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Commit 6a2748bf authored by Leonardo Solis's avatar Leonardo Solis
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gradient kernel ready to debug

parent 43aa19f1
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Makefile
View file @ 6a2748bf
......@@ -202,8 +202,8 @@ odock: check-env-all stringify $(SRC)
# 3tmn: for testing gradients of torsion genes (1 torsion)
PDB := 7cpa
NRUN := 1
POPSIZE := 1
NRUN := 100
POPSIZE := 500
TESTNAME:= test
test: odock
......
common/defines.h
View file @ 6a2748bf
......@@ -55,8 +55,9 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#define LS_CONT_FACTOR 0.5f
// Improvements over Pechan's implementation
#define NATIVE_PRECISION
#define IMPROVE_GRID
//#define NATIVE_PRECISION
#define MAPPED_COPY
#define GRADIENT_ENABLED
#endif /* DEFINES_H_ */
device/auxiliary_genetic.cl
View file @ 6a2748bf
......@@ -70,13 +70,7 @@ float gpu_randf(
#if defined (REPRO)
state = 0.55f; //0.55f;
#else
#if defined (NATIVE_PRECISION)
state = native_divide(gpu_rand(prng_states),MAX_UINT)*0.999999f;
#elif defined (HALF_PRECISION)
state = half_divide(gpu_rand(prng_states),MAX_UINT)*0.999999f;
#else // Full precision
state = (((float) gpu_rand(prng_states))/MAX_UINT)*0.999999f;
#endif
#endif
return state;
......
device/auxiliary_gradient.cl
View file @ 6a2748bf
#define DEBUG_GRADDESC_ENABLED
//#define DEBUG_GRADDESC_ENABLED
// Implementation of auxiliary functions
// for the gradient-based minimizer
void is_gradDescent_enabled(
__local bool* is_perturb_gt_gene_min,
__local float* local_gNorm,
float gradMin_tol,
__local bool* is_genotype_valid,
__local uint* local_nIter,
uint gradMin_maxiter,
__local float* local_perturbation,
__local float* local_genotype,
__constant float* gradMin_conformation_min_perturbation,
__local float* local_candidate_genotype,
uint gradMin_numElements,
__local bool* is_gradDescentEn
)
{
bool is_gNorm_gt_gMin;
bool is_nIter_lt_maxIter;
bool is_perturb_gt_genotype;
bool is_valid;
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_valid = 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 ((local_candidate_genotype[get_local_id(0)] < 0.0f) && (local_candidate_genotype[get_local_id(0)] > 1.0f)) {
local_candidate_genotype[get_local_id(0)] = 0.0f;
}
}
*/
#if 0
// For every gene, let's determine
// if perturbation is greater than min conformation
// Using every of its genes, let's determine
// if candidate genotype is valid
for(uint i = get_local_id(0);
i < gradMin_numElements;
i+= NUM_OF_THREADS_PER_BLOCK) {
is_perturb_gt_gene_min[i] = (local_perturbation[i] >= gradMin_conformation_min_perturbation[i]);
is_genotype_valid[i] = !isnan(local_candidate_genotype[i]) && !isinf(local_candidate_genotype[i]);
}
#endif
barrier(CLK_LOCAL_MEM_FENCE);
if (get_local_id(0) == 0) {
#if 0
// Reduce all is_perturb_gt_gene_min's
// Reduce all "valid" values of genes
// 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_valid = is_valid && is_genotype_valid[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");
//printf("is_genotype_valid[%u]?: %s\n", i, (is_genotype_valid[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_nIter_lt_maxIter;
// Reduce all previous partial evaluations (nIter, valid) into a final one
*is_gradDescentEn = is_nIter_lt_maxIter && is_valid;
#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("Continue gradient iteration?: %s\n", (*is_gradDescentEn == 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_valid?: %s\n", (is_valid == true)?"yes":"no");
printf("Continue grad-mini?: %s\n", (*is_gradDescentEn == true)?"yes":"no");
#endif
#endif
}
}
void gradient_norm(
__local float* vector1,
uint inputSize,
__local float* init,
__local float* inner_product
) {
float temp = 0.0f;
// Element-wise multiplication
for(uint i = get_local_id(0);
i < inputSize;
i+= NUM_OF_THREADS_PER_BLOCK) {
init[i] = vector1[i] * vector1[i];
}
barrier(CLK_LOCAL_MEM_FENCE);
// Accumulating dot product,
// and then getting the norm
if(get_local_id(0) == 0) {
for(uint i = 0;
i < inputSize;
i ++) {
temp += init[i];
}
*inner_product = native_sqrt(temp);
}
}
device/calcenergy.cl
View file @ 6a2748bf
This diff is collapsed.
