void PetscMatTools::SetOption(Mat matrix, MatOption option)
{
#if (PETSC_VERSION_MAJOR == 3) //PETSc 3.x.x
MatSetOption(matrix, option, PETSC_TRUE);
#else
MatSetOption(matrix, option);
#endif
}
EXTERN_C_END
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "MatConvert_SeqAIJ_SeqSBAIJ"
PetscErrorCode PETSCMAT_DLLEXPORT MatConvert_SeqAIJ_SeqSBAIJ(Mat A,const MatType newtype,MatReuse reuse,Mat *newmat) {
Mat B;
Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
Mat_SeqSBAIJ *b;
PetscErrorCode ierr;
PetscInt *ai=a->i,*aj,m=A->rmap->N,n=A->cmap->N,i,j,*bi,*bj,*rowlengths;
MatScalar *av,*bv;
PetscFunctionBegin;
if (n != m) SETERRQ(PETSC_ERR_ARG_WRONG,"Matrix must be square");
ierr = PetscMalloc(m*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr);
for (i=0; i<m; i++) {
rowlengths[i] = ai[i+1] - a->diag[i];
}
ierr = MatCreate(((PetscObject)A)->comm,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,m,n,m,n);CHKERRQ(ierr);
ierr = MatSetType(B,newtype);CHKERRQ(ierr);
ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(B,1,0,rowlengths);CHKERRQ(ierr);
ierr = MatSetOption(B,MAT_ROW_ORIENTED,PETSC_TRUE);CHKERRQ(ierr);
b = (Mat_SeqSBAIJ*)(B->data);
bi = b->i;
bj = b->j;
bv = b->a;
bi[0] = 0;
for (i=0; i<m; i++) {
aj = a->j + a->diag[i];
av = a->a + a->diag[i];
for (j=0; j<rowlengths[i]; j++){
*bj = *aj; bj++; aj++;
*bv = *av; bv++; av++;
}
bi[i+1] = bi[i] + rowlengths[i];
b->ilen[i] = rowlengths[i];
}
ierr = PetscFree(rowlengths);CHKERRQ(ierr);
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (A->hermitian){
ierr = MatSetOption(B,MAT_HERMITIAN,PETSC_TRUE);CHKERRQ(ierr);
}
if (reuse == MAT_REUSE_MATRIX) {
ierr = MatHeaderReplace(A,B);CHKERRQ(ierr);
} else {
*newmat = B;
}
PetscFunctionReturn(0);
}
/*
MatConvert_Basic - Converts from any input format to another format. For
parallel formats, the new matrix distribution is determined by PETSc.
Does not do preallocation so in general will be slow
*/
PETSC_INTERN PetscErrorCode MatConvert_Basic(Mat mat, MatType newtype,MatReuse reuse,Mat *newmat)
{
Mat M;
const PetscScalar *vwork;
PetscErrorCode ierr;
PetscInt nz,i,m,n,rstart,rend,lm,ln;
const PetscInt *cwork;
PetscBool isSBAIJ;
PetscFunctionBegin;
ierr = PetscObjectTypeCompare((PetscObject)mat,MATSEQSBAIJ,&isSBAIJ);CHKERRQ(ierr);
if (!isSBAIJ) {
ierr = PetscObjectTypeCompare((PetscObject)mat,MATMPISBAIJ,&isSBAIJ);CHKERRQ(ierr);
}
if (isSBAIJ) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot convert from SBAIJ matrix since cannot obtain entire rows of matrix");
ierr = MatGetSize(mat,&m,&n);CHKERRQ(ierr);
ierr = MatGetLocalSize(mat,&lm,&ln);CHKERRQ(ierr);
if (ln == n) ln = PETSC_DECIDE; /* try to preserve column ownership */
ierr = MatCreate(PetscObjectComm((PetscObject)mat),&M);CHKERRQ(ierr);
ierr = MatSetSizes(M,lm,ln,m,n);CHKERRQ(ierr);
ierr = MatSetBlockSizesFromMats(M,mat,mat);CHKERRQ(ierr);
ierr = MatSetType(M,newtype);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(M,NULL);CHKERRQ(ierr);
ierr = MatMPIDenseSetPreallocation(M,NULL);CHKERRQ(ierr);
ierr = MatSetUp(M);CHKERRQ(ierr);
ierr = MatSetOption(M,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatSetOption(M,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)M,MATSEQSBAIJ,&isSBAIJ);CHKERRQ(ierr);
if (!isSBAIJ) {
ierr = PetscObjectTypeCompare((PetscObject)M,MATMPISBAIJ,&isSBAIJ);CHKERRQ(ierr);
}
if (isSBAIJ) {
ierr = MatSetOption(M,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = MatGetOwnershipRange(mat,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
ierr = MatGetRow(mat,i,&nz,&cwork,&vwork);CHKERRQ(ierr);
ierr = MatSetValues(M,1,&i,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatRestoreRow(mat,i,&nz,&cwork,&vwork);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (reuse == MAT_INPLACE_MATRIX) {
ierr = MatHeaderReplace(mat,&M);CHKERRQ(ierr);
} else {
*newmat = M;
}
PetscFunctionReturn(0);
}
PetscErrorCode AssemblePressureMatrx( UserContext* uc )
{
PetscErrorCode ierr;
PetscScalar val[5];
PetscInt i, j;
BCNode *bcn;
Node *n;
PetscFunctionBegin;
ierr = MatCreate(PETSC_COMM_WORLD, &uc->A); CHKERRQ(ierr);
ierr = MatSetSizes(uc->A, PETSC_DECIDE, PETSC_DECIDE, uc->numNodes, uc->numNodes); CHKERRQ(ierr);
ierr = MatSetType(uc->A, MATUMFPACK); CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(uc->A, 5, PETSC_NULL); CHKERRQ(ierr);
// ierr = MatCreateSeqSBAIJ(PETSC_COMM_WORLD,1,uc->numNodes, uc->numNodes,3, PETSC_NULL, &uc->A); CHKERRQ(ierr);
// ierr = MatSetOption(uc->A, MAT_SYMMETRIC); CHKERRQ(ierr);
// ierr = MatSetOption(uc->A, MAT_USE_INODES); CHKERRQ(ierr);
// ierr = MatSetOption(uc->A, MAT_IGNORE_LOWER_TRIANGULAR); CHKERRQ(ierr);
for (i = 0; i < uc->numNodes; ++i)
{
n = &uc->nodes[i];
for (j = 0; j < n->numNei; ++j)
{
val[j] = negone;
}
val[n->numNei] = n->numNei;
ierr = MatSetValues(uc->A, 1, &i, n->numNei+1, n->nei, val, INSERT_VALUES); CHKERRQ(ierr);
}
PetscInt idx;
for( i = 0; i < uc->numBC; ++i)
{
idx = uc->imageToNode[uc->bcToImage[i]];
n = &uc->nodes[idx];
for( j = 0; j < n->numNei; ++j)
{
ierr = MatSetValue(uc->A, idx, n->nei[j], zero, INSERT_VALUES); CHKERRQ(ierr);
ierr = MatSetValue(uc->A, n->nei[j], idx, zero, INSERT_VALUES); CHKERRQ(ierr);
}
ierr = MatSetValue(uc->A, idx, idx, one, INSERT_VALUES); CHKERRQ(ierr);
}
ierr = MatSetOption(uc->A, MAT_NEW_NONZERO_LOCATION_ERR); CHKERRQ(ierr);
ierr = MatSetOption(uc->A, MAT_NO_NEW_NONZERO_LOCATIONS); CHKERRQ(ierr);
ierr = MatAssemblyBegin(uc->A, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(uc->A, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatStoreValues(uc->A); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
MatSetFromOptions - Creates a matrix where the type is determined
from the options database. Generates a parallel MPI matrix if the
communicator has more than one processor. The default matrix type is
AIJ, using the routines MatCreateSeqAIJ() and MatCreateAIJ() if
you do not select a type in the options database.
Collective on Mat
Input Parameter:
. A - the matrix
Options Database Keys:
+ -mat_type seqaij - AIJ type, uses MatCreateSeqAIJ()
. -mat_type mpiaij - AIJ type, uses MatCreateAIJ()
. -mat_type seqdense - dense type, uses MatCreateSeqDense()
. -mat_type mpidense - dense type, uses MatCreateDense()
. -mat_type seqbaij - block AIJ type, uses MatCreateSeqBAIJ()
- -mat_type mpibaij - block AIJ type, uses MatCreateBAIJ()
Even More Options Database Keys:
See the manpages for particular formats (e.g., MatCreateSeqAIJ())
for additional format-specific options.
Level: beginner
.keywords: matrix, create
.seealso: MatCreateSeqAIJ((), MatCreateAIJ(),
MatCreateSeqDense(), MatCreateDense(),
MatCreateSeqBAIJ(), MatCreateBAIJ(),
MatCreateSeqSBAIJ(), MatCreateSBAIJ(),
MatConvert()
@*/
PetscErrorCode MatSetFromOptions(Mat B)
{
PetscErrorCode ierr;
const char *deft = MATAIJ;
char type[256];
PetscBool flg,set;
PetscFunctionBegin;
PetscValidHeaderSpecific(B,MAT_CLASSID,1);
ierr = PetscObjectOptionsBegin((PetscObject)B);CHKERRQ(ierr);
if (B->rmap->bs < 0) {
PetscInt newbs = -1;
ierr = PetscOptionsInt("-mat_block_size","Set the blocksize used to store the matrix","MatSetBlockSize",newbs,&newbs,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscLayoutSetBlockSize(B->rmap,newbs);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(B->cmap,newbs);CHKERRQ(ierr);
}
}
ierr = PetscOptionsFList("-mat_type","Matrix type","MatSetType",MatList,deft,type,256,&flg);CHKERRQ(ierr);
if (flg) {
ierr = MatSetType(B,type);CHKERRQ(ierr);
} else if (!((PetscObject)B)->type_name) {
ierr = MatSetType(B,deft);CHKERRQ(ierr);
}
ierr = PetscOptionsName("-mat_is_symmetric","Checks if mat is symmetric on MatAssemblyEnd()","MatIsSymmetric",&B->checksymmetryonassembly);CHKERRQ(ierr);
ierr = PetscOptionsReal("-mat_is_symmetric","Checks if mat is symmetric on MatAssemblyEnd()","MatIsSymmetric",0.0,&B->checksymmetrytol,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-mat_null_space_test","Checks if provided null space is correct in MatAssemblyEnd()","MatSetNullSpaceTest",PETSC_FALSE,&B->checknullspaceonassembly,NULL);CHKERRQ(ierr);
if (B->ops->setfromoptions) {
ierr = (*B->ops->setfromoptions)(B);CHKERRQ(ierr);
}
flg = PETSC_FALSE;
ierr = PetscOptionsBool("-mat_new_nonzero_location_err","Generate an error if new nonzeros are created in the matrix structure (useful to test preallocation)","MatSetOption",flg,&flg,&set);CHKERRQ(ierr);
if (set) {ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,flg);CHKERRQ(ierr);}
flg = PETSC_FALSE;
ierr = PetscOptionsBool("-mat_new_nonzero_allocation_err","Generate an error if new nonzeros are allocated in the matrix structure (useful to test preallocation)","MatSetOption",flg,&flg,&set);CHKERRQ(ierr);
if (set) {ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,flg);CHKERRQ(ierr);}
/* process any options handlers added with PetscObjectAddOptionsHandler() */
ierr = PetscObjectProcessOptionsHandlers((PetscObject)B);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode Assemble(MPI_Comm comm,PetscInt n,MatType mtype)
{
Mat A;
PetscInt first,last,i;
PetscErrorCode ierr;
PetscMPIInt rank,size;
PetscFunctionBegin;
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A, PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetType(A,MATMPISBAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
if (rank < size-1) {
ierr = MatMPISBAIJSetPreallocation(A,1,1,PETSC_NULL,1,PETSC_NULL);CHKERRQ(ierr);
} else {
ierr = MatMPISBAIJSetPreallocation(A,1,2,PETSC_NULL,0,PETSC_NULL);CHKERRQ(ierr);
}
ierr = MatGetOwnershipRange(A,&first,&last);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
last--;
for (i=first; i<=last; i++){
ierr = MatSetValue(A,i,i,2.,INSERT_VALUES);CHKERRQ(ierr);
if (i != n-1) {ierr = MatSetValue(A,i,n-1,-1.,INSERT_VALUES);CHKERRQ(ierr);}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
KSPComputeExplicitOperator - Computes the explicit preconditioned operator.
