EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "MatCreate_Scatter"
PetscErrorCode PETSCMAT_DLLEXPORT MatCreate_Scatter(Mat A)
{
Mat_Scatter *b;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscMemcpy(A->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr);
ierr = PetscNewLog(A,Mat_Scatter,&b);CHKERRQ(ierr);
A->data = (void*)b;
ierr = PetscLayoutSetBlockSize(A->rmap,1);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(A->cmap,1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr);
A->assembled = PETSC_TRUE;
A->preallocated = PETSC_FALSE;
ierr = PetscObjectChangeTypeName((PetscObject)A,MATSCATTER);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);
}
/*@
MatCreateTranspose - Creates a new matrix object that behaves like A'
Collective on Mat
Input Parameter:
. A - the (possibly rectangular) matrix
Output Parameter:
. N - the matrix that represents A'
Level: intermediate
Notes: The transpose A' is NOT actually formed! Rather the new matrix
object performs the matrix-vector product by using the MatMultTranspose() on
the original matrix
.seealso: MatCreateNormal(), MatMult(), MatMultTranspose(), MatCreate()
@*/
PetscErrorCode MatCreateTranspose(Mat A,Mat *N)
{
PetscErrorCode ierr;
PetscInt m,n;
Mat_Transpose *Na;
PetscFunctionBegin;
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatCreate(PetscObjectComm((PetscObject)A),N);CHKERRQ(ierr);
ierr = MatSetSizes(*N,n,m,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)*N,MATTRANSPOSEMAT);CHKERRQ(ierr);
ierr = PetscNewLog(*N,&Na);CHKERRQ(ierr);
(*N)->data = (void*) Na;
ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr);
Na->A = A;
(*N)->ops->destroy = MatDestroy_Transpose;
(*N)->ops->mult = MatMult_Transpose;
(*N)->ops->multadd = MatMultAdd_Transpose;
(*N)->ops->multtranspose = MatMultTranspose_Transpose;
(*N)->ops->multtransposeadd = MatMultTransposeAdd_Transpose;
(*N)->assembled = PETSC_TRUE;
ierr = PetscLayoutSetBlockSize((*N)->rmap,A->cmap->bs);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize((*N)->cmap,A->rmap->bs);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((*N)->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((*N)->cmap);CHKERRQ(ierr);
ierr = MatSetUp(*N);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 DMSetUp_Composite(DM dm)
{
PetscErrorCode ierr;
PetscInt nprev = 0;
PetscMPIInt rank,size;
DM_Composite *com = (DM_Composite*)dm->data;
struct DMCompositeLink *next = com->next;
PetscLayout map;
PetscFunctionBegin;
if (com->setup) SETERRQ(((PetscObject)dm)->comm,PETSC_ERR_ARG_WRONGSTATE,"Packer has already been setup");
ierr = PetscLayoutCreate(((PetscObject)dm)->comm,&map);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(map,com->n);CHKERRQ(ierr);
ierr = PetscLayoutSetSize(map,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(map,1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(map);CHKERRQ(ierr);
ierr = PetscLayoutGetSize(map,&com->N);CHKERRQ(ierr);
ierr = PetscLayoutGetRange(map,&com->rstart,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&map);CHKERRQ(ierr);
/* now set the rstart for each linked vector */
ierr = MPI_Comm_rank(((PetscObject)dm)->comm,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(((PetscObject)dm)->comm,&size);CHKERRQ(ierr);
while (next) {
next->rstart = nprev;
nprev += next->n;
next->grstart = com->rstart + next->rstart;
ierr = PetscMalloc(size*sizeof(PetscInt),&next->grstarts);CHKERRQ(ierr);
ierr = MPI_Allgather(&next->grstart,1,MPIU_INT,next->grstarts,1,MPIU_INT,((PetscObject)dm)->comm);CHKERRQ(ierr);
next = next->next;
}
com->setup = PETSC_TRUE;
PetscFunctionReturn(0);
}
static PetscErrorCode ISSetBlockSize_Block(IS is,PetscInt bs)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLayoutSetBlockSize(is->map, bs);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "MatMPIAdjSetPreallocation_MPIAdj"
PetscErrorCode PETSCMAT_DLLEXPORT MatMPIAdjSetPreallocation_MPIAdj(Mat B,PetscInt *i,PetscInt *j,PetscInt *values)
{
Mat_MPIAdj *b = (Mat_MPIAdj *)B->data;
PetscErrorCode ierr;
#if defined(PETSC_USE_DEBUG)
PetscInt ii;
#endif
PetscFunctionBegin;
ierr = PetscLayoutSetBlockSize(B->rmap,1);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(B->cmap,1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr);
#if defined(PETSC_USE_DEBUG)
if (i[0] != 0) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"First i[] index must be zero, instead it is %D\n",i[0]);
for (ii=1; ii<B->rmap->n; ii++) {
if (i[ii] < 0 || i[ii] < i[ii-1]) {
SETERRQ4(PETSC_ERR_ARG_OUTOFRANGE,"i[%D]=%D index is out of range: i[%D]=%D",ii,i[ii],ii-1,i[ii-1]);
}
}
for (ii=0; ii<i[B->rmap->n]; ii++) {
if (j[ii] < 0 || j[ii] >= B->cmap->N) {
SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column index %D out of range %D\n",ii,j[ii]);
}
}
#endif
B->preallocated = PETSC_TRUE;
b->j = j;
b->i = i;
b->values = values;
b->nz = i[B->rmap->n];
b->diag = 0;
b->symmetric = PETSC_FALSE;
b->freeaij = PETSC_TRUE;
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode ISSetBlockSize_Stride(IS is,PetscInt bs)
{
IS_Stride *sub = (IS_Stride*)is->data;
PetscErrorCode ierr;
PetscFunctionBegin;
if (sub->step != 1 && bs != 1) SETERRQ2(PetscObjectComm((PetscObject)is),PETSC_ERR_ARG_SIZ,"ISSTRIDE has stride %D, cannot be blocked of size %D",sub->step,bs);
ierr = PetscLayoutSetBlockSize(is->map, bs);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode ISBlockSetIndices_Block(IS is,PetscInt bs,PetscInt n,const PetscInt idx[],PetscCopyMode mode)
{
PetscErrorCode ierr;
PetscInt i,min,max;
IS_Block *sub = (IS_Block*)is->data;
PetscFunctionBegin;
if (bs < 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"block size < 1");
if (n < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"length < 0");
if (n) PetscValidIntPointer(idx,3);
ierr = PetscLayoutSetLocalSize(is->map, n*bs);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(is->map, bs);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(is->map);CHKERRQ(ierr);
if (sub->allocated) {ierr = PetscFree(sub->idx);CHKERRQ(ierr);}
if (mode == PETSC_COPY_VALUES) {
ierr = PetscMalloc1(n,&sub->idx);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)is,n*sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(sub->idx,idx,n*sizeof(PetscInt));CHKERRQ(ierr);
sub->allocated = PETSC_TRUE;
} else if (mode == PETSC_OWN_POINTER) {
sub->idx = (PetscInt*) idx;
ierr = PetscLogObjectMemory((PetscObject)is,n*sizeof(PetscInt));CHKERRQ(ierr);
sub->allocated = PETSC_TRUE;
} else if (mode == PETSC_USE_POINTER) {
sub->idx = (PetscInt*) idx;
sub->allocated = PETSC_FALSE;
}
sub->sorted = PETSC_TRUE;
for (i=1; i<n; i++) {
if (idx[i] < idx[i-1]) {sub->sorted = PETSC_FALSE; break;}
}
if (n) {
min = max = idx[0];
for (i=1; i<n; i++) {
if (idx[i] < min) min = idx[i];
if (idx[i] > max) max = idx[i];
}
is->min = bs*min;
is->max = bs*max+bs-1;
} else {
is->min = PETSC_MAX_INT;
is->max = PETSC_MIN_INT;
}
is->isperm = PETSC_FALSE;
is->isidentity = PETSC_FALSE;
PetscFunctionReturn(0);
}
/*@C
VecCreateNest - Creates a new vector containing several nested subvectors, each stored separately
Collective on Vec
Input Parameter:
+ comm - Communicator for the new Vec
. nb - number of nested blocks
. is - array of nb index sets describing each nested block, or NULL to pack subvectors contiguously
- x - array of nb sub-vectors
Output Parameter:
. Y - new vector
Level: advanced
.seealso: VecCreate(), MatCreateNest(), DMSetVecType(), VECNEST
@*/
PetscErrorCode VecCreateNest(MPI_Comm comm,PetscInt nb,IS is[],Vec x[],Vec *Y)
{
Vec V;
Vec_Nest *s;
PetscInt n,N;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = VecCreate(comm,&V);CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)V,VECNEST);CHKERRQ(ierr);
/* allocate and set pointer for implememtation data */
ierr = PetscMalloc(sizeof(Vec_Nest),&s);CHKERRQ(ierr);
ierr = PetscMemzero(s,sizeof(Vec_Nest));CHKERRQ(ierr);
V->data = (void*)s;
s->setup_called = PETSC_FALSE;
s->nb = -1;
s->v = NULL;
ierr = VecSetUp_Nest_Private(V,nb,x);CHKERRQ(ierr);
n = N = 0;
ierr = VecSize_Nest_Recursive(V,PETSC_TRUE,&N);CHKERRQ(ierr);
ierr = VecSize_Nest_Recursive(V,PETSC_FALSE,&n);CHKERRQ(ierr);
ierr = PetscLayoutSetSize(V->map,N);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(V->map,n);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(V->map,1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(V->map);CHKERRQ(ierr);
ierr = VecSetUp_NestIS_Private(V,nb,is);CHKERRQ(ierr);
ierr = VecNestSetOps_Private(V->ops);CHKERRQ(ierr);
V->petscnative = PETSC_FALSE;
/* expose block api's */
