PetscErrorCode MatTransposeMatMultSymbolic_SeqAIJ_SeqDense(Mat A,Mat B,PetscReal fill,Mat *C)
{
PetscErrorCode ierr;
PetscInt m=A->rmap->n,n=A->cmap->n,BN=B->cmap->N;
Mat_MatTransMatMult *atb;
Mat Cdense;
Vec bt,ct;
Mat_SeqDense *c;
PetscFunctionBegin;
ierr = PetscNew(&atb);CHKERRQ(ierr);
/* create output dense matrix C = A^T*B */
ierr = MatCreate(PETSC_COMM_SELF,&Cdense);CHKERRQ(ierr);
ierr = MatSetSizes(Cdense,n,BN,n,BN);CHKERRQ(ierr);
ierr = MatSetType(Cdense,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(Cdense,NULL);CHKERRQ(ierr);
/* create vectors bt and ct to hold locally transposed arrays of B and C */
ierr = VecCreate(PETSC_COMM_SELF,&bt);CHKERRQ(ierr);
ierr = VecSetSizes(bt,m*BN,m*BN);CHKERRQ(ierr);
ierr = VecSetType(bt,VECSTANDARD);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&ct);CHKERRQ(ierr);
ierr = VecSetSizes(ct,n*BN,n*BN);CHKERRQ(ierr);
ierr = VecSetType(ct,VECSTANDARD);CHKERRQ(ierr);
atb->bt = bt;
atb->ct = ct;
*C = Cdense;
c = (Mat_SeqDense*)Cdense->data;
c->atb = atb;
atb->destroy = Cdense->ops->destroy;
Cdense->ops->destroy = MatDestroy_SeqDense_MatTransMatMult;
PetscFunctionReturn(0);
}
PetscErrorCode test_vec_ops( void )
{
Vec X, a,b;
Vec c,d,e,f;
PetscScalar val;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscPrintf( PETSC_COMM_WORLD, "\n\n============== %s ==============\n",PETSC_FUNCTION_NAME);
ierr = VecCreate( PETSC_COMM_WORLD, &X );CHKERRQ(ierr);
ierr = VecSetSizes( X, 2, 2 );CHKERRQ(ierr);
ierr = VecSetType( X, VECNEST );CHKERRQ(ierr);
ierr = VecCreate( PETSC_COMM_WORLD, &a );CHKERRQ(ierr);
ierr = VecSetSizes( a, 2, 2 );CHKERRQ(ierr);
ierr = VecSetType( a, VECNEST );CHKERRQ(ierr);
ierr = VecCreate( PETSC_COMM_WORLD, &b );CHKERRQ(ierr);
ierr = VecSetSizes( b, 2, 2 );CHKERRQ(ierr);
ierr = VecSetType( b, VECNEST );CHKERRQ(ierr);
/* assemble X */
ierr = VecNestSetSubVec( X, 0, a );CHKERRQ(ierr);
ierr = VecNestSetSubVec( X, 1, b );CHKERRQ(ierr);
ierr = VecAssemblyBegin(X);CHKERRQ(ierr);
ierr = VecAssemblyEnd(X);CHKERRQ(ierr);
ierr = VecCreate( PETSC_COMM_WORLD, &c );CHKERRQ(ierr);
ierr = VecSetSizes( c, 3, 3 );CHKERRQ(ierr);
ierr = VecSetType( c, VECSEQ );CHKERRQ(ierr);
ierr = VecDuplicate( c, &d );CHKERRQ(ierr);
ierr = VecDuplicate( c, &e );CHKERRQ(ierr);
ierr = VecDuplicate( c, &f );CHKERRQ(ierr);
ierr = VecSet( c, 1.0 );CHKERRQ(ierr);
ierr = VecSet( d, 2.0 );CHKERRQ(ierr);
ierr = VecSet( e, 3.0 );CHKERRQ(ierr);
ierr = VecSet( f, 4.0 );CHKERRQ(ierr);
/* assemble a */
ierr = VecNestSetSubVec( a, 0, c );CHKERRQ(ierr);
ierr = VecNestSetSubVec( a, 1, d );CHKERRQ(ierr);
ierr = VecAssemblyBegin(a);CHKERRQ(ierr);
ierr = VecAssemblyEnd(a);CHKERRQ(ierr);
/* assemble b */
ierr = VecNestSetSubVec( b, 0, e );CHKERRQ(ierr);
ierr = VecNestSetSubVec( b, 1, f );CHKERRQ(ierr);
ierr = VecAssemblyBegin(b);CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);CHKERRQ(ierr);
//PetscPrintf( PETSC_COMM_WORLD, "X \n");
//VecView( X, PETSC_VIEWER_STDOUT_WORLD );
ierr = VecDot( X,X, &val );CHKERRQ(ierr);
PetscPrintf( PETSC_COMM_WORLD, "X.X = %f \n", val );
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt n = 5;
PetscScalar one = 1.0,two = 2.0;
Vec x,y;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
/* create vector */
ierr = VecCreate(PETSC_COMM_SELF,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetType(x,"mpi");CHKERRQ(ierr);
ierr = VecSetType(x,"seq");CHKERRQ(ierr);
ierr = VecDuplicate(x,&y);CHKERRQ(ierr);
ierr = VecSetType(x,"mpi");CHKERRQ(ierr);
ierr = VecSet(x,one);CHKERRQ(ierr);
ierr = VecSet(y,two);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = VecDestroy(y);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int DA::createActiveVector(Vec &arr, bool isElemental, bool isGhosted, unsigned int dof) {
// first determine the length of the vector ...
unsigned int sz = 0;
if(m_bIamActive) {
if (isElemental) {
sz = m_uiElementSize;
if (isGhosted) {
sz += (m_uiPreGhostElementSize);
}
} else {
sz = m_uiNodeSize + m_uiBoundaryNodeSize;
if (isGhosted) {
sz += (m_uiPreGhostNodeSize + m_uiPreGhostBoundaryNodeSize + m_uiPostGhostNodeSize);
}
}
// now for dof ...
sz *= dof;
// now create the PETSc Vector
VecCreate(m_mpiCommActive, &arr);
VecSetSizes(arr, sz, PETSC_DECIDE);
if (m_iNpesActive > 1) {
VecSetType(arr, VECMPI);
} else {
VecSetType(arr, VECSEQ);
}
}//end if active
return 0;
}
PetscErrorCode gen_test_vector( MPI_Comm comm, PetscInt length, PetscInt start_value, PetscInt stride, Vec *_v )
{
int nproc;
Vec v;
PetscInt i;
PetscScalar vx;
PetscErrorCode ierr;
MPI_Comm_size( comm, &nproc );
ierr = VecCreate( comm, &v );CHKERRQ(ierr);
ierr = VecSetSizes( v, PETSC_DECIDE, length );CHKERRQ(ierr);
if ( nproc == 1 ) { ierr = VecSetType( v, VECSEQ );CHKERRQ(ierr); }
else { ierr = VecSetType( v, VECMPI );CHKERRQ(ierr); }
for ( i=0; i<length; i++ ) {
vx = (PetscScalar)( start_value + i * stride );
ierr = VecSetValue( v, i, vx, INSERT_VALUES );CHKERRQ(ierr);
}
ierr = VecAssemblyBegin( v );CHKERRQ(ierr);
ierr = VecAssemblyEnd( v );CHKERRQ(ierr);
*_v = v;
PetscFunctionReturn(0);
}
EXTERN_C_END
/*MC
VECSTANDARD = "standard" - A VECSEQ on one process and VECMPI on more than one process
Options Database Keys:
. -vec_type standard - sets a vector type to standard on calls to VecSetFromOptions()
Level: beginner
.seealso: VecCreateSeq(), VecCreateMPI()
M*/
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "VecCreate_Standard"
PetscErrorCode VecCreate_Standard(Vec v)
{
PetscErrorCode ierr;
PetscMPIInt size;
PetscFunctionBegin;
ierr = MPI_Comm_size(((PetscObject)v)->comm,&size);CHKERRQ(ierr);
if (size == 1) {
ierr = VecSetType(v,VECSEQ);CHKERRQ(ierr);
} else {
ierr = VecSetType(v,VECMPI);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*@C
DMDAGetRay - Returns a vector on process zero that contains a row or column of the values in a DMDA vector
Collective on DMDA
Input Parameters:
+ da - the distributed array
. vec - the vector
. dir - Cartesian direction, either DMDA_X, DMDA_Y, or DMDA_Z
- gp - global grid point number in this direction
Output Parameters:
+ newvec - the new vector that can hold the values (size zero on all processes except process 0)
- scatter - the VecScatter that will map from the original vector to the slice
Level: advanced
Notes:
All processors that share the DMDA must call this with the same gp value
.keywords: distributed array, get, processor subset
@*/
PetscErrorCode DMDAGetRay(DM da,DMDADirection dir,PetscInt gp,Vec *newvec,VecScatter *scatter)
{
PetscMPIInt rank;
DM_DA *dd = (DM_DA*)da->data;
PetscErrorCode ierr;
IS is;
AO ao;
Vec vec;
PetscInt *indices,i,j;
PetscFunctionBegin;
if (dd->dim == 1) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot get slice from 1d DMDA");
if (dd->dim == 3) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot get slice from 3d DMDA");
ierr = DMDAGetAO(da,&ao);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)da),&rank);CHKERRQ(ierr);
if (!rank) {
if (dir == DMDA_Y) {
ierr = PetscMalloc(dd->w*dd->M*sizeof(PetscInt),&indices);CHKERRQ(ierr);
indices[0] = gp*dd->M*dd->w;
for (i=1; i<dd->M*dd->w; i++) indices[i] = indices[i-1] + 1;
ierr = AOApplicationToPetsc(ao,dd->M*dd->w,indices);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,newvec);CHKERRQ(ierr);
ierr = VecSetBlockSize(*newvec,dd->w);CHKERRQ(ierr);
ierr = VecSetSizes(*newvec,dd->M*dd->w,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetType(*newvec,VECSEQ);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,dd->w*dd->M,indices,PETSC_OWN_POINTER,&is);CHKERRQ(ierr);
} else if (dir == DMDA_X) {
ierr = PetscMalloc(dd->w*dd->N*sizeof(PetscInt),&indices);CHKERRQ(ierr);
indices[0] = dd->w*gp;
for (j=1; j<dd->w; j++) indices[j] = indices[j-1] + 1;
for (i=1; i<dd->N; i++) {
indices[i*dd->w] = indices[i*dd->w-1] + dd->w*dd->M - dd->w + 1;
for (j=1; j<dd->w; j++) indices[i*dd->w + j] = indices[i*dd->w + j - 1] + 1;
}
ierr = AOApplicationToPetsc(ao,dd->w*dd->N,indices);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,newvec);CHKERRQ(ierr);
ierr = VecSetBlockSize(*newvec,dd->w);CHKERRQ(ierr);
