/* Defines the basic matrix operations for the SBAIJ (compressed row) matrix storage format. */ #include <../src/mat/impls/baij/seq/baij.h> /*I "petscmat.h" I*/ #include <../src/mat/impls/sbaij/seq/sbaij.h> #include #include <../src/mat/impls/sbaij/seq/relax.h> #define USESHORT #include <../src/mat/impls/sbaij/seq/relax.h> extern PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat,PetscBool); #if defined(PETSC_HAVE_ELEMENTAL) PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_Elemental(Mat,MatType,MatReuse,Mat*); #endif /* Checks for missing diagonals */ #undef __FUNCT__ #define __FUNCT__ "MatMissingDiagonal_SeqSBAIJ" PetscErrorCode MatMissingDiagonal_SeqSBAIJ(Mat A,PetscBool *missing,PetscInt *dd) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscInt *diag,*ii = a->i,i; PetscFunctionBegin; ierr = MatMarkDiagonal_SeqSBAIJ(A);CHKERRQ(ierr); *missing = PETSC_FALSE; if (A->rmap->n > 0 && !ii) { *missing = PETSC_TRUE; if (dd) *dd = 0; ierr = PetscInfo(A,"Matrix has no entries therefore is missing diagonal\n");CHKERRQ(ierr); } else { diag = a->diag; for (i=0; imbs; i++) { if (diag[i] >= ii[i+1]) { *missing = PETSC_TRUE; if (dd) *dd = i; break; } } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatMarkDiagonal_SeqSBAIJ" PetscErrorCode MatMarkDiagonal_SeqSBAIJ(Mat A) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscInt i,j; PetscFunctionBegin; if (!a->diag) { ierr = PetscMalloc1(a->mbs,&a->diag);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)A,a->mbs*sizeof(PetscInt));CHKERRQ(ierr); a->free_diag = PETSC_TRUE; } for (i=0; imbs; i++) { a->diag[i] = a->i[i+1]; for (j=a->i[i]; ji[i+1]; j++) { if (a->j[j] == i) { a->diag[i] = j; break; } } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatGetRowIJ_SeqSBAIJ" static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *inia[],const PetscInt *inja[],PetscBool *done) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscInt i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs; PetscInt **ia = (PetscInt**)inia,**ja = (PetscInt**)inja; PetscErrorCode ierr; PetscFunctionBegin; *nn = n; if (!ia) PetscFunctionReturn(0); if (!blockcompressed) { /* malloc & create the natural set of indices */ ierr = PetscMalloc2((n+1)*bs,ia,nz*bs,ja);CHKERRQ(ierr); for (i=0; ii[i]*bs+j+oshift; } } for (i=0; ij[i]*bs+j+oshift; } } } else { /* blockcompressed */ if (oshift == 1) { /* temporarily add 1 to i and j indices */ for (i=0; ij[i]++; for (i=0; ii[i]++; } *ia = a->i; *ja = a->j; } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatRestoreRowIJ_SeqSBAIJ" static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscBool *done) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscInt i,n = a->mbs,nz = a->i[n]; PetscErrorCode ierr; PetscFunctionBegin; if (!ia) PetscFunctionReturn(0); if (!blockcompressed) { ierr = PetscFree2(*ia,*ja);CHKERRQ(ierr); } else if (oshift == 1) { /* blockcompressed */ for (i=0; ij[i]--; for (i=0; ii[i]--; } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatDestroy_SeqSBAIJ" PetscErrorCode MatDestroy_SeqSBAIJ(Mat A) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscFunctionBegin; #if defined(PETSC_USE_LOG) PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz); #endif ierr = MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);CHKERRQ(ierr); if (a->free_diag) {ierr = PetscFree(a->diag);CHKERRQ(ierr);} ierr = ISDestroy(&a->row);CHKERRQ(ierr); ierr = ISDestroy(&a->col);CHKERRQ(ierr); ierr = ISDestroy(&a->icol);CHKERRQ(ierr); ierr = PetscFree(a->idiag);CHKERRQ(ierr); ierr = PetscFree(a->inode.size);CHKERRQ(ierr); if (a->free_imax_ilen) {ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr);} ierr = PetscFree(a->solve_work);CHKERRQ(ierr); ierr = PetscFree(a->sor_work);CHKERRQ(ierr); ierr = PetscFree(a->solves_work);CHKERRQ(ierr); ierr = PetscFree(a->mult_work);CHKERRQ(ierr); ierr = PetscFree(a->saved_values);CHKERRQ(ierr); if (a->free_jshort) {ierr = PetscFree(a->jshort);CHKERRQ(ierr);} ierr = PetscFree(a->inew);CHKERRQ(ierr); ierr = MatDestroy(&a->parent);CHKERRQ(ierr); ierr = PetscFree(A->data);CHKERRQ(ierr); ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C",NULL);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C",NULL);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C",NULL);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C",NULL);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C",NULL);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqsbstrm_C",NULL);CHKERRQ(ierr); #if defined(PETSC_HAVE_ELEMENTAL) ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_elemental_C",NULL);CHKERRQ(ierr); #endif PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSetOption_SeqSBAIJ" PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool flg) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscFunctionBegin; switch (op) { case MAT_ROW_ORIENTED: a->roworiented = flg; break; case MAT_KEEP_NONZERO_PATTERN: a->keepnonzeropattern = flg; break; case MAT_NEW_NONZERO_LOCATIONS: a->nonew = (flg ? 0 : 1); break; case MAT_NEW_NONZERO_LOCATION_ERR: a->nonew = (flg ? -1 : 0); break; case MAT_NEW_NONZERO_ALLOCATION_ERR: a->nonew = (flg ? -2 : 0); break; case MAT_UNUSED_NONZERO_LOCATION_ERR: a->nounused = (flg ? -1 : 0); break; case MAT_NEW_DIAGONALS: case MAT_IGNORE_OFF_PROC_ENTRIES: case MAT_USE_HASH_TABLE: ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); break; case MAT_HERMITIAN: if (!A->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first"); if (A->cmap->n < 65536 && A->cmap->bs == 1) { A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort; } else if (A->cmap->bs == 1) { A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian; } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1"); break; case MAT_SPD: /* These options are handled directly by MatSetOption() */ break; case MAT_SYMMETRIC: case MAT_STRUCTURALLY_SYMMETRIC: case MAT_SYMMETRY_ETERNAL: /* These options are handled directly by MatSetOption() */ break; case MAT_IGNORE_LOWER_TRIANGULAR: a->ignore_ltriangular = flg; break; case MAT_ERROR_LOWER_TRIANGULAR: a->ignore_ltriangular = flg; break; case MAT_GETROW_UPPERTRIANGULAR: a->getrow_utriangular = flg; break; default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatGetRow_SeqSBAIJ" PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscFunctionBegin; if (A && !a->getrow_utriangular) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MatGetRow is not supported for SBAIJ matrix format. Getting the upper triangular part of row, run with -mat_getrow_uppertriangular, call MatSetOption(mat,MAT_GETROW_UPPERTRIANGULAR,PETSC_TRUE) or MatGetRowUpperTriangular()"); /* Get the upper triangular part of the row */ ierr = MatGetRow_SeqBAIJ_private(A,row,nz,idx,v,a->i,a->j,a->a);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatRestoreRow_SeqSBAIJ" PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) { PetscErrorCode ierr; PetscFunctionBegin; if (idx) {ierr = PetscFree(*idx);CHKERRQ(ierr);} if (v) {ierr = PetscFree(*v);CHKERRQ(ierr);} PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatGetRowUpperTriangular_SeqSBAIJ" PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscFunctionBegin; a->getrow_utriangular = PETSC_TRUE; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatRestoreRowUpperTriangular_SeqSBAIJ" PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscFunctionBegin; a->getrow_utriangular = PETSC_FALSE; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatTranspose_SeqSBAIJ" PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B) { PetscErrorCode ierr; PetscFunctionBegin; if (reuse == MAT_INITIAL_MATRIX || *B != A) { ierr = MatDuplicate(A,MAT_COPY_VALUES,B);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatView_SeqSBAIJ_ASCII" PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscInt i,j,bs = A->rmap->bs,k,l,bs2=a->bs2; PetscViewerFormat format; PetscInt *diag; PetscFunctionBegin; ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); } else if (format == PETSC_VIEWER_ASCII_MATLAB) { Mat aij; const char *matname; if (A->factortype && bs>1) { ierr = PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored with bs>1. MatView() with PETSC_VIEWER_ASCII_MATLAB is not supported and ignored!