void JacobiSmoothFG( VT &sol, const MT &A, const VT &def )
// changes only the fine unknowns
// result in sol_vec; def_vec: correct defect before call, after call destroyed
{
typename VT::Iterator viter(sol);
typename VT::VectorEntry ve;
const FAMGSparseVector *svsol = sol.GetSparseVectorPtr();
const FAMGSparseVector *svdef = def.GetSparseVectorPtr();
const FAMGSparseBlock *sb = A.GetDiagSparseBlockPtr();
double *solptr, *defptr, *matptr;
short nr = sb->Get_nr();
if(nr != sb->Get_nc()) assert(0);
if(nr != svsol->Get_n()) assert(0);
if(nr != svdef->Get_n()) assert(0);
// todo: implement for more general vectors
for(short i = 1; i < nr; i++)
{
if(svsol->Get_comp(i) - svsol->Get_comp(i-1) != 1) assert(0);
if(svdef->Get_comp(i) - svdef->Get_comp(i-1) != 1) assert(0);
}
short sol_off = svsol->Get_comp(0);
short def_off = svdef->Get_comp(0);
double *decomp = new double[nr*nr];
short *pivotmap = new short[nr];
while(viter(ve))
{
if( sol.IsFG(ve) )
{
solptr = sol.GetValuePtr(ve)+sol_off;
defptr = def.GetValuePtr(ve)+def_off;
matptr = A.GetDiagValuePtr(ve);
SparseBlockMCopyDense(decomp,sb,matptr);
if(LR_Decomp(nr,decomp,pivotmap)) assert(0);
if(LR_Solve(nr,decomp,pivotmap,solptr,defptr)) assert(0);
}
#ifdef USE_UG_DS
else
{
// set coarse components to 0
SparseBlockVSet(svsol,sol.GetValuePtr(ve),0.0);
}
#endif
}
delete decomp;
delete pivotmap;
return;
}
// split this M-tree into a list of trees having height level, which is used in the "splitting" phase of the BulkLoad algorithm
// nCreated is the number of created subtrees,
// level is the split level for the tree,
// children is the list of the parents of each subtree,
// name is the root for the subtrees names
// the return value is the list of splitted subtrees's names
GiSTlist<char *> *
MT::SplitTree (int *nCreated, int level, GiSTlist<MTentry *> *parentEntries, const char *name)
{
GiSTlist<MTnode *> *oldList = new GiSTlist<MTnode *>; // upper level nodes
MTnode *node = new MTnode; // this is because the first operation on node is a delete
GiSTpath path;
path.MakeRoot ();
oldList->Append((MTnode *) ReadNode(path)); // insert the root
do { // build the roots list
GiSTlist<MTnode *> *newList = new GiSTlist<MTnode *>; // lower level nodes
while (!oldList->IsEmpty()) {
delete node; // delete the old node created by ReadNode
node = oldList->RemoveFront(); // retrieve next node to be examined
path = node->Path();
for (int i=0; i<node->NumEntries(); i++) { // append all its children to the new list
path.MakeChild ((*node)[i].Ptr()->Ptr());
newList->Append((MTnode *)ReadNode(path));
path.MakeParent ();
}
}
delete oldList;
oldList = newList;
} while (node->Level() > level); // stop if we're at the split level
delete node;
GiSTlist<char *> *newTreeNames = new GiSTlist<char *>; // this is the results list
while (!oldList->IsEmpty()) { // now append each sub-tree to its root
char newName[50];
sprintf (newName, "%s.%i", name, ++(*nCreated));
unlink (newName); // if this M-tree already exists, delete it
MT *newTree = new MT;
newTree->Create(newName); // create a new M-tree
path.MakeRoot ();
MTnode *rootNode = (MTnode *) newTree->ReadNode(path); // read the root of the new tree
node = oldList->RemoveFront();
newTree->Append(rootNode, (MTnode *)node->Copy()); // append the current node to the root of new tree
parentEntries->Append(node->ParentEntry()); // insert the original parent entry into the list
newTreeNames->Append(strdup(newName)); // insert the new M-tree name into the list
delete node;
delete rootNode;
delete newTree;
}
delete oldList;
return newTreeNames;
}
void VecMinusMatVec( VT &d, const VT &f, const MT &M, const VT &u )
{
typename VT::Iterator viter(d);
typename VT::VectorEntry row;
typename MT::MatrixEntry col;
double *dptr, *fptr, *uptr, *mptr;
const FAMGSparseVector *svu = u.GetSparseVectorPtr();
const FAMGSparseVector *svf = f.GetSparseVectorPtr();
const FAMGSparseVector *svd = d.GetSparseVectorPtr();
const FAMGSparseBlock *sb = M.GetSparseBlockPtr();
const FAMGSparseBlock *sbd = M.GetDiagSparseBlockPtr();
FAMGSparseVector svsum_d, svsum_o;
svsum_d.Product(sbd,svu);
svsum_o.Product(sb,svu);
double *sum_d = new double[svsum_d.Get_maxcomp()+1];
double *sum_o = new double[svsum_o.Get_maxcomp()+1];
while(viter(row))
{
typename MT::Iterator miter(M,row);
dptr = d.GetValuePtr(row);
fptr = f.GetValuePtr(row);
// diagonal
miter(col);
uptr = u.GetValuePtr(col.dest());
mptr = M.GetValuePtr(col);
SparseBlockVSet(&svsum_d,sum_d,0.0);
SparseBlockVSet(&svsum_o,sum_o,0.0);
SparseBlockMVAddProduct(&svsum_d,sbd,svu,sum_d,mptr,uptr,1.0);
while(miter(col))
{
uptr = u.GetValuePtr(col.dest());
mptr = M.GetValuePtr(col);
SparseBlockMVAddProduct(&svsum_o,sb,svu,sum_o,mptr,uptr,1.0);
}
SparseBlockVSub(svd,svf,&svsum_o,dptr,fptr,sum_o);