ierr = VecSetSizes(*newvec,dd->N*dd->w,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetType(*newvec,VECSEQ);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,dd->w*dd->N,indices,PETSC_OWN_POINTER,&is);CHKERRQ(ierr);
} else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Unknown DMDADirection");
} else {
ierr = VecCreateSeq(PETSC_COMM_SELF,0,newvec);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,0,0,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
}
ierr = DMGetGlobalVector(da,&vec);CHKERRQ(ierr);
ierr = VecScatterCreate(vec,is,*newvec,NULL,scatter);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(da,&vec);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode VecCreate_Standard(Vec v)
{
PetscErrorCode ierr;
PetscMPIInt size;
PetscFunctionBegin;
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)v),&size);CHKERRQ(ierr);
if (size == 1) {
ierr = VecSetType(v,VECSEQ);CHKERRQ(ierr);
} else {
ierr = VecSetType(v,VECMPI);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*@
DMDACreateNaturalVector - Creates a parallel PETSc vector that
will hold vector values in the natural numbering, rather than in
the PETSc parallel numbering associated with the DMDA.
Collective
Input Parameter:
. da - the distributed array
Output Parameter:
. g - the distributed global vector
Level: developer
Note:
The output parameter, g, is a regular PETSc vector that should be destroyed
with a call to VecDestroy() when usage is finished.
The number of local entries in the vector on each process is the same
as in a vector created with DMCreateGlobalVector().
.keywords: distributed array, create, global, distributed, vector
.seealso: DMCreateLocalVector(), VecDuplicate(), VecDuplicateVecs(),
DMDACreate1d(), DMDACreate2d(), DMDACreate3d(), DMGlobalToLocalBegin(),
DMGlobalToLocalEnd(), DMDALocalToGlobalBegin()
@*/
PetscErrorCode DMDACreateNaturalVector(DM da,Vec *g)
{
PetscErrorCode ierr;
PetscInt cnt;
DM_DA *dd = (DM_DA*)da->data;
PetscFunctionBegin;
PetscValidHeaderSpecificType(da,DM_CLASSID,1,DMDA);
PetscValidPointer(g,2);
if (dd->natural) {
ierr = PetscObjectGetReference((PetscObject)dd->natural,&cnt);CHKERRQ(ierr);
if (cnt == 1) { /* object is not currently used by anyone */
ierr = PetscObjectReference((PetscObject)dd->natural);CHKERRQ(ierr);
*g = dd->natural;
} else {
ierr = VecDuplicate(dd->natural,g);CHKERRQ(ierr);
}
} else { /* create the first version of this guy */
ierr = VecCreate(PetscObjectComm((PetscObject)da),g);CHKERRQ(ierr);
ierr = VecSetSizes(*g,dd->Nlocal,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetBlockSize(*g, dd->w);CHKERRQ(ierr);
ierr = VecSetType(*g,da->vectype);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)*g);CHKERRQ(ierr);
dd->natural = *g;
}
PetscFunctionReturn(0);
}
PetscErrorCode CreateStructures(DM da, UserContext *user)
{
const PetscInt *necon;
PetscInt ne,nc;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMDAGetElements(da,&ne,&nc,&necon);CHKERRQ(ierr);
ierr = DMDARestoreElements(da,&ne,&nc,&necon);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_n.rho);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_n.rho_u);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_n.rho_v);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_n.rho_e);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_n.p);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_n.u);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_n.v);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_n.t);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD, &user->sol_phi.rho);CHKERRQ(ierr);
ierr = VecSetSizes(user->sol_phi.rho, ne, PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetType(user->sol_phi.rho,VECMPI);CHKERRQ(ierr);
ierr = VecDuplicate(user->sol_phi.rho, &user->sol_phi.rho_u);CHKERRQ(ierr);
ierr = VecDuplicate(user->sol_phi.rho, &user->sol_phi.rho_v);CHKERRQ(ierr);
ierr = VecDuplicate(user->sol_phi.rho, &user->sol_phi.u);CHKERRQ(ierr);