ierr = PetscObjectComposeFunction((PetscObject)V,"VecNestGetSubVec_C",VecNestGetSubVec_Nest);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)V,"VecNestGetSubVecs_C",VecNestGetSubVecs_Nest);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)V,"VecNestSetSubVec_C",VecNestSetSubVec_Nest);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)V,"VecNestSetSubVecs_C",VecNestSetSubVecs_Nest);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)V,"VecNestGetSize_C",VecNestGetSize_Nest);CHKERRQ(ierr);
*Y = V;
PetscFunctionReturn(0);
}
static PetscErrorCode ISSetBlockSize_General(IS is,PetscInt bs)
{
#if defined(PETSC_USE_DEBUG)
IS_General *sub = (IS_General*)is->data;
PetscInt n;
#endif
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLayoutSetBlockSize(is->map, bs);CHKERRQ(ierr);
#if defined(PETSC_USE_DEBUG)
ierr = PetscLayoutGetLocalSize(is->map, &n);CHKERRQ(ierr);
{
PetscInt i,j;
for (i=0; i<n; i+=bs) {
for (j=0; j<bs; j++) {
if (sub->idx[i+j] != sub->idx[i]+j) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Index set does not have block structure, cannot set block size to %D",bs);
}
}
}
#endif
PetscFunctionReturn(0);
}
PetscErrorCode ISBlockSetIndices_Block(IS is,PetscInt bs,PetscInt n,const PetscInt idx[],PetscCopyMode mode)
{
PetscErrorCode ierr;
PetscInt i,min,max;
IS_Block *sub = (IS_Block*)is->data;
PetscBool sorted = PETSC_TRUE;
PetscFunctionBegin;
ierr = PetscFree(sub->idx);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(is->map, n*bs);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(is->map, bs);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(is->map);CHKERRQ(ierr);
for (i=1; i<n; i++) {
if (idx[i] < idx[i-1]) {sorted = PETSC_FALSE; break;}
}
if (n) min = max = idx[0];
else min = max = 0;
for (i=1; i<n; i++) {
if (idx[i] < min) min = idx[i];
if (idx[i] > max) max = idx[i];
}
if (mode == PETSC_COPY_VALUES) {
ierr = PetscMalloc1(n,&sub->idx);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)is,n*sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(sub->idx,idx,n*sizeof(PetscInt));CHKERRQ(ierr);
} else if (mode == PETSC_OWN_POINTER) sub->idx = (PetscInt*) idx;
else SETERRQ(PetscObjectComm((PetscObject)is),PETSC_ERR_SUP,"Only supports PETSC_COPY_VALUES and PETSC_OWN_POINTER");
sub->sorted = sorted;
is->min = bs*min;
is->max = bs*max+bs-1;
is->data = (void*)sub;
ierr = PetscMemcpy(is->ops,&myops,sizeof(myops));CHKERRQ(ierr);
is->isperm = PETSC_FALSE;
PetscFunctionReturn(0);
}
PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints)
{
MPI_Comm comm = ctx->comm;
PetscScalar *a;
PetscInt p, q, i;
PetscMPIInt rank, size;
PetscErrorCode ierr;
Vec pointVec;
IS cellIS;
PetscLayout layout;
PetscReal *globalPoints;
PetscScalar *globalPointsScalar;
const PetscInt *ranges;
PetscMPIInt *counts, *displs;
const PetscInt *foundCells;
PetscMPIInt *foundProcs, *globalProcs;
PetscInt n, N;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set");
/* Locate points */
n = ctx->nInput;
if (!redundantPoints) {
ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(layout, n);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr);
ierr = PetscLayoutGetSize(layout, &N);CHKERRQ(ierr);
/* Communicate all points to all processes */
ierr = PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);CHKERRQ(ierr);
ierr = PetscLayoutGetRanges(layout, &ranges);CHKERRQ(ierr);
for (p = 0; p < size; ++p) {
counts[p] = (ranges[p+1] - ranges[p])*ctx->dim;
displs[p] = ranges[p]*ctx->dim;
}
ierr = MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);CHKERRQ(ierr);
} else {
N = n;
globalPoints = ctx->points;
counts = displs = NULL;
layout = NULL;
}
#if 0
ierr = PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);CHKERRQ(ierr);
/* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */
#else
#if defined(PETSC_USE_COMPLEX)
ierr = PetscMalloc1(N,&globalPointsScalar);CHKERRQ(ierr);
for (i=0; i<N; i++) globalPointsScalar[i] = globalPoints[i];
#else
globalPointsScalar = globalPoints;
#endif
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);CHKERRQ(ierr);
ierr = PetscMalloc2(N,&foundProcs,N,&globalProcs);CHKERRQ(ierr);
ierr = DMLocatePoints(dm, pointVec, &cellIS);CHKERRQ(ierr);
ierr = ISGetIndices(cellIS, &foundCells);CHKERRQ(ierr);
#endif
for (p = 0; p < N; ++p) {
if (foundCells[p] >= 0) foundProcs[p] = rank;
else foundProcs[p] = size;
}
/* Let the lowest rank process own each point */
ierr = MPI_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);CHKERRQ(ierr);
ctx->n = 0;
for (p = 0; p < N; ++p) {
if (globalProcs[p] == size) SETERRQ4(comm, PETSC_ERR_PLIB, "Point %d: %g %g %g not located in mesh", p, globalPoints[p*ctx->dim+0], ctx->dim > 1 ? globalPoints[p*ctx->dim+1] : 0.0, ctx->dim > 2 ? globalPoints[p*ctx->dim+2] : 0.0);
else if (globalProcs[p] == rank) ctx->n++;
}
/* Create coordinates vector and array of owned cells */
ierr = PetscMalloc1(ctx->n, &ctx->cells);CHKERRQ(ierr);
ierr = VecCreate(comm, &ctx->coords);CHKERRQ(ierr);
ierr = VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetBlockSize(ctx->coords, ctx->dim);CHKERRQ(ierr);
ierr = VecSetType(ctx->coords,VECSTANDARD);CHKERRQ(ierr);
ierr = VecGetArray(ctx->coords, &a);CHKERRQ(ierr);
for (p = 0, q = 0, i = 0; p < N; ++p) {
if (globalProcs[p] == rank) {
PetscInt d;
for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d];
ctx->cells[q++] = foundCells[p];
}
}
ierr = VecRestoreArray(ctx->coords, &a);CHKERRQ(ierr);
#if 0
ierr = PetscFree3(foundCells,foundProcs,globalProcs);CHKERRQ(ierr);
#else
ierr = PetscFree2(foundProcs,globalProcs);CHKERRQ(ierr);
ierr = ISRestoreIndices(cellIS, &foundCells);CHKERRQ(ierr);
ierr = ISDestroy(&cellIS);CHKERRQ(ierr);
ierr = VecDestroy(&pointVec);CHKERRQ(ierr);
#endif
if ((void*)globalPointsScalar != (void*)globalPoints) {ierr = PetscFree(globalPointsScalar);CHKERRQ(ierr);}
if (!redundantPoints) {ierr = PetscFree3(globalPoints,counts,displs);CHKERRQ(ierr);}
ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatGetMultiProcBlock_MPIBAIJ(Mat mat, MPI_Comm subComm, MatReuse scall,Mat *subMat)
{
PetscErrorCode ierr;
Mat_MPIBAIJ *aij = (Mat_MPIBAIJ*)mat->data;
Mat_SeqBAIJ *aijB = (Mat_SeqBAIJ*)aij->B->data;
PetscMPIInt commRank,subCommSize,subCommRank;
PetscMPIInt *commRankMap,subRank,rank,commsize;
PetscInt *garrayCMap,col,i,j,*nnz,newRow,newCol,*newbRow,*newbCol,k,k1;
PetscInt bs=mat->rmap->bs;
PetscScalar *vals,*aijBvals;
PetscFunctionBegin;
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&commsize);CHKERRQ(ierr);
ierr = MPI_Comm_size(subComm,&subCommSize);CHKERRQ(ierr);
/* create subMat object with the relavent layout */
if (scall == MAT_INITIAL_MATRIX) {
ierr = MatCreate(subComm,subMat);CHKERRQ(ierr);
ierr = MatSetType(*subMat,MATMPIBAIJ);CHKERRQ(ierr);
ierr = MatSetSizes(*subMat,mat->rmap->n,mat->cmap->n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetBlockSizes(*subMat,mat->rmap->bs,mat->cmap->bs);CHKERRQ(ierr);
/* need to setup rmap and cmap before Preallocation */
ierr = PetscLayoutSetBlockSize((*subMat)->rmap,mat->rmap->bs);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize((*subMat)->cmap,mat->cmap->bs);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((*subMat)->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((*subMat)->cmap);CHKERRQ(ierr);
}
/* create a map of comm_rank from subComm to comm - should commRankMap and garrayCMap be kept for reused? */
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&commRank);CHKERRQ(ierr);
ierr = MPI_Comm_rank(subComm,&subCommRank);CHKERRQ(ierr);
ierr = PetscMalloc(subCommSize*sizeof(PetscMPIInt),&commRankMap);CHKERRQ(ierr);
ierr = MPI_Allgather(&commRank,1,MPI_INT,commRankMap,1,MPI_INT,subComm);CHKERRQ(ierr);
/* Traverse garray and identify blocked column indices [of offdiag mat] that
should be discarded. For the ones not discarded, store the newCol+1
value in garrayCMap */
ierr = PetscMalloc(aij->B->cmap->n/bs*sizeof(PetscInt),&garrayCMap);CHKERRQ(ierr);
ierr = PetscMemzero(garrayCMap,aij->B->cmap->n/bs*sizeof(PetscInt));CHKERRQ(ierr);
for (i=0; i<aij->B->cmap->n/bs; i++) {
col = aij->garray[i]; /* blocked column index */
for (subRank=0; subRank<subCommSize; subRank++) {
rank = commRankMap[subRank];
if ((col >= mat->cmap->range[rank]/bs) && (col < mat->cmap->range[rank+1]/bs)) {
garrayCMap[i] = (((*subMat)->cmap->range[subRank]- mat->cmap->range[rank])/bs + col + 1);
break;
}
}
}
if (scall == MAT_INITIAL_MATRIX) {
/* Now compute preallocation for the offdiag mat */
ierr = PetscMalloc(aij->B->rmap->n/bs*sizeof(PetscInt),&nnz);CHKERRQ(ierr);
ierr = PetscMemzero(nnz,aij->B->rmap->n/bs*sizeof(PetscInt));CHKERRQ(ierr);
for (i=0; i<aij->B->rmap->n/bs; i++) {
for (j=aijB->i[i]; j<aijB->i[i+1]; j++) {
if (garrayCMap[aijB->j[j]]) nnz[i]++;
}
}