SparseBlockVSub(svd,svd,&svsum_d,dptr,dptr,sum_d);
}
delete sum_d;
delete sum_o;
}
// append the subtree rooted at from to the node to, which is used in the "append" phase of the BulkLoad algorithm
void
MT::Append (MTnode *to, MTnode *from)
{
GiSTlist<MTnode *> *oldList = new GiSTlist<MTnode *>; // upper level nodes to append
oldList->Append(from);
GiSTlist<GiSTpath> pathList;
pathList.Append (to->Path());
MTnode *node = new MTnode, *newNode = NULL;
MT *fromTree = (MT *) from->Tree();
do {
GiSTlist<MTnode *> *newList = new GiSTlist<MTnode *>; // lower level nodes to append
while (!oldList->IsEmpty()) {
delete node;
node = oldList->RemoveFront();
GiSTpath path = pathList.RemoveFront ();
newNode = (MTnode *) ReadNode (path); // node to be appended
for (int i=0; i<node->NumEntries(); i++) {
MTentry *entry = (MTentry *) (*node)[i].Ptr()->Copy();
if (node->Level() > 0) { // if node isn't a leaf, we've to allocate its children
GiSTpath nodePath = node->Path();
nodePath.MakeChild (entry->Ptr());
newList->Append((MTnode *) fromTree->ReadNode(nodePath));
entry->SetPtr(Store()->Allocate()); // allocate its child in the inserted tree
path.MakeChild (entry->Ptr());
MTnode *childNode = (MTnode *) CreateNode ();
childNode->Path() = path;
childNode->SetTree(this);
WriteNode (childNode); // write the empty node
delete childNode;
pathList.Append (path);
path.MakeParent ();
}
newNode->Insert(*entry);
delete entry;
}
newNode->SetLevel(node->Level());
WriteNode (newNode); // write the node
delete newNode;
}
delete oldList;
oldList = newList;
} while (node->Level() > 0); // until we reach the leaves' level
delete node;
delete oldList;
}
void SGSSmoother( VT &sol, const MT &M, VT &def )
// backward Gauss-Seidel
// result in sol_vec; def_vec: correct defect before call, after call destroyed
{
typename VT::Iterator viter(def);
typename VT::RevIterator vReviter(def);
typename VT::VectorEntry row, col;
typename MT::MatrixEntry me;
register double sum, diag;
int row_index;
/* symmetric Gauss-Seidel */
while(viter(row))
{
typename MT::Iterator miter(M,row);
row_index = row.GetIndex();
sum = def[row];
miter(me);
diag = M[me];
while(miter(me))
{
col = me.dest();
if( col.GetIndex() < row_index )
sum -= M[me] * def[col];
}
def[row] = sum / diag;
}
viter.reset();
while(viter(row))
def[row] *= M.DiagValue(row);
while(vReviter(row))
{
typename MT::Iterator miter(M,row);
row_index = row.GetIndex();
sum = def[row];
miter(me);
diag = M[me];
while(miter(me))
{
col = me.dest();
if( col.GetIndex() > row_index )
sum -= M[me] * def[col];
}
def[row] = sum / diag;
}
sol += def; // update solution
return;
}
void JacobiSmoother( VT &sol, const MT &M, const VT &def )
// result in sol_vec; def_vec: correct defect before call, after call destroyed
{
typename VT::Iterator viter(sol);
typename VT::VectorEntry ve;
while(viter(ve))
sol[ve] += def[ve] / M.DiagValue(ve);
return;
}
void JacobiSmoothFG( VT &sol, const MT &M, const VT &def )
// changes only the fine unknowns
// result in sol_vec; def_vec: correct defect before call, after call destroyed
{
typename VT::Iterator viter(sol);
typename VT::VectorEntry ve;
#ifdef USE_UG_DS
while(viter(ve))
if( sol.IsFG(ve) )
sol[ve] = def[ve] / M.DiagValue(ve);
else
sol[ve] = 0; // init other components
#else
while(viter(ve))
if( sol.IsFG(ve) )
sol[ve] += def[ve] / M.DiagValue(ve);
#endif
return;
}
void dampedJacobiSmoother( VT &sol, const MT &M, const VT &def )
// result in sol_vec; def_vec: correct defect before call, after call destroyed
{
static const double omega = 2.0/3.0;
typename VT::Iterator viter(sol);
typename VT::VectorEntry ve;
while(viter(ve))
sol[ve] += omega * def[ve] / M.DiagValue(ve);
return;
}
void JacobiSmoothFGSimple( VT &sol, const MT &D, const VT &def )
// changes only the fine unknowns
// result in sol_vec; def_vec: correct defect before call, after call destroyed
{
typename VT::Iterator viter(sol);
typename VT::VectorEntry ve;
const FAMGSparseVector *svsol = sol.GetSparseVectorPtr();
const FAMGSparseVector *svdef = def.GetSparseVectorPtr();
const FAMGSparseBlock *sb = D.GetDiagSparseBlockPtr();
double *solptr, *defptr, *matptr;
while(viter(ve))
{
if( sol.IsFG(ve) )
{
solptr = sol.GetValuePtr(ve);
defptr = def.GetValuePtr(ve);
matptr = D.GetDiagValuePtr(ve);
SparseBlockMVAddProduct(svsol,sb,svdef,solptr,matptr,defptr,1.0);
}
}
return;
}
int ConstructGalerkinMatrix( MT &Mcg, const FAMGGrid &fg )
// this matrix lives on the coarse grid
// calculates Mcg := R * Mfg * P and with indices:
// Mcg_(i,j) := \sum_{s,t} R_(i,s) * Mfg_(s,t) * P_(t,j)
{
typedef typename MT::Vector VT;
const FAMGTransfer &transfer = *fg.GetTransfer();
const typename MT::GridVector& fg_gridvec = (typename MT::GridVector&)fg.GetGridVector();
const MT& Mfg = (MT&)*fg.GetConsMatrix(); // consistent matrix is essential here!
