merging fastergrad onto master

Makefile

@@ -50,7 +50,10 @@ 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_minSD"
+K6_NAME="gradient_minFire"
+K7_NAME="gradient_minAD"
+K_NAMES=-DK1=$(K1_NAME) -DK2=$(K2_NAME) -DK3=$(K3_NAME) -DK4=$(K4_NAME) -DK5=$(K5_NAME) -DK6=$(K6_NAME) -DK7=$(K7_NAME)
 # Kernel flags
 KFLAGS=-DKRNL_SOURCE=$(KRNL_DIR)/$(KRNL_MAIN) -DKRNL_DIRECTORY=$(KRNL_DIR) -DKCMN_DIRECTORY=$(KCMN_DIR) $(K_NAMES)
 
@@ -95,8 +98,10 @@ else
 endif
 
 # ------------------------------------------------------
-# Configuration (Host)
-# Valid values: RELEASE, DEBUG
+# Configuration
+# FDEBUG (full) : enables debugging on both host + device
+# LDEBUG (light): enables debugging on host
+# RELEASE
 CONFIG=RELEASE
 
 OCL_DEBUG_BASIC=-DPLATFORM_ATTRIBUTES_DISPLAY\
@@ -113,7 +118,9 @@ OCL_DEBUG_ALL=$(OCL_DEBUG_BASIC) \
 	      -DKERNEL_WORK_GROUP_INFO_DISPLAY \
 	      -DBUFFER_OBJECT_INFO_DISPLAY
 
-ifeq ($(CONFIG),DEBUG)
+ifeq ($(CONFIG),FDEBUG)
+	OPT =-O0 -g3 -Wall $(OCL_DEBUG_ALL) -DDOCK_DEBUG
+else ifeq ($(CONFIG),LDEBUG)
 	OPT =-O0 -g3 -Wall $(OCL_DEBUG_BASIC)
 else ifeq ($(CONFIG),RELEASE)
 	OPT =-O3
@@ -122,18 +129,9 @@ else
 endif
 
 # ------------------------------------------------------
-# Host and Device Debug
-DOCK_DEBUG=NO
-
 # Reproduce results (remove randomness)
 REPRO=NO
 
-ifeq ($(DOCK_DEBUG),YES)
-	DD =-DDOCK_DEBUG
-else
-	DD =
-endif
-
 ifeq ($(REPRO),YES)
 	REP =-DREPRO
 else
@@ -188,11 +186,66 @@ check-env-gpu:
 
 check-env-all: check-env-dev check-env-cpu check-env-gpu
 
+# ------------------------------------------------------
+# Priting out its git version hash
+
+GIT_VERSION := $(shell git describe --abbrev=40 --dirty --always --tags)
+
+CFLAGS+=-DVERSION=\"$(GIT_VERSION)\"
+
+# ------------------------------------------------------
+
 stringify:
 	./stringify_ocl_krnls.sh
 
 odock: check-env-all stringify $(SRC)
-	g++ $(SRC) $(CFLAGS) -lOpenCL -o$(BIN_DIR)/$(TARGET) $(DEV) $(NWI) $(OPT) $(DD) $(REP) $(KFLAGS)
+	g++ \
+	$(SRC) \
+	$(CFLAGS) \
+	-lOpenCL \
+	-o$(BIN_DIR)/$(TARGET) \
+	$(DEV) $(NWI) $(OPT) $(DD) $(REP) $(KFLAGS)
+
+# Example
+# 1ac8: for testing gradients of translation and rotation genes
+# 7cpa: for testing gradients of torsion genes (15 torsions) 
+# 3tmn: for testing gradients of torsion genes (1 torsion)
+
+PDB      := 3ce3
+NRUN     := 100
+NGEN     := 27000
+POPSIZE  := 150
+TESTNAME := test
+TESTLS   := sw
+
+test: odock
+	$(BIN_DIR)/$(TARGET) \
+	-ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld \
+	-lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt \
+	-nrun $(NRUN) \
+	-ngen $(NGEN) \
+	-psize $(POPSIZE) \
+	-resnam $(TESTNAME) \
+	-gfpop 0 \
+	-lsmet $(TESTLS)
+
+ASTEX_PDB := 2bsm
+ASTEX_NRUN:= 10
+ASTEX_POPSIZE := 10
+ASTEX_TESTNAME := test_astex
+ASTEX_LS := sw
+
+astex: odock
+	$(BIN_DIR)/$(TARGET) \
+	-ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld \
+	-lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt \
+	-nrun $(ASTEX_NRUN) \
+	-psize $(ASTEX_POPSIZE) \
+	-resnam $(ASTEX_TESTNAME) \
+	-gfpop 1 \
+	-lsmet $(ASTEX_LS)
+
+#	$(BIN_DIR)/$(TARGET) -ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld -lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt -nrun $(ASTEX_NRUN) -psize $(ASTEX_POPSIZE) -resnam $(ASTEX_TESTNAME) -gfpop 1 | tee ./input_tsri/search-set-astex/intrapairs/$(ASTEX_PDB)_intrapair.txt
 