\n");CHKERRQ(ierr); PetscFunctionReturn(0); } ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);CHKERRQ(ierr); ierr = PetscObjectGetName((PetscObject)A,&matname);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)aij,matname);CHKERRQ(ierr); ierr = MatView(aij,viewer);CHKERRQ(ierr); ierr = MatDestroy(&aij);CHKERRQ(ierr); } else if (format == PETSC_VIEWER_ASCII_COMMON) { ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); for (i=0; imbs; i++) { for (j=0; ji[i]; ki[i+1]; k++) { for (l=0; la[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l, (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l, (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); } #else if (a->a[bs2*k + l*bs + j] != 0.0) { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); } #endif } } ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); } } ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { PetscFunctionReturn(0); } else { ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); if (A->factortype) { /* for factored matrix */ if (bs>1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"matrix is factored with bs>1. Not implemented yet"); diag=a->diag; for (i=0; imbs; i++) { /* for row block i */ ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); /* diagonal entry */ #if defined(PETSC_USE_COMPLEX) if (PetscImaginaryPart(a->a[diag[i]]) > 0.0) { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]),(double)PetscImaginaryPart(1.0/a->a[diag[i]]));CHKERRQ(ierr); } else if (PetscImaginaryPart(a->a[diag[i]]) < 0.0) { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]),-(double)PetscImaginaryPart(1.0/a->a[diag[i]]));CHKERRQ(ierr); } else { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]));CHKERRQ(ierr); } #else ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)(1.0/a->a[diag[i]]));CHKERRQ(ierr); #endif /* off-diagonal entries */ for (k=a->i[i]; ki[i+1]-1; k++) { #if defined(PETSC_USE_COMPLEX) if (PetscImaginaryPart(a->a[k]) > 0.0) { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),(double)PetscImaginaryPart(a->a[k]));CHKERRQ(ierr); } else if (PetscImaginaryPart(a->a[k]) < 0.0) { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),-(double)PetscImaginaryPart(a->a[k]));CHKERRQ(ierr); } else { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k],(double)PetscRealPart(a->a[k]));CHKERRQ(ierr); } #else ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[k],(double)a->a[k]);CHKERRQ(ierr); #endif } ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); } } else { /* for non-factored matrix */ for (i=0; imbs; i++) { /* for row block i */ for (j=0; ji[i]; ki[i+1]; k++) { /* for column block */ for (l=0; la[bs2*k + l*bs + j]) > 0.0) { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l, (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l, (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); } else { ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); } #else ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); #endif } } ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); } } } ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); } ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); PetscFunctionReturn(0); } #include #undef __FUNCT__ #define __FUNCT__ "MatView_SeqSBAIJ_Draw_Zoom" static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa) { Mat A = (Mat) Aa; Mat_SeqSBAIJ *a=(Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscInt row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2; PetscMPIInt rank; PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r; MatScalar *aa; MPI_Comm comm; PetscViewer viewer; PetscFunctionBegin; /* This is nasty. If this is called from an originally parallel matrix then all processes call this,but only the first has the matrix so the rest should return immediately. */ ierr = PetscObjectGetComm((PetscObject)draw,&comm);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); if (rank) PetscFunctionReturn(0); ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr); ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric"); /* loop over matrix elements drawing boxes */ color = PETSC_DRAW_BLUE; for (i=0,row=0; ii[i]; ji[i+1]; j++) { y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; x_l = a->j[j]*bs; x_r = x_l + 1.0; aa = a->a + j*bs2; for (k=0; k= 0.) continue; ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); } } } } color = PETSC_DRAW_CYAN; for (i=0,row=0; ii[i]; ji[i+1]; j++) { y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; x_l = a->j[j]*bs; x_r = x_l + 1.0; aa = a->a + j*bs2; for (k=0; ki[i]; ji[i+1]; j++) { y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; x_l = a->j[j]*bs; x_r = x_l + 1.0; aa = a->a + j*bs2; for (k=0; krmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0; xr += w; yr += h; xl = -w; yl = -h; ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr); ierr = PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",NULL);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatView_SeqSBAIJ" PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer) { PetscErrorCode ierr; PetscBool iascii,isdraw; FILE *file = 0; PetscFunctionBegin; ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); if (iascii) { ierr = MatView_SeqSBAIJ_ASCII(A,viewer);CHKERRQ(ierr); } else if (isdraw) { ierr = MatView_SeqSBAIJ_Draw(A,viewer);CHKERRQ(ierr); } else { Mat B; const char *matname; ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); ierr = PetscObjectGetName((PetscObject)A,&matname);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)B,matname);CHKERRQ(ierr); ierr = MatView(B,viewer);CHKERRQ(ierr); ierr = MatDestroy(&B);CHKERRQ(ierr); ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); if (file) { fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs); } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatGetValues_SeqSBAIJ" PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[]) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j; PetscInt *ai = a->i,*ailen = a->ilen; PetscInt brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2; MatScalar *ap,*aa = a->a; PetscFunctionBegin; for (k=0; k= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1); rp = aj + ai[brow]; ap = aa + bs2*ai[brow]; nrow = ailen[brow]; for (l=0; l= A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->cmap->n-1); col = in[l]; bcol = col/bs; cidx = col%bs; ridx = row%bs; high = nrow; low = 0; /* assume unsorted */ while (high-low > 5) { t = (low+high)/2; if (rp[t] > bcol) high = t; else low = t; } for (i=low; i bcol) break; if (rp[i] == bcol) { *v++ = ap[bs2*i+bs*cidx+ridx]; goto