const MT& Dfg = (MT&)*fg.GetDiagMatrix();
const VT &tvA = *fg.GetVector(FAMGTVA);
const VT &tvB = *fg.GetVector(FAMGTVB);
typename MT::MatrixEntry mij, mis;
typename VT::VectorEntry i_fg, i_cg, j_fg, j_cg, s_fg, s_cg, t_cg;
FAMGTransferEntry *pjs, *pij, *pst;
typename VT::Iterator viter(fg_gridvec);
#ifdef ModelP
abort();// check the consistent mode of ALL occuring matrices!!! and remove this line then
#endif
// cast because GetSparseBlockPtr returns a const FAMGSparseBlock * pointer
FAMGSparseBlock *cmatsb_d = (FAMGSparseBlock *)Mcg.GetDiagSparseBlockPtr();
FAMGSparseBlock *cmatsb_o = (FAMGSparseBlock *)Mcg.GetSparseBlockPtr();
const FAMGSparseBlock *dmatsb = Dfg.GetDiagSparseBlockPtr();
const FAMGSparseBlock *fmatsb_o = Mfg.GetSparseBlockPtr();
const FAMGSparseBlock *fmatsb_d = Mfg.GetDiagSparseBlockPtr();
const FAMGSparseVector *sp = transfer.Get_sp();
const FAMGSparseVector *sr = transfer.Get_sr();
const FAMGSparseVector *tvAsv = tvA.GetSparseVectorPtr();
const FAMGSparseVector *tvBsv = tvB.GetSparseVectorPtr();
double *tvAptr, *tvBptr;
FAMGSparseBlock sb_o_p, sb_r_o, sb_r_o_p, sb_r_d_p, sb_r_dmat_p; // only offdiagonal blocks
sb_o_p.Product(fmatsb_o,sp);
sb_r_o.Product(sr,fmatsb_o);
sb_r_o_p.Product(sr,fmatsb_o,sp);
// sb_r_dmat_p.Product(sr,dmatsb,sp);
sb_r_dmat_p = (*fmatsb_o);
sb_r_d_p.Product(sr,fmatsb_d,sp);
// chech sparse block structure
if(cmatsb_o->CheckStructureforAdd(fmatsb_o)) return 1;
if(cmatsb_o->CheckStructureforAdd(&sb_o_p)) return 1;
if(cmatsb_o->CheckStructureforAdd(&sb_r_o)) return 1;
if(cmatsb_o->CheckStructureforAdd(&sb_r_o_p)) return 1;
if(cmatsb_o->CheckStructureforAdd(&sb_r_dmat_p)) return 1;
if(cmatsb_d->CheckStructureforAdd(fmatsb_d)) return 1;
if(cmatsb_d->CheckStructureforAdd(&sb_r_d_p)) return 1;
if(cmatsb_d->CheckStructureforAdd(&sb_o_p)) return 1;
if(cmatsb_d->CheckStructureforAdd(&sb_r_o)) return 1;
if(cmatsb_d->CheckStructureforAdd(&sb_r_o_p)) return 1;
if(cmatsb_d->CheckStructureforAdd(&sb_r_dmat_p)) return 1;
short maxoffset = sb_o_p.Get_maxoffset();
maxoffset = Max(maxoffset,sb_r_o.Get_maxoffset());
maxoffset = Max(maxoffset,sb_r_o_p.Get_maxoffset());
maxoffset = Max(maxoffset,sb_r_dmat_p.Get_maxoffset());
maxoffset = Max(maxoffset,sb_r_d_p.Get_maxoffset());
double *val = new double[maxoffset+1];
double *diaginv = new double[dmatsb->Get_maxoffset()+1];
while (viter(i_fg) )
{
#ifdef ModelP
if ( IS_FAMG_GHOST(((FAMGugVectorEntryRef*)(i_fg.GetPointer()))->myvector()) )
{
// repair coarse grid matrix of border vector, if it has no diagonal matrix entry
if (fg_gridvec.IsCG(i_fg) )
{
transfer.GetFirstEntry(i_fg)->GetColInVar(i_cg);
typename MT::Iterator mijiter(Mcg,i_cg);
if( mijiter(mij) ) // test first matrix entry of i_cg
{
if( mij.dest() != i_cg )
Mcg.AddEntry(0.0, i_cg, i_cg); // has no diag entry yet
}
else // i_cg has no matrix entry
{
Mcg.AddEntry(0.0, i_cg, i_cg);
}
}
continue;
}
#endif
// i is now in core partition
if (fg_gridvec.IsCG(i_fg) )
{
// i is coarse
transfer.GetFirstEntry(i_fg)->GetColInVar(i_cg);
typename MT::Iterator mijiter(Mfg,i_fg);
while( mijiter(mij) )
{
j_fg = mij.dest();
if( fg_gridvec.IsCG(j_fg) )
{
transfer.GetFirstEntry(j_fg)->GetColInVar(j_cg);
// Mcg.AddEntry(Mfg[mij], i_cg, j_cg); // Mcc
if(i_cg == j_cg) Mcg.AddEntry(fmatsb_d,Mfg.GetValuePtr(mij), i_cg, j_cg);
else Mcg.AddEntry(fmatsb_o,Mfg.GetValuePtr(mij), i_cg, j_cg); // Mcc
}
else
{
for( pjs=transfer.GetFirstEntry(j_fg); pjs != NULL; pjs = pjs->GetNext())
{
pjs->GetColInVar(s_cg);
SparseBlockMMProduct(&sb_o_p,fmatsb_o,sp,val,Mfg.GetValuePtr(mij),pjs->GetProlongationPtr());
Mcg.AddEntry(&sb_o_p,val,i_cg, s_cg);
// Mcg.AddEntry(Mfg[mij]*pjs->GetProlongation(), i_cg, s_cg); // Mcf*P
}
}
}
}
else
{
// i is fine
typename MT::Iterator misiter(Mfg,i_fg);
while( misiter(mis) )
{
s_fg = mis.dest();
for( pij=transfer.GetFirstEntry(i_fg); pij != NULL; pij = pij->GetNext())