 PDB      := 3ce3
 NRUN     := 100

README.md

@@ -98,6 +98,7 @@ By default the output log file is written in the current working folder. Example
 | -lsrat   | Local-search rate                | 6 (%)         |
 | -trat    | Tournament rate                  | 60 (%)        |
 | -resnam  | Name for docking output log      | _"docking"_   |
+| -hsym    | Handle symmetry in RMSD calc.    | 1             |
 
 For a complete list of available arguments and their default values, check: [getparameters.cpp](host/src/getparameters.cpp).
 

common/calcenergy_basic.h

@@ -27,19 +27,19 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
 #include "defines.h"
 
-#define RLIST_ATOMID_MASK 	 0x000000FF
-#define RLIST_RBONDID_MASK 	 0x0000FF00
-#define RLIST_RBONDID_SHIFT  8
-#define RLIST_FIRSTROT_MASK  0x00010000
-#define RLIST_GENROT_MASK 	 0x00020000
-#define RLIST_DUMMY_MASK 	 	 0x00040000
-#define DEG_TO_RAD 					 0.0174533f
+#define RLIST_ATOMID_MASK 	0x000000FF
+#define RLIST_RBONDID_MASK 	0x0000FF00
+#define RLIST_RBONDID_SHIFT  	8
+#define RLIST_FIRSTROT_MASK  	0x00010000
+#define RLIST_GENROT_MASK 	0x00020000
+#define RLIST_DUMMY_MASK 	0x00040000
+#define DEG_TO_RAD 		0.0174533f
 
 // LCG: linear congruential generator constants
-#define RAND_A 							1103515245u
-#define RAND_C 							12345u
+#define RAND_A 			1103515245u
+#define RAND_C 			12345u
 // WARNING: it is supposed that unsigned int is 32 bit long
-#define MAX_UINT 						4294967296.0f
+#define MAX_UINT 		4294967296.0f
 
 // Macro for capturing grid values
 	// Original
@@ -57,4 +57,49 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 				       cube[0][0][1]*weights[0][0][1] +cube[1][0][1]*weights[1][0][1] + \
 				       cube[0][1][1]*weights[0][1][1] +cube[1][1][1]*weights[1][1][1])
 
+// Constants for dielelectric term of the 
+// electrostatic component of the intramolecular energy/gradient
+#define DIEL_A 			-8.5525f
+#define DIEL_WAT 		78.4f
+#define DIEL_B 			(DIEL_WAT - DIEL_A)
+#define DIEL_LAMBDA		0.003627f
+#define DIEL_H			DIEL_LAMBDA
+#define DIEL_K			7.7839f
+#define DIEL_B_TIMES_H		(DIEL_B * DIEL_H)
+#define DIEL_B_TIMES_H_TIMES_K	(DIEL_B_TIMES_H * DIEL_K)
+
+// Used for Shoemake to quaternion transformation
+#define PI_TIMES_2 		(float)(2.0f*M_PI)
+#define PI_FLOAT		(float)(M_PI)
+
+
+// -------------------------------------------
+// Gradient-related defines
+// -------------------------------------------
+
+#define INFINITESIMAL_RADIAN		1E-3
+#define HALF_INFINITESIMAL_RADIAN 	(0.5f * INFINITESIMAL_RADIAN)
+#define INV_INFINITESIMAL_RADIAN	(1/INFINITESIMAL_RADIAN)
+#define COS_HALF_INFINITESIMAL_RADIAN	cos(HALF_INFINITESIMAL_RADIAN)
+#define SIN_HALF_INFINITESIMAL_RADIAN	sin(HALF_INFINITESIMAL_RADIAN)
+
+
+/*
+#define TRANGENE_ALPHA 1E-3
+#define ROTAGENE_ALPHA 1E-8
+#define TORSGENE_ALPHA 1E-13
+*/
+
+#define STEP_INCREASE 		1.2f
+#define STEP_DECREASE 		0.2f
+#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_ROTATION	0.5f/DEG_TO_RAD	// 0.5f RAD
+#define MAX_DEV_TORSION		0.5f/DEG_TO_RAD	// 0.5f RAD
+
+
+
+
+
 #endif /* CALCENERGY_BASIC_H_ */