ierr = VecDuplicate(user->sol_phi.rho, &user->sol_phi.v);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_np1.rho);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_np1.rho_u);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_np1.rho_v);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_np1.rho_e);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_np1.p);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_np1.u);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->sol_np1.v);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->mu);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da, &user->kappa);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void
PetscSparseMtrx :: times(const FloatArray &x, FloatArray &answer) const
{
if ( this->giveNumberOfColumns() != x.giveSize() ) {
OOFEM_ERROR("Dimension mismatch");
}
#ifdef __PARALLEL_MODE
if ( emodel->isParallel() ) {
OOFEM_ERROR("PetscSparseMtrx :: times - Not implemented");
}
#endif
Vec globX, globY;
VecCreateSeqWithArray(PETSC_COMM_SELF, 1, x.giveSize(), x.givePointer(), & globX);
VecCreate(PETSC_COMM_SELF, & globY);
VecSetType(globY, VECSEQ);
VecSetSizes(globY, PETSC_DECIDE, this->nRows);
MatMult(this->mtrx, globX, globY);
double *ptr;
VecGetArray(globY, & ptr);
answer.resize(this->nRows);
for ( int i = 0; i < this->nRows; i++ ) {
answer(i) = ptr [ i ];
}
VecRestoreArray(globY, & ptr);
VecDestroy(&globX);
VecDestroy(&globY);
}
PetscErrorCode StokesSetupVectors(Stokes* s) {
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* solution vector x */
ierr = VecCreate(PETSC_COMM_WORLD, &s->x);
CHKERRQ(ierr);
ierr = VecSetSizes(s->x, PETSC_DECIDE, 3 * s->nx * s->ny);
CHKERRQ(ierr);
ierr = VecSetType(s->x, VECMPI);
CHKERRQ(ierr);
/* ierr = VecSetRandom(s->x, NULL);CHKERRQ(ierr); */
/* ierr = VecView(s->x, (PetscViewer) PETSC_VIEWER_DEFAULT);CHKERRQ(ierr); */
/* exact solution y */
ierr = VecDuplicate(s->x, &s->y);
CHKERRQ(ierr);
ierr = StokesExactSolution(s);
CHKERRQ(ierr);
/* ierr = VecView(s->y, (PetscViewer) PETSC_VIEWER_DEFAULT);CHKERRQ(ierr); */
/* rhs vector b */
ierr = VecDuplicate(s->x, &s->b);
CHKERRQ(ierr);
ierr = StokesRhs(s);
CHKERRQ(ierr);
/*ierr = VecView(s->b, (PetscViewer) PETSC_VIEWER_DEFAULT);CHKERRQ(ierr);*/
PetscFunctionReturn(0);
}
PetscErrorCode DMCreateGlobalVector_DA(DM da,Vec *g)
{
PetscErrorCode ierr;
DM_DA *dd = (DM_DA*)da->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(da,DM_CLASSID,1);
PetscValidPointer(g,2);
if (da->defaultSection) {
ierr = DMCreateGlobalVector_Section_Private(da,g);CHKERRQ(ierr);
/* The view and load functions break for general layouts */
PetscFunctionReturn(0);
} else {
ierr = VecCreate(PetscObjectComm((PetscObject)da),g);CHKERRQ(ierr);
ierr = VecSetSizes(*g,dd->Nlocal,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetBlockSize(*g,dd->w);CHKERRQ(ierr);
ierr = VecSetType(*g,da->vectype);CHKERRQ(ierr);
ierr = VecSetDM(*g, da);CHKERRQ(ierr);
ierr = VecSetLocalToGlobalMapping(*g,da->ltogmap);CHKERRQ(ierr);
}
ierr = VecSetOperation(*g,VECOP_VIEW,(void (*)(void))VecView_MPI_DA);CHKERRQ(ierr);
ierr = VecSetOperation(*g,VECOP_LOAD,(void (*)(void))VecLoad_Default_DA);CHKERRQ(ierr);
ierr = VecSetOperation(*g,VECOP_DUPLICATE,(void (*)(void))VecDuplicate_MPI_DA);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexDistributeField - Distribute field data to match a given PetscSF, usually the SF from mesh distribution
Collective on DM
Input Parameters:
+ dm - The DMPlex object
. pointSF - The PetscSF describing the communication pattern
. originalSection - The PetscSection for existing data layout
- originalVec - The existing data
Output Parameters:
+ newSection - The PetscSF describing the new data layout
- newVec - The new data
Level: developer
.seealso: DMPlexDistribute(), DMPlexDistributeData()
@*/
PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec)
{
PetscSF fieldSF;
PetscInt *remoteOffsets, fieldSize;
PetscScalar *originalValues, *newValues;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr);
ierr = VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetType(newVec,dm->vectype);CHKERRQ(ierr);
ierr = VecGetArray(originalVec, &originalValues);CHKERRQ(ierr);
ierr = VecGetArray(newVec, &newValues);CHKERRQ(ierr);
ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr);
ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr);
ierr = VecRestoreArray(newVec, &newValues);CHKERRQ(ierr);
ierr = VecRestoreArray(originalVec, &originalValues);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode StokesSetupApproxSchur(Stokes *s)
{
