CHKERRQ(ierr); ierr = VecSet(x,value);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr); ierr = VecSetSizes(b,PETSC_DECIDE,n);CHKERRQ(ierr); ierr = VecSetFromOptions(b);CHKERRQ(ierr); /* create multiple vectors RHS and SOLU */ ierr = MatCreate(PETSC_COMM_WORLD,&RHS);CHKERRQ(ierr); ierr = MatSetSizes(RHS,PETSC_DECIDE,PETSC_DECIDE,n,nrhs);CHKERRQ(ierr); ierr = MatSetType(RHS,MATDENSE);CHKERRQ(ierr); ierr = MatSetFromOptions(RHS);CHKERRQ(ierr); ierr = MatSeqDenseSetPreallocation(RHS,NULL);CHKERRQ(ierr); ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr); ierr = MatDenseGetArray(RHS,&array);CHKERRQ(ierr); for (j=0; j<nrhs; j++) { for (i=0; i<n; i++) { ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr); array[n*j+i] = rval; } } ierr = MatDenseRestoreArray(RHS,&array);CHKERRQ(ierr); ierr = MatDuplicate(RHS,MAT_DO_NOT_COPY_VALUES,&SOLU);CHKERRQ(ierr); /* create matrix */ ierr = MatCreateSeqDense(PETSC_COMM_WORLD,m,n,NULL,&mat);CHKERRQ(ierr); ierr = MatGetOwnershipRange(mat,&rstart,&rend);CHKERRQ(ierr); for (i=rstart; i<rend; i++) { value = (PetscReal)i+1; ierr = MatSetValues(mat,1,&i,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr); } ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"matrix nonzeros = %D, allocated nonzeros = %D\n", (PetscInt)info.nz_used,(PetscInt)info.nz_allocated);CHKERRQ(ierr); /* Cholesky factorization - perm and factinfo are ignored by LAPACK */ /* in-place Cholesky */ ierr = MatMult(mat,x,b);CHKERRQ(ierr); ierr = MatDuplicate(mat,MAT_COPY_VALUES,&F);CHKERRQ(ierr); ierr = MatCholeskyFactor(F,0,0);CHKERRQ(ierr); ierr = MatSolve(F,b,y);CHKERRQ(ierr); ierr = MatDestroy(&F);CHKERRQ(ierr); value = -1.0; ierr = VecAXPY(y,value,x);CHKERRQ(ierr); ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr); if (norm > tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: Norm of error for Cholesky %G\n",norm);CHKERRQ(ierr); } /* out-place Cholesky */ ierr = MatGetFactor(mat,MATSOLVERPETSC,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr); ierr = MatCholeskyFactorSymbolic(F,mat,0,0);CHKERRQ(ierr); ierr = MatCholeskyFactorNumeric(F,mat,0);CHKERRQ(ierr); ierr = MatSolve(F,b,y);CHKERRQ(ierr); value = -1.0; ierr = VecAXPY(y,value,x);CHKERRQ(ierr); ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr); if (norm > tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: Norm of error for Cholesky %G\n",norm);CHKERRQ(ierr); } ierr = MatDestroy(&F);CHKERRQ(ierr); /* LU factorization - perms and factinfo are ignored by LAPACK */ i = m-1; value = 1.0; ierr = MatSetValues(mat,1,&i,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatMult(mat,x,b);CHKERRQ(ierr); ierr = MatDuplicate(mat,MAT_COPY_VALUES,&F);CHKERRQ(ierr); /* in-place LU */ ierr = MatLUFactor(F,0,0,0);CHKERRQ(ierr); ierr = MatSolve(F,b,y);CHKERRQ(ierr); value = -1.0; ierr = VecAXPY(y,value,x);CHKERRQ(ierr); ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr); if (norm > tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: Norm of error for LU %G\n",norm);CHKERRQ(ierr); } ierr = MatMatSolve(F,RHS,SOLU);CHKERRQ(ierr); ierr = MatDenseGetArray(SOLU,&solu_array);CHKERRQ(ierr); ierr = MatDenseGetArray(RHS,&rhs_array);CHKERRQ(ierr); for (j=0; j<nrhs; j++) { ierr = VecPlaceArray(y,solu_array+j*m);CHKERRQ(ierr); ierr = VecPlaceArray(b,rhs_array+j*m);CHKERRQ(ierr); ierr = MatMult(mat,y,ytmp);CHKERRQ(ierr); ierr = VecAXPY(ytmp,-1.0,b);CHKERRQ(ierr); /* ytmp = mat*SOLU[:,j] - RHS[:,j] */ ierr = VecNorm(ytmp,NORM_2,&norm);CHKERRQ(ierr); if (norm > tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: Norm of residual for LU %G\n",norm);CHKERRQ(ierr); } ierr = VecResetArray(b);CHKERRQ(ierr); ierr = VecResetArray(y);CHKERRQ(ierr); } ierr = MatDenseRestoreArray(RHS,&rhs_array);CHKERRQ(ierr); ierr = MatDenseRestoreArray(SOLU,&solu_array);CHKERRQ(ierr); ierr = MatDestroy(&F);CHKERRQ(ierr); /* out-place LU */ ierr = MatGetFactor(mat,MATSOLVERPETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr); ierr = MatLUFactorSymbolic(F,mat,0,0,0);CHKERRQ(ierr); ierr = MatLUFactorNumeric(F,mat,0);CHKERRQ(ierr); ierr = MatSolve(F,b,y);CHKERRQ(ierr); value = -1.0; ierr = VecAXPY(y,value,x);CHKERRQ(ierr); ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr); if (norm > tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: Norm of error for LU %G\n",norm);CHKERRQ(ierr); } /* free space */ ierr = MatDestroy(&F);CHKERRQ(ierr); ierr = MatDestroy(&mat);CHKERRQ(ierr); ierr = MatDestroy(&RHS);CHKERRQ(ierr); ierr = MatDestroy(&SOLU);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = VecDestroy(&y);CHKERRQ(ierr); ierr = VecDestroy(&ytmp);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
static PetscErrorCode PCSetUp_Cholesky(PC pc) { PetscErrorCode ierr; PetscBool flg; PC_Cholesky *dir = (PC_Cholesky*)pc->data; PetscFunctionBegin; if (dir->reusefill && pc->setupcalled) ((PC_Factor*)dir)->info.fill = dir->actualfill; if (dir->inplace) { if (dir->row && dir->col && (dir->row != dir->col)) { ierr = ISDestroy(&dir->row);CHKERRQ(ierr); } ierr = ISDestroy(&dir->col);CHKERRQ(ierr); ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);CHKERRQ(ierr); if (dir->col && (dir->row != dir->col)) { /* only use row ordering for SBAIJ */ ierr = ISDestroy(&dir->col);CHKERRQ(ierr); } if (dir->row) {ierr = PetscLogObjectParent(pc,dir->row);CHKERRQ(ierr);} ierr = MatCholeskyFactor(pc->pmat,dir->row,&((PC_Factor*)dir)->info);CHKERRQ(ierr); ((PC_Factor*)dir)->fact = pc->pmat; } else { MatInfo info; if (!pc->setupcalled) { ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);CHKERRQ(ierr); /* check if dir->row == dir->col */ ierr = ISEqual(dir->row,dir->col,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"row and column permutations must equal"); ierr = ISDestroy(&dir->col);CHKERRQ(ierr); /* only pass one ordering into CholeskyFactor */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) { PetscReal tol = 1.e-10; ierr = PetscOptionsGetReal(((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&tol,PETSC_NULL);CHKERRQ(ierr); ierr = MatReorderForNonzeroDiagonal(pc->pmat,tol,dir->row,dir->row);CHKERRQ(ierr); } if (dir->row) {ierr = PetscLogObjectParent(pc,dir->row);CHKERRQ(ierr);} if (!((PC_Factor*)dir)->fact){ ierr = MatGetFactor(pc->pmat,((PC_Factor*)dir)->solvertype,MAT_FACTOR_CHOLESKY,&((PC_Factor*)dir)->fact);CHKERRQ(ierr); } ierr = MatCholeskyFactorSymbolic(((PC_Factor*)dir)->fact,pc->pmat,dir->row,&((PC_Factor*)dir)->info);CHKERRQ(ierr); ierr = MatGetInfo(((PC_Factor*)dir)->fact,MAT_LOCAL,&info);CHKERRQ(ierr); dir->actualfill = info.fill_ratio_needed; ierr = PetscLogObjectParent(pc,((PC_Factor*)dir)->fact);CHKERRQ(ierr); } else if (pc->flag != SAME_NONZERO_PATTERN) { if (!dir->reuseordering) { ierr = ISDestroy(&dir->row);CHKERRQ(ierr); ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);CHKERRQ(ierr); ierr = ISDestroy(&dir->col);CHKERRQ(ierr); /* only use dir->row ordering in CholeskyFactor */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) { PetscReal tol = 1.e-10; ierr = PetscOptionsGetReal(((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&tol,PETSC_NULL);CHKERRQ(ierr); ierr = MatReorderForNonzeroDiagonal(pc->pmat,tol,dir->row,dir->row);CHKERRQ(ierr); } if (dir->row) {ierr = PetscLogObjectParent(pc,dir->row);CHKERRQ(ierr);} } ierr = MatDestroy(&((PC_Factor*)dir)->fact);CHKERRQ(ierr); ierr = MatGetFactor(pc->pmat,((PC_Factor*)dir)->solvertype,MAT_FACTOR_CHOLESKY,&((PC_Factor*)dir)->fact);CHKERRQ(ierr); ierr = MatCholeskyFactorSymbolic(((PC_Factor*)dir)->fact,pc->pmat,dir->row,&((PC_Factor*)dir)->info);CHKERRQ(ierr); ierr = MatGetInfo(((PC_Factor*)dir)->fact,MAT_LOCAL,&info);CHKERRQ(ierr); dir->actualfill = info.fill_ratio_needed; ierr = PetscLogObjectParent(pc,((PC_Factor*)dir)->fact);CHKERRQ(ierr); } ierr = MatCholeskyFactorNumeric(((PC_Factor*)dir)->fact,pc->pmat,&((PC_Factor*)dir)->info);CHKERRQ(ierr); } PetscFunctionReturn(0); }
static PetscErrorCode PCSetUp_ILU(PC pc) { PetscErrorCode ierr; PC_ILU *ilu = (PC_ILU*)pc->data; MatInfo info; PetscBool flg; PetscFunctionBegin; /* ugly hack to change default, since it is not support by some matrix types */ if (((PC_Factor*)ilu)->info.shifttype == (PetscReal)MAT_SHIFT_NONZERO) { ierr = PetscObjectTypeCompare((PetscObject)pc->pmat,MATSEQAIJ,&flg);CHKERRQ(ierr); if (!flg) { ierr = PetscObjectTypeCompare((PetscObject)pc->pmat,MATMPIAIJ,&flg);CHKERRQ(ierr); if (!flg) { ((PC_Factor*)ilu)->info.shifttype = (PetscReal)MAT_SHIFT_INBLOCKS; PetscInfo(pc,"Changing shift type from NONZERO to INBLOCKS because block matrices do not support NONZERO");CHKERRQ(ierr); } } } if (ilu->inplace) { CHKMEMQ; if (!pc->setupcalled) { /* In-place factorization only makes sense with the natural ordering, so we only need to get the ordering once, even if nonzero structure changes */ ierr = MatGetOrdering(pc->pmat,((PC_Factor*)ilu)->ordering,&ilu->row,&ilu->col);CHKERRQ(ierr); if (ilu->row) {ierr = PetscLogObjectParent(pc,ilu->row);CHKERRQ(ierr);} if (ilu->col) {ierr = PetscLogObjectParent(pc,ilu->col);CHKERRQ(ierr);} } /* In place ILU only makes sense with fill factor of 1.0 because cannot have levels of fill */ ((PC_Factor*)ilu)->info.fill = 1.0; ((PC_Factor*)ilu)->info.diagonal_fill = 0.0; ierr = MatILUFactor(pc->pmat,ilu->row,ilu->col,&((PC_Factor*)ilu)->info);CHKERRQ(ierr);CHKMEMQ; ((PC_Factor*)ilu)->fact = pc->pmat; } else { if (!pc->setupcalled) { /* first time in so compute reordering and symbolic factorization */ ierr = MatGetOrdering(pc->pmat,((PC_Factor*)ilu)->ordering,&ilu->row,&ilu->col);CHKERRQ(ierr); if (ilu->row) {ierr = PetscLogObjectParent(pc,ilu->row);CHKERRQ(ierr);} if (ilu->col) {ierr = PetscLogObjectParent(pc,ilu->col);CHKERRQ(ierr);} /* Remove zeros along diagonal? */ if (ilu->nonzerosalongdiagonal) { ierr = MatReorderForNonzeroDiagonal(pc->pmat,ilu->nonzerosalongdiagonaltol,ilu->row,ilu->col);CHKERRQ(ierr); } if (!((PC_Factor*)ilu)->fact){ ierr = MatGetFactor(pc->pmat,((PC_Factor*)ilu)->solvertype,MAT_FACTOR_ILU,&((PC_Factor*)ilu)->fact);CHKERRQ(ierr); } ierr = MatILUFactorSymbolic(((PC_Factor*)ilu)->fact,pc->pmat,ilu->row,ilu->col,&((PC_Factor*)ilu)->info);CHKERRQ(ierr); ierr = MatGetInfo(((PC_Factor*)ilu)->fact,MAT_LOCAL,&info);CHKERRQ(ierr); ilu->actualfill = info.fill_ratio_needed; ierr = PetscLogObjectParent(pc,((PC_Factor*)ilu)->fact);CHKERRQ(ierr); } else if (pc->flag != SAME_NONZERO_PATTERN) { if (!ilu->reuseordering) { /* compute a new ordering for the ILU */ ierr = ISDestroy(&ilu->row);CHKERRQ(ierr); ierr = ISDestroy(&ilu->col);CHKERRQ(ierr); ierr = MatGetOrdering(pc->pmat,((PC_Factor*)ilu)->ordering,&ilu->row,&ilu->col);CHKERRQ(ierr); if (ilu->row) {ierr = PetscLogObjectParent(pc,ilu->row);CHKERRQ(ierr);} if (ilu->col) {ierr = PetscLogObjectParent(pc,ilu->col);CHKERRQ(ierr);} /* Remove zeros along diagonal? */ if (ilu->nonzerosalongdiagonal) { ierr = MatReorderForNonzeroDiagonal(pc->pmat,ilu->nonzerosalongdiagonaltol,ilu->row,ilu->col);CHKERRQ(ierr); } } ierr = MatDestroy(&((PC_Factor*)ilu)->fact);CHKERRQ(ierr); ierr = MatGetFactor(pc->pmat,((PC_Factor*)ilu)->solvertype,MAT_FACTOR_ILU,&((PC_Factor*)ilu)->fact);CHKERRQ(ierr); ierr = MatILUFactorSymbolic(((PC_Factor*)ilu)->fact,pc->pmat,ilu->row,ilu->col,&((PC_Factor*)ilu)->info);CHKERRQ(ierr); ierr = MatGetInfo(((PC_Factor*)ilu)->fact,MAT_LOCAL,&info);CHKERRQ(ierr); ilu->actualfill = info.fill_ratio_needed; ierr = PetscLogObjectParent(pc,((PC_Factor*)ilu)->fact);CHKERRQ(ierr); } CHKMEMQ; ierr = MatLUFactorNumeric(((PC_Factor*)ilu)->fact,pc->pmat,&((PC_Factor*)ilu)->info);CHKERRQ(ierr); CHKMEMQ; } PetscFunctionReturn(0); }
static PetscErrorCode PCSetUp_ILU(PC pc) { PetscErrorCode ierr; PC_ILU *ilu = (PC_ILU*)pc->data; MatInfo info; PetscBool flg; const MatSolverPackage stype; MatFactorError err; PetscFunctionBegin; pc->failedreason = PC_NOERROR; /* ugly hack to change default, since it is not support by some matrix types */ if (((PC_Factor*)ilu)->info.shifttype == (PetscReal)MAT_SHIFT_NONZERO) { ierr = PetscObjectTypeCompare((PetscObject)pc->pmat,MATSEQAIJ,&flg);CHKERRQ(ierr); if (!flg) { ierr = PetscObjectTypeCompare((PetscObject)pc->pmat,MATMPIAIJ,&flg);CHKERRQ(ierr); if (!flg) { ((PC_Factor*)ilu)->info.shifttype = (PetscReal)MAT_SHIFT_INBLOCKS; PetscInfo(pc,"Changing shift type from NONZERO to INBLOCKS because block matrices do not support NONZERO\n");CHKERRQ(ierr); } } } ierr = MatSetErrorIfFailure(pc->pmat,pc->erroriffailure);CHKERRQ(ierr); if (ilu->hdr.inplace) { if (!pc->setupcalled) { /* In-place factorization only makes sense with the natural ordering, so we only need to get the