device/calcgradient.cl
View file @ 6a2748bf
......@@ -38,7 +38,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//#define DEBUG_GRAD_TRANSLATION_GENES
//#define DEBUG_GRAD_ROTATION_GENES
//#define DEBUG_GRAD_TORSION_GENES
//#define DEBUG_GRAD
//#define DEBUG_ENERGY_KERNEL5
void gpu_calc_gradient(
int dockpars_rotbondlist_length,
......@@ -53,11 +53,13 @@ void gpu_calc_gradient(
float dockpars_coeff_elec,
float dockpars_qasp,
float 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.
__local float* genotype,
__local float* energy,
__local int* run_id,
__local float* calc_coords_x,
......@@ -212,8 +214,6 @@ void gpu_calc_gradient(
atom_to_rotate[2] -= rotation_movingvec[2];
// Transforming torsion angles into quaternions
// FIXME: add precision choices with preprocessor directives:
// NATIVE_PRECISION, HALF_PRECISION, Full precision
rotation_angle = native_divide(rotation_angle, 2.0f);
float sin_angle = native_sin(rotation_angle);
quatrot_left_q = native_cos(rotation_angle);
......@@ -331,6 +331,17 @@ void gpu_calc_gradient(
//printf("%-15s %-5u %-10.8f %-10.8f %-10.8f\n", "dx,dy,dz", atom_id, dx, dy, dz);
// Calculating interpolation weights
float weights[2][2][2];
weights [0][0][0] = (1-dx)*(1-dy)*(1-dz);
weights [1][0][0] = dx*(1-dy)*(1-dz);
weights [0][1][0] = (1-dx)*dy*(1-dz);
weights [1][1][0] = dx*dy*(1-dz);
weights [0][0][1] = (1-dx)*(1-dy)*dz;
weights [1][0][1] = dx*(1-dy)*dz;
weights [0][1][1] = (1-dx)*dy*dz;
weights [1][1][1] = dx*dy*dz;
// Capturing affinity values
uint ylow_times_g1 = y_low*g1;
uint yhigh_times_g1 = y_high*g1;
......@@ -401,16 +412,6 @@ void gpu_calc_gradient(
// -------------------------------------------------------------------
// Vector in x-direction
/*
x10 = grid[int(vertices[1])] - grid[int(vertices[0])] # z = 0
x52 = grid[int(vertices[5])] - grid[int(vertices[2])] # z = 0
x43 = grid[int(vertices[4])] - grid[int(vertices[3])] # z = 1
x76 = grid[int(vertices[7])] - grid[int(vertices[6])] # z = 1
vx_z0 = (1-yd) * x10 + yd * x52 # z = 0
vx_z1 = (1-yd) * x43 + yd * x76 # z = 1
gradient[0] = (1-zd) * vx_z0 + zd * vx_z1
*/
x10 = cube [1][0][0] - cube [0][0][0]; // z = 0
x52 = cube [1][1][0] - cube [0][1][0]; // z = 0
x43 = cube [1][0][1] - cube [0][0][1]; // z = 1
......@@ -420,16 +421,6 @@ void gpu_calc_gradient(
gradient_inter_x[atom_id] += (1 - dz) * vx_z0 + dz * vx_z1;
// Vector in y-direction
/*
y20 = grid[int(vertices[2])] - grid[int(vertices[0])] # z = 0
y51 = grid[int(vertices[5])] - grid[int(vertices[1])] # z = 0
y63 = grid[int(vertices[6])] - grid[int(vertices[3])] # z = 1
y74 = grid[int(vertices[7])] - grid[int(vertices[4])] # z = 1
vy_z0 = (1-xd) * y20 + xd * y51 # z = 0
y_z1 = (1-xd) * y63 + xd * y74 # z = 1
gradient[1] = (1-zd) * vy_z0 + zd * vy_z1
*/
y20 = cube[0][1][0] - cube [0][0][0]; // z = 0
y51 = cube[1][1][0] - cube [1][0][0]; // z = 0
y63 = cube[0][1][1] - cube [0][0][1]; // z = 1
......@@ -439,16 +430,6 @@ void gpu_calc_gradient(