Collective on KSP
Input Parameter:
. ksp - the Krylov subspace context
Output Parameter:
. mat - the explict preconditioned operator
Notes:
This computation is done by applying the operators to columns of the
identity matrix.
Currently, this routine uses a dense matrix format when 1 processor
is used and a sparse format otherwise. This routine is costly in general,
and is recommended for use only with relatively small systems.
Level: advanced
.keywords: KSP, compute, explicit, operator
.seealso: KSPComputeEigenvaluesExplicitly(), PCComputeExplicitOperator()
@*/
PetscErrorCode KSPComputeExplicitOperator(KSP ksp,Mat *mat)
{
Vec in,out;
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt i,M,m,*rows,start,end;
Mat A;
MPI_Comm comm;
PetscScalar *array,one = 1.0;
PetscFunctionBegin;
PetscValidHeaderSpecific(ksp,KSP_CLASSID,1);
PetscValidPointer(mat,2);
comm = ((PetscObject)ksp)->comm;
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = VecDuplicate(ksp->vec_sol,&in);CHKERRQ(ierr);
ierr = VecDuplicate(ksp->vec_sol,&out);CHKERRQ(ierr);
ierr = VecGetSize(in,&M);CHKERRQ(ierr);
ierr = VecGetLocalSize(in,&m);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(in,&start,&end);CHKERRQ(ierr);
ierr = PetscMalloc(m*sizeof(PetscInt),&rows);CHKERRQ(ierr);
for (i=0; i<m; i++) {rows[i] = start + i;}
ierr = MatCreate(comm,mat);CHKERRQ(ierr);
ierr = MatSetSizes(*mat,m,m,M,M);CHKERRQ(ierr);
if (size == 1) {
ierr = MatSetType(*mat,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(*mat,PETSC_NULL);CHKERRQ(ierr);
} else {
ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(*mat,0,PETSC_NULL,0,PETSC_NULL);CHKERRQ(ierr);
}
ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
if (!ksp->pc) {ierr = KSPGetPC(ksp,&ksp->pc);CHKERRQ(ierr);}
ierr = PCGetOperators(ksp->pc,&A,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
for (i=0; i<M; i++) {
ierr = VecSet(in,0.0);CHKERRQ(ierr);
ierr = VecSetValues(in,1,&i,&one,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(in);CHKERRQ(ierr);
ierr = VecAssemblyEnd(in);CHKERRQ(ierr);
ierr = KSP_MatMult(ksp,A,in,out);CHKERRQ(ierr);
ierr = KSP_PCApply(ksp,out,in);CHKERRQ(ierr);
ierr = VecGetArray(in,&array);CHKERRQ(ierr);
ierr = MatSetValues(*mat,m,rows,1,&i,array,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecRestoreArray(in,&array);CHKERRQ(ierr);
}
ierr = PetscFree(rows);CHKERRQ(ierr);
ierr = VecDestroy(&in);CHKERRQ(ierr);
ierr = VecDestroy(&out);CHKERRQ(ierr);
ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatBlockMatSetPreallocation_BlockMat(Mat A,PetscInt bs,PetscInt nz,PetscInt *nnz)
{
Mat_BlockMat *bmat = (Mat_BlockMat*)A->data;
PetscErrorCode ierr;
PetscInt i;
PetscFunctionBegin;
ierr = PetscLayoutSetBlockSize(A->rmap,bs);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(A->cmap,bs);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr);
ierr = PetscLayoutGetBlockSize(A->rmap,&bs);CHKERRQ(ierr);
if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5;
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<A->rmap->n/bs; i++) {
if (nnz[i] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be less than 0: local row %d value %d",i,nnz[i]);
if (nnz[i] > A->cmap->n/bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than row length: local row %d value %d rowlength %d",i,nnz[i],A->cmap->n/bs);
}
}
bmat->mbs = A->rmap->n/bs;
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,bs,NULL,&bmat->right);CHKERRQ(ierr);
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,bs,NULL,&bmat->middle);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,bs,&bmat->left);CHKERRQ(ierr);
if (!bmat->imax) {
ierr = PetscMalloc2(A->rmap->n,&bmat->imax,A->rmap->n,&bmat->ilen);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)A,2*A->rmap->n*sizeof(PetscInt));CHKERRQ(ierr);
}
if (nnz) {
nz = 0;
for (i=0; i<A->rmap->n/A->rmap->bs; i++) {
bmat->imax[i] = nnz[i];
nz += nnz[i];
}
} else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Currently requires block row by row preallocation");
/* bmat->ilen will count nonzeros in each row so far. */
for (i=0; i<bmat->mbs; i++) bmat->ilen[i] = 0;
/* allocate the matrix space */
ierr = MatSeqXAIJFreeAIJ(A,(PetscScalar**)&bmat->a,&bmat->j,&bmat->i);CHKERRQ(ierr);
ierr = PetscMalloc3(nz,&bmat->a,nz,&bmat->j,A->rmap->n+1,&bmat->i);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)A,(A->rmap->n+1)*sizeof(PetscInt)+nz*(sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr);
bmat->i[0] = 0;
for (i=1; i<bmat->mbs+1; i++) {
bmat->i[i] = bmat->i[i-1] + bmat->imax[i-1];
}
bmat->singlemalloc = PETSC_TRUE;
bmat->free_a = PETSC_TRUE;
bmat->free_ij = PETSC_TRUE;
bmat->nz = 0;
bmat->maxnz = nz;
A->info.nz_unneeded = (double)bmat->maxnz;
ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode Assemble(MPI_Comm comm,PetscInt bs,const MatType mtype)
{
const PetscInt rc[] = {0,1,2,3};
const PetscScalar vals[] = {1, 2, 3, 4, 5, 6, 7, 8,
9,10,11,12,13,14,15,16,
17,18,19,20,21,22,23,24,
25,26,27,28,29,30,31,32,
33,34,35,36,37,38,39,40,
41,42,43,44,45,46,47,48,
49,50,51,52,53,54,55,56,
57,58,49,60,61,62,63,64};
Mat A;
PetscViewer viewer;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatCreate(comm,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,4*bs,4*bs);CHKERRQ(ierr);
ierr = MatSetType(A,mtype);CHKERRQ(ierr);
ierr = MatMPIBAIJSetPreallocation(A,bs,2,NULL,2,NULL);CHKERRQ(ierr);
ierr = MatMPISBAIJSetPreallocation(A,bs,2,NULL,2,NULL);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
/* All processes contribute a global matrix */
ierr = MatSetValuesBlocked(A,4,rc,4,rc,vals,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Matrix %s(%D)\n",mtype,bs);CHKERRQ(ierr);
ierr = PetscViewerASCIIGetStdout(comm,&viewer);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_ASCII_INFO_DETAIL);CHKERRQ(ierr);
ierr = MatView(A,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = MatView(A,viewer);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
RHSMatrixHeat - User-provided routine to compute the right-hand-side
matrix for the heat equation.