ierr = MatMPIBAIJSetPreallocation(*(subMat),bs,0,NULL,0,nnz);CHKERRQ(ierr);
/* reuse diag block with the new submat */
ierr = MatDestroy(&((Mat_MPIBAIJ*)((*subMat)->data))->A);CHKERRQ(ierr);
((Mat_MPIBAIJ*)((*subMat)->data))->A = aij->A;
ierr = PetscObjectReference((PetscObject)aij->A);CHKERRQ(ierr);
} else if (((Mat_MPIBAIJ*)(*subMat)->data)->A != aij->A) {
PetscObject obj = (PetscObject)((Mat_MPIBAIJ*)((*subMat)->data))->A;
ierr = PetscObjectReference((PetscObject)obj);CHKERRQ(ierr);
((Mat_MPIBAIJ*)((*subMat)->data))->A = aij->A;
ierr = PetscObjectReference((PetscObject)aij->A);CHKERRQ(ierr);
}
/* Now traverse aij->B and insert values into subMat */
ierr = PetscMalloc3(bs,PetscInt,&newbRow,bs,PetscInt,&newbCol,bs*bs,PetscScalar,&vals);CHKERRQ(ierr);
for (i=0; i<aij->B->rmap->n/bs; i++) {
newRow = (*subMat)->rmap->range[subCommRank] + i*bs;
for (j=aijB->i[i]; j<aijB->i[i+1]; j++) {
newCol = garrayCMap[aijB->j[j]];
if (newCol) {
newCol--; /* remove the increment */
newCol *= bs;
for (k=0; k<bs; k++) {
newbRow[k] = newRow + k;
newbCol[k] = newCol + k;
}
/* copy column-oriented aijB->a into row-oriented vals */
aijBvals = aijB->a + j*bs*bs;
for (k1=0; k1<bs; k1++) {
for (k=0; k<bs; k++) {
vals[k1+k*bs] = *aijBvals++;
}
}
ierr = MatSetValues(*subMat,bs,newbRow,bs,newbCol,vals,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
ierr = MatAssemblyBegin(*subMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*subMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* deallocate temporary data */
ierr = PetscFree3(newbRow,newbCol,vals);CHKERRQ(ierr);
ierr = PetscFree(commRankMap);CHKERRQ(ierr);
ierr = PetscFree(garrayCMap);CHKERRQ(ierr);
if (scall == MAT_INITIAL_MATRIX) {
ierr = PetscFree(nnz);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode DMPlexVTKWriteAll_ASCII(DM dm, PetscViewer viewer)
{
MPI_Comm comm;
PetscViewer_VTK *vtk = (PetscViewer_VTK*) viewer->data;
FILE *fp;
PetscViewerVTKObjectLink link;
PetscSection coordSection, globalCoordSection;
PetscLayout vLayout;
Vec coordinates;
PetscReal lengthScale;
PetscInt vMax, totVertices, totCells;
PetscBool hasPoint = PETSC_FALSE, hasCell = PETSC_FALSE, writePartition = PETSC_FALSE;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscFOpen(comm, vtk->filename, "wb", &fp);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "# vtk DataFile Version 2.0\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "Simplicial Mesh Example\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "ASCII\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "DATASET UNSTRUCTURED_GRID\n");CHKERRQ(ierr);
/* Vertices */
ierr = DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionCreateGlobalSection(coordSection, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalCoordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, NULL, NULL, NULL, &vMax);CHKERRQ(ierr);
if (vMax >= 0) {
PetscInt pStart, pEnd, p, localSize = 0;
ierr = PetscSectionGetChart(globalCoordSection, &pStart, &pEnd);CHKERRQ(ierr);
pEnd = PetscMin(pEnd, vMax);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof;
ierr = PetscSectionGetDof(globalCoordSection, p, &dof);CHKERRQ(ierr);
if (dof > 0) ++localSize;
}
ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &vLayout);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(vLayout, localSize);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr);
} else {
ierr = PetscSectionGetPointLayout(PetscObjectComm((PetscObject)dm), globalCoordSection, &vLayout);CHKERRQ(ierr);
}
ierr = PetscLayoutGetSize(vLayout, &totVertices);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "POINTS %d double\n", totVertices);CHKERRQ(ierr);
ierr = DMPlexVTKWriteSection_ASCII(dm, coordSection, globalCoordSection, coordinates, fp, 3, PETSC_DETERMINE, lengthScale);CHKERRQ(ierr);
/* Cells */
ierr = DMPlexVTKWriteCells_ASCII(dm, fp, &totCells);CHKERRQ(ierr);
/* Vertex fields */
for (link = vtk->link; link; link = link->next) {
if ((link->ft == PETSC_VTK_POINT_FIELD) || (link->ft == PETSC_VTK_POINT_VECTOR_FIELD)) hasPoint = PETSC_TRUE;
if ((link->ft == PETSC_VTK_CELL_FIELD) || (link->ft == PETSC_VTK_CELL_VECTOR_FIELD)) hasCell = PETSC_TRUE;
}
if (hasPoint) {
ierr = PetscFPrintf(comm, fp, "POINT_DATA %d\n", totVertices);CHKERRQ(ierr);
for (link = vtk->link; link; link = link->next) {
Vec X = (Vec) link->vec;
DM dmX;
PetscSection section, globalSection, newSection = NULL;
const char *name;
PetscInt enforceDof = PETSC_DETERMINE;
if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
if (link->ft == PETSC_VTK_POINT_VECTOR_FIELD) enforceDof = 3;
ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
if (dmX) {
DMLabel subpointMap, subpointMapX;
PetscInt dim, dimX, pStart, pEnd, qStart, qEnd;
ierr = DMGetDefaultSection(dmX, §ion);CHKERRQ(ierr);
/* Here is where we check whether dmX is a submesh of dm */
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetDimension(dmX, &dimX);CHKERRQ(ierr);
ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
ierr = DMPlexGetChart(dmX, &qStart, &qEnd);CHKERRQ(ierr);
ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr);
ierr = DMPlexGetSubpointMap(dmX, &subpointMapX);CHKERRQ(ierr);
if (((dim != dimX) || ((pEnd-pStart) < (qEnd-qStart))) && subpointMap && !subpointMapX) {
const PetscInt *ind = NULL;
IS subpointIS;
PetscInt n = 0, q;
ierr = PetscSectionGetChart(section, &qStart, &qEnd);CHKERRQ(ierr);
ierr = DMPlexCreateSubpointIS(dm, &subpointIS);CHKERRQ(ierr);
if (subpointIS) {
ierr = ISGetLocalSize(subpointIS, &n);CHKERRQ(ierr);
ierr = ISGetIndices(subpointIS, &ind);CHKERRQ(ierr);
}
ierr = PetscSectionCreate(comm, &newSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(newSection, pStart, pEnd);CHKERRQ(ierr);
for (q = qStart; q < qEnd; ++q) {
PetscInt dof, off, p;
ierr = PetscSectionGetDof(section, q, &dof);CHKERRQ(ierr);
if (dof) {
ierr = PetscFindInt(q, n, ind, &p);CHKERRQ(ierr);
if (p >= pStart) {
ierr = PetscSectionSetDof(newSection, p, dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, q, &off);CHKERRQ(ierr);
ierr = PetscSectionSetOffset(newSection, p, off);CHKERRQ(ierr);
}
}
}
if (subpointIS) {
ierr = ISRestoreIndices(subpointIS, &ind);CHKERRQ(ierr);
ierr = ISDestroy(&subpointIS);CHKERRQ(ierr);
}
/* No need to setup section */
section = newSection;
}
} else {
ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) §ion);CHKERRQ(ierr);
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
}
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
if (newSection) {ierr = PetscSectionDestroy(&newSection);CHKERRQ(ierr);}
}
}
/* Cell Fields */
ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_view_partition", &writePartition, NULL);CHKERRQ(ierr);
if (hasCell || writePartition) {
ierr = PetscFPrintf(comm, fp, "CELL_DATA %d\n", totCells);CHKERRQ(ierr);
for (link = vtk->link; link; link = link->next) {
Vec X = (Vec) link->vec;
DM dmX;
PetscSection section, globalSection;
const char *name;
PetscInt enforceDof = PETSC_DETERMINE;
if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
if (link->ft == PETSC_VTK_CELL_VECTOR_FIELD) enforceDof = 3;
ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
if (dmX) {
ierr = DMGetDefaultSection(dmX, §ion);CHKERRQ(ierr);
} else {
PetscContainer c;
ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) &c);CHKERRQ(ierr);
if (!c) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscContainerGetPointer(c, (void**) §ion);CHKERRQ(ierr);
}
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
}
if (writePartition) {
ierr = PetscFPrintf(comm, fp, "SCALARS partition int 1\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "LOOKUP_TABLE default\n");CHKERRQ(ierr);
ierr = DMPlexVTKWritePartition_ASCII(dm, fp);CHKERRQ(ierr);
}
}
/* Cleanup */
ierr = PetscSectionDestroy(&globalCoordSection);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr);
ierr = PetscFClose(comm, fp);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode MatSetupDM_HYPRESStruct(Mat mat,DM da)
{
PetscErrorCode ierr;
Mat_HYPRESStruct *ex = (Mat_HYPRESStruct*) mat->data;
PetscInt dim,dof,sw[3],nx,ny,nz;
PetscInt ilower[3],iupper[3],ssize,i;
DMBoundaryType px,py,pz;
DMDAStencilType st;
PetscInt nparts= 1; /* assuming only one part */
PetscInt part = 0;
ISLocalToGlobalMapping ltog;
PetscFunctionBegin;
ex->da = da;
ierr = PetscObjectReference((PetscObject)da);CHKERRQ(ierr);
ierr = DMDAGetInfo(ex->da,&dim,0,0,0,0,0,0,&dof,&sw[0],&px,&py,&pz,&st);CHKERRQ(ierr);
ierr = DMDAGetCorners(ex->da,&ilower[0],&ilower[1],&ilower[2],&iupper[0],&iupper[1],&iupper[2]);CHKERRQ(ierr);
iupper[0] += ilower[0] - 1;
iupper[1] += ilower[1] - 1;
iupper[2] += ilower[2] - 1;
/* the hypre_Box is used to zero out the matrix entries in MatZeroValues() */
ex->hbox.imin[0] = ilower[0];
ex->hbox.imin[1] = ilower[1];
ex->hbox.imin[2] = ilower[2];
ex->hbox.imax[0] = iupper[0];
ex->hbox.imax[1] = iupper[1];
ex->hbox.imax[2] = iupper[2];
ex->dofs_order = 0;
/* assuming that the same number of dofs on each gridpoint. Also assume all cell-centred based */
ex->nvars= dof;
/* create the hypre grid object and set its information */
if (px || py || pz) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Ask us to add periodic support by calling HYPRE_SStructGridSetPeriodic()");
PetscStackCallStandard(HYPRE_SStructGridCreate,(ex->hcomm,dim,nparts,&ex->ss_grid));
PetscStackCallStandard(HYPRE_SStructGridSetExtents,(ex->ss_grid,part,ex->hbox.imin,ex->hbox.imax));
{
HYPRE_SStructVariable *vartypes;
ierr = PetscMalloc1(ex->nvars,&vartypes);CHKERRQ(ierr);
for (i= 0; i< ex->nvars; i++) vartypes[i]= HYPRE_SSTRUCT_VARIABLE_CELL;
PetscStackCallStandard(HYPRE_SStructGridSetVariables,(ex->ss_grid, part, ex->nvars,vartypes));
ierr = PetscFree(vartypes);CHKERRQ(ierr);
}
PetscStackCallStandard(HYPRE_SStructGridAssemble,(ex->ss_grid));
sw[1] = sw[0];
sw[2] = sw[1];
/* PetscStackCallStandard(HYPRE_SStructGridSetNumGhost,(ex->ss_grid,sw)); */
/* create the hypre stencil object and set its information */
if (sw[0] > 1) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Ask us to add support for wider stencils");
if (st == DMDA_STENCIL_BOX) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Ask us to add support for box stencils");
if (dim == 1) {
PetscInt offsets[3][1] = {{-1},{0},{1}};
PetscInt j, cnt;
ssize = 3*(ex->nvars);
PetscStackCallStandard(HYPRE_SStructStencilCreate,(dim,ssize,&ex->ss_stencil));
cnt= 0;
for (i = 0; i < (ex->nvars); i++) {
for (j = 0; j < 3; j++) {
PetscStackCallStandard(HYPRE_SStructStencilSetEntry,(ex->ss_stencil, cnt, (HYPRE_Int *)offsets[j], i));
cnt++;
}
}
} else if (dim == 2) {
PetscInt offsets[5][2] = {{0,-1},{-1,0},{0,0},{1,0},{0,1}};
PetscInt j, cnt;
ssize = 5*(ex->nvars);
PetscStackCallStandard(HYPRE_SStructStencilCreate,(dim,ssize,&ex->ss_stencil));
cnt= 0;
for (i= 0; i< (ex->nvars); i++) {
for (j= 0; j< 5; j++) {
PetscStackCallStandard(HYPRE_SStructStencilSetEntry,(ex->ss_stencil, cnt, (HYPRE_Int *)offsets[j], i));
cnt++;
}
}
} else if (dim == 3) {
PetscInt offsets[7][3] = {{0,0,-1},{0,-1,0},{-1,0,0},{0,0,0},{1,0,0},{0,1,0},{0,0,1}};
PetscInt j, cnt;
ssize = 7*(ex->nvars);
PetscStackCallStandard(HYPRE_SStructStencilCreate,(dim,ssize,&ex->ss_stencil));
cnt= 0;
for (i= 0; i< (ex->nvars); i++) {
for (j= 0; j< 7; j++) {
PetscStackCallStandard(HYPRE_SStructStencilSetEntry,(ex->ss_stencil, cnt, (HYPRE_Int *)offsets[j], i));
cnt++;
}
}
}
/* create the HYPRE graph */
PetscStackCallStandard(HYPRE_SStructGraphCreate,(ex->hcomm, ex->ss_grid, &(ex->ss_graph)));
/* set the stencil graph. Note that each variable has the same graph. This means that each
variable couples to all the other variable and with the same stencil pattern. */
for (i= 0; i< (ex->nvars); i++) {
PetscStackCallStandard(HYPRE_SStructGraphSetStencil,(ex->ss_graph,part,i,ex->ss_stencil));
}
PetscStackCallStandard(HYPRE_SStructGraphAssemble,(ex->ss_graph));
/* create the HYPRE sstruct vectors for rhs and solution */
PetscStackCallStandard(HYPRE_SStructVectorCreate,(ex->hcomm,ex->ss_grid,&ex->ss_b));
PetscStackCallStandard(HYPRE_SStructVectorCreate,(ex->hcomm,ex->ss_grid,&ex->ss_x));
PetscStackCallStandard(HYPRE_SStructVectorInitialize,(ex->ss_b));
PetscStackCallStandard(HYPRE_SStructVectorInitialize,(ex->ss_x));
PetscStackCallStandard(HYPRE_SStructVectorAssemble,(ex->ss_b));
PetscStackCallStandard(HYPRE_SStructVectorAssemble,(ex->ss_x));
/* create the hypre matrix object and set its information */
PetscStackCallStandard(HYPRE_SStructMatrixCreate,(ex->hcomm,ex->ss_graph,&ex->ss_mat));
PetscStackCallStandard(HYPRE_SStructGridDestroy,(ex->ss_grid));
PetscStackCallStandard(HYPRE_SStructStencilDestroy,(ex->ss_stencil));
if (ex->needsinitialization) {
PetscStackCallStandard(HYPRE_SStructMatrixInitialize,(ex->ss_mat));
ex->needsinitialization = PETSC_FALSE;
}
/* set the global and local sizes of the matrix */
ierr = DMDAGetCorners(da,0,0,0,&nx,&ny,&nz);CHKERRQ(ierr);
ierr = MatSetSizes(mat,dof*nx*ny*nz,dof*nx*ny*nz,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(mat->rmap,1);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(mat->cmap,1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(mat->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(mat->cmap);CHKERRQ(ierr);
if (dim == 3) {
mat->ops->setvalueslocal = MatSetValuesLocal_HYPRESStruct_3d;
mat->ops->zerorowslocal = MatZeroRowsLocal_HYPRESStruct_3d;
mat->ops->zeroentries = MatZeroEntries_HYPRESStruct_3d;
ierr = MatZeroEntries_HYPRESStruct_3d(mat);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Only support for 3d DMDA currently");
/* get values that will be used repeatedly in MatSetValuesLocal() and MatZeroRowsLocal() repeatedly */
ierr = MatGetOwnershipRange(mat,&ex->rstart,NULL);CHKERRQ(ierr);
ierr = DMGetLocalToGlobalMapping(ex->da,<og);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetIndices(ltog, (const PetscInt **) &ex->gindices);CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(ex->da,0,0,0,&ex->gnx,&ex->gnxgny,&ex->gnxgnygnz);CHKERRQ(ierr);
ex->gnxgny *= ex->gnx;
ex->gnxgnygnz *= ex->gnxgny;
ierr = DMDAGetCorners(ex->da,&ex->xs,&ex->ys,&ex->zs,&ex->nx,&ex->ny,&ex->nz);CHKERRQ(ierr);
ex->nxny = ex->nx*ex->ny;
ex->nxnynz = ex->nz*ex->nxny;
PetscFunctionReturn(0);
}
PetscErrorCode DMPlexPreallocateOperator(DM dm, PetscInt bs, PetscSection section, PetscSection sectionGlobal, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix)
{
MPI_Comm comm;
MatType mtype;
PetscSF sf, sfDof, sfAdj;
PetscSection leafSectionAdj, rootSectionAdj, sectionAdj, anchorSectionAdj;
PetscInt nroots, nleaves, l, p;
const PetscInt *leaves;
const PetscSFNode *remotes;
PetscInt dim, pStart, pEnd, numDof, globalOffStart, globalOffEnd, numCols;
PetscInt *tmpAdj = NULL, *adj, *rootAdj, *anchorAdj = NULL, *cols, *remoteOffsets;
PetscInt adjSize;
PetscLayout rLayout;
PetscInt locRows, rStart, rEnd, r;
PetscMPIInt size;
PetscBool doCommLocal, doComm, debug = PETSC_FALSE, isSymBlock, isSymSeqBlock, isSymMPIBlock;
PetscBool useAnchors;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 3);
PetscValidHeaderSpecific(sectionGlobal, PETSC_SECTION_CLASSID, 4);
PetscValidHeaderSpecific(A, MAT_CLASSID, 9);
if (dnz) PetscValidPointer(dnz,5);
if (onz) PetscValidPointer(onz,6);
if (dnzu) PetscValidPointer(dnzu,7);
if (onzu) PetscValidPointer(onzu,8);
ierr = PetscLogEventBegin(DMPLEX_Preallocate,dm,0,0,0);CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL, "-dm_view_preallocation", &debug, NULL);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr);
ierr = PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL);CHKERRQ(ierr);
doCommLocal = (size > 1) && (nroots >= 0) ? PETSC_TRUE : PETSC_FALSE;
ierr = MPI_Allreduce(&doCommLocal, &doComm, 1, MPIU_BOOL, MPI_LAND, comm);CHKERRQ(ierr);
/* Create dof SF based on point SF */
if (debug) {
ierr = PetscPrintf(comm, "Input Section for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Input Global Section for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSectionView(sectionGlobal, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Input SF for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSFView(sf, NULL);CHKERRQ(ierr);
}
ierr = PetscSFCreateRemoteOffsets(sf, section, section, &remoteOffsets);CHKERRQ(ierr);
ierr = PetscSFCreateSectionSF(sf, section, remoteOffsets, section, &sfDof);CHKERRQ(ierr);
if (debug) {
ierr = PetscPrintf(comm, "Dof SF for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSFView(sfDof, NULL);CHKERRQ(ierr);
}
/* Create section for dof adjacency (dof ==> # adj dof) */
ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(section, &numDof);CHKERRQ(ierr);
ierr = PetscSectionCreate(comm, &leafSectionAdj);CHKERRQ(ierr);
ierr = PetscSectionSetChart(leafSectionAdj, 0, numDof);CHKERRQ(ierr);
ierr = PetscSectionCreate(comm, &rootSectionAdj);CHKERRQ(ierr);
ierr = PetscSectionSetChart(rootSectionAdj, 0, numDof);CHKERRQ(ierr);
/* Fill in the ghost dofs on the interface */
ierr = PetscSFGetGraph(sf, NULL, &nleaves, &leaves, &remotes);CHKERRQ(ierr);
/* use constraints in finding adjacency in this routine */
ierr = DMPlexGetAdjacencyUseAnchors(dm,&useAnchors);CHKERRQ(ierr);
ierr = DMPlexSetAdjacencyUseAnchors(dm,PETSC_TRUE);CHKERRQ(ierr);
/*
section - maps points to (# dofs, local dofs)
sectionGlobal - maps points to (# dofs, global dofs)