Vec diag;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* Schur complement approximation: myS = A11 - A10 diag(A00)^(-1) A01 */
/* note: A11 is zero */
/* note: in real life this matrix would be build directly, */
/* i.e. without MatMatMult */
/* inverse of diagonal of A00 */
ierr = VecCreate(PETSC_COMM_WORLD,&diag);CHKERRQ(ierr);
ierr = VecSetSizes(diag,PETSC_DECIDE,2*s->nx*s->ny);CHKERRQ(ierr);
ierr = VecSetType(diag,VECMPI);CHKERRQ(ierr);
ierr = MatGetDiagonal(s->subA[0],diag);
ierr = VecReciprocal(diag);
/* compute: - A10 diag(A00)^(-1) A01 */
ierr = MatDiagonalScale(s->subA[1],diag,NULL); /* (*warning* overwrites subA[1]) */
ierr = MatMatMult(s->subA[2],s->subA[1],MAT_INITIAL_MATRIX,PETSC_DEFAULT,&s->myS);CHKERRQ(ierr);
ierr = MatScale(s->myS,-1.0);CHKERRQ(ierr);
/* restore A10 */
ierr = MatGetDiagonal(s->subA[0],diag);
ierr = MatDiagonalScale(s->subA[1],diag,NULL);
ierr = VecDestroy(&diag);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMCreateGlobalVector_Section_Private(DM dm,Vec *vec)
{
PetscSection gSection;
PetscInt localSize, bs, blockSize = -1, pStart, pEnd, p;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMGetDefaultGlobalSection(dm, &gSection);CHKERRQ(ierr);
ierr = PetscSectionGetChart(gSection, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof, cdof;
ierr = PetscSectionGetDof(gSection, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(gSection, p, &cdof);CHKERRQ(ierr);
if ((blockSize < 0) && (dof > 0) && (dof-cdof > 0)) blockSize = dof-cdof;
if ((dof > 0) && (dof-cdof != blockSize)) {
blockSize = 1;
break;
}
}
if (blockSize < 0) blockSize = PETSC_MAX_INT;
ierr = MPIU_Allreduce(&blockSize, &bs, 1, MPIU_INT, MPI_MIN, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr);
if (blockSize == PETSC_MAX_INT) blockSize = 1; /* Everyone was empty */
ierr = PetscSectionGetConstrainedStorageSize(gSection, &localSize);CHKERRQ(ierr);
if (localSize%blockSize) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Mismatch between blocksize %d and local storage size %d", blockSize, localSize);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), vec);CHKERRQ(ierr);
ierr = VecSetSizes(*vec, localSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetBlockSize(*vec, bs);CHKERRQ(ierr);
ierr = VecSetType(*vec,dm->vectype);CHKERRQ(ierr);
ierr = VecSetDM(*vec, dm);CHKERRQ(ierr);
/* ierr = VecSetLocalToGlobalMapping(*vec, dm->ltogmap);CHKERRQ(ierr); */
PetscFunctionReturn(0);
}
PetscErrorCode DMCreateLocalVector_Section_Private(DM dm,Vec *vec)
{
PetscSection section;
PetscInt localSize, blockSize = -1, pStart, pEnd, p;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
if ((blockSize < 0) && (dof > 0)) blockSize = dof;
if ((dof > 0) && (dof != blockSize)) {
blockSize = 1;
break;
}
}
ierr = PetscSectionGetStorageSize(section, &localSize);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF, vec);CHKERRQ(ierr);
ierr = VecSetSizes(*vec, localSize, localSize);CHKERRQ(ierr);
ierr = VecSetBlockSize(*vec, blockSize);CHKERRQ(ierr);
ierr = VecSetType(*vec,dm->vectype);CHKERRQ(ierr);
ierr = VecSetDM(*vec, dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
UniqueVec::UniqueVec(PetscInt local_n, PetscInt global_n) :
data_(new Vec, PetscVecDeleter()), local_n_(local_n) {
VecCreate(PETSC_COMM_WORLD, data_.get());
Vec &vec = *data_.get();
VecSetType(vec, VECMPI);
VecSetSizes(vec, local_n, global_n);
VecSet(vec, 0.0);
}
void SparseVector::allocate(int m)
{
VecCreate(PETSC_COMM_WORLD, &vec_);
VecSetSizes(vec_, PETSC_DECIDE, m);
VecSetType(vec_, VECSTANDARD);
// Get MPI ranges
VecGetOwnershipRange(vec_, &iLower_, &iUpper_);
}
void
PetscSparseMtrx :: times(const FloatMatrix &B, FloatMatrix &answer) const
{
if ( this->giveNumberOfColumns() != B.giveNumberOfRows() ) {
OOFEM_ERROR("Dimension mismatch");
}
#ifdef __PARALLEL_MODE
if ( emodel->isParallel() ) {
OOFEM_ERROR("PetscSparseMtrx :: times - Not implemented");
}
#endif
// I'm opting to work with a set of vectors, as i think it might be faster and more robust. / Mikael
int nr = this->giveNumberOfRows();
int nc = B.giveNumberOfColumns();
answer.resize(nr, nc);
double *aptr = answer.givePointer();
#if 0
// Approach using several vectors. Not sure if it is optimal, but it includes petsc calls which i suspect are inefficient. / Mikael
// UNTESTED!
