void TestInterleavedVecScatter()
{
// Vectors will be twice PROBLEM_SIZE, since this is to be used in bidomain code.
const unsigned PROBLEM_SIZE = 10;
DistributedVectorFactory factory(PROBLEM_SIZE);
// Source vector = [-1 1 -2 2 ... -PROBLEM_SIZE/2+1 PROBLEM_SIZE/2+1]
Vec interleaved_vec=factory.CreateVec(2);
DistributedVector interleaved_dist_vec = factory.CreateDistributedVector(interleaved_vec);
DistributedVector::Stripe first_variable(interleaved_dist_vec, 0);
DistributedVector::Stripe second_variable(interleaved_dist_vec, 1);
for (DistributedVector::Iterator index = interleaved_dist_vec.Begin();
index!= interleaved_dist_vec.End();
++index)
{
first_variable[index] = -1.0 * (index.Global+1);
second_variable[index] = (index.Global+1);
}
// Destination vectors. It is important they have a compatible parallel layout with the source vector, hence the 2nd param of CreateVec()
PetscInt local_num_rows;
VecGetLocalSize(interleaved_vec, &local_num_rows);
Vec first_variable_vec = PetscTools::CreateVec(PROBLEM_SIZE, local_num_rows/2);
Vec second_variable_vec = PetscTools::CreateVec(PROBLEM_SIZE, local_num_rows/2);
// Setup and perform scatter operation
VecScatter first_variable_context;
VecScatter second_variable_context;
PetscVecTools::SetupInterleavedVectorScatterGather(interleaved_vec, first_variable_context, second_variable_context);
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 6) //PETSc 3.6 or later
// When used in the preconditioner code within a KSP solve, the main (bidomain) vector will be locked.
// Lock the vector so that modern PETSc (3.6) won't want to change it
VecLockPush(interleaved_vec);
#endif
PetscVecTools::DoInterleavedVecScatter(interleaved_vec, first_variable_context, first_variable_vec, second_variable_context, second_variable_vec);
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 6) //PETSc 3.6 or later
// Unlock the vector (for symmetry)
VecLockPop(interleaved_vec);
#endif
// Check destination vectors are [-1 -2 -3 ...] and [1 2 3 ...] respectively.
DistributedVector dist_1st_var_vec = factory.CreateDistributedVector(first_variable_vec);
DistributedVector dist_2nd_var_vec = factory.CreateDistributedVector(second_variable_vec);
for (DistributedVector::Iterator index = dist_1st_var_vec.Begin();
index!= dist_1st_var_vec.End();
++index)
{
TS_ASSERT_EQUALS(dist_1st_var_vec[index], -1.0 * (index.Global+1));
TS_ASSERT_EQUALS(dist_2nd_var_vec[index], index.Global+1);
}
PetscTools::Destroy(interleaved_vec);
PetscTools::Destroy(first_variable_vec);
PetscTools::Destroy(second_variable_vec);
VecScatterDestroy(PETSC_DESTROY_PARAM(first_variable_context));
VecScatterDestroy(PETSC_DESTROY_PARAM(second_variable_context));
}
/*
Helper rutine to handle user postenvents and recording
*/
static PetscErrorCode TSPostEvent(TS ts,PetscReal t,Vec U)
{
PetscErrorCode ierr;
TSEvent event = ts->event;
PetscBool terminate = PETSC_FALSE;
PetscBool restart = PETSC_FALSE;
PetscInt i,ctr,stepnum;
PetscBool inflag[2],outflag[2];
PetscBool forwardsolve = PETSC_TRUE; /* Flag indicating that TS is doing a forward solve */
PetscFunctionBegin;
if (event->postevent) {
PetscObjectState state_prev,state_post;
ierr = PetscObjectStateGet((PetscObject)U,&state_prev);CHKERRQ(ierr);
ierr = (*event->postevent)(ts,event->nevents_zero,event->events_zero,t,U,forwardsolve,event->ctx);CHKERRQ(ierr);
ierr = PetscObjectStateGet((PetscObject)U,&state_post);CHKERRQ(ierr);
if (state_prev != state_post) restart = PETSC_TRUE;
}
/* Handle termination events and step restart */
for (i=0; i<event->nevents_zero; i++) if (event->terminate[event->events_zero[i]]) terminate = PETSC_TRUE;
inflag[0] = restart; inflag[1] = terminate;
ierr = MPIU_Allreduce(inflag,outflag,2,MPIU_BOOL,MPI_LOR,((PetscObject)ts)->comm);CHKERRQ(ierr);
restart = outflag[0]; terminate = outflag[1];
if (restart) {ierr = TSRestartStep(ts);CHKERRQ(ierr);}
if (terminate) {ierr = TSSetConvergedReason(ts,TS_CONVERGED_EVENT);CHKERRQ(ierr);}
event->status = terminate ? TSEVENT_NONE : TSEVENT_RESET_NEXTSTEP;
/* Reset event residual functions as states might get changed by the postevent callback */
if (event->postevent) {
ierr = VecLockPush(U);CHKERRQ(ierr);
ierr = (*event->eventhandler)(ts,t,U,event->fvalue,event->ctx);CHKERRQ(ierr);
ierr = VecLockPop(U);CHKERRQ(ierr);
}
/* Cache current time and event residual functions */
event->ptime_prev = t;
for (i=0; i<event->nevents; i++)
event->fvalue_prev[i] = event->fvalue[i];
/* Record the event in the event recorder */
ierr = TSGetStepNumber(ts,&stepnum);CHKERRQ(ierr);
ctr = event->recorder.ctr;
if (ctr == event->recsize) {
ierr = TSEventRecorderResize(event);CHKERRQ(ierr);
}
event->recorder.time[ctr] = t;
event->recorder.stepnum[ctr] = stepnum;
event->recorder.nevents[ctr] = event->nevents_zero;
for (i=0; i<event->nevents_zero; i++) event->recorder.eventidx[ctr][i] = event->events_zero[i];
event->recorder.ctr++;
PetscFunctionReturn(0);
}
void TestReadOnlyDistributedVector()
{
DistributedVectorFactory factory(10);
Vec petsc_vec = factory.CreateVec();
{
DistributedVector distributed_vector = factory.CreateDistributedVector(petsc_vec);
for (DistributedVector::Iterator index = distributed_vector.Begin();
index!= distributed_vector.End();
++index)
{
distributed_vector[index] = (double) PetscTools::GetMyRank();
}
}
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 6) //PETSc 3.6 or later
// Lock the vector so that modern PETSc (3.6) won't want to change it
EXCEPT_IF_NOT(VecLockPush(petsc_vec) == 0);
#endif
{
DistributedVector distributed_vector_read = factory.CreateDistributedVector(petsc_vec, true);
for (DistributedVector::Iterator index = distributed_vector_read.Begin();
index!= distributed_vector_read.End();
++index)
{
TS_ASSERT_EQUALS(distributed_vector_read[index], (double) PetscTools::GetMyRank());
distributed_vector_read[index] = 2.0;
}
}
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 6) //PETSc 3.6 or later
// Take the lock back
EXCEPT_IF_NOT(VecLockPop(petsc_vec) == 0);
#endif
PetscTools::Destroy(petsc_vec);
}
PetscErrorCode TSEventHandler(TS ts)
{
PetscErrorCode ierr;
TSEvent event;
PetscReal t;
Vec U;
PetscInt i;
PetscReal dt,dt_min;
PetscInt rollback=0,in[2],out[2];
PetscInt fvalue_sign,fvalueprev_sign;
PetscFunctionBegin;
PetscValidHeaderSpecific(ts,TS_CLASSID,1);
if (!ts->event) PetscFunctionReturn(0);
event = ts->event;
ierr = TSGetTime(ts,&t);CHKERRQ(ierr);
ierr = TSGetTimeStep(ts,&dt);CHKERRQ(ierr);
ierr = TSGetSolution(ts,&U);CHKERRQ(ierr);
if (event->status == TSEVENT_NONE) {
if (ts->steps == 1) /* After first successful step */
event->timestep_orig = ts->ptime - ts->ptime_prev;
event->timestep_prev = dt;
}
if (event->status == TSEVENT_RESET_NEXTSTEP) {
/* Restore time step */
dt = PetscMin(event->timestep_orig,event->timestep_prev);
ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr);
event->status = TSEVENT_NONE;
}
if (event->status == TSEVENT_NONE) {
event->ptime_end = t;
}
ierr = VecLockPush(U);CHKERRQ(ierr);
ierr = (*event->eventhandler)(ts,t,U,event->fvalue,event->ctx);CHKERRQ(ierr);
ierr = VecLockPop(U);CHKERRQ(ierr);
for (i=0; i < event->nevents; i++) {
if (PetscAbsScalar(event->fvalue[i]) < event->vtol[i]) {
event->status = TSEVENT_ZERO;
event->fvalue_right[i] = event->fvalue[i];
continue;
}
fvalue_sign = PetscSign(PetscRealPart(event->fvalue[i]));
fvalueprev_sign = PetscSign(PetscRealPart(event->fvalue_prev[i]));
if (fvalueprev_sign != 0 && (fvalue_sign != fvalueprev_sign) && (PetscAbsScalar(event->fvalue_prev[i]) > event->vtol[i])) {
switch (event->direction[i]) {
case -1:
if (fvalue_sign < 0) {
rollback = 1;
/* Compute new time step */
