Skip to content
GitLab
Commit 43aa19f1 authored by Leonardo Solis's avatar Leonardo Solis
Browse files

hardcoded different alphas for gene-type

parent d6f2d704
Hide whitespace changes
Inline Side-by-side
Makefile
View file @ 43aa19f1
......@@ -203,7 +203,7 @@ odock: check-env-all stringify $(SRC)
PDB := 7cpa
NRUN := 1
POPSIZE := 10
POPSIZE := 1
TESTNAME:= test
test: odock
......
device/auxiliary_gradient.cl
View file @ 43aa19f1
#define DEBUG_GRADDESC_ENABLED
// Implementation of auxiliary functions
// for the gradient-based minimizer
......@@ -8,6 +10,7 @@ void is_gradDescent_enabled(
__local uint* local_nIter,
uint gradMin_maxiter,
__local float* local_perturbation,
__local float* local_genotype,
__constant float* gradMin_conformation_min_perturbation,
uint gradMin_numElements,
__local bool* is_gradDescentEn
......@@ -18,11 +21,23 @@ void is_gradDescent_enabled(
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;
}
// Verifying that Shoemake genes do not get out of valid range.
// If they do so, then set them to 0.0f
if (get_local_id(0) < 3){
if ((local_genotype[get_local_id(0)] < 0.0f) && (local_genotype[get_local_id(0)] > 1.0f)) {
local_genotype[get_local_id(0)] = 0.0f;
}
}
#if 0
// For every gene, let's determine
// if perturbation is greater than min conformation
for(uint i = get_local_id(0);
......@@ -30,41 +45,45 @@ void is_gradDescent_enabled(
i+= NUM_OF_THREADS_PER_BLOCK) {
is_perturb_gt_gene_min[i] = (local_perturbation[i] >= gradMin_conformation_min_perturbation[i]);
}
#endif
barrier(CLK_LOCAL_MEM_FENCE);
if (get_local_id(0) == 0) {
#if 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];
/*
#if defined (DEBUG_GRADDESC_ENABLED)
printf("is_perturb_gt_gene_min[%u]?: %s\n", i, (is_perturb_gt_gene_min[i] == true)?"yes":"no");
*/
#endif
}
#endif
// Reduce all three previous
// partial evaluations (gNorm, nIter, perturb) into a final one
//*is_gradDescentEn = 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;
/*
*is_gradDescentEn = is_nIter_lt_maxIter;
#if 1
#if defined (DEBUG_GRADDESC_ENABLED)
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("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");
}
*/
}
#endif
#endif
/*
barrier(CLK_LOCAL_MEM_FENCE);
return *is_gradDescentEn;
*/
}
}
void gradient_norm(
......
device/calcgradient.cl
View file @ 43aa19f1
......@@ -574,9 +574,8 @@ void gpu_calc_gradient(
// Getting atom IDs
uint atom1_id = intraE_contributors_const[3*contributor_counter];
uint atom2_id = intraE_contributors_const[3*contributor_counter+1];
///*
printf ("%-5u %-5u %-5u\n", contributor_counter, atom1_id, atom2_id);
//*/
//printf ("%-5u %-5u %-5u\n", contributor_counter, atom1_id, atom2_id);
// Calculating vector components of vector going
// from first atom's to second atom's coordinates
......
device/kernel_gradient.cl
View file @ 43aa19f1
......@@ -5,6 +5,10 @@
#define DEBUG_MINIMIZER
#define TRANGENE_ALPHA 1E-8
#define ROTAGENE_ALPHA 1E-15
#define TORSGENE_ALPHA 1E-3
// FIXME: original call of stepGPU
// stepGPU<<<iDivUp(M, BLOCK_SIZE), BLOCK_SIZE>>>
......@@ -209,6 +213,7 @@ gradient_minimizer(
// -----------------------------------------------------------------------------
// Perform gradient-descent iterations
#if 0
// 7cpa
float grid_center_x = 49.836;
float grid_center_y = 17.609;
......@@ -219,26 +224,25 @@ gradient_minimizer(
float shoemake_gene_u1 = 0.02;
float shoemake_gene_u2 = 0.23;
float shoemake_gene_u3 = 0.95;
#endif
/*
// 3tmn
float grid_center_x = 52.340;
float grid_center_y = 15.029;
float grid_center_z = -2.932;
float ligand_center_x = 52.22740741;
float ligand_center_y = 15.51751852;
float ligand_center_z = -2.40896296;
*/
#if 0
// 3tmn
float grid_center_x = 52.340;
float grid_center_y = 15.029;
float grid_center_z = -2.932;
float ligand_center_x = 52.22740741;
float ligand_center_y = 15.51751852;
float ligand_center_z = -2.40896296;
#endif
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]).
// However, for testing purposes,
// we start using translation values in real space (Angstrom): {31.79575, 93.743875, 47.699875}
// Rotation genes are exp5.96902604 / (2*math.pi)
resed in the Shoemake space: local_genotype [3|4|5]
// Rotation genes are expresed in the Shoemake space: local_genotype [3|4|5]
// xyz_gene_gridspace = gridcenter_gridspace + (input_gene_realspace - gridcenter_realspace)/gridsize
// 1ac8
......@@ -248,11 +252,10 @@ resed in the Shoemake space: local_genotype [3|4|5]
local_genotype[3] = 0.1f;
local_genotype[4] = 0.5f;
local_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;
......@@ -274,9 +277,7 @@ resed in the Shoemake space: local_genotype [3|4|5]
local_genotype[18] = 0.0f;
local_genotype[19] = 0.0f;
local_genotype[20] = 0.0f;
//*/
#endif
// Calculating gradient
// =============================================================
......@@ -342,20 +343,24 @@ resed in the Shoemake space: local_genotype [3|4|5]
barrier(CLK_LOCAL_MEM_FENCE);
#if defined (DEBUG_MINIMIZER)
if (get_local_id(0) == 0) {
for (uint i=0; i<dockpars_num_of_genes; i++) {
printf("AFTER- GRADIENT - local_gradient[%u]: %f\n", i, local_gradient[i]);
}
}
#endif
float alpha;
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];
//local_genotype_new[i] = local_genotype[i] - gradMin_alpha * local_gradient[i];
if (i<3) { alpha = TRANGENE_ALPHA; }
else if (i<6) { alpha = ROTAGENE_ALPHA; }
else { alpha = TORSGENE_ALPHA; }
local_genotype_new[i] = local_genotype[i] - alpha * local_gradient[i];
#if defined (DEBUG_MINIMIZER)
printf("(%u) %-15.15f %-10.10f %-10.10f %-10.10f\n", i, alpha, local_genotype[i], local_gradient[i], local_genotype_new[i]);
#endif
// Updating termination metrics
local_genotype_diff[i] = local_genotype_new[i] - local_genotype[i];
......@@ -370,8 +375,15 @@ resed in the Shoemake space: local_genotype [3|4|5]
// Updating number of stepest-descent iterations
if (get_local_id(0) == 0) {
local_nIter = local_nIter + 1;
#if defined (DEBUG_MINIMIZER)
printf("Number of grad-minimizer iterations: %u\n", local_nIter);
#endif
}
// Storing the norm of all gradients
gradient_norm(local_gradient, dockpars_num_of_genes, dotProduct, &local_gNorm);
......@@ -389,13 +401,6 @@ resed in the Shoemake space: local_genotype [3|4|5]
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);
}
//*/
is_gradDescent_enabled(
is_perturb_gt_gene_min,
&local_gNorm,
......@@ -403,6 +408,7 @@ resed in the Shoemake space: local_genotype [3|4|5]
&local_nIter,
gradMin_maxiter,
local_perturbation,
local_genotype,
gradMin_conformation_min_perturbation,
dockpars_num_of_genes,
&is_gradDescentEn
......@@ -411,7 +417,7 @@ resed in the Shoemake space: local_genotype [3|4|5]
// -----------------------------------------------------------------------------
/*
#if 0
// 1ac8
local_genotype[0] = 30 + (31.79575 - 31.924) / 0.375;
local_genotype[1] = 30 + (93.743875 - 93.444) / 0.375;
......@@ -419,33 +425,32 @@ resed in the Shoemake space: local_genotype [3|4|5]
local_genotype[3] = 0.1f;
local_genotype[4] = 0.5f;
local_genotype[5] = 0.9f;
*/
#endif
///*
#if 0
// 7cpa
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;
//*/
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;
#endif
// Calculating energy
// =============================================================
......
host/src/getparameters.cpp
View file @ 43aa19f1
......@@ -785,13 +785,13 @@ void gen_initpop_and_reflig(Dockpars* mypars,
// These specific values for the rotation genes (in Shoemake space)
// correspond to a quaternion for NO rotation.
ref_ori_angles[3*i] = 0.0f;
ref_ori_angles[3*i+1] = 0.25f;
ref_ori_angles[3*i+2] = 0.0f;
//ref_ori_angles[3*i] = 0.0f;
//ref_ori_angles[3*i+1] = 0.25f;
//ref_ori_angles[3*i+2] = 0.0f;
//#else
// ref_ori_angles[3*i] = ((float) rand()/ (float) RAND_MAX); // u1
// ref_ori_angles[3*i+1] = ((float) rand()/ (float) RAND_MAX); // u2
// ref_ori_angles[3*i+2] = ((float) rand()/ (float) RAND_MAX); // u3
ref_ori_angles[3*i] = ((float) rand()/ (float) RAND_MAX); // u1
ref_ori_angles[3*i+1] = ((float) rand()/ (float) RAND_MAX); // u2
ref_ori_angles[3*i+2] = ((float) rand()/ (float) RAND_MAX); // u3
//printf("u1, u2, u3: %10f %10f %10f \n", ref_ori_angles[3*i], ref_ori_angles[3*i+1], ref_ori_angles[3*i+2]);
//#endif
}
......
host/src/performdocking.cpp
View file @ 43aa19f1
......@@ -409,23 +409,23 @@ filled with clock() */
// This should be ultimately configurable by the user as program exec. flags.
Gradientparameters gradientpars;
gradientpars.tolerance = 1.e-6;
gradientpars.max_num_of_iters = 300; // Same as Solis-Wetts local search
gradientpars.alpha = 0.00001f; //0.001f; // TODO: find out why 0.001f, 0.0001f (100 runs, 500 popsize) throws segmentation fault
gradientpars.max_num_of_iters = 4; // Same as Solis-Wetts local search
gradientpars.alpha = 0.000001f; //0.001f; // TODO: find out why 0.001f, 0.0001f (100 runs, 500 popsize) throws segmentation fault
gradientpars.h = 0.0001f;
// Set minimum values for input conformation (translation genes as x, y, z)
for (unsigned int gene_cnt=0; gene_cnt<3; gene_cnt++) {
gradientpars.conformation_min_perturbation[0] = 1e-5; // FIXME: set right min values
gradientpars.conformation_min_perturbation[0] = 1e-5; // FIXME: set right min values max .1/.375
}
// Set minimum values for input conformation (rotation genes as Shoemake genes)
for (unsigned int gene_cnt=3; gene_cnt<6; gene_cnt++) {
gradientpars.conformation_min_perturbation[0] = 0.01f;
gradientpars.conformation_min_perturbation[0] = 0.0005f; //max 0.01
}
// Set minimum values for input conformations (torsion genes as angles)
for (unsigned int gene_cnt=6; gene_cnt<(dockpars.num_of_genes - 6); gene_cnt++) {
gradientpars.conformation_min_perturbation[0] = 5.0f; // FIXME: set right min values
gradientpars.conformation_min_perturbation[0] = 0.1f; // FIXME: set right min values max 1.0
}
cl_mem mem_gradpars_conformation_min_perturbation;
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment