#include /*I "petscmat.h" I*/ typedef struct { Mat A; Mat D; /* local submatrix for diagonal part */ Vec w, left, right, leftwork, rightwork; PetscScalar scale; } Mat_Normal; PetscErrorCode MatScale_Normal(Mat inA, PetscScalar scale) { Mat_Normal *a = (Mat_Normal *)inA->data; PetscFunctionBegin; a->scale *= scale; PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatDiagonalScale_Normal(Mat inA, Vec left, Vec right) { Mat_Normal *a = (Mat_Normal *)inA->data; PetscFunctionBegin; if (left) { if (!a->left) { PetscCall(VecDuplicate(left, &a->left)); PetscCall(VecCopy(left, a->left)); } else { PetscCall(VecPointwiseMult(a->left, left, a->left)); } } if (right) { if (!a->right) { PetscCall(VecDuplicate(right, &a->right)); PetscCall(VecCopy(right, a->right)); } else { PetscCall(VecPointwiseMult(a->right, right, a->right)); } } PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatIncreaseOverlap_Normal(Mat A, PetscInt is_max, IS is[], PetscInt ov) { Mat_Normal *a = (Mat_Normal *)A->data; Mat pattern; PetscFunctionBegin; PetscCheck(ov >= 0, PetscObjectComm((PetscObject)A), PETSC_ERR_ARG_OUTOFRANGE, "Negative overlap specified"); PetscCall(MatProductCreate(a->A, a->A, NULL, &pattern)); PetscCall(MatProductSetType(pattern, MATPRODUCT_AtB)); PetscCall(MatProductSetFromOptions(pattern)); PetscCall(MatProductSymbolic(pattern)); PetscCall(MatIncreaseOverlap(pattern, is_max, is, ov)); PetscCall(MatDestroy(&pattern)); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatCreateSubMatrices_Normal(Mat mat, PetscInt n, const IS irow[], const IS icol[], MatReuse scall, Mat *submat[]) { Mat_Normal *a = (Mat_Normal *)mat->data; Mat B = a->A, *suba; IS *row; PetscInt M; PetscFunctionBegin; PetscCheck(!a->left && !a->right && irow == icol, PetscObjectComm((PetscObject)mat), PETSC_ERR_SUP, "Not implemented"); if (scall != MAT_REUSE_MATRIX) PetscCall(PetscCalloc1(n, submat)); PetscCall(MatGetSize(B, &M, NULL)); PetscCall(PetscMalloc1(n, &row)); PetscCall(ISCreateStride(PETSC_COMM_SELF, M, 0, 1, &row[0])); PetscCall(ISSetIdentity(row[0])); for (M = 1; M < n; ++M) row[M] = row[0]; PetscCall(MatCreateSubMatrices(B, n, row, icol, MAT_INITIAL_MATRIX, &suba)); for (M = 0; M < n; ++M) { PetscCall(MatCreateNormal(suba[M], *submat + M)); ((Mat_Normal *)(*submat)[M]->data)->scale = a->scale; } PetscCall(ISDestroy(&row[0])); PetscCall(PetscFree(row)); PetscCall(MatDestroySubMatrices(n, &suba)); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatPermute_Normal(Mat A, IS rowp, IS colp, Mat *B) { Mat_Normal *a = (Mat_Normal *)A->data; Mat C, Aa = a->A; IS row; PetscFunctionBegin; PetscCheck(rowp == colp, PetscObjectComm((PetscObject)A), PETSC_ERR_ARG_INCOMP, "Row permutation and column permutation must be the same"); PetscCall(ISCreateStride(PetscObjectComm((PetscObject)Aa), Aa->rmap->n, Aa->rmap->rstart, 