void RadialBasisFunction::Train(HostMatrix<float> &Input, HostMatrix<float> &Target){
//std::cout << "Training" << std::endl;
// c_width = (float*) malloc(sizeof(float)*network_size);
// memset(c_width,0,sizeof(float)*network_size);
DeviceMatrix<float> device_X(Input);
//std::cout << "KMeans" << std::endl;
clock_t initialTime = clock();
KMeans KM;
KM.SetSeed(seed);
dCenters = KM.Execute(device_X,network_size);
cudaThreadSynchronize();
times[0] = (clock() - initialTime);
//std::cout << "Adjust Widths" << std::endl;
/*Adjust width using mean of distance to neighbours*/
initialTime = clock();
AdjustWidths(number_neighbours);
cudaThreadSynchronize();
times[1] = (clock() - initialTime);
/*Training weights and scaling factor*/
HostMatrix<float> TargetArr(Target.Rows(),NumClasses);
memset(TargetArr.Pointer(),0,sizeof(float)*TargetArr.Elements());
for(int i = 0; i < Target.Rows(); i++){
TargetArr(i,((int)Target(i,0)-1)) = 1;
}
DeviceMatrix<float> d_Target(TargetArr);
//std::cout << "Calculating Weights" << std::endl;
initialTime = clock();
DeviceMatrix<float> device_activ_matrix(device_X.Rows(),dCenters.Rows(),ColumnMajor);
KernelActivationMatrix(device_activ_matrix.Pointer(),device_X.Pointer(),dCenters.Pointer(),device_X.Columns(),dCenters.Columns(),device_activ_matrix.Columns(),device_activ_matrix.Rows(),scaling_factor,device_c_width.Pointer());
DeviceMatrix<float> d_Aplus = UTILS::pseudoinverse(device_activ_matrix);
dWeights = DeviceMatrix<float>(d_Aplus.Rows(),d_Target.Columns());
d_Aplus.Multiply(d_Aplus,d_Target,dWeights);
/*Return Weights and Centers*/
cudaThreadSynchronize();
times[2] = (clock() - initialTime);
// cudaMemcpy(c_width,device_c_width.Pointer(),sizeof(float)*device_c_width.Length(),cudaMemcpyDeviceToHost);
// this->Weights = HostMatrix<float>(dWeights);
// this->Centers = HostMatrix<float>(dCenters);
}
void writeHeader(HostMatrix<float> &Input, int number_classes, int seed){
cout << "\n=== Run information ===\n\n";
cout << std::left << setw(50) << "Random Seed" << std::left << setw(20) << seed << endl;
cout << std::left << setw(50) << "Number of Basis Functions" << std::left << setw(20) << NETWORK_SIZE << endl;
cout << std::left << setw(50) << "Number of Neighbours for Width Estimation" << std::left << setw(20) << RNEIGHBOURS << endl;
cout << std::left << setw(50) << "Number of Folds" << std::left << setw(20) << KFOLDS << endl;
cout << std::left << setw(50) << "Number of Attributes" << std::left << setw(20) << Input.Columns() << endl;
cout << std::left << setw(50) << "Number of Classes" << std::left << setw(20) << number_classes << endl;
cout << std::left << setw(50) << "Number of Instances" << std::left << setw(20) << Input.Rows() << endl;
}
void OCLAcceleratorMatrixBCSR<ValueType>::CopyFromHost(const HostMatrix<ValueType> &src) {
const HostMatrixBCSR<ValueType> *cast_mat;
// copy only in the same format
assert(this->get_mat_format() == src.get_mat_format());
// CPU to OCL copy
if ((cast_mat = dynamic_cast<const HostMatrixBCSR<ValueType>*> (&src)) != NULL) {
if (this->get_nnz() == 0)
this->AllocateBCSR(src.get_nnz(), src.get_nrow(), src.get_ncol() );
assert((this->get_nnz() == src.get_nnz()) &&
(this->get_nrow() == src.get_nrow()) &&
