performdocking.cpp 104 KB
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/*
 * (C) 2013. Evopro Innovation Kft.
 *
 * performdocking.cu
 *
 * Created on: 2010.04.20.
 * Author: pechan.imre
 */

//// ------------------------
//// Correct time measurement
//// Moved from main.cpp to performdocking.cpp
//// to skip measuring build time
//#include <sys/time.h>
//// ------------------------
#include "performdocking.h"

//// --------------------------------
//// Altera OpenCL Helper Variables
//// --------------------------------
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <cstring>
#include "CL/opencl.h"
#include "AOCLUtils/aocl_utils.h"

using namespace aocl_utils;

#define STRING_BUFFER_LEN 1024

// OpenCL runtime configuration
static cl_platform_id   platform      = NULL;
static cl_device_id     device        = NULL;
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static cl_context       context       = NULL;

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#if 0
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// Unique command queue
static cl_command_queue command_queue = NULL;
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#endif
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// Kernel name as defined in the CL file
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#ifdef ENABLE_KRNL_GA
static cl_command_queue command_queue_ga = NULL;
static cl_kernel kernel_ga  = NULL;
static const char *name_krnl_ga = "Krnl_GA";
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#endif

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#ifdef ENABLE_KRNL_CONFORM
static cl_command_queue command_queue_conform = NULL;
static cl_kernel kernel_conform  = NULL;
static const char *name_krnl_conform = "Krnl_Conform";
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#endif

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#ifdef ENABLE_KRNL_INTERE
static cl_command_queue command_queue_intere = NULL;
static cl_kernel kernel_intere  = NULL;
static const char *name_krnl_intere = "Krnl_InterE";
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#endif

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#ifdef ENABLE_KRNL_INTRAE
static cl_command_queue command_queue_intrae = NULL;
static cl_kernel kernel_intrae  = NULL;
static const char *name_krnl_intrae = "Krnl_IntraE";
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#endif

#ifdef ENABLE_KRNL_PRNG_BT_USHORT_FLOAT
static cl_command_queue command_queue_prng_bt_ushort_float = NULL;
static cl_kernel kernel_prng_bt_ushort_float  = NULL;
static const char *name_krnl_prng_bt_ushort_float = "Krnl_Prng_BT_ushort_float";
#endif

#ifdef ENABLE_KRNL_PRNG_GG_UCHAR
static cl_command_queue command_queue_prng_gg_uchar = NULL;
static cl_kernel kernel_prng_gg_uchar  = NULL;
static const char *name_krnl_prng_gg_uchar = "Krnl_Prng_GG_uchar";
#endif

#ifdef ENABLE_KRNL_PRNG_GG_FLOAT
static cl_command_queue command_queue_prng_gg_float = NULL;
static cl_kernel kernel_prng_gg_float  = NULL;
static const char *name_krnl_prng_gg_float = "Krnl_Prng_GG_float";
#endif

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#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
static cl_command_queue command_queue_prng_ls123_ushort = NULL;
static cl_kernel kernel_prng_ls123_ushort  = NULL;
static const char *name_krnl_prng_ls123_ushort = "Krnl_Prng_LS123_ushort";
#endif

#ifdef ENABLE_KRNL_PRNG_LS_FLOAT
static cl_command_queue command_queue_prng_ls_float = NULL;
static cl_kernel kernel_prng_ls_float  = NULL;
static const char *name_krnl_prng_ls_float = "Krnl_Prng_LS_float";
#endif

#ifdef ENABLE_KRNL_PRNG_LS2_FLOAT
static cl_command_queue command_queue_prng_ls2_float = NULL;
static cl_kernel kernel_prng_ls2_float  = NULL;
static const char *name_krnl_prng_ls2_float = "Krnl_Prng_LS2_float";
#endif

#ifdef ENABLE_KRNL_PRNG_LS3_FLOAT
static cl_command_queue command_queue_prng_ls3_float = NULL;
static cl_kernel kernel_prng_ls3_float  = NULL;
static const char *name_krnl_prng_ls3_float = "Krnl_Prng_LS3_float";
#endif

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#ifdef ENABLE_KRNL_PRNG_LS4_FLOAT
static cl_command_queue command_queue_prng_ls4_float = NULL;
static cl_kernel kernel_prng_ls4_float  = NULL;
static const char *name_krnl_prng_ls4_float = "Krnl_Prng_LS4_float";
#endif

#ifdef ENABLE_KRNL_PRNG_LS5_FLOAT
static cl_command_queue command_queue_prng_ls5_float = NULL;
static cl_kernel kernel_prng_ls5_float  = NULL;
static const char *name_krnl_prng_ls5_float = "Krnl_Prng_LS5_float";
#endif
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#ifdef ENABLE_KRNL_PRNG_LS6_FLOAT
static cl_command_queue command_queue_prng_ls6_float = NULL;
static cl_kernel kernel_prng_ls6_float  = NULL;
static const char *name_krnl_prng_ls6_float = "Krnl_Prng_LS6_float";
#endif
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#ifdef ENABLE_KRNL_PRNG_LS7_FLOAT
static cl_command_queue command_queue_prng_ls7_float = NULL;
static cl_kernel kernel_prng_ls7_float  = NULL;
static const char *name_krnl_prng_ls7_float = "Krnl_Prng_LS7_float";
#endif
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#ifdef ENABLE_KRNL_PRNG_LS8_FLOAT
static cl_command_queue command_queue_prng_ls8_float = NULL;
static cl_kernel kernel_prng_ls8_float  = NULL;
static const char *name_krnl_prng_ls8_float = "Krnl_Prng_LS8_float";
#endif
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#ifdef ENABLE_KRNL_PRNG_LS9_FLOAT
static cl_command_queue command_queue_prng_ls9_float = NULL;
static cl_kernel kernel_prng_ls9_float  = NULL;
static const char *name_krnl_prng_ls9_float = "Krnl_Prng_LS9_float";
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#endif










#ifdef ENABLE_KERNEL12
static cl_command_queue command_queue12 = NULL;
static cl_kernel kernel12  = NULL;
static const char *name_k12 = "Krnl_LS";
#endif



#ifdef ENABLE_KERNEL15
static cl_command_queue command_queue15 = NULL;
static cl_kernel kernel15  = NULL;
static const char *name_k15 = "Krnl_LS2";
#endif



#ifdef ENABLE_KERNEL21
static cl_command_queue command_queue21 = NULL;
static cl_kernel kernel21  = NULL;
static const char *name_k21 = "Krnl_LS3";
#endif

#ifdef ENABLE_KERNEL27
static cl_command_queue command_queue27 = NULL;
static cl_kernel kernel27  = NULL;
static const char *name_k27 = "Krnl_IGL_Arbiter";
#endif

#ifdef ENABLE_KERNEL39
static cl_command_queue command_queue39 = NULL;
static cl_kernel kernel39  = NULL;
static const char *name_k39 = "Krnl_LS4";
#endif