finished; } } *v++ = 0.0; finished:; } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSetValuesBlocked_SeqSBAIJ" PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscInt *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1; PetscInt *imax =a->imax,*ai=a->i,*ailen=a->ilen; PetscInt *aj =a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval; PetscBool roworiented=a->roworiented; const PetscScalar *value = v; MatScalar *ap,*aa = a->a,*bap; PetscFunctionBegin; if (roworiented) stepval = (n-1)*bs; else stepval = (m-1)*bs; for (k=0; k= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Block index row too large %D max %D",row,a->mbs-1); #endif rp = aj + ai[row]; ap = aa + bs2*ai[row]; rmax = imax[row]; nrow = ailen[row]; low = 0; high = nrow; for (l=0; l= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Block index column too large %D max %D",col,a->nbs-1); #endif if (col < row) { if (a->ignore_ltriangular) continue; /* ignore lower triangular block */ else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Lower triangular value cannot be set for sbaij format. Ignoring these values, run with -mat_ignore_lower_triangular or call MatSetOption(mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE)"); } if (roworiented) value = v + k*(stepval+bs)*bs + l*bs; else value = v + l*(stepval+bs)*bs + k*bs; if (col <= lastcol) low = 0; else high = nrow; lastcol = col; while (high-low > 7) { t = (low+high)/2; if (rp[t] > col) high = t; else low = t; } for (i=low; i col) break; if (rp[i] == col) { bap = ap + bs2*i; if (roworiented) { if (is == ADD_VALUES) { for (ii=0; iimbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); N = nrow++ - 1; high++; /* shift up all the later entries in this row */ for (ii=N; ii>=i; ii--) { rp[ii+1] = rp[ii]; ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); } if (N >= i) { ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); } rp[i] = col; bap = ap + bs2*i; if (roworiented) { for (ii=0; iidata; PetscErrorCode ierr; const PetscInt *ai = a->i, *aj = a->j,*cols; PetscInt i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts; PetscBool flag; PetscFunctionBegin; ierr = PetscMalloc1(m,&ns);CHKERRQ(ierr); while (i < m) { nzx = ai[i+1] - ai[i]; /* Number of nonzeros */ /* Limits the number of elements in a node to 'a->inode.limit' */ for (j=i+1,blk_size=1; jinode.limit; ++j,++blk_size) { nzy = ai[j+1] - ai[j]; if (nzy != (nzx - j + i)) break; ierr = PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);CHKERRQ(ierr); if (!flag) break; } ns[node_count++] = blk_size; i = j; } if (!a->inode.size && m && node_count > .9*m) { ierr = PetscFree(ns);CHKERRQ(ierr); ierr = PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);CHKERRQ(ierr); } else { a->inode.node_count = node_count; ierr = PetscMalloc1(node_count,&a->inode.size);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)A,node_count*sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscFree(ns);CHKERRQ(ierr); ierr = PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);CHKERRQ(ierr); /* count collections of adjacent columns in each inode */ row = 0; cnt = 0; for (i=0; iinode.size[i]; nz = ai[row+1] - ai[row] - a->inode.size[i]; for (j=1; jinode.size[i]; } ierr = PetscMalloc1(2*cnt,&counts);CHKERRQ(ierr); cnt = 0; row = 0; for (i=0; iinode.size[i]; counts[2*cnt] = cols[0]; nz = ai[row+1] - ai[row] - a->inode.size[i]; cnt2 = 1; for (j=1; jinode.size[i]; } ierr = PetscIntView(2*cnt,counts,0);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ" PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax; PetscInt m = A->rmap->N,*ip,N,*ailen = a->ilen; PetscInt mbs = a->mbs,bs2 = a->bs2,rmax = 0; MatScalar *aa = a->a,*ap; PetscFunctionBegin; if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); if (m) rmax = ailen[0]; for (i=1; inz = ai[mbs]; /* diagonals may have moved, reset it */ if (a->diag) { ierr = PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));CHKERRQ(ierr); } if (fshift && a->nounused == -1) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Unused space detected in matrix: %D X %D block size %D, %D unneeded", m, A->cmap->n, A->rmap->bs, fshift*bs2); ierr = PetscInfo5(A,"Matrix size: %D X %D, block size %D; storage space: %D unneeded, %D used\n",m,A->rmap->N,A->rmap->bs,fshift*bs2,a->nz*bs2);CHKERRQ(ierr); ierr = PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);CHKERRQ(ierr); ierr = PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);CHKERRQ(ierr); A->info.mallocs += a->reallocs; a->reallocs = 0; A->info.nz_unneeded = (PetscReal)fshift*bs2; a->idiagvalid = PETSC_FALSE; a->rmax = rmax; if (A->cmap->n < 65536 && A->cmap->bs == 1) { if (a->jshort && a->free_jshort) { /* when matrix data structure is changed, previous jshort must be replaced */ ierr = PetscFree(a->jshort);CHKERRQ(ierr); } ierr = PetscMalloc1(a->i[A->rmap->n],&a->jshort);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)A,a->i[A->rmap->n]*sizeof(unsigned short));CHKERRQ(ierr); for (i=0; ii[A->rmap->n]; i++) a->jshort[i] = a->j[i]; A->ops->mult = MatMult_SeqSBAIJ_1_ushort; A->ops->sor = MatSOR_SeqSBAIJ_ushort; a->free_jshort = PETSC_TRUE; } PetscFunctionReturn(0); } /* This function returns an array of flags which indicate the locations of contiguous blocks that should be zeroed. for eg: if bs = 3 and is = [0,1,2,3,5,6,7,8,9] then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)] Assume: sizes should be long enough to hold all the values. */ #undef __FUNCT__ #define __FUNCT__ "MatZeroRows_SeqSBAIJ_Check_Blocks" PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max) { PetscInt i,j,k,row; PetscBool flg; PetscFunctionBegin; for (i=0,j=0; i n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */ sizes[j] = 1; /* Also makes sure atleast 'bs' values exist for next else */ i++; } else { /* Begining of the block, so check if the complete block exists */ flg = PETSC_TRUE; for (k=1; kj input by user is ingored. */ #undef __FUNCT__ #define __FUNCT__ "MatSetValues_SeqSBAIJ" PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1; PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented; PetscInt *aj =a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol; PetscInt ridx,cidx,bs2=a->bs2; MatScalar *ap,value,*aa=a->a,*bap; PetscFunctionBegin; for (k=0; k= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1); #endif rp = aj + ai[brow]; /*ptr to beginning of column value of the row block*/ ap = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/ rmax = imax[brow]; /* maximum space allocated for this row */ nrow = ailen[brow]; /* actual length of this row */ low = 0; for (l=0; l= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->rmap->N-1); #endif col = in[l]; bcol = col/bs; /* block col number */ if (brow > bcol) { if (a->ignore_ltriangular) continue; /* ignore lower triangular values */ else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Lower triangular value cannot be set for sbaij format. Ignoring these values, run with -mat_ignore_lower_triangular or call MatSetOption(mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE)"); } ridx = row % bs; cidx = col % bs; /*row and col index inside the block */ if ((brow==bcol && ridx<=cidx) || (brow 7) { t = (low+high)/2; if (rp[t] > bcol) high = t; else low = t; } for (i=low; i bcol) break; if (rp[i] == bcol) { bap = ap + bs2*i + bs*cidx + ridx; if (is == ADD_VALUES) *bap += value; else *bap = value; /* for diag block, add/insert its symmetric element a(cidx,ridx) */ if (brow == bcol && ridx < cidx) { bap = ap + bs2*i + bs*ridx + cidx; if (is == ADD_VALUES) *bap += value; else *bap = value; } goto noinsert1; } } if (nonew == 1) goto noinsert1; if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); N = nrow++ - 1; high++; /* shift up all the later entries in this row */ for (ii=N; ii>=i; ii--) { rp[ii+1] = rp[ii]; ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); } if (N>=i) { ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); } rp[i] = bcol; ap[bs2*i + bs*cidx + ridx] = value; A->nonzerostate++; noinsert1:; low = i; } } /* end of loop over added columns */ ailen[brow] = nrow; } /* end of loop over added rows */ PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatICCFactor_SeqSBAIJ" PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)inA->data; Mat outA; PetscErrorCode ierr; PetscBool row_identity; PetscFunctionBegin; if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc"); ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr); if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported"); if (inA->rmap->bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix block size %D is not supported",inA->rmap->bs); /* Need to replace MatCholeskyFactorSymbolic_SeqSBAIJ_MSR()! */ outA = inA; inA->factortype = MAT_FACTOR_ICC; ierr = MatMarkDiagonal_SeqSBAIJ(inA);CHKERRQ(ierr); ierr = MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); ierr = ISDestroy(&a->row);CHKERRQ(ierr); a->row = row; ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); ierr = ISDestroy(&a->col);CHKERRQ(ierr); a->col = row; /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */ if (a->icol) {ierr = ISInvertPermutation(row,PETSC_DECIDE, &a->icol);CHKERRQ(ierr);} ierr = PetscLogObjectParent((PetscObject)inA,(PetscObject)a->icol);CHKERRQ(ierr); if (!a->solve_work) { ierr = PetscMalloc1(inA->rmap->N+inA->rmap->bs,&a->solve_work);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));CHKERRQ(ierr); } ierr = MatCholeskyFactorNumeric(outA,inA,info);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSeqSBAIJSetColumnIndices_SeqSBAIJ" PetscErrorCode MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices) { Mat_SeqSBAIJ *baij = (Mat_SeqSBAIJ*)mat->data; PetscInt i,nz,n; PetscErrorCode ierr; PetscFunctionBegin; nz = baij->maxnz; n = mat->cmap->n; for (i=0; ij[i] = indices[i]; baij->nz = nz; for (i=0; iilen[i] = baij->imax[i]; ierr = MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSeqSBAIJSetColumnIndices" /*@ MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows in the matrix. Input Parameters: + mat - the SeqSBAIJ matrix - indices - the column indices Level: advanced Notes: This can be called if you have precomputed the nonzero structure of the matrix and want to provide it to the matrix object to improve the performance of the MatSetValues() operation. You MUST have set the correct numbers of nonzeros per row in the call to MatCreateSeqSBAIJ(), and the columns indices MUST be sorted. MUST be called before any calls to MatSetValues() .seealso: MatCreateSeqSBAIJ @*/ PetscErrorCode MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(mat,MAT_CLASSID,1); PetscValidPointer(indices,2); ierr = PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt*),(mat,indices));CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatCopy_SeqSBAIJ" PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str) { PetscErrorCode ierr; PetscFunctionBegin; /* If the two matrices have the same copy implementation, use fast copy. */ if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; if (a->i[A->rmap->N] != b->i[B->rmap->N]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of nonzeros in two matrices are different"); ierr = PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));CHKERRQ(ierr); } else { ierr = MatGetRowUpperTriangular(A);CHKERRQ(ierr); ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); ierr = MatRestoreRowUpperTriangular(A);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSetUp_SeqSBAIJ" PetscErrorCode MatSetUp_SeqSBAIJ(Mat A) { PetscErrorCode ierr; PetscFunctionBegin; ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,A->rmap->bs,PETSC_DEFAULT,0);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSeqSBAIJGetArray_SeqSBAIJ" PetscErrorCode MatSeqSBAIJGetArray_SeqSBAIJ(Mat A,PetscScalar *array[]) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscFunctionBegin; *array = a->a; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSeqSBAIJRestoreArray_SeqSBAIJ" PetscErrorCode MatSeqSBAIJRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[]) { PetscFunctionBegin; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatAXPYGetPreallocation_SeqSBAIJ" PetscErrorCode MatAXPYGetPreallocation_SeqSBAIJ(Mat Y,Mat X,PetscInt *nnz) { PetscInt bs = Y->rmap->bs,mbs = Y->rmap->N/bs; Mat_SeqSBAIJ *x = (Mat_SeqSBAIJ*)X->data; Mat_SeqSBAIJ *y = (Mat_SeqSBAIJ*)Y->data; PetscErrorCode ierr; PetscFunctionBegin; /* Set the number of nonzeros in the new matrix */ ierr = MatAXPYGetPreallocation_SeqX_private(mbs,x->i,x->j,y->i,y->j,nnz);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatAXPY_SeqSBAIJ" PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) { Mat_SeqSBAIJ *x=(Mat_SeqSBAIJ*)X->data, *y=(Mat_SeqSBAIJ*)Y->data; PetscErrorCode ierr; PetscInt bs=Y->rmap->bs,bs2=bs*bs; PetscBLASInt one = 1; PetscFunctionBegin; if (str == SAME_NONZERO_PATTERN) { PetscScalar alpha = a; PetscBLASInt bnz; ierr = PetscBLASIntCast(x->nz*bs2,&bnz);CHKERRQ(ierr); PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ ierr = MatSetOption(X,MAT_GETROW_UPPERTRIANGULAR,PETSC_TRUE);CHKERRQ(ierr); ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); ierr = MatSetOption(X,MAT_GETROW_UPPERTRIANGULAR,PETSC_FALSE);CHKERRQ(ierr); } else { Mat B; PetscInt *nnz; if (bs != X->rmap->bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrices must have same block size"); ierr = MatGetRowUpperTriangular(X);CHKERRQ(ierr); ierr = MatGetRowUpperTriangular(Y);CHKERRQ(ierr); ierr = PetscMalloc1(Y->rmap->N,&nnz);CHKERRQ(ierr); ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); ierr = MatSetType(B,(MatType) ((PetscObject)Y)->type_name);CHKERRQ(ierr); ierr = MatAXPYGetPreallocation_SeqSBAIJ(Y,X,nnz);CHKERRQ(ierr); ierr = MatSeqSBAIJSetPreallocation(B,bs,0,nnz);CHKERRQ(ierr); ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); ierr = MatHeaderReplace(Y,B);CHKERRQ(ierr); ierr = PetscFree(nnz);CHKERRQ(ierr); ierr = MatRestoreRowUpperTriangular(X);CHKERRQ(ierr); ierr = MatRestoreRowUpperTriangular(Y);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatIsSymmetric_SeqSBAIJ" PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) { PetscFunctionBegin; *flg = PETSC_TRUE; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatIsStructurallySymmetric_SeqSBAIJ" PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool *flg) { PetscFunctionBegin; *flg = PETSC_TRUE; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatIsHermitian_SeqSBAIJ" PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) { PetscFunctionBegin; *flg = PETSC_FALSE; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatRealPart_SeqSBAIJ" PetscErrorCode MatRealPart_SeqSBAIJ(Mat A) { Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; PetscInt i,nz = a->bs2*a->i[a->mbs]; MatScalar *aa = a->a; PetscFunctionBegin; for (i=0; idata; PetscInt i,nz = a->bs2*a->i[a->mbs]; MatScalar *aa = a->a; PetscFunctionBegin; for (i=0; idata; PetscErrorCode ierr; PetscInt i,j,k,count; PetscInt bs =A->rmap->bs,bs2=baij->bs2,row,col; PetscScalar zero = 0.0; MatScalar *aa; const PetscScalar *xx; PetscScalar *bb; PetscBool *zeroed,vecs = PETSC_FALSE; PetscFunctionBegin; /* fix right hand side if needed */ if (x && b) { ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); ierr = VecGetArray(b,&bb);CHKERRQ(ierr); vecs = PETSC_TRUE; } /* zero the columns */ ierr = PetscCalloc1(A->rmap->n,&zeroed);CHKERRQ(ierr); for (i=0; i= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range",is_idx[i]); zeroed[is_idx[i]] = PETSC_TRUE; } if (vecs) { for (i=0; irmap->N; i++) { row = i/bs; for (j=baij->i[row]; ji[row+1]; j++) { for (k=0; kj[j] + k; if (col <= i) continue; aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; if (!zeroed[i] && zeroed[col]) bb[i] -= aa[0]*xx[col]; if (zeroed[i] && !zeroed[col]) bb[col] -= aa[0]*xx[i]; } } } for (i=0; irmap->N; i++) { if (!zeroed[i]) { row = i/bs; for (j=baij->i[row]; ji[row+1]; j++) { for (k=0; kj[j] + k; if (zeroed[col]) { aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; aa[0] = 0.0; } } } } } ierr = PetscFree(zeroed);CHKERRQ(ierr); if (vecs) { ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); } /* zero the rows */ for (i=0; ii[row/bs +1] - baij->i[row/bs])*bs; aa = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs); for (k=0; kops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); } } ierr = MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatShift_SeqSBAIJ" PetscErrorCode MatShift_SeqSBAIJ(Mat Y,PetscScalar a) { PetscErrorCode ierr; Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)Y->data; PetscFunctionBegin; if (!Y->preallocated || !aij->nz) { ierr = MatSeqSBAIJSetPreallocation(Y,Y->rmap->bs,1,NULL);CHKERRQ(ierr); } ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); PetscFunctionReturn(0); } /* -------------------------------------------------------------------*/ static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ, MatGetRow_SeqSBAIJ, MatRestoreRow_SeqSBAIJ, MatMult_SeqSBAIJ_N, /* 4*/ MatMultAdd_SeqSBAIJ_N, MatMult_SeqSBAIJ_N, /* transpose versions are same as non-transpose versions */ MatMultAdd_SeqSBAIJ_N, 0, 0, 0, /* 10*/ 0, 0, MatCholeskyFactor_SeqSBAIJ, MatSOR_SeqSBAIJ, MatTranspose_SeqSBAIJ, /* 15*/ MatGetInfo_SeqSBAIJ, MatEqual_SeqSBAIJ, MatGetDiagonal_SeqSBAIJ, MatDiagonalScale_SeqSBAIJ, MatNorm_SeqSBAIJ, /* 20*/ 0, MatAssemblyEnd_SeqSBAIJ, MatSetOption_SeqSBAIJ, MatZeroEntries_SeqSBAIJ, /* 24*/ 0, 0, 0, 0, 0, /* 29*/ MatSetUp_SeqSBAIJ, 0, 0, 0, 0, /* 34*/ MatDuplicate_SeqSBAIJ, 0, 0, 0, MatICCFactor_SeqSBAIJ, /* 39*/ MatAXPY_SeqSBAIJ, MatGetSubMatrices_SeqSBAIJ, MatIncreaseOverlap_SeqSBAIJ, MatGetValues_SeqSBAIJ, MatCopy_SeqSBAIJ, /* 44*/ 0, MatScale_SeqSBAIJ, MatShift_SeqSBAIJ, 0, MatZeroRowsColumns_SeqSBAIJ, /* 49*/ 0, MatGetRowIJ_SeqSBAIJ, MatRestoreRowIJ_SeqSBAIJ, 0, 0, /* 54*/ 0, 0, 0, 0, MatSetValuesBlocked_SeqSBAIJ, /* 59*/ MatGetSubMatrix_SeqSBAIJ, 0, 0, 0, 0, /* 64*/ 0, 0, 0, 0, 0, /* 69*/ MatGetRowMaxAbs_SeqSBAIJ, 0, 0, 0, 0, /* 74*/ 0, 0, 0, 0, 0, /* 79*/ 0, 0, 0, MatGetInertia_SeqSBAIJ, MatLoad_SeqSBAIJ, /* 84*/ MatIsSymmetric_SeqSBAIJ, MatIsHermitian_SeqSBAIJ, MatIsStructurallySymmetric_SeqSBAIJ, 0, 0, /* 89*/ 0, 0, 0, 0, 0, /* 94*/ 0, 0, 0, 0, 0, /* 99*/ 0, 0, 0, 0, 0, /*104*/ 0, MatRealPart_SeqSBAIJ, MatImaginaryPart_SeqSBAIJ, MatGetRowUpperTriangular_SeqSBAIJ, MatRestoreRowUpperTriangular_SeqSBAIJ, /*109*/ 0, 0, 0, 0, MatMissingDiagonal_SeqSBAIJ, /*114*/ 0, 0, 0, 0, 0, /*119*/ 0, 0, 0, 0, 0, /*124*/ 0, 0, 0, 0, 0, /*129*/ 0, 0, 0, 0, 0, /*134*/ 0, 0, 0, 0, 0, /*139*/ 0, 0, 0, 0, 0, /*144*/MatCreateMPIMatConcatenateSeqMat_SeqSBAIJ }; #undef __FUNCT__ #define __FUNCT__ "MatStoreValues_SeqSBAIJ" PetscErrorCode MatStoreValues_SeqSBAIJ(Mat mat) { Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)mat->data; PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; PetscErrorCode ierr; PetscFunctionBegin; if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); /* allocate space for values if not already there */ if (!aij->saved_values) { ierr = PetscMalloc1(nz+1,&aij->saved_values);CHKERRQ(ierr); } /* copy values over */ ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatRetrieveValues_SeqSBAIJ" PetscErrorCode MatRetrieveValues_SeqSBAIJ(Mat mat) { Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)mat->data; PetscErrorCode ierr; PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; PetscFunctionBegin; if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first"); /* copy values over */ ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSeqSBAIJSetPreallocation_SeqSBAIJ" PetscErrorCode MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz) { Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; PetscErrorCode ierr; PetscInt i,mbs,nbs,bs2; PetscBool skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE; PetscFunctionBegin; if (nz >= 0 || nnz) realalloc = PETSC_TRUE; B->preallocated = PETSC_TRUE; ierr = MatSetBlockSize(B,PetscAbs(bs));CHKERRQ(ierr); ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); mbs = B->rmap->N/bs; nbs = B->cmap->n/bs; bs2 = bs*bs; if (mbs*bs != B->rmap->N || nbs*bs!=B->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize"); if (nz == MAT_SKIP_ALLOCATION) { skipallocation = PETSC_TRUE; nz = 0; } if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3; if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz); if (nnz) { for (i=0; i nbs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than block row length: local row %D value %D block rowlength %D",i,nnz[i],nbs); } } B->ops->mult = MatMult_SeqSBAIJ_N; B->ops->multadd = MatMultAdd_SeqSBAIJ_N; B->ops->multtranspose = MatMult_SeqSBAIJ_N; B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N; ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);CHKERRQ(ierr); if (!flg) { switch (bs) { case 1: B->ops->mult = MatMult_SeqSBAIJ_1; B->ops->multadd = MatMultAdd_SeqSBAIJ_1; B->ops->multtranspose = MatMult_SeqSBAIJ_1; B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1; break; case 2: B->ops->mult = MatMult_SeqSBAIJ_2; B->ops->multadd = MatMultAdd_SeqSBAIJ_2; B->ops->multtranspose = MatMult_SeqSBAIJ_2; B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2; break; case 3: B->ops->mult = MatMult_SeqSBAIJ_3; B->ops->multadd = MatMultAdd_SeqSBAIJ_3; B->ops->multtranspose = MatMult_SeqSBAIJ_3; B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3; break; case 4: B->ops->mult = MatMult_SeqSBAIJ_4; B->ops->multadd = MatMultAdd_SeqSBAIJ_4; B->ops->multtranspose = MatMult_SeqSBAIJ_4; B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4; break; case 5: B->ops->mult = MatMult_SeqSBAIJ_5; B->ops->multadd = MatMultAdd_SeqSBAIJ_5; B->ops->multtranspose = MatMult_SeqSBAIJ_5; B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5; break; case 6: B->ops->mult = MatMult_SeqSBAIJ_6; B->ops->multadd = MatMultAdd_SeqSBAIJ_6; B->ops->multtranspose = MatMult_SeqSBAIJ_6; B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6; break; case 7: B->ops->mult = MatMult_SeqSBAIJ_7; B->ops->multadd = MatMultAdd_SeqSBAIJ_7; B->ops->multtranspose = MatMult_SeqSBAIJ_7; B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7; break; } } b->mbs = mbs; b->nbs = nbs; if (!skipallocation) { if (!b->imax) { ierr = PetscMalloc2(mbs,&b->imax,mbs,&b->ilen);CHKERRQ(ierr); b->free_imax_ilen = PETSC_TRUE; ierr = PetscLogObjectMemory((PetscObject)B,2*mbs*sizeof(PetscInt));CHKERRQ(ierr); } if (!nnz) { if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5; else if (nz <= 0) nz = 1; for (i=0; iimax[i] = nz; nz = nz*mbs; /* total nz */ } else { nz = 0; for (i=0; iimax[i] = nnz[i]; nz += nnz[i];} } /* b->ilen will count nonzeros in each block row so far. */ for (i=0; iilen[i] = 0; /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */ /* allocate the matrix space */ ierr = MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);CHKERRQ(ierr); ierr = PetscMalloc3(bs2*nz,&b->a,nz,&b->j,B->rmap->N+1,&b->i);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr); ierr = PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); ierr = PetscMemzero(b->j,nz*sizeof(PetscInt));CHKERRQ(ierr); b->singlemalloc = PETSC_TRUE; /* pointer to beginning of each row */ b->i[0] = 0; for (i=1; ii[i] = b->i[i-1] + b->imax[i-1]; b->free_a = PETSC_TRUE; b->free_ij = PETSC_TRUE; } else { b->free_a = PETSC_FALSE; b->free_ij = PETSC_FALSE; } B->rmap->bs = bs; b->bs2 = bs2; b->nz = 0; b->maxnz = nz; b->inew = 0; b->jnew = 0; b->anew = 0; b->a2anew = 0; b->permute = PETSC_FALSE; if (realalloc) {ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);} PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ" PetscErrorCode MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[], const PetscScalar V[]) { PetscInt i,j,m,nz,nz_max=0,*nnz; PetscScalar *values=0; PetscBool roworiented = ((Mat_SeqSBAIJ*)B->data)->roworiented; PetscErrorCode ierr; PetscFunctionBegin; if (bs < 1) SETERRQ1(PetscObjectComm((PetscObject)B),PETSC_ERR_ARG_OUTOFRANGE,"Invalid block size specified, must be positive but it is %D",bs); ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); m = B->rmap->n/bs; if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]); ierr = PetscMalloc1(m+1,&nnz);CHKERRQ(ierr); for (i=0; irmap->bs; PetscFunctionBegin; ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);CHKERRQ(ierr); if (flg) bs = 8; if (!natural) { switch (bs) { case 1: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace; break; case 2: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2; break; case 3: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3; break; case 4: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4; break; case 5: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5; break; case 6: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6; break; case 7: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7; break; default: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N; break; } } else { switch (bs) { case 1: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace; break; case 2: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering; break; case 3: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering; break; case 4: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering; break; case 5: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering; break; case 6: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering; break; case 7: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering; break; default: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering; break; } } PetscFunctionReturn(0); } PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*); PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*); #undef __FUNCT__ #define __FUNCT__ "MatGetFactor_seqsbaij_petsc" PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B) { PetscInt n = A->rmap->n; PetscErrorCode ierr; PetscFunctionBegin; #if defined(PETSC_USE_COMPLEX) if (A->hermitian) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported"); #endif ierr = MatCreate(PetscObjectComm((PetscObject)A),B);CHKERRQ(ierr); ierr = MatSetSizes(*B,n,n,n,n);CHKERRQ(ierr); if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { ierr = MatSetType(*B,MATSEQSBAIJ);CHKERRQ(ierr); ierr = MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,NULL);CHKERRQ(ierr); (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ; (*B)->ops->iccfactorsymbolic = MatICCFactorSymbolic_SeqSBAIJ; } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported"); (*B)->factortype = ftype; PetscFunctionReturn(0); } /*MC MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices, based on block compressed sparse row format. Only the upper triangular portion of the matrix is stored. For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd() Options Database Keys: . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions() Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use the options database -mat_ignore_lower_triangular false it will generate an error if you try to set a value in the lower triangular portion. Level: beginner .seealso: MatCreateSeqSBAIJ M*/ PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*); #undef __FUNCT__ #define __FUNCT__ "MatCreate_SeqSBAIJ" PETSC_EXTERN PetscErrorCode MatCreate_SeqSBAIJ(Mat B) { Mat_SeqSBAIJ *b; PetscErrorCode ierr; PetscMPIInt size; PetscBool no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE; PetscFunctionBegin; ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1"); ierr = PetscNewLog(B,&b);CHKERRQ(ierr); B->data = (void*)b; ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); B->ops->destroy = MatDestroy_SeqSBAIJ; B->ops->view = MatView_SeqSBAIJ; b->row = 0; b->icol = 0; b->reallocs = 0; b->saved_values = 0; b->inode.limit = 5; b->inode.max_limit = 5; b->roworiented = PETSC_TRUE; b->nonew = 0; b->diag = 0; b->solve_work = 0; b->mult_work = 0; B->spptr = 0; B->info.nz_unneeded = (PetscReal)b->maxnz*b->bs2; b->keepnonzeropattern = PETSC_FALSE; b->inew = 0; b->jnew = 0; b->anew = 0; b->a2anew = 0; b->permute = PETSC_FALSE; b->ignore_ltriangular = PETSC_TRUE; ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,NULL);CHKERRQ(ierr); b->getrow_utriangular = PETSC_FALSE; ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,NULL);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqSBAIJ);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqSBAIJ);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",MatSeqSBAIJSetColumnIndices_SeqSBAIJ);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",MatConvert_SeqSBAIJ_SeqAIJ);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",MatConvert_SeqSBAIJ_SeqBAIJ);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",MatSeqSBAIJSetPreallocation_SeqSBAIJ);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocationCSR_C",MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ);CHKERRQ(ierr); ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C",MatConvert_SeqSBAIJ_SeqSBSTRM);CHKERRQ(ierr); #if defined(PETSC_HAVE_ELEMENTAL) ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_elemental_C",MatConvert_SeqSBAIJ_Elemental);CHKERRQ(ierr); #endif B->symmetric = PETSC_TRUE; B->structurally_symmetric = PETSC_TRUE; B->symmetric_set = PETSC_TRUE; B->structurally_symmetric_set = PETSC_TRUE; ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);CHKERRQ(ierr); ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)B),((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");CHKERRQ(ierr); ierr = PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",NULL,no_unroll,&no_unroll,NULL);CHKERRQ(ierr); if (no_unroll) { ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");CHKERRQ(ierr); } ierr = PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",NULL,no_inode,&no_inode,NULL);CHKERRQ(ierr); if (no_inode) { ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");CHKERRQ(ierr); } ierr = PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",NULL,b->inode.limit,&b->inode.limit,NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); b->inode.use = (PetscBool)(!