(this->get_ncol() == src.get_ncol()) );
cast_mat->get_nnz();
FATAL_ERROR(__FILE__, __LINE__);
} else {
LOG_INFO("Error unsupported OCL matrix type");
this->info();
src.info();
FATAL_ERROR(__FILE__, __LINE__);
}
}
/*Calculate the root mean square error of outputs against targets*/
double rmse_error(HostMatrix<float> &Target,HostMatrix<float> &Output){
//check global error
float sum = 0;
int i;
for(i = 0; i < Target.Rows(); i++){
sum = sum + pow(Target(i,0) - Output(i,0),2);
}
return sqrt(sum/Target.Rows());
}
void MICAcceleratorMatrixHYB<ValueType>::CopyFromHost(const HostMatrix<ValueType> &src) {
const HostMatrixHYB<ValueType> *cast_mat;
// copy only in the same format
assert(this->get_mat_format() == src.get_mat_format());
// CPU to MIC copy
if ((cast_mat = dynamic_cast<const HostMatrixHYB<ValueType>*> (&src)) != NULL) {
if (this->get_nnz() == 0)
this->AllocateHYB(cast_mat->get_ell_nnz(), cast_mat->get_coo_nnz(), cast_mat->get_ell_max_row(),
cast_mat->get_nrow(), cast_mat->get_ncol());
assert((this->get_nnz() == src.get_nnz()) &&
(this->get_nrow() == src.get_nrow()) &&
(this->get_ncol() == src.get_ncol()) );
if (this->get_ell_nnz() > 0) {
copy_to_mic(this->local_backend_.MIC_dev,
cast_mat->mat_.ELL.val, this->mat_.ELL.val, this->get_ell_nnz());
copy_to_mic(this->local_backend_.MIC_dev,
cast_mat->mat_.ELL.col, this->mat_.ELL.col, this->get_ell_nnz());
}
if (this->get_coo_nnz() > 0) {
copy_to_mic(this->local_backend_.MIC_dev,
cast_mat->mat_.COO.row, this->mat_.COO.row, this->get_coo_nnz());
copy_to_mic(this->local_backend_.MIC_dev,
cast_mat->mat_.COO.col, this->mat_.COO.col, this->get_coo_nnz());
copy_to_mic(this->local_backend_.MIC_dev,
cast_mat->mat_.COO.val, this->mat_.COO.val, this->get_coo_nnz());
}
} else {
LOG_INFO("Error unsupported MIC matrix type");
this->info();
src.info();
FATAL_ERROR(__FILE__, __LINE__);
}
}
void MICAcceleratorMatrixDIA<ValueType>::CopyFromHost(const HostMatrix<ValueType> &src) {
const HostMatrixDIA<ValueType> *cast_mat;
// copy only in the same format
assert(this->get_mat_format() == src.get_mat_format());
// CPU to MIC copy
if ((cast_mat = dynamic_cast<const HostMatrixDIA<ValueType>*> (&src)) != NULL) {
if (this->get_nnz() == 0)
this->AllocateDIA(cast_mat->get_nnz(), cast_mat->get_nrow(), cast_mat->get_ncol(), cast_mat->get_ndiag());
assert((this->get_nnz() == src.get_nnz()) &&
(this->get_nrow() == src.get_nrow()) &&
(this->get_ncol() == src.get_ncol()) );
if (this->get_nnz() > 0) {
copy_to_mic(cast_mat->mat_.val, this->mat_.val, this->get_nnz());
copy_to_mic(cast_mat->mat_.offset, this->mat_.offset, this->mat_.num_diag);
/*
// TODO
for (int j=0; j<this->get_nnz(); ++j)
this->mat_.val[j] = cast_mat->mat_.val[j];
for (int j=0; j<this->mat_.num_diag; ++j)
this->mat_.offset[j] = cast_mat->mat_.offset[j];
*/
}
} else {
LOG_INFO("Error unsupported MIC matrix type");
this->info();
src.info();
FATAL_ERROR(__FILE__, __LINE__);
}
}
void OCLAcceleratorMatrixCOO<ValueType>::CopyFromHost(const HostMatrix<ValueType> &src) {
const HostMatrixCOO<ValueType> *cast_mat;
// copy only in the same format
assert(this->get_mat_format() == src.get_mat_format());
// CPU to OCL copy
if ((cast_mat = dynamic_cast<const HostMatrixCOO<ValueType>*> (&src)) != NULL) {