Vec globX, globY;
VecCreate(PETSC_COMM_SELF, &globY);
VecSetType(globY, VECSEQ);
VecSetSizes(globY, PETSC_DECIDE, nr);
int nrB = B.giveNumberOfRows();
for (int k = 0; k < nc; k++) {
double colVals[nrB];
for (int i = 0; i < nrB; i++) colVals[i] = B(i,k); // B.copyColumn(Bk,k);
VecCreateSeqWithArray(PETSC_COMM_SELF, nrB, colVals, &globX);
MatMult(this->mtrx, globX, globY );
double *ptr;
VecGetArray(globY, &ptr);
for (int i = 0; i < nr; i++) *aptr++ = ptr[i]; // answer.setColumn(Ak,k);
VecRestoreArray(globY, &ptr);
VecDestroy(globX);
}
VecDestroy(globY);
#endif
Mat globB, globC;
MatCreateSeqDense(PETSC_COMM_SELF, B.giveNumberOfRows(), B.giveNumberOfColumns(), B.givePointer(), & globB);
MatMatMult(this->mtrx, globB, MAT_INITIAL_MATRIX, PETSC_DEFAULT, & globC);
const double *vals;
for ( int r = 0; r < nr; r++ ) {
MatGetRow(globC, r, NULL, NULL, & vals);
for ( int i = 0, i2 = r; i < nc; i++, i2 += nr ) {
aptr [ i2 ] = vals [ i ];
}
MatRestoreRow(globC, r, NULL, NULL, & vals);
}
MatDestroy(&globB);
MatDestroy(&globC);
}
static PetscErrorCode MatHermitianTransposeMatMult_MPIAIJ_MPIDense0(Mat A,PetscScalar *Barray, PetscInt BN, PRIMME_INT ldb,PetscScalar *Carray, PetscInt ldc)
{
PetscErrorCode ierr;
PetscInt i,j,m=A->rmap->n,n=A->cmap->n;
PetscScalar *btarray,*ctarray;
Vec bt,ct;
Mat mA;
PetscFunctionBegin;
/* create MAIJ matrix mA from A -- should be done in symbolic phase */
ierr = MatCreateMAIJ(A,BN,&mA);CHKERRQ(ierr);
/* create vectors bt and ct to hold locally transposed arrays of B and C */
ierr = VecCreate(PetscObjectComm((PetscObject)A),&bt);CHKERRQ(ierr);
ierr = VecSetSizes(bt,m*BN,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetType(bt,VECSTANDARD);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)A),&ct);CHKERRQ(ierr);
ierr = VecSetSizes(ct,n*BN,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetType(ct,VECSTANDARD);CHKERRQ(ierr);
/* transpose local arry of B, then copy it to vector bt */
ierr = VecGetArray(bt,&btarray);CHKERRQ(ierr);
for (j=0; j<BN; j++) {
for (i=0; i<m; i++) btarray[i*BN + j] = PetscConj(Barray[ldb*j+i]);
}
ierr = VecRestoreArray(bt,&btarray);CHKERRQ(ierr);
/* compute ct = mA^T * cb */
ierr = MatMultTranspose(mA,bt,ct);CHKERRQ(ierr);
/* transpose local arry of ct to matrix C */
ierr = VecGetArray(ct,&ctarray);CHKERRQ(ierr);
for (j=0; j<BN; j++) {
for (i=0; i<n; i++) Carray[j*ldc+i] = PetscConj(ctarray[i*BN + j]);
}
ierr = VecRestoreArray(ct,&ctarray);CHKERRQ(ierr);
ierr = VecDestroy(&bt);CHKERRQ(ierr);
ierr = VecDestroy(&ct);CHKERRQ(ierr);
ierr = MatDestroy(&mA);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
VecCreateMPI - Creates a parallel vector.