dt = TSEventComputeStepSize(event->ptime_prev,t,event->ptime_right,event->fvalue_prev[i],event->fvalue[i],event->fvalue_right[i],event->side[i],dt);
if (event->monitor) {
ierr = PetscViewerASCIIPrintf(event->monitor,"TSEvent: iter %D - Event %D interval detected [%g - %g]\n",event->iterctr,i,(double)event->ptime_prev,(double)t);CHKERRQ(ierr);
}
event->fvalue_right[i] = event->fvalue[i];
event->side[i] = 1;
if (!event->iterctr) event->zerocrossing[i] = PETSC_TRUE;
event->status = TSEVENT_LOCATED_INTERVAL;
}
break;
case 1:
if (fvalue_sign > 0) {
rollback = 1;
/* Compute new time step */
dt = TSEventComputeStepSize(event->ptime_prev,t,event->ptime_right,event->fvalue_prev[i],event->fvalue[i],event->fvalue_right[i],event->side[i],dt);
if (event->monitor) {
ierr = PetscViewerASCIIPrintf(event->monitor,"TSEvent: iter %D - Event %D interval detected [%g - %g]\n",event->iterctr,i,(double)event->ptime_prev,(double)t);CHKERRQ(ierr);
}
event->fvalue_right[i] = event->fvalue[i];
event->side[i] = 1;
if (!event->iterctr) event->zerocrossing[i] = PETSC_TRUE;
event->status = TSEVENT_LOCATED_INTERVAL;
}
break;
case 0:
rollback = 1;
/* Compute new time step */
dt = TSEventComputeStepSize(event->ptime_prev,t,event->ptime_right,event->fvalue_prev[i],event->fvalue[i],event->fvalue_right[i],event->side[i],dt);
if (event->monitor) {
ierr = PetscViewerASCIIPrintf(event->monitor,"TSEvent: iter %D - Event %D interval detected [%g - %g]\n",event->iterctr,i,(double)event->ptime_prev,(double)t);CHKERRQ(ierr);
}
event->fvalue_right[i] = event->fvalue[i];
event->side[i] = 1;
if (!event->iterctr) event->zerocrossing[i] = PETSC_TRUE;
event->status = TSEVENT_LOCATED_INTERVAL;
break;
}
}
}
in[0] = event->status; in[1] = rollback;
ierr = MPIU_Allreduce(in,out,2,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr);
event->status = (TSEventStatus)out[0]; rollback = out[1];
if (rollback) event->status = TSEVENT_LOCATED_INTERVAL;
event->nevents_zero = 0;
if (event->status == TSEVENT_ZERO) {
for (i=0; i < event->nevents; i++) {
if (PetscAbsScalar(event->fvalue[i]) < event->vtol[i]) {
event->events_zero[event->nevents_zero++] = i;
if (event->monitor) {
ierr = PetscViewerASCIIPrintf(event->monitor,"TSEvent: Event %D zero crossing at time %g located in %D iterations\n",i,(double)t,event->iterctr);CHKERRQ(ierr);
}
event->zerocrossing[i] = PETSC_FALSE;
}
event->side[i] = 0;
}
ierr = TSPostEvent(ts,t,U);CHKERRQ(ierr);
dt = event->ptime_end - t;
if (PetscAbsReal(dt) < PETSC_SMALL) { /* we hit the event, continue with the candidate time step */
dt = event->timestep_prev;
event->status = TSEVENT_NONE;
}
ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr);
event->iterctr = 0;
PetscFunctionReturn(0);
}
if (event->status == TSEVENT_LOCATED_INTERVAL) {
ierr = TSRollBack(ts);CHKERRQ(ierr);
ierr = TSSetConvergedReason(ts,TS_CONVERGED_ITERATING);CHKERRQ(ierr);
event->status = TSEVENT_PROCESSING;
event->ptime_right = t;
} else {
for (i=0; i < event->nevents; i++) {
if (event->status == TSEVENT_PROCESSING && event->zerocrossing[i]) {
/* Compute new time step */
dt = TSEventComputeStepSize(event->ptime_prev,t,event->ptime_right,event->fvalue_prev[i],event->fvalue[i],event->fvalue_right[i],event->side[i],dt);
event->side[i] = -1;
}
event->fvalue_prev[i] = event->fvalue[i];
}
if (event->monitor && event->status == TSEVENT_PROCESSING) {
ierr = PetscViewerASCIIPrintf(event->monitor,"TSEvent: iter %D - Stepping forward as no event detected in interval [%g - %g]\n",event->iterctr,(double)event->ptime_prev,(double)t);CHKERRQ(ierr);
}
event->ptime_prev = t;
}
if (event->status == TSEVENT_PROCESSING) event->iterctr++;
ierr = MPIU_Allreduce(&dt,&dt_min,1,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr);
ierr = TSSetTimeStep(ts,dt_min);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
MatNullSpaceCreate - Creates a data structure used to project vectors
out of null spaces.
