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);
}
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "MatCreate_Shell"
PetscErrorCode MatCreate_Shell(Mat A)
{
Mat_Shell *b;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscMemcpy(A->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr);
ierr = PetscNewLog(A,Mat_Shell,&b);CHKERRQ(ierr);
A->data = (void*)b;
ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr);
b->ctx = 0;
b->vshift = 0.0;
b->vscale = 1.0;
b->mult = 0;
b->multtranspose = 0;
b->getdiagonal = 0;
A->assembled = PETSC_TRUE;
A->preallocated = PETSC_FALSE;
ierr = PetscObjectChangeTypeName((PetscObject)A,MATSHELL);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 = PetscLayoutSetUp((*N)->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((*N)->cmap);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)->ops->duplicate = MatDuplicate_Transpose;
(*N)->ops->getvecs = MatCreateVecs_Transpose;
(*N)->ops->axpy = MatAXPY_Transpose;
(*N)->assembled = PETSC_TRUE;
ierr = PetscObjectComposeFunction((PetscObject)(*N),"MatTransposeGetMat_C",MatTransposeGetMat_Transpose);CHKERRQ(ierr);
ierr = MatSetBlockSizes(*N,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr);
ierr = MatSetUp(*N);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 PETSCMAT_DLLEXPORT MatCreateTranspose(Mat A,Mat *N)
{
PetscErrorCode ierr;
PetscInt m,n;
Mat_Transpose *Na;
PetscFunctionBegin;
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatCreate(((PetscObject)A)->comm,N);CHKERRQ(ierr);
ierr = MatSetSizes(*N,n,m,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)*N,MATTRANSPOSEMAT);CHKERRQ(ierr);
ierr = PetscNewLog(*N,Mat_Transpose,&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);
PetscFunctionReturn(0);
}
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);
}
PETSC_EXTERN PetscErrorCode 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 = 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);
}
/*@
MatXAIJSetPreallocation - set preallocation for serial and parallel AIJ, BAIJ, and SBAIJ matrices
Collective on Mat
Input Arguments:
+ A - matrix being preallocated
. bs - block size
. dnnz - number of nonzero blocks per block row of diagonal part of parallel matrix
. onnz - number of nonzero blocks per block row of off-diagonal part of parallel matrix
. dnnzu - number of nonzero blocks per block row of upper-triangular part of diagonal part of parallel matrix
- onnzu - number of nonzero blocks per block row of upper-triangular part of off-diagonal part of parallel matrix
Level: beginner
.seealso: MatSeqAIJSetPreallocation(), MatMPIAIJSetPreallocation(), MatSeqBAIJSetPreallocation(), MatMPIBAIJSetPreallocation(), MatSeqSBAIJSetPreallocation(), MatMPISBAIJSetPreallocation(),
PetscSplitOwnership()
@*/
PetscErrorCode MatXAIJSetPreallocation(Mat A,PetscInt bs,const PetscInt dnnz[],const PetscInt onnz[],const PetscInt dnnzu[],const PetscInt onnzu[])
{
PetscErrorCode ierr;
void (*aij)(void);
PetscFunctionBegin;
ierr = MatSetBlockSize(A,bs);
CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->rmap);
CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->cmap);
CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation(A,bs,0,dnnz);
CHKERRQ(ierr);
ierr = MatMPIBAIJSetPreallocation(A,bs,0,dnnz,0,onnz);
CHKERRQ(ierr);
ierr = MatSeqSBAIJSetPreallocation(A,bs,0,dnnzu);
CHKERRQ(ierr);
ierr = MatMPISBAIJSetPreallocation(A,bs,0,dnnzu,0,onnzu);
CHKERRQ(ierr);
/*
In general, we have to do extra work to preallocate for scalar (AIJ) matrices so we check whether it will do any
good before going on with it.
