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Commit 588ac909 authored by Leonardo Solis's avatar Leonardo Solis
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corrected optimized step

parent 9fad58a3
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Makefile
View file @ 588ac909
......@@ -210,8 +210,8 @@ 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
ASTEX_PDB := 2bsm
ASTEX_NRUN:= 1
ASTEX_POPSIZE := 1
ASTEX_NRUN:= 10
ASTEX_POPSIZE := 10
ASTEX_TESTNAME := test_astex
astex: odock
......
common/calcenergy_basic.h
View file @ 588ac909
......@@ -85,7 +85,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
// Enable printf statements for debugging
// the gradient-based minimizer
#define DEBUG_MINIMIZER
//#define DEBUG_MINIMIZER
/*
......@@ -96,8 +96,8 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#define STEP_INCREASE 1.2f
#define STEP_DECREASE 0.2f
#define STEP_START 1E3 // Might look gigantic, but will cap
#define MAX_DEV_TRANSLATION 2.0f // 2 Angstrom, but must be divided by the gridspacing
#define STEP_START 1E3 // Starting step size. This might look gigantic but will cap
#define MAX_DEV_TRANSLATION 2.0f // 2 Angstrom, but must be divided by the gridspacing (store in variable)
#define MAX_DEV_ROTATION 0.2f // Shoemake range [0, 1]
#define MAX_DEV_TORSION 0.5f/DEG_TO_RAD // 0.5f RAD
......
device/kernel_gradient.cl
View file @ 588ac909
......@@ -44,13 +44,11 @@ gradient_minimizer(
__constant int* rotbonds_atoms_const,
__constant int* num_rotating_atoms_per_rotbond_const,
// Specific gradient-minimizer args
uint gradMin_maxiters,
uint gradMin_maxfails
/*
uint gradMin_maxiters
/*
,
float gradMin_alpha,
__constant float* gradMin_conformation_min_perturbation // minimal values for gene perturbation, originally as the scalar "dxmin"
*/
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.
......@@ -74,8 +72,10 @@ gradient_minimizer(
__local bool exit;
*/
/*
// Number of energy-evaluations counter
__local int evaluation_cnt;
*/
// Stepsize for the minimizer
__local float stepsize;
......@@ -107,7 +107,7 @@ gradient_minimizer(
energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
#if defined (DEBUG_MINIMIZER)
printf("\nrun_id: %5u entity_id: %5u initial_energy: %.5f\n", run_id, entity_id, energy);
printf("\nrun_id: %5u entity_id: %5u initial_energy: %.7f\n", run_id, entity_id, energy);
#endif
// Initializing gradient-minimizer counters and flags
......@@ -115,7 +115,9 @@ gradient_minimizer(
/*
failure_cnt = 0;
*/
/*
evaluation_cnt = 0;
*/
stepsize = STEP_START;
}
......@@ -237,9 +239,17 @@ gradient_minimizer(
lower_bounds_genotype [gene_counter] = 0.0f;
upper_bounds_genotype [gene_counter] = 360.0f;
}
#if defined (DEBUG_MINIMIZER)
//printf("(%-3u) %-0.7f %-10.7f %-10.7f %-10.7f\n", gene_counter, stepsize, genotype[gene_counter], lower_bounds_genotype[gene_counter], upper_bounds_genotype[gene_counter]);
#endif
}
barrier(CLK_LOCAL_MEM_FENCE);
// 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)
do {
#if 0
// Specific input genotypes for a ligand with no rotatable bonds (1ac8).
......@@ -293,53 +303,40 @@ gradient_minimizer(
if (get_local_id(0) == 0) {
// Finding maximum of the absolute value
// for the three translation genes
if (fabs(genotype[0]) > fabs(genotype[1])) {
max_trans_gene = fabs(genotype[0]);
}
else {
max_trans_gene = fabs(genotype[1]);
}
if (max_trans_gene < fabs(genotype[2])) {
max_trans_gene = fabs(genotype[2]);
}
max_trans_gene = max(fabs(genotype[0]), fabs(genotype[1]));
max_trans_gene = max(max_trans_gene, fabs(genotype[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);
// Finding maximum of the absolute value
// for the three Shoemake rotation genes
if (fabs(genotype[3]) > fabs(genotype[4])) {
max_rota_gene = fabs(genotype[3]);
}
else {
max_rota_gene = fabs(genotype[4]);
}
if (max_trans_gene < fabs(genotype[5])) {
max_rota_gene = fabs(genotype[5]);
}
max_rota_gene = max(fabs(genotype[3]), fabs(genotype[4]));//printf("max_rota_gene: %-10.7f\n", max_rota_gene);
max_rota_gene = max(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]
max_rota_stepsize = native_divide(MAX_DEV_ROTATION, max_rota_gene);
}
// Copying torsions genes
__local float torsions_genotype[ACTUAL_GENOTYPE_LENGTH];
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(genotype[i+6]);
}
barrier(CLK_LOCAL_MEM_FENCE);
// Calculating maximum absolute torsional gene
for (uint i=(dockpars_num_of_genes-6); i>=1; i/=2){
for (uint i=(dockpars_num_of_genes-6)+1; i>=1; i/=2){
if (get_local_id(0) < i) {
#if defined (DEBUG_MINIMIZER)
//printf("---====--- %u %u %-10.10f %-10.10f\n", i, get_local_id(0), torsions_genotype[get_local_id(0)], torsions_genotype[get_local_id(0) + i]);
#endif
if (torsions_genotype[get_local_id(0)] < torsions_genotype[get_local_id(0) + i]) {
torsions_genotype[get_local_id(0)] = torsions_genotype[get_local_id(0) + i];
}
......@@ -353,25 +350,21 @@ gradient_minimizer(
barrier(CLK_LOCAL_MEM_FENCE);
// Calculating the maximum stepsize using previous three
if (get_local_id(0) == 0) {
if (max_trans_stepsize < max_rota_stepsize) {
max_stepsize = max_trans_stepsize;
}
else {
max_stepsize = max_rota_stepsize;
}
// Calculating the maximum stepsize using previous three
max_stepsize = min(max_trans_stepsize, max_rota_stepsize);
max_stepsize = min(max_stepsize, max_tors_stepsize);
if (max_stepsize > max_tors_stepsize) {
max_stepsize = max_tors_stepsize;
}
// Capping the stepsize
stepsize = min(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_steps: %-0.7f %-10.7f %-10.7f %-10.7f\n", max_trans_stepsize, max_rota_stepsize, max_tors_stepsize, max_stepsize);
#endif
}
barrier(CLK_LOCAL_MEM_FENCE);
// Capping the stepsize
if (get_local_id(0) == 0) {
stepsize = (stepsize<max_stepsize)?stepsize:max_stepsize;
}
barrier(CLK_LOCAL_MEM_FENCE);
// Calculating gradient
......@@ -449,7 +442,7 @@ gradient_minimizer(
candidate_genotype[i] = genotype[i] - stepsize * gradient[i];
#if defined (DEBUG_MINIMIZER)
//printf("(%-3u) %-0.15f %-10.10f %-10.10f %-10.10f\n", i, stepsize, genotype[i], gradient[i], candidate_genotype[i]);
//printf("(%-3u) %-0.7f %-10.7f %-10.7f %-10.7f\n", i, stepsize, genotype[i], gradient[i], candidate_genotype[i]);
#endif
// Putting genes back within bounds
......@@ -509,10 +502,12 @@ 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)
......@@ -534,7 +529,7 @@ gradient_minimizer(
genotype[i] = candidate_genotype[i];
#if defined (DEBUG_MINIMIZER)
//printf("(%-3u) %-15.15f %-10.10f %-10.10f %-10.10f\n", i, alpha, genotype[i], gradient[i], candidate_genotype[i]);
//printf("(%-3u) %-15.7f %-10.7f %-10.7f %-10.7f\n", i, alpha, genotype[i], gradient[i], candidate_genotype[i]);
#endif
}
}
......@@ -546,30 +541,30 @@ gradient_minimizer(
barrier(CLK_LOCAL_MEM_FENCE);
// Updating number of stepest-descent iterations
// Updating number of stepest-descent iterations (energy evaluations)
if (get_local_id(0) == 0) {
iteration_cnt = iteration_cnt + 1;
#if defined (DEBUG_MINIMIZER)
printf("# mini-iters: %-3u, # ener-evals: %-3u, stepsize: %f, energy: %f\n", iteration_cnt, evaluation_cnt, stepsize, energy);
printf("# minimizer-iters: %-3u, stepsize: %10.7f, E: %10.7f\n", iteration_cnt, stepsize, energy);
#endif
#if defined (DEBUG_ENERGY_KERNEL5)
printf("%-18s [%-5s]---{%-5s} [%-10.8f]---{%-10.8f}\n", "-ENERGY-KERNEL5-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
printf("%-18s [%-5s]---{%-5s} [%-10.7f]---{%-10.7f}\n", "-ENERGY-KERNEL5-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
#endif
}
} while (iteration_cnt < gradMin_maxiters);
} while ((iteration_cnt < gradMin_maxiters) && (stepsize > 1E-8));
// -----------------------------------------------------------------------------
// Updating eval counter and energy
if (get_local_id(0) == 0) {
dockpars_evals_of_new_entities[run_id*dockpars_pop_size+entity_id] += evaluation_cnt;
dockpars_evals_of_new_entities[run_id*dockpars_pop_size+entity_id] += iteration_cnt;
dockpars_energies_next[run_id*dockpars_pop_size+entity_id] = energy;
#if defined (DEBUG_MINIMIZER)
printf("-------> End of grad-min cycle, num of evals: %u, final energy: %.5f\n", evaluation_cnt, energy);
printf("-------> End of grad-min cycle, num of evals: %u, final energy: %.7f\n", iteration_cnt, energy);
#endif
}
......
host/inc/performdocking.h
View file @ 588ac909
......@@ -58,8 +58,8 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
typedef struct {
unsigned int max_num_of_iters;
unsigned int max_num_of_consec_fails;
/*
unsigned int max_num_of_consec_fails;
float alpha;
float conformation_min_perturbation [ACTUAL_GENOTYPE_LENGTH];
*/
......
host/src/performdocking.cpp
View file @ 588ac909
......@@ -412,10 +412,11 @@ filled with clock() */
// Setup here (temporarily?) the gradient and associated parameters.
// This should be ultimately configurable by the user as program exec. flags.
Gradientparameters gradientpars;
gradientpars.max_num_of_iters = 30;
gradientpars.max_num_of_consec_fails = (unsigned int)(0.05 * gradientpars.max_num_of_iters);
gradientpars.max_num_of_iters = 300;
/*
gradientpars.max_num_of_consec_fails = (unsigned int)(0.05 * gradientpars.max_num_of_iters);
gradientpars.alpha = 0.000001f;
// Set minimum values for input conformation (translation genes as x, y, z)
......@@ -441,16 +442,16 @@ filled with clock() */
*/
/*
///*
// Initially, the number of entities that undergo gradient-minimization,
// by default, it is the same as the number of entities that undergo gradient-based minimizer
blocksPerGridForEachGradMinimizerEntity = dockpars.num_of_lsentities*mypars->num_of_runs;
*/
//*/
///*
/*
// test, only one entity per reach run, undergoes gradient minimization
blocksPerGridForEachGradMinimizerEntity = mypars->num_of_runs;
//*/
*/
clock_start_docking = clock();
......@@ -683,8 +684,8 @@ filled with clock() */
setKernelArg(kernel5,38,sizeof(mem_num_rotating_atoms_per_rotbond_const),&mem_num_rotating_atoms_per_rotbond_const);
// Specific gradient-minimizer args
setKernelArg(kernel5,39,sizeof(gradientpars.max_num_of_iters), &gradientpars.max_num_of_iters);
setKernelArg(kernel5,40,sizeof(gradientpars.max_num_of_consec_fails), &gradientpars.max_num_of_consec_fails);
/*
setKernelArg(kernel5,40,sizeof(gradientpars.max_num_of_consec_fails), &gradientpars.max_num_of_consec_fails);
setKernelArg(kernel5,39,sizeof(gradientpars.alpha), &gradientpars.alpha);
setKernelArg(kernel5,40,sizeof(mem_gradpars_conformation_min_perturbation), &mem_gradpars_conformation_min_perturbation);
*/
......
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