1, &row)); PetscCall(ISSetIdentity(row)); PetscCall(MatPermute(Aa, row, colp, &C)); PetscCall(ISDestroy(&row)); PetscCall(MatCreateNormal(C, B)); PetscCall(MatDestroy(&C)); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatDuplicate_Normal(Mat A, MatDuplicateOption op, Mat *B) { Mat_Normal *a = (Mat_Normal *)A->data; Mat C; PetscFunctionBegin; PetscCheck(!a->left && !a->right, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Not implemented"); PetscCall(MatDuplicate(a->A, op, &C)); PetscCall(MatCreateNormal(C, B)); PetscCall(MatDestroy(&C)); if (op == MAT_COPY_VALUES) ((Mat_Normal *)(*B)->data)->scale = a->scale; PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatCopy_Normal(Mat A, Mat B, MatStructure str) { Mat_Normal *a = (Mat_Normal *)A->data, *b = (Mat_Normal *)B->data; PetscFunctionBegin; PetscCheck(!a->left && !a->right, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Not implemented"); PetscCall(MatCopy(a->A, b->A, str)); b->scale = a->scale; PetscCall(VecDestroy(&b->left)); PetscCall(VecDestroy(&b->right)); PetscCall(VecDestroy(&b->leftwork)); PetscCall(VecDestroy(&b->rightwork)); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatMult_Normal(Mat N, Vec x, Vec y) { Mat_Normal *Na = (Mat_Normal *)N->data; Vec in; PetscFunctionBegin; in = x; if (Na->right) { if (!Na->rightwork) PetscCall(VecDuplicate(Na->right, &Na->rightwork)); PetscCall(VecPointwiseMult(Na->rightwork, Na->right, in)); in = Na->rightwork; } PetscCall(MatMult(Na->A, in, Na->w)); PetscCall(MatMultTranspose(Na->A, Na->w, y)); if (Na->left) PetscCall(VecPointwiseMult(y, Na->left, y)); PetscCall(VecScale(y, Na->scale)); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatMultAdd_Normal(Mat N, Vec v1, Vec v2, Vec v3) { Mat_Normal *Na = (Mat_Normal *)N->data; Vec in; PetscFunctionBegin; in = v1; if (Na->right) { if (!Na->rightwork) PetscCall(VecDuplicate(Na->right, &Na->rightwork)); PetscCall(VecPointwiseMult(Na->rightwork, Na->right, in)); in = Na->rightwork; } PetscCall(MatMult(Na->A, in, Na->w)); PetscCall(VecScale(Na->w, Na->scale)); if (Na->left) { PetscCall(MatMultTranspose(Na->A, Na->w, v3)); PetscCall(VecPointwiseMult(v3, Na->left, v3)); PetscCall(VecAXPY(v3, 1.0, v2)); } else { PetscCall(MatMultTransposeAdd(Na->A, Na->w, v2, v3)); } PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatMultTranspose_Normal(Mat N, Vec x, Vec y) { Mat_Normal *Na = (Mat_Normal *)N->data; Vec in; PetscFunctionBegin; in = x; if (Na->left) { if (!Na->leftwork) PetscCall(VecDuplicate(Na->left, &Na->leftwork)); PetscCall(VecPointwiseMult(Na->leftwork, Na->left, in)); in = Na->leftwork; } PetscCall(MatMult(Na->A, in, Na->w)); PetscCall(MatMultTranspose(Na->A, Na->w, y)); if (Na->right) PetscCall(VecPointwiseMult(y, Na->right, y)); PetscCall(VecScale(y, Na->scale)); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatMultTransposeAdd_Normal(Mat N, Vec v1, Vec v2, Vec v3) { Mat_Normal *Na = (Mat_Normal *)N->data; Vec in; PetscFunctionBegin; in = v1; if (Na->left) { if (!Na->leftwork) PetscCall(VecDuplicate(Na->left, &Na->leftwork)); PetscCall(VecPointwiseMult(Na->leftwork, Na->left, in)); in = Na->leftwork; } PetscCall(MatMult(Na->A, in, Na->w)); PetscCall(VecScale(Na->w, Na->scale)); if (Na->right) { PetscCall(MatMultTranspose(Na->A, Na->w, v3)); PetscCall(VecPointwiseMult(v3, Na->right, v3)); PetscCall(VecAXPY(v3, 1.0, v2)); } else { PetscCall(MatMultTransposeAdd(Na->A, Na->w, v2, v3)); } PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatDestroy_Normal(Mat N) { Mat_Normal *Na = (Mat_Normal *)N->data; PetscFunctionBegin; PetscCall(MatDestroy(&Na->A)); PetscCall(MatDestroy(&Na->D)); PetscCall(VecDestroy(&Na->w)); PetscCall(VecDestroy(&Na->left)); PetscCall(VecDestroy(&Na->right)); PetscCall(VecDestroy(&Na->leftwork)); PetscCall(VecDestroy(&Na->rightwork)); PetscCall(PetscFree(N->data)); PetscCall(PetscObjectComposeFunction((PetscObject)N, "MatNormalGetMat_C", NULL)); PetscCall(PetscObjectComposeFunction((PetscObject)N, "MatConvert_normal_seqaij_C", NULL)); PetscCall(PetscObjectComposeFunction((PetscObject)N, "MatConvert_normal_mpiaij_C", NULL)); #if defined(PETSC_HAVE_HYPRE) PetscCall(PetscObjectComposeFunction((PetscObject)N, "MatConvert_normal_hypre_C", NULL)); #endif PetscCall(PetscObjectComposeFunction((PetscObject)N, "MatProductSetFromOptions_normal_seqdense_C", NULL)); PetscCall(PetscObjectComposeFunction((PetscObject)N, "MatProductSetFromOptions_normal_mpidense_C", NULL)); PetscCall(PetscObjectComposeFunction((PetscObject)N, "MatProductSetFromOptions_normal_dense_C", NULL)); PetscFunctionReturn(PETSC_SUCCESS); } /* Slow, nonscalable version */ PetscErrorCode MatGetDiagonal_Normal(Mat N, Vec v) { Mat_Normal *Na = (Mat_Normal *)N->data; Mat A = Na->A; PetscInt i, j, rstart, rend, nnz; const PetscInt *cols; PetscScalar *diag, *work, *values; const PetscScalar *mvalues; PetscFunctionBegin; PetscCall(PetscMalloc2(A->cmap->N, &diag, A->cmap->N, &work)); PetscCall(PetscArrayzero(work, A->cmap->N)); PetscCall(MatGetOwnershipRange(A, &rstart, &rend)); for (i = rstart; i < rend; i++) { PetscCall(MatGetRow(A, i, &nnz, &cols, &mvalues)); for (j = 0; j < nnz; j++) work[cols[j]] += mvalues[j] * mvalues[j]; PetscCall(MatRestoreRow(A, i, &nnz, &cols, &mvalues)); } PetscCall(MPIU_Allreduce(work, diag, A->cmap->N, MPIU_SCALAR, MPIU_SUM, PetscObjectComm((PetscObject)N))); rstart = N->cmap->rstart; rend = N->cmap->rend; PetscCall(VecGetArray(v, &values)); PetscCall(PetscArraycpy(values, diag + rstart, rend - rstart)); PetscCall(VecRestoreArray(v, &values)); PetscCall(PetscFree2(diag, work)); PetscCall(VecScale(v, Na->scale)); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatGetDiagonalBlock_Normal(Mat N, Mat *D) { Mat_Normal *Na = (Mat_Normal *)N->data; Mat M, A = Na->A; PetscFunctionBegin; PetscCall(MatGetDiagonalBlock(A, &M)); PetscCall(MatCreateNormal(M, &Na->D)); *D = Na->D; PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatNormalGetMat_Normal(Mat A, Mat *M) { Mat_Normal *Aa = (Mat_Normal *)A->data; PetscFunctionBegin; *M = Aa->A; PetscFunctionReturn(PETSC_SUCCESS); } /*@ MatNormalGetMat - Gets the `Mat` object stored inside a `MATNORMAL` Logically Collective Input Parameter: . A - the `MATNORMAL` matrix Output Parameter: . M - the matrix object stored inside `A` Level: intermediate .seealso: [](ch_matrices), `Mat`, `MATNORMAL`, `MATNORMALHERMITIAN`, `MatCreateNormal()` @*/ PetscErrorCode MatNormalGetMat(Mat A, Mat *M) { PetscFunctionBegin; PetscValidHeaderSpecific(A, MAT_CLASSID, 1); PetscValidType(A, 1); PetscValidPointer(M, 2); PetscUseMethod(A, "MatNormalGetMat_C", (Mat, Mat *), (A, M)); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatConvert_Normal_AIJ(Mat A, MatType newtype, MatReuse reuse, Mat *newmat) { Mat_Normal *Aa = (Mat_Normal *)A->data; Mat B; PetscInt m, n, M, N; PetscFunctionBegin; PetscCall(MatGetSize(A, &M, &N)); PetscCall(MatGetLocalSize(A, &m, &n)); if (reuse == MAT_REUSE_MATRIX) { B = *newmat; PetscCall(MatProductReplaceMats(Aa->A, Aa->A, NULL, B)); } else { PetscCall(MatProductCreate(Aa->A, Aa->A, NULL, &B)); PetscCall(MatProductSetType(B, MATPRODUCT_AtB)); PetscCall(MatProductSetFromOptions(B)); PetscCall(MatProductSymbolic(B)); PetscCall(MatSetOption(B, MAT_SYMMETRIC, PETSC_TRUE)); } PetscCall(MatProductNumeric(B)); if (reuse == MAT_INPLACE_MATRIX) { PetscCall(MatHeaderReplace(A, &B)); } else if (reuse == MAT_INITIAL_MATRIX) *newmat = B; PetscCall(MatConvert(*newmat, MATAIJ, MAT_INPLACE_MATRIX, newmat)); PetscFunctionReturn(PETSC_SUCCESS); } #if defined(PETSC_HAVE_HYPRE) PetscErrorCode MatConvert_Normal_HYPRE(Mat A, MatType type, MatReuse reuse, Mat *B) { PetscFunctionBegin; if (reuse == MAT_INITIAL_MATRIX) { PetscCall(MatConvert(A, MATAIJ, reuse, B)); PetscCall(MatConvert(*B, type, MAT_INPLACE_MATRIX, B)); } else PetscCall(MatConvert_Basic(A, type, reuse, B)); /* fall back to basic convert */ PetscFunctionReturn(PETSC_SUCCESS); } #endif typedef struct { Mat work[2]; } Normal_Dense; PetscErrorCode MatProductNumeric_Normal_Dense(Mat C) { Mat A, B; Normal_Dense *contents; Mat_Normal *a; PetscScalar *array; PetscFunctionBegin; MatCheckProduct(C, 1); A = C->product->A; a = (Mat_Normal *)A->data; B = C->product->B; contents = (Normal_Dense *)C->product->data; PetscCheck(contents, PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Product data empty"); if (a->right) { PetscCall(MatCopy(B, C, SAME_NONZERO_PATTERN)); PetscCall(MatDiagonalScale(C, a->right, NULL)); } PetscCall(MatProductNumeric(contents->work[0])); PetscCall(MatDenseGetArrayWrite(C, &array)); PetscCall(MatDensePlaceArray(contents->work[1], array)); PetscCall(MatProductNumeric(contents->work[1])); PetscCall(MatDenseRestoreArrayWrite(C, &array)); PetscCall(MatDenseResetArray(contents->work[1])); PetscCall(MatSetOption(C, MAT_NO_OFF_PROC_ENTRIES, PETSC_TRUE)); PetscCall(MatAssemblyBegin(C, MAT_FINAL_ASSEMBLY)); PetscCall(MatAssemblyEnd(C, MAT_FINAL_ASSEMBLY)); PetscCall(MatScale(C, a->scale)); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatNormal_DenseDestroy(void *ctx) { Normal_Dense *contents = (Normal_Dense *)ctx; PetscFunctionBegin; PetscCall(MatDestroy(contents->work)); PetscCall(MatDestroy(contents->work + 1)); PetscCall(PetscFree(contents)); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatProductSymbolic_Normal_Dense(Mat C) { Mat A, B; Normal_Dense *contents = NULL; Mat_Normal *a; PetscScalar *array; PetscInt n, N, m, M; PetscFunctionBegin; MatCheckProduct(C, 1); PetscCheck(!C->product->data, PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Product data not empty"); A = C->product->A; a = (Mat_Normal *)A->data; PetscCheck(!a->left, PetscObjectComm((PetscObject)C), PETSC_ERR_SUP, "Not implemented"); B = C->product->B; PetscCall(MatGetLocalSize(C, &m, &n)); PetscCall(MatGetSize(C, &M, &N)); if (m == PETSC_DECIDE || n == PETSC_DECIDE || M == PETSC_DECIDE || N == PETSC_DECIDE) { PetscCall(MatGetLocalSize(B, NULL, &n)); PetscCall(MatGetSize(B, NULL, &N)); PetscCall(MatGetLocalSize(A, &m, NULL)); PetscCall(MatGetSize(A, &M, NULL)); PetscCall(MatSetSizes(C, m, n, M, N)); } PetscCall(MatSetType(C, ((PetscObject)B)->type_name)); PetscCall(MatSetUp(C)); PetscCall(PetscNew(&contents)); C->product->data = contents; C->product->destroy = MatNormal_DenseDestroy; if (a->right) { PetscCall(MatProductCreate(a->A, C, NULL, contents->work)); } else { PetscCall(MatProductCreate(a->A, B, NULL, contents->work)); } PetscCall(MatProductSetType(contents->work[0], MATPRODUCT_AB)); PetscCall(MatProductSetFromOptions(contents->work[0])); PetscCall(MatProductSymbolic(contents->work[0])); PetscCall(MatProductCreate(a->A, contents->work[0], NULL, contents->work + 1)); PetscCall(MatProductSetType(contents->work[1], MATPRODUCT_AtB)); PetscCall(MatProductSetFromOptions(contents->work[1])); PetscCall(MatProductSymbolic(contents->work[1])); PetscCall(MatDenseGetArrayWrite(C, &array)); PetscCall(MatSeqDenseSetPreallocation(contents->work[1], array)); PetscCall(MatMPIDenseSetPreallocation(contents->work[1], array)); PetscCall(MatDenseRestoreArrayWrite(C, &array)); C->ops->productnumeric = MatProductNumeric_Normal_Dense; PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatProductSetFromOptions_Normal_Dense_AB(Mat C) { PetscFunctionBegin; C->ops->productsymbolic = MatProductSymbolic_Normal_Dense; PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode MatProductSetFromOptions_Normal_Dense(Mat C) { Mat_Product *product = C->product; PetscFunctionBegin; if (product->type == MATPRODUCT_AB) PetscCall(MatProductSetFromOptions_Normal_Dense_AB(C)); PetscFunctionReturn(PETSC_SUCCESS); } /*MC MATNORMAL - a matrix that behaves like A'*A for `MatMult()` while only containing A Level: intermediate .seealso: [](ch_matrices), `Mat`, `MatCreateNormal()`, `MatMult()`, `MatNormalGetMat()`, `MATNORMALHERMITIAN`, `MatCreateNormalHermitian()` M*/ /*@ MatCreateNormal - Creates a new `MATNORMAL` matrix object that behaves like A'*A. Collective