if (this->get_nnz() == 0)
this->AllocateCOO(src.get_nnz(), src.get_nrow(), src.get_ncol() );
if (this->get_nnz() > 0) {
assert((this->get_nnz() == src.get_nnz()) &&
(this->get_nrow() == src.get_nrow()) &&
(this->get_ncol() == src.get_ncol()) );
// Copy object from host to device memory
ocl_host2dev<int>(this->get_nnz(), // size
cast_mat->mat_.row, // src
this->mat_.row, // dst
OCL_HANDLE(this->local_backend_.OCL_handle)->OCL_cmdQueue );
// Copy object from host to device memory
ocl_host2dev<int>(this->get_nnz(), // size
cast_mat->mat_.col, // src
this->mat_.col, // dst
OCL_HANDLE(this->local_backend_.OCL_handle)->OCL_cmdQueue );
// Copy object from host to device memory
ocl_host2dev<ValueType>(this->get_nnz(), // size
cast_mat->mat_.val, // src
this->mat_.val, // dst
OCL_HANDLE(this->local_backend_.OCL_handle)->OCL_cmdQueue );
}
} else {
LOG_INFO("Error unsupported OCL matrix type");
this->info();
src.info();
FATAL_ERROR(__FILE__, __LINE__);
}
}
HostMatrix<T> operator*(const HostMatrix<T>& m)
{
HostMatrix<T> mult(m.width_,height_);
for(int row=0; row<mult.height_; ++row)
for(int col=0; col<mult.width_; ++col)
{
T v = 0.0;
for(int k=0; k<width_; ++k)
{
v+=getData(row,k)*m.getData(k,col);
}
mult.setData(row,col,v);
}
return mult;
}
/*Count number of miscalculated outputs against targets*/
int error_calc(HostMatrix<float> &Target,HostMatrix<float> &Output){
//check global error
int i;
int error = 0;
for(i = 0; i < Target.Rows(); i++){
if(Target(i,0) - Output(i,0) != 0){
error += 1;
}
}
return error;
}
void PointGroup<scalar_type>::solve(Timers& timers, bool compute_rmm, bool lda, bool compute_forces, bool compute_energy,
double& energy, double* fort_forces_ptr)
{
HostMatrix<scalar_type> rmm_output;
uint group_m = total_functions();
if (compute_rmm) { rmm_output.resize(group_m, group_m); rmm_output.zero(); }
#if CPU_RECOMPUTE
/** Compute functions **/
timers.functions.start();
compute_functions(compute_forces, !lda);
timers.functions.pause();
#endif
// prepare rmm_input for this group
timers.density.start();
HostMatrix<scalar_type> rmm_input(group_m, group_m);
get_rmm_input(rmm_input);
timers.density.pause();
HostMatrix<vec_type3> forces(total_nucleii(), 1); forces.zero();
HostMatrix<vec_type3> dd;
/******** each point *******/
uint point = 0;
for (list<Point>::const_iterator point_it = points.begin(); point_it != points.end(); ++point_it, ++point)
{
timers.density.start();
/** density **/
scalar_type partial_density = 0;
vec_type3 dxyz(0,0,0);
vec_type3 dd1(0,0,0);
vec_type3 dd2(0,0,0);
if (lda) {
for (uint i = 0; i < group_m; i++) {
float w = 0.0;
float Fi = function_values(i, point);
for (uint j = i; j < group_m; j++) {
scalar_type Fj = function_values(j, point);
w += rmm_input(j, i) * Fj;
}
partial_density += Fi * w;
}
}
else {
for (uint i = 0; i < group_m; i++) {
float w = 0.0;
vec_type3 w3(0,0,0);
vec_type3 ww1(0,0,0);
vec_type3 ww2(0,0,0);
scalar_type Fi = function_values(i, point);
vec_type3 Fgi(gradient_values(i, point));
vec_type3 Fhi1(hessian_values(2 * (i + 0) + 0, point));
vec_type3 Fhi2(hessian_values(2 * (i + 0) + 1, point));
for (uint j = 0; j <= i; j++) {
scalar_type rmm = rmm_input(j,i);
scalar_type Fj = function_values(j, point);
