performdocking.cpp 56.7 KB
Newer Older
lvs's avatar
lvs committed
1
2
3
4
5
#include "performdocking.h"

//// --------------------------------
//// Device memory buffers
//// --------------------------------
Leonardo Solis's avatar
Leonardo Solis committed
6

lvs's avatar
lvs committed
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27

/*								                  // 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
*/

//// --------------------------------
//// Docking
//// --------------------------------
28
29
30
31
32
33
34
int docking_with_fpga( const    Gridinfo*   mygrid,
	              /*const*/ float*      cpu_floatgrids,
                                Dockpars*   mypars,
		      const     Liganddata* myligand_init,
		      const     int*        argc,
		                char**      argv,
		                clock_t     clock_start_program)
lvs's avatar
lvs committed
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
/* 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() */
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
{
	// The get_xil_devices will return vector of Xilinx Devices 
	std::vector<cl::Device> devices = xcl::get_xil_devices();
	cl::Device device = devices[0];

	//Creating Context and Command Queue for selected Device 
	cl::Context context(device);
    	std::string device_name = device.getInfo<CL_DEVICE_NAME>(); 
	std::cout << "Found Device=" << device_name.c_str() << std::endl;

	#ifdef ENABLE_KRNL_GA
	cl::CommandQueue command_queue_ga			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_CONFORM
	cl::CommandQueue command_queue_conform			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_INTERE
	cl::CommandQueue command_queue_intere			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_INTRAE
	cl::CommandQueue command_queue_intrae			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_BT_USHORT_FLOAT
	cl::CommandQueue command_queue_prng_bt_ushort_float	(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_GG_UCHAR
	cl::CommandQueue command_queue_prng_gg_uchar		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_GG_FLOAT
	cl::CommandQueue command_queue_prng_gg_float		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
	cl::CommandQueue command_queue_prng_ls123_ushort	(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS_FLOAT
	cl::CommandQueue command_queue_prng_ls_float		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS2_FLOAT
	cl::CommandQueue command_queue_prng_ls2_float		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS3_FLOAT
	cl::CommandQueue command_queue_prng_ls3_float		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS4_FLOAT
	cl::CommandQueue command_queue_prng_ls4_float		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS5_FLOAT
	cl::CommandQueue command_queue_prng_ls5_float		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS6_FLOAT
	cl::CommandQueue command_queue_prng_ls6_float		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS7_FLOAT
	cl::CommandQueue command_queue_prng_ls7_float		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS8_FLOAT
	cl::CommandQueue command_queue_prng_ls8_float		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS9_FLOAT
	cl::CommandQueue command_queue_prng_ls9_float		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_LS
	cl::CommandQueue command_queue_ls			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_LS2
	cl::CommandQueue command_queue_ls2			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_LS3
	cl::CommandQueue command_queue_ls3			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_LS4
	cl::CommandQueue command_queue_ls4			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_LS5
	cl::CommandQueue command_queue_ls5			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_LS6
	cl::CommandQueue command_queue_ls6			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif	
	#ifdef ENABLE_KRNL_LS7
	cl::CommandQueue command_queue_ls7			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_LS8
	cl::CommandQueue command_queue_ls8			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_LS9
	cl::CommandQueue command_queue_ls9			(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif
	#ifdef ENABLE_KRNL_IGL_ARBITER
	cl::CommandQueue command_queue_igl_arbiter		(context, device, CL_QUEUE_PROFILING_ENABLE);
	#endif

    	// import_binary() command will find the OpenCL binary file created using the 
    	// xocc compiler load into OpenCL Binary and return as Binaries
    	// OpenCL and it can contain many functions which can be executed on the
   	// device.
    	std::string binaryFile = xcl::find_binary_file(device_name,"Krnl_GA");
    	cl::Program::Binaries bins = xcl::import_binary_file(binaryFile);
    	devices.resize(1);
    	cl::Program program(context, devices, bins);

    	// This call will extract a kernel out of the program we loaded in the
    	// previous line. A kernel is an OpenCL function that is executed on the
    	// FPGA. This function is defined in the device/Krnl_GA.cl file.
	#ifdef ENABLE_KRNL_GA
	cl::Kernel kernel_ga			(program, "Krnl_GA");
	#endif
	#ifdef ENABLE_KRNL_CONFORM
	cl::Kernel kernel_conform		(program, "Krnl_Conform");
	#endif
	#ifdef ENABLE_KRNL_INTERE
	cl::Kernel kernel_intere		(program, "Krnl_InterE");
	#endif
	#ifdef ENABLE_KRNL_INTRAE
	cl::Kernel kernel_intrae		(program, "Krnl_IntraE");
	#endif
	#ifdef ENABLE_KRNL_PRNG_BT_USHORT_FLOAT
	cl::Kernel kernel_prng_bt_ushort_float	(program, "Krnl_Prng_BT_ushort_float");
	#endif
	#ifdef ENABLE_KRNL_PRNG_GG_UCHAR
	cl::Kernel kernel_prng_gg_uchar		(program, "Krnl_Prng_GG_uchar");
	#endif
	#ifdef ENABLE_KRNL_PRNG_GG_FLOAT
	cl::Kernel kernel_prng_gg_float		(program, "Krnl_Prng_GG_float");
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
	cl::Kernel kernel_prng_ls123_ushort	(program, "Krnl_Prng_LS123_ushort");
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS_FLOAT
	cl::Kernel kernel_prng_ls_float		(program, "Krnl_Prng_LS_float");
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS2_FLOAT
	cl::Kernel kernel_prng_ls2_float	(program, "Krnl_Prng_LS2_float");
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS3_FLOAT
	cl::Kernel kernel_prng_ls3_float	(program, "Krnl_Prng_LS3_float");
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS4_FLOAT
	cl::Kernel kernel_prng_ls4_float	(program, "Krnl_Prng_LS4_float");
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS5_FLOAT
	cl::Kernel kernel_prng_ls5_float	(program, "Krnl_Prng_LS5_float");
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS6_FLOAT
	cl::Kernel kernel_prng_ls6_float	(program, "Krnl_Prng_LS6_float");
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS7_FLOAT
	cl::Kernel kernel_prng_ls7_float	(program, "Krnl_Prng_LS7_float");
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS8_FLOAT
	cl::Kernel kernel_prng_ls8_float	(program, "Krnl_Prng_LS8_float");
	#endif
	#ifdef ENABLE_KRNL_PRNG_LS9_FLOAT
	cl::Kernel kernel_prng_ls9_float	(program, "Krnl_Prng_LS9_float");
	#endif
	#ifdef ENABLE_KRNL_LS
	cl::Kernel kernel_ls			(program, "Krnl_LS");
	#endif
	#ifdef ENABLE_KRNL_LS2
	cl::Kernel kernel_ls2			(program, "Krnl_LS2");
	#endif
	#ifdef ENABLE_KRNL_LS3
	cl::Kernel kernel_ls3			(program, "Krnl_LS3");
	#endif
	#ifdef ENABLE_KRNL_LS4
	cl::Kernel kernel_ls4			(program, "Krnl_LS4");
	#endif
	#ifdef ENABLE_KRNL_LS5
	cl::Kernel kernel_ls5			(program, "Krnl_LS5");
	#endif
	#ifdef ENABLE_KRNL_LS6
	cl::Kernel kernel_ls6			(program, "Krnl_LS6");
	#endif
	#ifdef ENABLE_KRNL_LS7
	cl::Kernel kernel_ls7			(program, "Krnl_LS7");
	#endif
	#ifdef ENABLE_KRNL_LS8
	cl::Kernel kernel_ls8			(program, "Krnl_LS8");
	#endif
	#ifdef ENABLE_KRNL_LS9
	cl::Kernel kernel_ls9			(program, "Krnl_LS9");
	#endif
	#ifdef ENABLE_KRNL_IGL_ARBITER
	cl::Kernel kernel_igl_arbiter		(program, "Krnl_IGL_Arbiter");
	#endif
lvs's avatar
lvs committed
237

238
239
240
	clock_t clock_start_docking;
	clock_t	clock_stop_docking;
	clock_t clock_stop_program_before_clustering;
lvs's avatar
lvs committed
241

242
243
	Liganddata myligand_reference;

244
 	//allocating FPGA memory for floatgrids,
245
246
	size_t size_floatgrids_nbytes = sizeof(float) * (mygrid->num_of_atypes+2) *
					(mygrid->size_xyz[0]) * (mygrid->size_xyz[1]) * (mygrid->size_xyz[2]);
lvs's avatar
lvs committed
247

248
249
	size_t size_populations_nbytes = mypars->num_of_runs * mypars->pop_size * ACTUAL_GENOTYPE_LENGTH * sizeof(float);
	size_t size_populations_nelems = mypars->num_of_runs * mypars->pop_size * ACTUAL_GENOTYPE_LENGTH;
lvs's avatar
lvs committed
250

251
252
	size_t size_energies_nbytes = mypars->num_of_runs * mypars->pop_size * sizeof(float);
	size_t size_energies_nelems = mypars->num_of_runs * mypars->pop_size;
lvs's avatar
lvs committed
253

254
255
256
257
258
	//allocating and initializing CPU memory for initial population
	vector<float,aligned_allocator<float>> cpu_init_populations (size_populations_nelems, 0.0f);

	//allocating CPU memory for final population
	vector<float,aligned_allocator<float>> cpu_final_populations (size_populations_nelems);
lvs's avatar
lvs committed
259

260
261
262
263
264
265
266
267
	//allocating CPU memory for results
	vector<float,aligned_allocator<float>> cpu_energies (size_energies_nelems);

	//allocating CPU memory for resulting ligands
	vector<Ligandresult,aligned_allocator<Ligandresult>> cpu_result_ligands (mypars->num_of_runs);

	//allocating memory in CPU for reference orientation angles
	vector<float,aligned_allocator<float>> cpu_ref_ori_angles (mypars->num_of_runs*3);
lvs's avatar
lvs committed
268
269
270
271

	//generating initial populations and random orientation angles of reference ligand
	//(ligand will be moved to origo and scaled as well)
	myligand_reference = *myligand_init;
272
	gen_initpop_and_reflig(mypars, cpu_init_populations.data(), cpu_ref_ori_angles.data(), &myligand_reference, mygrid);
273
274
275
276
277
278
279
280
281
282
283

	//allocating memory in CPU for pseudorandom number generator seeds
	const unsigned int num_of_prng_blocks = 25;
	size_t size_prng_seeds_nelems = num_of_prng_blocks * mypars->num_of_runs;
	vector<unsigned int,aligned_allocator<unsigned int>> cpu_prng_seeds (size_prng_seeds_nelems);
	
	//initializing seed generator
	genseed(time(NULL));	

	//generating seeds (for each thread during GA)
	for (unsigned int i=0; i<size_prng_seeds_nelems; i++) {
lvs's avatar
lvs committed
284
285
		cpu_prng_seeds[i] = genseed(0u);
	}
286
287
288
289

	size_t size_evals_of_runs_nbytes = mypars->num_of_runs*sizeof(int);
	size_t size_evals_of_runs_nelems = mypars->num_of_runs;

lvs's avatar
lvs committed
290
	// allocating memory in CPU for evaluation counters
291
292
293
294
	vector<int,aligned_allocator<int>> cpu_evals_of_runs (size_evals_of_runs_nelems, 0);
	
	// allocating memory in CPU for generation counters
	vector<int,aligned_allocator<int>> cpu_gens_of_runs (size_evals_of_runs_nelems, 0);
lvs's avatar
lvs committed
295

296
	//preparing the constant data fields for the FPGA (calcenergy.cpp)
297
298
	// -----------------------------------------------------------------------------------------------------
	kernelconstant_static  KerConstStatic;
299
	if (prepare_conststatic_fields_for_fpga(&myligand_reference, mypars, cpu_ref_ori_angles.data(), &KerConstStatic) == 1)
lvs's avatar
lvs committed
300
301
		return 1;

302
303
304
305
306
	//preparing parameter struct
	Dockparameters dockpars;
	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);
307
308
309
310
311
312
313
	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);
314
	dockpars.rotbondlist_length 		= ((unsigned int) myligand_reference.num_of_rotcyc);
315
	dockpars.coeff_elec    			= ((float) mypars->coeffs.scaled_AD4_coeff_elec);
316
	dockpars.coeff_desolv  			= ((float) mypars->coeffs.AD4_coeff_desolv);
317
318
319
	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;
320
	dockpars.num_of_genes  			= (unsigned char)(myligand_reference.num_of_rotbonds + 6);
321
322
323
324
325
326
327
328
329
330
331
332
333
334
	dockpars.tournament_rate 		= (mypars->tournament_rate)/100;
	dockpars.crossover_rate  		= (mypars->crossover_rate)/100;
	dockpars.mutation_rate   		= (mypars->mutation_rate)/100;
	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;
lvs's avatar
lvs committed
335
336
337
338
339
340
341
342
343
344

	// 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
	const unsigned int mul_tmp2 = dockpars.num_of_atypes * dockpars.g3;
	const unsigned int mul_tmp3 = (dockpars.num_of_atypes + 1) * dockpars.g3;
345

346
	// -----------------------------------------------------------------------------------------------------
347
	// Replaced by cl_mem extensions (custom connections to DDR banks)
348
	#if 0
349

350
351
352
353
354
355
        // These commands will allocate memory on the FPGA. The cl::Buffer objects can
        // be used to reference the memory locations on the device. The cl::Buffer
	// object cannot be referenced directly and must be passed to other OpenCL
	// functions.