ordering once, even if nonzero structure changes */ ierr = MatGetOrdering(pc->pmat,((PC_Factor*)ilu)->ordering,&ilu->row,&ilu->col);CHKERRQ(ierr); if (ilu->row) {ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)ilu->row);CHKERRQ(ierr);} if (ilu->col) {ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)ilu->col);CHKERRQ(ierr);} } /* In place ILU only makes sense with fill factor of 1.0 because cannot have levels of fill */ ((PC_Factor*)ilu)->info.fill = 1.0; ((PC_Factor*)ilu)->info.diagonal_fill = 0.0; ierr = MatILUFactor(pc->pmat,ilu->row,ilu->col,&((PC_Factor*)ilu)->info);CHKERRQ(ierr);CHKERRQ(ierr); ierr = MatFactorGetError(pc->pmat,&err);CHKERRQ(ierr); if (err) { /* Factor() fails */ pc->failedreason = (PCFailedReason)err; PetscFunctionReturn(0); } ((PC_Factor*)ilu)->fact = pc->pmat; /* must update the pc record of the matrix state or the PC will attempt to run PCSetUp() yet again */ ierr = PetscObjectStateGet((PetscObject)pc->pmat,&pc->matstate);CHKERRQ(ierr); } else { if (!pc->setupcalled) { /* first time in so compute reordering and symbolic factorization */ ierr = MatGetOrdering(pc->pmat,((PC_Factor*)ilu)->ordering,&ilu->row,&ilu->col);CHKERRQ(ierr); if (ilu->row) {ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)ilu->row);CHKERRQ(ierr);} if (ilu->col) {ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)ilu->col);CHKERRQ(ierr);} /* Remove zeros along diagonal? */ if (ilu->nonzerosalongdiagonal) { ierr = MatReorderForNonzeroDiagonal(pc->pmat,ilu->nonzerosalongdiagonaltol,ilu->row,ilu->col);CHKERRQ(ierr); } if (!((PC_Factor*)ilu)->fact) { ierr = MatGetFactor(pc->pmat,((PC_Factor*)ilu)->solvertype,MAT_FACTOR_ILU,&((PC_Factor*)ilu)->fact);CHKERRQ(ierr); } ierr = MatILUFactorSymbolic(((PC_Factor*)ilu)->fact,pc->pmat,ilu->row,ilu->col,&((PC_Factor*)ilu)->info);CHKERRQ(ierr); ierr = MatGetInfo(((PC_Factor*)ilu)->fact,MAT_LOCAL,&info);CHKERRQ(ierr); ilu->hdr.actualfill = info.fill_ratio_needed; ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)((PC_Factor*)ilu)->fact);CHKERRQ(ierr); } else if (pc->flag != SAME_NONZERO_PATTERN) { if (!ilu->hdr.reuseordering) { /* compute a new ordering for the ILU */ ierr = ISDestroy(&ilu->row);CHKERRQ(ierr); ierr = ISDestroy(&ilu->col);CHKERRQ(ierr); ierr = MatGetOrdering(pc->pmat,((PC_Factor*)ilu)->ordering,&ilu->row,&ilu->col);CHKERRQ(ierr); if (ilu->row) {ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)ilu->row);CHKERRQ(ierr);} if (ilu->col) {ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)ilu->col);CHKERRQ(ierr);} /* Remove zeros along diagonal? */ if (ilu->nonzerosalongdiagonal) { ierr = MatReorderForNonzeroDiagonal(pc->pmat,ilu->nonzerosalongdiagonaltol,ilu->row,ilu->col);CHKERRQ(ierr); } } ierr = MatDestroy(&((PC_Factor*)ilu)->fact);CHKERRQ(ierr); ierr = MatGetFactor(pc->pmat,((PC_Factor*)ilu)->solvertype,MAT_FACTOR_ILU,&((PC_Factor*)ilu)->fact);CHKERRQ(ierr); ierr = MatILUFactorSymbolic(((PC_Factor*)ilu)->fact,pc->pmat,ilu->row,ilu->col,&((PC_Factor*)ilu)->info);CHKERRQ(ierr); ierr = MatGetInfo(((PC_Factor*)ilu)->fact,MAT_LOCAL,&info);CHKERRQ(ierr); ilu->hdr.actualfill = info.fill_ratio_needed; ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)((PC_Factor*)ilu)->fact);CHKERRQ(ierr); } ierr = MatFactorGetError(((PC_Factor*)ilu)->fact,&err);CHKERRQ(ierr); if (err) { /* FactorSymbolic() fails */ pc->failedreason = (PCFailedReason)err; PetscFunctionReturn(0); } ierr = MatLUFactorNumeric(((PC_Factor*)ilu)->fact,pc->pmat,&((PC_Factor*)ilu)->info);CHKERRQ(ierr); ierr = MatFactorGetError(((PC_Factor*)ilu)->fact,&err);CHKERRQ(ierr); if (err) { /* FactorNumeric() fails */ pc->failedreason = (PCFailedReason)err; } } ierr = PCFactorGetMatSolverPackage(pc,&stype);CHKERRQ(ierr); if (!stype) { const MatSolverPackage solverpackage; ierr = MatFactorGetSolverPackage(((PC_Factor*)ilu)->fact,&solverpackage);CHKERRQ(ierr); ierr = PCFactorSetMatSolverPackage(pc,solverpackage);CHKERRQ(ierr); } PetscFunctionReturn(0); }
static PetscErrorCode PCSetUp_Cholesky(PC pc) { PetscErrorCode ierr; PetscBool flg; PC_Cholesky *dir = (PC_Cholesky*)pc->data; const MatSolverPackage stype; MatFactorError err; PetscFunctionBegin; pc->failedreason = PC_NOERROR; if (dir->hdr.reusefill && pc->setupcalled) ((PC_Factor*)dir)->info.fill = dir->hdr.actualfill; ierr = MatSetErrorIfFailure(pc->pmat,pc->erroriffailure); CHKERRQ(ierr); if (dir->hdr.inplace) { if (dir->row && dir->col && (dir->row != dir->col)) { ierr = ISDestroy(&dir->row); CHKERRQ(ierr); } ierr = ISDestroy(&dir->col); CHKERRQ(ierr); ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col); CHKERRQ(ierr); if (dir->col && (dir->row != dir->col)) { /* only use row ordering for SBAIJ */ ierr = ISDestroy(&dir->col); CHKERRQ(ierr); } if (dir->row) { ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)dir->row); CHKERRQ(ierr); } ierr = MatCholeskyFactor(pc->pmat,dir->row,&((PC_Factor*)dir)->info); CHKERRQ(ierr); ierr = MatFactorGetError(pc->pmat,&err); CHKERRQ(ierr); if (err) { /* Factor() fails */ pc->failedreason = (PCFailedReason)err; PetscFunctionReturn(0); } ((PC_Factor*)dir)->fact = pc->pmat; } else { MatInfo info; if (!pc->setupcalled) { ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col); CHKERRQ(ierr); /* check if dir->row == dir->col */ ierr = ISEqual(dir->row,dir->col,&flg); CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"row and column permutations must equal"); ierr = ISDestroy(&dir->col); CHKERRQ(ierr); /* only pass one ordering into CholeskyFactor */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(((PetscObject)pc)->options,((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&flg,NULL); CHKERRQ(ierr); if (flg) { PetscReal tol = 1.e-10; ierr = PetscOptionsGetReal(((PetscObject)pc)->options,((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&tol,NULL); CHKERRQ(ierr); ierr = MatReorderForNonzeroDiagonal(pc->pmat,tol,dir->row,dir->row); CHKERRQ(ierr); } if (dir->row) { ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)dir->row); CHKERRQ(ierr); } if (!