Input Parameters:
ts - the TS context
t - current time
global_in - global input vector
dummy - optional user-defined context, as set by TSetRHSJacobian()
Output Parameters:
AA - Jacobian matrix
BB - optionally different preconditioning matrix
str - flag indicating matrix structure
Notes:
RHSMatrixHeat computes entries for the locally owned part of the system.
- Currently, all PETSc parallel matrix formats are partitioned by
contiguous chunks of rows across the processors.
- Each processor needs to insert only elements that it owns
locally (but any non-local elements will be sent to the
appropriate processor during matrix assembly).
- Always specify global row and columns of matrix entries when
using MatSetValues(); we could alternatively use MatSetValuesLocal().
- Here, we set all entries for a particular row at once.
- Note that MatSetValues() uses 0-based row and column numbers
in Fortran as well as in C.
*/
PetscErrorCode RHSMatrixHeat(TS ts,PetscReal t,Vec X,Mat AA,Mat BB,void *ctx)
{
Mat A = AA; /* Jacobian matrix */
AppCtx *appctx = (AppCtx*)ctx; /* user-defined application context */
PetscErrorCode ierr;
PetscInt i,mstart,mend,idx[3];
PetscScalar v[3],stwo = -2./(appctx->h*appctx->h),sone = -.5*stwo;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute entries for the locally owned part of the matrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatGetOwnershipRange(A,&mstart,&mend);CHKERRQ(ierr);
/*
Set matrix rows corresponding to boundary data
*/
if (mstart == 0) { /* first processor only */
v[0] = 1.0;
ierr = MatSetValues(A,1,&mstart,1,&mstart,v,INSERT_VALUES);CHKERRQ(ierr);
mstart++;
}
if (mend == appctx->m) { /* last processor only */
mend--;
v[0] = 1.0;
ierr = MatSetValues(A,1,&mend,1,&mend,v,INSERT_VALUES);CHKERRQ(ierr);
}
/*
Set matrix rows corresponding to interior data. We construct the
matrix one row at a time.
*/
v[0] = sone; v[1] = stwo; v[2] = sone;
for (i=mstart; i<mend; i++) {
idx[0] = i-1; idx[1] = i; idx[2] = i+1;
ierr = MatSetValues(A,1,&i,3,idx,v,INSERT_VALUES);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Complete the matrix assembly process and set some options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Assemble matrix, using the 2-step process:
MatAssemblyBegin(), MatAssemblyEnd()
Computations can be done while messages are in transition
by placing code between these two statements.
*/
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/*
Set and option to indicate that we will never add a new nonzero location
to the matrix. If we do, it will generate an error.
*/
ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
return 0;
}
PetscErrorCode StokesSetupMatBlock01(Stokes *s)
{
PetscInt row, start, end, size, i, j;
PetscInt cols[5];
PetscScalar vals[5];
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* A[1] is 2N-by-N */
ierr = MatCreate(PETSC_COMM_WORLD, &s->subA[1]);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(s->subA[1],"a01_");
ierr = MatSetSizes(s->subA[1],PETSC_DECIDE,PETSC_DECIDE,2*s->nx*s->ny,s->nx*s->ny);CHKERRQ(ierr);
ierr = MatSetType(s->subA[1],MATMPIAIJ);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(s->subA[1],5,NULL,5,NULL);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(s->subA[1],&start,&end);CHKERRQ(ierr);
ierr = MatSetOption(s->subA[1],MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
for (row = start; row < end; row++) {
ierr = StokesGetPosition(s, row, &i, &j);CHKERRQ(ierr);
/* first part: rows 0 to (nx*ny-1) */
if (row < s->nx*s->ny) {
ierr = StokesStencilGradientX(s, i, j, &size, cols, vals);CHKERRQ(ierr);
}
/* second part: rows (nx*ny) to (2*nx*ny-1) */
else {
ierr = StokesStencilGradientY(s, i, j, &size, cols, vals);CHKERRQ(ierr);
}
ierr = MatSetValues(s->subA[1], 1, &row, size, cols, vals, INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(s->subA[1], MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(s->subA[1], MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode MatConvert_SeqAIJ_SeqBAIJ(Mat A,MatType newtype,MatReuse reuse,Mat *newmat)
{
Mat B;
Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
Mat_SeqBAIJ *b;
PetscErrorCode ierr;
PetscInt *ai=a->i,m=A->rmap->N,n=A->cmap->N,i,*rowlengths;
PetscFunctionBegin;
if (n != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Matrix must be square");
if (A->rmap->bs > 1) {
ierr = MatConvert_Basic(A,newtype,reuse,newmat);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
ierr = PetscMalloc1(m,&rowlengths);
CHKERRQ(ierr);
for (i=0; i<m; i++) {
rowlengths[i] = ai[i+1] - ai[i];
}
ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);
CHKERRQ(ierr);
ierr = MatSetSizes(B,m,n,m,n);
CHKERRQ(ierr);
ierr = MatSetType(B,MATSEQBAIJ);
CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation_SeqBAIJ(B,1,0,rowlengths);
CHKERRQ(ierr);
ierr = PetscFree(rowlengths);
CHKERRQ(ierr);
ierr = MatSetOption(B,MAT_ROW_ORIENTED,PETSC_TRUE);
CHKERRQ(ierr);
b = (Mat_SeqBAIJ*)(B->data);