Collective on MPI_Comm
Input Parameters:
+ comm - the MPI communicator to use
. n - local vector length (or PETSC_DECIDE to have calculated if N is given)
- N - global vector length (or PETSC_DETERMINE to have calculated if n is given)
Output Parameter:
. vv - the vector
Notes:
Use VecDuplicate() or VecDuplicateVecs() to form additional vectors of the
same type as an existing vector.
Level: intermediate
Concepts: vectors^creating parallel
.seealso: VecCreateSeq(), VecCreate(), VecDuplicate(), VecDuplicateVecs(), VecCreateGhost(),
VecCreateMPIWithArray(), VecCreateGhostWithArray(), VecMPISetGhost()
@*/
PetscErrorCode VecCreateMPI(MPI_Comm comm,PetscInt n,PetscInt N,Vec *v)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = VecCreate(comm,v);CHKERRQ(ierr);
ierr = VecSetSizes(*v,n,N);CHKERRQ(ierr);
ierr = VecSetType(*v,VECMPI);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt n = 9,bs = 3,indices[2],i;
PetscScalar values[6];
Vec x;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_SELF,1,"Must be run with one processor");
/* create vector */
ierr = VecCreate(PETSC_COMM_SELF,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,n,n);CHKERRQ(ierr);
ierr = VecSetBlockSize(x,bs);CHKERRQ(ierr);
ierr = VecSetType(x,VECSEQ);CHKERRQ(ierr);
for (i=0; i<6; i++) values[i] = 4.0*i;
indices[0] = 0;
indices[1] = 2;
ierr = VecSetValuesBlocked(x,2,indices,values,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
/*
Resulting vector should be 0 4 8 0 0 0 12 16 20
*/
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* test insertion with negative indices */
ierr = VecSetOption(x,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);CHKERRQ(ierr);
for (i=0; i<6; i++) values[i] = -4.0*i;
indices[0] = -1;
indices[1] = 2;
ierr = VecSetValuesBlocked(x,2,indices,values,ADD_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
/*
Resulting vector should be 0 4 8 0 0 0 0 0 0
*/
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode DMInterpolationGetVector(DMInterpolationInfo ctx, Vec *v)
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidPointer(v, 2);
if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup.");
ierr = VecCreate(ctx->comm, v);CHKERRQ(ierr);
ierr = VecSetSizes(*v, ctx->n*ctx->dof, PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetBlockSize(*v, ctx->dof);CHKERRQ(ierr);
ierr = VecSetType(*v,VECSTANDARD);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexCopyCoordinates - Copy coordinates from one mesh to another with the same vertices
Collective on DM
Input Parameter:
. dmA - The DMPlex object with initial coordinates
Output Parameter:
. dmB - The DMPlex object with copied coordinates
Level: intermediate
Note: This is typically used when adding pieces other than vertices to a mesh
.keywords: mesh
.seealso: DMCopyLabels(), DMGetCoordinates(), DMGetCoordinatesLocal(), DMGetCoordinateDM(), DMGetCoordinateSection()
@*/
PetscErrorCode DMPlexCopyCoordinates(DM dmA, DM dmB)
{
Vec coordinatesA, coordinatesB;
PetscSection coordSectionA, coordSectionB;
PetscScalar *coordsA, *coordsB;
PetscInt spaceDim, vStartA, vStartB, vEndA, vEndB, coordSizeB, v, d;
PetscErrorCode ierr;
PetscFunctionBegin;
if (dmA == dmB) PetscFunctionReturn(0);
ierr = DMPlexGetDepthStratum(dmA, 0, &vStartA, &vEndA);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dmB, 0, &vStartB, &vEndB);CHKERRQ(ierr);
if ((vEndA-vStartA) != (vEndB-vStartB)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "The number of vertices in first DM %d != %d in the second DM", vEndA-vStartA, vEndB-vStartB);
ierr = DMGetCoordinateSection(dmA, &coordSectionA);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dmB, &coordSectionB);CHKERRQ(ierr);
if (!coordSectionB) {
PetscInt dim;
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) coordSectionA), &coordSectionB);CHKERRQ(ierr);
ierr = DMGetCoordinateDim(dmA, &dim);CHKERRQ(ierr);
ierr = DMSetCoordinateSection(dmB, dim, coordSectionB);CHKERRQ(ierr);
ierr = PetscObjectDereference((PetscObject) coordSectionB);CHKERRQ(ierr);
}
ierr = PetscSectionSetNumFields(coordSectionB, 1);CHKERRQ(ierr);
ierr = PetscSectionGetFieldComponents(coordSectionA, 0, &spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSectionB, 0, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSectionB, vStartB, vEndB);CHKERRQ(ierr);
for (v = vStartB; v < vEndB; ++v) {
