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Commit a9ca2fd8 authored by Leonardo Solis's avatar Leonardo Solis
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added kernel_gradients in the ocl string

parent 071eec04
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Makefile
View file @ a9ca2fd8
......@@ -50,7 +50,8 @@ K1_NAME="gpu_calc_initpop"
K2_NAME="gpu_sum_evals"
K3_NAME="perform_LS"
K4_NAME="gpu_gen_and_eval_newpops"
K_NAMES=-DK1=$(K1_NAME) -DK2=$(K2_NAME) -DK3=$(K3_NAME) -DK4=$(K4_NAME)
K5_NAME="gradient_minimizer"
K_NAMES=-DK1=$(K1_NAME) -DK2=$(K2_NAME) -DK3=$(K3_NAME) -DK4=$(K4_NAME) -DK5=$(K5_NAME)
# Kernel flags
KFLAGS=-DKRNL_SOURCE=$(KRNL_DIR)/$(KRNL_MAIN) -DKRNL_DIRECTORY=$(KRNL_DIR) -DKCMN_DIRECTORY=$(KCMN_DIR) $(K_NAMES)
......
device/auxiliary_gradient.cl
View file @ a9ca2fd8
......@@ -6,19 +6,20 @@ bool is_gradDescent_enabled(__local float* a_gNorm,
unsigned int gradMin_maxiter,
__local float* a_perturbation,
__constant float* gradMin_conformation_min_perturbation,
__local bool* is_gradDescentEn)
__local bool* is_gradDescentEn,
uint gradMin_numElements)
{
bool is_gNorm_gt_gMin = (a_gNorm >= gradMin_tol);
bool is_nIter_lt_maxIter = (a_niter <= gradMin_maxiter);
bool is_gNorm_gt_gMin = (a_gNorm[0] >= gradMin_tol);
bool is_nIter_lt_maxIter = (a_nIter[0] <= gradMin_maxiter);
bool is_perturb_gt_gene_min [ACTUAL_GENOTYPE_LENGTH];
bool is perturb_gt_genotype = true;
bool is_perturb_gt_genotype = true;
// For every gene, let's determine
// if perturbation is greater than min conformation
for(unsigned int i=get_local_id(0);
i<dockpars_num_of_genes;
i+=NUM_OF_THREADS_PER_BLOCK) {
for(uint i=get_local_id(0);
i<gradMin_numElements;
i+=NUM_OF_THREADS_PER_BLOCK) {
is_perturb_gt_gene_min[i] = (a_perturbation[i] >= gradMin_conformation_min_perturbation[i]);
}
......@@ -26,9 +27,9 @@ bool is_gradDescent_enabled(__local float* a_gNorm,
// Reduce all is_perturb_gt_gene_min's
// into their corresponding genotype
for(unsigned int i=get_local_id(0);
i<dockpars_num_of_genes;
i+=NUM_OF_THREADS_PER_BLOCK) {
for(uint i=get_local_id(0);
i<gradMin_numElements;
i+=NUM_OF_THREADS_PER_BLOCK) {
is_perturb_gt_genotype = is_perturb_gt_genotype && is_perturb_gt_gene_min[i];
}
......@@ -114,7 +115,9 @@ void stepGPU (// Args for minimization
__local bool* is_enabled_gradient_calc,
__local float* gradient_inter_x,
__local float* gradient_inter_y,
__local float* gradient_inter_z
__local float* gradient_inter_z,
__local float* gradient_genotype
)
{
// Calculate gradient
......@@ -133,8 +136,8 @@ void stepGPU (// Args for minimization
dockpars_qasp,
dockpars_coeff_desolv,
genotype,
&energy,
&run_id,
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,
......@@ -166,10 +169,12 @@ void stepGPU (// Args for minimization
// Derived from autodockdev/maps.py
// -------------------------------------------------------------------
,
&is_enabled_gradient_calc,
is_enabled_gradient_calc,
gradient_inter_x,
gradient_inter_y,
gradient_inter_z
gradient_inter_z,
gradient_genotype
);
// -------------------------------------------------------------------
// =============================================================
......
device/calcenergy.cl
View file @ a9ca2fd8
......@@ -896,6 +896,19 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
}
}
// -------------------------------------------------------------------
// Calculate gradients (forces) corresponding to (interE + intraE)
// Derived from autodockdev/motions.py/forces_to_delta()
......@@ -1104,3 +1117,5 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
#include "auxiliary_genetic.cl"
#include "kernel4.cl"
#include "kernel3.cl"
#include "auxiliary_gradient.cl"
#include "kernel_gradient.cl"
device/kernel_gradient.cl
View file @ a9ca2fd8
......@@ -33,12 +33,12 @@ gradient_minimizer( char dockpars_num_of_atoms,
__global float* restrict dockpars_conformations_next,
__global float* restrict dockpars_energies_next,
//__global int* restrict dockpars_evals_of_new_entities,
//__global unsigned int* restrict dockpars_prng_states,
__global unsigned int* restrict dockpars_prng_states,
#else
__global float* dockpars_conformations_next,
__global float* dockpars_energies_next,
//__global int* dockpars_evals_of_new_entities,
//__global unsigned int* dockpars_prng_states,
__global unsigned int* dockpars_prng_states,
#endif
int dockpars_pop_size,
......@@ -50,7 +50,7 @@ gradient_minimizer( char dockpars_num_of_atoms,
//float dockpars_base_dang_mul_sqrt3,
//unsigned int dockpars_cons_limit,
//unsigned int dockpars_max_num_of_iters,
//float dockpars_qasp,
float dockpars_qasp,
__constant float* atom_charges_const,
__constant char* atom_types_const,
......@@ -74,7 +74,7 @@ gradient_minimizer( char dockpars_num_of_atoms,
unsigned int gradMin_maxiter,
float gradMin_alpha,
float gradMin_h,
__constant float* gradMin_conformation_min_perturbation, // minimal values for gene perturbation, originally as the scalar "dxmin"
__constant float* gradMin_conformation_min_perturbation // minimal values for gene perturbation, originally as the scalar "dxmin"
//unsigned int gradMin_M, // dimensionality of the input data (=num_of_genes)
// __global float* restrict dockpars_conformations_next, // optimized genotype are to be store back here, originally as "d_xopt"
// __global float* restrict dockpars_energies_next, // minimized energy, originally as "fopt"
......@@ -106,7 +106,7 @@ gradient_minimizer( char dockpars_num_of_atoms,
// Since entity-ID=0 is the best one due to elitism, it should be subjected to random selection
if (entity_id == 0)
if (100.0f*gpu_randf(dockpar_prng_states) > dockpars_lsearch_rate)
if (100.0f*gpu_randf(dockpars_prng_states) > dockpars_lsearch_rate)
entity_id = dockpars_num_of_lsentities; // If entity-ID=0 is not selected according to LS-rate,
// then choose another entity
......@@ -188,11 +188,12 @@ gradient_minimizer( char dockpars_num_of_atoms,
// Perform gradient-descent iterations
while (is_gradDescent_enabled(&local_gNorm,
gradMin_tol,
&local_iter,
&local_nIter,
gradMin_maxiter,
local_perturbation,
gradMin_conformation_min_perturbation,
&is_gradDescentEn) == true) {
&is_gradDescentEn,
dockpars_num_of_genes) == true) {
stepGPU(// Args for minimization
local_genotype,
......
host/inc/stringify.h
View file @ a9ca2fd8
This diff is collapsed.
host/src/performdocking.cpp
View file @ a9ca2fd8
......@@ -32,6 +32,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#define KRNL2 STRINGIZE(K2)
#define KRNL3 STRINGIZE(K3)
#define KRNL4 STRINGIZE(K4)
#define KRNL5 STRINGIZE(K5)
#else
#define KRNL_FILE KRNL_SOURCE
......@@ -41,6 +42,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#define KRNL2 K2
#define KRNL3 K3
#define KRNL4 K4
#define KRNL5 K5
#endif
#define INC " -I " KRNL_FOLDER " -I " KRNL_COMMON
......
stringify_ocl_krnls.sh
View file @ a9ca2fd8
......@@ -18,6 +18,8 @@ IN_KERNEL2=$KERNEL_DIR/"kernel2.cl"
IN_KERNELa=$KERNEL_DIR/"auxiliary_genetic.cl"
IN_KERNEL3=$KERNEL_DIR/"kernel3.cl"
IN_KERNEL4=$KERNEL_DIR/"kernel4.cl"
IN_KERNELb=$KERNEL_DIR/"auxiliary_gradient.cl"
IN_KERNEL5=$KERNEL_DIR/"kernel_gradient.cl"
echo " "
echo "Stringified input kernel-files: "
......@@ -27,6 +29,8 @@ echo $IN_KERNEL2
echo $IN_KERNELa
echo $IN_KERNEL3
echo $IN_KERNEL4
echo $IN_KERNELb
echo $IN_KERNEL5
# output file
OUT=host/inc/stringify.h
......@@ -52,6 +56,8 @@ sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNEL2 >> $TMP
sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNELa >> $TMP
sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNEL3 >> $TMP
sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNEL4 >> $TMP
sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNELb >> $TMP
sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNEL5 >> $TMP
echo ";" >>$TMP
echo "#endif // End of STRINGIFY_H" >>$TMP
......
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