ierr = PetscMemcpy(b->i,a->i,(m+1)*sizeof(PetscInt));
CHKERRQ(ierr);
ierr = PetscMemcpy(b->ilen,a->ilen,m*sizeof(PetscInt));
CHKERRQ(ierr);
ierr = PetscMemcpy(b->j,a->j,a->nz*sizeof(PetscInt));
CHKERRQ(ierr);
ierr = PetscMemcpy(b->a,a->a,a->nz*sizeof(MatScalar));
CHKERRQ(ierr);
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
if (reuse == MAT_REUSE_MATRIX) {
ierr = MatHeaderReplace(A,B);
CHKERRQ(ierr);
} else {
*newmat = B;
}
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
Mat A,B;
PetscInt m = 7,n,i,rstart,rend,cols[3];
PetscErrorCode ierr;
PetscScalar v[3];
PetscBool equal;
const char *eq[2];
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
n = m;
/* ------- Assemble matrix, --------- */
ierr = MatCreateAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,m,n,0,0,0,0,&A);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
if (!rstart) {
cols[0] = 0;
cols[1] = 1;
v[0] = 2.0; v[1] = -1.0;
ierr = MatSetValues(A,1,&rstart,2,cols,v,INSERT_VALUES);CHKERRQ(ierr);
rstart++;
}
if (rend == m) {
rend--;
cols[0] = rend-1;
cols[1] = rend;
v[0] = -1.0; v[1] = 2.0;
ierr = MatSetValues(A,1,&rend,2,cols,v,INSERT_VALUES);CHKERRQ(ierr);
}
v[0] = -1.0; v[1] = 2.0; v[2] = -1.0;
for (i=rstart; i<rend; i++) {
cols[0] = i-1;
cols[1] = i;
cols[2] = i+1;
ierr = MatSetValues(A,1,&i,3,cols,v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
ierr = MatEqual(A,B,&equal);
eq[0] = "not equal";
eq[1] = "equal";
ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrices are %s\n",eq[equal]);CHKERRQ(ierr);
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/*
RHSMatrixLaplacian - User-provided routine to compute the right-hand-side
matrix for the Laplacian operator
Input Parameters:
ts - the TS context
t - current time (ignored)
X - current solution (ignored)
dummy - optional user-defined context, as set by TSetRHSJacobian()
Output Parameters:
AA - Jacobian matrix
BB - optionally different matrix from which the preconditioner is built
str - flag indicating matrix structure
*/
PetscErrorCode RHSMatrixLaplaciangllDM(TS ts,PetscReal t,Vec X,Mat A,Mat BB,void *ctx)
{
PetscReal **temp;
PetscReal vv;
AppCtx *appctx = (AppCtx*)ctx; /* user-defined application context */
PetscErrorCode ierr;
PetscInt i,xs,xn,l,j;
PetscInt *rowsDM;
PetscBool flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-gll_mf",&flg,NULL);CHKERRQ(ierr);
if (!flg) {
/*
Creates the element stiffness matrix for the given gll
*/
ierr = PetscGLLElementLaplacianCreate(&appctx->SEMop.gll,&temp);CHKERRQ(ierr);
/* workarround for clang analyzer warning: Division by zero */
if (appctx->param.N <= 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Spectral element order should be > 1");
/* scale by the size of the element */
for (i=0; i<appctx->param.N; i++) {
vv=-appctx->param.mu*2.0/appctx->param.Le;
for (j=0; j<appctx->param.N; j++) temp[i][j]=temp[i][j]*vv;
}
ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = DMDAGetCorners(appctx->da,&xs,NULL,NULL,&xn,NULL,NULL);CHKERRQ(ierr);
xs = xs/(appctx->param.N-1);
xn = xn/(appctx->param.N-1);
ierr = PetscMalloc1(appctx->param.N,&rowsDM);CHKERRQ(ierr);
/*
loop over local elements
*/
for (j=xs; j<xs+xn; j++) {
for (l=0; l<appctx->param.N; l++) {
rowsDM[l] = 1+(j-xs)*(appctx->param.N-1)+l;
}
ierr = MatSetValuesLocal(A,appctx->param.N,rowsDM,appctx->param.N,rowsDM,&temp[0][0],ADD_VALUES);CHKERRQ(ierr);
}
ierr = PetscFree(rowsDM);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecReciprocal(appctx->SEMop.mass);CHKERRQ(ierr);
ierr = MatDiagonalScale(A,appctx->SEMop.mass,0);CHKERRQ(ierr);
ierr = VecReciprocal(appctx->SEMop.mass);CHKERRQ(ierr);
ierr = PetscGLLElementLaplacianDestroy(&appctx->SEMop.gll,&temp);CHKERRQ(ierr);
} else {
ierr = MatSetType(A,MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatShellSetContext(A,appctx);CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_MULT,(void (*)(void))MatMult_Laplacian);CHKERRQ(ierr);
}
return 0;
}
PetscErrorCode MatSetOption_IS(Mat A,MatOption op,PetscBool flg)
{
Mat_IS *a = (Mat_IS*)A->data;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "MatConvert_SeqBAIJ_SeqAIJ"
PetscErrorCode MatConvert_SeqBAIJ_SeqAIJ(Mat A, MatType newtype,MatReuse reuse,Mat *newmat)
{
Mat B;
Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data;
PetscErrorCode ierr;
PetscInt bs = A->rmap->bs,*ai = a->i,*aj = a->j,n = A->rmap->N/bs,i,j,k;
PetscInt *rowlengths,*rows,*cols,maxlen = 0,ncols;
MatScalar *aa = a->a;
PetscFunctionBegin;
ierr = PetscMalloc(n*bs*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr);
for (i=0; i<n; i++) {
maxlen = PetscMax(maxlen,(ai[i+1] - ai[i]));
for (j=0; j<bs; j++) {
rowlengths[i*bs+j] = bs*(ai[i+1] - ai[i]);
}
}
ierr = MatCreate(((PetscObject)A)->comm,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N);CHKERRQ(ierr);
ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(B,0,rowlengths);CHKERRQ(ierr);
ierr = MatSetOption(B,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscFree(rowlengths);CHKERRQ(ierr);
