SparseOptimizerIncremental::~SparseOptimizerIncremental()
{
_updateMat.clear(true);
delete _cholmodSparse;
if (_cholmodFactor) {
cholmod_free_factor(&_cholmodFactor, &_cholmodCommon);
_cholmodFactor = 0;
}
cholmod_free_triplet(&_permutedUpdate, &_cholmodCommon);
cholmod_finish(&_cholmodCommon);
}
double GaussianProcessInterpolationRestraintSparse::unprotected_evaluate(
DerivativeAccumulator *accum) const
{
//check if the functions have changed
const_cast<GaussianProcessInterpolationRestraintSparse*>(this)->
update_mean_and_covariance();
double ene = mvn_->evaluate();
if (accum)
{
cholmod_dense *dmv = mvn_->evaluate_derivative_FM();
if (dmv->xtype != CHOLMOD_REAL)
IMP_THROW("matrix type is not real, update code here first",
ModelException);
double *dmvx=(double*) dmv->x;
//derivatives for mean particles
for (size_t i=0; i<M_; i++)
{
DerivativeAccumulator a(*accum, dmvx[i]);
gpi_->mean_function_->add_to_derivatives(gpi_->x_[i], a);
}
cholmod_free_dense(&dmv, c_);
//derivatives for covariance particles
cholmod_sparse *tmp(mvn_->evaluate_derivative_Sigma());
cholmod_triplet *dmvS = cholmod_sparse_to_triplet(tmp, c_);
cholmod_free_sparse(&tmp, c_);
if ((dmvS->itype != CHOLMOD_INT) && (dmvS->xtype != CHOLMOD_REAL))
IMP_THROW("matrix type is not real or coefficients are not int!",
ModelException);
int *dmvi=(int*) dmvS->i;
int *dmvj=(int*) dmvS->j;
dmvx=(double*) dmvS->x;
for (size_t p=0; p<dmvS->nzmax; ++p)
{
int i=dmvi[p];
int j=dmvj[p];
double val=dmvx[p];
DerivativeAccumulator a(*accum, val);
gpi_->covariance_function_->add_to_derivatives(
gpi_->x_[i],gpi_->x_[j], a);
}
cholmod_free_triplet(&dmvS,c_);
}
return ene;
}
// doing cholesky decomposition
void Algebra::CK_decomp(Matrix &A, cholmod_factor *&L, cholmod_common *cm, size_t &peak_mem, size_t & CK_mem){
// doing factorization first
cholmod_triplet * T;
size_t n_row = A.get_row();
size_t n_col = A.get_row();
size_t nnz = A.size();
int *Ti;
int *Tj;
double *Tx;
int stype = -1;// lower triangular storage
T = cholmod_allocate_triplet(n_row, n_col, nnz, stype,
CHOLMOD_REAL, cm);
Ti = static_cast<int *>(T->i);
Tj = static_cast<int *>(T->j);
Tx = static_cast<double *>(T->x);
// copy data into T
for(size_t k=0;k<nnz;k++){
Ti[k] = A.Ti[k];
Tj[k] = A.Tj[k];
Tx[k] = A.Tx[k];
}
T->nnz = nnz;
A.Ti.clear();
A.Tj.clear();
A.Tx.clear();
cholmod_sparse * A_cholmod;
A_cholmod = cholmod_triplet_to_sparse(T, nnz, cm);
// free the triplet pointer
cholmod_free_triplet(&T, cm);
//cm->supernodal = -1;
L = cholmod_analyze(A_cholmod, cm);
//L->ordering = CHOLMOD_NATURAL;
cholmod_factorize(A_cholmod, L, cm);
//cholmod_print_factor(L, "L", cm);
//if(peak_mem < cm->memory_usage)
//peak_mem = cm->memory_usage;
//CK_mem += cm->lnz;
cholmod_free_sparse(&A_cholmod, cm);
}
