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Commit 9b20069a authored by lvs's avatar lvs
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removed comments

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Makefile
View file @ 9b20069a
......@@ -205,11 +205,11 @@ PDB := 3ce3
NRUN := 100
POPSIZE := 150
TESTNAME := test
TESTLS := sw
TESTLS := sd
NUM_LSIT := 300
test: odock
$(BIN_DIR)/$(TARGET) -ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -psize $(POPSIZE) -resnam $(TESTNAME) -gfpop 1 -lsmet $(TESTLS) -lsit $(NUM_LSIT) -smooth 0.5
$(BIN_DIR)/$(TARGET) -ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -psize $(POPSIZE) -resnam $(TESTNAME) -gfpop 1 -lsmet $(TESTLS) -lsit $(NUM_LSIT) -smooth 0.0
ASTEX_PDB := 2bsm
ASTEX_NRUN:= 10
......
device/calcenergy.cl
View file @ 9b20069a
......@@ -96,8 +96,8 @@ void gpu_calc_energy(
#endif
uchar g1 = dockpars_gridsize_x;
uint g2 = dockpars_gridsize_x_times_y /*dockpars_gridsize_x * dockpars_gridsize_y*/;
uint g3 = dockpars_gridsize_x_times_y_times_z /*dockpars_gridsize_x * dockpars_gridsize_y * dockpars_gridsize_z*/;
uint g2 = dockpars_gridsize_x_times_y;
uint g3 = dockpars_gridsize_x_times_y_times_z;
// ================================================
// CALCULATING ATOMIC POSITIONS AFTER ROTATIONS
......@@ -172,14 +172,7 @@ void gpu_calc_energy(
atom_to_rotate[2] -= rotation_movingvec[2];
// Transforming torsion angles into quaternions
//----------------------------------
// fastergrad
//----------------------------------
/*
rotation_angle = native_divide(rotation_angle, 2.0f);
*/
rotation_angle = rotation_angle * 0.5f;
//----------------------------------
float sin_angle = native_sin(rotation_angle);
quatrot_left_q = native_cos(rotation_angle);
quatrot_left_x = sin_angle*rotation_unitvec[0];
......@@ -578,6 +571,5 @@ void gpu_calc_energy(
#include "auxiliary_genetic.cl"
#include "kernel4.cl"
#include "kernel3.cl"
//#include "auxiliary_gradient.cl"
#include "calcgradient.cl"
#include "kernel_gradient.cl"
device/calcgradient.cl
View file @ 9b20069a
......@@ -34,13 +34,11 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
// whose population includes the current entity (which can be determined with get_group_id(0)),
// since this determines which reference orientation should be used.
//#define DEBUG_GRAD_TRANSLATION_GENES
//#define DEBUG_GRAD_ROTATION_GENES
//#define DEBUG_GRAD_TORSION_GENES
//#define DEBUG_ENERGY_KERNEL5
// Atomic operations used in gradients of intra contributors.
// Only atomic_cmpxchg() works on floats.
// So for atomic add on floats, this link was used:
......@@ -142,11 +140,6 @@ void gpu_calc_gradient(
__local float* gradient_intra_x,
__local float* gradient_intra_y,
__local float* gradient_intra_z,
/*
__local float* gradient_x,
__local float* gradient_y,
__local float* gradient_z,
*/
__local float* gradient_genotype
)
{
......@@ -174,8 +167,8 @@ void gpu_calc_gradient(
barrier(CLK_LOCAL_MEM_FENCE);
uchar g1 = dockpars_gridsize_x;
uint g2 = dockpars_gridsize_x_times_y /*dockpars_gridsize_x * dockpars_gridsize_y*/;
uint g3 = dockpars_gridsize_x_times_y_times_z /*dockpars_gridsize_x * dockpars_gridsize_y * dockpars_gridsize_z*/;
uint g2 = dockpars_gridsize_x_times_y;
uint g3 = dockpars_gridsize_x_times_y_times_z;
// ================================================
// CALCULATING ATOMIC POSITIONS AFTER ROTATIONS
......@@ -250,15 +243,7 @@ void gpu_calc_gradient(
atom_to_rotate[2] -= rotation_movingvec[2];
// Transforming torsion angles into quaternions
//----------------------------------
// fastergrad
//----------------------------------
/*
rotation_angle = native_divide(rotation_angle, 2.0f);
*/
rotation_angle = rotation_angle * 0.5f;
//----------------------------------
float sin_angle = native_sin(rotation_angle);
quatrot_left_q = native_cos(rotation_angle);
quatrot_left_x = sin_angle*rotation_unitvec[0];
......@@ -727,10 +712,10 @@ void gpu_calc_gradient(
} // End contributor_counter for-loop (INTRAMOLECULAR ENERGY)
//----------------------------------