ierr = PetscSectionSetDof(coordSectionB, v, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSectionB, v, 0, spaceDim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSectionB);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSectionB, &coordSizeB);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dmA, &coordinatesA);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject) dmB), &coordinatesB);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinatesB, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinatesB, coordSizeB, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetType(coordinatesB,VECSTANDARD);CHKERRQ(ierr);
ierr = VecGetArray(coordinatesA, &coordsA);CHKERRQ(ierr);
ierr = VecGetArray(coordinatesB, &coordsB);CHKERRQ(ierr);
for (v = 0; v < vEndB-vStartB; ++v) {
for (d = 0; d < spaceDim; ++d) {
coordsB[v*spaceDim+d] = coordsA[v*spaceDim+d];
}
}
ierr = VecRestoreArray(coordinatesA, &coordsA);CHKERRQ(ierr);
ierr = VecRestoreArray(coordinatesB, &coordsB);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dmB, coordinatesB);CHKERRQ(ierr);
ierr = VecDestroy(&coordinatesB);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
END_TEST
START_TEST( WriteVector_test )
{
PetscErrorCode ierr;
Vec v;
VecCreate( PETSC_COMM_SELF, &v);
VecSetSizes(v, 10, 10);
VecSetType(v, VECSEQ );
VecSet(v, one);
ierr = WriteVector("testwrite.bin", v); CHKERRQ(ierr);
}
static PetscErrorCode DMCreateLocalVector_Redundant(DM dm,Vec *lvec)
{
PetscErrorCode ierr;
DM_Redundant *red = (DM_Redundant*)dm->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscValidPointer(lvec,2);
*lvec = 0;
ierr = VecCreate(PETSC_COMM_SELF,lvec);CHKERRQ(ierr);
ierr = VecSetSizes(*lvec,red->N,red->N);CHKERRQ(ierr);
ierr = VecSetType(*lvec,dm->vectype);CHKERRQ(ierr);
ierr = VecSetDM(*lvec,dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int Epetra_PETScAIJMatrix::ExtractDiagonalCopy(Epetra_Vector & Diagonal) const
{
//TODO optimization: only get this diagonal once
Vec petscDiag;
double *vals=0;
int length;
int ierr=VecCreate(Comm_->Comm(),&petscDiag);CHKERRQ(ierr);
VecSetSizes(petscDiag,NumMyRows_,NumGlobalRows_);
# ifdef HAVE_MPI
ierr = VecSetType(petscDiag,VECMPI);CHKERRQ(ierr);
# else //TODO untested!!
VecSetType(petscDiag,VECSEQ);
# endif
MatGetDiagonal(Amat_, petscDiag);
VecGetArray(petscDiag,&vals);
VecGetLocalSize(petscDiag,&length);
for (int i=0; i<length; i++) Diagonal[i] = vals[i];
VecRestoreArray(petscDiag,&vals);
VecDestroy(petscDiag);
return(0);
}
PetscErrorCode VecDuplicate_Seq(Vec win,Vec *V)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = VecCreate(PetscObjectComm((PetscObject)win),V);CHKERRQ(ierr);
ierr = VecSetSizes(*V,win->map->n,win->map->n);CHKERRQ(ierr);
ierr = VecSetType(*V,((PetscObject)win)->type_name);CHKERRQ(ierr);
ierr = PetscLayoutReference(win->map,&(*V)->map);CHKERRQ(ierr);
ierr = PetscObjectListDuplicate(((PetscObject)win)->olist,&((PetscObject)(*V))->olist);CHKERRQ(ierr);
ierr = PetscFunctionListDuplicate(((PetscObject)win)->qlist,&((PetscObject)(*V))->qlist);CHKERRQ(ierr);
(*V)->ops->view = win->ops->view;
(*V)->stash.ignorenegidx = win->stash.ignorenegidx;
PetscFunctionReturn(0);
}
EXTERN_C_END
#endif
#undef __FUNCT__
#define __FUNCT__ "VecCreateShared"
/*@
VecCreateShared - Creates a parallel vector that uses shared memory.
Input Parameters:
. comm - the MPI communicator to use
. n - local vector length (or PETSC_DECIDE to have calculated if N is given)
. N - global vector length (or PETSC_DECIDE to have calculated if n is given)
Output Parameter:
. vv - the vector
Collective on MPI_Comm
Notes:
Currently VecCreateShared() is available only on the SGI; otherwise,
this routine is the same as VecCreateMPI().
Use VecDuplicate() or VecDuplicateVecs() to form additional vectors of the
same type as an existing vector.
Level: advanced
Concepts: vectors^creating with shared memory
.seealso: VecCreateSeq(), VecCreate(), VecCreateMPI(), VecDuplicate(), VecDuplicateVecs(),
VecCreateGhost(), VecCreateMPIWithArray(), VecCreateGhostWithArray()
@*/
PetscErrorCode VecCreateShared(MPI_Comm comm,PetscInt n,PetscInt N,Vec *v)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = VecCreate(comm,v);CHKERRQ(ierr);
ierr = VecSetSizes(*v,n,N);CHKERRQ(ierr);
ierr = VecSetType(*v,VECSHARED);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