leafSectionAdj - maps unowned local dofs to # adj dofs
rootSectionAdj - maps owned local dofs to # adj dofs
adj - adj global dofs indexed by leafSectionAdj
rootAdj - adj global dofs indexed by rootSectionAdj
sf - describes shared points across procs
sfDof - describes shared dofs across procs
sfAdj - describes shared adjacent dofs across procs
** The bootstrapping process involves six rounds with similar structure of visiting neighbors of each point.
(0). If there are point-to-point constraints, add the adjacencies of constrained points to anchors in anchorAdj
(This is done in DMPlexComputeAnchorAdjacencies())
1. Visit unowned points on interface, count adjacencies placing in leafSectionAdj
Reduce those counts to rootSectionAdj (now redundantly counting some interface points)
2. Visit owned points on interface, count adjacencies placing in rootSectionAdj
Create sfAdj connecting rootSectionAdj and leafSectionAdj
3. Visit unowned points on interface, write adjacencies to adj
Gather adj to rootAdj (note that there is redundancy in rootAdj when multiple procs find the same adjacencies)
4. Visit owned points on interface, write adjacencies to rootAdj
Remove redundancy in rootAdj
** The last two traversals use transitive closure
5. Visit all owned points in the subdomain, count dofs for each point (sectionAdj)
Allocate memory addressed by sectionAdj (cols)
6. Visit all owned points in the subdomain, insert dof adjacencies into cols
** Knowing all the column adjacencies, check ownership and sum into dnz and onz
*/
ierr = DMPlexComputeAnchorAdjacencies(dm,section,sectionGlobal,&anchorSectionAdj,&anchorAdj);CHKERRQ(ierr);
for (l = 0; l < nleaves; ++l) {
PetscInt dof, off, d, q, anDof;
PetscInt p = leaves[l], numAdj = PETSC_DETERMINE;
if ((p < pStart) || (p >= pEnd)) continue;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof;
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
ierr = PetscSectionAddDof(leafSectionAdj, d, ndof-ncdof);CHKERRQ(ierr);
}
}
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
if (anDof) {
for (d = off; d < off+dof; ++d) {
ierr = PetscSectionAddDof(leafSectionAdj, d, anDof);CHKERRQ(ierr);
}
}
}
ierr = PetscSectionSetUp(leafSectionAdj);CHKERRQ(ierr);
if (debug) {
ierr = PetscPrintf(comm, "Adjacency Section for Preallocation on Leaves:\n");CHKERRQ(ierr);
ierr = PetscSectionView(leafSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Get maximum remote adjacency sizes for owned dofs on interface (roots) */
if (doComm) {
ierr = PetscSFReduceBegin(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM);CHKERRQ(ierr);
ierr = PetscSFReduceEnd(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM);CHKERRQ(ierr);
}
if (debug) {
ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots:\n");CHKERRQ(ierr);
ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Add in local adjacency sizes for owned dofs on interface (roots) */
for (p = pStart; p < pEnd; ++p) {
PetscInt numAdj = PETSC_DETERMINE, adof, dof, off, d, q, anDof;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
if (!dof) continue;
ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr);
if (adof <= 0) continue;
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof;
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
ierr = PetscSectionAddDof(rootSectionAdj, d, ndof-ncdof);CHKERRQ(ierr);
}
}
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
if (anDof) {
for (d = off; d < off+dof; ++d) {
ierr = PetscSectionAddDof(rootSectionAdj, d, anDof);CHKERRQ(ierr);
}
}
}
ierr = PetscSectionSetUp(rootSectionAdj);CHKERRQ(ierr);
if (debug) {
ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots after local additions:\n");CHKERRQ(ierr);
ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Create adj SF based on dof SF */
ierr = PetscSFCreateRemoteOffsets(sfDof, rootSectionAdj, leafSectionAdj, &remoteOffsets);CHKERRQ(ierr);
ierr = PetscSFCreateSectionSF(sfDof, rootSectionAdj, remoteOffsets, leafSectionAdj, &sfAdj);CHKERRQ(ierr);
if (debug) {
ierr = PetscPrintf(comm, "Adjacency SF for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSFView(sfAdj, NULL);CHKERRQ(ierr);
}
ierr = PetscSFDestroy(&sfDof);CHKERRQ(ierr);
/* Create leaf adjacency */
ierr = PetscSectionSetUp(leafSectionAdj);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(leafSectionAdj, &adjSize);CHKERRQ(ierr);
ierr = PetscCalloc1(adjSize, &adj);CHKERRQ(ierr);
for (l = 0; l < nleaves; ++l) {
PetscInt dof, off, d, q, anDof, anOff;
PetscInt p = leaves[l], numAdj = PETSC_DETERMINE;
if ((p < pStart) || (p >= pEnd)) continue;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(anchorSectionAdj, p, &anOff);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
PetscInt aoff, i = 0;
ierr = PetscSectionGetOffset(leafSectionAdj, d, &aoff);CHKERRQ(ierr);
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof, ngoff, nd;
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, padj, &ngoff);CHKERRQ(ierr);
for (nd = 0; nd < ndof-ncdof; ++nd) {
adj[aoff+i] = (ngoff < 0 ? -(ngoff+1) : ngoff) + nd;
++i;
}
}
for (q = 0; q < anDof; q++) {
adj[aoff+i] = anchorAdj[anOff+q];
++i;
}
}
}
/* Debugging */
if (debug) {
IS tmp;
ierr = PetscPrintf(comm, "Leaf adjacency indices\n");CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, adjSize, adj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
ierr = ISView(tmp, NULL);CHKERRQ(ierr);
ierr = ISDestroy(&tmp);CHKERRQ(ierr);
}
/* Gather adjacenct indices to root */
ierr = PetscSectionGetStorageSize(rootSectionAdj, &adjSize);CHKERRQ(ierr);
ierr = PetscMalloc1(adjSize, &rootAdj);CHKERRQ(ierr);
for (r = 0; r < adjSize; ++r) rootAdj[r] = -1;
if (doComm) {
ierr = PetscSFGatherBegin(sfAdj, MPIU_INT, adj, rootAdj);CHKERRQ(ierr);
ierr = PetscSFGatherEnd(sfAdj, MPIU_INT, adj, rootAdj);CHKERRQ(ierr);
}
ierr = PetscSFDestroy(&sfAdj);CHKERRQ(ierr);
ierr = PetscFree(adj);CHKERRQ(ierr);
/* Debugging */
if (debug) {
IS tmp;
ierr = PetscPrintf(comm, "Root adjacency indices after gather\n");CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
ierr = ISView(tmp, NULL);CHKERRQ(ierr);
ierr = ISDestroy(&tmp);CHKERRQ(ierr);
}
/* Add in local adjacency indices for owned dofs on interface (roots) */
for (p = pStart; p < pEnd; ++p) {
PetscInt numAdj = PETSC_DETERMINE, adof, dof, off, d, q, anDof, anOff;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
if (!dof) continue;
ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr);
if (adof <= 0) continue;
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(anchorSectionAdj, p, &anOff);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
PetscInt adof, aoff, i;
ierr = PetscSectionGetDof(rootSectionAdj, d, &adof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(rootSectionAdj, d, &aoff);CHKERRQ(ierr);
i = adof-1;
for (q = 0; q < anDof; q++) {
rootAdj[aoff+i] = anchorAdj[anOff+q];
--i;
}
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof, ngoff, nd;
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, padj, &ngoff);CHKERRQ(ierr);
for (nd = 0; nd < ndof-ncdof; ++nd) {
rootAdj[aoff+i] = ngoff < 0 ? -(ngoff+1)+nd : ngoff+nd;
--i;
}
}
}
}
/* Debugging */
if (debug) {
IS tmp;
ierr = PetscPrintf(comm, "Root adjacency indices\n");CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
ierr = ISView(tmp, NULL);CHKERRQ(ierr);
ierr = ISDestroy(&tmp);CHKERRQ(ierr);
}
/* Compress indices */
ierr = PetscSectionSetUp(rootSectionAdj);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof, cdof, off, d;
PetscInt adof, aoff;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
if (!dof) continue;
ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr);
if (adof <= 0) continue;
for (d = off; d < off+dof-cdof; ++d) {
ierr = PetscSectionGetDof(rootSectionAdj, d, &adof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(rootSectionAdj, d, &aoff);CHKERRQ(ierr);
ierr = PetscSortRemoveDupsInt(&adof, &rootAdj[aoff]);CHKERRQ(ierr);
ierr = PetscSectionSetDof(rootSectionAdj, d, adof);CHKERRQ(ierr);
}
}
/* Debugging */
if (debug) {
IS tmp;
ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots after compression:\n");CHKERRQ(ierr);
ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Root adjacency indices after compression\n");CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
ierr = ISView(tmp, NULL);CHKERRQ(ierr);
ierr = ISDestroy(&tmp);CHKERRQ(ierr);
}
/* Build adjacency section: Maps global indices to sets of adjacent global indices */
ierr = PetscSectionGetOffsetRange(sectionGlobal, &globalOffStart, &globalOffEnd);CHKERRQ(ierr);
ierr = PetscSectionCreate(comm, §ionAdj);CHKERRQ(ierr);
ierr = PetscSectionSetChart(sectionAdj, globalOffStart, globalOffEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt numAdj = PETSC_DETERMINE, dof, cdof, off, goff, d, q, anDof;
PetscBool found = PETSC_TRUE;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
for (d = 0; d < dof-cdof; ++d) {
PetscInt ldof, rdof;
ierr = PetscSectionGetDof(leafSectionAdj, off+d, &ldof);CHKERRQ(ierr);
ierr = PetscSectionGetDof(rootSectionAdj, off+d, &rdof);CHKERRQ(ierr);
if (ldof > 0) {
/* We do not own this point */
} else if (rdof > 0) {
ierr = PetscSectionSetDof(sectionAdj, goff+d, rdof);CHKERRQ(ierr);
} else {
found = PETSC_FALSE;
}
}
if (found) continue;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof, noff;
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, padj, &noff);CHKERRQ(ierr);
for (d = goff; d < goff+dof-cdof; ++d) {