// eliminate unnecessary local storage
//----------------------------------
/*
// Commented to remove unnecessary local storage which was
// required by gradient_per_intracontributor[MAX_INTRAE_CONTRIBUTORS]
/*
barrier(CLK_LOCAL_MEM_FENCE);
// Accumulating gradients from "gradient_per_intracontributor" for each each
......@@ -768,7 +753,7 @@ void gpu_calc_gradient(
//printf("%-20s %-10u %-5u %-5u %-10.8f\n", "grad_intracontrib", contributor_counter, atom1_id, atom2_id, gradient_per_intracontributor[contributor_counter]);
}
}
*/
*/
barrier(CLK_LOCAL_MEM_FENCE);
......@@ -786,22 +771,14 @@ void gpu_calc_gradient(
gradient_inter_y[atom_cnt] = native_divide(gradient_inter_y[atom_cnt], dockpars_grid_spacing);
gradient_inter_z[atom_cnt] = native_divide(gradient_inter_z[atom_cnt], dockpars_grid_spacing);
/*
gradient_x[atom_cnt] = gradient_inter_x[atom_cnt] + gradient_intra_x[atom_cnt];
gradient_y[atom_cnt] = gradient_inter_y[atom_cnt] + gradient_intra_y[atom_cnt];
gradient_z[atom_cnt] = gradient_inter_z[atom_cnt] + gradient_intra_z[atom_cnt];
*/
// Re-using "gradient_inter_*" for total gradient (inter+intra)
gradient_inter_x[atom_cnt] += gradient_intra_x[atom_cnt];
gradient_inter_y[atom_cnt] += gradient_intra_y[atom_cnt];
gradient_inter_z[atom_cnt] += gradient_intra_z[atom_cnt];
//printf("%-15s %-5u %-10.8f %-10.8f %-10.8f\n", "grad_grid", atom_cnt, gradient_inter_x[atom_cnt], gradient_inter_y[atom_cnt], gradient_inter_z[atom_cnt]);
//printf("%-15s %-5u %-10.8f %-10.8f %-10.8f\n", "grad_intra", atom_cnt, gradient_intra_x[atom_cnt], gradient_intra_y[atom_cnt], gradient_intra_z[atom_cnt]);
//printf("%-15s %-5u %-10.8f %-10.8f %-10.8f\n", "calc_coords", atom_cnt, calc_coords_x[atom_cnt], calc_coords_y[atom_cnt], calc_coords_z[atom_cnt]);
}
barrier(CLK_LOCAL_MEM_FENCE);
......@@ -813,11 +790,8 @@ void gpu_calc_gradient(
for (uint lig_atom_id = 0;
lig_atom_id<dockpars_num_of_atoms;
lig_atom_id++) {
/*
gradient_genotype[0] += gradient_x[lig_atom_id]; // gradient for gene 0: gene x
gradient_genotype[1] += gradient_y[lig_atom_id]; // gradient for gene 1: gene y
gradient_genotype[2] += gradient_z[lig_atom_id]; // gradient for gene 2: gene z
*/
// Re-using "gradient_inter_*" for total gradient (inter+intra)
gradient_genotype[0] += gradient_inter_x[lig_atom_id]; // gradient for gene 0: gene x
gradient_genotype[1] += gradient_inter_y[lig_atom_id]; // gradient for gene 1: gene y
gradient_genotype[2] += gradient_inter_z[lig_atom_id]; // gradient for gene 2: gene z
......@@ -832,14 +806,9 @@ void gpu_calc_gradient(
gradient_genotype[2] *= dockpars_grid_spacing;
#if defined (DEBUG_GRAD_TRANSLATION_GENES)
/*
printf("gradient_x:%f\n", gradient_genotype [0]);
printf("gradient_y:%f\n", gradient_genotype [1]);
printf("gradient_z:%f\n", gradient_genotype [2]);
*/
printf("gradient_inter_x:%f\n", gradient_genotype [0]);
printf("gradient_inter_y:%f\n", gradient_genotype [1]);
printf("gradient_inter_z:%f\n", gradient_genotype [2]);
#endif
}
......@@ -885,12 +854,8 @@ void gpu_calc_gradient(
r.y = (calc_coords_y[lig_atom_id] - about.y) * dockpars_grid_spacing;
r.z = (calc_coords_z[lig_atom_id] - about.z) * dockpars_grid_spacing;
// Re-using "gradient_inter_*" for total gradient (inter+intra)
float3 force;
/*
force.x = gradient_x[lig_atom_id];
force.y = gradient_y[lig_atom_id];
force.z = gradient_z[lig_atom_id];
*/
force.x = gradient_inter_x[lig_atom_id];
force.y = gradient_inter_y[lig_atom_id];
force.z = gradient_inter_z[lig_atom_id];
......@@ -1119,12 +1084,8 @@ void gpu_calc_gradient(
r.y = (atom_coords.y - atomRef_coords.y) * dockpars_grid_spacing;
r.z = (atom_coords.z - atomRef_coords.z) * dockpars_grid_spacing;
// Re-using "gradient_inter_*" for total gradient (inter+intra)
float3 atom_force;
/*
atom_force.x = gradient_x[lig_atom_id];
atom_force.y = gradient_y[lig_atom_id];
atom_force.z = gradient_z[lig_atom_id];
*/
atom_force.x = gradient_inter_x[lig_atom_id];
atom_force.y = gradient_inter_y[lig_atom_id];
atom_force.z = gradient_inter_z[lig_atom_id];
......
device/kernel_gradient.cl
View file @ 9b20069a
......@@ -48,10 +48,6 @@ gradient_minimizer(
__constant int* num_rotating_atoms_per_rotbond_const,
// Specific gradient-minimizer args
uint gradMin_maxiters
/*
,
uint gradMin_maxfails
*/
)
//The GPU global function performs gradient-based minimization on (some) entities of conformations_next.
//The number of OpenCL compute units (CU) which should be started equals to num_of_minEntities*num_of_runs.
......@@ -68,17 +64,8 @@ gradient_minimizer(
__local float energy;
__local float genotype[ACTUAL_GENOTYPE_LENGTH];
// Variables for gradient minimizer
__local uint iteration_cnt; // minimizer iteration counter
/*
__local uint failure_cnt; // minimizer failure counter
__local bool exit;
*/
/*
// Number of energy-evaluations counter
__local int evaluation_cnt;
*/
// Iteration counter fot the minimizer
__local uint iteration_cnt;
// Stepsize for the minimizer
__local float stepsize;
......@@ -92,7 +79,6 @@ gradient_minimizer(
entity_id = 0;
*/
///*
run_id = get_group_id(0) / dockpars_num_of_lsentities;
entity_id = get_group_id(0) % dockpars_num_of_lsentities;
......@@ -105,7 +91,6 @@ gradient_minimizer(
entity_id = dockpars_num_of_lsentities;
}
}
//*/
energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
......@@ -115,12 +100,6 @@ gradient_minimizer(
// Initializing gradient-minimizer counters and flags
iteration_cnt = 0;
/*
failure_cnt = 0;
*/
/*
evaluation_cnt = 0;
*/
stepsize = STEP_START;
}
......@@ -146,6 +125,7 @@ gradient_minimizer(
// Derived from autodockdev/maps.py
// -------------------------------------------------------------------
// Gradient of the intermolecular energy per each ligand atom
// Also used to store the accummulated gradient per each ligand atom
__local float gradient_inter_x[MAX_NUM_OF_ATOMS];
__local float gradient_inter_y[MAX_NUM_OF_ATOMS];
__local float gradient_inter_z[MAX_NUM_OF_ATOMS];
......@@ -155,14 +135,7 @@ gradient_minimizer(
__local float gradient_intra_y[MAX_NUM_OF_ATOMS];
__local float gradient_intra_z[MAX_NUM_OF_ATOMS];
// Accummulated gradient per each ligand atom
/*
__local float gradient_x[MAX_NUM_OF_ATOMS];
__local float gradient_y[MAX_NUM_OF_ATOMS];
__local float gradient_z[MAX_NUM_OF_ATOMS];
*/
// -------------------------------------------------------------------
// Ligand-atom position and partial energies
__local float calc_coords_x[MAX_NUM_OF_ATOMS];
__local float calc_coords_y[MAX_NUM_OF_ATOMS];
......@@ -173,28 +146,8 @@ gradient_minimizer(
__local float partial_interE[NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE[NUM_OF_THREADS_PER_BLOCK];
#endif
// -----------------------------------------------------------------------------
/*
// Step size of the steepest descent
float alpha;
*/
#if 0
// Initilizing each (work-item)-specific alpha
for(uint i = get_local_id(0);
i < dockpars_num_of_genes;
i+= NUM_OF_THREADS_PER_BLOCK) {
if (i<3) { alpha = TRANGENE_ALPHA; }
else if (i<6) { alpha = ROTAGENE_ALPHA; }
else { alpha = TORSGENE_ALPHA; }
#if defined (DEBUG_MINIMIZER)
//printf("(%-3u) %-15.15f\n", i, alpha);
#endif
}
#endif
// -----------------------------------------------------------------------------
// Perform gradient-descent iterations
#if 0
......@@ -249,21 +202,13 @@ gradient_minimizer(
}
barrier(CLK_LOCAL_MEM_FENCE);
//----------------------------------
// fastergrad
//----------------------------------
// Calculating maximum possible stepsize (alpha)
__local float max_trans_gene, max_rota_gene, max_tors_gene;
__local float max_trans_stepsize, max_rota_stepsize, max_tors_stepsize;
__local float max_stepsize;
// Storing torsion genotypes here
__local float torsions_genotype[ACTUAL_GENOTYPE_LENGTH];
//----------------------------------
// Asynchronous copy should be finished by here
wait_group_events(1,&ev);
......@@ -318,8 +263,8 @@ gradient_minimizer(
if (get_local_id(0) == 0) {
// Finding maximum of the absolute value
// for the three translation genes
max_trans_gene = fmax/*max*/(fabs(genotype[0]), fabs(genotype[1]));
max_trans_gene = fmax/*max*/(max_trans_gene, fabs(genotype[2]));
max_trans_gene = fmax(fabs(genotype[0]), fabs(genotype[1]));
max_trans_gene = fmax(max_trans_gene, fabs(genotype[2]));
// Note that MAX_DEV_TRANSLATION needs to be
// expressed in grid size first
......@@ -327,8 +272,8 @@ gradient_minimizer(
// Finding maximum of the absolute value
// for the three Shoemake rotation genes
max_rota_gene = fmax/*max*/(fabs(genotype[3]), fabs(genotype[4]));//printf("max_rota_gene: %-10.7f\n", max_rota_gene);
max_rota_gene = fmax/*max*/(max_rota_gene, fabs(genotype[5])); //printf("max_rota_gene: %-10.7f\n", max_rota_gene);
max_rota_gene = fmax(fabs(genotype[3]), fabs(genotype[4])); //printf("max_rota_gene: %-10.7f\n", max_rota_gene);
max_rota_gene = fmax(max_rota_gene, fabs(genotype[5])); //printf("max_rota_gene: %-10.7f\n", max_rota_gene);
// Note that MAX_DEV_ROTATION
// is already expressed within [0, 1]
......@@ -367,11 +312,11 @@ gradient_minimizer(
if (get_local_id(0) == 0) {
// Calculating the maximum stepsize using previous three
max_stepsize = fmin/*min*/(max_trans_stepsize, max_rota_stepsize);
max_stepsize = fmin/*min*/(max_stepsize, max_tors_stepsize);
max_stepsize = fmin(max_trans_stepsize, max_rota_stepsize);
max_stepsize = fmin(max_stepsize, max_tors_stepsize);
// Capping the stepsize
stepsize = fmin/*min*/(stepsize, max_stepsize);
stepsize = fmin(stepsize, max_stepsize);
#if defined (DEBUG_MINIMIZER)
//printf("max_genes: %-0.7f %-10.7f %-10.7f %-10.7f\n", max_trans_gene, max_rota_gene, max_tors_gene, stepsize);
......@@ -442,20 +387,10 @@ gradient_minimizer(
gradient_intra_x,
gradient_intra_y,
gradient_intra_z,
/*
gradient_x,
gradient_y,
gradient_z,
*/
gradient
);
// =============================================================
/*barrier(CLK_LOCAL_MEM_FENCE);*/
//----------------------------------
// fastergrad
//----------------------------------
/*
if ((get_group_id(0) == 0) && (get_local_id(0) == 0)) {
for(uint i = 0; i < dockpars_num_of_genes; i++) {
......@@ -463,8 +398,6 @@ gradient_minimizer(
}
}
*/
//----------------------------------
for(uint i = get_local_id(0); i < dockpars_num_of_genes; i+= NUM_OF_THREADS_PER_BLOCK) {
......@@ -476,8 +409,8 @@ gradient_minimizer(
#endif
// Putting genes back within bounds
candidate_genotype[i] = fmin/*min*/(candidate_genotype[i], upper_bounds_genotype[i]);
candidate_genotype[i] = fmax/*max*/(candidate_genotype[i], lower_bounds_genotype[i]);
candidate_genotype[i] = fmin(candidate_genotype[i], upper_bounds_genotype[i]);
candidate_genotype[i] = fmax(candidate_genotype[i], lower_bounds_genotype[i]);
}
// Evaluating candidate
......@@ -510,7 +443,7 @@ gradient_minimizer(
calc_coords_y,
calc_coords_z,
partial_energies,
#if defined (DEBUG_ENERGY_KERNEL1)
#if defined (DEBUG_ENERGY_KERNEL5)
partial_interE,
partial_intraE,
#endif
......@@ -535,14 +468,6 @@ gradient_minimizer(
);
// =============================================================
/*
// Updating number of energy-evaluations counter
if (get_local_id(0) == 0) {
evaluation_cnt = evaluation_cnt + 1;
}
*/
/*barrier(CLK_LOCAL_MEM_FENCE);*/
// Checking if E(candidate_genotype) < E(genotype)
if (candidate_energy < energy){
......
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