performdocking.cpp 45 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
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51

/*								                  // 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
//// --------------------------------
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() */
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
244
	Liganddata myligand_reference;

 	//allocating GPU 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
297
	//preparing the constant data fields for the FPGA
	// -----------------------------------------------------------------------------------------------------
lvs's avatar
lvs committed
298
299
300
301
	// 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.
302
303
304
	// -----------------------------------------------------------------------------------------------------
	kernelconstant_static  KerConstStatic;
	if (prepare_conststatic_fields_for_gpu(&myligand_reference, mypars, cpu_ref_ori_angles.data(), &KerConstStatic) == 1)
lvs's avatar
lvs committed
305
306
		return 1;

307
308
309
310
311
	//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);
312
313
314
315
316
317
318
	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);
319
	dockpars.rotbondlist_length 		= ((unsigned int) myligand_reference.num_of_rotcyc);
320
	dockpars.coeff_elec    			= ((float) mypars->coeffs.scaled_AD4_coeff_elec);
321
	dockpars.coeff_desolv  			= ((float) mypars->coeffs.AD4_coeff_desolv);
322
323
324
	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;
325
	dockpars.num_of_genes  			= (unsigned char)(myligand_reference.num_of_rotbonds + 6);
326
327
328
329
330
331
332
333
334
335
336
337
338
339
	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
340
341
342
343
344
345
346
347
348
349

	// 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;
350

351
	// -----------------------------------------------------------------------------------------------------
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
	#if 0
	// Hardware specific configuration (valid if 4 DDR banks are available, e.g.: AWS)
	// Specifiying precisely which DDR memory bank is 
	// being pointed to by a kernel globgal memory pointer.

	cl_mem_ext_ptr_t d_bank0_ext; // Ideally: DDR bank0 <-> Krnl_GA
	cl_mem_ext_ptr_t d_bank1_ext; // Ideally: DDR bank1 <-> Krnl_Conform
	cl_mem_ext_ptr_t d_bank2_ext; // Ideally: DDR bank2 <-> Krnl_InterE
	cl_mem_ext_ptr_t d_bank3_ext; // Ideally: DDR bank3 <-> 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;
	#endif
	// -----------------------------------------------------------------------------------------------------
368

369
370
371
372
373
374
        // 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
375
376
	cl::Buffer mem_dockpars_conformations_current_Initial
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY, 
377
							size_populations_nbytes,	cpu_init_populations.data());
378
379
380
	cl::Buffer mem_dockpars_conformations_current_Final
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_WRITE_ONLY, 
							size_populations_nbytes,	cpu_final_populations.data());
381
	cl::Buffer mem_dockpars_energies_current     	(context, CL_MEM_USE_HOST_PTR | CL_MEM_WRITE_ONLY, 
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
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
							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);	
443

444
445
	// 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
446
	cl::Buffer mem_dummy				(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY, sizeof(int), cpu_dummy.data());
447
	#endif
448

449
	// -----------------------------------------------------------------------------------------------------
450
451
452
453
	//Separate Read/write Buffer vector is needed to migrate data between host/device
	std::vector<cl::Memory> inBufVec, outBufVec;

	// Krnl_GA
454
	inBufVec.push_back(mem_dockpars_conformations_current_Initial);
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
	// 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
479
480
        outBufVec.push_back(mem_dockpars_conformations_current_Final);
	outBufVec.push_back(mem_dockpars_energies_current);
481
482
	outBufVec.push_back(mem_evals_performed);
	outBufVec.push_back(mem_gens_performed);
Leonardo Solis's avatar
Leonardo Solis committed
483

484
485
486
487
488
489
490
	// -----------------------------------------------------------------------------------------------------
    	// 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
491
492

	clock_start_docking = clock();
493
494
495
496

	int narg;
	#ifdef ENABLE_KRNL_GA
	narg = 0;
497
498
	kernel_ga.setArg(narg++, mem_dockpars_conformations_current_Initial);
	kernel_ga.setArg(narg++, mem_dockpars_conformations_current_Final);
499
500
501
502
503
504
505
506
507
508
509
510
511
512
	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);
513
514
	kernel_ga.setArg(narg++, dockpars.num_of_genes);
	// Other kernel args are configured at every docking run
lvs's avatar
lvs committed
515
516
	#endif

517
518
519
520
521
522
523
524
525
526
	#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);
527
	// Other kernel args are configured at every docking run
lvs's avatar
lvs committed
528
529
530
531
	#endif

	unsigned char gridsizex_minus1 = dockpars.gridsize_x - 1;
	unsigned char gridsizey_minus1 = dockpars.gridsize_y - 1;
lvs's avatar
lvs committed
532
	unsigned char gridsizez_minus1 = dockpars.gridsize_z - 1;
lvs's avatar
lvs committed
533
534
	float fgridsizex_minus1 = (float) gridsizex_minus1;
	float fgridsizey_minus1 = (float) gridsizey_minus1;
lvs's avatar
lvs committed
535
536
	float fgridsizez_minus1 = (float) gridsizez_minus1;

537
538
539
540
541
542
543
544
545
546
547
548
549
550
	#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
551
	#endif
lvs's avatar
lvs committed
552

553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
	#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

576
577
578
	#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);
579
	#if !defined(SW_EMU)
580
	kernel_prng_bt_ushort_float.setArg(3, mem_dummy);
581
	#endif
582
	#endif
583

584
585
586
	#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);
587
	#if !defined(SW_EMU)
588
	kernel_prng_gg_uchar.setArg(2, mem_dummy);
589
	#endif
590
	#endif
lvs's avatar
lvs committed
591