	// Krnl_GA buffers
356
357
	cl::Buffer mem_dockpars_conformations_current_Initial
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY, 
358
							size_populations_nbytes,	cpu_init_populations.data());
359
360
361
	cl::Buffer mem_dockpars_conformations_current_Final
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_WRITE_ONLY, 
							size_populations_nbytes,	cpu_final_populations.data());
362
	cl::Buffer mem_dockpars_energies_current     	(context, CL_MEM_USE_HOST_PTR | CL_MEM_WRITE_ONLY, 
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
							size_energies_nbytes,     	cpu_energies.data());
	cl::Buffer mem_evals_performed			(context, CL_MEM_USE_HOST_PTR | CL_MEM_WRITE_ONLY, 
							size_evals_of_runs_nbytes, 	cpu_evals_of_runs.data());
	cl::Buffer mem_gens_performed			(context, CL_MEM_USE_HOST_PTR | CL_MEM_WRITE_ONLY, 
							size_evals_of_runs_nbytes,	cpu_gens_of_runs.data());
	// Krnl_Conform buffers
	cl::Buffer mem_KerConstStatic_rotlist_const	(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ROTATIONS*sizeof(int),	&KerConstStatic.rotlist_const[0]);
	cl::Buffer mem_KerConstStatic_ref_coords_const	(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ATOMS*sizeof(cl_float3),	&KerConstStatic.ref_coords_const[0]);	
	cl::Buffer mem_KerConstStatic_rotbonds_moving_vectors_const
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,  
							MAX_NUM_OF_ROTBONDS*sizeof(cl_float3),	&KerConstStatic.rotbonds_moving_vectors_const[0]);
	cl::Buffer mem_KerConstStatic_rotbonds_unit_vectors_const
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ROTBONDS*sizeof(cl_float3),	&KerConstStatic.rotbonds_unit_vectors_const[0]);
	cl::Buffer mem_KerConstStatic_ref_orientation_quats_const
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_RUNS*sizeof(cl_float4),   	&KerConstStatic.ref_orientation_quats_const[0]);
	
	// Krnl_InterE buffers
	cl::Buffer mem_dockpars_fgrids			(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							size_floatgrids_nbytes,		cpu_floatgrids);	
	cl::Buffer mem_KerConstStatic_InterE_atom_charges_const
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ATOMS*sizeof(float),	&KerConstStatic.atom_charges_const[0]);
	cl::Buffer mem_KerConstStatic_InterE_atom_types_const
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ATOMS*sizeof(char),	&KerConstStatic.atom_types_const[0]);
	
	// Krnl_IntraE buffers
	cl::Buffer mem_KerConstStatic_IntraE_atom_charges_const
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ATOMS*sizeof(float),	&KerConstStatic.atom_charges_const[0]);
	cl::Buffer mem_KerConstStatic_IntraE_atom_types_const
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ATOMS*sizeof(char), &KerConstStatic.atom_types_const[0]);
	cl::Buffer mem_KerConstStatic_intraE_contributors_const
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_INTRAE_CONTRIBUTORS*sizeof(cl_char3), &KerConstStatic.intraE_contributors_const[0]);
	cl::Buffer mem_KerConstStatic_reqm_const	(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							ATYPE_NUM*sizeof(float),	&KerConstStatic.reqm_const);	
	cl::Buffer mem_KerConstStatic_reqm_hbond_const	(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							ATYPE_NUM*sizeof(float),	&KerConstStatic.reqm_hbond_const);
	cl::Buffer mem_KerConstStatic_atom1_types_reqm_const
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							ATYPE_NUM*sizeof(unsigned int),	&KerConstStatic.atom1_types_reqm_const);
	cl::Buffer mem_KerConstStatic_atom2_types_reqm_const
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							ATYPE_NUM*sizeof(unsigned int),	&KerConstStatic.atom2_types_reqm_const);
	cl::Buffer mem_KerConstStatic_VWpars_AC_const	(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float),	&KerConstStatic.VWpars_AC_const[0]);
	cl::Buffer mem_KerConstStatic_VWpars_BD_const	(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float),	&KerConstStatic.VWpars_BD_const[0]);
	cl::Buffer mem_KerConstStatic_dspars_S_const	(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ATYPES*sizeof(float),			&KerConstStatic.dspars_S_const[0]);
	cl::Buffer mem_KerConstStatic_dspars_V_const	(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY,
							MAX_NUM_OF_ATYPES*sizeof(float),			&KerConstStatic.dspars_V_const[0]);
	#if !defined(SW_EMU)
	//allocating CPU memory for dummy data (one integer)
	vector<int,aligned_allocator<int>> cpu_dummy (1);	
424

425
426
	// IMPORTANT: enable this dummy global argument only for "hw" build.
	// https://forums.xilinx.com/t5/SDAccel/ERROR-KernelCheck-83-114-in-sdx-2017-4/td-p/818135
427
	cl::Buffer mem_dummy				(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY, sizeof(int), cpu_dummy.data());
428
	#endif
429

430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
	#endif
	// -----------------------------------------------------------------------------------------------------
        // For Allocating Buffer to specific Global Memory Bank, 
	// user has to use cl_mem_ext_ptr_t and provide the Banks

	// Declaring two extensions for both buffers

	// Krnl_GA cl_mem extensions
	cl_mem_ext_ptr_t memExt_dockpars_conformations_current_Initial;
	cl_mem_ext_ptr_t memExt_dockpars_conformations_current_Final;
	cl_mem_ext_ptr_t memExt_dockpars_energies_current;
	cl_mem_ext_ptr_t memExt_evals_performed;
	cl_mem_ext_ptr_t memExt_gens_performed;

	// Krnl_Conform cl_mem extensions
	cl_mem_ext_ptr_t memExt_KerConstStatic_rotlist_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_ref_coords_const;	
	cl_mem_ext_ptr_t memExt_KerConstStatic_rotbonds_moving_vectors_const;			
	cl_mem_ext_ptr_t memExt_KerConstStatic_rotbonds_unit_vectors_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_ref_orientation_quats_const;

	// Krnl_InterE cl_mem extensions
	cl_mem_ext_ptr_t memExt_dockpars_fgrids;	
	cl_mem_ext_ptr_t memExt_KerConstStatic_InterE_atom_charges_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_InterE_atom_types_const;

	// Krnl_IntraE cl_mem extensions
	cl_mem_ext_ptr_t memExt_KerConstStatic_IntraE_atom_charges_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_IntraE_atom_types_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_intraE_contributors_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_reqm_const;	
	cl_mem_ext_ptr_t memExt_KerConstStatic_reqm_hbond_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_atom1_types_reqm_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_atom2_types_reqm_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_VWpars_AC_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_VWpars_BD_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_dspars_S_const;
	cl_mem_ext_ptr_t memExt_KerConstStatic_dspars_V_const;