{
pij->GetColInVar(j_cg);
if( fg_gridvec.IsCG(s_fg) )
{
transfer.GetFirstEntry(s_fg)->GetColInVar(s_cg);
// pij is equivalent to rji
// Mcg.AddEntry(pij->GetRestriction()*Mfg[mis], j_cg, s_cg); // R*Mfc
SparseBlockMMProduct(&sb_r_o,sr,fmatsb_o,val,pij->GetRestrictionPtr(),Mfg.GetValuePtr(mis));
Mcg.AddEntry(&sb_r_o,val,j_cg, s_cg);
}
else
{
// s is fine
if(s_fg == i_fg)
{
// special treatment for the A_{i,i} to keep block sparsity pattern
for( pst=transfer.GetFirstEntry(s_fg); pst != NULL; pst = pst->GetNext())
{
pst->GetColInVar(t_cg);
// pij is equivalent to rji
// Mcg.AddEntry(pij->GetRestriction()*Mfg[mis]*pst->GetProlongation(), j_cg, t_cg);// R*Mff*P
SparseBlockMMProduct(&sb_r_d_p,sr,fmatsb_d,sp,val,pij->GetRestrictionPtr(),Mfg.GetValuePtr(mis),pst->GetProlongationPtr());
//Mcg.AddEntry(&sb_r_d_p,val,j_cg, j_cg); // lump to diagonal
Mcg.AddEntry(&sb_r_d_p,val,t_cg, t_cg); // lump to diagonal
// todo: make sure lumping preserves filter condition
if(j_cg != t_cg)
{
// SparseBlockMInvertDiag(dmatsb, diaginv, Dfg.GetValuePtr(mis));
// SparseBlockMMProduct(&sb_r_dmat_p,sr,dmatsb,sp,val,pij->GetRestrictionPtr(),diaginv,pst->GetProlongationPtr());
tvAptr = tvA.GetValuePtr(t_cg); tvBptr = tvB.GetValuePtr(t_cg);
SparseBlockGalDiagApprox(&sb_r_dmat_p,sr,fmatsb_d,sp,tvAsv,val,pij->GetRestrictionPtr(),Mfg.GetValuePtr(mis),pst->GetProlongationPtr(),tvAptr);
// SparseBlockGalDiagApproxT(&sb_r_dmat_p,sr,fmatsb_d,sp,tvBsv,val,pij->GetRestrictionPtr(),Mfg.GetValuePtr(mis),pst->GetProlongationPtr(),tvBptr);
Mcg.AddEntry(&sb_r_dmat_p,val,j_cg, t_cg);
// Mcg.AddEntry(&sb_r_dmat_p,val,j_cg, j_cg,-1.0);
Mcg.AddEntry(&sb_r_dmat_p,val,t_cg, t_cg,-1.0);
}
}
}
else
{
for( pst=transfer.GetFirstEntry(s_fg); pst != NULL; pst = pst->GetNext())
{
pst->GetColInVar(t_cg);
// pij is equivalent to rji
// Mcg.AddEntry(pij->GetRestriction()*Mfg[mis]*pst->GetProlongation(), j_cg, t_cg);// R*Mff*P
SparseBlockMMProduct(&sb_r_o_p,sr,fmatsb_o,sp,val,pij->GetRestrictionPtr(),Mfg.GetValuePtr(mis),pst->GetProlongationPtr());
Mcg.AddEntry(&sb_r_o_p,val,j_cg, t_cg);
}
}
}
}
}
}
}
delete val;
delete diaginv;
return 0;
}
void MarkStrongLinks(const MT &A, const FAMGGrid &grid)
{
typedef typename MT::Vector VT;
const typename MT::GridVector& gridvec = (typename MT::GridVector&)grid.GetGridVector();
typename MT::MatrixEntry matij;
typename VT::VectorEntry vi;
typename VT::Iterator viter(gridvec);
double rlist[20], llist[20], mij, mji, rmax, lmax;
int z, y;
const double sigma = FAMGGetParameter()->Getsigma();
const int minsl = 2 - 1;
while (viter(vi))
{
for(z = 0; z <= minsl; z++)
{
rlist[z] = llist[z] = 0.0;
}
typename MT::Iterator mij_iter(A,vi);
mij_iter(matij); // skip diagonal
while( mij_iter(matij) )
{
mij = Abs(A[matij]);
mji = Abs(A.GetAdjData(matij));
for(z = minsl; z >= 0; z--)
{
if (mij < rlist[z]) break;
}
for(y = minsl; y > z+1; y--)
{
rlist[y] = rlist[y-1];
}
if(z+1 <= minsl) rlist[z+1] = mij;
for(z = minsl; z >= 0; z--)
{
if (mji < llist[z]) break;
}
for(y = minsl; y > z+1; y--)
{
llist[y] = llist[y-1];
}
if(z+1 <= minsl) llist[z+1] = mji;
}
rmax = rlist[minsl]*sigma;
lmax = llist[minsl]*sigma;
mij_iter.reset();
mij_iter(matij);
matij.set_strong(1);
while( mij_iter(matij) )
{
mij = Abs(A[matij]);
mji = Abs(A.GetAdjData(matij));
if((mij > rmax) || (mji > lmax))
{
matij.set_strong(1);
}
else matij.set_strong(0);
}
}
return;
}
int ConstructGalerkinMatrix( MT &Mcg, const FAMGGrid &fg )
// this matrix lives on the coarse grid
// calculates Mcg := R * Mfg * P and with indices:
// Mcg_(i,j) := \sum_{s,t} R_(i,s) * Mfg_(s,t) * P_(t,j)
{
typedef typename MT::Vector VT;
const FAMGTransfer &transfer = *fg.GetTransfer();
const typename MT::GridVector& fg_gridvec = (typename MT::GridVector&)fg.GetGridVector();
const MT& Mfg = (MT&)*fg.GetConsMatrix(); // consistent matrix is essential here!
typename MT::MatrixEntry mij, mis;
typename VT::VectorEntry i_fg, i_cg, j_fg, j_cg, s_fg, s_cg, t_cg;
FAMGTransferEntry *pjs, *pij, *pst;
typename VT::Iterator viter(fg_gridvec);
// the next lines are for debugging only:
//MATDATA_DESC *tmpA = ((FAMGugMatrix*)fg.GetConsMatrix())->GetMatDesc();
//GRID *tmpgrid = fg.GetugGrid();
//int tmpflevel = GLEVEL(tmpgrid);
//printf("%d: GalerkinAss finelevel = %d\n",me,tmpflevel); prvGeom(tmpflevel,0); primGeom(tmpflevel); prmGeom(tmpflevel,MD_SCALCMP(tmpA)); prvGeom(tmpflevel-1,0);
while (viter(i_fg) )
{
#ifdef ModelP
if ( IS_FAMG_GHOST(((FAMGugVectorEntryRef*)(i_fg.GetPointer()))->myvector()) )
{
// repair coarse grid matrix of border vector, if it has no diagonal matrix entry
if (fg_gridvec.IsCG(i_fg) )
{
transfer.GetFirstEntry(i_fg)->GetColInVar(i_cg);
typename MT::Iterator mijiter(Mcg,i_cg);
if( mijiter(mij) ) // test first matrix entry of i_cg
{
if( mij.dest() != i_cg )
Mcg.AddEntry(0.0, i_cg, i_cg); // has no diag entry yet
}
else // i_cg has no matrix entry
{
Mcg.AddEntry(0.0, i_cg, i_cg);
}
}
continue;
}
#endif
// i is now in core partition
if (fg_gridvec.IsCG(i_fg) )
{
// i is coarse
transfer.GetFirstEntry(i_fg)->GetColInVar(i_cg);
typename MT::Iterator mijiter(Mfg,i_fg);
while( mijiter(mij) )
{
j_fg = mij.dest();
if( fg_gridvec.IsCG(j_fg) )
{
transfer.GetFirstEntry(j_fg)->GetColInVar(j_cg);
Mcg.AddEntry(Mfg[mij], i_cg, j_cg); // Mcc
//printf("%d: G%d[%d] Mcc i f%d[%d] c%d[%d] j f%d[%d] c%d[%d] Mfg[mij]=%g\n",me, prvec(i_cg),
// prvec(i_fg),prvec(i_cg),prvec(j_fg),prvec(j_cg),Mfg[mij]);
}
else
{
for( pjs=transfer.GetFirstEntry(j_fg); pjs != NULL; pjs = pjs->GetNext())
{
pjs->GetColInVar(s_cg);
Mcg.AddEntry(Mfg[mij]*pjs->GetProlongation(), i_cg, s_cg); // Mcf*P
//printf("%d: G%d[%d] Mcf*P i f%d[%d] c%d[%d] j f%d[%d] s c%d[%d] Mfg[mij]=%g pjs=%g Mfg[mij]*pjs=%g\n",me, prvec(i_cg),
// prvec(i_fg),prvec(i_cg),prvec(j_fg),prvec(s_cg),Mfg[mij],pjs->GetProlongation(),Mfg[mij]*pjs->GetProlongation());
}
}
}
}
else
{
// i is fine
typename MT::Iterator misiter(Mfg,i_fg);
while( misiter(mis) )
{
s_fg = mis.dest();
for( pij=transfer.GetFirstEntry(i_fg); pij != NULL; pij = pij->GetNext())
{
pij->GetColInVar(j_cg);
if( fg_gridvec.IsCG(s_fg) )
{
transfer.GetFirstEntry(s_fg)->GetColInVar(s_cg);
// pij is equivalent to rji
Mcg.AddEntry(pij->GetRestriction()*Mfg[mis], j_cg, s_cg); // R*Mfc
//printf("%d: G%d[%d] R*Mfc j c%d[%d] i f%d[%d] s f%d[%d] c%d[%d] rji=%g Mfg[mis]=%g rji*Mfg[mis]=%g\n",me, prvec(j_cg),
// prvec(j_cg),prvec(i_fg),prvec(s_fg),prvec(s_cg),pij->GetRestriction(), Mfg[mis], pij->GetRestriction()*Mfg[mis] );
}
else
{ // s is fine
for( pst=transfer.GetFirstEntry(s_fg); pst != NULL; pst = pst->GetNext())
{
pst->GetColInVar(t_cg);
// pij is equivalent to rji
Mcg.AddEntry(pij->GetRestriction()*Mfg[mis]*pst->GetProlongation(), j_cg, t_cg);// R*Mff*P
//printf("%d: G%d[%d] R*Mff*P j c%d[%d] i f%d[%d] s f%d[%d] t c%d[%d] rji=%g Mfg[mis]=%g pst=%g rji*Mfg[mis]*pst=%g\n",me, prvec(j_cg),
// prvec(j_cg),prvec(i_fg),prvec(s_fg),prvec(t_cg),pij->GetRestriction(),Mfg[mis],pst->GetProlongation(),pij->GetRestriction()*Mfg[mis]*pst->GetProlongation() );
}
}
}
}
}
}
return 0;
}
// no need of special traversal
template<typename MT> V_type fortran_view (MT const &x) { return (x.indexmap().memory_layout_is_c() ? x.transpose() : x);}
// load this M-tree with n data using the BulkLoad algorithm [CP98]
// data is an array of n entries
// padFactor is the maximum node utilization (use 1)
// name is the name of the tree
void
MT::BulkLoad (MTentry **data, int n, double padFactor, const char *name)
{
int size = 0;
if (EntrySize()) {
size = n * (sizeof(GiSTpage) + EntrySize()); // (only valid if we've fixed size entries)
} else {
for (int i=0; i<n; i++) {
size += sizeof(GiSTlte) + sizeof(GiSTpage) + data[i]->CompressedLength();
}
}
int totSize = size + GIST_PAGE_HEADER_SIZE + sizeof(GiSTlte);
if (totSize > Store()->PageSize()) { // we need to split the entries into several sub-trees
int numEntries = (int)(Store()->PageSize()*padFactor*n) / totSize;
int s = (int) MAX (MIN (numEntries, ceil(((float)n)/numEntries)), numEntries*MIN_UTIL); // initial number of samples
int nSamples, *samples = new int[s], *sizes = NULL, *ns = NULL, iter = 0, MAXITER = s * s;