#ifdef ENABLE_KERNEL40
static cl_command_queue command_queue40 = NULL;
static cl_kernel kernel40  = NULL;
static const char *name_k40 = "Krnl_LS5";
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#endif

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#ifdef ENABLE_KERNEL45
static cl_command_queue command_queue45 = NULL;
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static cl_kernel kernel45  = NULL;
static const char *name_k45 = "Krnl_LS6";
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#endif

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#ifdef ENABLE_KERNEL46
static cl_command_queue command_queue46 = NULL;
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static cl_kernel kernel46  = NULL;
static const char *name_k46 = "Krnl_LS7";
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#endif

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#ifdef ENABLE_KERNEL47
static cl_command_queue command_queue47 = NULL;
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static cl_kernel kernel47  = NULL;
static const char *name_k47 = "Krnl_LS8";
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#endif

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#ifdef ENABLE_KERNEL48
static cl_command_queue command_queue48 = NULL;
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static cl_kernel kernel48  = NULL;
static const char *name_k48 = "Krnl_LS9";
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#endif

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static cl_program program = NULL;

// Function prototypes
bool init();
void cleanup();
static void device_info_ulong( cl_device_id device, cl_device_info param, const char* name);
static void device_info_uint ( cl_device_id device, cl_device_info param, const char* name);
static void device_info_bool ( cl_device_id device, cl_device_info param, const char* name);
static void device_info_string( cl_device_id device, cl_device_info param, const char* name);
static void display_device_info( cl_device_id device );

//// --------------------------------
//// Host constant struct
//// --------------------------------
Dockparameters dockpars;
kernelconstant_static  KerConstStatic;
#if defined(SINGLE_COPY_POP_ENE)

#else
kernelconstant_dynamic KerConstDynamic;
#endif

//// --------------------------------
//// Host memory buffers
//// --------------------------------
float* cpu_init_populations;
float* cpu_final_populations;
float* cpu_energies;
Ligandresult* cpu_result_ligands;
unsigned int* cpu_prng_seeds;
#if defined(SINGLE_COPY_POP_ENE)
int *cpu_evals_of_runs;
int *cpu_gens_of_runs;
#endif
float* cpu_ref_ori_angles;

//// --------------------------------
//// Device memory buffers
//// --------------------------------
// Altera Issue
// Constant data holding struct data
// Created because structs containing array
// are not supported as OpenCL kernel args

#if defined (FIXED_POINT_INTERE)
cl_mem mem_KerConstStatic_fixpt64_atom_charges_const;
#endif
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cl_mem mem_KerConstStatic_InterE_atom_charges_const;
cl_mem mem_KerConstStatic_InterE_atom_types_const;

cl_mem mem_KerConstStatic_IntraE_atom_charges_const;
cl_mem mem_KerConstStatic_IntraE_atom_types_const;

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cl_mem mem_KerConstStatic_intraE_contributors_const;

cl_mem mem_KerConstStatic_reqm_const;
cl_mem mem_KerConstStatic_reqm_hbond_const;
cl_mem mem_KerConstStatic_atom1_types_reqm_const;
cl_mem mem_KerConstStatic_atom2_types_reqm_const;

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cl_mem mem_KerConstStatic_VWpars_AC_const;
cl_mem mem_KerConstStatic_VWpars_BD_const;
cl_mem mem_KerConstStatic_dspars_S_const;
cl_mem mem_KerConstStatic_dspars_V_const;
cl_mem mem_KerConstStatic_rotlist_const;
cl_mem mem_KerConstStatic_ref_coords_const;
cl_mem mem_KerConstStatic_rotbonds_moving_vectors_const;
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cl_mem mem_KerConstStatic_rotbonds_unit_vectors_const;
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cl_mem mem_KerConstStatic_ref_orientation_quats_const;

/*								                  // Nr elements	// Nr bytes
cl_mem mem_atom_charges_const;		// float [MAX_NUM_OF_ATOMS];			// 90	 = 90	//360
cl_mem mem_atom_types_const;		// char  [MAX_NUM_OF_ATOMS];			// 90	 = 90	//360
cl_mem mem_intraE_contributors_const;	// char  [3*MAX_INTRAE_CONTRIBUTORS];		// 3*8128=28384 //24384	
cl_mem mem_VWpars_AC_const;		// float [MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES];	// 14*14 = 196  //784
cl_mem mem_VWpars_BD_const;		// float [MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES]; // 14*14 = 196	//784
cl_mem mem_dspars_S_const;		// float [MAX_NUM_OF_ATYPES];			// 14    = 14   //56
cl_mem mem_dspars_V_const;		// float [MAX_NUM_OF_ATYPES];			// 14    = 14   //56
cl_mem mem_rotlist_const;		// int   [MAX_NUM_OF_ROTATIONS];		// 4096  = 4096 //16384
cl_mem mem_ref_coords_x_const;		// float [MAX_NUM_OF_ATOMS];			// 90    = 90   //360
cl_mem mem_ref_coords_y_const;		// float [MAX_NUM_OF_ATOMS];			// 90    = 90   //360
cl_mem mem_ref_coords_z_const;		// float [MAX_NUM_OF_ATOMS];			// 90	 = 90   //360
cl_mem mem_rotbonds_moving_vectors_const;// float [3*MAX_NUM_OF_ROTBONDS];		// 3*32  = 96   //384
cl_mem mem_rotbonds_unit_vectors_const;	// float [3*MAX_NUM_OF_ROTBONDS];		// 3*32  = 96   //384
cl_mem mem_ref_orientation_quats_const;	// float [4*MAX_NUM_OF_RUNS];			// 4*100 = 400  //1600
*/

cl_mem mem_dockpars_fgrids;

#if defined(SEPARATE_FGRID_INTERE)
cl_mem mem_dockpars_fgrids2;
cl_mem mem_dockpars_fgrids3;
#endif

cl_mem mem_dockpars_conformations_current;
cl_mem mem_dockpars_energies_current;
/*
cl_mem mem_dockpars_prng_states;
*/

#if defined(SINGLE_COPY_POP_ENE)
cl_mem mem_evals_performed;
cl_mem mem_gens_performed;
#else
cl_mem mem_evals_and_generations_performed;
#endif


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#if !defined(SW_EMU)
// IMPORTANT: enable this dummy global argument only for "hw" build.
// Check ../common_xilinx/utility/boards.mk
// https://forums.xilinx.com/t5/SDAccel/ERROR-KernelCheck-83-114-in-sdx-2017-4/td-p/818135
cl_mem mem_dummy;
#endif
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//#if defined (FIXED_POINT_INTERE)
#if 0
//#include "defines_fixedpt_64.h"
fixedpt64* cpu_fixedpt64grids;