	// Specify Bank0 Memory for Krnl_GA & Krnl_Conform
	memExt_dockpars_conformations_current_Initial.flags = XCL_MEM_DDR_BANK0;
	memExt_dockpars_conformations_current_Final.flags   = XCL_MEM_DDR_BANK0;
	memExt_dockpars_energies_current.flags              = XCL_MEM_DDR_BANK0;
	memExt_evals_performed.flags                        = XCL_MEM_DDR_BANK0;
	memExt_gens_performed.flags                         = XCL_MEM_DDR_BANK0;
	memExt_KerConstStatic_rotlist_const.flags	          = XCL_MEM_DDR_BANK0;
	memExt_KerConstStatic_ref_coords_const.flags		  = XCL_MEM_DDR_BANK0;	
	memExt_KerConstStatic_rotbonds_moving_vectors_const.flags = XCL_MEM_DDR_BANK0;			
	memExt_KerConstStatic_rotbonds_unit_vectors_const.flags   = XCL_MEM_DDR_BANK0;
	memExt_KerConstStatic_ref_orientation_quats_const.flags   = XCL_MEM_DDR_BANK0;

	// Specify Bank1 Memory for Krnl_InterE & Krnl_IntraE
	memExt_dockpars_fgrids.flags				= XCL_MEM_DDR_BANK1;	
	memExt_KerConstStatic_InterE_atom_charges_const.flags	= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_InterE_atom_types_const.flags	= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_IntraE_atom_charges_const.flags	= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_IntraE_atom_types_const.flags	= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_intraE_contributors_const.flags	= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_reqm_const.flags			= XCL_MEM_DDR_BANK1;	
	memExt_KerConstStatic_reqm_hbond_const.flags		= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_atom1_types_reqm_const.flags	= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_atom2_types_reqm_const.flags	= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_VWpars_AC_const.flags		= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_VWpars_BD_const.flags		= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_dspars_S_const.flags		= XCL_MEM_DDR_BANK1;
	memExt_KerConstStatic_dspars_V_const.flags		= XCL_MEM_DDR_BANK1;

	// Specifying the mapping from host arrays to Krnl_GA & Krnl_Conform
	memExt_dockpars_conformations_current_Initial.obj = cpu_init_populations.data();
	memExt_dockpars_conformations_current_Final.obj   = cpu_final_populations.data();
	memExt_dockpars_energies_current.obj              = cpu_energies.data();
	memExt_evals_performed.obj                        = cpu_evals_of_runs.data();
	memExt_gens_performed.obj                         = cpu_gens_of_runs.data();
	memExt_KerConstStatic_rotlist_const.obj                 = &KerConstStatic.rotlist_const[0];
	memExt_KerConstStatic_ref_coords_const.obj              = &KerConstStatic.ref_coords_const[0];	
	memExt_KerConstStatic_rotbonds_moving_vectors_const.obj = &KerConstStatic.rotbonds_moving_vectors_const[0];			
	memExt_KerConstStatic_rotbonds_unit_vectors_const.obj   = &KerConstStatic.rotbonds_unit_vectors_const[0];
	memExt_KerConstStatic_ref_orientation_quats_const.obj   = &KerConstStatic.ref_orientation_quats_const[0];

	// Specifying the mapping from host arrays to Krnl_InterE & Krnl_IntraE
	memExt_dockpars_fgrids.obj                              = cpu_floatgrids;	
	memExt_KerConstStatic_InterE_atom_charges_const.obj     = &KerConstStatic.atom_charges_const[0];
	memExt_KerConstStatic_InterE_atom_types_const.obj       = &KerConstStatic.atom_types_const[0];
	memExt_KerConstStatic_IntraE_atom_charges_const.obj     = &KerConstStatic.atom_charges_const[0];
	memExt_KerConstStatic_IntraE_atom_types_const.obj       = &KerConstStatic.atom_types_const[0];
	memExt_KerConstStatic_intraE_contributors_const.obj     = &KerConstStatic.intraE_contributors_const[0];
	memExt_KerConstStatic_reqm_const.obj                    = &KerConstStatic.reqm_const;	
	memExt_KerConstStatic_reqm_hbond_const.obj              = &KerConstStatic.reqm_hbond_const;
	memExt_KerConstStatic_atom1_types_reqm_const.obj        = &KerConstStatic.atom1_types_reqm_const;
	memExt_KerConstStatic_atom2_types_reqm_const.obj        = &KerConstStatic.atom2_types_reqm_const; 
	memExt_KerConstStatic_VWpars_AC_const.obj               = &KerConstStatic.VWpars_AC_const[0];
	memExt_KerConstStatic_VWpars_BD_const.obj               = &KerConstStatic.VWpars_BD_const[0];
	memExt_KerConstStatic_dspars_S_const.obj                = &KerConstStatic.dspars_S_const[0];
	memExt_KerConstStatic_dspars_V_const.obj                = &KerConstStatic.dspars_V_const[0];

	// Setting param to zero
	memExt_dockpars_conformations_current_Initial.param = 0;
	memExt_dockpars_conformations_current_Final.param   = 0;
	memExt_dockpars_energies_current.param              = 0;
	memExt_evals_performed.param                        = 0;
	memExt_gens_performed.param                         = 0;
	memExt_KerConstStatic_rotlist_const.param                 = 0;
	memExt_KerConstStatic_ref_coords_const.param              = 0;	
	memExt_KerConstStatic_rotbonds_moving_vectors_const.param = 0;			
	memExt_KerConstStatic_rotbonds_unit_vectors_const.param   = 0;
	memExt_KerConstStatic_ref_orientation_quats_const.param   = 0;
	memExt_dockpars_fgrids.param                          = 0;	
	memExt_KerConstStatic_InterE_atom_charges_const.param = 0;
	memExt_KerConstStatic_InterE_atom_types_const.param   = 0;
	memExt_KerConstStatic_IntraE_atom_charges_const.param = 0;
	memExt_KerConstStatic_IntraE_atom_types_const.param   = 0;
	memExt_KerConstStatic_intraE_contributors_const.param = 0;
	memExt_KerConstStatic_reqm_const.param                = 0;	
	memExt_KerConstStatic_reqm_hbond_const.param          = 0;
	memExt_KerConstStatic_atom1_types_reqm_const.param    = 0;
	memExt_KerConstStatic_atom2_types_reqm_const.param    = 0; 
	memExt_KerConstStatic_VWpars_AC_const.param           = 0;
	memExt_KerConstStatic_VWpars_BD_const.param           = 0;
	memExt_KerConstStatic_dspars_S_const.param            = 0;
	memExt_KerConstStatic_dspars_V_const.param            = 0;

