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Commit dace836e authored by lvs's avatar lvs
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corrected error in steepest-descent

parent c9b5d2e2
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device/kernel_gradient.cl
View file @ dace836e
......@@ -83,11 +83,11 @@ gradient_minimizer(
if (get_local_id(0) == 0)
{
// Choosing a random entity out of the entire population
/*
/*
run_id = get_group_id(0);
//entity_id = (uint)(dockpars_pop_size * gpu_randf(dockpars_prng_states));
entity_id = 0;
*/
*/
run_id = get_group_id(0) / dockpars_num_of_lsentities;
entity_id = get_group_id(0) % dockpars_num_of_lsentities;
......@@ -104,9 +104,9 @@ gradient_minimizer(
energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
// #if defined (DEBUG_MINIMIZER)
#if defined (DEBUG_MINIMIZER)
printf("\nrun_id: %5u entity_id: %5u initial_energy: %.7f\n", run_id, entity_id, energy);
// #endif
#endif
// Initializing gradient-minimizer counters and flags
iteration_cnt = 0;
......@@ -123,16 +123,16 @@ gradient_minimizer(
wait_group_events(1,&ev);
// -----------------------------------------------------------------------------
// Some OpenCL compilers don't allow declaring
// local variables within non-kernel functions.
// These local variables must be declared in a kernel,
// and then passed to non-kernel functions.
// Partial results of the gradient step
__local float gradient [ACTUAL_GENOTYPE_LENGTH];
__local float candidate_energy;
__local float candidate_genotype[ACTUAL_GENOTYPE_LENGTH];
// Dummy variable used only for the first gpu_calc_gradient() call.
// The corresponding energy for "genotype" is stored in "energy"
__local float dummy_energy;
// -------------------------------------------------------------------
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
......@@ -148,7 +148,6 @@ gradient_minimizer(
__local float gradient_intra_y[MAX_NUM_OF_ATOMS];
__local float gradient_intra_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];
......@@ -161,6 +160,79 @@ gradient_minimizer(
#endif
// -----------------------------------------------------------------------------
// Calculating gradient
barrier(CLK_LOCAL_MEM_FENCE);
// =============================================================
gpu_calc_gradient(
dockpars_rotbondlist_length,
dockpars_num_of_atoms,
dockpars_gridsize_x,
dockpars_gridsize_y,
dockpars_gridsize_z,
// g1 = gridsize_x
dockpars_gridsize_x_times_y, // g2 = gridsize_x * gridsize_y
dockpars_gridsize_x_times_y_times_z, // g3 = gridsize_x * gridsize_y * gridsize_z
dockpars_fgrids,
dockpars_num_of_atypes,
dockpars_num_of_intraE_contributors,
dockpars_grid_spacing,
dockpars_coeff_elec,
dockpars_qasp,
dockpars_coeff_desolv,
// Some OpenCL compilers don't allow declaring
// local variables within non-kernel functions.
// These local variables must be declared in a kernel,
// and then passed to non-kernel functions.
genotype,
&dummy_energy,
&run_id,
calc_coords_x,
calc_coords_y,
calc_coords_z,
atom_charges_const,
atom_types_const,
intraE_contributors_const,
dockpars_smooth,
reqm,
reqm_hbond,
atom1_types_reqm,
atom2_types_reqm,
VWpars_AC_const,
VWpars_BD_const,
dspars_S_const,
dspars_V_const,
rotlist_const,
ref_coords_x_const,
ref_coords_y_const,
ref_coords_z_const,
rotbonds_moving_vectors_const,
rotbonds_unit_vectors_const,
ref_orientation_quats_const,
rotbonds_const,
rotbonds_atoms_const,
num_rotating_atoms_per_rotbond_const
,
angle_const,
dependence_on_theta_const,
dependence_on_rotangle_const
// Gradient-related arguments
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
,
dockpars_num_of_genes,
gradient_inter_x,
gradient_inter_y,
gradient_inter_z,
gradient_intra_x,
gradient_intra_y,
gradient_intra_z,
gradient
);
// =============================================================
// Perform gradient-descent iterations
#if 0
......@@ -186,7 +258,8 @@ gradient_minimizer(
float ligand_center_z = -2.40896296;
#endif
#if 0
// No need for defining upper and lower genotype bounds
#if 0
// Defining lower and upper bounds for genotypes
__local float lower_bounds_genotype[ACTUAL_GENOTYPE_LENGTH];
__local float upper_bounds_genotype[ACTUAL_GENOTYPE_LENGTH];
......@@ -212,25 +285,20 @@ gradient_minimizer(
#endif
}
barrier(CLK_LOCAL_MEM_FENCE);
#endif
#endif
// Calculating maximum possible stepsize (alpha)
__local float max_trans_gene, max_rota_gene, max_tors_gene;
__local float max_trans_grad, max_rota_grad, max_tors_grad;
__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];
// The termination criteria is based on
// a maximum number of iterations, and
// the minimum step size allowed for single-floating point numbers
// (IEEE-754 single float has a precision of about 7 decimal digits)
// (IEEE-754 single float has a precision of about 6 decimal digits)
do {
#if 0
// Specific input genotypes for a ligand with no rotatable bonds (1ac8).