w += Fj * rmm;
vec_type3 Fgj(gradient_values(j, point));
w3 += Fgj * rmm;
vec_type3 Fhj1(hessian_values(2 * (j + 0) + 0, point));
vec_type3 Fhj2(hessian_values(2 * (j + 0) + 1, point));
ww1 += Fhj1 * rmm;
ww2 += Fhj2 * rmm;
}
partial_density += Fi * w;
dxyz += Fgi * w + w3 * Fi;
dd1 += Fgi * w3 * 2 + Fhi1 * w + ww1 * Fi;
vec_type3 FgXXY(Fgi.x(), Fgi.x(), Fgi.y());
vec_type3 w3YZZ(w3.y(), w3.z(), w3.z());
vec_type3 FgiYZZ(Fgi.y(), Fgi.z(), Fgi.z());
vec_type3 w3XXY(w3.x(), w3.x(), w3.y());
dd2 += FgXXY * w3YZZ + FgiYZZ * w3XXY + Fhi2 * w + ww2 * Fi;
}
}
timers.density.pause();
timers.forces.start();
/** density derivatives **/
if (compute_forces) {
dd.resize(total_nucleii(), 1); dd.zero();
for (uint i = 0, ii = 0; i < total_functions_simple(); i++) {
uint nuc = func2local_nuc(ii);
uint inc_i = small_function_type(i);
vec_type3 this_dd = vec_type3(0,0,0);
for (uint k = 0; k < inc_i; k++, ii++) {
scalar_type w = 0.0;
for (uint j = 0; j < group_m; j++) {
scalar_type Fj = function_values(j, point);
w += rmm_input(j, ii) * Fj * (ii == j ? 2 : 1);
}
this_dd -= gradient_values(ii, point) * w;
}
dd(nuc) += this_dd;
}
}
timers.forces.pause();
timers.pot.start();
timers.density.start();
/** energy / potential **/
scalar_type exc = 0, corr = 0, y2a = 0;
if (lda)
cpu_pot(partial_density, exc, corr, y2a);
else {
cpu_potg(partial_density, dxyz, dd1, dd2, exc, corr, y2a);
}
timers.pot.pause();
if (compute_energy)
energy += (partial_density * point_it->weight) * (exc + corr);
timers.density.pause();
/** forces **/
timers.forces.start();
if (compute_forces) {
scalar_type factor = point_it->weight * y2a;
for (uint i = 0; i < total_nucleii(); i++)
forces(i) += dd(i) * factor;
}
timers.forces.pause();
/** RMM **/
timers.rmm.start();
if (compute_rmm) {
scalar_type factor = point_it->weight * y2a;
HostMatrix<scalar_type>::blas_ssyr(LowerTriangle, factor, function_values, rmm_output, point);
}
timers.rmm.pause();
}
timers.forces.start();
/* accumulate force results for this group */
if (compute_forces) {
FortranMatrix<double> fort_forces(fort_forces_ptr, fortran_vars.atoms, 3, fortran_vars.max_atoms); // TODO: mover esto a init.cpp
for (uint i = 0; i < total_nucleii(); i++) {
uint global_atom = local2global_nuc[i];
vec_type3 this_force = forces(i);
fort_forces(global_atom,0) += this_force.x();
fort_forces(global_atom,1) += this_force.y();
fort_forces(global_atom,2) += this_force.z();
}
}
timers.forces.pause();
timers.rmm.start();
/* accumulate RMM results for this group */
if (compute_rmm) {
for (uint i = 0, ii = 0; i < total_functions_simple(); i++) {
uint inc_i = small_function_type(i);
for (uint k = 0; k < inc_i; k++, ii++) {
uint big_i = local2global_func[i] + k;
for (uint j = 0, jj = 0; j < total_functions_simple(); j++) {
uint inc_j = small_function_type(j);
for (uint l = 0; l < inc_j; l++, jj++) {
uint big_j = local2global_func[j] + l;
if (big_i > big_j) continue;
uint big_index = (big_i * fortran_vars.m - (big_i * (big_i - 1)) / 2) + (big_j - big_i);
fortran_vars.rmm_output(big_index) += rmm_output(ii, jj);
}
}
}
}
}
timers.rmm.pause();
#if CPU_RECOMPUTE
/* clear functions */
function_values.deallocate();
gradient_values.deallocate();
hessian_values.deallocate();
#endif
}