ierr = PetscMalloc(bs*sizeof(PetscInt),&rows);CHKERRQ(ierr);
ierr = PetscMalloc(bs*maxlen*sizeof(PetscInt),&cols);CHKERRQ(ierr);
for (i=0; i<n; i++) {
for (j=0; j<bs; j++) {
rows[j] = i*bs+j;
}
ncols = ai[i+1] - ai[i];
for (k=0; k<ncols; k++) {
for (j=0; j<bs; j++) {
cols[k*bs+j] = bs*(*aj) + j;
}
aj++;
}
ierr = MatSetValues(B,bs,rows,bs*ncols,cols,aa,INSERT_VALUES);CHKERRQ(ierr);
aa += ncols*bs*bs;
}
ierr = PetscFree(cols);CHKERRQ(ierr);
ierr = PetscFree(rows);CHKERRQ(ierr);
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
B->rmap->bs = A->rmap->bs;
if (reuse == MAT_REUSE_MATRIX) {
ierr = MatHeaderReplace(A,B);CHKERRQ(ierr);
} else {
*newmat = B;
}
PetscFunctionReturn(0);
}
PetscErrorCode MatShift_Basic(Mat Y,PetscScalar a)
{
PetscErrorCode ierr;
PetscInt i,start,end;
PetscScalar alpha = a;
PetscBool prevoption;
PetscFunctionBegin;
ierr = MatGetOption(Y,MAT_NO_OFF_PROC_ENTRIES,&prevoption);CHKERRQ(ierr);
ierr = MatSetOption(Y,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(Y,&start,&end);CHKERRQ(ierr);
for (i=start; i<end; i++) {
ierr = MatSetValues(Y,1,&i,1,&i,&alpha,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(Y,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Y,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatSetOption(Y,MAT_NO_OFF_PROC_ENTRIES,prevoption);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode FormRHSJacobian(TS ts,PetscReal t,Vec X,Mat Amat,Mat Pmat,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
const PetscScalar **x;
PetscInt M = user->Nspec+1,i,j,xs,xm;;
DM dm;
PetscFunctionBeginUser;
if (user->reactions) {
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = MatZeroEntries(Pmat);CHKERRQ(ierr);
ierr = MatSetOption(Pmat,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatSetOption(Pmat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOFRead(dm,X,&x);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
for (i=xs; i<xs+xm; i++) {
ierr = PetscMemcpy(user->tchemwork,x[i],(user->Nspec+1)*sizeof(x[xs][0]));CHKERRQ(ierr);
user->tchemwork[0] *= user->Tini; /* Dimensionalize temperature (first row) because that is what Tchem wants */
ierr = TC_getJacTYN(user->tchemwork,user->Nspec,user->Jdense,1);CHKERRQ(ierr);
for (j=0; j<M; j++) user->Jdense[j + 0*M] /= user->Tini; /* Non-dimensionalize first column */
for (j=0; j<M; j++) user->Jdense[0 + j*M] /= user->Tini; /* Non-dimensionalize first row */
for (j=0; j<M; j++) user->rows[j] = i*M+j;
ierr = MatSetValues(Pmat,M,user->rows,M,user->rows,user->Jdense,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = DMDAVecRestoreArrayDOFRead(dm,X,&x);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Pmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Pmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
} else {
ierr = MatZeroEntries(Pmat);CHKERRQ(ierr);
}
if (user->diffusion) {
ierr = FormDiffusionJacobian(ts,t,X,Amat,Pmat,ptr);CHKERRQ(ierr);
}
if (Amat != Pmat) {
ierr = MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode AlgJacobian(SNES snes,Vec X,Mat A,Mat B,void *ctx)
{
PetscErrorCode ierr;
Userctx *user=(Userctx*)ctx;
PetscFunctionBegin;
ierr = ResidualJacobian(snes,X,A,B,ctx);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatZeroRowsIS(A,user->is_diff,1.0,NULL,NULL);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode PadMatrix(Mat A,Vec v,PetscScalar c,Mat *B)
{
PetscErrorCode ierr;
PetscInt n = A->rmap->n,i,*cnt,*indices;
Mat_SeqAIJ *aij = (Mat_SeqAIJ*)A->data;
PetscScalar *vv;
PetscFunctionBegin;
ierr = VecGetArray(v,&vv);
CHKERRQ(ierr);
ierr = PetscMalloc(n*sizeof(PetscInt),&indices);
CHKERRQ(ierr);
for (i=0; i<n; i++) indices[i] = i;
/* determine number of nonzeros per row in the new matrix */
ierr = PetscMalloc((n+1)*sizeof(PetscInt),&cnt);
CHKERRQ(ierr);
for (i=0; i<n; i++) {
cnt[i] = aij->i[i+1] - aij->i[i] + (vv[i] != 0.0);
}
cnt[n] = 1;
for (i=0; i<n; i++) {
cnt[n] += (vv[i] != 0.0);
}
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,n+1,n+1,0,cnt,B);
CHKERRQ(ierr);
ierr = MatSetOption(*B,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE);
CHKERRQ(ierr);
/* copy over the matrix entries from the matrix and then the vector */
for (i=0; i<n; i++) {
ierr = MatSetValues(*B,1,&i,aij->i[i+1] - aij->i[i],aij->j + aij->i[i],aij->a + aij->i[i],INSERT_VALUES);
CHKERRQ(ierr);
}
ierr = MatSetValues(*B,1,&n,n,indices,vv,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatSetValues(*B,n,indices,1,&n,vv,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatSetValues(*B,1,&n,1,&n,&c,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = VecRestoreArray(v,&vv);
CHKERRQ(ierr);
ierr = PetscFree(cnt);
CHKERRQ(ierr);
ierr = PetscFree(indices);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatPreallocatorPreallocate_Preallocator(Mat mat, PetscBool fill, Mat A)
{
Mat_Preallocator *p = (Mat_Preallocator *) mat->data;
PetscInt *udnz = NULL, *uonz = NULL;