*/
ierr = PetscObjectQueryFunction((PetscObject)A,"MatMPIAIJSetPreallocation_C",&aij);
CHKERRQ(ierr);
if (!aij) {
ierr = PetscObjectQueryFunction((PetscObject)A,"MatSeqAIJSetPreallocation_C",&aij);
CHKERRQ(ierr);
}
if (aij) {
if (bs == 1) {
ierr = MatSeqAIJSetPreallocation(A,0,dnnz);
CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(A,0,dnnz,0,onnz);
CHKERRQ(ierr);
} else { /* Convert block-row precallocation to scalar-row */
PetscInt i,m,*sdnnz,*sonnz;
ierr = MatGetLocalSize(A,&m,NULL);
CHKERRQ(ierr);
ierr = PetscMalloc2((!!dnnz)*m,PetscInt,&sdnnz,(!!onnz)*m,PetscInt,&sonnz);
CHKERRQ(ierr);
for (i=0; i<m; i++) {
if (dnnz) sdnnz[i] = dnnz[i/bs] * bs;
if (onnz) sonnz[i] = onnz[i/bs] * bs;
}
ierr = MatSeqAIJSetPreallocation(A,0,dnnz ? sdnnz : NULL);
CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(A,0,dnnz ? sdnnz : NULL,0,onnz ? sonnz : NULL);
CHKERRQ(ierr);
ierr = PetscFree2(sdnnz,sonnz);
CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
/*@
MatSchurComplementSet - Sets the matrices that define the Schur complement
Collective on Mat
Input Parameter:
+ N - matrix obtained with MatCreate() and MatSetType(MATSCHURCOMPLEMENT);
- A00,A01,A10,A11 - the four parts of the original matrix (A00 is optional)
Level: intermediate
Notes: The Schur complement is NOT actually formed! Rather this
object performs the matrix-vector product by using the the formula for
the Schur complement and a KSP solver to approximate the action of inv(A)
All four matrices must have the same MPI communicator
A00 and A11 must be square matrices
.seealso: MatCreateNormal(), MatMult(), MatCreate(), MatSchurComplementGetKSP(), MatSchurComplementUpdate(), MatCreateTranspose(), MatGetSchurComplement()
@*/
PetscErrorCode MatSchurComplementSet(Mat N,Mat A00,Mat Ap00,Mat A01,Mat A10,Mat A11)
{
PetscErrorCode ierr;
PetscInt m,n;
Mat_SchurComplement *Na = (Mat_SchurComplement*)N->data;
PetscFunctionBegin;
if (N->assembled) SETERRQ(((PetscObject)N)->comm,PETSC_ERR_ARG_WRONGSTATE,"Use MatSchurComplementUpdate() for already used matrix");
PetscValidHeaderSpecific(A00,MAT_CLASSID,1);
PetscValidHeaderSpecific(Ap00,MAT_CLASSID,2);
PetscValidHeaderSpecific(A01,MAT_CLASSID,3);
PetscValidHeaderSpecific(A10,MAT_CLASSID,4);
PetscCheckSameComm(A00,1,Ap00,2);
PetscCheckSameComm(A00,1,A01,3);
PetscCheckSameComm(A00,1,A10,4);
if (A00->rmap->n != A00->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of A00 %D do not equal local columns %D",A00->rmap->n,A00->cmap->n);
if (A00->rmap->n != Ap00->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of A00 %D do not equal local rows of Ap00 %D",A00->rmap->n,Ap00->rmap->n);
if (Ap00->rmap->n != Ap00->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of Ap00 %D do not equal local columns %D",Ap00->rmap->n,Ap00->cmap->n);
if (A00->cmap->n != A01->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local columns of A00 %D do not equal local rows of A01 %D",A00->cmap->n,A01->rmap->n);
if (A10->cmap->n != A00->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local columns of A10 %D do not equal local rows of A00 %D",A10->cmap->n,A00->rmap->n);
if (A11) {
PetscValidHeaderSpecific(A11,MAT_CLASSID,5);
PetscCheckSameComm(A00,1,A11,5);
if (A11->rmap->n != A11->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of A11 %D do not equal local columns %D",A11->rmap->n,A11->cmap->n);
if (A10->rmap->n != A11->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local rows of A10 %D do not equal local rows A11 %D",A10->rmap->n,A11->rmap->n);
}
ierr = MatGetLocalSize(A01,PETSC_NULL,&n);CHKERRQ(ierr);
ierr = MatGetLocalSize(A10,&m,PETSC_NULL);CHKERRQ(ierr);
ierr = MatSetSizes(N,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)A00);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)Ap00);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)A01);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)A10);CHKERRQ(ierr);
Na->A = A00;
Na->Ap = Ap00;
Na->B = A01;
Na->C = A10;
Na->D = A11;
if (A11) {
ierr = PetscObjectReference((PetscObject)A11);CHKERRQ(ierr);
}
N->assembled = PETSC_TRUE;
N->preallocated = PETSC_TRUE;
ierr = PetscLayoutSetUp((N)->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp((N)->cmap);CHKERRQ(ierr);
ierr = KSPSetOperators(Na->ksp,A00,Ap00,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode MatCreate_IS(Mat A)