GiSTlist<double *> *distm = (GiSTlist<double *> *) calloc (s, sizeof(GiSTlist<double *>)); // relative distances between samples
int MINSIZE = (int) (Store()->PageSize()*MIN_UTIL), addEntrySize = EntrySize() ? sizeof(GiSTpage) : sizeof(GiSTlte)+sizeof(GiSTpage);
GiSTlist<int> *lists = NULL; // set for each sample set
GiSTlist<double> *dists = NULL; // set for distance between each sample and its members
BOOL *bSampled = new BOOL[n]; // is this entry in the samples set?
// sampling phase
do {
iter++;
if (iter > 1) { // this is a new sampling phase
while (!lists[0].IsEmpty()) {
lists[0].RemoveFront ();
dists[0].RemoveFront ();
}
delete []lists;
delete []dists;
delete []sizes;
delete []ns;
while (!distm[0].IsEmpty()) {
delete []distm[0].RemoveFront(); // empty the distance list
}
for (int i=1; i<s; i++) {
distm[i].front = distm[i].rear = NULL;
}
}
if (iter >= MAXITER) {
cout << "Too many loops in BulkLoad!"<<endl<<"Please select a lower minimum node utilization or a bigger node size."<<endl;
exit(1);
}
for (int i=0; i<n; i++) {
bSampled[i] = FALSE;
}
nSamples = 0;
// pick s samples to create parents
while (nSamples < s) {
int i;
do {
i = PickRandom (0, n);
} while (bSampled[i]);
bSampled[i] = TRUE;
samples[nSamples++] = i;
}
lists = new GiSTlist<int>[s];
dists = new GiSTlist<double>[s];
sizes = new int[s];
ns = new int[s];
for (int i=0; i<s; i++) {
sizes[i] = GIST_PAGE_HEADER_SIZE + sizeof(GiSTlte);
ns[i] = 1;
distm[i].Prepend (new double[s]);
}
// compute the relative distances between samples
for (int i=0; i<s; i++) {
for (int j=0; j<i; j++) {
distm[j].front->entry[i] = distm[i].front->entry[j] = data[samples[j]]->object().distance(data[samples[i]]->object());
}
distm[i].front->entry[i] = 0;
}
// assign each entry to its nearest parent
for (int i=0; i<n; i++) {
if (bSampled[i]) {
int j = 0;
for (; samples[j]!=i; j++); // find this entry in the samples set and return position in it
lists[j].Prepend (i); // insert the entry in the right sample
dists[j].Prepend (0); // distance between sample and data[i]
sizes[j] += addEntrySize + data[i]->CompressedLength();
} else { // here we optimize the distance computations (like we do in the insert algorithm)
double *dist = new double[s]; // distance between this non-sample and samples
dist[0] = data[samples[0]]->object().distance(data[i]->object());
int minIndex = 0;
for (int j=1; j<s; j++) { // seek the nearest sample
dist[j] = -MaxDist();
if (fabs (data[samples[j]]->Key()->distance - data[i]->Key()->distance) >= dist[minIndex]) { // pruning
continue;
}
BOOL flag = TRUE;
for (int k=0; k<j && flag; k++) { // pruning (other samples)
if (dist[k] < 0) {
continue;
} else {
flag = fabs (dist[k] - distm[j].front->entry[k]) < dist[minIndex];
}
}
if (!flag) {
continue;
}
dist[j] = data[samples[j]]->object().distance(data[i]->object()); // have to compute this distance
if (dist[j] < dist[minIndex]) {
minIndex = j;
}
}
lists[minIndex].Append (i); // insert the entry in the right sample
dists[minIndex].Append (dist[minIndex]); // distance between sample and data[i]
sizes[minIndex] += addEntrySize + data[i]->CompressedLength();
ns[minIndex]++;
sizes[minIndex] >= MINSIZE ? delete []dist : distm[minIndex].Append (dist); // correspond with lists
}
}
// redistribute underfilled parents
int i;
while (sizes[i = FindMin (sizes, nSamples)] < MINSIZE) {
GiSTlist<int> list = lists[i]; // each sample set
while (!dists[i].IsEmpty()) { // clear distance between each sample and its members
dists[i].RemoveFront ();
}
// substitute this set with last set
for (int j=0; j<nSamples; j++) {
for (GiSTlistnode<double *> *node=distm[j].front; node; node=node->next) {
node->entry[i] = node->entry[nSamples-1];
}
}
GiSTlist<double *> dlist = distm[i]; // relative distances between sample[i] and other samples, reposition by myself
distm[i] = distm[nSamples-1];
lists[i] = lists[nSamples-1];
dists[i] = dists[nSamples-1];
samples[i] = samples[nSamples-1];
sizes[i] = sizes[nSamples-1];
ns[i] = ns[nSamples-1];
nSamples--;
while (!list.IsEmpty()) { // assign each entry to its nearest parent
double *dist = dlist.RemoveFront (); // relative distances between sample[i] (old) and other samples (old)
int minIndex = -1;
for (int j=0; j<nSamples && minIndex<0; j++) { // search for a computed distance
if (dist[j] > 0) {
minIndex = j;
}
}
int k = list.RemoveFront ();
if (minIndex < 0) { // no distance was computed (i.e. all distances were pruned)
dist[0] = data[samples[0]]->object().distance(data[k]->object());
minIndex = 0;
}
for (int j=0; j<nSamples; j++) {
if (j == minIndex) {
continue;
}
if (dist[j] < 0) { // distance wasn't computed
if (fabs (data[samples[j]]->Key()->distance - data[k]->Key()->distance) >= dist[minIndex]) {
continue; // pruning
}
BOOL flag = TRUE;
for (int i=0; i<j && flag; i++) { // pruning (other samples)
if (dist[i] < 0) {
continue;
} else {
flag = fabs (dist[i] - distm[j].front->entry[i]) < dist[minIndex];
}
}
if (!flag) {
continue;
}
dist[j] = data[samples[j]]->object().distance(data[k]->object()); // have to compute this distance
}
if (dist[j] < dist[minIndex]) {
minIndex = j;
}
}
lists[minIndex].Append (k);
dists[minIndex].Append (dist[minIndex]);
sizes[minIndex] += addEntrySize + data[k]->CompressedLength();
ns[minIndex]++;
sizes[minIndex] >= MINSIZE ? delete []dist : distm[minIndex].Append (dist); // correspond with lists
}
assert (dlist.IsEmpty()); // so is the list
}
} while (nSamples == 1); // if there's only one child, repeat the sampling phase
MTentry ***array = new MTentry **[nSamples]; // array of the entries for each sub-tree
for (int i=0; i<nSamples; i++) { // convert the lists into arrays
array[i] = new MTentry *[ns[i]];
for (int j=0; j<ns[i]; j++) {
array[i][j] = (MTentry *) data[lists[i].RemoveFront ()]->Copy();
array[i][j]->Key()->distance = dists[i].RemoveFront ();
}
assert (lists[i].IsEmpty());
assert (dists[i].IsEmpty());
}
delete []lists;
delete []dists;
delete []sizes;
delete []bSampled;
for (int i=0; i<nSamples; i++) {
while (!distm[i].IsEmpty()) {
delete [](distm[i].RemoveFront());
}
}
free (distm);
// build an M-tree under each parent
int nInit = nSamples;
MT *subtree = new MT;
GiSTlist<char *> subtreeNames; // list of the subtrees names
GiSTlist<MTentry *> topEntries; // list of the parent entries of each subtree
int nCreated = 0, minHeight = MAXINT;
char newName[50];
for (int i=0; i<nInit; i++) {
sprintf (newName, "%s.%i", name, ++nCreated);
unlink (newName);
subtree->Create(newName); // create the new subtree
subtree->BulkLoad(array[i], ns[i], padFactor, newName); // build the subtree
GiSTpath path;
path.MakeRoot ();
MTnode *subtreeRoot = (MTnode *) subtree->ReadNode(path);
if (subtreeRoot->IsUnderFull(*Store())) { // if the subtree root node is underfilled, we have to split the tree
GiSTlist<MTentry *> *parentEntries = new GiSTlist<MTentry *>;
GiSTlist<char *> *newTreeNames = subtree->SplitTree(&nCreated, subtree->TreeHeight()-1, parentEntries, name); // split the tree
nSamples--;
while (!newTreeNames->IsEmpty()) { // insert all the new trees in the subtrees list
subtreeNames.Append (newTreeNames->RemoveFront());
MTentry *entry = parentEntries->RemoveFront();
for (int j=0; j<n; j++) {
if (data[j]->object() == entry->object()) { // append the parent entry to the list
topEntries.Append (data[j]);
break;
}
}
delete entry;
nSamples++;
}
delete newTreeNames;
delete parentEntries;
minHeight = MIN (minHeight, subtree->TreeHeight()-1);
} else {
subtreeNames.Append (strdup(newName));
topEntries.Append (data[samples[i]]);
minHeight = MIN (minHeight, subtree->TreeHeight());
}
delete subtreeRoot;
subtree->Close();
delete subtree->Store(); // it was created in subtree->Create()
}
delete []samples;
for (int i=0; i<nInit; i++) {
for (int j=0; j<ns[i]; j++) {
delete array[i][j];
}
delete []array[i];
}
delete []array;
delete []ns;
// fix the subtree height
GiSTlist<char *> subtreeNames2; // list of the subtrees names
GiSTlist<MTentry *> topEntries2; // list of the parent entries of each subtree
while (!topEntries.IsEmpty()) { // insert the trees in the list (splitting trees if necessary)
MTentry *parentEntry = topEntries.RemoveFront ();
char *tmp = subtreeNames.RemoveFront ();
strcpy (newName, tmp);
delete []tmp;
subtree->Open(newName);
if (subtree->TreeHeight() > minHeight) { // we have to split the tree to reduce its height
nSamples--;
GiSTlist<MTentry *> *parentEntries = new GiSTlist<MTentry *>;
GiSTlist<char *> *newTreeNames = subtree->SplitTree(&nCreated, minHeight, parentEntries, name); // split the tree
while (!newTreeNames->IsEmpty()) { // insert all the new trees in the subtrees list
