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Commit e6dc04f8 authored by Leonardo Solis's avatar Leonardo Solis
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dynamic step adaption

parent 6a2748bf
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Makefile
View file @ e6dc04f8
......@@ -202,8 +202,8 @@ odock: check-env-all stringify $(SRC)
# 3tmn: for testing gradients of torsion genes (1 torsion)
PDB := 7cpa
NRUN := 100
POPSIZE := 500
NRUN := 1
POPSIZE := 1
TESTNAME:= test
test: odock
......
device/kernel_gradient.cl
View file @ e6dc04f8
// Gradient-based steepest descent minimizer
// Alternative to Solis-Wetts
//#define DEBUG_MINIMIZER
#define DEBUG_MINIMIZER
#define TRANGENE_ALPHA 1E-3//1E-8
#define ROTAGENE_ALPHA 1E-8//1E-15
......@@ -47,7 +47,8 @@ gradient_minimizer(
__constant int* rotbonds_atoms_const,
__constant int* num_rotating_atoms_per_rotbond_const,
// Specific gradient-minimizer args
uint gradMin_maxiter,
uint gradMin_maxiters,
uint gradMin_maxfails,
float gradMin_alpha,
__constant float* gradMin_conformation_min_perturbation // minimal values for gene perturbation, originally as the scalar "dxmin"
)
......@@ -59,16 +60,20 @@ gradient_minimizer(
//it is always tested according to the ls probability, and if it not to be
//subjected to local search, the entity with ID num_of_lsentities is selected instead of the first one (with ID 0).
{
// -----------------------------------------------------------------------------
// Number of energy-evaluations counter
__local int evaluation_cnt;
// -----------------------------------------------------------------------------
// Determining entity, and its run, energy, and genotype
__local int entity_id;
__local int run_id;
__local float local_energy;
__local float local_genotype[ACTUAL_GENOTYPE_LENGTH];
__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;
if (get_local_id(0) == 0)
{
......@@ -84,35 +89,25 @@ gradient_minimizer(
entity_id = get_group_id(0) % dockpars_num_of_lsentities;
*/
local_energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
#if defined (DEBUG_MINIMIZER)
printf("run_id: %5u entity_id: %5u initial_energy: %.5f\n", run_id, entity_id, local_energy);
//printf("%-50s %f\n", "Initial energy: ", local_energy);
printf("\nrun_id: %5u entity_id: %5u initial_energy: %.5f\n", run_id, entity_id, energy);
#endif
// Initializing gradient-minimizer counters and flags
iteration_cnt = 0;
failure_cnt = 0;
/*exit = false;*/
evaluation_cnt = 0;
}
barrier(CLK_LOCAL_MEM_FENCE);
async_work_group_copy(local_genotype,
async_work_group_copy(genotype,
dockpars_conformations_next+(run_id*dockpars_pop_size+entity_id)*GENOTYPE_LENGTH_IN_GLOBMEM,
dockpars_num_of_genes, 0);
// -----------------------------------------------------------------------------
// Initializing variables for gradient minimizer
__local uint local_nIter; // iteration counter
__local uint failure_cnt; // Failure counter
__local bool exit;
if (get_local_id(0) == 0) {
local_nIter = 0;
failure_cnt = 0;
exit = false;
evaluation_cnt = 0;
}
barrier(CLK_LOCAL_MEM_FENCE);
// -----------------------------------------------------------------------------
// Some OpenCL compilers don't allow declaring
// local variables within non-kernel functions.
......@@ -120,12 +115,12 @@ gradient_minimizer(
// and then passed to non-kernel functions.
// Partial results for checking validity of genotype
__local bool is_genotype_valid [ACTUAL_GENOTYPE_LENGTH];
__local bool is_candidate_genotype_valid [ACTUAL_GENOTYPE_LENGTH];
// Partial results of the gradient step
__local float local_gradient [ACTUAL_GENOTYPE_LENGTH];
__local float local_candidate_energy;
__local float local_candidate_genotype[ACTUAL_GENOTYPE_LENGTH];
__local float gradient [ACTUAL_GENOTYPE_LENGTH];
__local float candidate_energy;
__local float candidate_genotype[ACTUAL_GENOTYPE_LENGTH];
// -------------------------------------------------------------------
// Calculate gradients (forces) for intermolecular energy
......@@ -164,10 +159,16 @@ gradient_minimizer(
float alpha;
// Initilizing each (work-item)-specific alpha
for(uint i = get_local_id(0); i < dockpars_num_of_genes; i+= NUM_OF_THREADS_PER_BLOCK) {
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
}
// Perform gradient-descent iterations
......@@ -198,44 +199,44 @@ gradient_minimizer(
do {
#if 0
// Specific input genotypes for a ligand with no rotatable bonds (1ac8).