PetscInt bs;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatGetBlockSize(mat, &bs);CHKERRQ(ierr);
ierr = MatXAIJSetPreallocation(A, bs, p->dnz, p->onz, udnz, uonz);CHKERRQ(ierr);
ierr = MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode MatConvert_MPIBAIJ_MPISBAIJ(Mat A, MatType newtype,MatReuse reuse,Mat *newmat)
{
PetscErrorCode ierr;
Mat M;
Mat_MPIBAIJ *mpimat = (Mat_MPIBAIJ*)A->data;
Mat_SeqBAIJ *Aa = (Mat_SeqBAIJ*)mpimat->A->data,*Ba = (Mat_SeqBAIJ*)mpimat->B->data;
PetscInt *d_nnz,*o_nnz;
PetscInt i,j,nz;
PetscInt m,n,lm,ln;
PetscInt rstart,rend;
const PetscScalar *vwork;
const PetscInt *cwork;
PetscInt bs = A->rmap->bs;
PetscFunctionBegin;
ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&lm,&ln);CHKERRQ(ierr);
ierr = PetscMalloc2(lm/bs,&d_nnz,lm/bs,&o_nnz);CHKERRQ(ierr);
ierr = MatMarkDiagonal_SeqBAIJ(mpimat->A);CHKERRQ(ierr);
for (i=0; i<lm/bs; i++) {
d_nnz[i] = Aa->i[i+1] - Aa->diag[i];
o_nnz[i] = Ba->i[i+1] - Ba->i[i];
}
ierr = MatCreate(PetscObjectComm((PetscObject)A),&M);CHKERRQ(ierr);
ierr = MatSetSizes(M,lm,ln,m,n);CHKERRQ(ierr);
ierr = MatSetType(M,MATMPISBAIJ);CHKERRQ(ierr);
ierr = MatSeqSBAIJSetPreallocation(M,bs,0,d_nnz);CHKERRQ(ierr);
ierr = MatMPISBAIJSetPreallocation(M,bs,0,d_nnz,0,o_nnz);CHKERRQ(ierr);
ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
ierr = MatSetOption(M,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
ierr = MatGetRow(A,i,&nz,&cwork,&vwork);CHKERRQ(ierr);
j = 0;
ierr = MatSetValues(M,1,&i,nz,cwork+j,vwork+j,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatRestoreRow(A,i,&nz,&cwork,&vwork);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (reuse == MAT_REUSE_MATRIX) {
ierr = MatHeaderReplace(A,&M);CHKERRQ(ierr);
} else {
*newmat = M;
}
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat C=0;
PetscScalar v;
PetscInt Ii,J,Istart,Iend;
PetscErrorCode ierr;
PetscInt i,j,m = 3,n = 2;
PetscMPIInt size,rank;
PetscInt solve_count;
const MatType type;
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;
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);
for (solve_count=0; solve_count<3; solve_count++){
if (solve_count == 1){
ierr = MatSetType(C,MATSBAIJ);CHKERRQ(ierr);
ierr = MatSetOption(C,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE);CHKERRQ(ierr);
} else {
ierr = MatSetType(C,MATMPIDENSE);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);
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetType(C,&type);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," case %D, matrix type: %s\n",solve_count,type);
}
/* Free work space. */
ierr = MatDestroy(C);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
PetscErrorCode TestMatZeroRows_with_no_allocation(Mat A,IS is,PetscScalar diag)
{
Mat B;
PetscErrorCode ierr;
/* Now copy A into B, and test it with MatZeroRows() */
ierr = MatDuplicate(A,MAT_COPY_VALUES,&B);CHKERRQ(ierr);
/* Set this flag after assembly. This way, it affects only MatZeroRows() */
ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatZeroRowsIS(B,is,diag,0,0);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
return 0;
}
/*
RHSMatrixAdvection - User-provided routine to compute the right-hand-side
matrix for the Advection (gradient) operator.
Input Parameters:
ts - the TS context
t - current time
global_in - global input vector
dummy - optional user-defined context, as set by TSetRHSJacobian()
Output Parameters:
AA - Jacobian matrix
BB - optionally different preconditioning matrix
str - flag indicating matrix structure
*/
PetscErrorCode RHSMatrixAdvectiongllDM(TS ts,PetscReal t,Vec X,Mat A,Mat BB,void *ctx)
{
PetscReal **temp;
AppCtx *appctx = (AppCtx*)ctx; /* user-defined application context */
PetscErrorCode ierr;
PetscInt xs,xn,l,j;
PetscInt *rowsDM;
PetscBool flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-gll_mf",&flg,NULL);CHKERRQ(ierr);
if (!flg) {
/*
Creates the advection matrix for the given gll
*/
ierr = PetscGLLElementAdvectionCreate(&appctx->SEMop.gll,&temp);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = DMDAGetCorners(appctx->da,&xs,NULL,NULL,&xn,NULL,NULL);CHKERRQ(ierr);
xs = xs/(appctx->param.N-1);
xn = xn/(appctx->param.N-1);
ierr = PetscMalloc1(appctx->param.N,&rowsDM);CHKERRQ(ierr);
for (j=xs; j<xs+xn; j++) {
for (l=0; l<appctx->param.N; l++) {
rowsDM[l] = 1+(j-xs)*(appctx->param.N-1)+l;
}
ierr = MatSetValuesLocal(A,appctx->param.N,rowsDM,appctx->param.N,rowsDM,&temp[0][0],ADD_VALUES);CHKERRQ(ierr);
}
ierr = PetscFree(rowsDM);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecReciprocal(appctx->SEMop.mass);CHKERRQ(ierr);
ierr = MatDiagonalScale(A,appctx->SEMop.mass,0);CHKERRQ(ierr);
ierr = VecReciprocal(appctx->SEMop.mass);CHKERRQ(ierr);
ierr = PetscGLLElementAdvectionDestroy(&appctx->SEMop.gll,&temp);CHKERRQ(ierr);
} else {
ierr = MatSetType(A,MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatShellSetContext(A,appctx);CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_MULT,(void (*)(void))MatMult_Advection);CHKERRQ(ierr);
}
return 0;