subtreeNames2.Append (newTreeNames->RemoveFront());
MTentry *entry = parentEntries->RemoveFront();
for (int j=0; j<n; j++) {
if (data[j]->object() == entry->object()) { // append the parent entry to the parents list
topEntries2.Append (data[j]);
break;;
}
}
delete entry;
nSamples++;
}
delete newTreeNames;
delete parentEntries;
} else { // simply insert the tree and its parent entry to the lists
subtreeNames2.Append (strdup(newName));
topEntries2.Append (parentEntry);
}
subtree->Close();
delete subtree->Store(); // it was created in tree->Open()
}
// build the super tree upon the parents
MTentry **topEntrArr = new MTentry *[nSamples]; // array of the parent entries for each subtree
char **subNameArr = new char *[nSamples]; // array of the subtrees names
for (int i=0; i<nSamples; i++) { // convert the lists into arrays
topEntrArr[i] = topEntries2.RemoveFront ();
subNameArr[i] = subtreeNames2.RemoveFront ();
}
assert (topEntries2.IsEmpty());
assert (subtreeNames2.IsEmpty());
sprintf (newName, "%s.0", name);
BulkLoad (topEntrArr, nSamples, padFactor, newName);
// attach each subtree to the leaves of the super tree
GiSTpath path;
path.MakeRoot ();
MTnode *node = (MTnode *) ReadNode (path);
GiSTlist<MTnode *> *oldList = new GiSTlist<MTnode *>; // upper level nodes
oldList->Append(node);
int level = node->Level();
while (level > 0) { // build the leaves list for super tree
GiSTlist<MTnode *> *newList = new GiSTlist<MTnode *>; // lower level nodes
while (!oldList->IsEmpty()) {
node = oldList->RemoveFront();
path = node->Path();
node->SetLevel(node->Level() + minHeight); // update level of the upper nodes of the super tree
WriteNode (node);
for (int i=0; i<node->NumEntries(); i++) {
MTentry *entry = (MTentry *) (*node)[i].Ptr();
path.MakeChild (entry->Ptr());
newList->Append((MTnode *)ReadNode(path));
path.MakeParent ();
}
delete node;
}
delete oldList;
oldList = newList;
level--;
}
while (!oldList->IsEmpty()) { // attach each subtree to its leaf
node = oldList->RemoveFront(); // retrieve next leaf (root of subtree)
node->SetLevel(minHeight); // update level of the root of the subtree
path = node->Path();
for (int i=0; i<node->NumEntries(); i++) {
MTentry *entry = (MTentry *) (*node)[i].Ptr();
path.MakeChild(Store()->Allocate());
MTnode *newNode = (MTnode *) CreateNode ();
newNode->Path() = path;
entry->SetPtr(path.Page());
path.MakeParent ();
int j = 0;
for (; entry->object() != topEntrArr[j]->object(); j++); // search the position to append
subtree->Open(subNameArr[j]);
GiSTpath rootPath;
rootPath.MakeRoot ();
Append (newNode, (MTnode *)subtree->ReadNode(rootPath)); // append this subtree to the super tree
subtree->Close();
delete subtree->Store(); // it was created in tree->Open()
delete newNode;
}
WriteNode (node);
delete node;
}
subtree->Open(subNameArr[0]); // in order to destroy the object tree
delete subtree;
for (int i=0; i<nSamples; i++) {
delete []subNameArr[i];
}
delete []subNameArr;
delete []topEntrArr;
// update radii of the upper nodes of the result M-tree
path.MakeRoot ();
node = (MTnode *) ReadNode (path);
oldList->Append(node);
level = node->Level();
while (level >= minHeight) { // build the list of the nodes which radii should be recomputed
GiSTlist<MTnode *> *newList = new GiSTlist<MTnode *>;
while (!oldList->IsEmpty()) {
node = oldList->RemoveFront();
path = node->Path();
for (int i=0; i<node->NumEntries(); i++) {
path.MakeChild ((*node)[i].Ptr()->Ptr());
newList->Append((MTnode *)ReadNode(path));
path.MakeParent ();
}
delete node;
}
delete oldList;
oldList = newList;
level--;
}
while (!oldList->IsEmpty()) { // adjust the radii of the nodes
MTnode *node = oldList->RemoveFront();
AdjKeys (node);
delete node;
}
delete oldList;
for (int i=0; i<=nCreated; i++) { // delete all temporary subtrees
sprintf (newName, "%s.%i", name, i);
unlink (newName);
}
} else { // we can insert all the entries in a single node
GiSTpath path;
path.MakeRoot ();
GiSTnode *node = ReadNode (path);
for (int i=0; i<n; i++) {
node->Insert(*(data[i]));
}
assert (!node->IsOverFull(*Store()));
WriteNode (node);
delete node;
}
}
// no need of special traversal
template <typename MT> V_type fortran_view(MT const &x) {
if (x.indexmap().memory_layout_is_c())
return x.transpose();
else
return x;
}