// Translation genes must be expressed in grids in OCLADock (local_genotype [0|1|2]).
// Translation genes must be expressed in grids in OCLADock (genotype [0|1|2]).
// However, for testing purposes,
// we start using translation values in real space (Angstrom): {31.79575, 93.743875, 47.699875}
// Rotation genes are expresed in the Shoemake space: local_genotype [3|4|5]
// Rotation genes are expresed in the Shoemake space: genotype [3|4|5]
// xyz_gene_gridspace = gridcenter_gridspace + (input_gene_realspace - gridcenter_realspace)/gridsize
// 1ac8
local_genotype[0] = 30 + (31.79575 - 31.924) / 0.375;
local_genotype[1] = 30 + (93.743875 - 93.444) / 0.375;
local_genotype[2] = 30 + (47.699875 - 47.924) / 0.375;
local_genotype[3] = 0.1f;
local_genotype[4] = 0.5f;
local_genotype[5] = 0.9f;
genotype[0] = 30 + (31.79575 - 31.924) / 0.375;
genotype[1] = 30 + (93.743875 - 93.444) / 0.375;
genotype[2] = 30 + (47.699875 - 47.924) / 0.375;
genotype[3] = 0.1f;
genotype[4] = 0.5f;
genotype[5] = 0.9f;
#endif
#if 0
// 3tmn
local_genotype[0] = 30 + (ligand_center_x - grid_center_x) / 0.375;
local_genotype[1] = 30 + (ligand_center_y - grid_center_y) / 0.375;
local_genotype[2] = 30 + (ligand_center_z - grid_center_z) / 0.375;
local_genotype[3] = shoemake_gene_u1;
local_genotype[4] = shoemake_gene_u2;
local_genotype[5] = shoemake_gene_u3;
local_genotype[6] = 0.0f;
local_genotype[7] = 0.0f;
local_genotype[8] = 0.0f;
local_genotype[9] = 0.0f;
local_genotype[10] = 0.0f;
local_genotype[11] = 0.0f;
local_genotype[12] = 0.0f;
local_genotype[13] = 0.0f;
local_genotype[14] = 0.0f;
local_genotype[15] = 0.0f;
local_genotype[16] = 0.0f;
local_genotype[17] = 0.0f;
local_genotype[18] = 0.0f;
local_genotype[19] = 0.0f;
local_genotype[20] = 0.0f;
genotype[0] = 30 + (ligand_center_x - grid_center_x) / 0.375;
genotype[1] = 30 + (ligand_center_y - grid_center_y) / 0.375;
genotype[2] = 30 + (ligand_center_z - grid_center_z) / 0.375;
genotype[3] = shoemake_gene_u1;
genotype[4] = shoemake_gene_u2;
genotype[5] = shoemake_gene_u3;
genotype[6] = 0.0f;
genotype[7] = 0.0f;
genotype[8] = 0.0f;
genotype[9] = 0.0f;
genotype[10] = 0.0f;
genotype[11] = 0.0f;
genotype[12] = 0.0f;
genotype[13] = 0.0f;
genotype[14] = 0.0f;
genotype[15] = 0.0f;
genotype[16] = 0.0f;
genotype[17] = 0.0f;
genotype[18] = 0.0f;
genotype[19] = 0.0f;
genotype[20] = 0.0f;
#endif
// Calculating gradient
......@@ -257,8 +258,8 @@ gradient_minimizer(
// local variables within non-kernel functions.
// These local variables must be declared in a kernel,
// and then passed to non-kernel functions.
local_genotype,
&local_energy,
genotype,
&energy,
&run_id,
calc_coords_x,
......@@ -297,7 +298,7 @@ gradient_minimizer(
gradient_y,
gradient_z,
gradient_per_intracontributor,
local_gradient
gradient
);
// =============================================================
......@@ -307,23 +308,24 @@ gradient_minimizer(
for(uint i = get_local_id(0); i < dockpars_num_of_genes; i+= NUM_OF_THREADS_PER_BLOCK) {
// Taking step
local_candidate_genotype[i] = local_genotype[i] - alpha * local_gradient[i];
candidate_genotype[i] = genotype[i] - alpha * gradient[i];
#if defined (DEBUG_MINIMIZER)
//printf("(%-3u) %-0.15f %-10.10f %-10.10f %-10.10f\n", i, alpha, local_genotype[i], local_gradient[i], local_candidate_genotype[i]);
//printf("(%-3u) %-0.15f %-10.10f %-10.10f %-10.10f\n", i, alpha, genotype[i], gradient[i], candidate_genotype[i]);
#endif
// Checking if every gene of candidate_genotype is valid
is_genotype_valid[i] = (isnan(local_candidate_genotype[i]) == 0) && (isinf(local_candidate_genotype[i]) == 0);
// Checking if every gene of candidate_genotype
// is neither a nan, not inf
is_candidate_genotype_valid[i] = (isnan(candidate_genotype[i]) == 0) && (isinf(candidate_genotype[i]) == 0);
// Verifying the Shoemake genes
// Verifying that Shoemake genes
// do not get out of valid region
if ((i > 2) && (i < 6)) {
if (is_genotype_valid[i] == true) {
//printf("BEFORE is_genotype_valid[%u]?: %s\n", i, (is_genotype_valid[i] == true)?"yes":"no");
if ((local_candidate_genotype[i] < 0.0f) || (local_candidate_genotype[i] > 1.0f)){
is_genotype_valid[i] = false;
//printf("AFTER is_genotype_valid[%u]?: %s\n", i, (is_genotype_valid[i] == true)?"yes":"no");
if (is_candidate_genotype_valid[i] == true) {
//printf("BEFORE is_candidate_genotype_valid[%u]?: %s\n", i, (is_candidate_genotype_valid[i] == true)?"yes":"no");
if ((candidate_genotype[i] < 0.0f) || (candidate_genotype[i] > 1.0f)){
is_candidate_genotype_valid[i] = false;
//printf("AFTER is_candidate_genotype_valid[%u]?: %s\n", i, (is_candidate_genotype_valid[i] == true)?"yes":"no");
}
}
}
......@@ -339,26 +341,29 @@ gradient_minimizer(
is_valid = true;
for(uint i = 0; i < dockpars_num_of_genes;i++) {
is_valid = is_valid && is_genotype_valid[i];
is_valid = is_valid && is_candidate_genotype_valid[i];
#if defined (DEBUG_MINIMIZER)
//printf("is_genotype_valid[%u]?: %s\n", i, (is_genotype_valid[i] == true)?"yes":"no");
//printf("is_candidate_genotype_valid[%u]?: %s\n", i, (is_candidate_genotype_valid[i] == true)?"yes":"no");
#endif
}
/*
if (is_valid == false) {
exit = true;
}
*/
#if defined (DEBUG_MINIMIZER)
//printf("is_valid?: %s, exit?: %s\n", (is_valid == true)?"yes":"no", (exit == true)?"yes":"no");
if (is_valid == false) {
printf("Candidate genome is invalid!\n");
}
#endif
}
barrier(CLK_LOCAL_MEM_FENCE);
if (exit == false) {
if (is_valid == true) {
/*if (exit == false) {*/
if (is_valid == true) {
// =============================================================
gpu_calc_energy(dockpars_rotbondlist_length,
dockpars_num_of_atoms,
......@@ -372,8 +377,8 @@ gradient_minimizer(
dockpars_coeff_elec,
dockpars_qasp,
dockpars_coeff_desolv,
local_candidate_genotype,
&local_candidate_energy,
candidate_genotype,
&candidate_energy,
&run_id,
// Some OpenCL compilers don't allow declaring
// local variables within non-kernel functions.
......@@ -407,15 +412,15 @@ gradient_minimizer(
// Updating number of energy-evaluations counter
if (get_local_id(0) == 0) {
evaluation_cnt++;
evaluation_cnt = evaluation_cnt + 1;
}
barrier(CLK_LOCAL_MEM_FENCE);
// Checking if E(candidate_genotype) < E(genotype)
//if (local_candidate_energy < local_energy){
if (local_candidate_energy - local_energy < 0.1){
if (candidate_energy < energy){
// Updating energy
if (get_local_id(0) == 0) {
local_energy = local_candidate_energy;
energy = candidate_energy;
}
for(uint i = get_local_id(0);
......@@ -423,55 +428,72 @@ gradient_minimizer(
i+= NUM_OF_THREADS_PER_BLOCK) {
// Updating genotype
local_genotype [i] = local_candidate_genotype[i];
genotype [i] = candidate_genotype[i];
// Up-scaling alpha by one order magnitud
alpha = alpha*10;
alpha = alpha*/*10*/(5/(failure_cnt == 0?(failure_cnt+1):(failure_cnt)));
#if defined (DEBUG_MINIMIZER)
//printf("(%u) %-15.15f %-10.10f %-10.10f %-10.10f\n", i, alpha, local_genotype[i], local_gradient[i], local_candidate_genotype[i]);
//printf("(%-3u) %-15.15f %-10.10f %-10.10f %-10.10f\n", i, alpha, genotype[i], gradient[i], candidate_genotype[i]);
#endif
}
}
// If E (candidate) is worse
else {
// Update failure counter
if (get_local_id(0) == 0) {
failure_cnt = failure_cnt + 1;
#if defined (DEBUG_MINIMIZER)
printf("Candidate energy has not improved!\n");
#endif
}
barrier(CLK_LOCAL_MEM_FENCE);
// Down-scaling alpha by one order magnitud.
// Genotype is not updated, meaning that search will be
// started over from the same point from with different alpha
for(uint i = get_local_id(0);
i < dockpars_num_of_genes;
i+= NUM_OF_THREADS_PER_BLOCK) {
alpha = native_divide(alpha, 10);
}
alpha = native_divide(alpha, 5*failure_cnt/*10*/);
// Update failure counter
if (get_local_id(0) == 0) {
failure_cnt = failure_cnt++;
}
#if defined (DEBUG_MINIMIZER)
//printf("(%-3u) %-15.15f\n", i, alpha);
#endif
}
} // End of energy comparison
} // End of if(valid genotypes)
/*} // End of if(valid genotypes)*/
}
else {
// Update failure counter
if (get_local_id(0) == 0) {
failure_cnt = failure_cnt + 1;
}
barrier(CLK_LOCAL_MEM_FENCE);
// Down-scaling alpha by one order magnitud.
// Genotype is not updated, meaning that search will be
// started over from the same point from with different alpha
for(uint i = get_local_id(0);
i < dockpars_num_of_genes;
i+= NUM_OF_THREADS_PER_BLOCK) {
alpha = native_divide(alpha, 10);
alpha = native_divide(alpha, 5*failure_cnt/*10*/);
#if defined (DEBUG_MINIMIZER)
//printf("(%-3u) %-15.15f\n", i, alpha);
#endif
}
} // End of if(exit==false)
barrier(CLK_LOCAL_MEM_FENCE);
// Updating number of stepest-descent iterations
if (get_local_id(0) == 0) {
local_nIter = local_nIter + 1;
iteration_cnt = iteration_cnt + 1;
#if defined (DEBUG_MINIMIZER)
//printf("# grad-mini cycles: %-3u, energy: %f\n", local_nIter, local_energy);
printf("# mini-iters: %-3u, # ener-evals: %-3u, # failures: %-3u, energy: %f\n", iteration_cnt, evaluation_cnt, failure_cnt, energy);
#endif
#if defined (DEBUG_ENERGY_KERNEL5)
......@@ -479,17 +501,17 @@ gradient_minimizer(
#endif
}
} while ((local_nIter < gradMin_maxiter) && (failure_cnt < 5) && (exit == false));
} while ((iteration_cnt < gradMin_maxiters) && (failure_cnt < gradMin_maxfails) /*&& (exit == false)*/);
// -----------------------------------------------------------------------------
// 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_energies_next[run_id*dockpars_pop_size+entity_id] = local_energy;
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, local_energy);
printf("-------> End of grad-min cycle, num of evals: %u, final energy: %.5f\n", evaluation_cnt, energy);
#endif
}
......@@ -498,15 +520,14 @@ gradient_minimizer(
gene_counter < dockpars_num_of_genes;
gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
if (gene_counter >= 6) {
map_angle(&(local_genotype[gene_counter]));
map_angle(&(genotype[gene_counter]));
}
}
// Updating old offspring in population
barrier(CLK_LOCAL_MEM_FENCE);
async_work_group_copy(dockpars_conformations_next+(run_id*dockpars_pop_size+entity_id)*GENOTYPE_LENGTH_IN_GLOBMEM,
local_genotype,
genotype,
dockpars_num_of_genes, 0);
}
host/inc/performdocking.h
View file @ e6dc04f8
......@@ -58,6 +58,7 @@ 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;
float alpha;
float conformation_min_perturbation [ACTUAL_GENOTYPE_LENGTH];
} Gradientparameters;
......
host/src/performdocking.cpp
View file @ e6dc04f8
......@@ -408,7 +408,8 @@ 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 = 40; // Same as Solis-Wetts local search
gradientpars.max_num_of_iters = 100;
gradientpars.max_num_of_consec_fails = gradientpars.max_num_of_iters / 5;
gradientpars.alpha = 0.000001f; //0.001f; // TODO: find out why 0.001f, 0.0001f (100 runs, 500 popsize) throws segmentation fault
// Set minimum values for input conformation (translation genes as x, y, z)
......@@ -647,8 +648,9 @@ filled with clock() */
setKernelArg(kernel5,36,sizeof(mem_num_rotating_atoms_per_rotbond_const),&mem_num_rotating_atoms_per_rotbond_const);
// Specific gradient-minimizer args
setKernelArg(kernel5,37,sizeof(gradientpars.max_num_of_iters), &gradientpars.max_num_of_iters);
setKernelArg(kernel5,38,sizeof(gradientpars.alpha), &gradientpars.alpha);
setKernelArg(kernel5,39,sizeof(mem_gradpars_conformation_min_perturbation), &mem_gradpars_conformation_min_perturbation);
setKernelArg(kernel5,38,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);
kernel5_gxsize = blocksPerGridForEachGradMinimizerEntity * threadsPerBlock;
kernel5_lxsize = threadsPerBlock;
......
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