Collective on MPI_Comm
Input Parameters:
+ comm - the MPI communicator associated with the object
. has_cnst - PETSC_TRUE if the null space contains the constant vector; otherwise PETSC_FALSE
. n - number of vectors (excluding constant vector) in null space
- vecs - the vectors that span the null space (excluding the constant vector);
these vectors must be orthonormal. These vectors are NOT copied, so do not change them
after this call. You should free the array that you pass in and destroy the vectors (this will reduce the reference count
for them by one).
Output Parameter:
. SP - the null space context
Level: advanced
Notes:
See MatNullSpaceSetFunction() as an alternative way of providing the null space information instead of setting vecs.
If has_cnst is PETSC_TRUE you do not need to pass a constant vector in as a fourth argument to this routine, nor do you
need to pass in a function that eliminates the constant function into MatNullSpaceSetFunction().
Users manual sections:
. sec_singular
.keywords: PC, null space, create
.seealso: MatNullSpaceDestroy(), MatNullSpaceRemove(), MatSetNullSpace(), MatNullSpace, MatNullSpaceSetFunction()
@*/
PetscErrorCode MatNullSpaceCreate(MPI_Comm comm,PetscBool has_cnst,PetscInt n,const Vec vecs[],MatNullSpace *SP)
{
MatNullSpace sp;
PetscErrorCode ierr;
PetscInt i;
PetscFunctionBegin;
if (n < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Number of vectors (given %D) cannot be negative",n);
if (n) PetscValidPointer(vecs,4);
for (i=0; i<n; i++) PetscValidHeaderSpecific(vecs[i],VEC_CLASSID,4);
PetscValidPointer(SP,5);
if (n) {
for (i=0; i<n; i++) {
/* prevent the user from changes values in the vector */
ierr = VecLockPush(vecs[i]);CHKERRQ(ierr);
}
}
#if defined(PETSC_USE_DEBUG)
if (n) {
PetscScalar *dots;
for (i=0; i<n; i++) {
PetscReal norm;
ierr = VecNorm(vecs[i],NORM_2,&norm);CHKERRQ(ierr);
if (PetscAbsReal(norm - 1) > PETSC_SQRT_MACHINE_EPSILON) SETERRQ2(PetscObjectComm((PetscObject)vecs[i]),PETSC_ERR_ARG_WRONG,"Vector %D must have 2-norm of 1.0, it is %g",i,(double)norm);
}
if (has_cnst) {
for (i=0; i<n; i++) {
PetscScalar sum;
ierr = VecSum(vecs[i],&sum);CHKERRQ(ierr);
if (PetscAbsScalar(sum) > PETSC_SQRT_MACHINE_EPSILON) SETERRQ2(PetscObjectComm((PetscObject)vecs[i]),PETSC_ERR_ARG_WRONG,"Vector %D must be orthogonal to constant vector, inner product is %g",i,(double)PetscAbsScalar(sum));
}
}
ierr = PetscMalloc1(n-1,&dots);CHKERRQ(ierr);
for (i=0; i<n-1; i++) {
PetscInt j;
ierr = VecMDot(vecs[i],n-i-1,vecs+i+1,dots);CHKERRQ(ierr);
for (j=0;j<n-i-1;j++) {
if (PetscAbsScalar(dots[j]) > PETSC_SQRT_MACHINE_EPSILON) SETERRQ3(PetscObjectComm((PetscObject)vecs[i]),PETSC_ERR_ARG_WRONG,"Vector %D must be orthogonal to vector %D, inner product is %g",i,i+j+1,(double)PetscAbsScalar(dots[j]));
}
}
PetscFree(dots);CHKERRQ(ierr);
}
#endif
*SP = NULL;
ierr = MatInitializePackage();CHKERRQ(ierr);
ierr = PetscHeaderCreate(sp,MAT_NULLSPACE_CLASSID,"MatNullSpace","Null space","Mat",comm,MatNullSpaceDestroy,MatNullSpaceView);CHKERRQ(ierr);
sp->has_cnst = has_cnst;
sp->n = n;
sp->vecs = 0;
sp->alpha = 0;
sp->remove = 0;
sp->rmctx = 0;
if (n) {
ierr = PetscMalloc1(n,&sp->vecs);CHKERRQ(ierr);
ierr = PetscMalloc1(n,&sp->alpha);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)sp,n*(sizeof(Vec)+sizeof(PetscScalar)));CHKERRQ(ierr);
for (i=0; i<n; i++) {
ierr = PetscObjectReference((PetscObject)vecs[i]);CHKERRQ(ierr);
sp->vecs[i] = vecs[i];
}
}
*SP = sp;
PetscFunctionReturn(0);
}