ierr = PetscSectionAddDof(sectionAdj, d, ndof-ncdof);CHKERRQ(ierr);
}
}
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
if (anDof) {
for (d = goff; d < goff+dof-cdof; ++d) {
ierr = PetscSectionAddDof(sectionAdj, d, anDof);CHKERRQ(ierr);
}
}
}
ierr = PetscSectionSetUp(sectionAdj);CHKERRQ(ierr);
if (debug) {
ierr = PetscPrintf(comm, "Adjacency Section for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSectionView(sectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Get adjacent indices */
ierr = PetscSectionGetStorageSize(sectionAdj, &numCols);CHKERRQ(ierr);
ierr = PetscMalloc1(numCols, &cols);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt numAdj = PETSC_DETERMINE, dof, cdof, off, goff, d, q, anDof, anOff;
PetscBool found = PETSC_TRUE;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
for (d = 0; d < dof-cdof; ++d) {
PetscInt ldof, rdof;
ierr = PetscSectionGetDof(leafSectionAdj, off+d, &ldof);CHKERRQ(ierr);
ierr = PetscSectionGetDof(rootSectionAdj, off+d, &rdof);CHKERRQ(ierr);
if (ldof > 0) {
/* We do not own this point */
} else if (rdof > 0) {
PetscInt aoff, roff;
ierr = PetscSectionGetOffset(sectionAdj, goff+d, &aoff);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(rootSectionAdj, off+d, &roff);CHKERRQ(ierr);
ierr = PetscMemcpy(&cols[aoff], &rootAdj[roff], rdof * sizeof(PetscInt));CHKERRQ(ierr);
} else {
found = PETSC_FALSE;
}
}
if (found) continue;
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(anchorSectionAdj, p, &anOff);CHKERRQ(ierr);
for (d = goff; d < goff+dof-cdof; ++d) {
PetscInt adof, aoff, i = 0;
ierr = PetscSectionGetDof(sectionAdj, d, &adof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionAdj, d, &aoff);CHKERRQ(ierr);
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof, ngoff, nd;
const PetscInt *ncind;
/* Adjacent points may not be in the section chart */
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintIndices(section, padj, &ncind);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, padj, &ngoff);CHKERRQ(ierr);
for (nd = 0; nd < ndof-ncdof; ++nd, ++i) {
cols[aoff+i] = ngoff < 0 ? -(ngoff+1)+nd : ngoff+nd;
}
}
for (q = 0; q < anDof; q++, i++) {
cols[aoff+i] = anchorAdj[anOff + q];
}
if (i != adof) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of entries %D != %D for dof %D (point %D)", i, adof, d, p);
}
}
ierr = PetscSectionDestroy(&anchorSectionAdj);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&leafSectionAdj);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&rootSectionAdj);CHKERRQ(ierr);
ierr = PetscFree(anchorAdj);CHKERRQ(ierr);
ierr = PetscFree(rootAdj);CHKERRQ(ierr);
ierr = PetscFree(tmpAdj);CHKERRQ(ierr);
/* Debugging */
if (debug) {
IS tmp;
ierr = PetscPrintf(comm, "Column indices\n");CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, numCols, cols, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
ierr = ISView(tmp, NULL);CHKERRQ(ierr);
ierr = ISDestroy(&tmp);CHKERRQ(ierr);
}
/* Create allocation vectors from adjacency graph */
ierr = MatGetLocalSize(A, &locRows, NULL);CHKERRQ(ierr);
ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)A), &rLayout);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(rLayout, locRows);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(rLayout, 1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(rLayout);CHKERRQ(ierr);
ierr = PetscLayoutGetRange(rLayout, &rStart, &rEnd);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&rLayout);CHKERRQ(ierr);
/* Only loop over blocks of rows */
if (rStart%bs || rEnd%bs) SETERRQ3(PetscObjectComm((PetscObject)A), PETSC_ERR_ARG_WRONG, "Invalid layout [%d, %d) for matrix, must be divisible by block size %d", rStart, rEnd, bs);
for (r = rStart/bs; r < rEnd/bs; ++r) {
const PetscInt row = r*bs;
PetscInt numCols, cStart, c;
ierr = PetscSectionGetDof(sectionAdj, row, &numCols);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionAdj, row, &cStart);CHKERRQ(ierr);
for (c = cStart; c < cStart+numCols; ++c) {
if ((cols[c] >= rStart*bs) && (cols[c] < rEnd*bs)) {
++dnz[r-rStart];
if (cols[c] >= row) ++dnzu[r-rStart];
} else {
++onz[r-rStart];
if (cols[c] >= row) ++onzu[r-rStart];
}
}
}
if (bs > 1) {
for (r = 0; r < locRows/bs; ++r) {
dnz[r] /= bs;
onz[r] /= bs;
dnzu[r] /= bs;
onzu[r] /= bs;
}
}
/* Set matrix pattern */
ierr = MatXAIJSetPreallocation(A, bs, dnz, onz, dnzu, onzu);CHKERRQ(ierr);
ierr = MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
/* Check for symmetric storage */
ierr = MatGetType(A, &mtype);CHKERRQ(ierr);
ierr = PetscStrcmp(mtype, MATSBAIJ, &isSymBlock);CHKERRQ(ierr);
ierr = PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock);CHKERRQ(ierr);
ierr = PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock);CHKERRQ(ierr);
if (isSymBlock || isSymSeqBlock || isSymMPIBlock) {ierr = MatSetOption(A, MAT_IGNORE_LOWER_TRIANGULAR, PETSC_TRUE);CHKERRQ(ierr);}
/* Fill matrix with zeros */
if (fillMatrix) {
PetscScalar *values;
PetscInt maxRowLen = 0;
for (r = rStart; r < rEnd; ++r) {
PetscInt len;
ierr = PetscSectionGetDof(sectionAdj, r, &len);CHKERRQ(ierr);
maxRowLen = PetscMax(maxRowLen, len);
}
ierr = PetscCalloc1(maxRowLen, &values);CHKERRQ(ierr);
for (r = rStart; r < rEnd; ++r) {
PetscInt numCols, cStart;
ierr = PetscSectionGetDof(sectionAdj, r, &numCols);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionAdj, r, &cStart);CHKERRQ(ierr);
ierr = MatSetValues(A, 1, &r, numCols, &cols[cStart], values, INSERT_VALUES);CHKERRQ(ierr);
}
ierr = PetscFree(values);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
/* restore original useAnchors */
ierr = DMPlexSetAdjacencyUseAnchors(dm,useAnchors);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionAdj);CHKERRQ(ierr);
ierr = PetscFree(cols);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_Preallocate,dm,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
MatCreateSubMatrix - Creates a composite matrix that acts as a submatrix
Collective on Mat
Input Parameters:
+ A - matrix that we will extract a submatrix of
. isrow - rows to be present in the submatrix
- iscol - columns to be present in the submatrix
Output Parameters:
. newmat - new matrix
Level: developer
Notes:
Most will use MatGetSubMatrix which provides a more efficient representation if it is available.
.seealso: MatGetSubMatrix(), MatSubMatrixUpdate()
@*/
PetscErrorCode MatCreateSubMatrix(Mat A,IS isrow,IS iscol,Mat *newmat)
{
Vec left,right;
PetscInt m,n;
Mat N;
Mat_SubMatrix *Na;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(A,MAT_CLASSID,1);
PetscValidHeaderSpecific(isrow,IS_CLASSID,2);
PetscValidHeaderSpecific(iscol,IS_CLASSID,3);
PetscValidPointer(newmat,4);
*newmat = 0;
ierr = MatCreate(PetscObjectComm((PetscObject)A),&N);CHKERRQ(ierr);
ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr);
ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr);
ierr = MatSetSizes(N,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)N,MATSUBMATRIX);CHKERRQ(ierr);
ierr = PetscNewLog(N,Mat_SubMatrix,&Na);CHKERRQ(ierr);
N->data = (void*)Na;
ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)isrow);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)iscol);CHKERRQ(ierr);
Na->A = A;
Na->isrow = isrow;
Na->iscol = iscol;
Na->scale = 1.0;
N->ops->destroy = MatDestroy_SubMatrix;
N->ops->mult = MatMult_SubMatrix;
N->ops->multadd = MatMultAdd_SubMatrix;
N->ops->multtranspose = MatMultTranspose_SubMatrix;
N->ops->multtransposeadd = MatMultTransposeAdd_SubMatrix;
N->ops->scale = MatScale_SubMatrix;
N->ops->diagonalscale = MatDiagonalScale_SubMatrix;
ierr = PetscLayoutSetBlockSize(N->rmap,A->rmap->bs);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(N->cmap,A->cmap->bs);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(N->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(N->cmap);CHKERRQ(ierr);
ierr = MatGetVecs(A,&Na->rwork,&Na->lwork);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)isrow),&left);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)iscol),&right);CHKERRQ(ierr);
ierr = VecSetSizes(left,m,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetSizes(right,n,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetUp(left);CHKERRQ(ierr);
ierr = VecSetUp(right);CHKERRQ(ierr);
ierr = VecScatterCreate(Na->lwork,isrow,left,NULL,&Na->lrestrict);CHKERRQ(ierr);
ierr = VecScatterCreate(right,NULL,Na->rwork,iscol,&Na->rprolong);CHKERRQ(ierr);
ierr = VecDestroy(&left);CHKERRQ(ierr);
ierr = VecDestroy(&right);CHKERRQ(ierr);
N->assembled = PETSC_TRUE;
ierr = MatSetUp(N);CHKERRQ(ierr);
*newmat = N;
PetscFunctionReturn(0);
}
static PetscErrorCode PCSetUp_Redistribute(PC pc)
{
PC_Redistribute *red = (PC_Redistribute*)pc->data;
PetscErrorCode ierr;
MPI_Comm comm;
PetscInt rstart,rend,i,nz,cnt,*rows,ncnt,dcnt,*drows;
PetscLayout map,nmap;
PetscMPIInt size,imdex,tag,n;
PetscInt *source = PETSC_NULL;
PetscMPIInt *nprocs = PETSC_NULL,nrecvs;
PetscInt j,nsends;
PetscInt *owner = PETSC_NULL,*starts = PETSC_NULL,count,slen;
PetscInt *rvalues,*svalues,recvtotal;
PetscMPIInt *onodes1,*olengths1;
MPI_Request *send_waits = PETSC_NULL,*recv_waits = PETSC_NULL;
MPI_Status recv_status,*send_status;
Vec tvec,diag;
Mat tmat;
const PetscScalar *d;
PetscFunctionBegin;
if (pc->setupcalled) {
ierr = KSPGetOperators(red->ksp,PETSC_NULL,&tmat,PETSC_NULL);CHKERRQ(ierr);
ierr = MatGetSubMatrix(pc->pmat,red->is,red->is,MAT_REUSE_MATRIX,&tmat);CHKERRQ(ierr);
ierr = KSPSetOperators(red->ksp,tmat,tmat,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