{
PetscErrorCode ierr;
Mat_IS *b;
PetscFunctionBegin;
ierr = PetscNewLog(A,&b);CHKERRQ(ierr);
A->data = (void*)b;
ierr = PetscMemzero(A->ops,sizeof(struct _MatOps));CHKERRQ(ierr);
A->ops->mult = MatMult_IS;
A->ops->multadd = MatMultAdd_IS;
A->ops->multtranspose = MatMultTranspose_IS;
A->ops->multtransposeadd = MatMultTransposeAdd_IS;
A->ops->destroy = MatDestroy_IS;
A->ops->setlocaltoglobalmapping = MatSetLocalToGlobalMapping_IS;
A->ops->setvalues = MatSetValues_IS;
A->ops->setvalueslocal = MatSetValuesLocal_IS;
A->ops->setvaluesblockedlocal = MatSetValuesBlockedLocal_IS;
A->ops->zerorows = MatZeroRows_IS;
A->ops->zerorowslocal = MatZeroRowsLocal_IS;
A->ops->assemblybegin = MatAssemblyBegin_IS;
A->ops->assemblyend = MatAssemblyEnd_IS;
A->ops->view = MatView_IS;
A->ops->zeroentries = MatZeroEntries_IS;
A->ops->scale = MatScale_IS;
A->ops->getdiagonal = MatGetDiagonal_IS;
A->ops->setoption = MatSetOption_IS;
A->ops->ishermitian = MatIsHermitian_IS;
A->ops->issymmetric = MatIsSymmetric_IS;
A->ops->duplicate = MatDuplicate_IS;
ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr);
/* zeros pointer */
b->A = 0;
b->ctx = 0;
b->x = 0;
b->y = 0;
b->mapping = 0;
/* special MATIS functions */
ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetLocalMat_C",MatISGetLocalMat_IS);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetLocalMat_C",MatISSetLocalMat_IS);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetMPIXAIJ_C",MatISGetMPIXAIJ_IS);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetPreallocation_C",MatISSetPreallocation_IS);CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)A,MATIS);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ISCreateGeneral_Private(IS is)
{
PetscErrorCode ierr;
IS_General *sub = (IS_General*)is->data;
const PetscInt *idx = sub->idx;
PetscBool sorted = PETSC_TRUE;
PetscInt n,i,min,max;
PetscFunctionBegin;
ierr = PetscLayoutGetLocalSize(is->map, &n);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];
}
sub->sorted = sorted;
is->min = min;
is->max = max;
is->isperm = PETSC_FALSE;
is->isidentity = PETSC_FALSE;
ierr = ISViewFromOptions(is,NULL,"-is_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode VecCreate_Seq_Private(Vec v,const PetscScalar array[])
{
Vec_Seq *s;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscNewLog(v,&s);CHKERRQ(ierr);
ierr = PetscMemcpy(v->ops,&DvOps,sizeof(DvOps));CHKERRQ(ierr);
v->data = (void*)s;
v->petscnative = PETSC_TRUE;
s->array = (PetscScalar*)array;
s->array_allocated = 0;
ierr = PetscLayoutSetUp(v->map);CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)v,VECSEQ);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MATLAB_ENGINE)
ierr = PetscObjectComposeFunction((PetscObject)v,"PetscMatlabEnginePut_C",VecMatlabEnginePut_Default);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)v,"PetscMatlabEngineGet_C",VecMatlabEngineGet_Default);CHKERRQ(ierr);
#endif
#if defined(PETSC_USE_MIXED_PRECISION)
((PetscObject)v)->precision = (PetscPrecision)sizeof(PetscReal);
#endif
PetscFunctionReturn(0);
}
PetscErrorCode ISGeneralSetIndices_General(IS is,PetscInt n,const PetscInt idx[],PetscCopyMode mode)
{
PetscErrorCode ierr;
IS_General *sub = (IS_General*)is->data;
PetscFunctionBegin;
if (n < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"length < 0");
if (n) PetscValidIntPointer(idx,3);
ierr = PetscLayoutSetLocalSize(is->map,n);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 {
sub->idx = (PetscInt*)idx;
sub->allocated = PETSC_FALSE;
}
ierr = ISSetUp_General(is);CHKERRQ(ierr);
ierr = ISViewFromOptions(is,NULL,"-is_view");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);
}
PetscErrorCode MatSetUp_Preallocator(Mat A)
{
Mat_Preallocator *p = (Mat_Preallocator *) A->data;
PetscInt m, bs;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr);
ierr = MatGetLocalSize(A, &m, NULL);CHKERRQ(ierr);
ierr = PetscHSetIJCreate(&p->ht);CHKERRQ(ierr);
ierr = MatGetBlockSize(A, &bs);CHKERRQ(ierr);
ierr = MatStashCreate_Private(PetscObjectComm((PetscObject) A), bs, &A->stash);CHKERRQ(ierr);
ierr = PetscCalloc2(m, &p->dnz, m, &p->onz);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);
}
EXTERN_C_END
/*MC
MATDAAD - MATDAAD = "daad" - A matrix type that can do matrix-vector products using a local function that
is differentiated with ADIFOR or ADIC.