gradient_inter_y[atom_id] += (1 - dz) * vy_z0 + dz * vy_z1;
// Vectors in z-direction
/*
z30 = grid[int(vertices[3])] - grid[int(vertices[0])] # y = 0
z41 = grid[int(vertices[4])] - grid[int(vertices[1])] # y = 0
z62 = grid[int(vertices[6])] - grid[int(vertices[2])] # y = 1
z75 = grid[int(vertices[7])] - grid[int(vertices[5])] # y = 1
vz_y0 = (1-xd) * z30 + xd * z41 # y = 0
vz_y1 = (1-xd) * z62 + xd * z75 # y = 1
gradient[2] = (1-yd) * vz_y0 + yd * vz_y1
*/
z30 = cube [0][0][1] - cube [0][0][0]; // y = 0
z41 = cube [1][0][1] - cube [1][0][0]; // y = 0
z62 = cube [0][1][1] - cube [0][1][0]; // y = 1
......@@ -605,7 +586,6 @@ void gpu_calc_gradient(
gradient_per_intracontributor[contributor_counter] += native_divide (10*VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],
native_powr(atomic_distance, 11)
);
}
else { //van der Waals
gradient_per_intracontributor[contributor_counter] += native_divide (6*VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],
......@@ -651,16 +631,20 @@ void gpu_calc_gradient(
float subz = (calc_coords_z[atom2_id] - calc_coords_z[atom1_id]);
float dist = native_sqrt(subx*subx + suby*suby + subz*subz);
float subx_div_dist = native_divide(subx, dist);
float suby_div_dist = native_divide(suby, dist);
float subz_div_dist = native_divide(subz, dist);
// Calculating gradients in xyz components.
// Gradients for both atoms in a single contributor pair
// have the same magnitude, but opposite directions
gradient_intra_x[atom1_id] -= gradient_per_intracontributor[contributor_counter] * subx / dist;
gradient_intra_y[atom1_id] -= gradient_per_intracontributor[contributor_counter] * suby / dist;
gradient_intra_z[atom1_id] -= gradient_per_intracontributor[contributor_counter] * subz / dist;
gradient_intra_x[atom1_id] -= gradient_per_intracontributor[contributor_counter] * subx_div_dist;
gradient_intra_y[atom1_id] -= gradient_per_intracontributor[contributor_counter] * suby_div_dist;
gradient_intra_z[atom1_id] -= gradient_per_intracontributor[contributor_counter] * subz_div_dist;
gradient_intra_x[atom2_id] += gradient_per_intracontributor[contributor_counter] * subx / dist;
gradient_intra_y[atom2_id] += gradient_per_intracontributor[contributor_counter] * suby / dist;
gradient_intra_z[atom2_id] += gradient_per_intracontributor[contributor_counter] * subz / dist;
gradient_intra_x[atom2_id] += gradient_per_intracontributor[contributor_counter] * subx_div_dist;
gradient_intra_y[atom2_id] += gradient_per_intracontributor[contributor_counter] * suby_div_dist;
gradient_intra_z[atom2_id] += gradient_per_intracontributor[contributor_counter] * subz_div_dist;
//printf("%-20s %-10u %-5u %-5u %-10.8f\n", "grad_intracontrib", contributor_counter, atom1_id, atom2_id, gradient_per_intracontributor[contributor_counter]);
}
......@@ -679,9 +663,9 @@ void gpu_calc_gradient(
// Intramolecular gradients were already in Angstrom,
// so no scaling for them is required.
gradient_inter_x[atom_cnt] = gradient_inter_x[atom_cnt] / dockpars_grid_spacing;
gradient_inter_y[atom_cnt] = gradient_inter_y[atom_cnt] / dockpars_grid_spacing;
gradient_inter_z[atom_cnt] = gradient_inter_z[atom_cnt] / dockpars_grid_spacing;
gradient_inter_x[atom_cnt] = native_divide(gradient_inter_x[atom_cnt], dockpars_grid_spacing);
gradient_inter_y[atom_cnt] = native_divide(gradient_inter_y[atom_cnt], dockpars_grid_spacing);
gradient_inter_z[atom_cnt] = native_divide(gradient_inter_z[atom_cnt], dockpars_grid_spacing);
gradient_x[atom_cnt] = gradient_inter_x[atom_cnt] + gradient_intra_x[atom_cnt];
gradient_y[atom_cnt] = gradient_inter_y[atom_cnt] + gradient_intra_y[atom_cnt];
......@@ -722,7 +706,6 @@ void gpu_calc_gradient(
printf("gradient_y:%f\n", gradient_genotype [1]);
printf("gradient_z:%f\n", gradient_genotype [2]);
#endif
}
// ------------------------------------------
......@@ -748,13 +731,13 @@ void gpu_calc_gradient(
printf("%-20s %-10.5f %-10.5f %-10.5f\n", "initial torque: ", torque_rot.x, torque_rot.y, torque_rot.z);
#endif
// Center of rotation
// Declaring a variable to hold the center of rotation
// In getparameters.cpp, it indicates
// translation genes are in grid spacing (instead of Angstroms)
float3 about;
about.x = /*30*/genotype[0];
about.y = /*30*/genotype[1];
about.z = /*30*/genotype[2];
about.x = genotype[0];
about.y = genotype[1];
about.z = genotype[2];
// Temporal variable to calculate translation differences.
// They are converted back to Angstroms here
......@@ -1004,9 +987,9 @@ void gpu_calc_gradient(
// Assignment of gene-based gradient
gradient_genotype[rotbond_id+6] = torque_on_axis * (M_PI / 180.0f);
//#if defined (DEBUG_GRAD_TORSION_GENES)
//printf("gradient_torsion [%u] :%f\n", rotbond_id+6, gradient_genotype [rotbond_id+6]);
//#endif
#if defined (DEBUG_GRAD_TORSION_GENES)
printf("gradient_torsion [%u] :%f\n", rotbond_id+6, gradient_genotype [rotbond_id+6]);
#endif
} // End of iterations over rotatable bonds
}
......
device/kernel1.cl
View file @ 6a2748bf
......@@ -20,8 +20,6 @@ along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))
gpu_calc_initpop(
char dockpars_num_of_atoms,
......@@ -67,9 +65,9 @@ gpu_calc_initpop(
__local float calc_coords_y[MAX_NUM_OF_ATOMS];
__local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
#if defined (DEBUG_ENERGY)
__local float partial_interE [NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE [NUM_OF_THREADS_PER_BLOCK];
#if defined (DEBUG_ENERGY_KERNEL1)
__local float partial_interE[NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE[NUM_OF_THREADS_PER_BLOCK];
#endif
// Copying genotype from global memory
......@@ -109,7 +107,7 @@ gpu_calc_initpop(
calc_coords_y,
calc_coords_z,
partial_energies,
#if defined (DEBUG_ENERGY)
#if defined (DEBUG_ENERGY_KERNEL1)
partial_interE,
partial_intraE,
#endif
......@@ -134,5 +132,9 @@ gpu_calc_initpop(
if (get_local_id(0) == 0) {
dockpars_energies_current[get_group_id(0)] = energy;
dockpars_evals_of_new_entities[get_group_id(0)] = 1;
#if defined (DEBUG_ENERGY_KERNEL1)
printf("%-18s [%-5s]---{%-5s} [%-10.8f]---{%-10.8f}\n", "-ENERGY-KERNEL1-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
#endif
}
}
device/kernel3.cl
View file @ 6a2748bf
......@@ -97,7 +97,7 @@ perform_LS(
__local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
#if defined (DEBUG_ENERGY)
#if defined (DEBUG_ENERGY_KERNEL3)
__local float partial_interE [NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE [NUM_OF_THREADS_PER_BLOCK];
#endif
......@@ -209,7 +209,7 @@ perform_LS(
calc_coords_y,
calc_coords_z,
partial_energies,
#if defined (DEBUG_ENERGY)
#if defined (DEBUG_ENERGY_KERNEL3)
partial_interE,
partial_intraE,
#endif
......@@ -233,6 +233,10 @@ perform_LS(
if (get_local_id(0) == 0) {
evaluation_cnt++;
#if defined (DEBUG_ENERGY_KERNEL3)
printf("%-18s [%-5s]---{%-5s} [%-10.8f]---{%-10.8f}\n", "-ENERGY-KERNEL3-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
#endif
}
barrier(CLK_LOCAL_MEM_FENCE);
......@@ -307,7 +311,7 @@ perform_LS(
calc_coords_y,
calc_coords_z,
partial_energies,
#if defined (DEBUG_ENERGY)
#if defined (DEBUG_ENERGY_KERNEL3)
partial_interE,
partial_intraE,
#endif
......@@ -331,6 +335,10 @@ perform_LS(
if (get_local_id(0) == 0) {
evaluation_cnt++;
#if defined (DEBUG_ENERGY_KERNEL3)
printf("%-18s [%-5s]---{%-5s} [%-10.8f]---{%-10.8f}\n", "-ENERGY-KERNEL3-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
#endif
}
barrier(CLK_LOCAL_MEM_FENCE);
......
device/kernel4.cl
View file @ 6a2748bf
......@@ -89,7 +89,7 @@ gpu_gen_and_eval_newpops(
__local float calc_coords_y[MAX_NUM_OF_ATOMS];
__local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
#if defined (DEBUG_ENERGY)
#if defined (DEBUG_ENERGY_KERNEL4)
__local float partial_interE [NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE [NUM_OF_THREADS_PER_BLOCK];
#endif
......@@ -259,7 +259,7 @@ gpu_gen_and_eval_newpops(
calc_coords_y,
calc_coords_z,
partial_energies,
#if defined (DEBUG_ENERGY)
#if defined (DEBUG_ENERGY_KERNEL4)
partial_interE,
partial_intraE,
#endif
......@@ -284,6 +284,10 @@ gpu_gen_and_eval_newpops(
if (get_local_id(0) == 0) {
dockpars_evals_of_new_entities[get_group_id(0)] = 1;
dockpars_energies_next[get_group_id(0)] = energy;
#if defined (DEBUG_ENERGY_KERNEL4)
printf("%-18s [%-5s]---{%-5s} [%-10.8f]---{%-10.8f}\n", "-ENERGY-KERNEL4-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
#endif
}
// Copying new offspring to next generation
......
device/kernel_gradient.cl
View file @ 6a2748bf
This diff is collapsed.
host/inc/performdocking.h
View file @ 6a2748bf
......@@ -57,10 +57,8 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
// This should be ultimately configurable by the user as program exec. flags.
typedef struct {
float tolerance;
unsigned int max_num_of_iters;
float alpha;
float h;
float conformation_min_perturbation [ACTUAL_GENOTYPE_LENGTH];
} Gradientparameters;
......
host/src/performdocking.cpp
View file @ 6a2748bf
......@@ -408,10 +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.tolerance = 1.e-6;
gradientpars.max_num_of_iters = 4; // Same as Solis-Wetts local search
gradientpars.max_num_of_iters = 40; // 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++) {
......@@ -440,8 +438,10 @@ filled with clock() */
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();
......@@ -558,6 +558,8 @@ filled with clock() */
#endif
// End of Kernel4
#if !defined (GRADIENT_ENABLED)
// Kernel3
setKernelArg(kernel3,0,sizeof(dockpars.num_of_atoms), &dockpars.num_of_atoms);
setKernelArg(kernel3,1,sizeof(dockpars.num_of_atypes), &dockpars.num_of_atypes);
......@@ -600,12 +602,11 @@ filled with clock() */
setKernelArg(kernel3,38,sizeof(mem_ref_orientation_quats_const), &mem_ref_orientation_quats_const);
kernel3_gxsize = blocksPerGridForEachLSEntity * threadsPerBlock;
kernel3_lxsize = threadsPerBlock;
#ifdef DOCK_DEBUG
printf("%-25s %10s %8u %10s %4u\n", "K_LOCAL_SEARCH: ", "gSize: ", kernel3_gxsize, "lSize: ", kernel3_lxsize); fflush(stdout);
#endif
#ifdef DOCK_DEBUG
printf("%-25s %10s %8u %10s %4u\n", "K_LOCAL_SEARCH: ", "gSize: ", kernel3_gxsize, "lSize: ", kernel3_lxsize); fflush(stdout);
#endif
// End of Kernel3
#else
// Kernel5
setKernelArg(kernel5,0, sizeof(dockpars.num_of_atoms), &dockpars.num_of_atoms);
setKernelArg(kernel5,1, sizeof(dockpars.num_of_atypes), &dockpars.num_of_atypes);
......@@ -620,43 +621,42 @@ filled with clock() */
setKernelArg(kernel5,10,sizeof(dockpars.coeff_desolv), &dockpars.coeff_desolv);
setKernelArg(kernel5,11,sizeof(mem_dockpars_conformations_next), &mem_dockpars_conformations_next);
setKernelArg(kernel5,12,sizeof(mem_dockpars_energies_next), &mem_dockpars_energies_next);
setKernelArg(kernel5,13,sizeof(mem_dockpars_prng_states), &mem_dockpars_prng_states);
setKernelArg(kernel5,14,sizeof(dockpars.pop_size), &dockpars.pop_size);
setKernelArg(kernel5,15,sizeof(dockpars.num_of_genes), &dockpars.num_of_genes);
setKernelArg(kernel5,16,sizeof(dockpars.lsearch_rate), &dockpars.lsearch_rate);
setKernelArg(kernel5,17,sizeof(dockpars.num_of_lsentities), &dockpars.num_of_lsentities);
setKernelArg(kernel5,18,sizeof(dockpars.qasp), &dockpars.qasp);
setKernelArg(kernel5,19,sizeof(mem_atom_charges_const), &mem_atom_charges_const);
setKernelArg(kernel5,20,sizeof(mem_atom_types_const), &mem_atom_types_const);
setKernelArg(kernel5,21,sizeof(mem_intraE_contributors_const), &mem_intraE_contributors_const);
setKernelArg(kernel5,22,sizeof(mem_VWpars_AC_const), &mem_VWpars_AC_const);
setKernelArg(kernel5,23,sizeof(mem_VWpars_BD_const), &mem_VWpars_BD_const);
setKernelArg(kernel5,24,sizeof(mem_dspars_S_const), &mem_dspars_S_const);
setKernelArg(kernel5,25,sizeof(mem_dspars_V_const), &mem_dspars_V_const);
setKernelArg(kernel5,26,sizeof(mem_rotlist_const), &mem_rotlist_const);
setKernelArg(kernel5,27,sizeof(mem_ref_coords_x_const), &mem_ref_coords_x_const);
setKernelArg(kernel5,28,sizeof(mem_ref_coords_y_const), &mem_ref_coords_y_const);
setKernelArg(kernel5,29,sizeof(mem_ref_coords_z_const), &mem_ref_coords_z_const);
setKernelArg(kernel5,30,sizeof(mem_rotbonds_moving_vectors_const), &mem_rotbonds_moving_vectors_const);
setKernelArg(kernel5,31,sizeof(mem_rotbonds_unit_vectors_const), &mem_rotbonds_unit_vectors_const);
setKernelArg(kernel5,32,sizeof(mem_ref_orientation_quats_const), &mem_ref_orientation_quats_const);
setKernelArg(kernel5,33,sizeof(mem_rotbonds_const), &mem_rotbonds_const);
setKernelArg(kernel5,34,sizeof(mem_rotbonds_atoms_const), &mem_rotbonds_atoms_const);
setKernelArg(kernel5,35,sizeof(mem_num_rotating_atoms_per_rotbond_const),&mem_num_rotating_atoms_per_rotbond_const);
setKernelArg(kernel5,13,sizeof(mem_dockpars_evals_of_new_entities), &mem_dockpars_evals_of_new_entities);
setKernelArg(kernel5,14,sizeof(mem_dockpars_prng_states), &mem_dockpars_prng_states);
setKernelArg(kernel5,15,sizeof(dockpars.pop_size), &dockpars.pop_size);
setKernelArg(kernel5,16,sizeof(dockpars.num_of_genes), &dockpars.num_of_genes);
setKernelArg(kernel5,17,sizeof(dockpars.lsearch_rate), &dockpars.lsearch_rate);
setKernelArg(kernel5,18,sizeof(dockpars.num_of_lsentities), &dockpars.num_of_lsentities);
setKernelArg(kernel5,19,sizeof(dockpars.qasp), &dockpars.qasp);
setKernelArg(kernel5,20,sizeof(mem_atom_charges_const), &mem_atom_charges_const);
setKernelArg(kernel5,21,sizeof(mem_atom_types_const), &mem_atom_types_const);
setKernelArg(kernel5,22,sizeof(mem_intraE_contributors_const), &mem_intraE_contributors_const);
setKernelArg(kernel5,23,sizeof(mem_VWpars_AC_const), &mem_VWpars_AC_const);
setKernelArg(kernel5,24,sizeof(mem_VWpars_BD_const), &mem_VWpars_BD_const);
setKernelArg(kernel5,25,sizeof(mem_dspars_S_const), &mem_dspars_S_const);
setKernelArg(kernel5,26,sizeof(mem_dspars_V_const), &mem_dspars_V_const);
setKernelArg(kernel5,27,sizeof(mem_rotlist_const), &mem_rotlist_const);
setKernelArg(kernel5,28,sizeof(mem_ref_coords_x_const), &mem_ref_coords_x_const);
setKernelArg(kernel5,29,sizeof(mem_ref_coords_y_const), &mem_ref_coords_y_const);
setKernelArg(kernel5,30,sizeof(mem_ref_coords_z_const), &mem_ref_coords_z_const);
setKernelArg(kernel5,31,sizeof(mem_rotbonds_moving_vectors_const), &mem_rotbonds_moving_vectors_const);
setKernelArg(kernel5,32,sizeof(mem_rotbonds_unit_vectors_const), &mem_rotbonds_unit_vectors_const);
setKernelArg(kernel5,33,sizeof(mem_ref_orientation_quats_const), &mem_ref_orientation_quats_const);
setKernelArg(kernel5,34,sizeof(mem_rotbonds_const), &mem_rotbonds_const);
setKernelArg(kernel5,35,sizeof(mem_rotbonds_atoms_const), &mem_rotbonds_atoms_const);
setKernelArg(kernel5,36,sizeof(mem_num_rotating_atoms_per_rotbond_const),&mem_num_rotating_atoms_per_rotbond_const);
// Specific gradient-minimizer args
setKernelArg(kernel5,36,sizeof(gradientpars.tolerance), &gradientpars.tolerance);
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(gradientpars.h), &gradientpars.h);
setKernelArg(kernel5,40,sizeof(mem_gradpars_conformation_min_perturbation), &mem_gradpars_conformation_min_perturbation);
setKernelArg(kernel5,39,sizeof(mem_gradpars_conformation_min_perturbation), &mem_gradpars_conformation_min_perturbation);
kernel5_gxsize = blocksPerGridForEachGradMinimizerEntity * threadsPerBlock;
kernel5_lxsize = threadsPerBlock;