#endif



//// --------------------------------
//// Docking
//// --------------------------------
int docking_with_gpu(const Gridinfo*   mygrid,
	             /*const*/ float*  cpu_floatgrids,
                           Dockpars*   mypars,
		     const Liganddata* myligand_init,
		     const int*        argc,
		           char**      argv,
		           clock_t     clock_start_program)
/* The function performs the docking algorithm and generates the corresponding result files.
parameter mygrid:
		describes the grid
		filled with get_gridinfo()
parameter cpu_floatgrids:
		points to the memory region containing the grids
		filled with get_gridvalues_f()
parameter mypars:
		describes the docking parameters
		filled with get_commandpars()
parameter myligand_init:
		describes the ligands
		filled with get_liganddata()
parameters argc and argv:
		are the corresponding command line arguments parameter clock_start_program:
		contains the state of the clock tick counter at the beginning of the program
filled with clock() */
{
	//// ------------------------
	//// OpenCL Host Setup
        //// ------------------------
	if(!init()) {
    		return -1;
  	}
	printf("Init complete!\n"); fflush(stdout);

	Liganddata myligand_reference;
	//Dockparameters dockpars;
	

//#if defined (FIXED_POINT_INTERE)
#if 0
	size_t size_fixedpt64grids;
#else
	size_t size_floatgrids;

	#if defined(SEPARATE_FGRID_INTERE)
	size_t size_floatgrids2;
	size_t size_floatgrids3;
	#endif

#endif

	size_t size_populations;
	size_t size_energies;
	size_t size_prng_seeds;
#if defined(SINGLE_COPY_POP_ENE)
	size_t size_evals_of_runs;
#endif

	clock_t clock_start_docking;
	clock_t	clock_stop_docking;
	clock_t clock_stop_program_before_clustering;

	//allocating CPU memory for initial populations
#if defined(SINGLE_COPY_POP_ENE)
	size_populations = mypars->num_of_runs * mypars->pop_size * ACTUAL_GENOTYPE_LENGTH * sizeof(float);
#else
	//size_populations = mypars->pop_size * GENOTYPE_LENGTH_IN_GLOBMEM * sizeof(float);
	size_populations = mypars->pop_size * ACTUAL_GENOTYPE_LENGTH * sizeof(float);
#endif
        cpu_init_populations = (float*) alignedMalloc(size_populations);
	memset(cpu_init_populations, 0, size_populations);

	//allocating CPU memory for results
#if defined(SINGLE_COPY_POP_ENE)
	size_energies = mypars->num_of_runs * mypars->pop_size * sizeof(float);
#else
	size_energies = mypars->pop_size * sizeof(float);
#endif
	cpu_energies = (float*) alignedMalloc(size_energies);		
	cpu_result_ligands = (Ligandresult*) alignedMalloc(sizeof(Ligandresult)*(mypars->num_of_runs));	
	cpu_final_populations = (float*) alignedMalloc(size_populations);

	//allocating memory in CPU for reference orientation angles
#if defined(SINGLE_COPY_POP_ENE)
	cpu_ref_ori_angles = (float*) alignedMalloc(mypars->num_of_runs*3*sizeof(float));
#else
	cpu_ref_ori_angles = (float*) alignedMalloc(3*sizeof(float));
#endif

	//generating initial populations and random orientation angles of reference ligand
	//(ligand will be moved to origo and scaled as well)
	myligand_reference = *myligand_init;
	gen_initpop_and_reflig(mypars, cpu_init_populations, cpu_ref_ori_angles, &myligand_reference, mygrid);

	//allocating memory in CPU for pseudorandom number generator seeds and
	//generating them (seed for each thread during GA)
	unsigned int num_of_prng_blocks = 25;
	size_prng_seeds = num_of_prng_blocks * mypars->num_of_runs * sizeof(unsigned int);
	cpu_prng_seeds = (unsigned int*) alignedMalloc(size_prng_seeds);
	genseed(time(NULL));	//initializing seed generator

	for (unsigned int i=0; i<num_of_prng_blocks*mypars->num_of_runs; i++) {
#if defined (REPRO)
		cpu_prng_seeds[i] = 1u;
#else
		cpu_prng_seeds[i] = genseed(0u);
#endif
	}

	//srand(time(NULL));

#if defined(SINGLE_COPY_POP_ENE)
	// allocating memory in CPU for evaluation counters
	size_evals_of_runs = mypars->num_of_runs*sizeof(int);
	cpu_evals_of_runs = (int*) alignedMalloc(size_evals_of_runs);
	memset(cpu_evals_of_runs, 0, size_evals_of_runs);

	// allocating memory in CPU for generation counters
	cpu_gens_of_runs = (int*) alignedMalloc(size_evals_of_runs);
	memset(cpu_gens_of_runs, 0, size_evals_of_runs);
#endif

	//preparing the constant data fields for the GPU
	// ----------------------------------------------------------------------
	// The original function does CUDA calls initializing const Kernel data.
	// We create a struct to hold those constants
	// and return them <here> (<here> = where prepare_const_fields_for_gpu() is called),
	// so we can send them to Kernels from <here>, instead of from calcenergy.cpp as originally.
	// ----------------------------------------------------------------------
#if defined(SINGLE_COPY_POP_ENE)
	if (prepare_conststatic_fields_for_gpu(&myligand_reference, mypars, cpu_ref_ori_angles, &KerConstStatic) == 1)
#else
	if (prepare_conststatic_fields_for_gpu(&myligand_reference, mypars, &KerConstStatic) == 1)
#endif
		return 1;

	//preparing parameter struct
	dockpars.num_of_atoms  = ((unsigned char) myligand_reference.num_of_atoms);
	dockpars.num_of_atypes = ((unsigned char) myligand_reference.num_of_atypes);
	dockpars.num_of_intraE_contributors = ((unsigned int) myligand_reference.num_of_intraE_contributors);
	dockpars.gridsize_x    = ((unsigned char)  mygrid->size_xyz[0]);
	dockpars.gridsize_y    = ((unsigned char)  mygrid->size_xyz[1]);
	dockpars.gridsize_z    = ((unsigned char)  mygrid->size_xyz[2]);
	dockpars.g1	       = dockpars.gridsize_x ;
	dockpars.g2	       = dockpars.gridsize_x * dockpars.gridsize_y;
	dockpars.g3	       = dockpars.gridsize_x * dockpars.gridsize_y * dockpars.gridsize_z;
	dockpars.grid_spacing  = ((float) mygrid->spacing);
	dockpars.rotbondlist_length = ((unsigned int) NUM_OF_THREADS_PER_BLOCK*(myligand_reference.num_of_rotcyc));
	dockpars.coeff_elec    = ((float) mypars->coeffs.scaled_AD4_coeff_elec);
	dockpars.coeff_desolv  = ((float) mypars->coeffs.AD4_coeff_desolv);
	// L30nardoSV added
	dockpars.num_of_energy_evals = (unsigned int) mypars->num_of_energy_evals;
	dockpars.num_of_generations  = (unsigned int) mypars->num_of_generations;

	dockpars.pop_size      = (unsigned int) mypars->pop_size;
	dockpars.num_of_genes  = (unsigned int)(myligand_reference.num_of_rotbonds + 6);
	dockpars.tournament_rate = (mypars->tournament_rate)/100;//dockpars.tournament_rate = mypars->tournament_rate;
	dockpars.crossover_rate  = (mypars->crossover_rate)/100; //dockpars.crossover_rate  = mypars->crossover_rate;
	dockpars.mutation_rate   = (mypars->mutation_rate)/100;	 //dockpars.mutation_rate   = mypars->mutation_rate;
	dockpars.abs_max_dang    = mypars->abs_max_dang;
	dockpars.abs_max_dmov    = mypars->abs_max_dmov;
	dockpars.lsearch_rate    = mypars->lsearch_rate;
	dockpars.num_of_lsentities = (unsigned int) (mypars->lsearch_rate/100.0*mypars->pop_size + 0.5);
	dockpars.rho_lower_bound   = mypars->rho_lower_bound;
	dockpars.base_dmov_mul_sqrt3 = mypars->base_dmov_mul_sqrt3;
	dockpars.base_dang_mul_sqrt3 = mypars->base_dang_mul_sqrt3;
	dockpars.cons_limit        = (unsigned int) mypars->cons_limit;
	dockpars.max_num_of_iters  = (unsigned int) mypars->max_num_of_iters;
	dockpars.qasp = mypars->qasp;
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	dockpars.smooth = mypars->smooth;
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/*
// passed correctly
printf("%i %i\n", dockpars.num_of_intraE_contributors, myligand_reference.num_of_intraE_contributors);
*/

	// these variables hold multiplications between kernel-constants
	// better calculate them here and then pass them to Krnl_GA
	const float two_absmaxdmov = 2.0 * dockpars.abs_max_dmov;
	const float two_absmaxdang = 2.0 * dockpars.abs_max_dang;

	// these variables hold multiplications between kernel-constants
	// better calculate them here and then pass them to Krnl_InterE and Krnl_InterE2
	#if defined(SEPARATE_FGRID_INTERE)

	#else
	const unsigned int mul_tmp2 = dockpars.num_of_atypes * dockpars.g3;
	const unsigned int mul_tmp3 = (dockpars.num_of_atypes + 1) * dockpars.g3;
	#endif

	// this variable holds a multiplication between kernel-constants
	// better calculate them it and then pass them to Krnl_IntraE and Krnl_IntraE2
	const unsigned int square_num_of_atypes = dockpars.num_of_atypes * dockpars.num_of_atypes;

	// num of rotbonds
	const unsigned char num_rotbonds = myligand_reference.num_of_rotbonds;

 	//allocating GPU memory for populations, floatgrids,
	//energies, evaluation counters and random number generator states
//#if defined (FIXED_POINT_INTERE)
#if 0
	size_fixedpt64grids = (sizeof(fixedpt64)) * (mygrid->num_of_atypes+2) * (mygrid->size_xyz[0]) * (mygrid->size_xyz[1]) * (mygrid->size_xyz[2]);
#else
	#if defined(SEPARATE_FGRID_INTERE)
	size_floatgrids = sizeof(float) * mygrid->num_of_atypes * mygrid->size_xyz[0]*mygrid->size_xyz[1]* mygrid->size_xyz[2];
	size_floatgrids2= sizeof(float) * mygrid->size_xyz[0] * mygrid->size_xyz[1] * mygrid->size_xyz[2];
	size_floatgrids3= sizeof(float) * mygrid->size_xyz[0] * mygrid->size_xyz[1] * mygrid->size_xyz[2];
	#else
	size_floatgrids = (sizeof(float)) * (mygrid->num_of_atypes+2) * (mygrid->size_xyz[0]) * (mygrid->size_xyz[1]) * (mygrid->size_xyz[2]);
	#endif
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#endif



// -----------------------------------------------------------------------------------------------------
// Hardware specific
// Specifiying exact memory bank from host code
// Only valid if 4 banks are available (AWS)
	cl_mem_ext_ptr_t d_bank0_ext; // Krnl_GA
	cl_mem_ext_ptr_t d_bank1_ext; // Krnl_Conform
	cl_mem_ext_ptr_t d_bank2_ext; // Krnl_InterE
	cl_mem_ext_ptr_t d_bank3_ext; // Krnl_IntraE

	d_bank0_ext.flags = XCL_MEM_DDR_BANK0;
	d_bank0_ext.obj   = NULL;
	d_bank0_ext.param = 0;

	d_bank1_ext.flags = XCL_MEM_DDR_BANK1;
	d_bank1_ext.obj   = NULL;
	d_bank1_ext.param = 0;

	d_bank2_ext.flags = XCL_MEM_DDR_BANK2;
	d_bank2_ext.obj   = NULL;
	d_bank2_ext.param = 0;

	d_bank3_ext.flags = XCL_MEM_DDR_BANK3;
	d_bank3_ext.obj   = NULL;
	d_bank3_ext.param = 0;

// Replacing common buffer creation with 
// a Xilinx-specific where DDR banks can be specified
#if 0
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#if defined (FIXED_POINT_INTERE)
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATOMS*sizeof(fixedpt64),                &mem_KerConstStatic_fixpt64_atom_charges_const);
#endif
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATOMS*sizeof(float),                    &mem_KerConstStatic_atom_charges_const);

	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATOMS*sizeof(char),                     &mem_KerConstStatic_atom_types_const);

/*
	mallocBufferObject(context,CL_MEM_READ_ONLY, 3*MAX_INTRAE_CONTRIBUTORS*sizeof(char),            &mem_KerConstStatic_intraE_contributors_const);
*/
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	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_INTRAE_CONTRIBUTORS*sizeof(cl_char3),          &mem_KerConstStatic_intraE_contributors_const);

        mallocBufferObject(context,CL_MEM_READ_ONLY, ATYPE_NUM*sizeof(float),				&mem_KerConstStatic_reqm_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY, ATYPE_NUM*sizeof(float),				&mem_KerConstStatic_reqm_hbond_const);
  	mallocBufferObject(context,CL_MEM_READ_ONLY, ATYPE_NUM*sizeof(unsigned int),			&mem_KerConstStatic_atom1_types_reqm_const);
  	mallocBufferObject(context,CL_MEM_READ_ONLY, ATYPE_NUM*sizeof(unsigned int),                    &mem_KerConstStatic_atom2_types_reqm_const);
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	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float), &mem_KerConstStatic_VWpars_AC_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float), &mem_KerConstStatic_VWpars_BD_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATYPES*sizeof(float), 			&mem_KerConstStatic_dspars_S_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATYPES*sizeof(float), 			&mem_KerConstStatic_dspars_V_const);
	#if defined (FIXED_POINT_CONFORM)
	// fixed-point
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ROTATIONS*sizeof(fixedpt), 		&mem_KerConstStatic_rotlist_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATOMS*sizeof(cl_int3), 		        &mem_KerConstStatic_ref_coords_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ROTBONDS*sizeof(cl_int3), 		&mem_KerConstStatic_rotbonds_moving_vectors_const);
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	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ROTBONDS*sizeof(cl_int3), 		&mem_KerConstStatic_rotbonds_unit_vectors_const);
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	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_RUNS*sizeof(cl_int4),			&mem_KerConstStatic_ref_orientation_quats_const);
	#else
	// floating-point (original)
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ROTATIONS*sizeof(int), 			&mem_KerConstStatic_rotlist_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATOMS*sizeof(cl_float3), 		&mem_KerConstStatic_ref_coords_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ROTBONDS*sizeof(cl_float3), 		&mem_KerConstStatic_rotbonds_moving_vectors_const);
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	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ROTBONDS*sizeof(cl_float3), 		&mem_KerConstStatic_rotbonds_unit_vectors_const);
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	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_RUNS*sizeof(cl_float4),			&mem_KerConstStatic_ref_orientation_quats_const);
	#endif

//#if defined (FIXED_POINT_INTERE)
#if 0
	mallocBufferObject(context,CL_MEM_READ_ONLY,size_fixedpt64grids,   	&mem_dockpars_fgrids);
#else
	mallocBufferObject(context,CL_MEM_READ_ONLY,size_floatgrids,   		&mem_dockpars_fgrids);

	#if defined(SEPARATE_FGRID_INTERE)
	mallocBufferObject(context,CL_MEM_READ_ONLY,size_floatgrids2,   	&mem_dockpars_fgrids2);
	mallocBufferObject(context,CL_MEM_READ_ONLY,size_floatgrids3,   	&mem_dockpars_fgrids3);
	#endif
#endif

	mallocBufferObject(context,CL_MEM_READ_WRITE,size_populations,  	&mem_dockpars_conformations_current);
	mallocBufferObject(context,CL_MEM_READ_WRITE,size_energies,    		&mem_dockpars_energies_current);

#if defined(SINGLE_COPY_POP_ENE)
	mallocBufferObject(context,CL_MEM_WRITE_ONLY,size_evals_of_runs,  	&mem_evals_performed);
	mallocBufferObject(context,CL_MEM_WRITE_ONLY,size_evals_of_runs,  	&mem_gens_performed);
#else
	mallocBufferObject(context,CL_MEM_WRITE_ONLY,2*sizeof(unsigned int),  	&mem_evals_and_generations_performed);
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#endif
#endif



#if defined (FIXED_POINT_INTERE)
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATOMS*sizeof(fixedpt64),                &d_bank2_ext, &mem_KerConstStatic_fixpt64_atom_charges_const);	
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#endif
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	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATOMS*sizeof(float),                    &d_bank2_ext, &mem_KerConstStatic_InterE_atom_charges_const);	// InterE
  	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATOMS*sizeof(char),                     &d_bank2_ext, &mem_KerConstStatic_InterE_atom_types_const);	// InterE

	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATOMS*sizeof(float),                    &d_bank3_ext, &mem_KerConstStatic_IntraE_atom_charges_const);	// IntraE
  	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATOMS*sizeof(char),                     &d_bank3_ext, &mem_KerConstStatic_IntraE_atom_types_const);	// IntraE

/*
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, 3*MAX_INTRAE_CONTRIBUTORS*sizeof(char),            &d_bank3_ext, &mem_KerConstStatic_intraE_contributors_const);	// IntraE
*/
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_INTRAE_CONTRIBUTORS*sizeof(cl_char3),          &d_bank3_ext, &mem_KerConstStatic_intraE_contributors_const);	// IntraE

        mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, ATYPE_NUM*sizeof(float),			        &d_bank3_ext, &mem_KerConstStatic_reqm_const);			// IntraE
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, ATYPE_NUM*sizeof(float),			        &d_bank3_ext, &mem_KerConstStatic_reqm_hbond_const);		// IntraE
  	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, ATYPE_NUM*sizeof(unsigned int),		        &d_bank3_ext, &mem_KerConstStatic_atom1_types_reqm_const);	// IntraE
  	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, ATYPE_NUM*sizeof(unsigned int),                    &d_bank3_ext, &mem_KerConstStatic_atom2_types_reqm_const);	// IntraE

	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float), &d_bank3_ext, &mem_KerConstStatic_VWpars_AC_const);		// IntraE
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float), &d_bank3_ext, &mem_KerConstStatic_VWpars_BD_const);		// IntraE
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATYPES*sizeof(float), 		        &d_bank3_ext, &mem_KerConstStatic_dspars_S_const);		// IntraE
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATYPES*sizeof(float), 			&d_bank3_ext, &mem_KerConstStatic_dspars_V_const);		// IntraE
	#if defined (FIXED_POINT_CONFORM)
	// fixed-point
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ROTATIONS*sizeof(fixedpt), 		&d_bank1_ext, &mem_KerConstStatic_rotlist_const);			// Conform
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATOMS*sizeof(cl_int3), 		        &d_bank1_ext, &mem_KerConstStatic_ref_coords_const);			// Conform
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ROTBONDS*sizeof(cl_int3), 		&d_bank1_ext, &mem_KerConstStatic_rotbonds_moving_vectors_const);	// Conform
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ROTBONDS*sizeof(cl_int3), 		&d_bank1_ext, &mem_KerConstStatic_rotbonds_unit_vectors_const);		// Conform
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_RUNS*sizeof(cl_int4),			&d_bank1_ext, &mem_KerConstStatic_ref_orientation_quats_const);		// Conform
	#else
	// floating-point (original)
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ROTATIONS*sizeof(int), 			&d_bank1_ext, &mem_KerConstStatic_rotlist_const);			// Conform
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ATOMS*sizeof(cl_float3), 		&d_bank1_ext, &mem_KerConstStatic_ref_coords_const); 			// Conform
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ROTBONDS*sizeof(cl_float3), 		&d_bank1_ext, &mem_KerConstStatic_rotbonds_moving_vectors_const);	// Conform
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_ROTBONDS*sizeof(cl_float3), 		&d_bank1_ext, &mem_KerConstStatic_rotbonds_unit_vectors_const);		// Conform
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX, MAX_NUM_OF_RUNS*sizeof(cl_float4),			&d_bank1_ext, &mem_KerConstStatic_ref_orientation_quats_const);		// Conform
	#endif

//#if defined (FIXED_POINT_INTERE)
#if 0
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX,size_fixedpt64grids,   	&d_bank2_ext,	&mem_dockpars_fgrids);	// InterE
#else
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX,size_floatgrids,   		&d_bank2_ext,	&mem_dockpars_fgrids);	// InterE

	#if defined(SEPARATE_FGRID_INTERE)
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX,size_floatgrids2,   	&d_bank2_ext,	&mem_dockpars_fgrids2);	// InterE
	mallocBufferObject(context,CL_MEM_READ_ONLY | CL_MEM_EXT_PTR_XILINX,size_floatgrids3,   	&d_bank2_ext,	&mem_dockpars_fgrids3);	// InterE
	#endif
#endif

	mallocBufferObject(context,CL_MEM_READ_WRITE | CL_MEM_EXT_PTR_XILINX,size_populations,  	&d_bank0_ext,	&mem_dockpars_conformations_current);	// GA
	mallocBufferObject(context,CL_MEM_READ_WRITE | CL_MEM_EXT_PTR_XILINX,size_energies,    		&d_bank0_ext,	&mem_dockpars_energies_current);	// GA

#if defined(SINGLE_COPY_POP_ENE)
	mallocBufferObject(context,CL_MEM_WRITE_ONLY | CL_MEM_EXT_PTR_XILINX,size_evals_of_runs,  	&d_bank0_ext,	&mem_evals_performed);			// GA
					
	mallocBufferObject(context,CL_MEM_WRITE_ONLY | CL_MEM_EXT_PTR_XILINX,size_evals_of_runs,  	&d_bank0_ext,	&mem_gens_performed);			// GA
#else
	mallocBufferObject(context,CL_MEM_WRITE_ONLY | CL_MEM_EXT_PTR_XILINX,2*sizeof(unsigned int),  	&d_bank0_ext,	&mem_evals_and_generations_performed);	// GA
#endif















// -----------------------------------------------------------------------------------------------------

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#if defined(SINGLE_COPY_POP_ENE)

#else
	unsigned int array_evals_and_generations_performed [2]; // [0]: evals, [1]: generations 
#endif

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#if defined (FIXED_POINT_INTERE)
	#if 0
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	memcopyBufferObjectToDevice(command_queue,mem_KerConstStatic_fixpt64_atom_charges_const,            &KerConstStatic.fixpt64_atom_charges_const[0],            MAX_NUM_OF_ATOMS*sizeof(fixedpt64));
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	#endif
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	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_fixpt64_atom_charges_const,            &KerConstStatic.fixpt64_atom_charges_const[0],            MAX_NUM_OF_ATOMS*sizeof(fixedpt64));
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#endif
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	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_InterE_atom_charges_const,            &KerConstStatic.atom_charges_const[0],            MAX_NUM_OF_ATOMS*sizeof(float));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_InterE_atom_types_const,              &KerConstStatic.atom_types_const[0],              MAX_NUM_OF_ATOMS*sizeof(char));
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	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_IntraE_atom_charges_const,            &KerConstStatic.atom_charges_const[0],            MAX_NUM_OF_ATOMS*sizeof(float));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_IntraE_atom_types_const,              &KerConstStatic.atom_types_const[0],              MAX_NUM_OF_ATOMS*sizeof(char));
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/*
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	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_intraE_contributors_const,     &KerConstStatic.intraE_contributors_const[0],     3*MAX_INTRAE_CONTRIBUTORS*sizeof(char));
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*/
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	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_intraE_contributors_const,     &KerConstStatic.intraE_contributors_const[0],     MAX_INTRAE_CONTRIBUTORS*sizeof(cl_char3));
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	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_reqm_const,         	     &KerConstStatic.reqm_const,           	           ATYPE_NUM*sizeof(float));
  	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_reqm_hbond_const,              &KerConstStatic.reqm_hbond_const,                 ATYPE_NUM*sizeof(float));
  	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_atom1_types_reqm_const,        &KerConstStatic.atom1_types_reqm_const,           ATYPE_NUM*sizeof(unsigned int));
  	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_atom2_types_reqm_const,        &KerConstStatic.atom2_types_reqm_const,           ATYPE_NUM*sizeof(unsigned int));
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	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_VWpars_AC_const,               &KerConstStatic.VWpars_AC_const[0],               MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_VWpars_BD_const,               &KerConstStatic.VWpars_BD_const[0],               MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_dspars_S_const,                &KerConstStatic.dspars_S_const[0], 	       MAX_NUM_OF_ATYPES*sizeof(float));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_dspars_V_const,                &KerConstStatic.dspars_V_const[0], 	       MAX_NUM_OF_ATYPES*sizeof(float));
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	#if defined (FIXED_POINT_CONFORM)
	// fixed-point
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	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_rotlist_const,                 &KerConstStatic.rotlist_const[0], 		       MAX_NUM_OF_ROTATIONS*sizeof(fixedpt));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_ref_coords_const, 	     &KerConstStatic.ref_coords_const[0],              MAX_NUM_OF_ATOMS*sizeof(cl_int3));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_rotbonds_moving_vectors_const, &KerConstStatic.rotbonds_moving_vectors_const[0], MAX_NUM_OF_ROTBONDS*sizeof(cl_int3));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_rotbonds_unit_vectors_const,   &KerConstStatic.rotbonds_unit_vectors_const[0],   MAX_NUM_OF_ROTBONDS*sizeof(cl_int3));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_ref_orientation_quats_const,   &KerConstStatic.ref_orientation_quats_const[0],   MAX_NUM_OF_RUNS*sizeof(cl_int4));
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	#else
	// floating-point (original)
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	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_rotlist_const,                 &KerConstStatic.rotlist_const[0], 		       MAX_NUM_OF_ROTATIONS*sizeof(int));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_ref_coords_const, 	     &KerConstStatic.ref_coords_const[0],              MAX_NUM_OF_ATOMS*sizeof(cl_float3));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_rotbonds_moving_vectors_const, &KerConstStatic.rotbonds_moving_vectors_const[0], MAX_NUM_OF_ROTBONDS*sizeof(cl_float3));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_rotbonds_unit_vectors_const,   &KerConstStatic.rotbonds_unit_vectors_const[0],   MAX_NUM_OF_ROTBONDS*sizeof(cl_float3));
	memcopyBufferObjectToDevice(command_queue_ga,mem_KerConstStatic_ref_orientation_quats_const,   &KerConstStatic.ref_orientation_quats_const[0],   MAX_NUM_OF_RUNS*sizeof(cl_float4));
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	#endif

//#if defined (FIXED_POINT_INTERE)
#if 0
/*
	cpu_fixedpt64grids = (fixedpt64*) alignedMalloc((sizeof(fixedpt64))*(mygrid->num_of_atypes+2)*
						  			    (mygrid->size_xyz[0])*
			   					            (mygrid->size_xyz[1])*
									    (mygrid->size_xyz[2]));
*/
	cpu_fixedpt64grids = (fixedpt64*) alignedMalloc(size_fixedpt64grids);

	float* mypoi;
	fixedpt64* myqoi;
	mypoi = cpu_floatgrids;
	myqoi = cpu_fixedpt64grids;

	for (int t=0; t < mygrid->num_of_atypes+2; t++) {
		//reading values
		for (int z=0; z < mygrid->size_xyz[2]; z++)
			for (int y=0; y < mygrid->size_xyz[1]; y++)
				for (int x=0; x < mygrid->size_xyz[0]; x++)
				{
					//fscanf(fp, "%f", mypoi);
					//mypoi++;
					float tmp_grids = *mypoi;
					mypoi++;
					*myqoi = fixedpt64_fromfloat(tmp_grids);

					// test to prove that it requires 32.32
					// and 16.16 is not enough
					//fixedpt myqoi16 = fixedpt_fromfloat(tmp_grids);
					//printf("%-10f %-10f %-10f\n", tmp_grids, fixedpt64_tofloat(*myqoi), fixedpt_tofloat(myqoi16));
					
					myqoi++;

					
				}
	}

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	memcopyBufferObjectToDevice(command_queue_ga,mem_dockpars_fgrids, 	cpu_fixedpt64grids,       size_fixedpt64grids);
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#else
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	memcopyBufferObjectToDevice(command_queue_ga,mem_dockpars_fgrids, 	cpu_floatgrids,       size_floatgrids);
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	#if defined(SEPARATE_FGRID_INTERE)
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	memcopyBufferObjectToDevice(command_queue_ga,mem_dockpars_fgrids2, 	cpu_floatgrids + mygrid->num_of_atypes     * mygrid->size_xyz[0]*mygrid->size_xyz[1]* mygrid->size_xyz[2],       size_floatgrids2);
	memcopyBufferObjectToDevice(command_queue_ga,mem_dockpars_fgrids3, 	cpu_floatgrids + (mygrid->num_of_atypes+1) * mygrid->size_xyz[0]*mygrid->size_xyz[1]* mygrid->size_xyz[2],       size_floatgrids3);
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	#endif
#endif

	clock_start_docking = clock();

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#ifdef ENABLE_KRNL_GA
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	#if defined(SINGLE_COPY_POP_ENE)
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        setKernelArg(kernel_ga,0,  sizeof(mem_dockpars_conformations_current),    &mem_dockpars_conformations_current);
        setKernelArg(kernel_ga,1,  sizeof(mem_dockpars_energies_current),         &mem_dockpars_energies_current);
	setKernelArg(kernel_ga,2,  sizeof(mem_evals_performed),   		&mem_evals_performed);
	setKernelArg(kernel_ga,3,  sizeof(mem_gens_performed),    		&mem_gens_performed);
	setKernelArg(kernel_ga,4,  sizeof(unsigned int),                  	&dockpars.pop_size);
	setKernelArg(kernel_ga,5,  sizeof(unsigned int),                 		&dockpars.num_of_energy_evals);
	setKernelArg(kernel_ga,6,  sizeof(unsigned int),                 		&dockpars.num_of_generations);
	setKernelArg(kernel_ga,7,  sizeof(float),                          	&dockpars.tournament_rate);
	setKernelArg(kernel_ga,8,  sizeof(float),                          	&dockpars.mutation_rate);
	setKernelArg(kernel_ga,9,  sizeof(float),                          	&dockpars.abs_max_dmov);
	setKernelArg(kernel_ga,10, sizeof(float),                          	&dockpars.abs_max_dang);
	setKernelArg(kernel_ga,11, sizeof(float),                                 &two_absmaxdmov);
	setKernelArg(kernel_ga,12, sizeof(float),                                 &two_absmaxdang);
	setKernelArg(kernel_ga,13, sizeof(float),                          	&dockpars.crossover_rate);
	setKernelArg(kernel_ga,14, sizeof(unsigned int),                          &dockpars.num_of_lsentities);
	setKernelArg(kernel_ga,15, sizeof(unsigned char),                         &dockpars.num_of_genes);
	//setKernelArg(kernel_ga,16, sizeof(unsigned short),                      run_cnt);
	//setKernelArg(kernel_ga,17, sizeof(unsigned int),                        offset_pop);
	//setKernelArg(kernel_ga,18, sizeof(unsigned int),                        offset_ene);
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	#else
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        setKernelArg(kernel_ga,0,  sizeof(mem_dockpars_conformations_current),    &mem_dockpars_conformations_current);
        setKernelArg(kernel_ga,1,  sizeof(mem_dockpars_energies_current),         &mem_dockpars_energies_current);
	setKernelArg(kernel_ga,2,  sizeof(mem_evals_and_generations_performed),   &mem_evals_and_generations_performed);
	setKernelArg(kernel_ga,3,  sizeof(unsigned int),                  	&dockpars.pop_size);
	setKernelArg(kernel_ga,4,  sizeof(unsigned int),                 		&dockpars.num_of_energy_evals);
	setKernelArg(kernel_ga,5,  sizeof(unsigned int),                 		&dockpars.num_of_generations);
	setKernelArg(kernel_ga,6,  sizeof(float),                          	&dockpars.tournament_rate);
	setKernelArg(kernel_ga,7,  sizeof(float),                          	&dockpars.mutation_rate);
	setKernelArg(kernel_ga,8,  sizeof(float),                          	&dockpars.abs_max_dmov);
	setKernelArg(kernel_ga,9,  sizeof(float),                          	&dockpars.abs_max_dang);
	setKernelArg(kernel_ga,10, sizeof(float),                                 &two_absmaxdmov);
	setKernelArg(kernel_ga,11, sizeof(float),                                 &two_absmaxdang);
	setKernelArg(kernel_ga,12, sizeof(float),                          	&dockpars.crossover_rate);
	setKernelArg(kernel_ga,13, sizeof(unsigned int),                          &dockpars.num_of_lsentities);
	setKernelArg(kernel_ga,14, sizeof(unsigned char),                         &dockpars.num_of_genes);
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	#endif
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#endif // End of ENABLE_KRNL_GA
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#ifdef ENABLE_KRNL_CONFORM // Krnl_Conform
	setKernelArg(kernel_conform,0,  sizeof(mem_KerConstStatic_rotlist_const),      	   &mem_KerConstStatic_rotlist_const);
	setKernelArg(kernel_conform,1,  sizeof(mem_KerConstStatic_ref_coords_const),              &mem_KerConstStatic_ref_coords_const);
	setKernelArg(kernel_conform,2,  sizeof(mem_KerConstStatic_rotbonds_moving_vectors_const), &mem_KerConstStatic_rotbonds_moving_vectors_const);
	setKernelArg(kernel_conform,3,  sizeof(mem_KerConstStatic_rotbonds_unit_vectors_const),   &mem_KerConstStatic_rotbonds_unit_vectors_const);
	setKernelArg(kernel_conform,4,  sizeof(unsigned int),       &dockpars.rotbondlist_length);
	setKernelArg(kernel_conform,5,  sizeof(unsigned char),      &dockpars.num_of_atoms);
	setKernelArg(kernel_conform,6,  sizeof(unsigned char),      &dockpars.num_of_genes);
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/*
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	setKernelArg(kernel_conform,7,  sizeof(unsigned char),      &num_rotbonds);
	setKernelArg(kernel_conform,8,  sizeof(mem_KerConstStatic_ref_orientation_quats_const),   &mem_KerConstStatic_ref_orientation_quats_const);
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*/
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	setKernelArg(kernel_conform,7,  sizeof(mem_KerConstStatic_ref_orientation_quats_const),   &mem_KerConstStatic_ref_orientation_quats_const);
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	#if defined(SINGLE_COPY_POP_ENE)

	#else
		#if defined (FIXED_POINT_CONFORM)
	// fixed-point
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	setKernelArg(kernel_conform,8,  sizeof(fixedpt),            &KerConstDynamic.ref_orientation_quats_const[0]);
	setKernelArg(kernel_conform,9,  sizeof(fixedpt),            &KerConstDynamic.ref_orientation_quats_const[1]);
	setKernelArg(kernel_conform,10, sizeof(fixedpt),            &KerConstDynamic.ref_orientation_quats_const[2]);
	setKernelArg(kernel_conform,11, sizeof(fixedpt),            &KerConstDynamic.ref_orientation_quats_const[3]);
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		#else
	// floating-point (original)
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	setKernelArg(kernel_conform,8,  sizeof(float),              &KerConstDynamic.ref_orientation_quats_const[0]);
	setKernelArg(kernel_conform,9,  sizeof(float),              &KerConstDynamic.ref_orientation_quats_const[1]);
	setKernelArg(kernel_conform,10, sizeof(float),              &KerConstDynamic.ref_orientation_quats_const[2]);
	setKernelArg(kernel_conform,11, sizeof(float),              &KerConstDynamic.ref_orientation_quats_const[3]);
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		#endif
	#endif
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#endif // End of ENABLE_KRNL_CONFORM
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	unsigned char gridsizex_minus1 = dockpars.gridsize_x - 1;
	unsigned char gridsizey_minus1 = dockpars.gridsize_y - 1;
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	unsigned char gridsizez_minus1 = dockpars.gridsize_z - 1;

#if defined (FIXED_POINT_INTERE)

#else
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	float fgridsizex_minus1 = (float) gridsizex_minus1;
	float fgridsizey_minus1 = (float) gridsizey_minus1;
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	float fgridsizez_minus1 = (float) gridsizez_minus1;

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#endif


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#ifdef ENABLE_KRNL_INTERE // Krnl_InterE
        setKernelArg(kernel_intere,0,  sizeof(mem_dockpars_fgrids),                    &mem_dockpars_fgrids);
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	#if defined (FIXED_POINT_INTERE)
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	setKernelArg(kernel_intere,1,  sizeof(mem_KerConstStatic_fixpt64_atom_charges_const),  &mem_KerConstStatic_fixpt64_atom_charges_const);
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	#else
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	setKernelArg(kernel_intere,1,  sizeof(mem_KerConstStatic_InterE_atom_charges_const),  &mem_KerConstStatic_InterE_atom_charges_const);
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	#endif
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	setKernelArg(kernel_intere,2,  sizeof(mem_KerConstStatic_InterE_atom_types_const),    &mem_KerConstStatic_InterE_atom_types_const);
	setKernelArg(kernel_intere,3,  sizeof(unsigned char),                          &dockpars.g1);
	setKernelArg(kernel_intere,4,  sizeof(unsigned int),                           &dockpars.g2);
	setKernelArg(kernel_intere,5,  sizeof(unsigned int),                           &dockpars.g3);
	setKernelArg(kernel_intere,6,  sizeof(unsigned char),                          &dockpars.num_of_atoms);
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	#if defined (FIXED_POINT_INTERE)
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	setKernelArg(kernel_intere,7,  sizeof(unsigned char),                          &gridsizex_minus1);
	setKernelArg(kernel_intere,8,  sizeof(unsigned char),                          &gridsizey_minus1);
	setKernelArg(kernel_intere,9,  sizeof(unsigned char),                          &gridsizez_minus1);
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	#else
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	setKernelArg(kernel_intere,7,  sizeof(float),                          	 &fgridsizex_minus1);
	setKernelArg(kernel_intere,8,  sizeof(float),                          	 &fgridsizey_minus1);
	setKernelArg(kernel_intere,9,  sizeof(float),                          	 &fgridsizez_minus1);
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	#endif
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	#if defined(SEPARATE_FGRID_INTERE)
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	setKernelArg(kernel_intere,10, sizeof(mem_dockpars_fgrids2),                   &mem_dockpars_fgrids2);
	setKernelArg(kernel_intere,11, sizeof(mem_dockpars_fgrids3),                   &mem_dockpars_fgrids3);
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	#else
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	setKernelArg(kernel_intere,10, sizeof(unsigned int),                           &mul_tmp2);
	setKernelArg(kernel_intere,11, sizeof(unsigned int),                           &mul_tmp3);
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	#endif
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#endif // End of ENABLE_KRNL_INTERE

#ifdef ENABLE_KRNL_INTRAE // Krnl_IntraE
	setKernelArg(kernel_intrae,0,  sizeof(mem_KerConstStatic_IntraE_atom_charges_const),        &mem_KerConstStatic_IntraE_atom_charges_const);
	setKernelArg(kernel_intrae,1,  sizeof(mem_KerConstStatic_IntraE_atom_types_const),          &mem_KerConstStatic_IntraE_atom_types_const);
	setKernelArg(kernel_intrae,2,  sizeof(mem_KerConstStatic_intraE_contributors_const), &mem_KerConstStatic_intraE_contributors_const);

  	setKernelArg(kernel_intrae,3,  sizeof(dockpars.smooth),                              &dockpars.smooth);
  	setKernelArg(kernel_intrae,4,  sizeof(mem_KerConstStatic_reqm_const),                &mem_KerConstStatic_reqm_const);
  	setKernelArg(kernel_intrae,5,  sizeof(mem_KerConstStatic_reqm_hbond_const),          &mem_KerConstStatic_reqm_hbond_const);
  	setKernelArg(kernel_intrae,6,  sizeof(mem_KerConstStatic_atom1_types_reqm_const),    &mem_KerConstStatic_atom1_types_reqm_const);
  	setKernelArg(kernel_intrae,7,  sizeof(mem_KerConstStatic_atom2_types_reqm_const),    &mem_KerConstStatic_atom2_types_reqm_const);

	setKernelArg(kernel_intrae,8,  sizeof(mem_KerConstStatic_VWpars_AC_const),           &mem_KerConstStatic_VWpars_AC_const);
	setKernelArg(kernel_intrae,9,  sizeof(mem_KerConstStatic_VWpars_BD_const),           &mem_KerConstStatic_VWpars_BD_const);
	setKernelArg(kernel_intrae,10, sizeof(mem_KerConstStatic_dspars_S_const),            &mem_KerConstStatic_dspars_S_const);
	setKernelArg(kernel_intrae,11, sizeof(mem_KerConstStatic_dspars_V_const),            &mem_KerConstStatic_dspars_V_const);

	setKernelArg(kernel_intrae,12, sizeof(unsigned char),                    	       &dockpars.num_of_atoms);
	setKernelArg(kernel_intrae,13, sizeof(unsigned int),                     	       &dockpars.num_of_intraE_contributors);
	setKernelArg(kernel_intrae,14, sizeof(float),                          	       &dockpars.grid_spacing);
	setKernelArg(kernel_intrae,15, sizeof(unsigned char),                    	       &dockpars.num_of_atypes);
	setKernelArg(kernel_intrae,16, sizeof(float),                          	       &dockpars.coeff_elec);
	setKernelArg(kernel_intrae,17, sizeof(float),                          	       &dockpars.qasp);
	setKernelArg(kernel_intrae,18, sizeof(float),                          	       &dockpars.coeff_desolv);
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/*
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	setKernelArg(kernel_intrae,14, sizeof(unsigned int),                     	&square_num_of_atypes);
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*/
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