Level: intermediate
.seealso: MatCreateDAAD
M*/
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "MatCreate_DAAD"
PetscErrorCode MatCreate_DAAD(Mat B)
{
Mat_DAAD *b;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscNewLog(B,Mat_DAAD,&b);
CHKERRQ(ierr);
B->data = (void*)b;
ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));
CHKERRQ(ierr);
ierr = PetscLayoutSetUp(B->rmap);
CHKERRQ(ierr);
ierr = PetscLayoutSetUp(B->cmap);
CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)B,MATDAAD);
CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatMFFDSetBase_C","MatMFFDSetBase_AD",MatMFFDSetBase_AD);
CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatDAADSetDA_C","MatDAADSetDA_AD",MatDAADSetDA_AD);
CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatDAADSetSNES_C","MatDAADSetSNES_AD",MatDAADSetSNES_AD);
CHKERRQ(ierr);
ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatDAADSetCtx_C","MatDAADSetCtx_AD",MatDAADSetCtx_AD);
CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)B,MATDAAD);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatAllocate_LMVM(Mat B, Vec X, Vec F)
{
Mat_LMVM *lmvm = (Mat_LMVM*)B->data;
PetscErrorCode ierr;
PetscBool same, allocate = PETSC_FALSE;
PetscInt m, n, M, N;
VecType type;
PetscFunctionBegin;
if (lmvm->allocated) {
VecCheckMatCompatible(B, X, 2, F, 3);
ierr = VecGetType(X, &type);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)lmvm->Xprev, type, &same);CHKERRQ(ierr);
if (!same) {
/* Given X vector has a different type than allocated X-type data structures.
We need to destroy all of this and duplicate again out of the given vector. */
allocate = PETSC_TRUE;
ierr = MatLMVMReset(B, PETSC_TRUE);CHKERRQ(ierr);
}
} else {
allocate = PETSC_TRUE;
}
if (allocate) {
ierr = VecGetLocalSize(X, &n);CHKERRQ(ierr);
ierr = VecGetSize(X, &N);CHKERRQ(ierr);
ierr = VecGetLocalSize(F, &m);CHKERRQ(ierr);
ierr = VecGetSize(F, &M);CHKERRQ(ierr);
ierr = MatSetSizes(B, m, n, M, N);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr);
ierr = VecDuplicate(X, &lmvm->Xprev);CHKERRQ(ierr);
ierr = VecDuplicate(F, &lmvm->Fprev);CHKERRQ(ierr);
if (lmvm->m > 0) {
ierr = VecDuplicateVecs(lmvm->Xprev, lmvm->m, &lmvm->S);CHKERRQ(ierr);
ierr = VecDuplicateVecs(lmvm->Fprev, lmvm->m, &lmvm->Y);CHKERRQ(ierr);
}
lmvm->allocated = PETSC_TRUE;
B->preallocated = PETSC_TRUE;
B->assembled = PETSC_TRUE;
}
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode MatCreate_Composite(Mat A)
{
Mat_Composite *b;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscNewLog(A,&b);CHKERRQ(ierr);
A->data = (void*)b;
ierr = PetscMemcpy(A->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr);
A->assembled = PETSC_TRUE;
A->preallocated = PETSC_TRUE;
b->type = MAT_COMPOSITE_ADDITIVE;
b->scale = 1.0;
ierr = PetscObjectChangeTypeName((PetscObject)A,MATCOMPOSITE);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatAssemblyBegin_Preallocator(Mat A, MatAssemblyType type)
{
PetscInt nstash, reallocs;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr);
ierr = MatStashScatterBegin_Private(A, &A->stash, A->rmap->range);CHKERRQ(ierr);
ierr = MatStashGetInfo_Private(&A->stash, &nstash, &reallocs);CHKERRQ(ierr);
ierr = PetscInfo2(A, "Stash has %D entries, uses %D mallocs.\n", nstash, reallocs);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);
}
/*
VecCreate_MPI_Private - Basic create routine called by VecCreate_MPI() (i.e. VecCreateMPI()),
VecCreateMPIWithArray(), VecCreate_Shared() (i.e. VecCreateShared()), VecCreateGhost(),
VecDuplicate_MPI(), VecCreateGhostWithArray(), VecDuplicate_MPI(), and VecDuplicate_Shared()
If alloc is true and array is NULL then this routine allocates the space, otherwise
no space is allocated.
*/
PetscErrorCode VecCreate_MPI_Private(Vec v,PetscBool alloc,PetscInt nghost,const PetscScalar array[])
{
Vec_MPI *s;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscNewLog(v,&s);CHKERRQ(ierr);
v->data = (void*)s;
ierr = PetscMemcpy(v->ops,&DvOps,sizeof(DvOps));CHKERRQ(ierr);
s->nghost = nghost;
v->petscnative = PETSC_TRUE;
ierr = PetscLayoutSetUp(v->map);CHKERRQ(ierr);
s->array = (PetscScalar*)array;
s->array_allocated = 0;
if (alloc && !array) {
PetscInt n = v->map->n+nghost;
ierr = PetscMalloc1(n,&s->array);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)v,n*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = PetscMemzero(s->array,n*sizeof(PetscScalar));CHKERRQ(ierr);
s->array_allocated = s->array;
}
/* By default parallel vectors do not have local representation */
s->localrep = 0;
s->localupdate = 0;
v->stash.insertmode = NOT_SET_VALUES;
v->bstash.insertmode = NOT_SET_VALUES;
/* create the stashes. The block-size for bstash is set later when
VecSetValuesBlocked is called.
*/
ierr = VecStashCreate_Private(PetscObjectComm((PetscObject)v),1,&v->stash);CHKERRQ(ierr);
ierr = VecStashCreate_Private(PetscObjectComm((PetscObject)v),PetscAbs(v->map->bs),&v->bstash);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MATLAB_ENGINE)
ierr = PetscObjectComposeFunction((PetscObject)v,"PetscMatlabEnginePut_C",VecMatlabEnginePut_Default);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)v,"PetscMatlabEngineGet_C",VecMatlabEngineGet_Default);CHKERRQ(ierr);
#endif
ierr = PetscObjectChangeTypeName((PetscObject)v,VECMPI);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode ISSortRemoveDups_General(IS is)
{
IS_General *sub = (IS_General*)is->data;
PetscInt n;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLayoutGetLocalSize(is->map, &n);CHKERRQ(ierr);
if (sub->sorted) {
ierr = PetscSortedRemoveDupsInt(&n,sub->idx);CHKERRQ(ierr);
} else {
ierr = PetscSortRemoveDupsInt(&n,sub->idx);CHKERRQ(ierr);
}
ierr = PetscLayoutSetLocalSize(is->map, n);CHKERRQ(ierr);
ierr = PetscLayoutSetSize(is->map, PETSC_DECIDE);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(is->map);CHKERRQ(ierr);
sub->sorted = PETSC_TRUE;
PetscFunctionReturn(0);
}
static PetscErrorCode ISSortRemoveDups_Block(IS is)
{
IS_Block *sub = (IS_Block*)is->data;
PetscInt bs, n, nb;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLayoutGetBlockSize(is->map, &bs);CHKERRQ(ierr);
ierr = PetscLayoutGetLocalSize(is->map, &n);CHKERRQ(ierr);
nb = n/bs;
if (sub->sorted) {
ierr = PetscSortedRemoveDupsInt(&nb,sub->idx);CHKERRQ(ierr);
} else {
ierr = PetscSortRemoveDupsInt(&nb,sub->idx);CHKERRQ(ierr);
}
ierr = PetscLayoutSetLocalSize(is->map, nb*bs);CHKERRQ(ierr);
ierr = PetscLayoutSetSize(is->map, PETSC_DECIDE);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(is->map);CHKERRQ(ierr);
sub->sorted = PETSC_TRUE;
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 MatSetLocalToGlobalMapping_IS(Mat A,ISLocalToGlobalMapping rmapping,ISLocalToGlobalMapping cmapping)
{
PetscErrorCode ierr;
PetscInt nr,rbs,nc,cbs;
Mat_IS *is = (Mat_IS*)A->data;
IS from,to;
Vec cglobal,rglobal;
PetscFunctionBegin;
PetscCheckSameComm(A,1,rmapping,2);
PetscCheckSameComm(A,1,cmapping,3);
/* Destroy any previous data */
ierr = VecDestroy(&is->x);CHKERRQ(ierr);
ierr = VecDestroy(&is->y);CHKERRQ(ierr);
ierr = VecScatterDestroy(&is->rctx);CHKERRQ(ierr);
ierr = VecScatterDestroy(&is->cctx);CHKERRQ(ierr);
ierr = MatDestroy(&is->A);CHKERRQ(ierr);
ierr = PetscSFDestroy(&is->sf);CHKERRQ(ierr);
ierr = PetscFree2(is->sf_rootdata,is->sf_leafdata);CHKERRQ(ierr);
/* Setup Layout and set local to global maps */
ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr);
ierr = PetscLayoutSetISLocalToGlobalMapping(A->rmap,rmapping);CHKERRQ(ierr);
ierr = PetscLayoutSetISLocalToGlobalMapping(A->cmap,cmapping);CHKERRQ(ierr);
/* Create the local matrix A */
ierr = ISLocalToGlobalMappingGetSize(rmapping,&nr);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetBlockSize(rmapping,&rbs);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetSize(cmapping,&nc);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetBlockSize(cmapping,&cbs);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&is->A);CHKERRQ(ierr);
ierr = MatSetType(is->A,MATAIJ);CHKERRQ(ierr);
ierr = MatSetSizes(is->A,nr,nc,nr,nc);CHKERRQ(ierr);
ierr = MatSetBlockSizes(is->A,rbs,cbs);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(is->A,((PetscObject)A)->prefix);CHKERRQ(ierr);
ierr = MatAppendOptionsPrefix(is->A,"is_");CHKERRQ(ierr);
ierr = MatSetFromOptions(is->A);CHKERRQ(ierr);
/* Create the local work vectors */
ierr = MatCreateVecs(is->A,&is->x,&is->y);CHKERRQ(ierr);
/* setup the global to local scatters */
ierr = MatCreateVecs(A,&cglobal,&rglobal);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,nr,0,1,&to);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApplyIS(rmapping,to,&from);CHKERRQ(ierr);
ierr = VecScatterCreate(rglobal,from,is->y,to,&is->rctx);CHKERRQ(ierr);
if (rmapping != cmapping) {
ierr = ISDestroy(&to);CHKERRQ(ierr);
ierr = ISDestroy(&from);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,nc,0,1,&to);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApplyIS(cmapping,to,&from);CHKERRQ(ierr);
ierr = VecScatterCreate(cglobal,from,is->x,to,&is->cctx);CHKERRQ(ierr);
} else {
ierr = PetscObjectReference((PetscObject)is->rctx);CHKERRQ(ierr);
is->cctx = is->rctx;
}
ierr = VecDestroy(&rglobal);CHKERRQ(ierr);
ierr = VecDestroy(&cglobal);CHKERRQ(ierr);
ierr = ISDestroy(&to);CHKERRQ(ierr);
ierr = ISDestroy(&from);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);
}
PETSC_EXTERN PetscErrorCode AOCreate_MemoryScalable(AO ao)
{
PetscErrorCode ierr;
IS isapp=ao->isapp,ispetsc=ao->ispetsc;
const PetscInt *mypetsc,*myapp;
PetscInt napp,n_local,N,i,start,*petsc,*lens,*disp;
MPI_Comm comm;
AO_MemoryScalable *aomems;
PetscLayout map;
PetscMPIInt size,rank;
PetscFunctionBegin;
/* create special struct aomems */
ierr = PetscNewLog(ao, AO_MemoryScalable, &aomems);
CHKERRQ(ierr);
ao->data = (void*) aomems;
ierr = PetscMemcpy(ao->ops,&AOOps_MemoryScalable,sizeof(struct _AOOps));
CHKERRQ(ierr);
ierr = PetscObjectChangeTypeName((PetscObject)ao,AOMEMORYSCALABLE);
CHKERRQ(ierr);
/* transmit all local lengths of isapp to all processors */
ierr = PetscObjectGetComm((PetscObject)isapp,&comm);
CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &size);
CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);
CHKERRQ(ierr);
ierr = PetscMalloc2(size,PetscInt,&lens,size,PetscInt,&disp);
CHKERRQ(ierr);
ierr = ISGetLocalSize(isapp,&napp);
CHKERRQ(ierr);
ierr = MPI_Allgather(&napp, 1, MPIU_INT, lens, 1, MPIU_INT, comm);
CHKERRQ(ierr);
N = 0;
for (i = 0; i < size; i++) {
disp[i] = N;
N += lens[i];
}
/* If ispetsc is 0 then use "natural" numbering */
if (napp) {
if (!ispetsc) {
start = disp[rank];
ierr = PetscMalloc((napp+1) * sizeof(PetscInt), &petsc);
CHKERRQ(ierr);
for (i=0; i<napp; i++) petsc[i] = start + i;
} else {
ierr = ISGetIndices(ispetsc,&mypetsc);
CHKERRQ(ierr);
petsc = (PetscInt*)mypetsc;
}
}
/* create a map with global size N - used to determine the local sizes of ao - shall we use local napp instead of N? */
ierr = PetscLayoutCreate(comm,&map);
CHKERRQ(ierr);
map->bs = 1;
map->N = N;
ierr = PetscLayoutSetUp(map);
CHKERRQ(ierr);
ao->N = N;
ao->n = map->n;
aomems->map = map;
/* create distributed indices app_loc: petsc->app and petsc_loc: app->petsc */
n_local = map->n;
ierr = PetscMalloc2(n_local,PetscInt, &aomems->app_loc,n_local,PetscInt,&aomems->petsc_loc);
CHKERRQ(ierr);
ierr = PetscLogObjectMemory(ao,2*n_local*sizeof(PetscInt));
CHKERRQ(ierr);
ierr = PetscMemzero(aomems->app_loc,n_local*sizeof(PetscInt));
CHKERRQ(ierr);
ierr = PetscMemzero(aomems->petsc_loc,n_local*sizeof(PetscInt));
CHKERRQ(ierr);
ierr = ISGetIndices(isapp,&myapp);
CHKERRQ(ierr);
ierr = AOCreateMemoryScalable_private(comm,napp,petsc,myapp,ao,aomems->app_loc);
CHKERRQ(ierr);
ierr = AOCreateMemoryScalable_private(comm,napp,myapp,petsc,ao,aomems->petsc_loc);
CHKERRQ(ierr);
ierr = ISRestoreIndices(isapp,&myapp);
CHKERRQ(ierr);
if (napp) {
if (ispetsc) {
ierr = ISRestoreIndices(ispetsc,&mypetsc);
CHKERRQ(ierr);
} else {
ierr = PetscFree(petsc);
CHKERRQ(ierr);
}
}
ierr = PetscFree2(lens,disp);
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);
}
PetscErrorCode MatSetUpMultiply_MPIAIJ(Mat mat)
{
Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data;
Mat_SeqAIJ *B = (Mat_SeqAIJ*)(aij->B->data);
PetscErrorCode ierr;
PetscInt i,j,*aj = B->j,ec = 0,*garray;
IS from,to;
Vec gvec;
#if defined(PETSC_USE_CTABLE)
PetscTable gid1_lid1;
PetscTablePosition tpos;
PetscInt gid,lid;
#else
PetscInt N = mat->cmap->N,*indices;
#endif
PetscFunctionBegin;
if (!aij->garray) {
#if defined(PETSC_USE_CTABLE)
/* use a table */
ierr = PetscTableCreate(aij->B->rmap->n,mat->cmap->N+1,&gid1_lid1);CHKERRQ(ierr);
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
PetscInt data,gid1 = aj[B->i[i] + j] + 1;
ierr = PetscTableFind(gid1_lid1,gid1,&data);CHKERRQ(ierr);
if (!data) {
/* one based table */
ierr = PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
/* form array of columns we need */
ierr = PetscMalloc1(ec+1,&garray);CHKERRQ(ierr);
ierr = PetscTableGetHeadPosition(gid1_lid1,&tpos);CHKERRQ(ierr);
while (tpos) {
ierr = PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);CHKERRQ(ierr);
gid--;
lid--;
garray[lid] = gid;
}
ierr = PetscSortInt(ec,garray);CHKERRQ(ierr); /* sort, and rebuild */
ierr = PetscTableRemoveAll(gid1_lid1);CHKERRQ(ierr);
for (i=0; i<ec; i++) {
ierr = PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr);
}
/* compact out the extra columns in B */
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
PetscInt gid1 = aj[B->i[i] + j] + 1;
ierr = PetscTableFind(gid1_lid1,gid1,&lid);CHKERRQ(ierr);
lid--;
aj[B->i[i] + j] = lid;
}
}
aij->B->cmap->n = aij->B->cmap->N = ec;
aij->B->cmap->bs = 1;
ierr = PetscLayoutSetUp((aij->B->cmap));CHKERRQ(ierr);
ierr = PetscTableDestroy(&gid1_lid1);CHKERRQ(ierr);
#else
/* Make an array as long as the number of columns */
/* mark those columns that are in aij->B */
ierr = PetscCalloc1(N+1,&indices);CHKERRQ(ierr);
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
if (!indices[aj[B->i[i] + j]]) ec++;
indices[aj[B->i[i] + j]] = 1;
}
}
/* form array of columns we need */
ierr = PetscMalloc1(ec+1,&garray);CHKERRQ(ierr);
ec = 0;
for (i=0; i<N; i++) {
if (indices[i]) garray[ec++] = i;
}
/* make indices now point into garray */
for (i=0; i<ec; i++) {
indices[garray[i]] = i;
}
/* compact out the extra columns in B */
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
}
}
aij->B->cmap->n = aij->B->cmap->N = ec;
aij->B->cmap->bs = 1;
ierr = PetscLayoutSetUp((aij->B->cmap));CHKERRQ(ierr);
ierr = PetscFree(indices);CHKERRQ(ierr);
#endif
} else {
garray = aij->garray;
}
if (!aij->lvec) {
/* create local vector that is used to scatter into */
ierr = VecCreateSeq(PETSC_COMM_SELF,ec,&aij->lvec);CHKERRQ(ierr);
} else {
ierr = VecGetSize(aij->lvec,&ec);CHKERRQ(ierr);
}
/* create two temporary Index sets for build scatter gather */
ierr = ISCreateGeneral(((PetscObject)mat)->comm,ec,garray,PETSC_COPY_VALUES,&from);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,ec,0,1,&to);CHKERRQ(ierr);
/* create temporary global vector to generate scatter context */
/* This does not allocate the array's memory so is efficient */
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);CHKERRQ(ierr);
/* generate the scatter context */
if (aij->Mvctx_mpi1_flg) {
ierr = VecScatterDestroy(&aij->Mvctx_mpi1);CHKERRQ(ierr);
ierr = VecScatterCreate(gvec,from,aij->lvec,to,&aij->Mvctx_mpi1);CHKERRQ(ierr);
ierr = VecScatterSetType(aij->Mvctx_mpi1,VECSCATTERMPI1);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)aij->Mvctx_mpi1);CHKERRQ(ierr);
} else {
ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr);
ierr = VecScatterCreate(gvec,from,aij->lvec,to,&aij->Mvctx);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)aij->Mvctx);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)aij->lvec);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)mat,(ec+1)*sizeof(PetscInt));CHKERRQ(ierr);
}
aij->garray = garray;
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)from);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)to);CHKERRQ(ierr);
ierr = ISDestroy(&from);CHKERRQ(ierr);
ierr = ISDestroy(&to);CHKERRQ(ierr);
ierr = VecDestroy(&gvec);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
