Skip to content

GitLab

Commit f79a7104 authored by Leonardo Solis's avatar Leonardo Solis
Browse files

corrections + code-restructure in grad

parent d266192b
Expand all Hide whitespace changes
Inline Side-by-side
Makefile
View file @ f79a7104
......@@ -198,8 +198,8 @@ odock: check-env-all stringify $(SRC)
# Example
PDB := 3ce3
NRUN := 100
POPSIZE := 500
NRUN := 200
POPSIZE := 2048
TESTNAME:= test
test: odock
......
device/auxiliary_genetic.cl
View file @ f79a7104
......@@ -172,7 +172,6 @@ void gpu_perform_elitist_selection(
for (gene_counter = get_local_id(0);
gene_counter < dockpars_num_of_genes;
gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0) +
GENOTYPE_LENGTH_IN_GLOBMEM*best_ID[0]+gene_counter];
dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0) + GENOTYPE_LENGTH_IN_GLOBMEM*best_ID[0]+gene_counter];
}
}
device/auxiliary_gradient.cl
View file @ f79a7104
......@@ -2,11 +2,7 @@
// Implementation of auxiliary functions
// for the gradient-based minimizer
bool is_gradDescent_enabled(
__local bool* is_gNorm_gt_gMin,
__local bool* is_nIter_lt_maxIter,
__local bool* is_perturb_gt_gene_min,
__local bool* is_perturb_gt_genotype,
__local float* local_gNorm,
float gradMin_tol,
__local uint* local_nIter,
......@@ -16,10 +12,14 @@ bool is_gradDescent_enabled(
__local bool* is_gradDescentEn,
uint gradMin_numElements)
{
bool is_gNorm_gt_gMin;
bool is_nIter_lt_maxIter;
bool is_perturb_gt_genotype;
if (get_local_id(0) == 0) {
*is_gNorm_gt_gMin = (local_gNorm[0] >= gradMin_tol);
*is_nIter_lt_maxIter = (local_nIter[0] <= gradMin_maxiter);
*is_perturb_gt_genotype = true;
is_gNorm_gt_gMin = (local_gNorm[0] >= gradMin_tol);
is_nIter_lt_maxIter = (local_nIter[0] <= gradMin_maxiter);
is_perturb_gt_genotype = true;
}
// For every gene, let's determine
......@@ -35,153 +35,35 @@ bool is_gradDescent_enabled(
if (get_local_id(0) == 0) {
// Reduce all is_perturb_gt_gene_min's
// into their corresponding genotype
for(uint i = 0;
i < gradMin_numElements;
i++) {
*is_perturb_gt_genotype = *is_perturb_gt_genotype && is_perturb_gt_gene_min[i];
is_perturb_gt_genotype = is_perturb_gt_genotype && is_perturb_gt_gene_min[i];
/*
printf("is_perturb_gt_gene_min[%u]?: %s\n", i, (is_perturb_gt_gene_min[i] == true)?"yes":"no");
*/
}
// Reduce all three previous
// partial evaluations (gNorm, nIter, perturb) into a final one
is_gradDescentEn[0] = *is_gNorm_gt_gMin && *is_nIter_lt_maxIter && *is_perturb_gt_genotype;
*is_gradDescentEn = is_gNorm_gt_gMin && is_nIter_lt_maxIter && is_perturb_gt_genotype;
/*
if (get_local_id(0) == 0) {
printf("is_gNorm_gt_gMin?: %s\n", (is_gNorm_gt_gMin == true)?"yes":"no");
printf("is_nIter_lt_maxIter?: %s\n", (is_nIter_lt_maxIter == true)?"yes":"no");
printf("is_perturb_gt_genotype?: %s\n", (is_perturb_gt_genotype == true)?"yes":"no");
printf("Continue gradient iteration?: %s\n", (*is_gradDescentEn == true)?"yes":"no");
}
*/
}
barrier(CLK_LOCAL_MEM_FENCE);
return is_gradDescentEn[0];
}
void stepGPU (// Args for minimization
__local float* local_genotype, // originally as "d_x"
__local float* local_genotype_new, // originally as "d_xnew"
__local float* local_genotype_diff, // originally as "d_xdiff"
__local float* local_gradient, // originally as "d_g"
float gradMin_alpha, // originally as "alpha"
float gradMin_h, // originally as "h"
uint gradMin_inputSize, // originally as "M". initially labelled as "gradMin_M"
// Args for energy and gradient calculation
int dockpars_rotbondlist_length,
char dockpars_num_of_atoms,
char dockpars_gridsize_x,
char dockpars_gridsize_y,
char dockpars_gridsize_z,
__global const float* restrict dockpars_fgrids, // This is too large to be allocated in __constant
char dockpars_num_of_atypes,
int dockpars_num_of_intraE_contributors,
float dockpars_grid_spacing,
float dockpars_coeff_elec,
float dockpars_qasp,
float dockpars_coeff_desolv,
__local float* genotype,
__local float* energy,
__local int* run_id,
// 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.
__local float* calc_coords_x,
__local float* calc_coords_y,
__local float* calc_coords_z,
__local float* partial_energies,
__constant float* atom_charges_const,
__constant char* atom_types_const,
__constant char* intraE_contributors_const,
__constant float* VWpars_AC_const,
__constant float* VWpars_BD_const,
__constant float* dspars_S_const,
__constant float* dspars_V_const,
__constant int* rotlist_const,
__constant float* ref_coords_x_const,
__constant float* ref_coords_y_const,
__constant float* ref_coords_z_const,
__constant float* rotbonds_moving_vectors_const,
__constant float* rotbonds_unit_vectors_const,
__constant float* ref_orientation_quats_const
// Gradient-related arguments
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
// "is_enabled_gradient_calc": enables gradient calculation.
// In Genetic-Generation: no need for gradients
// In Gradient-Minimizer: must calculate gradients
,
__local bool* is_enabled_gradient_calc,
__local float* gradient_inter_x,
__local float* gradient_inter_y,
__local float* gradient_inter_z,
__local float* gradient_genotype
)
{
// Calculate gradient
// =============================================================
gpu_calc_energy(dockpars_rotbondlist_length,
dockpars_num_of_atoms,
dockpars_gridsize_x,
dockpars_gridsize_y,
dockpars_gridsize_z,
dockpars_fgrids,
dockpars_num_of_atypes,
dockpars_num_of_intraE_contributors,
dockpars_grid_spacing,
dockpars_coeff_elec,
dockpars_qasp,
dockpars_coeff_desolv,
genotype,
energy,
run_id,
// 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.
calc_coords_x,
calc_coords_y,
calc_coords_z,
partial_energies,
atom_charges_const,
atom_types_const,
intraE_contributors_const,
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
// Gradient-related arguments
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
,
is_enabled_gradient_calc,
gradient_inter_x,
gradient_inter_y,
gradient_inter_z,
gradient_genotype
);
// =============================================================
for(uint i = get_local_id(0);
i < gradMin_inputSize;
i+= NUM_OF_THREADS_PER_BLOCK) {
// Taking step
local_genotype_new[i] = local_genotype[i] - gradMin_alpha * local_gradient[i];
// Updating termination metrics
local_genotype_diff[i] = local_genotype_new[i] - local_genotype[i];
// Updating current solution
local_genotype[i] = local_genotype_new[i];
}
return *is_gradDescentEn;
}
float inner_product(__local float* vector1,
......
device/calcenergy.cl
View file @ f79a7104
This diff is collapsed.
device/calcgradient.cl 0 → 100644
View file @ f79a7104
This diff is collapsed.
device/kernel1.cl
View file @ f79a7104
......@@ -59,7 +59,7 @@ gpu_calc_initpop(
// local variables within non-kernel functions.
// These local variables must be declared in a kernel,
// and then passed to non-kernel functions.
__local float genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
__local float genotype[ACTUAL_GENOTYPE_LENGTH];
__local float energy;
__local int run_id;
......@@ -80,27 +80,6 @@ gpu_calc_initpop(
run_id = get_group_id(0) / dockpars_pop_size;
}
// -------------------------------------------------------------------
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
// -------------------------------------------------------------------
// Disabling gradient calculation for this kernel
__local bool is_enabled_gradient_calc;
if (get_local_id(0) == 0) {
is_enabled_gradient_calc = false;
}
// Variables to store gradient of
// the intermolecular energy 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];
// Final gradient resulting out of gradient calculation
__local float gradient_genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
// -------------------------------------------------------------------
// =============================================================
// WARNING: only energy of work-item=0 will be valid
gpu_calc_energy(dockpars_rotbondlist_length,
......@@ -141,15 +120,6 @@ gpu_calc_initpop(
rotbonds_moving_vectors_const,
rotbonds_unit_vectors_const,
ref_orientation_quats_const
// Gradient-related arguments
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
,
&is_enabled_gradient_calc,
gradient_inter_x,
gradient_inter_y,
gradient_inter_z,
gradient_genotype
);
// =============================================================
......
device/kernel3.cl
View file @ f79a7104
......@@ -97,27 +97,6 @@ perform_LS(
__local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
// -------------------------------------------------------------------
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
// -------------------------------------------------------------------
// Disabling gradient calculation for this kernel
__local bool is_enabled_gradient_calc;
if (get_local_id(0) == 0) {
is_enabled_gradient_calc = false;
}
// Variables to store gradient of
// the intermolecular energy 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];
// Final gradient resulting out of gradient calculation
__local float gradient_genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
// -------------------------------------------------------------------
// Determining run ID and entity ID
// Initializing offspring genotype
if (get_local_id(0) == 0)
......@@ -240,15 +219,6 @@ perform_LS(
rotbonds_moving_vectors_const,
rotbonds_unit_vectors_const,
ref_orientation_quats_const
// Gradient-related arguments
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
,
&is_enabled_gradient_calc,
gradient_inter_x,
gradient_inter_y,
gradient_inter_z,
gradient_genotype
);
// =================================================================
......@@ -291,7 +261,7 @@ perform_LS(
// Shoemake genes (u1, u2, u3) ranges between [0,1]
if ((gene_counter >= 3) && (gene_counter <= 5)) {
genotype_candidate[gene_counter] = gpu_randf(dockpars_prng_states);
genotype_candidate[gene_counter] = gpu_randf(dockpars_prng_states);
}
// Other genes: translation and torsions
else {
......@@ -343,15 +313,6 @@ perform_LS(
rotbonds_moving_vectors_const,
rotbonds_unit_vectors_const,
ref_orientation_quats_const
// Gradient-related arguments
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
,
&is_enabled_gradient_calc,
gradient_inter_x,
gradient_inter_y,
gradient_inter_z,
gradient_genotype
);
// =================================================================
......
device/kernel4.cl
View file @ f79a7104
......@@ -90,27 +90,6 @@ gpu_gen_and_eval_newpops(
__local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
// -------------------------------------------------------------------
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
// -------------------------------------------------------------------
// Disabling gradient calculation for this kernel
__local bool is_enabled_gradient_calc;
if (get_local_id(0) == 0) {
is_enabled_gradient_calc = false;
}
// Variables to store gradient of
// the intermolecular energy 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];
// Final gradient resulting out of gradient calculation
__local float gradient_genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
// -------------------------------------------------------------------
// In this case this compute-unit is responsible for elitist selection
if ((get_group_id(0) % dockpars_pop_size) == 0) {
gpu_perform_elitist_selection(dockpars_pop_size,
......@@ -291,16 +270,6 @@ gpu_gen_and_eval_newpops(
rotbonds_moving_vectors_const,
rotbonds_unit_vectors_const,
ref_orientation_quats_const
// Gradient-related arguments
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
,
&is_enabled_gradient_calc,
gradient_inter_x,
gradient_inter_y,
gradient_inter_z,
gradient_genotype
);
// =============================================================
......
device/kernel_gradient.cl
View file @ f79a7104
......@@ -45,7 +45,6 @@ gradient_minimizer(
__constant float* rotbonds_moving_vectors_const,
__constant float* rotbonds_unit_vectors_const,
__constant float* ref_orientation_quats_const,
// Specific gradient-minimizer args
// __global float* restrict dockpars_conformations_next, // initial population
// whose (some) entities (genotypes) are to be minimized
......@@ -97,6 +96,15 @@ gradient_minimizer(
}
local_energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
/*
printf("run_id: %u, entity_id: %u, local_energy: %f\n", run_id, entity_id, local_energy);
*/
/*
printf("BEFORE GRADIENT - local_energy: %f\n", local_energy);
*/
}
barrier(CLK_LOCAL_MEM_FENCE);
......@@ -106,7 +114,7 @@ gradient_minimizer(
__local float local_gNorm; // gradient norm (shared in the CU), originally as "gnorm"
__local uint local_nIter; // iteration counter, originally as "niter"
__local float local_perturbation [ACTUAL_GENOTYPE_LENGTH]; // perturbation, originally as "dx"
__local float local_genotype[ACTUAL_GENOTYPE_LENGTH]; // optimization vector, originally as "d_x"
__local float local_genotype [ACTUAL_GENOTYPE_LENGTH]; // optimization vector, originally as "d_x"
if (get_local_id(0) == 0) {
local_gNorm = FLT_MAX;
......@@ -132,13 +140,10 @@ gradient_minimizer(
// and then passed to non-kernel functions.
// Partial results in "is_gradDescent_enabled()"
__local bool is_gNorm_gt_gMin;
__local bool is_nIter_lt_maxIter;
__local bool is_perturb_gt_gene_min [ACTUAL_GENOTYPE_LENGTH];
__local bool is_perturb_gt_genotype;
__local bool is_gradDescentEn;
// Partial results in "stepGPU()"
// Partial results of the gradient step
__local float local_gradient [ACTUAL_GENOTYPE_LENGTH]; // gradient, originally as "d_g"
__local float local_genotype_new [ACTUAL_GENOTYPE_LENGTH]; // new actual solution, originally as "d_xnew"
__local float local_genotype_diff [ACTUAL_GENOTYPE_LENGTH]; // difference between actual and old solution, originally as "d_xdiff"
......@@ -155,15 +160,6 @@ gradient_minimizer(
__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];
// Enable gradient calculation for this kernel
__local bool is_enabled_gradient_calc;
if (get_local_id(0) == 0) {
is_enabled_gradient_calc = true;
}
// Final gradient resulting out of gradient calculation
__local float gradient_genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
// -------------------------------------------------------------------
// Variables to store partial energies
......@@ -175,10 +171,7 @@ gradient_minimizer(
// -----------------------------------------------------------------------------
// Perform gradient-descent iterations
while (is_gradDescent_enabled(
&is_gNorm_gt_gMin,
&is_nIter_lt_maxIter,
is_perturb_gt_gene_min,
&is_perturb_gt_genotype,
&local_gNorm,
gradMin_tol,
&local_nIter,
......@@ -187,18 +180,113 @@ gradient_minimizer(
gradMin_conformation_min_perturbation,
&is_gradDescentEn,
dockpars_num_of_genes) == true) {
// Calculating gradient
// =============================================================
gpu_calc_gradient(
dockpars_rotbondlist_length,
dockpars_num_of_atoms,
dockpars_gridsize_x,
dockpars_gridsize_y,
dockpars_gridsize_z,
dockpars_fgrids,
dockpars_num_of_atypes,
dockpars_num_of_intraE_contributors,
dockpars_grid_spacing,
dockpars_coeff_elec,
dockpars_qasp,
dockpars_coeff_desolv,
local_genotype,
/*
&local_energy,
*/
&run_id,
// 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.
calc_coords_x,
calc_coords_y,
calc_coords_z,
atom_charges_const,
atom_types_const,
intraE_contributors_const,
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
// 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,
local_gradient
);
// =============================================================
stepGPU(// Args for minimization
local_genotype,
local_genotype_new,
local_genotype_diff,
local_gradient,
gradMin_alpha,
gradMin_h,
dockpars_num_of_genes, //gradMin_M
// Args for energy and gradient calculation
dockpars_rotbondlist_length,
for(uint i = get_local_id(0);
i < dockpars_num_of_genes;
i+= NUM_OF_THREADS_PER_BLOCK) {
// Taking step
local_genotype_new[i] = local_genotype[i] - gradMin_alpha * local_gradient[i];
// Updating terminatiodockpars_num_of_genesn metrics
local_genotype_diff[i] = local_genotype_new[i] - local_genotype[i];
// Updating current solution
local_genotype[i] = local_genotype_new[i];
}
// Updating number of stepest-descent iterations
if (get_local_id(0) == 0) {
local_nIter = local_nIter + 1;
}
// Storing the norm of all gradients
local_gNorm = inner_product(local_gradient, local_gradient, dockpars_num_of_genes, dotProduct);
if (get_local_id(0) == 0) {
local_gNorm = native_sqrt(local_gNorm);
}
barrier(CLK_LOCAL_MEM_FENCE);
// Storing all gene-based perturbations
for(uint i = get_local_id(0);
i < dockpars_num_of_genes;
i+= NUM_OF_THREADS_PER_BLOCK) {
local_perturbation[i] = local_genotype_diff [i];
}
/*
if (get_local_id(0) == 0) {
printf("Entity: %u, Run: %u, minimized E: %f\n", entity_id, run_id, local_energy);
}
*/
/*
if (get_local_id(0) == 0) {
printf("Number of gradient iterations: %u\n", local_nIter);
}
*/
}
// -----------------------------------------------------------------------------
// Calculating energy
// =============================================================
gpu_calc_energy(dockpars_rotbondlist_length,
dockpars_num_of_atoms,
dockpars_gridsize_x,
dockpars_gridsize_y,
......@@ -236,64 +324,15 @@ gradient_minimizer(
rotbonds_moving_vectors_const,
rotbonds_unit_vectors_const,
ref_orientation_quats_const
// Gradient-related arguments
// Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py
,
&is_enabled_gradient_calc,
gradient_inter_x,
gradient_inter_y,
gradient_inter_z,
gradient_genotype
);
// -------------------------------------------------------------------
// Updating number of stepest-descent iterations
if (get_local_id(0) == 0) {
local_nIter = local_nIter + 1;
}
// Storing the norm of all gradients
/*
local_gNorm = native_sqrt(inner_product(local_gradient,
local_gradient,
dockpars_num_of_genes,
dotProduct));
*/
local_gNorm = inner_product(local_gradient, local_gradient, dockpars_num_of_genes, dotProduct);
if (get_local_id(0) == 0) {
local_gNorm = native_sqrt(local_gNorm);
}
barrier(CLK_LOCAL_MEM_FENCE);