	// -----------------------------------------------------------------------------------------------------
	// Krnl_GA buffers
	cl::Buffer mem_dockpars_conformations_current_Initial
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX, 
							size_populations_nbytes,	&memExt_dockpars_conformations_current_Initial);
	cl::Buffer mem_dockpars_conformations_current_Final
							(context, CL_MEM_WRITE_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX, 
							size_populations_nbytes,	&memExt_dockpars_conformations_current_Final);
	cl::Buffer mem_dockpars_energies_current     	(context, CL_MEM_WRITE_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX, 
							size_energies_nbytes,     	&memExt_dockpars_energies_current);
	cl::Buffer mem_evals_performed			(context, CL_MEM_WRITE_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX, 
							size_evals_of_runs_nbytes, 	&memExt_evals_performed);
	cl::Buffer mem_gens_performed			(context, CL_MEM_WRITE_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX, 
							size_evals_of_runs_nbytes,	&memExt_gens_performed);
	// Krnl_Conform buffers
	cl::Buffer mem_KerConstStatic_rotlist_const	(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ROTATIONS*sizeof(int),	&memExt_KerConstStatic_rotlist_const);
	cl::Buffer mem_KerConstStatic_ref_coords_const	(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ATOMS*sizeof(cl_float3),	&memExt_KerConstStatic_ref_coords_const);	
	cl::Buffer mem_KerConstStatic_rotbonds_moving_vectors_const
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,  
							MAX_NUM_OF_ROTBONDS*sizeof(cl_float3),	&memExt_KerConstStatic_rotbonds_moving_vectors_const);
	cl::Buffer mem_KerConstStatic_rotbonds_unit_vectors_const
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ROTBONDS*sizeof(cl_float3),	&memExt_KerConstStatic_rotbonds_unit_vectors_const);
	cl::Buffer mem_KerConstStatic_ref_orientation_quats_const
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_RUNS*sizeof(cl_float4),   	&memExt_KerConstStatic_ref_orientation_quats_const);
	
	// Krnl_InterE buffers
	cl::Buffer mem_dockpars_fgrids			(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							size_floatgrids_nbytes,		&memExt_dockpars_fgrids);	
	cl::Buffer mem_KerConstStatic_InterE_atom_charges_const
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ATOMS*sizeof(float),	&memExt_KerConstStatic_InterE_atom_charges_const);
	cl::Buffer mem_KerConstStatic_InterE_atom_types_const
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ATOMS*sizeof(char),	&memExt_KerConstStatic_InterE_atom_types_const);
	
	// Krnl_IntraE buffers
	cl::Buffer mem_KerConstStatic_IntraE_atom_charges_const
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ATOMS*sizeof(float),	&memExt_KerConstStatic_IntraE_atom_charges_const);
	cl::Buffer mem_KerConstStatic_IntraE_atom_types_const
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ATOMS*sizeof(char),  &memExt_KerConstStatic_IntraE_atom_types_const);
	cl::Buffer mem_KerConstStatic_intraE_contributors_const
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_INTRAE_CONTRIBUTORS*sizeof(cl_char3), &memExt_KerConstStatic_intraE_contributors_const);
	cl::Buffer mem_KerConstStatic_reqm_const	(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							ATYPE_NUM*sizeof(float),	&memExt_KerConstStatic_reqm_const);	
	cl::Buffer mem_KerConstStatic_reqm_hbond_const	(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							ATYPE_NUM*sizeof(float),	&memExt_KerConstStatic_reqm_hbond_const);
	cl::Buffer mem_KerConstStatic_atom1_types_reqm_const
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							ATYPE_NUM*sizeof(unsigned int),	&memExt_KerConstStatic_atom1_types_reqm_const);
	cl::Buffer mem_KerConstStatic_atom2_types_reqm_const
							(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							ATYPE_NUM*sizeof(unsigned int),	&memExt_KerConstStatic_atom2_types_reqm_const);
	cl::Buffer mem_KerConstStatic_VWpars_AC_const	(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float),	&memExt_KerConstStatic_VWpars_AC_const);
	cl::Buffer mem_KerConstStatic_VWpars_BD_const	(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float),	&memExt_KerConstStatic_VWpars_BD_const);
	cl::Buffer mem_KerConstStatic_dspars_S_const	(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ATYPES*sizeof(float),			&memExt_KerConstStatic_dspars_S_const);
	cl::Buffer mem_KerConstStatic_dspars_V_const	(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
							MAX_NUM_OF_ATYPES*sizeof(float),			&memExt_KerConstStatic_dspars_V_const);
	#if !defined(SW_EMU)
	//allocating CPU memory for dummy data (one integer)
	vector<int,aligned_allocator<int>> cpu_dummy (1);	

	// IMPORTANT: enable this dummy global argument only for "hw" build.
	// https://forums.xilinx.com/t5/SDAccel/ERROR-KernelCheck-83-114-in-sdx-2017-4/td-p/818135
	cl::Buffer mem_dummy				(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY, sizeof(int), cpu_dummy.data());
	#endif
626
	// -----------------------------------------------------------------------------------------------------
627
628
629
630
	//Separate Read/write Buffer vector is needed to migrate data between host/device
	std::vector<cl::Memory> inBufVec, outBufVec;

	// Krnl_GA
631
	inBufVec.push_back(mem_dockpars_conformations_current_Initial);
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
	// Krnl_Conform
	inBufVec.push_back(mem_KerConstStatic_rotlist_const);
	inBufVec.push_back(mem_KerConstStatic_ref_coords_const);
	inBufVec.push_back(mem_KerConstStatic_rotbonds_moving_vectors_const);
	inBufVec.push_back(mem_KerConstStatic_rotbonds_unit_vectors_const);
	inBufVec.push_back(mem_KerConstStatic_ref_orientation_quats_const);
	// Krnl_InterE
	inBufVec.push_back(mem_dockpars_fgrids);
	inBufVec.push_back(mem_KerConstStatic_InterE_atom_charges_const);
	inBufVec.push_back(mem_KerConstStatic_InterE_atom_types_const);
	// Krnl_IntraE
	inBufVec.push_back(mem_KerConstStatic_IntraE_atom_charges_const);
	inBufVec.push_back(mem_KerConstStatic_IntraE_atom_types_const);
	inBufVec.push_back(mem_KerConstStatic_intraE_contributors_const);
	inBufVec.push_back(mem_KerConstStatic_reqm_const);
	inBufVec.push_back(mem_KerConstStatic_reqm_hbond_const);
	inBufVec.push_back(mem_KerConstStatic_atom1_types_reqm_const);
	inBufVec.push_back(mem_KerConstStatic_atom2_types_reqm_const);
	inBufVec.push_back(mem_KerConstStatic_VWpars_AC_const);
	inBufVec.push_back(mem_KerConstStatic_VWpars_BD_const);
	inBufVec.push_back(mem_KerConstStatic_dspars_S_const);
	inBufVec.push_back(mem_KerConstStatic_dspars_V_const);

	// Krnl_GA
656
657
        outBufVec.push_back(mem_dockpars_conformations_current_Final);
	outBufVec.push_back(mem_dockpars_energies_current);
658
659
	outBufVec.push_back(mem_evals_performed);
	outBufVec.push_back(mem_gens_performed);
Leonardo Solis's avatar
Leonardo Solis committed
660

661
662
663
664
665
666
667
	// -----------------------------------------------------------------------------------------------------
    	// These commands will load CPU-sources vectors from the host
   	// application and into cl::Buffer objects. 
	// The data will be be transferred from system memory 
	// over PCIe to the FPGA on-board DDR memory.
	command_queue_ga.enqueueMigrateMemObjects(inBufVec,0/* 0 means from host*/);
	// -----------------------------------------------------------------------------------------------------
lvs's avatar
lvs committed
668
669

	clock_start_docking = clock();
670
671
672
673

	int narg;
	#ifdef ENABLE_KRNL_GA
	narg = 0;
674
675
	kernel_ga.setArg(narg++, mem_dockpars_conformations_current_Initial);
	kernel_ga.setArg(narg++, mem_dockpars_conformations_current_Final);
676
677
678
679
680
681
682
683
684
685
686
687
688
689
	kernel_ga.setArg(narg++, mem_dockpars_energies_current);
	kernel_ga.setArg(narg++, mem_evals_performed);
	kernel_ga.setArg(narg++, mem_gens_performed);
	kernel_ga.setArg(narg++, dockpars.pop_size);
	kernel_ga.setArg(narg++, dockpars.num_of_energy_evals);
	kernel_ga.setArg(narg++, dockpars.num_of_generations);
	kernel_ga.setArg(narg++, dockpars.tournament_rate);
	kernel_ga.setArg(narg++, dockpars.mutation_rate);
	kernel_ga.setArg(narg++, dockpars.abs_max_dmov);
	kernel_ga.setArg(narg++, dockpars.abs_max_dang);
	kernel_ga.setArg(narg++, two_absmaxdmov);
	kernel_ga.setArg(narg++, two_absmaxdang);
	kernel_ga.setArg(narg++, dockpars.crossover_rate);
	kernel_ga.setArg(narg++, dockpars.num_of_lsentities);
690
691
	kernel_ga.setArg(narg++, dockpars.num_of_genes);
	// Other kernel args are configured at every docking run
lvs's avatar
lvs committed
692
693
	#endif

694
695
696
697
698
699
700
701
702
703
	#ifdef ENABLE_KRNL_CONFORM
	narg = 0;
	kernel_conform.setArg(narg++, mem_KerConstStatic_rotlist_const);
	kernel_conform.setArg(narg++, mem_KerConstStatic_ref_coords_const);
	kernel_conform.setArg(narg++, mem_KerConstStatic_rotbonds_moving_vectors_const);
	kernel_conform.setArg(narg++, mem_KerConstStatic_rotbonds_unit_vectors_const);
	kernel_conform.setArg(narg++, dockpars.rotbondlist_length);
	kernel_conform.setArg(narg++, dockpars.num_of_atoms);
	kernel_conform.setArg(narg++, dockpars.num_of_genes);
	kernel_conform.setArg(narg++, mem_KerConstStatic_ref_orientation_quats_const);
704
	// Other kernel args are configured at every docking run
lvs's avatar
lvs committed
705
706
707
708
	#endif

	unsigned char gridsizex_minus1 = dockpars.gridsize_x - 1;
	unsigned char gridsizey_minus1 = dockpars.gridsize_y - 1;
lvs's avatar
lvs committed
709
	unsigned char gridsizez_minus1 = dockpars.gridsize_z - 1;
lvs's avatar
lvs committed
710
711
	float fgridsizex_minus1 = (float) gridsizex_minus1;
	float fgridsizey_minus1 = (float) gridsizey_minus1;
lvs's avatar
lvs committed
712
713
	float fgridsizez_minus1 = (float) gridsizez_minus1;

714
715
716
717
718
719
720
721
722
723
724
725
726
727
	#ifdef ENABLE_KRNL_INTERE
	narg = 0;
	kernel_intere.setArg(narg++, mem_dockpars_fgrids);
	kernel_intere.setArg(narg++, mem_KerConstStatic_InterE_atom_charges_const);
	kernel_intere.setArg(narg++, mem_KerConstStatic_InterE_atom_types_const);
	kernel_intere.setArg(narg++, dockpars.g1);
	kernel_intere.setArg(narg++, dockpars.g2);
	kernel_intere.setArg(narg++, dockpars.g3);
	kernel_intere.setArg(narg++, dockpars.num_of_atoms);
	kernel_intere.setArg(narg++, fgridsizex_minus1);
	kernel_intere.setArg(narg++, fgridsizey_minus1);
	kernel_intere.setArg(narg++, fgridsizez_minus1);
	kernel_intere.setArg(narg++, mul_tmp2);
	kernel_intere.setArg(narg++, mul_tmp3);
lvs's avatar
lvs committed
728
	#endif
lvs's avatar
lvs committed
729

730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
	#ifdef ENABLE_KRNL_INTRAE
	narg = 0;
	kernel_intrae.setArg(narg++, mem_KerConstStatic_IntraE_atom_charges_const);
	kernel_intrae.setArg(narg++, mem_KerConstStatic_IntraE_atom_types_const);
	kernel_intrae.setArg(narg++, mem_KerConstStatic_intraE_contributors_const);
	kernel_intrae.setArg(narg++, dockpars.smooth);
	kernel_intrae.setArg(narg++, mem_KerConstStatic_reqm_const);
	kernel_intrae.setArg(narg++, mem_KerConstStatic_reqm_hbond_const);
	kernel_intrae.setArg(narg++, mem_KerConstStatic_atom1_types_reqm_const);
	kernel_intrae.setArg(narg++, mem_KerConstStatic_atom2_types_reqm_const);
	kernel_intrae.setArg(narg++, mem_KerConstStatic_VWpars_AC_const);
	kernel_intrae.setArg(narg++, mem_KerConstStatic_VWpars_BD_const);
	kernel_intrae.setArg(narg++, mem_KerConstStatic_dspars_S_const);
	kernel_intrae.setArg(narg++, mem_KerConstStatic_dspars_V_const);
	kernel_intrae.setArg(narg++, dockpars.num_of_atoms);
	kernel_intrae.setArg(narg++, dockpars.num_of_intraE_contributors);
	kernel_intrae.setArg(narg++, dockpars.grid_spacing);
	kernel_intrae.setArg(narg++, dockpars.num_of_atypes);
	kernel_intrae.setArg(narg++, dockpars.coeff_elec);
	kernel_intrae.setArg(narg++, dockpars.qasp);
	kernel_intrae.setArg(narg++, dockpars.coeff_desolv);
	#endif

753
754
755
	#ifdef ENABLE_KRNL_PRNG_BT_USHORT_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_bt_ushort_float.setArg(2, dockpars.pop_size);
756
	#if !defined(SW_EMU)
757
	kernel_prng_bt_ushort_float.setArg(3, mem_dummy);
758
	#endif
759
	#endif
760

761
762
763
	#ifdef ENABLE_KRNL_PRNG_GG_UCHAR
	// Other kernel args are configured at every docking run
	kernel_prng_gg_uchar.setArg(1, dockpars.num_of_genes);
764
	#if !defined(SW_EMU)
765
	kernel_prng_gg_uchar.setArg(2, mem_dummy);
766
	#endif
767
	#endif
lvs's avatar
lvs committed
768

769
770
771
	#ifdef ENABLE_KRNL_PRNG_GG_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_gg_float.setArg(1, dockpars.num_of_genes);
Leonardo Solis's avatar
Leonardo Solis committed
772
	#if !defined(SW_EMU)
773
	kernel_prng_gg_float.setArg(2, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
774
	#endif
775
	#endif
776

777
778
779
	#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
	// Other kernel args are configured at every docking run
	kernel_prng_ls123_ushort.setArg(9, dockpars.pop_size);
780
	#if !defined(SW_EMU)
781
	kernel_prng_ls123_ushort.setArg(10, mem_dummy);
782
	#endif
783
	#endif
784

785
786
787
	#ifdef ENABLE_KRNL_PRNG_LS_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_ls_float.setArg(1, dockpars.num_of_genes);
788
	#if !defined(SW_EMU)
789
790
	kernel_prng_ls_float.setArg(2, mem_dummy);
	#endif
791
792
	#endif

793
794
795
	#ifdef ENABLE_KRNL_PRNG_LS2_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_ls2_float.setArg(1, dockpars.num_of_genes);
796
	#if !defined(SW_EMU)
797
	kernel_prng_ls2_float.setArg(2, mem_dummy);
798
	#endif
799
	#endif
800

801
802
803
	#ifdef ENABLE_KRNL_PRNG_LS3_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_ls3_float.setArg(1, dockpars.num_of_genes);
804
	#if !defined(SW_EMU)
805
	kernel_prng_ls3_float.setArg(2, mem_dummy);
806
	#endif
807
	#endif
808

809
810
811
	#ifdef ENABLE_KRNL_PRNG_LS4_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_ls4_float.setArg(1, dockpars.num_of_genes);
812
	#if !defined(SW_EMU)
813
	kernel_prng_ls4_float.setArg(2, mem_dummy);
814
	#endif
815
	#endif
816

817
818
819
	#ifdef ENABLE_KRNL_PRNG_LS5_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_ls5_float.setArg(1, dockpars.num_of_genes);
820
	#if !defined(SW_EMU)
821
	kernel_prng_ls5_float.setArg(2, mem_dummy);
822
	#endif
823
	#endif
824

825
826
827
	#ifdef ENABLE_KRNL_PRNG_LS6_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_ls6_float.setArg(1, dockpars.num_of_genes);
828
	#if !defined(SW_EMU)
829
	kernel_prng_ls6_float.setArg(2, mem_dummy);
830
	#endif
831
	#endif
832

833
834
835
	#ifdef ENABLE_KRNL_PRNG_LS7_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_ls7_float.setArg(1, dockpars.num_of_genes);
836
	#if !defined(SW_EMU)
837
	kernel_prng_ls7_float.setArg(2, mem_dummy);
838
	#endif
839
	#endif
840

841
842
843
	#ifdef ENABLE_KRNL_PRNG_LS8_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_ls8_float.setArg(1, dockpars.num_of_genes);
844
	#if !defined(SW_EMU)
845
	kernel_prng_ls8_float.setArg(2, mem_dummy);
846
	#endif
847
	#endif
848

849
850
851
	#ifdef ENABLE_KRNL_PRNG_LS9_FLOAT
	// Other kernel args are configured at every docking run
	kernel_prng_ls9_float.setArg(1, dockpars.num_of_genes);
852
	#if !defined(SW_EMU)
853
	kernel_prng_ls9_float.setArg(2, mem_dummy);
854
	#endif
855
	#endif
856

857
858
	unsigned short Host_max_num_of_iters = (unsigned short)dockpars.max_num_of_iters;
	unsigned char  Host_cons_limit       = (unsigned char) dockpars.cons_limit;
859

860
861
862
863
864
865
866
867
	#ifdef ENABLE_KRNL_LS
	narg = 0;
	kernel_ls.setArg(narg++, Host_max_num_of_iters);
	kernel_ls.setArg(narg++, dockpars.rho_lower_bound);
	kernel_ls.setArg(narg++, dockpars.base_dmov_mul_sqrt3);
	kernel_ls.setArg(narg++, dockpars.num_of_genes);
	kernel_ls.setArg(narg++, dockpars.base_dang_mul_sqrt3);
	kernel_ls.setArg(narg++, Host_cons_limit);
Leonardo Solis's avatar
Leonardo Solis committed
868
	#if !defined(SW_EMU)
869
	kernel_ls.setArg(narg++, mem_dummy);
lvs's avatar
lvs committed
870
	#endif
871
	#endif
872

873
874
875
876
877
878
879
880
	#ifdef ENABLE_KRNL_LS2
	narg = 0;
	kernel_ls2.setArg(narg++, Host_max_num_of_iters);
	kernel_ls2.setArg(narg++, dockpars.rho_lower_bound);
	kernel_ls2.setArg(narg++, dockpars.base_dmov_mul_sqrt3);
	kernel_ls2.setArg(narg++, dockpars.num_of_genes);
	kernel_ls2.setArg(narg++, dockpars.base_dang_mul_sqrt3);
	kernel_ls2.setArg(narg++, Host_cons_limit);
Leonardo Solis's avatar
Leonardo Solis committed
881
	#if !defined(SW_EMU)
882
883
	kernel_ls2.setArg(narg++, mem_dummy);
	#endif
Leonardo Solis's avatar
Leonardo Solis committed
884
	#endif
885