}
void linearSystemPETSc<scalar>::preAllocateEntries()
{
if (_entriesPreAllocated) return;
if (!_isAllocated) Msg::Fatal("system must be allocated first");
int blockSize = _getBlockSizeFromParameters();
std::vector<int> nByRowDiag (_localSize), nByRowOffDiag (_localSize);
if (_sparsity.getNbRows() == 0) {
PetscInt prealloc = 500;
PetscBool set;
PetscOptionsGetInt(PETSC_NULL, "-petsc_prealloc", &prealloc, &set);
prealloc = std::min(prealloc, _localSize);
nByRowDiag.resize(0);
nByRowDiag.resize(_localSize, prealloc);
} else {
for (int i = 0; i < _localSize; i++) {
int n;
const int *r = _sparsity.getRow(i, n);
for (int j = 0; j < n; j++) {
if (r[j] >= _localRowStart && r[j] < _localRowEnd)
nByRowDiag[i] ++;
else
nByRowOffDiag[i] ++;
}
}
_sparsity.clear();
}
//MatXAIJSetPreallocation is not available in petsc < 3.3
int commSize = 1;
MPI_Comm_size(_comm, &commSize);
if (commSize == 1){
if (blockSize == 1)
_try(MatSeqAIJSetPreallocation(_a, 0, &nByRowDiag[0]));
else
_try(MatSeqBAIJSetPreallocation(_a, blockSize, 0, &nByRowDiag[0]));
}
else {
if (blockSize == 1)
_try(MatMPIAIJSetPreallocation(_a, 0, &nByRowDiag[0], 0, &nByRowOffDiag[0]));
else
_try(MatMPIBAIJSetPreallocation(_a, blockSize, 0, &nByRowDiag[0], 0, &nByRowOffDiag[0]));
}
if (blockSize > 1)
_try(MatSetOption(_a, MAT_ROW_ORIENTED, PETSC_FALSE));
_entriesPreAllocated = true;
}
/* FormJacobianLocal - Evaluates Jacobian matrix on local process patch */
PetscErrorCode FormJacobianLocal(DMDALocalInfo *info,PetscScalar **x,Mat A,Mat jac, MatStructure *str,ObsCtx *user)
{
PetscErrorCode ierr;
PetscInt i,j;
MatStencil col[5],row;
PetscReal v[5],dx,dy,oxx,oyy;
PetscFunctionBeginUser;
dx = 4.0 / (PetscReal)(info->mx-1);
dy = 4.0 / (PetscReal)(info->my-1);
oxx = 1.0 / (dx * dx);
oyy = 1.0 / (dy * dy);
for (j=info->ys; j<info->ys+info->ym; j++) {
for (i=info->xs; i<info->xs+info->xm; i++) {
row.j = j; row.i = i;
if (i == 0 || j == 0 || i == info->mx-1 || j == info->my-1) { /* boundary */
v[0] = 1.0;
ierr = MatSetValuesStencil(jac,1,&row,1,&row,v,INSERT_VALUES);CHKERRQ(ierr);
} else { /* interior grid points */
v[0] = -oyy; col[0].j = j - 1; col[0].i = i;
v[1] = -oxx; col[1].j = j; col[1].i = i - 1;
v[2] = 2.0 * (oxx + oyy); col[2].j = j; col[2].i = i;
v[3] = -oxx; col[3].j = j; col[3].i = i + 1;
v[4] = -oyy; col[4].j = j + 1; col[4].i = i;
ierr = MatSetValuesStencil(jac,1,&row,5,col,v,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
/* Assemble matrix, using the 2-step process: */
ierr = MatAssemblyBegin(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (A != jac) {
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
*str = SAME_NONZERO_PATTERN;
/* Tell the matrix we will never add a new nonzero location to the
matrix. If we do, it will generate an error. */
ierr = MatSetOption(jac,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscLogFlops(2.0*info->ym*info->xm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void PETScLinearSolver::MatrixCreate( PetscInt m, PetscInt n)
{
MatCreate(PETSC_COMM_WORLD, &A);
// TEST MatSetSizes(A, m_size_loc, PETSC_DECIDE, m, n);
MatSetSizes(A, PETSC_DECIDE, PETSC_DECIDE, m, n);
//MatSetSizes(A, m_size_loc, PETSC_DECIDE, m, n);
MatSetType(A, MATMPIAIJ);
MatSetFromOptions(A);
MatSeqAIJSetPreallocation(A, d_nz, PETSC_NULL);
MatMPIAIJSetPreallocation(A, d_nz, PETSC_NULL, o_nz, PETSC_NULL);
MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);
MatSetUp(A); // KG44 this seems to work with petsc 3.3 ..the commands below result in problems when assembling the matrix with version 3.3
MatGetOwnershipRange(A, &i_start, &i_end);
}
int main(int argc,char **args)
{
Mat C;
PetscInt i,j,m = 5,n = 5,Ii,J;
PetscErrorCode ierr;
PetscScalar v,five = 5.0;
IS isrow;
PetscBool keepnonzeropattern;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
/* create the matrix for the five point stencil, YET AGAIN*/
ierr = MatCreate(PETSC_COMM_SELF,&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);
for (i=0; i<m; i++) {
for (j=0; j<n; 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);
}
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,(m*n)/2,0,2,&isrow);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL,"-keep_nonzero_pattern",&keepnonzeropattern);CHKERRQ(ierr);
if (keepnonzeropattern) {
ierr = MatSetOption(C,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = MatZeroRowsIS(C,isrow,five,0,0);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode TestMatZeroRows_Basic(Mat A,IS is,PetscScalar diag)
{
Mat B;
PetscErrorCode ierr;
PetscBool keepnonzeropattern;
/* Now copy A into B, and test it with MatZeroRows() */
ierr = MatDuplicate(A,MAT_COPY_VALUES,&B);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL,"-keep_nonzero_pattern",&keepnonzeropattern);CHKERRQ(ierr);
if (keepnonzeropattern) {
ierr = MatSetOption(B,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = MatZeroRowsIS(B,is,diag,0,0);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
return 0;
}