......@@ -325,30 +393,27 @@ gradient_minimizer(
#endif
if (get_local_id(0) == 0) {
// Finding maximum of the absolute value
// for the three translation genes
max_trans_gene = fmax(fabs(genotype[0]), fabs(genotype[1]));
max_trans_gene = fmax(max_trans_gene, fabs(genotype[2]));
// Finding maximum of the absolute value for the three translation gradients
max_trans_grad = fmax(fabs(gradient[0]), fabs(gradient[1]));
max_trans_grad = fmax(max_trans_grad, fabs(gradient[2]));
// Note that MAX_DEV_TRANSLATION needs to be
// expressed in grid size first
max_trans_stepsize = native_divide(native_divide(MAX_DEV_TRANSLATION, dockpars_grid_spacing), max_trans_gene);
// MAX_DEV_TRANSLATION needs to be expressed in grid size first
max_trans_stepsize = native_divide(native_divide(MAX_DEV_TRANSLATION, dockpars_grid_spacing), max_trans_grad);
// Finding maximum of the absolute value
// for the three rotation genes
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);
// Finding maximum of the absolute value for the three rotation gradients
max_rota_grad = fmax(fabs(gradient[3]), fabs(gradient[4])); //printf("max_rota_grad: %-10.7f\n", max_rota_grad);
max_rota_grad = fmax(max_rota_grad, fabs(gradient[5])); //printf("max_rota_grad: %-10.7f\n", max_rota_grad);
// Note that MAX_DEV_ROTATION
// is already expressed within [0, 1]
max_rota_stepsize = native_divide(MAX_DEV_ROTATION, max_rota_gene);
max_rota_stepsize = native_divide(MAX_DEV_ROTATION, max_rota_grad);
}
// Copying torsions genes
for(uint i = get_local_id(0);
i < dockpars_num_of_genes-6;
i+= NUM_OF_THREADS_PER_BLOCK) {
torsions_genotype[i] = fabs(genotype[i+6]);
torsions_genotype[i] = fabs(gradient[i+6]);
}
barrier(CLK_LOCAL_MEM_FENCE);
......@@ -367,13 +432,12 @@ gradient_minimizer(
barrier(CLK_LOCAL_MEM_FENCE);
}
if (get_local_id(0) == 0) {
max_tors_gene = torsions_genotype[get_local_id(0)];
max_tors_stepsize = native_divide(MAX_DEV_TORSION, max_tors_gene);
max_tors_grad = torsions_genotype[get_local_id(0)];
max_tors_stepsize = native_divide(MAX_DEV_TORSION, max_tors_grad);
}
barrier(CLK_LOCAL_MEM_FENCE);
if (get_local_id(0) == 0) {
// Calculating the maximum stepsize using previous three
max_stepsize = fmin(max_trans_stepsize, max_rota_stepsize);
......@@ -383,7 +447,7 @@ gradient_minimizer(
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);
//printf("max_genes: %-0.7f %-10.7f %-10.7f %-10.7f\n", max_trans_grad, max_rota_grad, max_tors_grad, stepsize);
//printf("max_steps: %-0.7f %-10.7f %-10.7f %-10.7f\n", max_trans_stepsize, max_rota_stepsize, max_tors_stepsize, max_stepsize);
#endif
}
......@@ -499,12 +563,12 @@ gradient_minimizer(
//printf("(%-3u) %-0.7f %-10.7f %-10.7f %-10.7f\n", i, stepsize, genotype[i], gradient[i], candidate_genotype[i]);
#endif
#if 0
// No need for defining upper and lower genotype bounds
#if 0
// Putting genes back within bounds
candidate_genotype[i] = fmin(candidate_genotype[i], upper_bounds_genotype[i]);
candidate_genotype[i] = fmax(candidate_genotype[i], lower_bounds_genotype[i]);
#endif
#endif
}
// Evaluating candidate
......@@ -526,7 +590,7 @@ gradient_minimizer(
dockpars_coeff_elec,
dockpars_qasp,
dockpars_coeff_desolv,
/*candidate_genotype,*/ genotype, /*WARNING: use genotype ONLY to reproduce results*/
/*candidate_genotype,*/ genotype, /*WARNING: use "genotype" ONLY to reproduce results*/
&candidate_energy,
&run_id,
// Some OpenCL compilers don't allow declaring
......
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