886
887
888
889
890
891
892
893
	#ifdef ENABLE_KRNL_LS3
	narg = 0;
	kernel_ls3.setArg(narg++, Host_max_num_of_iters);
	kernel_ls3.setArg(narg++, dockpars.rho_lower_bound);
	kernel_ls3.setArg(narg++, dockpars.base_dmov_mul_sqrt3);
	kernel_ls3.setArg(narg++, dockpars.num_of_genes);
	kernel_ls3.setArg(narg++, dockpars.base_dang_mul_sqrt3);
	kernel_ls3.setArg(narg++, Host_cons_limit);
Leonardo Solis's avatar
Leonardo Solis committed
894
	#if !defined(SW_EMU)
895
	kernel_ls3.setArg(narg++, mem_dummy);
lvs's avatar
lvs committed
896
	#endif
897
	#endif
898

899
900
901
902
903
904
905
906
	#ifdef ENABLE_KRNL_LS4
	narg = 0;
	kernel_ls4.setArg(narg++, Host_max_num_of_iters);
	kernel_ls4.setArg(narg++, dockpars.rho_lower_bound);
	kernel_ls4.setArg(narg++, dockpars.base_dmov_mul_sqrt3);
	kernel_ls4.setArg(narg++, dockpars.num_of_genes);
	kernel_ls4.setArg(narg++, dockpars.base_dang_mul_sqrt3);
	kernel_ls4.setArg(narg++, Host_cons_limit);
Leonardo Solis's avatar
Leonardo Solis committed
907
	#if !defined(SW_EMU)
908
	kernel_ls4.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
909
	#endif
910
	#endif
911

912
913
914
915
916
917
918
919
	#ifdef ENABLE_KRNL_LS5
	narg = 0;
	kernel_ls5.setArg(narg++, Host_max_num_of_iters);
	kernel_ls5.setArg(narg++, dockpars.rho_lower_bound);
	kernel_ls5.setArg(narg++, dockpars.base_dmov_mul_sqrt3);
	kernel_ls5.setArg(narg++, dockpars.num_of_genes);
	kernel_ls5.setArg(narg++, dockpars.base_dang_mul_sqrt3);
	kernel_ls5.setArg(narg++, Host_cons_limit);
Leonardo Solis's avatar
Leonardo Solis committed
920
	#if !defined(SW_EMU)
921
	kernel_ls5.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
922
	#endif
923
	#endif
924

925
926
927
928
929
930
931
932
	#ifdef ENABLE_KRNL_LS6
	narg = 0;
	kernel_ls6.setArg(narg++, Host_max_num_of_iters);
	kernel_ls6.setArg(narg++, dockpars.rho_lower_bound);
	kernel_ls6.setArg(narg++, dockpars.base_dmov_mul_sqrt3);
	kernel_ls6.setArg(narg++, dockpars.num_of_genes);
	kernel_ls6.setArg(narg++, dockpars.base_dang_mul_sqrt3);
	kernel_ls6.setArg(narg++, Host_cons_limit);
Leonardo Solis's avatar
Leonardo Solis committed
933
	#if !defined(SW_EMU)
934
	kernel_ls6.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
935
	#endif
936
	#endif
937

938
939
940
941
942
943
944
945
	#ifdef ENABLE_KRNL_LS7
	narg = 0;
	kernel_ls7.setArg(narg++, Host_max_num_of_iters);
	kernel_ls7.setArg(narg++, dockpars.rho_lower_bound);
	kernel_ls7.setArg(narg++, dockpars.base_dmov_mul_sqrt3);
	kernel_ls7.setArg(narg++, dockpars.num_of_genes);
	kernel_ls7.setArg(narg++, dockpars.base_dang_mul_sqrt3);
	kernel_ls7.setArg(narg++, Host_cons_limit);
Leonardo Solis's avatar
Leonardo Solis committed
946
	#if !defined(SW_EMU)
947
	kernel_ls7.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
948
	#endif
949
	#endif
950

951
952
953
954
955
956
957
958
	#ifdef ENABLE_KRNL_LS8
	narg = 0;
	kernel_ls8.setArg(narg++, Host_max_num_of_iters);
	kernel_ls8.setArg(narg++, dockpars.rho_lower_bound);
	kernel_ls8.setArg(narg++, dockpars.base_dmov_mul_sqrt3);
	kernel_ls8.setArg(narg++, dockpars.num_of_genes);
	kernel_ls8.setArg(narg++, dockpars.base_dang_mul_sqrt3);
	kernel_ls8.setArg(narg++, Host_cons_limit);
Leonardo Solis's avatar
Leonardo Solis committed
959
	#if !defined(SW_EMU)
960
	kernel_ls8.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
961
	#endif
962
	#endif
963

964
965
966
967
968
969
970
971
	#ifdef ENABLE_KRNL_LS9
	narg = 0;
	kernel_ls9.setArg(narg++, Host_max_num_of_iters);
	kernel_ls9.setArg(narg++, dockpars.rho_lower_bound);
	kernel_ls9.setArg(narg++, dockpars.base_dmov_mul_sqrt3);
	kernel_ls9.setArg(narg++, dockpars.num_of_genes);
	kernel_ls9.setArg(narg++, dockpars.base_dang_mul_sqrt3);
	kernel_ls9.setArg(narg++, Host_cons_limit);
Leonardo Solis's avatar
Leonardo Solis committed
972
	#if !defined(SW_EMU)
973
	kernel_ls9.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
974
	#endif
975
	#endif
976

977
	#ifdef ENABLE_KRNL_IGL_ARBITER
978
	#if !defined(SW_EMU)
979
980
	kernel_igl_arbiter.setArg(0, mem_dummy);
	#endif
981
	#endif
lvs's avatar
lvs committed
982

983
	printf("Docking runs to be executed: %lu\n", mypars->num_of_runs); 
lvs's avatar
lvs committed
984
	printf("Execution run: ");
lvs's avatar
lvs committed
985

986
	for (unsigned int run_cnt = 0; run_cnt < mypars->num_of_runs; run_cnt++) {
lvs's avatar
lvs committed
987
		printf(" %u", run_cnt+1); 
lvs's avatar
lvs committed
988
		fflush(stdout);
lvs's avatar
lvs committed
989

990
991
992
993
		#ifdef ENABLE_KRNL_GA
		unsigned short ushort_run_cnt  = (unsigned ushort) run_cnt;
		unsigned int   Host_Offset_Pop = run_cnt * dockpars.pop_size * ACTUAL_GENOTYPE_LENGTH;
		unsigned int   Host_Offset_Ene = run_cnt * dockpars.pop_size;
994
995
996
		kernel_ga.setArg(17, ushort_run_cnt);
		kernel_ga.setArg(18, Host_Offset_Pop);
		kernel_ga.setArg(19, Host_Offset_Ene);
lvs's avatar
lvs committed
997
		#endif
998

999
		#ifdef ENABLE_KRNL_CONFORM
Leonardo Solis's avatar
Leonardo Solis committed
1000
		kernel_conform.setArg(8, ushort_run_cnt);
For faster browsing, not all history is shown. View entire blame