((PC_Factor*)dir)->fact) { ierr = MatGetFactor(pc->pmat,((PC_Factor*)dir)->solvertype,MAT_FACTOR_CHOLESKY,&((PC_Factor*)dir)->fact); CHKERRQ(ierr); } ierr = MatCholeskyFactorSymbolic(((PC_Factor*)dir)->fact,pc->pmat,dir->row,&((PC_Factor*)dir)->info); CHKERRQ(ierr); ierr = MatGetInfo(((PC_Factor*)dir)->fact,MAT_LOCAL,&info); CHKERRQ(ierr); dir->hdr.actualfill = info.fill_ratio_needed; ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)((PC_Factor*)dir)->fact); CHKERRQ(ierr); } else if (pc->flag != SAME_NONZERO_PATTERN) { if (!dir->hdr.reuseordering) { ierr = ISDestroy(&dir->row); CHKERRQ(ierr); ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col); CHKERRQ(ierr); ierr = ISDestroy(&dir->col); CHKERRQ(ierr); /* only use dir->row ordering in CholeskyFactor */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(((PetscObject)pc)->options,((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&flg,NULL); CHKERRQ(ierr); if (flg) { PetscReal tol = 1.e-10; ierr = PetscOptionsGetReal(((PetscObject)pc)->options,((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&tol,NULL); CHKERRQ(ierr); ierr = MatReorderForNonzeroDiagonal(pc->pmat,tol,dir->row,dir->row); CHKERRQ(ierr); } if (dir->row) { ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)dir->row); CHKERRQ(ierr); } } ierr = MatDestroy(&((PC_Factor*)dir)->fact); CHKERRQ(ierr); ierr = MatGetFactor(pc->pmat,((PC_Factor*)dir)->solvertype,MAT_FACTOR_CHOLESKY,&((PC_Factor*)dir)->fact); CHKERRQ(ierr); ierr = MatCholeskyFactorSymbolic(((PC_Factor*)dir)->fact,pc->pmat,dir->row,&((PC_Factor*)dir)->info); CHKERRQ(ierr); ierr = MatGetInfo(((PC_Factor*)dir)->fact,MAT_LOCAL,&info); CHKERRQ(ierr); dir->hdr.actualfill = info.fill_ratio_needed; ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)((PC_Factor*)dir)->fact); CHKERRQ(ierr); } else { ierr = MatFactorGetError(((PC_Factor*)dir)->fact,&err); CHKERRQ(ierr); if (err == MAT_FACTOR_NUMERIC_ZEROPIVOT) { ierr = MatFactorClearError(((PC_Factor*)dir)->fact); CHKERRQ(ierr); pc->failedreason = PC_NOERROR; } } ierr = MatFactorGetError(((PC_Factor*)dir)->fact,&err); CHKERRQ(ierr); if (err) { /* FactorSymbolic() fails */ pc->failedreason = (PCFailedReason)err; PetscFunctionReturn(0); } ierr = MatCholeskyFactorNumeric(((PC_Factor*)dir)->fact,pc->pmat,&((PC_Factor*)dir)->info); CHKERRQ(ierr); ierr = MatFactorGetError(((PC_Factor*)dir)->fact,&err); CHKERRQ(ierr); if (err) { /* FactorNumeric() fails */ pc->failedreason = (PCFailedReason)err; } } ierr = PCFactorGetMatSolverPackage(pc,&stype); CHKERRQ(ierr); if (!stype) { const MatSolverPackage solverpackage; ierr = MatFactorGetSolverPackage(((PC_Factor*)dir)->fact,&solverpackage); CHKERRQ(ierr); ierr = PCFactorSetMatSolverPackage(pc,solverpackage); CHKERRQ(ierr); } PetscFunctionReturn(0); }
/*@C PCGAMGFilterGraph - filter (remove zero and possibly small values from the) graph and make it symmetric if requested Collective on Mat Input Parameter: + a_Gmat - the graph . vfilter - threshold paramter [0,1) - symm - make the result symmetric Level: developer Notes: This is called before graph coarsers are called. .seealso: PCGAMGSetThreshold() @*/ PetscErrorCode PCGAMGFilterGraph(Mat *a_Gmat,PetscReal vfilter,PetscBool symm) { PetscErrorCode ierr; PetscInt Istart,Iend,Ii,jj,ncols,nnz0,nnz1, NN, MM, nloc; PetscMPIInt rank; Mat Gmat = *a_Gmat, tGmat, matTrans; MPI_Comm comm; const PetscScalar *vals; const PetscInt *idx; PetscInt *d_nnz, *o_nnz; Vec diag; MatType mtype; PetscFunctionBegin; #if defined PETSC_GAMG_USE_LOG ierr = PetscLogEventBegin(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr); #endif /* scale Gmat for all values between -1 and 1 */ ierr = MatCreateVecs(Gmat, &diag, 0);CHKERRQ(ierr); ierr = MatGetDiagonal(Gmat, diag);CHKERRQ(ierr); ierr = VecReciprocal(diag);CHKERRQ(ierr); ierr = VecSqrtAbs(diag);CHKERRQ(ierr); ierr = MatDiagonalScale(Gmat, diag, diag);CHKERRQ(ierr); ierr = VecDestroy(&diag);CHKERRQ(ierr); if (vfilter < 0.0 && !symm) { /* Just use the provided matrix as the graph but make all values positive */ MatInfo info; PetscScalar *avals; PetscBool isaij,ismpiaij; ierr = PetscObjectBaseTypeCompare((PetscObject)Gmat,MATSEQAIJ,&isaij);CHKERRQ(ierr); ierr = PetscObjectBaseTypeCompare((PetscObject)Gmat,MATMPIAIJ,&ismpiaij);CHKERRQ(ierr); if (!isaij && !ismpiaij) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Require (MPI)AIJ matrix type"); if (isaij) { ierr = MatGetInfo(Gmat,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = MatSeqAIJGetArray(Gmat,&avals);CHKERRQ(ierr); for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]); ierr = MatSeqAIJRestoreArray(Gmat,&avals);CHKERRQ(ierr); } else { Mat_MPIAIJ *aij = (Mat_MPIAIJ*)Gmat->data; ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = MatSeqAIJGetArray(aij->A,&avals);CHKERRQ(ierr); for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]); ierr = MatSeqAIJRestoreArray(aij->A,&avals);CHKERRQ(ierr); ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = MatSeqAIJGetArray(aij->B,&avals);CHKERRQ(ierr); for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]); ierr = MatSeqAIJRestoreArray(aij->B,&avals);CHKERRQ(ierr); } #if defined PETSC_GAMG_USE_LOG ierr = PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr); #endif PetscFunctionReturn(0); } ierr = PetscObjectGetComm((PetscObject)Gmat,&comm);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr); nloc = Iend - Istart; ierr = MatGetSize(Gmat, &MM, &NN);CHKERRQ(ierr); if (symm) { ierr = MatTranspose(Gmat, MAT_INITIAL_MATRIX, &matTrans);CHKERRQ(ierr); } /* Determine upper bound on nonzeros needed in new filtered matrix */ ierr = PetscMalloc2(nloc, &d_nnz,nloc, &o_nnz);CHKERRQ(ierr); for (Ii = Istart, jj = 0; Ii < Iend; Ii++, jj++) { ierr = MatGetRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); d_nnz[jj] = ncols; o_nnz[jj] = ncols; ierr = MatRestoreRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); if (symm) { ierr = MatGetRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); d_nnz[jj] += ncols; o_nnz[jj] += ncols; ierr = MatRestoreRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); } if (d_nnz[jj] > nloc) d_nnz[jj] = nloc; if (o_nnz[jj] > (MM-nloc)) o_nnz[jj] = MM - nloc; } ierr = MatGetType(Gmat,&mtype);CHKERRQ(ierr); ierr = MatCreate(comm, &tGmat);CHKERRQ(ierr); ierr = MatSetSizes(tGmat,nloc,nloc,MM,MM);CHKERRQ(ierr); ierr = MatSetBlockSizes(tGmat, 1, 1);CHKERRQ(ierr); ierr = MatSetType(tGmat, mtype);CHKERRQ(ierr); ierr = MatSeqAIJSetPreallocation(tGmat,0,d_nnz);CHKERRQ(ierr); ierr = MatMPIAIJSetPreallocation(tGmat,0,d_nnz,0,o_nnz);CHKERRQ(ierr); ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); if (symm) { ierr = MatDestroy(&matTrans);CHKERRQ(ierr); } else { /* all entries are generated locally so MatAssembly will be slightly faster for large process counts */ ierr = MatSetOption(tGmat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); } for (Ii = Istart, nnz0 = nnz1 = 0; Ii < Iend; Ii++) { ierr = MatGetRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr); for (jj=0; jj<ncols; jj++,nnz0++) { PetscScalar sv = PetscAbs(PetscRealPart(vals[jj])); if (PetscRealPart(sv) > vfilter) { nnz1++; if (symm) { sv *= 0.5; ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValues(tGmat,1,&idx[jj],1,&Ii,&sv,ADD_VALUES);CHKERRQ(ierr); } else { ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr); } } } ierr = MatRestoreRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr); } ierr = MatAssemblyBegin(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); #if defined PETSC_GAMG_USE_LOG ierr = PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr); #endif #if defined(PETSC_USE_INFO) { double t1 = (!nnz0) ? 1. : 100.*(double)nnz1/(double)nnz0, t2 = (!nloc) ? 1. : (double)nnz0/(double)nloc; ierr = PetscInfo4(*a_Gmat,"\t %g%% nnz after filtering, with threshold %g, %g nnz ave. (N=%D)\n",t1,vfilter,t2,MM);CHKERRQ(ierr); } #endif ierr = MatDestroy(&Gmat);CHKERRQ(ierr); *a_Gmat = tGmat; PetscFunctionReturn(0); }
int main(int argc,char **args) { Vec x,y,b,s1,s2; Mat A; /* linear system matrix */ Mat sA; /* symmetric part of the matrices */ PetscInt n,mbs=16,bs=1,nz=3,prob=2,i,j,col[3],row,Ii,J,n1; const PetscInt *ip_ptr; PetscScalar neg_one = -1.0,value[3],alpha=0.1; PetscMPIInt size; PetscErrorCode ierr; IS ip, isrow, iscol; PetscRandom rdm; PetscBool reorder=PETSC_FALSE; MatInfo minfo1,minfo2; PetscReal norm1,norm2,tol=1.e-10; PetscInitialize(&argc,&args,(char *)0,help); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size != 1) SETERRQ(PETSC_COMM_WORLD,1,"This is a uniprocessor example only!"); ierr = PetscOptionsGetInt(PETSC_NULL,"-bs",&bs,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-mbs",&mbs,PETSC_NULL);CHKERRQ(ierr); n = mbs*bs; ierr=MatCreateSeqBAIJ(PETSC_COMM_WORLD,bs,n,n,nz,PETSC_NULL, &A);CHKERRQ(ierr); ierr=MatCreateSeqSBAIJ(PETSC_COMM_WORLD,bs,n,n,nz,PETSC_NULL, &sA);CHKERRQ(ierr); /* Test MatGetOwnershipRange() */ ierr = MatGetOwnershipRange(A,&Ii,&J);CHKERRQ(ierr); ierr = MatGetOwnershipRange(sA,&i,&j);CHKERRQ(ierr); if (i-Ii || j-J){ ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetOwnershipRange() in MatSBAIJ format\n");CHKERRQ(ierr); } /* Assemble matrix */ if (bs == 1){ ierr = PetscOptionsGetInt(PETSC_NULL,"-test_problem",&prob,PETSC_NULL);CHKERRQ(ierr); if (prob == 1){ /* tridiagonal matrix */ value[0] = -1.0; value[1] = 2.0; value[2] = -1.0; for (i=1; i<n-1; i++) { col[0] = i-1; col[1] = i; col[2] = i+1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } i = n - 1; col[0]=0; col[1] = n - 2; col[2] = n - 1; value[0]= 0.1; value[1]=-1; value[2]=2; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); i = 0; col[0] = 0; col[1] = 1; col[2]=n-1; value[0] = 2.0; value[1] = -1.0; value[2]=0.1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } else if (prob ==2){ /* matrix for the five point stencil */ n1 = (int) (PetscSqrtReal((PetscReal)n) + 0.001); if (n1*n1 - n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"sqrt(n) must be a positive interger!"); for (i=0; i<n1; i++) { for (j=0; j<n1; j++) { Ii = j + n1*i; if (i>0) { J = Ii - n1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } if (i<n1-1) { J = Ii + n1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } if (j>0) { J = Ii - 1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } if (j<n1-1) { J = Ii + 1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } /* ierr = MatSetValues(A,1,&I,1,&I,&four,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&I,1,&I,&four,INSERT_VALUES);CHKERRQ(ierr); */ } } } } else { /* bs > 1 */ #ifdef DIAGB for (block=0; block<n/bs; block++){ /* diagonal blocks */ value[0] = -1.0; value[1] = 4.0; value[2] = -1.0; for (i=1+block*bs; i<bs-1+block*bs; i++) { col[0] = i-1; col[1] = i; col[2] = i+1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } i = bs - 1+block*bs; col[0] = bs - 2+block*bs; col[1] = bs - 1+block*bs; value[0]=-1.0; value[1]=4.0; ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); i = 0+block*bs; col[0] = 0+block*bs; col[1] = 1+block*bs; value[0]=4.0; value[1] = -1.0; ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); } #endif /* off-diagonal blocks */ value[0]=-1.0; for (i=0; i<(n/bs-1)*bs; i++){ col[0]=i+bs; ierr = MatSetValues(A,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr); col[0]=i; row=i+bs; ierr = MatSetValues(A,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr); } } ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* PetscPrintf(PETSC_COMM_SELF,"\n The Matrix: \n"); MatView(A, VIEWER_DRAW_WORLD); MatView(A, VIEWER_STDOUT_WORLD); */ ierr = MatAssemblyBegin(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* PetscPrintf(PETSC_COMM_SELF,"\n Symmetric Part of Matrix: \n"); MatView(sA, VIEWER_DRAW_WORLD); MatView(sA, VIEWER_STDOUT_WORLD); */ /* Test MatNorm() */ ierr = MatNorm(A,NORM_FROBENIUS,&norm1);CHKERRQ(ierr); ierr = MatNorm(sA,NORM_FROBENIUS,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol){ ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm(), fnorm1-fnorm2=%16.14e\n",norm1);CHKERRQ(ierr); } ierr = MatNorm(A,NORM_INFINITY,&norm1);CHKERRQ(ierr); ierr = MatNorm(sA,NORM_INFINITY,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol){ ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm(), inf_norm1-inf_norm2=%16.14e\n",norm1);CHKERRQ(ierr); } /* Test MatGetInfo(), MatGetSize(), MatGetBlockSize() */ ierr = MatGetInfo(A,MAT_LOCAL,&minfo1);CHKERRQ(ierr); ierr = MatGetInfo(sA,MAT_LOCAL,&minfo2);CHKERRQ(ierr); /* printf("matrix nonzeros (BAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo1.nz_used,(int)minfo1.nz_allocated); printf("matrix nonzeros(SBAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo2.nz_used,(int)minfo2.nz_allocated); */ i = (int) (minfo1.nz_used - minfo2.nz_used); j = (int) (minfo1.nz_allocated - minfo2.nz_allocated); if (i<0 || j<0) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetInfo()\n");CHKERRQ(ierr); } ierr = MatGetSize(A,&Ii,&J);CHKERRQ(ierr); ierr = MatGetSize(sA,&i,&j);CHKERRQ(ierr); if (i-Ii || j-J) { PetscPrintf(PETSC_COMM_SELF,"Error: MatGetSize()\n");CHKERRQ(ierr); } ierr = MatGetBlockSize(A, &Ii);CHKERRQ(ierr); ierr = MatGetBlockSize(sA, &i);CHKERRQ(ierr); if (i-Ii){ ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetBlockSize()\n");CHKERRQ(ierr); } /* Test MatDiagonalScale(), MatGetDiagonal(), MatScale() */ ierr = PetscRandomCreate(PETSC_COMM_SELF,&rdm);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr); ierr = VecCreateSeq(PETSC_COMM_SELF,n,&x);CHKERRQ(ierr); ierr = VecDuplicate(x,&s1);CHKERRQ(ierr); ierr = VecDuplicate(x,&s2);CHKERRQ(ierr); ierr = VecDuplicate(x,&y);CHKERRQ(ierr); ierr = VecDuplicate(x,&b);CHKERRQ(ierr); ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); ierr = MatDiagonalScale(A,x,x);CHKERRQ(ierr); ierr = MatDiagonalScale(sA,x,x);CHKERRQ(ierr); ierr = MatGetDiagonal(A,s1);CHKERRQ(ierr); ierr = MatGetDiagonal(sA,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatGetDiagonal() \n");CHKERRQ(ierr); } ierr = MatScale(A,alpha);CHKERRQ(ierr); ierr = MatScale(sA,alpha);CHKERRQ(ierr); /* Test MatMult(), MatMultAdd() */ for (i=0; i<40; i++) { ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); ierr = MatMult(A,x,s1);CHKERRQ(ierr); ierr = MatMult(sA,x,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMult(), MatDiagonalScale() or MatScale()\n");CHKERRQ(ierr); } } for (i=0; i<40; i++) { ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); ierr = VecSetRandom(y,rdm);CHKERRQ(ierr); ierr = MatMultAdd(A,x,y,s1);CHKERRQ(ierr); ierr = MatMultAdd(sA,x,y,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMultAdd(), MatDiagonalScale() or MatScale() \n");CHKERRQ(ierr); } } /* Test MatReordering() */ ierr = MatGetOrdering(A,MATORDERINGNATURAL,&isrow,&iscol);CHKERRQ(ierr); ip = isrow; if (reorder){ IS nip; PetscInt *nip_ptr; ierr = PetscMalloc(mbs*sizeof(PetscInt),&nip_ptr);CHKERRQ(ierr); ierr = ISGetIndices(ip,&ip_ptr);CHKERRQ(ierr); ierr = PetscMemcpy(nip_ptr,ip_ptr,mbs*sizeof(PetscInt));CHKERRQ(ierr); i = nip_ptr[1]; nip_ptr[1] = nip_ptr[mbs-2]; nip_ptr[mbs-2] = i; i = nip_ptr[0]; nip_ptr[0] = nip_ptr[mbs-1]; nip_ptr[mbs-1] = i; ierr = ISRestoreIndices(ip,&ip_ptr);CHKERRQ(ierr); ierr = ISCreateGeneral(PETSC_COMM_SELF,mbs,nip_ptr,PETSC_COPY_VALUES,&nip);CHKERRQ(ierr); ierr = PetscFree(nip_ptr);CHKERRQ(ierr); ierr = MatReorderingSeqSBAIJ(sA, ip);CHKERRQ(ierr); ierr = ISDestroy(&nip);CHKERRQ(ierr); /* ierr = ISView(ip, VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = MatView(sA,VIEWER_DRAW_SELF);CHKERRQ(ierr); */ } ierr = ISDestroy(&iscol);CHKERRQ(ierr); /* ierr = ISDestroy(&isrow);CHKERRQ(ierr);*/ ierr = ISDestroy(&isrow);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&sA);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&y);CHKERRQ(ierr); ierr = VecDestroy(&s1);CHKERRQ(ierr); ierr = VecDestroy(&s2);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **args) { PetscMPIInt size; PetscErrorCode ierr; Vec x,y,b,s1,s2; Mat A; /* linear system matrix */ Mat sA,sB,sC; /* symmetric part of the matrices */ PetscInt n,mbs=16,bs=1,nz=3,prob=1,i,j,k1,k2,col[3],lf,block, row,Ii,J,n1,inc; PetscReal norm1,norm2,rnorm,tol=PETSC_SMALL; PetscScalar neg_one = -1.0,four=4.0,value[3]; IS perm, iscol; PetscRandom rdm; PetscBool doIcc=PETSC_TRUE,equal; MatInfo minfo1,minfo2; MatFactorInfo factinfo; MatType type; PetscInitialize(&argc,&args,(char*)0,help); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a uniprocessor example only!"); ierr = PetscOptionsGetInt(NULL,"-bs",&bs,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-mbs",&mbs,NULL);CHKERRQ(ierr); n = mbs*bs; ierr = MatCreate(PETSC_COMM_SELF,&A);CHKERRQ(ierr); ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); ierr = MatSetType(A,MATSEQBAIJ);CHKERRQ(ierr); ierr = MatSetFromOptions(A);CHKERRQ(ierr); ierr = MatSeqBAIJSetPreallocation(A,bs,nz,NULL);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_SELF,&sA);CHKERRQ(ierr); ierr = MatSetSizes(sA,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); ierr = MatSetType(sA,MATSEQSBAIJ);CHKERRQ(ierr); ierr = MatSetFromOptions(sA);CHKERRQ(ierr); ierr = MatGetType(sA,&type);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)sA,MATSEQSBAIJ,&doIcc);CHKERRQ(ierr); ierr = MatSeqSBAIJSetPreallocation(sA,bs,nz,NULL);CHKERRQ(ierr); ierr = MatSetOption(sA,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE);CHKERRQ(ierr); /* Test MatGetOwnershipRange() */ ierr = MatGetOwnershipRange(A,&Ii,&J);CHKERRQ(ierr); ierr = MatGetOwnershipRange(sA,&i,&j);CHKERRQ(ierr); if (i-Ii || j-J) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetOwnershipRange() in MatSBAIJ format\n");CHKERRQ(ierr); } /* Assemble matrix */ if (bs == 1) { ierr = PetscOptionsGetInt(NULL,"-test_problem",&prob,NULL);CHKERRQ(ierr); if (prob == 1) { /* tridiagonal matrix */ value[0] = -1.0; value[1] = 2.0; value[2] = -1.0; for (i=1; i<n-1; i++) { col[0] = i-1; col[1] = i; col[2] = i+1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } i = n - 1; col[0]=0; col[1] = n - 2; col[2] = n - 1; value[0]= 0.1; value[1]=-1; value[2]=2; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); i = 0; col[0] = n-1; col[1] = 1; col[2] = 0; value[0] = 0.1; value[1] = -1.0; value[2] = 2; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } else if (prob ==2) { /* matrix for the five point stencil */ n1 = (PetscInt) (PetscSqrtReal((PetscReal)n) + 0.001); if (n1*n1 - n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"sqrt(n) must be a positive interger!"); for (i=0; i<n1; i++) { for (j=0; j<n1; j++) { Ii = j + n1*i; if (i>0) { J = Ii - n1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } if (i<n1-1) { J = Ii + n1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } if (j>0) { J = Ii - 1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } if (j<n1-1) { J = Ii + 1; ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr); } ierr = MatSetValues(A,1,&Ii,1,&Ii,&four,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&Ii,1,&Ii,&four,INSERT_VALUES);CHKERRQ(ierr); } } } } else { /* bs > 1 */ for (block=0; block<n/bs; block++) { /* diagonal blocks */ value[0] = -1.0; value[1] = 4.0; value[2] = -1.0; for (i=1+block*bs; i<bs-1+block*bs; i++) { col[0] = i-1; col[1] = i; col[2] = i+1; ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr); } i = bs - 1+block*bs; col[0] = bs - 2+block*bs; col[1] = bs - 1+block*bs; value[0]=-1.0; value[1]=4.0; ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); i = 0+block*bs; col[0] = 0+block*bs; col[1] = 1+block*bs; value[0]=4.0; value[1] = -1.0; ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr); } /* off-diagonal blocks */ value[0]=-1.0; for (i=0; i<(n/bs-1)*bs; i++) { col[0]=i+bs; ierr = MatSetValues(A,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr); col[0]=i; row=i+bs; ierr = MatSetValues(A,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(sA,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr); } } ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyBegin(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* Test MatGetInfo() of A and sA */ ierr = MatGetInfo(A,MAT_LOCAL,&minfo1);CHKERRQ(ierr); ierr = MatGetInfo(sA,MAT_LOCAL,&minfo2);CHKERRQ(ierr); /* printf("A matrix nonzeros (BAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo1.nz_used,(int)minfo1.nz_allocated); printf("sA matrix nonzeros(SBAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo2.nz_used,(int)minfo2.nz_allocated); */ i = (int) (minfo1.nz_used - minfo2.nz_used); j = (int) (minfo1.nz_allocated - minfo2.nz_allocated); k1 = (int) (minfo1.nz_allocated - minfo1.nz_used); k2 = (int) (minfo2.nz_allocated - minfo2.nz_used); if (i < 0 || j < 0 || k1 < 0 || k2 < 0) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error (compare A and sA): MatGetInfo()\n");CHKERRQ(ierr); } /* Test MatDuplicate() */ ierr = MatNorm(A,NORM_FROBENIUS,&norm1);CHKERRQ(ierr); ierr = MatDuplicate(sA,MAT_COPY_VALUES,&sB);CHKERRQ(ierr); ierr = MatEqual(sA,sB,&equal);CHKERRQ(ierr); if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"Error in MatDuplicate()"); /* Test MatNorm() */ ierr = MatNorm(A,NORM_FROBENIUS,&norm1);CHKERRQ(ierr); ierr = MatNorm(sB,NORM_FROBENIUS,&norm2);CHKERRQ(ierr); rnorm = PetscAbsReal(norm1-norm2)/norm2; if (rnorm > tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_FROBENIUS, NormA=%16.14e NormsB=%16.14e\n",norm1,norm2);CHKERRQ(ierr); } ierr = MatNorm(A,NORM_INFINITY,&norm1);CHKERRQ(ierr); ierr = MatNorm(sB,NORM_INFINITY,&norm2);CHKERRQ(ierr); rnorm = PetscAbsReal(norm1-norm2)/norm2; if (rnorm > tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_INFINITY(), NormA=%16.14e NormsB=%16.14e\n",norm1,norm2);CHKERRQ(ierr); } ierr = MatNorm(A,NORM_1,&norm1);CHKERRQ(ierr); ierr = MatNorm(sB,NORM_1,&norm2);CHKERRQ(ierr); rnorm = PetscAbsReal(norm1-norm2)/norm2; if (rnorm > tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_INFINITY(), NormA=%16.14e NormsB=%16.14e\n",norm1,norm2);CHKERRQ(ierr); } /* Test MatGetInfo(), MatGetSize(), MatGetBlockSize() */ ierr = MatGetInfo(A,MAT_LOCAL,&minfo1);CHKERRQ(ierr); ierr = MatGetInfo(sB,MAT_LOCAL,&minfo2);CHKERRQ(ierr); /* printf("matrix nonzeros (BAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo1.nz_used,(int)minfo1.nz_allocated); printf("matrix nonzeros(SBAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo2.nz_used,(int)minfo2.nz_allocated); */ i = (int) (minfo1.nz_used - minfo2.nz_used); j = (int) (minfo1.nz_allocated - minfo2.nz_allocated); k1 = (int) (minfo1.nz_allocated - minfo1.nz_used); k2 = (int) (minfo2.nz_allocated - minfo2.nz_used); if (i < 0 || j < 0 || k1 < 0 || k2 < 0) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error(compare A and sB): MatGetInfo()\n");CHKERRQ(ierr); } ierr = MatGetSize(A,&Ii,&J);CHKERRQ(ierr); ierr = MatGetSize(sB,&i,&j);CHKERRQ(ierr); if (i-Ii || j-J) { PetscPrintf(PETSC_COMM_SELF,"Error: MatGetSize()\n");CHKERRQ(ierr); } ierr = MatGetBlockSize(A, &Ii);CHKERRQ(ierr); ierr = MatGetBlockSize(sB, &i);CHKERRQ(ierr); if (i-Ii) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetBlockSize()\n");CHKERRQ(ierr); } ierr = PetscRandomCreate(PETSC_COMM_SELF,&rdm);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr); ierr = VecCreateSeq(PETSC_COMM_SELF,n,&x);CHKERRQ(ierr); ierr = VecDuplicate(x,&s1);CHKERRQ(ierr); ierr = VecDuplicate(x,&s2);CHKERRQ(ierr); ierr = VecDuplicate(x,&y);CHKERRQ(ierr); ierr = VecDuplicate(x,&b);CHKERRQ(ierr); ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); /* Test MatDiagonalScale(), MatGetDiagonal(), MatScale() */ #if !defined(PETSC_USE_COMPLEX) /* Scaling matrix with complex numbers results non-spd matrix, causing crash of MatForwardSolve() and MatBackwardSolve() */ ierr = MatDiagonalScale(A,x,x);CHKERRQ(ierr); ierr = MatDiagonalScale(sB,x,x);CHKERRQ(ierr); ierr = MatMultEqual(A,sB,10,&equal);CHKERRQ(ierr); if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"Error in MatDiagonalScale"); ierr = MatGetDiagonal(A,s1);CHKERRQ(ierr); ierr = MatGetDiagonal(sB,s2);CHKERRQ(ierr); ierr = VecAXPY(s2,neg_one,s1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&norm1);CHKERRQ(ierr); if (norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatGetDiagonal(), ||s1-s2||=%G\n",norm1);CHKERRQ(ierr); } { PetscScalar alpha=0.1; ierr = MatScale(A,alpha);CHKERRQ(ierr); ierr = MatScale(sB,alpha);CHKERRQ(ierr); } #endif /* Test MatGetRowMaxAbs() */ ierr = MatGetRowMaxAbs(A,s1,NULL);CHKERRQ(ierr); ierr = MatGetRowMaxAbs(sB,s2,NULL);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatGetRowMaxAbs() \n");CHKERRQ(ierr); } /* Test MatMult() */ for (i=0; i<40; i++) { ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); ierr = MatMult(A,x,s1);CHKERRQ(ierr); ierr = MatMult(sB,x,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMult(), norm1-norm2: %G\n",norm1);CHKERRQ(ierr); } } /* MatMultAdd() */ for (i=0; i<40; i++) { ierr = VecSetRandom(x,rdm);CHKERRQ(ierr); ierr = VecSetRandom(y,rdm);CHKERRQ(ierr); ierr = MatMultAdd(A,x,y,s1);CHKERRQ(ierr); ierr = MatMultAdd(sB,x,y,s2);CHKERRQ(ierr); ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr); norm1 -= norm2; if (norm1<-tol || norm1>tol) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMultAdd(), norm1-norm2: %G\n",norm1);CHKERRQ(ierr); } } /* Test MatCholeskyFactor(), MatICCFactor() with natural ordering */ ierr = MatGetOrdering(A,MATORDERINGNATURAL,&perm,&iscol);CHKERRQ(ierr); ierr = ISDestroy(&iscol);CHKERRQ(ierr); norm1 = tol; inc = bs; /* initialize factinfo */ ierr = PetscMemzero(&factinfo,sizeof(MatFactorInfo));CHKERRQ(ierr); for (lf=-1; lf<10; lf += inc) { if (lf==-1) { /* Cholesky factor of sB (duplicate sA) */ factinfo.fill = 5.0; ierr = MatGetFactor(sB,MATSOLVERPETSC,MAT_FACTOR_CHOLESKY,&sC);CHKERRQ(ierr); ierr = MatCholeskyFactorSymbolic(sC,sB,perm,&factinfo);CHKERRQ(ierr); } else if (!doIcc) break; else { /* incomplete Cholesky factor */ factinfo.fill = 5.0; factinfo.levels = lf; ierr = MatGetFactor(sB,MATSOLVERPETSC,MAT_FACTOR_ICC,&sC);CHKERRQ(ierr); ierr = MatICCFactorSymbolic(sC,sB,perm,&factinfo);CHKERRQ(ierr); } ierr = MatCholeskyFactorNumeric(sC,sB,&factinfo);CHKERRQ(ierr); /* MatView(sC, PETSC_VIEWER_DRAW_WORLD); */ /* test MatGetDiagonal on numeric factor */ /* if (lf == -1) { ierr = MatGetDiagonal(sC,s1);CHKERRQ(ierr); printf(" in ex74.c, diag: \n"); ierr = VecView(s1,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); } */ ierr = MatMult(sB,x,b);CHKERRQ(ierr); /* test MatForwardSolve() and MatBackwardSolve() */ if (lf == -1) { ierr = MatForwardSolve(sC,b,s1);CHKERRQ(ierr); ierr = MatBackwardSolve(sC,s1,s2);CHKERRQ(ierr); ierr = VecAXPY(s2,neg_one,x);CHKERRQ(ierr); ierr = VecNorm(s2,NORM_2,&norm2);CHKERRQ(ierr); if (10*norm1 < norm2) { ierr = PetscPrintf(PETSC_COMM_SELF,"MatForwardSolve and BackwardSolve: Norm of error=%G, bs=%d\n",norm2,bs);CHKERRQ(ierr); } } /* test MatSolve() */ ierr = MatSolve(sC,b,y);CHKERRQ(ierr); ierr = MatDestroy(&sC);CHKERRQ(ierr); /* Check the error */ ierr = VecAXPY(y,neg_one,x);CHKERRQ(ierr); ierr = VecNorm(y,NORM_2,&norm2);CHKERRQ(ierr); /* printf("lf: %d, error: %G\n", lf,norm2); */ if (10*norm1 < norm2 && lf-inc != -1) { ierr = PetscPrintf(PETSC_COMM_SELF,"lf=%D, %D, Norm of error=%G, %G\n",lf-inc,lf,norm1,norm2);CHKERRQ(ierr); } norm1 = norm2; if (norm2 < tol && lf != -1) break; } ierr = ISDestroy(&perm);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&sB);CHKERRQ(ierr); ierr = MatDestroy(&sA);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&y);CHKERRQ(ierr); ierr = VecDestroy(&s1);CHKERRQ(ierr); ierr = VecDestroy(&s2);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
Matrix C is copied from ~petsc/src/ksp/ksp/examples/tutorials/ex5.c\n\n"; /* Example: ./ex132 -mat_view_info */ #include <petscmat.h> #undef __FUNCT__ #define __FUNCT__ "main" int main(int argc,char **args) { Mat C,C1,C2; /* matrix */ PetscScalar v; PetscInt Ii,J,Istart,Iend; PetscErrorCode ierr; PetscInt i,j,m = 3,n = 2; PetscMPIInt size,rank; PetscBool mat_nonsymmetric = PETSC_FALSE; MatInfo info; PetscInitialize(&argc,&args,(char *)0,help); ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); n = 2*size; /* Set flag if we are doing a nonsymmetric problem; the default is symmetric. */ ierr = PetscOptionsGetBool(PETSC_NULL,"-mat_nonsym",&mat_nonsymmetric,PETSC_NULL);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr); ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,m*n,m*n);CHKERRQ(ierr); ierr = MatSetFromOptions(C);CHKERRQ(ierr); ierr = MatSeqAIJSetPreallocation(C,5,PETSC_NULL);CHKERRQ(ierr); ierr = MatGetOwnershipRange(C,&Istart,&Iend);CHKERRQ(ierr); for (Ii=Istart; Ii<Iend; Ii++) { v = -1.0; i = Ii/n; j = Ii - i*n; if (i>0) {J = Ii - n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);} if (i<m-1) {J = Ii + n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);} if (j>0) {J = Ii - 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);} if (j<n-1) {J = Ii + 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);} v = 4.0; ierr = MatSetValues(C,1,&Ii,1,&Ii,&v,ADD_VALUES); } /* Make the matrix nonsymmetric if desired */ if (mat_nonsymmetric) { for (Ii=Istart; Ii<Iend; Ii++) { v = -1.5; i = Ii/n; if (i>1) {J = Ii-n-1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);} } } else { ierr = MatSetOption(C,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); ierr = MatSetOption(C,MAT_SYMMETRY_ETERNAL,PETSC_TRUE);CHKERRQ(ierr); } ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* First, create C1 = 2.0*C1 + C, C1 has less non-zeros than C */ ierr = PetscPrintf(PETSC_COMM_WORLD, "\ncreate C1 = 2.0*C1 + C, C1 has less non-zeros than C \n"); ierr = MatCreate(PETSC_COMM_WORLD,&C1);CHKERRQ(ierr); ierr = MatSetSizes(C1,PETSC_DECIDE,PETSC_DECIDE,m*n,m*n);CHKERRQ(ierr); ierr = MatSetFromOptions(C1);CHKERRQ(ierr); ierr = MatSeqAIJSetPreallocation(C1,1,PETSC_NULL);CHKERRQ(ierr); for (Ii=Istart; Ii<Iend; Ii++) { ierr = MatSetValues(C1,1,&Ii,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr); } ierr = MatAssemblyBegin(C1,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(C1,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD," MatAXPY(C1,2.0,C,DIFFERENT_NONZERO_PATTERN)...\n"); ierr = MatAXPY(C1,2.0,C,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); ierr = MatGetInfo(C1,MAT_GLOBAL_SUM,&info);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD," C1: nz_allocated = %g; nz_used = %g; nz_unneeded = %g\n",info.nz_allocated,info.nz_used, info.nz_unneeded); /* Secondly, create C2 = 2.0*C2 + C, C2 has non-zero pattern of C2 + C */ ierr = PetscPrintf(PETSC_COMM_WORLD, "\ncreate C2 = 2.0*C2 + C, C2 has non-zero pattern of C2 + C \n"); ierr = MatDuplicate(C,MAT_DO_NOT_COPY_VALUES,&C2);CHKERRQ(ierr); /* ierr = MatCreate(PETSC_COMM_WORLD,&C2);CHKERRQ(ierr); ierr = MatSetSizes(C2,PETSC_DECIDE,PETSC_DECIDE,m*n,m*n);CHKERRQ(ierr); ierr = MatSetFromOptions(C2);CHKERRQ(ierr); ierr = MatSeqAIJSetPreallocation(C2,5,PETSC_NULL);CHKERRQ(ierr); */ for (Ii=Istart; Ii<Iend; Ii++) { v = 1.0; ierr = MatSetValues(C2,1,&Ii,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr); } ierr = MatAssemblyBegin(C2,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(C2,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); printf(" MatAXPY(C2,2.0,C,SUBSET_NONZERO_PATTERN)...\n"); ierr = MatAXPY(C2,2.0,C,SUBSET_NONZERO_PATTERN);CHKERRQ(ierr); ierr = MatGetInfo(C2,MAT_GLOBAL_SUM,&info);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD," C2: nz_allocated = %g; nz_used = %g; nz_unneeded = %g\n",info.nz_allocated,info.nz_used, info.nz_unneeded); ierr = MatDestroy(&C1);CHKERRQ(ierr); ierr = MatDestroy(&C2);CHKERRQ(ierr); ierr = MatDestroy(&C);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }