performdocking.cpp

/*
 * (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;
static cl_context       context       = NULL;

// Unique command queue
static cl_command_queue command_queue = NULL;

// Kernel name, as defined in the CL file
#ifdef ENABLE_KERNEL1
/*
static cl_command_queue command_queue1 = NULL;
*/
static cl_kernel kernel1  = NULL;
static const char *name_k1 = "Krnl_GA";
#endif

#ifdef ENABLE_KERNEL2
/*
static cl_command_queue command_queue2 = NULL;
*/
static cl_kernel kernel2  = NULL;
static const char *name_k2 = "Krnl_Conform";
#endif

#ifdef ENABLE_KERNEL3
/*
static cl_command_queue command_queue3 = NULL;
*/
static cl_kernel kernel3  = NULL;
static const char *name_k3 = "Krnl_InterE";
#endif

#ifdef ENABLE_KERNEL4
/*
static cl_command_queue command_queue4 = NULL;
*/
static cl_kernel kernel4  = NULL;
static const char *name_k4 = "Krnl_IntraE";
#endif




#if 0
#ifdef ENABLE_KERNEL8
/*
static cl_command_queue command_queue8 = NULL;
*/
static cl_kernel kernel8  = NULL;
static const char *name_k8 = "Krnl_Prng_BT_ushort";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL5
/*
static cl_command_queue command_queue5 = NULL;
*/
static cl_kernel kernel5  = NULL;
static const char *name_k5 = "Krnl_Prng_BT_float";
#endif
#endif

#ifdef ENABLE_KERNEL10
/*
static cl_command_queue command_queue10 = NULL;
*/
static cl_kernel kernel10  = NULL;
static const char *name_k10 = "Krnl_Prng_GG_uchar";
#endif

#ifdef ENABLE_KERNEL6
/*
static cl_command_queue command_queue6 = NULL;
*/
static cl_kernel kernel6  = NULL;
static const char *name_k6 = "Krnl_Prng_GG_float";
#endif

#if 0
#ifdef ENABLE_KERNEL9
/*
static cl_command_queue command_queue9 = NULL;
*/
static cl_kernel kernel9  = NULL;
static const char *name_k9 = "Krnl_Prng_LS_ushort";
#endif
#endif

#ifdef ENABLE_KERNEL7
/*
static cl_command_queue command_queue7 = NULL;
*/
static cl_kernel kernel7  = NULL;
static const char *name_k7 = "Krnl_Prng_LS_float";
#endif

#if 0
#ifdef ENABLE_KERNEL11
/*
static cl_command_queue command_queue11 = NULL;
*/
static cl_kernel kernel11  = NULL;
static const char *name_k11 = "Krnl_Prng_Arbiter";
#endif
#endif

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

#if 0
#ifdef ENABLE_KERNEL13
/*
static cl_command_queue command_queue13 = NULL;
*/
static cl_kernel kernel13  = NULL;
static const char *name_k13 = "Krnl_LS_Arbiter";
#endif
#endif




#ifdef ENABLE_KERNEL14
/*
static cl_command_queue command_queue14 = NULL;
*/
static cl_kernel kernel14  = NULL;
static const char *name_k14 = "Krnl_Prng_LS2_float";
#endif

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

#if 0
#ifdef ENABLE_KERNEL16
/*
static cl_command_queue command_queue16 = NULL;
*/
static cl_kernel kernel16  = NULL;
static const char *name_k16 = "Krnl_LS2_Arbiter";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL17
/*
static cl_command_queue command_queue17 = NULL;
*/
static cl_kernel kernel17  = NULL;
static const char *name_k17 = "Krnl_Conform2";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL18
/*
static cl_command_queue command_queue18 = NULL;
*/
static cl_kernel kernel18  = NULL;
static const char *name_k18 = "Krnl_InterE2";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL19
/*
static cl_command_queue command_queue19 = NULL;
*/
static cl_kernel kernel19  = NULL;
static const char *name_k19 = "Krnl_IntraE2";
#endif
#endif








#ifdef ENABLE_KERNEL20
/*
static cl_command_queue command_queue20 = NULL;
*/
static cl_kernel kernel20  = NULL;
static const char *name_k20 = "Krnl_Prng_LS3_float";
#endif

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

#if 0
#ifdef ENABLE_KERNEL22
/*
static cl_command_queue command_queue22 = NULL;
*/
static cl_kernel kernel22  = NULL;
static const char *name_k22 = "Krnl_LS3_Arbiter";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL23
/*
static cl_command_queue command_queue23 = NULL;
*/
static cl_kernel kernel23  = NULL;
static const char *name_k23 = "Krnl_Conf_Arbiter";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL24
/*
static cl_command_queue command_queue24 = NULL;
*/
static cl_kernel kernel24  = NULL;
static const char *name_k24 = "Krnl_Conf_Arbiter2";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL25
/*
static cl_command_queue command_queue25 = NULL;
*/
static cl_kernel kernel25  = NULL;
static const char *name_k25 = "Krnl_Prng_LS2_ushort";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL26
/*
static cl_command_queue command_queue26 = NULL;
*/
static cl_kernel kernel26  = NULL;
static const char *name_k26 = "Krnl_Prng_LS3_ushort";
#endif
#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

#if 0
#ifdef ENABLE_KERNEL28
/*
static cl_command_queue command_queue28 = NULL;
*/
static cl_kernel kernel28  = NULL;
static const char *name_k28 = "Krnl_IA_pipeline_Arbiter";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL29
/*
static cl_command_queue command_queue29 = NULL;
*/
static cl_kernel kernel29  = NULL;
static const char *name_k29 = "Krnl_IA_pipeline";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL30
/*
static cl_command_queue command_queue30 = NULL;
*/
static cl_kernel kernel30  = NULL;
static const char *name_k30 = "Krnl_IA_pipeline2";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL31
static cl_command_queue command_queue31 = NULL;
static cl_kernel kernel31  = NULL;
static const char *name_k31 = "Krnl_Prng_BT_Arbiter";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL32
/*
static cl_command_queue command_queue32 = NULL;
*/
static cl_kernel kernel32  = NULL;
static const char *name_k32 = "Krnl_Prng_GG_Arbiter";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL33
/*
static cl_command_queue command_queue33 = NULL;
*/
static cl_kernel kernel33  = NULL;
static const char *name_k33 = "Krnl_Prng_LS_ushort_Arbiter";
#endif
#endif

#if 0
#ifdef ENABLE_KERNEL34
/*
static cl_command_queue command_queue34 = NULL;
*/
static cl_kernel kernel34  = NULL;
static const char *name_k34 = "Krnl_Prng_LS_float_Arbiter";
#endif
#endif

#ifdef ENABLE_KERNEL35
/*
static cl_command_queue command_queue35 = NULL;
*/
static cl_kernel kernel35  = NULL;
static const char *name_k35 = "Krnl_Prng_LS123_ushort";
#endif

#ifdef ENABLE_KERNEL36
/*
static cl_command_queue command_queue36 = NULL;
*/
static cl_kernel kernel36  = NULL;
static const char *name_k36 = "Krnl_Prng_BT_ushort_float";
#endif






#ifdef ENABLE_KERNEL37
/*
static cl_command_queue command_queue37 = NULL;
*/
static cl_kernel kernel37  = NULL;
static const char *name_k37 = "Krnl_Prng_LS4_float";
#endif

#ifdef ENABLE_KERNEL38
/*
static cl_command_queue command_queue38 = NULL;
*/
static cl_kernel kernel38  = NULL;
static const char *name_k38 = "Krnl_Prng_LS5_float";
#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";
#endif






#ifdef ENABLE_KERNEL41
/*
static cl_command_queue command_queue41 = NULL;
*/
static cl_kernel kernel41  = NULL;
static const char *name_k41 = "Krnl_Prng_LS6_float";
#endif

#ifdef ENABLE_KERNEL42
/*
static cl_command_queue command_queue42 = NULL;
*/
static cl_kernel kernel42  = NULL;
static const char *name_k42 = "Krnl_Prng_LS7_float";
#endif

#ifdef ENABLE_KERNEL43
/*
static cl_command_queue command_queue43 = NULL;
*/
static cl_kernel kernel43  = NULL;
static const char *name_k43 = "Krnl_Prng_LS8_float";
#endif

#ifdef ENABLE_KERNEL44
/*
static cl_command_queue command_queue44 = NULL;
*/
static cl_kernel kernel44  = NULL;
static const char *name_k44 = "Krnl_Prng_LS9_float";
#endif



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

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

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

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




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
cl_mem mem_KerConstStatic_atom_charges_const;
cl_mem mem_KerConstStatic_atom_types_const;
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;

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;
cl_mem mem_KerConstStatic_rotbonds_unit_vectors_const;
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



































//#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;
	dockpars.smooth = mypars->smooth;

/*
// 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
#endif

#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);
*/
	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);

	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);
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ROTBONDS*sizeof(cl_int3), 		&mem_KerConstStatic_rotbonds_unit_vectors_const);
	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);
	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ROTBONDS*sizeof(cl_float3), 		&mem_KerConstStatic_rotbonds_unit_vectors_const);
	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);
#endif

#if defined(SINGLE_COPY_POP_ENE)

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

#if defined (FIXED_POINT_INTERE)
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_fixpt64_atom_charges_const,            &KerConstStatic.fixpt64_atom_charges_const[0],            MAX_NUM_OF_ATOMS*sizeof(fixedpt64));
#endif
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_atom_charges_const,            &KerConstStatic.atom_charges_const[0],            MAX_NUM_OF_ATOMS*sizeof(float));

	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_atom_types_const,              &KerConstStatic.atom_types_const[0],              MAX_NUM_OF_ATOMS*sizeof(char));

/*
	memcopyBufferObjectToDevice(command_queue1,mem_KerConstStatic_intraE_contributors_const,     &KerConstStatic.intraE_contributors_const[0],     3*MAX_INTRAE_CONTRIBUTORS*sizeof(char));
*/
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_intraE_contributors_const,     &KerConstStatic.intraE_contributors_const[0],     MAX_INTRAE_CONTRIBUTORS*sizeof(cl_char3));

	memcopyBufferObjectToDevice(command_queue,mem_KerConstStatic_reqm_const,         	     	 &KerConstStatic.reqm_const,           	           ATYPE_NUM*sizeof(float));
  	memcopyBufferObjectToDevice(command_queue,mem_KerConstStatic_reqm_hbond_const,             	 &KerConstStatic.reqm_hbond_const,                 ATYPE_NUM*sizeof(float));
  	memcopyBufferObjectToDevice(command_queue,mem_KerConstStatic_atom1_types_reqm_const,        	 &KerConstStatic.atom1_types_reqm_const,           ATYPE_NUM*sizeof(unsigned int));
  	memcopyBufferObjectToDevice(command_queue,mem_KerConstStatic_atom2_types_reqm_const,        	 &KerConstStatic.atom2_types_reqm_const,           ATYPE_NUM*sizeof(unsigned int));

	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_VWpars_AC_const,               &KerConstStatic.VWpars_AC_const[0],               MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_VWpars_BD_const,               &KerConstStatic.VWpars_BD_const[0],               MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_dspars_S_const,                &KerConstStatic.dspars_S_const[0], 	       MAX_NUM_OF_ATYPES*sizeof(float));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_dspars_V_const,                &KerConstStatic.dspars_V_const[0], 	       MAX_NUM_OF_ATYPES*sizeof(float));
	#if defined (FIXED_POINT_CONFORM)
	// fixed-point
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_rotlist_const,                 &KerConstStatic.rotlist_const[0], 		       MAX_NUM_OF_ROTATIONS*sizeof(fixedpt));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_ref_coords_const, 	     &KerConstStatic.ref_coords_const[0],              MAX_NUM_OF_ATOMS*sizeof(cl_int3));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_rotbonds_moving_vectors_const, &KerConstStatic.rotbonds_moving_vectors_const[0], MAX_NUM_OF_ROTBONDS*sizeof(cl_int3));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_rotbonds_unit_vectors_const,   &KerConstStatic.rotbonds_unit_vectors_const[0],   MAX_NUM_OF_ROTBONDS*sizeof(cl_int3));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_ref_orientation_quats_const,   &KerConstStatic.ref_orientation_quats_const[0],   MAX_NUM_OF_RUNS*sizeof(cl_int4));
	#else
	// floating-point (original)
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_rotlist_const,                 &KerConstStatic.rotlist_const[0], 		       MAX_NUM_OF_ROTATIONS*sizeof(int));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_ref_coords_const, 	     &KerConstStatic.ref_coords_const[0],              MAX_NUM_OF_ATOMS*sizeof(cl_float3));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_rotbonds_moving_vectors_const, &KerConstStatic.rotbonds_moving_vectors_const[0], MAX_NUM_OF_ROTBONDS*sizeof(cl_float3));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_rotbonds_unit_vectors_const,   &KerConstStatic.rotbonds_unit_vectors_const[0],   MAX_NUM_OF_ROTBONDS*sizeof(cl_float3));
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_KerConstStatic_ref_orientation_quats_const,   &KerConstStatic.ref_orientation_quats_const[0],   MAX_NUM_OF_RUNS*sizeof(cl_float4));
	#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++;

					
				}
	}

	memcopyBufferObjectToDevice(command_queue1,mem_dockpars_fgrids, 	cpu_fixedpt64grids,       size_fixedpt64grids);
#else
	memcopyBufferObjectToDevice(command_queue/*1*/,mem_dockpars_fgrids, 	cpu_floatgrids,       size_floatgrids);