(no_unroll || no_inode)); if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSeqSBAIJSetPreallocation" /*@C MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block compressed row) format. For good matrix assembly performance the user should preallocate the matrix storage by setting the parameter nz (or the array nnz). By setting these parameters accurately, performance during matrix assembly can be increased by more than a factor of 50. Collective on Mat Input Parameters: + B - the symmetric matrix . bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs() . nz - number of block nonzeros per block row (same for all rows) - nnz - array containing the number of block nonzeros in the upper triangular plus diagonal portion of each block (possibly different for each block row) or NULL Options Database Keys: . -mat_no_unroll - uses code that does not unroll the loops in the block calculations (much slower) . -mat_block_size - size of the blocks to use (only works if a negative bs is passed in Level: intermediate Notes: Specify the preallocated storage with either nz or nnz (not both). Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory allocation. See Users-Manual: ch_mat for details. You can call MatGetInfo() to get information on how effective the preallocation was; for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; You can also run with the option -info and look for messages with the string malloc in them to see if additional memory allocation was needed. If the nnz parameter is given then the nz parameter is ignored .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() @*/ PetscErrorCode MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[]) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(B,MAT_CLASSID,1); PetscValidType(B,1); PetscValidLogicalCollectiveInt(B,bs,2); ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSeqSBAIJSetPreallocationCSR" /*@C MatSeqSBAIJSetPreallocationCSR - Allocates memory for a sparse sequential matrix in symmetric block AIJ format. Input Parameters: + B - the matrix . i - the indices into j for the start of each local row (starts with zero) . j - the column indices for each local row (starts with zero) these must be sorted for each row - v - optional values in the matrix Level: developer Notes: The order of the entries in values is specified by the MatOption MAT_ROW_ORIENTED. For example, C programs may want to use the default MAT_ROW_ORIENTED=PETSC_TRUE and use an array v[nnz][bs][bs] where the second index is over rows within a block and the last index is over columns within a block row. Fortran programs will likely set MAT_ROW_ORIENTED=PETSC_FALSE and use a Fortran array v(bs,bs,nnz) in which the first index is over rows within a block column and the second index is over columns within a block. .keywords: matrix, block, aij, compressed row, sparse .seealso: MatCreate(), MatCreateSeqSBAIJ(), MatSetValuesBlocked(), MatSeqSBAIJSetPreallocation(), MATSEQSBAIJ @*/ PetscErrorCode MatSeqSBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(B,MAT_CLASSID,1); PetscValidType(B,1); PetscValidLogicalCollectiveInt(B,bs,2); ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatCreateSeqSBAIJ" /*@C MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block compressed row) format. For good matrix assembly performance the user should preallocate the matrix storage by setting the parameter nz (or the array nnz). By setting these parameters accurately, performance during matrix assembly can be increased by more than a factor of 50. Collective on MPI_Comm Input Parameters: + comm - MPI communicator, set to PETSC_COMM_SELF . bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs() . m - number of rows, or number of columns . nz - number of block nonzeros per block row (same for all rows) - nnz - array containing the number of block nonzeros in the upper triangular plus diagonal portion of each block (possibly different for each block row) or NULL Output Parameter: . A - the symmetric matrix Options Database Keys: . -mat_no_unroll - uses code that does not unroll the loops in the block calculations (much slower) . -mat_block_size - size of the blocks to use Level: intermediate It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), MatXXXXSetPreallocation() paradgm instead of this routine directly. [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] Notes: The number of rows and columns must be divisible by blocksize. This matrix type does not support complex Hermitian operation. Specify the preallocated storage with either nz or nnz (not both). Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory allocation. See Users-Manual: ch_mat for details. If the nnz parameter is given then the nz parameter is ignored .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() @*/ PetscErrorCode MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A) { PetscErrorCode ierr; PetscFunctionBegin; ierr = MatCreate(comm,A);CHKERRQ(ierr); ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); ierr = MatSetType(*A,MATSEQSBAIJ);CHKERRQ(ierr); ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatDuplicate_SeqSBAIJ" PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B) { Mat C; Mat_SeqSBAIJ *c,*a = (Mat_SeqSBAIJ*)A->data; PetscErrorCode ierr; PetscInt i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2; PetscFunctionBegin; if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix"); *B = 0; ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr); ierr = MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);CHKERRQ(ierr); ierr = MatSetType(C,MATSEQSBAIJ);CHKERRQ(ierr); ierr = PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); c = (Mat_SeqSBAIJ*)C->data; C->preallocated = PETSC_TRUE; C->factortype = A->factortype; c->row = 0; c->icol = 0; c->saved_values = 0; c->keepnonzeropattern = a->keepnonzeropattern; C->assembled = PETSC_TRUE; ierr = PetscLayoutReference(A->rmap,&C->rmap);CHKERRQ(ierr); ierr = PetscLayoutReference(A->cmap,&C->cmap);CHKERRQ(ierr); c->bs2 = a->bs2; c->mbs = a->mbs; c->nbs = a->nbs; if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { c->imax = a->imax; c->ilen = a->ilen; c->free_imax_ilen = PETSC_FALSE; } else { ierr = PetscMalloc2((mbs+1),&c->imax,(mbs+1),&c->ilen);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)C,2*(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); for (i=0; iimax[i] = a->imax[i]; c->ilen[i] = a->ilen[i]; } c->free_imax_ilen = PETSC_TRUE; } /* allocate the matrix space */ if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { ierr = PetscMalloc1(bs2*nz,&c->a);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)C,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); c->i = a->i; c->j = a->j; c->singlemalloc = PETSC_FALSE; c->free_a = PETSC_TRUE; c->free_ij = PETSC_FALSE; c->parent = A; ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr); ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); } else { ierr = PetscMalloc3(bs2*nz,&c->a,nz,&c->j,mbs+1,&c->i);CHKERRQ(ierr); ierr = PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));CHKERRQ(ierr); c->singlemalloc = PETSC_TRUE; c->free_a = PETSC_TRUE; c->free_ij = PETSC_TRUE; } if (mbs > 0) { if (cpvalues != MAT_SHARE_NONZERO_PATTERN) { ierr = PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));CHKERRQ(ierr); } if (cpvalues == MAT_COPY_VALUES) { ierr = PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); } else { ierr = PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); } if (a->jshort) { /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */ /* if the parent matrix is reassembled, this child matrix will never notice */ ierr = PetscMalloc1(nz,&c->jshort);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)C,nz*sizeof(unsigned short));CHKERRQ(ierr); ierr = PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));CHKERRQ(ierr); c->free_jshort = PETSC_TRUE; } } c->roworiented = a->roworiented; c->nonew = a->nonew; if (a->diag) { if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { c->diag = a->diag; c->free_diag = PETSC_FALSE; } else { ierr = PetscMalloc1(mbs,&c->diag);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)C,mbs*sizeof(PetscInt));CHKERRQ(ierr); for (i=0; idiag[i] = a->diag[i]; c->free_diag = PETSC_TRUE; } } c->nz = a->nz; c->maxnz = a->nz; /* Since we allocate exactly the right amount */ c->solve_work = 0; c->mult_work = 0; *B = C; ierr = PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatLoad_SeqSBAIJ" PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer) { Mat_SeqSBAIJ *a; PetscErrorCode ierr; int fd; PetscMPIInt size; PetscInt i,nz,header[4],*rowlengths=0,M,N,bs = newmat->rmap->bs; PetscInt *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount; PetscInt kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols; PetscInt *masked,nmask,tmp,bs2,ishift; PetscScalar *aa; MPI_Comm comm; PetscFunctionBegin; /* force binary viewer to load .info file if it has not yet done so */ ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); ierr = PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,NULL);CHKERRQ(ierr); if (bs < 0) bs = 1; bs2 = bs*bs; ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor"); ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr); if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object"); M = header[1]; N = header[2]; nz = header[3]; if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ"); if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices"); /* This code adds extra rows to make sure the number of rows is divisible by the blocksize */ mbs = M/bs; extra_rows = bs - M + bs*(mbs); if (extra_rows == bs) extra_rows = 0; else mbs++; if (extra_rows) { ierr = PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");CHKERRQ(ierr); } /* Set global sizes if not already set */ if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) { ierr = MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);CHKERRQ(ierr); } else { /* Check if the matrix global sizes are correct */ ierr = MatGetSize(newmat,&rows,&cols);CHKERRQ(ierr); if (M != rows || N != cols) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix in file of different length (%d, %d) than the input matrix (%d, %d)",M,N,rows,cols); } /* read in row lengths */ ierr = PetscMalloc1(M+extra_rows,&rowlengths);CHKERRQ(ierr); ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); for (i=0; i= i) {masked[nmask++] = tmp; mask[tmp] = 1;} } rowcount++; } s_browlengths[i] += nmask; /* zero out the mask elements we set */ for (j=0; jdata; /* set matrix "i" values */ a->i[0] = 0; for (i=1; i<= mbs; i++) { a->i[i] = a->i[i-1] + s_browlengths[i-1]; a->ilen[i-1] = s_browlengths[i-1]; } a->nz = a->i[mbs]; /* read in nonzero values */ ierr = PetscMalloc1(nz+extra_rows,&aa);CHKERRQ(ierr); ierr = PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);CHKERRQ(ierr); for (i=0; i= i) { masked[nmask++] = tmp; mask[tmp] = 1;} } } /* sort the masked values */ ierr = PetscSortInt(nmask,masked);CHKERRQ(ierr); /* set "j" values into matrix */ maskcount = 1; for (j=0; jj[jcount++] = masked[j]; mask[masked[j]] = maskcount++; } /* set "a" values into matrix */ ishift = bs2*a->i[i]; for (j=0; j= i) { block = mask[tmp] - 1; point = jj[nzcountb] - bs*tmp; idx = ishift + bs2*block + j + bs*point; a->a[idx] = aa[nzcountb]; } nzcountb++; } } /* zero out the mask elements we set */ for (j=0; jnz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix"); ierr = PetscFree(rowlengths);CHKERRQ(ierr); ierr = PetscFree(s_browlengths);CHKERRQ(ierr); ierr = PetscFree(aa);CHKERRQ(ierr); ierr = PetscFree(jj);CHKERRQ(ierr); ierr = PetscFree2(mask,masked);CHKERRQ(ierr); ierr = MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatCreateSeqSBAIJWithArrays" /*@ MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements (upper triangular entries in CSR format) provided by the user. Collective on MPI_Comm Input Parameters: + comm - must be an MPI communicator of size 1 . bs - size of block . m - number of rows . n - number of columns . i - row indices . j - column indices - a - matrix values Output Parameter: . mat - the matrix Level: advanced Notes: The i, j, and a arrays are not copied by this routine, the user must free these arrays once the matrix is destroyed You cannot set new nonzero locations into this matrix, that will generate an error. The i and j indices are 0 based When block size is greater than 1 the matrix values must be stored using the SBAIJ storage format (see the SBAIJ code to determine this). For block size of 1 it is the regular CSR format excluding the lower triangular elements. .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ() @*/ PetscErrorCode MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt *i,PetscInt *j,PetscScalar *a,Mat *mat) { PetscErrorCode ierr; PetscInt ii; Mat_SeqSBAIJ *sbaij; PetscFunctionBegin; if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs); if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); ierr = MatCreate(comm,mat);CHKERRQ(ierr); ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); ierr = MatSetType(*mat,MATSEQSBAIJ);CHKERRQ(ierr); ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);CHKERRQ(ierr); sbaij = (Mat_SeqSBAIJ*)(*mat)->data; ierr = PetscMalloc2(m,&sbaij->imax,m,&sbaij->ilen);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)*mat,2*m*sizeof(PetscInt));CHKERRQ(ierr); sbaij->i = i; sbaij->j = j; sbaij->a = a; sbaij->singlemalloc = PETSC_FALSE; sbaij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/ sbaij->free_a = PETSC_FALSE; sbaij->free_ij = PETSC_FALSE; for (ii=0; iiilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii]; #if defined(PETSC_USE_DEBUG) if (i[ii+1] - i[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row length in i (row indices) row = %d length = %d",ii,i[ii+1] - i[ii]); #endif } #if defined(PETSC_USE_DEBUG) for (ii=0; iii[m]; ii++) { if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]); if (j[ii] > n - 1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column index to large at location = %d index = %d",ii,j[ii]); } #endif ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatCreateMPIMatConcatenateSeqMat_SeqSBAIJ" PetscErrorCode MatCreateMPIMatConcatenateSeqMat_SeqSBAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) { PetscErrorCode ierr; PetscFunctionBegin; ierr = MatCreateMPIMatConcatenateSeqMat_MPISBAIJ(comm,inmat,n,scall,outmat);CHKERRQ(ierr); PetscFunctionReturn(0); }