common/defines.h

@@ -39,7 +39,8 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 	#define NUM_OF_THREADS_PER_BLOCK 64
 #endif
 
-#define ATYPE_NUM 		22
+#define ATYPE_NUM 		22	// initial: 22
+#define ATYPE_GETBONDS		16	// initial: 16
 #define MAX_NUM_OF_ATOMS 	256
 #define MAX_NUM_OF_ATYPES 	14
 #define MAX_NUM_OF_ROTBONDS 	32
@@ -47,19 +48,27 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 #define MAX_NUM_OF_ROTATIONS 	(MAX_NUM_OF_ATOMS * MAX_NUM_OF_ROTBONDS)
 #define MAX_POPSIZE 		2048
 #define MAX_NUM_OF_RUNS 	1000
+#define MAX_NUM_GRIDPOINTS      256
 
 // Must be bigger than MAX_NUM_OF_ROTBONDS+6
 #define GENOTYPE_LENGTH_IN_GLOBMEM 64
 #define ACTUAL_GENOTYPE_LENGTH	(MAX_NUM_OF_ROTBONDS+6)
 
-#define LS_EXP_FACTOR 					2.0f
-#define LS_CONT_FACTOR 					0.5f
+#define LS_EXP_FACTOR 		2.0f
+#define LS_CONT_FACTOR 		0.5f
 
 // Improvements over Pechan's implementation
-#define NATIVE_PRECISION
-#define ASYNC_COPY
-#define IMPROVE_GRID
-#define RESTRICT_ARGS
 #define MAPPED_COPY
 
+
+
+
+
+// TODO: convert this into a program arg
+//#define GRADIENT_ENABLED
+
+
+
+
+
 #endif /* DEFINES_H_ */

device/auxiliary_genetic.cl

@@ -25,12 +25,8 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 // -------------------------------------------------------
 //
 // -------------------------------------------------------
-unsigned int gpu_rand(
-			#if defined (RESTRICT_ARGS)
-			__global unsigned int* restrict prng_states
-			#else
-			__global unsigned int* prng_states
-			#endif
+uint gpu_rand(
+		__global uint* restrict prng_states
 )
 //The GPU device function generates a random int
 //with a linear congruential generator.
@@ -39,20 +35,20 @@ unsigned int gpu_rand(
 //prng_states (thread with ID tx in block with ID bx stores its state in prng_states[bx*NUM_OF_THREADS_PER_BLOCK+$
 //The random number generator uses the gcc linear congruential generator constants.
 {
-  unsigned int state;
+	uint state;
 
 #if defined (REPRO)
 	state = 1;
 #else
-  //current state of the threads own PRNG
-  //state = prng_states[get_group_id(0)*NUM_OF_THREADS_PER_BLOCK + get_local_id(0)];
+  	// Current state of the threads own PRNG
+  	// state = prng_states[get_group_id(0)*NUM_OF_THREADS_PER_BLOCK + get_local_id(0)];
 	state = prng_states[get_global_id(0)];
 
-  //calculating next state
-  state = (RAND_A*state+RAND_C);
+	// Calculating next state
+  	state = (RAND_A*state+RAND_C);
 #endif
-  //saving next state to memory
-  //prng_states[get_group_id(0)*NUM_OF_THREADS_PER_BLOCK + get_local_id(0)] = state;
+  	// Saving next state to memory
+  	// prng_states[get_group_id(0)*NUM_OF_THREADS_PER_BLOCK + get_local_id(0)] = state;
 	prng_states[get_global_id(0)] = state;
 
   return state;
@@ -62,29 +58,19 @@ unsigned int gpu_rand(
 //
 // -------------------------------------------------------
 float gpu_randf(
-		#if defined (RESTRICT_ARGS)
-		__global unsigned int* restrict prng_states
-		#else
-		__global unsigned int* prng_states
-		#endif
+		__global uint* restrict prng_states
 )
 //The GPU device function generates a
 //random float greater than (or equal to) 0 and less than 1.
 //It uses gpu_rand() function.
 {
-  float state;
+  	float state;
 
-	//state will be between 0 and 1
+	// State will be between 0 and 1
 #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;
@@ -94,50 +80,33 @@ float gpu_randf(
 //
 // -------------------------------------------------------
 void map_angle(__local float* angle)
-//The GPU device function maps
-//the input parameter to the interval 0...360
-//(supposing that it is an angle).
+// The GPU device function maps
+// the input parameter to the interval 0...360
+// (supposing that it is an angle).
 {
-  while (*angle >= 360.0f)
-    *angle -= 360.0f;
+	while (*angle >= 360.0f) {
+		*angle -= 360.0f;
+	}
 
-  while (*angle < 0.0f)
-    *angle += 360.0f;
+	while (*angle < 0.0f) {
+		*angle += 360.0f;
+	}
 }
 
 // -------------------------------------------------------
 //
 // -------------------------------------------------------
-void gpu_perform_elitist_selection(int    dockpars_pop_size,
-
-	         #if defined (RESTRICT_ARGS)
+void gpu_perform_elitist_selection(
+					     int    dockpars_pop_size,
 				    __global float* restrict dockpars_energies_current,
 				    __global float* restrict dockpars_energies_next,
 				    __global int*   restrict dockpars_evals_of_new_entities,
-					#else
-				    __global float* dockpars_energies_current,
-				    __global float* dockpars_energies_next,
-				    __global int*   dockpars_evals_of_new_entities,
-					#endif
-
 					     int    dockpars_num_of_genes,
-
-					#if defined (RESTRICT_ARGS)
 				    __global float* restrict dockpars_conformations_next,
-		        __global const float* restrict dockpars_conformations_current
-					#else
-				    __global float* dockpars_conformations_next,
-		        __global const float* dockpars_conformations_current
-					#endif
-				
-					,
-                    // Some OpenCL compilers don't allow local var outside kernels
-                    // so this local vars are passed from a kernel
-				    __local float* best_energies,
-				    __local int*   best_IDs,
-				    __local int*   best_ID	
-
-
+		       		    __global const float* restrict dockpars_conformations_current,
+				    __local  float* best_energies,
+				    __local  int*   best_IDs,
+				    __local  int*   best_ID
 )
 //The GPU device function performs elitist selection,
 //that is, it looks for the best entity in conformations_current and
@@ -145,68 +114,58 @@ void gpu_perform_elitist_selection(int    dockpars_pop_size,
 //and copies it to the place of the first entity in
 //conformations_next and energies_next.
 {
-
 	int entity_counter;
 	int gene_counter;
 	float best_energy;
 
-        // Some OpenCL compilers don't allow local var outside kernels
-        // so this local vars are passed from a kernel
-	//__local float best_energies[NUM_OF_THREADS_PER_BLOCK];
-	//__local int best_IDs[NUM_OF_THREADS_PER_BLOCK];
-	//__local int best_ID;
-
-	if (get_local_id(0) < dockpars_pop_size)
-	{
+	if (get_local_id(0) < dockpars_pop_size) {
 		best_energies[get_local_id(0)] = dockpars_energies_current[get_group_id(0)+get_local_id(0)];
 		best_IDs[get_local_id(0)] = get_local_id(0);
 	}
 
-	for (entity_counter=NUM_OF_THREADS_PER_BLOCK+get_local_id(0);
-	     entity_counter<dockpars_pop_size;
-	     entity_counter+=NUM_OF_THREADS_PER_BLOCK)
+	for (entity_counter = NUM_OF_THREADS_PER_BLOCK+get_local_id(0);
+	     entity_counter < dockpars_pop_size;
+	     entity_counter+= NUM_OF_THREADS_PER_BLOCK) {
 
-	     if (dockpars_energies_current[get_group_id(0)+entity_counter] < best_energies[get_local_id(0)])
-	     {
+	     if (dockpars_energies_current[get_group_id(0)+entity_counter] < best_energies[get_local_id(0)]) {
 		best_energies[get_local_id(0)] = dockpars_energies_current[get_group_id(0)+entity_counter];
 		best_IDs[get_local_id(0)] = entity_counter;
 	     }
+	}
 
        barrier(CLK_LOCAL_MEM_FENCE);
 
-	//this could be implemented with a tree-like structure
-	//which may be slightly faster
+	// This could be implemented with a tree-like structure
+	// which may be slightly faster
 	if (get_local_id(0) == 0)
 	{
 		best_energy = best_energies[0];
-		//best_ID = best_IDs[0];
 		best_ID[0] = best_IDs[0];
 
-		for (entity_counter=1;
-		     entity_counter<NUM_OF_THREADS_PER_BLOCK;
-		     entity_counter++)
+		for (entity_counter = 1;
+		     entity_counter < NUM_OF_THREADS_PER_BLOCK;
+		     entity_counter++) {
 
-		     if ((best_energies[entity_counter] < best_energy) && (entity_counter < dockpars_pop_size))
-		     {
+		     if ((best_energies[entity_counter] < best_energy) && (entity_counter < dockpars_pop_size)) {
 			      best_energy = best_energies[entity_counter];
-			      //best_ID = best_IDs[entity_counter];
 			      best_ID[0] = best_IDs[entity_counter];
 		     }
+		}
 
-		//setting energy value of new entity
+		// Setting energy value of new entity
 		dockpars_energies_next[get_group_id(0)] = best_energy;
 
-		//0 evals were performed for entity selected with elitism (since it was copied only)
+		// Zero (0) evals were performed for entity selected with elitism (since it was copied only)
 		dockpars_evals_of_new_entities[get_group_id(0)] = 0;
 	}
 
-	//now best_id stores the id of the best entity in the population,
-	//copying genotype and energy value to the first entity of new population
+	// "best_id" stores the id of the best entity in the population,
+	// Copying genotype and energy value to the first entity of new population
 	barrier(CLK_LOCAL_MEM_FENCE);
 
-	for (gene_counter=get_local_id(0);
-	     gene_counter<dockpars_num_of_genes;
-	     gene_counter+=NUM_OF_THREADS_PER_BLOCK)
-	     //dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+GENOTYPE_LENGTH_IN_GLOBMEM*best_ID+gene_counter];
-	     dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+GENOTYPE_LENGTH_IN_GLOBMEM*best_ID[0]+gene_counter];
+	for (gene_counter = get_local_id(0);
+	     gene_counter < dockpars_num_of_genes;
+	     gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
+	     dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0) + GENOTYPE_LENGTH_IN_GLOBMEM*best_ID[0]+gene_counter];
+	}
 }

device/kernel1.cl

@@ -21,68 +21,68 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
 */
 
+//#define DEBUG_ENERGY_KERNEL1
 
 __kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))
-gpu_calc_initpop(	char   dockpars_num_of_atoms,
+gpu_calc_initpop(	
+			char   dockpars_num_of_atoms,
 			char   dockpars_num_of_atypes,
 			int    dockpars_num_of_intraE_contributors,
 			char   dockpars_gridsize_x,
 			char   dockpars_gridsize_y,
 			char   dockpars_gridsize_z,
+							    		// g1 = gridsize_x
+			uint   dockpars_gridsize_x_times_y, 		// g2 = gridsize_x * gridsize_y
+			uint   dockpars_gridsize_x_times_y_times_z,	// g3 = gridsize_x * gridsize_y * gridsize_z
 			float  dockpars_grid_spacing,
-		#if defined (RESTRICT_ARGS)
-		  __global const float* restrict dockpars_fgrids, // cannot be allocated in __constant (too large)
-		#else
-		  __global const float* dockpars_fgrids,          // cannot be allocated in __constant (too large)
-		#endif
+	 __global const float* restrict dockpars_fgrids, // This is too large to be allocated in __constant 
 			int    dockpars_rotbondlist_length,
 			float  dockpars_coeff_elec,
 			float  dockpars_coeff_desolv,
-
-		#if defined (RESTRICT_ARGS)
-			__global const float* restrict dockpars_conformations_current,
-			__global float* restrict dockpars_energies_current,
-		        __global int*   restrict dockpars_evals_of_new_entities,
-		#else
-			__global const float* dockpars_conformations_current,
-			__global float* dockpars_energies_current,
-		        __global int*   dockpars_evals_of_new_entities,
-		#endif
-
+	 __global const float* restrict dockpars_conformations_current,
+	 __global       float* restrict dockpars_energies_current,
+	 __global       int*   restrict dockpars_evals_of_new_entities,
 			int    dockpars_pop_size,
 			float  dockpars_qasp,
-                        float  dockpars_smooth,
+			float  dockpars_smooth,
 
-		   __constant     kernelconstant_interintra* 		kerconst_interintra,
-		   __global const kernelconstant_intracontrib*  	kerconst_intracontrib,
-		   __constant     kernelconstant_intra*			kerconst_intra,
-		   __constant     kernelconstant_rotlist*   		kerconst_rotlist,
-		   __constant     kernelconstant_conform*		kerconst_conform
+	 __constant     kernelconstant_interintra* 	kerconst_interintra,
+	 __global const kernelconstant_intracontrib*  	kerconst_intracontrib,
+	 __constant     kernelconstant_intra*		kerconst_intra,
+	 __constant     kernelconstant_rotlist*   	kerconst_rotlist,
+	 __constant     kernelconstant_conform*		kerconst_conform
 ){
+        // 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[ACTUAL_GENOTYPE_LENGTH];
 	__local float  energy;
 	__local int    run_id;
 
-        // Some OpenCL compilers don't allow local var outside kernels
-        // so this local vars are passed from a kernel
 	__local float calc_coords_x[MAX_NUM_OF_ATOMS];
 	__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_KERNEL)
+	__local float partial_interE[NUM_OF_THREADS_PER_BLOCK];
+	__local float partial_intraE[NUM_OF_THREADS_PER_BLOCK];
+	#endif
 
+	// Copying genotype from global memory
 	event_t ev = async_work_group_copy(genotype,
 			                   dockpars_conformations_current + GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0),
 			                   ACTUAL_GENOTYPE_LENGTH, 0);
 
-	//determining run ID
+	// Determining run-ID
 	if (get_local_id(0) == 0) {
 		run_id = get_group_id(0) / dockpars_pop_size;
 	}
 
 	// Asynchronous copy should be finished by here
-	wait_group_events(1,&ev);
+	wait_group_events(1, &ev);
 
-	// Evaluating initial genotype
+	// Evaluating initial genotypes
 	barrier(CLK_LOCAL_MEM_FENCE);
 
 	// =============================================================
@@ -91,6 +91,9 @@ gpu_calc_initpop(	char   dockpars_num_of_atoms,
 			dockpars_gridsize_x,
 			dockpars_gridsize_y,
 			dockpars_gridsize_z,
+							    	// g1 = gridsize_x
+			dockpars_gridsize_x_times_y, 		// g2 = gridsize_x * gridsize_y
+			dockpars_gridsize_x_times_y_times_z,	// g3 = gridsize_x * gridsize_y * gridsize_z
 			dockpars_fgrids,
 			dockpars_num_of_atypes,
 			dockpars_num_of_intraE_contributors,
@@ -103,22 +106,35 @@ gpu_calc_initpop(	char   dockpars_num_of_atoms,
 			genotype,
 			&energy,
 			&run_id,
-			// Some OpenCL compilers don't allow local var outside kernels
-			// so this local vars are passed from a kernel
+			// 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.
 			calc_coords_x,
 			calc_coords_y,
 			calc_coords_z,
 			partial_energies,
-
-	   		kerconst_interintra,
-	   		kerconst_intracontrib,
-	   		kerconst_intra,
-           		kerconst_rotlist,
-           		kerconst_conform);
+			#if defined (DEBUG_ENERGY_KERNEL)
+			partial_interE,
+			partial_intraE,
+			#endif
+#if 0
+			false,
+#endif
+		   	kerconst_interintra,
+		   	kerconst_intracontrib,
+		   	kerconst_intra,
+		   	kerconst_rotlist,
+		   	kerconst_conform
+			);
 	// =============================================================
 
 	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/kernel2.cl

@@ -23,16 +23,10 @@ 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_sum_evals(/*unsigned long pop_size,*/
-		unsigned int pop_size,
-	      /*unsigned long num_of_runs,*/
-#if defined (RESTRICT_ARGS)
+gpu_sum_evals(	       
+		       uint pop_size,
 	      __global int* restrict dockpars_evals_of_new_entities,
               __global int* restrict evals_of_runs
-#else
-	      __global int* dockpars_evals_of_new_entities,
-              __global int* evals_of_runs
-#endif
 )
 //The GPU global function sums the evaluation counter states