} else {
PetscInt NN;
ierr = PetscObjectGetComm((PetscObject)pc,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = PetscObjectGetNewTag((PetscObject)pc,&tag);CHKERRQ(ierr);
/* count non-diagonal rows on process */
ierr = MatGetOwnershipRange(pc->mat,&rstart,&rend);CHKERRQ(ierr);
cnt = 0;
for (i=rstart; i<rend; i++) {
ierr = MatGetRow(pc->mat,i,&nz,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
if (nz > 1) cnt++;
ierr = MatRestoreRow(pc->mat,i,&nz,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
}
ierr = PetscMalloc(cnt*sizeof(PetscInt),&rows);CHKERRQ(ierr);
ierr = PetscMalloc((rend - rstart - cnt)*sizeof(PetscInt),&drows);CHKERRQ(ierr);
/* list non-diagonal rows on process */
cnt = 0; dcnt = 0;
for (i=rstart; i<rend; i++) {
ierr = MatGetRow(pc->mat,i,&nz,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
if (nz > 1) rows[cnt++] = i;
else drows[dcnt++] = i - rstart;
ierr = MatRestoreRow(pc->mat,i,&nz,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
}
/* create PetscLayout for non-diagonal rows on each process */
ierr = PetscLayoutCreate(comm,&map);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(map,cnt);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(map,1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(map);CHKERRQ(ierr);
rstart = map->rstart;
rend = map->rend;
/* create PetscLayout for load-balanced non-diagonal rows on each process */
ierr = PetscLayoutCreate(comm,&nmap);CHKERRQ(ierr);
ierr = MPI_Allreduce(&cnt,&ncnt,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);
ierr = PetscLayoutSetSize(nmap,ncnt);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(nmap,1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(nmap);CHKERRQ(ierr);
ierr = MatGetSize(pc->pmat,&NN,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscInfo2(pc,"Number of diagonal rows eliminated %d, percentage eliminated %g\n",NN-ncnt,((PetscReal)(NN-ncnt))/((PetscReal)(NN)));CHKERRQ(ierr);
/*
this code is taken from VecScatterCreate_PtoS()
Determines what rows need to be moved where to
load balance the non-diagonal rows
*/
/* count number of contributors to each processor */
ierr = PetscMalloc2(size,PetscMPIInt,&nprocs,cnt,PetscInt,&owner);CHKERRQ(ierr);
ierr = PetscMemzero(nprocs,size*sizeof(PetscMPIInt));CHKERRQ(ierr);
j = 0;
nsends = 0;
for (i=rstart; i<rend; i++) {
if (i < nmap->range[j]) j = 0;
for (; j<size; j++) {
if (i < nmap->range[j+1]) {
if (!nprocs[j]++) nsends++;
owner[i-rstart] = j;
break;
}
}
}
/* inform other processors of number of messages and max length*/
ierr = PetscGatherNumberOfMessages(comm,PETSC_NULL,nprocs,&nrecvs);CHKERRQ(ierr);
ierr = PetscGatherMessageLengths(comm,nsends,nrecvs,nprocs,&onodes1,&olengths1);CHKERRQ(ierr);
ierr = PetscSortMPIIntWithArray(nrecvs,onodes1,olengths1);CHKERRQ(ierr);
recvtotal = 0; for (i=0; i<nrecvs; i++) recvtotal += olengths1[i];
/* post receives: rvalues - rows I will own; count - nu */
ierr = PetscMalloc3(recvtotal,PetscInt,&rvalues,nrecvs,PetscInt,&source,nrecvs,MPI_Request,&recv_waits);CHKERRQ(ierr);
count = 0;
for (i=0; i<nrecvs; i++) {
ierr = MPI_Irecv((rvalues+count),olengths1[i],MPIU_INT,onodes1[i],tag,comm,recv_waits+i);CHKERRQ(ierr);
count += olengths1[i];
}
/* do sends:
1) starts[i] gives the starting index in svalues for stuff going to
the ith processor
*/
ierr = PetscMalloc3(cnt,PetscInt,&svalues,nsends,MPI_Request,&send_waits,size,PetscInt,&starts);CHKERRQ(ierr);
starts[0] = 0;
for (i=1; i<size; i++) { starts[i] = starts[i-1] + nprocs[i-1];}
for (i=0; i<cnt; i++) {
svalues[starts[owner[i]]++] = rows[i];
}
for (i=0; i<cnt; i++) rows[i] = rows[i] - rstart;
red->drows = drows;
red->dcnt = dcnt;
ierr = PetscFree(rows);CHKERRQ(ierr);
starts[0] = 0;
for (i=1; i<size; i++) { starts[i] = starts[i-1] + nprocs[i-1];}
count = 0;
for (i=0; i<size; i++) {
if (nprocs[i]) {
ierr = MPI_Isend(svalues+starts[i],nprocs[i],MPIU_INT,i,tag,comm,send_waits+count++);CHKERRQ(ierr);
}
}
/* wait on receives */
count = nrecvs;
slen = 0;
while (count) {
ierr = MPI_Waitany(nrecvs,recv_waits,&imdex,&recv_status);CHKERRQ(ierr);
/* unpack receives into our local space */
ierr = MPI_Get_count(&recv_status,MPIU_INT,&n);CHKERRQ(ierr);
slen += n;
count--;
}
if (slen != recvtotal) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Total message lengths %D not expected %D",slen,recvtotal);
ierr = ISCreateGeneral(comm,slen,rvalues,PETSC_COPY_VALUES,&red->is);CHKERRQ(ierr);
/* free up all work space */
ierr = PetscFree(olengths1);CHKERRQ(ierr);
ierr = PetscFree(onodes1);CHKERRQ(ierr);
ierr = PetscFree3(rvalues,source,recv_waits);CHKERRQ(ierr);
ierr = PetscFree2(nprocs,owner);CHKERRQ(ierr);
if (nsends) { /* wait on sends */
ierr = PetscMalloc(nsends*sizeof(MPI_Status),&send_status);CHKERRQ(ierr);
ierr = MPI_Waitall(nsends,send_waits,send_status);CHKERRQ(ierr);
ierr = PetscFree(send_status);CHKERRQ(ierr);
}
ierr = PetscFree3(svalues,send_waits,starts);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&map);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&nmap);CHKERRQ(ierr);
ierr = VecCreateMPI(comm,slen,PETSC_DETERMINE,&red->b);CHKERRQ(ierr);
ierr = VecDuplicate(red->b,&red->x);CHKERRQ(ierr);
ierr = MatGetVecs(pc->pmat,&tvec,PETSC_NULL);CHKERRQ(ierr);
ierr = VecScatterCreate(tvec,red->is,red->b,PETSC_NULL,&red->scatter);CHKERRQ(ierr);
ierr = VecDestroy(&tvec);CHKERRQ(ierr);
ierr = MatGetSubMatrix(pc->pmat,red->is,red->is,MAT_INITIAL_MATRIX,&tmat);CHKERRQ(ierr);
ierr = KSPSetOperators(red->ksp,tmat,tmat,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatDestroy(&tmat);CHKERRQ(ierr);
}
/* get diagonal portion of matrix */
ierr = PetscMalloc(red->dcnt*sizeof(PetscScalar),&red->diag);CHKERRQ(ierr);
ierr = MatGetVecs(pc->pmat,&diag,PETSC_NULL);CHKERRQ(ierr);
ierr = MatGetDiagonal(pc->pmat,diag);CHKERRQ(ierr);
ierr = VecGetArrayRead(diag,&d);CHKERRQ(ierr);
for (i=0; i<red->dcnt; i++) {
red->diag[i] = 1.0/d[red->drows[i]];
}
ierr = VecRestoreArrayRead(diag,&d);CHKERRQ(ierr);
ierr = VecDestroy(&diag);CHKERRQ(ierr);
ierr = KSPSetUp(red->ksp);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
MatCreateLocalRef - Gets a logical reference to a local submatrix, for use in assembly
Not Collective
Input Arguments:
+ A - Full matrix, generally parallel
. isrow - Local index set for the rows
- iscol - Local index set for the columns
Output Arguments:
. newmat - New serial Mat
Level: developer
Notes:
Most will use MatGetLocalSubMatrix() which returns a real matrix corresponding to the local
block if it available, such as with matrix formats that store these blocks separately.
The new matrix forwards MatSetValuesLocal() and MatSetValuesBlockedLocal() to the global system.
In general, it does not define MatMult() or any other functions. Local submatrices can be nested.
.seealso: MatSetValuesLocal(), MatSetValuesBlockedLocal(), MatGetLocalSubMatrix(), MatCreateSubMatrix()
@*/
PetscErrorCode MatCreateLocalRef(Mat A,IS isrow,IS iscol,Mat *newmat)
{
PetscErrorCode ierr;
Mat_LocalRef *lr;
Mat B;
PetscInt m,n;
PetscBool islr;
PetscFunctionBegin;
PetscValidHeaderSpecific(A,MAT_CLASSID,1);
PetscValidHeaderSpecific(isrow,IS_CLASSID,2);
PetscValidHeaderSpecific(iscol,IS_CLASSID,3);
PetscValidPointer(newmat,4);
*newmat = 0;
ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr);
ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr);
ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr);
ierr = MatSetSizes(B,m,n,m,n);CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)B,MATLOCALREF);CHKERRQ(ierr);
ierr = MatSetUp(B);CHKERRQ(ierr);
B->ops->destroy = MatDestroy_LocalRef;
ierr = PetscNewLog(B,Mat_LocalRef,&lr);CHKERRQ(ierr);
B->data = (void*)lr;
ierr = PetscObjectTypeCompare((PetscObject)A,MATLOCALREF,&islr);CHKERRQ(ierr);
if (islr) {
Mat_LocalRef *alr = (Mat_LocalRef*)A->data;
lr->Top = alr->Top;
} else {
/* This does not increase the reference count because MatLocalRef is not allowed to live longer than its parent */
lr->Top = A;
}
{
ISLocalToGlobalMapping rltog,cltog;
PetscInt abs,rbs,cbs;
/* We will translate directly to global indices for the top level */
lr->SetValues = MatSetValues;
lr->SetValuesBlocked = MatSetValuesBlocked;
B->ops->setvalueslocal = MatSetValuesLocal_LocalRef_Scalar;
ierr = ISL2GCompose(isrow,A->rmap->mapping,&rltog);CHKERRQ(ierr);
if (isrow == iscol && A->rmap->mapping == A->cmap->mapping) {
ierr = PetscObjectReference((PetscObject)rltog);CHKERRQ(ierr);
cltog = rltog;
} else {
ierr = ISL2GCompose(iscol,A->cmap->mapping,&cltog);CHKERRQ(ierr);
}
ierr = MatSetLocalToGlobalMapping(B,rltog,cltog);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingDestroy(&rltog);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingDestroy(&cltog);CHKERRQ(ierr);
ierr = MatGetBlockSize(A,&abs);CHKERRQ(ierr);
ierr = ISGetBlockSize(isrow,&rbs);CHKERRQ(ierr);
ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr);
if (rbs == cbs) { /* submatrix has block structure, so user can insert values with blocked interface */
ierr = PetscLayoutSetBlockSize(B->rmap,rbs);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(B->cmap,cbs);CHKERRQ(ierr);
if (abs != rbs || abs == 1) {
/* Top-level matrix has different block size, so we have to call its scalar insertion interface */
B->ops->setvaluesblockedlocal = MatSetValuesBlockedLocal_LocalRef_Scalar;
} else {
/* Block sizes match so we can forward values to the top level using the block interface */
B->ops->setvaluesblockedlocal = MatSetValuesBlockedLocal_LocalRef_Block;
ierr = ISL2GComposeBlock(isrow,A->rmap->bmapping,&rltog);CHKERRQ(ierr);
if (isrow == iscol && A->rmap->bmapping == A->cmap->bmapping) {
ierr = PetscObjectReference((PetscObject)rltog);CHKERRQ(ierr);
cltog = rltog;
} else {
ierr = ISL2GComposeBlock(iscol,A->cmap->bmapping,&cltog);CHKERRQ(ierr);
}
ierr = MatSetLocalToGlobalMappingBlock(B,rltog,cltog);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingDestroy(&rltog);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingDestroy(&cltog);CHKERRQ(ierr);
}
}
}
*newmat = B;
PetscFunctionReturn(0);
}
PetscErrorCode MatGetMultiProcBlock_MPIAIJ(Mat mat, MPI_Comm subComm, MatReuse scall,Mat *subMat)
{
PetscErrorCode ierr;
Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data;
Mat_SeqAIJ *aijB = (Mat_SeqAIJ*)aij->B->data;
PetscMPIInt commRank,subCommSize,subCommRank;
PetscMPIInt *commRankMap,subRank,rank,commsize;
PetscInt *garrayCMap,col,i,j,*nnz,newRow,newCol;
PetscFunctionBegin;
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&commsize);CHKERRQ(ierr);
ierr = MPI_Comm_size(subComm,&subCommSize);CHKERRQ(ierr);
/* create subMat object with the relavent layout */
if (scall == MAT_INITIAL_MATRIX) {
ierr = MatCreate(subComm,subMat);CHKERRQ(ierr);
ierr = MatSetType(*subMat,MATMPIAIJ);CHKERRQ(ierr);
ierr = MatSetSizes(*subMat,mat->rmap->n,mat->cmap->n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetBlockSizes(*subMat,mat->rmap->bs,mat->cmap->bs);CHKERRQ(ierr);
/* need to setup rmap and cmap before Preallocation */
ierr = PetscLayoutSetBlockSize((*subMat)->rmap,mat->rmap->bs);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize((*subMat)->cmap,mat->cmap->bs);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((*subMat)->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((*subMat)->cmap);CHKERRQ(ierr);
}
/* create a map of comm_rank from subComm to comm - should commRankMap and garrayCMap be kept for reused? */
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&commRank);CHKERRQ(ierr);
ierr = MPI_Comm_rank(subComm,&subCommRank);CHKERRQ(ierr);
ierr = PetscMalloc1(subCommSize,&commRankMap);CHKERRQ(ierr);
ierr = MPI_Allgather(&commRank,1,MPI_INT,commRankMap,1,MPI_INT,subComm);CHKERRQ(ierr);
/* Traverse garray and identify column indices [of offdiag mat] that
should be discarded. For the ones not discarded, store the newCol+1
value in garrayCMap */
ierr = PetscCalloc1(aij->B->cmap->n,&garrayCMap);CHKERRQ(ierr);
for (i=0; i<aij->B->cmap->n; i++) {
col = aij->garray[i];
for (subRank=0; subRank<subCommSize; subRank++) {
rank = commRankMap[subRank];
if ((col >= mat->cmap->range[rank]) && (col < mat->cmap->range[rank+1])) {
garrayCMap[i] = (*subMat)->cmap->range[subRank] + col - mat->cmap->range[rank]+1;
break;
}
}
}
if (scall == MAT_INITIAL_MATRIX) {
/* Now compute preallocation for the offdiag mat */
ierr = PetscCalloc1(aij->B->rmap->n,&nnz);CHKERRQ(ierr);
for (i=0; i<aij->B->rmap->n; i++) {
for (j=aijB->i[i]; j<aijB->i[i+1]; j++) {
if (garrayCMap[aijB->j[j]]) nnz[i]++;
}
}
ierr = MatMPIAIJSetPreallocation(*(subMat),0,NULL,0,nnz);CHKERRQ(ierr);
/* reuse diag block with the new submat */
ierr = MatDestroy(&((Mat_MPIAIJ*)((*subMat)->data))->A);CHKERRQ(ierr);
((Mat_MPIAIJ*)((*subMat)->data))->A = aij->A;
ierr = PetscObjectReference((PetscObject)aij->A);CHKERRQ(ierr);
} else if (((Mat_MPIAIJ*)(*subMat)->data)->A != aij->A) {
PetscObject obj = (PetscObject)((Mat_MPIAIJ*)((*subMat)->data))->A;
ierr = PetscObjectReference((PetscObject)obj);CHKERRQ(ierr);
((Mat_MPIAIJ*)((*subMat)->data))->A = aij->A;
ierr = PetscObjectReference((PetscObject)aij->A);CHKERRQ(ierr);
}
/* Now traverse aij->B and insert values into subMat */
for (i=0; i<aij->B->rmap->n; i++) {
newRow = (*subMat)->rmap->range[subCommRank] + i;
for (j=aijB->i[i]; j<aijB->i[i+1]; j++) {
newCol = garrayCMap[aijB->j[j]];
if (newCol) {
newCol--; /* remove the increment */
ierr = MatSetValues(*subMat,1,&newRow,1,&newCol,(aijB->a+j),INSERT_VALUES);CHKERRQ(ierr);
}
}
}
/* assemble the submat */
ierr = MatAssemblyBegin(*subMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*subMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* deallocate temporary data */
ierr = PetscFree(commRankMap);CHKERRQ(ierr);
ierr = PetscFree(garrayCMap);CHKERRQ(ierr);
if (scall == MAT_INITIAL_MATRIX) {
ierr = PetscFree(nnz);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode MatSetupDM_HYPREStruct(Mat mat,DM da)
{
PetscErrorCode ierr;
Mat_HYPREStruct *ex = (Mat_HYPREStruct*) mat->data;
PetscInt dim,dof,sw[3],nx,ny,nz,ilower[3],iupper[3],ssize,i;
DMBoundaryType px,py,pz;
DMDAStencilType st;
ISLocalToGlobalMapping ltog;
PetscFunctionBegin;
ex->da = da;
ierr = PetscObjectReference((PetscObject)da);CHKERRQ(ierr);
ierr = DMDAGetInfo(ex->da,&dim,0,0,0,0,0,0,&dof,&sw[0],&px,&py,&pz,&st);CHKERRQ(ierr);
ierr = DMDAGetCorners(ex->da,&ilower[0],&ilower[1],&ilower[2],&iupper[0],&iupper[1],&iupper[2]);CHKERRQ(ierr);
iupper[0] += ilower[0] - 1;
iupper[1] += ilower[1] - 1;
iupper[2] += ilower[2] - 1;
/* the hypre_Box is used to zero out the matrix entries in MatZeroValues() */
ex->hbox.imin[0] = ilower[0];
ex->hbox.imin[1] = ilower[1];
ex->hbox.imin[2] = ilower[2];
ex->hbox.imax[0] = iupper[0];
ex->hbox.imax[1] = iupper[1];
ex->hbox.imax[2] = iupper[2];
/* create the hypre grid object and set its information */
if (dof > 1) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Currently only support for scalar problems");
if (px || py || pz) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Ask us to add periodic support by calling HYPRE_StructGridSetPeriodic()");
PetscStackCallStandard(HYPRE_StructGridCreate,(ex->hcomm,dim,&ex->hgrid));
PetscStackCallStandard(HYPRE_StructGridSetExtents,(ex->hgrid,(HYPRE_Int *)ilower,(HYPRE_Int *)iupper));
PetscStackCallStandard(HYPRE_StructGridAssemble,(ex->hgrid));
sw[1] = sw[0];
sw[2] = sw[1];
PetscStackCallStandard(HYPRE_StructGridSetNumGhost,(ex->hgrid,(HYPRE_Int *)sw));
/* create the hypre stencil object and set its information */
if (sw[0] > 1) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Ask us to add support for wider stencils");
if (st == DMDA_STENCIL_BOX) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Ask us to add support for box stencils");
if (dim == 1) {
PetscInt offsets[3][1] = {{-1},{0},{1}};
ssize = 3;
PetscStackCallStandard(HYPRE_StructStencilCreate,(dim,ssize,&ex->hstencil));
for (i=0; i<ssize; i++) {
PetscStackCallStandard(HYPRE_StructStencilSetElement,(ex->hstencil,i,(HYPRE_Int *)offsets[i]));
}
} else if (dim == 2) {
PetscInt offsets[5][2] = {{0,-1},{-1,0},{0,0},{1,0},{0,1}};
ssize = 5;
PetscStackCallStandard(HYPRE_StructStencilCreate,(dim,ssize,&ex->hstencil));
for (i=0; i<ssize; i++) {
PetscStackCallStandard(HYPRE_StructStencilSetElement,(ex->hstencil,i,(HYPRE_Int *)offsets[i]));
}
} else if (dim == 3) {
PetscInt offsets[7][3] = {{0,0,-1},{0,-1,0},{-1,0,0},{0,0,0},{1,0,0},{0,1,0},{0,0,1}};
ssize = 7;
PetscStackCallStandard(HYPRE_StructStencilCreate,(dim,ssize,&ex->hstencil));
for (i=0; i<ssize; i++) {
PetscStackCallStandard(HYPRE_StructStencilSetElement,(ex->hstencil,i,(HYPRE_Int *)offsets[i]));
}
}
/* create the HYPRE vector for rhs and solution */
PetscStackCallStandard(HYPRE_StructVectorCreate,(ex->hcomm,ex->hgrid,&ex->hb));
PetscStackCallStandard(HYPRE_StructVectorCreate,(ex->hcomm,ex->hgrid,&ex->hx));
PetscStackCallStandard(HYPRE_StructVectorInitialize,(ex->hb));
PetscStackCallStandard(HYPRE_StructVectorInitialize,(ex->hx));
PetscStackCallStandard(HYPRE_StructVectorAssemble,(ex->hb));
PetscStackCallStandard(HYPRE_StructVectorAssemble,(ex->hx));
/* create the hypre matrix object and set its information */
PetscStackCallStandard(HYPRE_StructMatrixCreate,(ex->hcomm,ex->hgrid,ex->hstencil,&ex->hmat));
PetscStackCallStandard(HYPRE_StructGridDestroy,(ex->hgrid));
PetscStackCallStandard(HYPRE_StructStencilDestroy,(ex->hstencil));
if (ex->needsinitialization) {
PetscStackCallStandard(HYPRE_StructMatrixInitialize,(ex->hmat));
ex->needsinitialization = PETSC_FALSE;
}
/* set the global and local sizes of the matrix */
ierr = DMDAGetCorners(da,0,0,0,&nx,&ny,&nz);CHKERRQ(ierr);
ierr = MatSetSizes(mat,dof*nx*ny*nz,dof*nx*ny*nz,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(mat->rmap,1);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(mat->cmap,1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(mat->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(mat->cmap);CHKERRQ(ierr);
if (dim == 3) {
mat->ops->setvalueslocal = MatSetValuesLocal_HYPREStruct_3d;
mat->ops->zerorowslocal = MatZeroRowsLocal_HYPREStruct_3d;
mat->ops->zeroentries = MatZeroEntries_HYPREStruct_3d;
ierr = MatZeroEntries_HYPREStruct_3d(mat);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Only support for 3d DMDA currently");
/* get values that will be used repeatedly in MatSetValuesLocal() and MatZeroRowsLocal() repeatedly */
ierr = MatGetOwnershipRange(mat,&ex->rstart,NULL);CHKERRQ(ierr);
ierr = DMGetLocalToGlobalMapping(ex->da,<og);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetIndices(ltog, (const PetscInt **) &ex->gindices);CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(ex->da,0,0,0,&ex->gnx,&ex->gnxgny,0);CHKERRQ(ierr);
ex->gnxgny *= ex->gnx;
ierr = DMDAGetCorners(ex->da,&ex->xs,&ex->ys,&ex->zs,&ex->nx,&ex->ny,0);CHKERRQ(ierr);
ex->nxny = ex->nx*ex->ny;
PetscFunctionReturn(0);
}