Input Parameter: . A - the (possibly rectangular) matrix Output Parameter: . N - the matrix that represents A'*A Level: intermediate Notes: The product A'*A is NOT actually formed! Rather the new matrix object performs the matrix-vector product, `MatMult()`, by first multiplying by A and then A' .seealso: [](ch_matrices), `Mat`, `MATNORMAL`, `MatMult()`, `MatNormalGetMat()`, `MATNORMALHERMITIAN`, `MatCreateNormalHermitian()` @*/ PetscErrorCode MatCreateNormal(Mat A, Mat *N) { PetscInt n, nn; Mat_Normal *Na; VecType vtype; PetscFunctionBegin; PetscCall(MatGetSize(A, NULL, &nn)); PetscCall(MatGetLocalSize(A, NULL, &n)); PetscCall(MatCreate(PetscObjectComm((PetscObject)A), N)); PetscCall(MatSetSizes(*N, n, n, nn, nn)); PetscCall(PetscObjectChangeTypeName((PetscObject)*N, MATNORMAL)); PetscCall(PetscLayoutReference(A->cmap, &(*N)->rmap)); PetscCall(PetscLayoutReference(A->cmap, &(*N)->cmap)); PetscCall(PetscNew(&Na)); (*N)->data = (void *)Na; PetscCall(PetscObjectReference((PetscObject)A)); Na->A = A; Na->scale = 1.0; PetscCall(MatCreateVecs(A, NULL, &Na->w)); (*N)->ops->destroy = MatDestroy_Normal; (*N)->ops->mult = MatMult_Normal; (*N)->ops->multtranspose = MatMultTranspose_Normal; (*N)->ops->multtransposeadd = MatMultTransposeAdd_Normal; (*N)->ops->multadd = MatMultAdd_Normal; (*N)->ops->getdiagonal = MatGetDiagonal_Normal; (*N)->ops->getdiagonalblock = MatGetDiagonalBlock_Normal; (*N)->ops->scale = MatScale_Normal; (*N)->ops->diagonalscale = MatDiagonalScale_Normal; (*N)->ops->increaseoverlap = MatIncreaseOverlap_Normal; (*N)->ops->createsubmatrices = MatCreateSubMatrices_Normal; (*N)->ops->permute = MatPermute_Normal; (*N)->ops->duplicate = MatDuplicate_Normal; (*N)->ops->copy = MatCopy_Normal; (*N)->assembled = PETSC_TRUE; (*N)->preallocated = PETSC_TRUE; PetscCall(PetscObjectComposeFunction((PetscObject)(*N), "MatNormalGetMat_C", MatNormalGetMat_Normal)); PetscCall(PetscObjectComposeFunction((PetscObject)(*N), "MatConvert_normal_seqaij_C", MatConvert_Normal_AIJ)); PetscCall(PetscObjectComposeFunction((PetscObject)(*N), "MatConvert_normal_mpiaij_C", MatConvert_Normal_AIJ)); #if defined(PETSC_HAVE_HYPRE) PetscCall(PetscObjectComposeFunction((PetscObject)(*N), "MatConvert_normal_hypre_C", MatConvert_Normal_HYPRE)); #endif PetscCall(PetscObjectComposeFunction((PetscObject)(*N), "MatProductSetFromOptions_normal_seqdense_C", MatProductSetFromOptions_Normal_Dense)); PetscCall(PetscObjectComposeFunction((PetscObject)(*N), "MatProductSetFromOptions_normal_mpidense_C", MatProductSetFromOptions_Normal_Dense)); PetscCall(PetscObjectComposeFunction((PetscObject)(*N), "MatProductSetFromOptions_normal_dense_C", MatProductSetFromOptions_Normal_Dense)); PetscCall(MatSetOption(*N, MAT_SYMMETRIC, PETSC_TRUE)); PetscCall(MatGetVecType(A, &vtype)); PetscCall(MatSetVecType(*N, vtype)); #if defined(PETSC_HAVE_DEVICE) PetscCall(MatBindToCPU(*N, A->boundtocpu)); #endif PetscFunctionReturn(PETSC_SUCCESS); }