592
593
594
	#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
595
	#if !defined(SW_EMU)
596
	kernel_prng_gg_float.setArg(2, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
597
	#endif
598
	#endif
599

600
601
602
	#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
	// Other kernel args are configured at every docking run
	kernel_prng_ls123_ushort.setArg(9, dockpars.pop_size);
603
	#if !defined(SW_EMU)
604
	kernel_prng_ls123_ushort.setArg(10, mem_dummy);
605
	#endif
606
	#endif
607

608
609
610
	#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);
611
	#if !defined(SW_EMU)
612
613
	kernel_prng_ls_float.setArg(2, mem_dummy);
	#endif
614
615
	#endif

616
617
618
	#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);
619
	#if !defined(SW_EMU)
620
	kernel_prng_ls2_float.setArg(2, mem_dummy);
621
	#endif
622
	#endif
623

624
625
626
	#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);
627
	#if !defined(SW_EMU)
628
	kernel_prng_ls3_float.setArg(2, mem_dummy);
629
	#endif
630
	#endif
631

632
633
634
	#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);
635
	#if !defined(SW_EMU)
636
	kernel_prng_ls4_float.setArg(2, mem_dummy);
637
	#endif
638
	#endif
639

640
641
642
	#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);
643
	#if !defined(SW_EMU)
644
	kernel_prng_ls5_float.setArg(2, mem_dummy);
645
	#endif
646
	#endif
647

648
649
650
	#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);
651
	#if !defined(SW_EMU)
652
	kernel_prng_ls6_float.setArg(2, mem_dummy);
653
	#endif
654
	#endif
655

656
657
658
	#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);
659
	#if !defined(SW_EMU)
660
	kernel_prng_ls7_float.setArg(2, mem_dummy);
661
	#endif
662
	#endif
663

664
665
666
	#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);
667
	#if !defined(SW_EMU)
668
	kernel_prng_ls8_float.setArg(2, mem_dummy);
669
	#endif
670
	#endif
671

672
673
674
	#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);
675
	#if !defined(SW_EMU)
676
	kernel_prng_ls9_float.setArg(2, mem_dummy);
677
	#endif
678
	#endif
679

680
681
	unsigned short Host_max_num_of_iters = (unsigned short)dockpars.max_num_of_iters;
	unsigned char  Host_cons_limit       = (unsigned char) dockpars.cons_limit;
682

683
684
685
686
687
688
689
690
	#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
691
	#if !defined(SW_EMU)
692
	kernel_ls.setArg(narg++, mem_dummy);
lvs's avatar
lvs committed
693
	#endif
694
	#endif
695

696
697
698
699
700
701
702
703
	#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
704
	#if !defined(SW_EMU)
705
706
	kernel_ls2.setArg(narg++, mem_dummy);
	#endif
Leonardo Solis's avatar
Leonardo Solis committed
707
	#endif
708

709
710
711
712
713
714
715
716
	#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
717
	#if !defined(SW_EMU)
718
	kernel_ls3.setArg(narg++, mem_dummy);
lvs's avatar
lvs committed
719
	#endif
720
	#endif
721

722
723
724
725
726
727
728
729
	#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
730
	#if !defined(SW_EMU)
731
	kernel_ls4.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
732
	#endif
733
	#endif
734

735
736
737
738
739
740
741
742
	#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
743
	#if !defined(SW_EMU)
744
	kernel_ls5.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
745
	#endif
746
	#endif
747

748
749
750
751
752
753
754
755
	#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
756
	#if !defined(SW_EMU)
757
	kernel_ls6.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
758
	#endif
759
	#endif
760

761
762
763
764
765
766
767
768
	#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
769
	#if !defined(SW_EMU)
770
	kernel_ls7.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
771
	#endif
772
	#endif
773

774
775
776
777
778
779
780
781
	#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
782
	#if !defined(SW_EMU)
783
	kernel_ls8.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
784
	#endif
785
	#endif
786

787
788
789
790
791
792
793
794
	#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
795
	#if !defined(SW_EMU)
796
	kernel_ls9.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
797
	#endif
798
	#endif
799

800
	#ifdef ENABLE_KRNL_IGL_ARBITER
801
	#if !defined(SW_EMU)
802
803
	kernel_igl_arbiter.setArg(0, mem_dummy);
	#endif
804
	#endif
lvs's avatar
lvs committed
805

806
	printf("Docking runs to be executed: %lu\n", mypars->num_of_runs); 
lvs's avatar
lvs committed
807
	printf("Execution run: ");
lvs's avatar
lvs committed
808

809
	for (unsigned int run_cnt = 0; run_cnt < mypars->num_of_runs; run_cnt++) {
lvs's avatar
lvs committed
810
		printf(" %u", run_cnt+1); 
lvs's avatar
lvs committed
811
		fflush(stdout);
lvs's avatar
lvs committed
812

813
814
815
816
		#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;
817
818
819
		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
820
		#endif
821

822
		#ifdef ENABLE_KRNL_CONFORM
Leonardo Solis's avatar
Leonardo Solis committed
823
		kernel_conform.setArg(8, ushort_run_cnt);
824
		#endif
825

826
		#ifdef ENABLE_KRNL_PRNG_BT_USHORT_FLOAT
827
828
		kernel_prng_bt_ushort_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt]);
		kernel_prng_bt_ushort_float.setArg(1, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 1]);
829
		#endif
830

831
832
833
		#ifdef ENABLE_KRNL_PRNG_GG_UCHAR
		kernel_prng_gg_uchar.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 2]);
		#endif
834

835
		#ifdef ENABLE_KRNL_PRNG_GG_FLOAT
836
		kernel_prng_gg_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 3]);
837
		#endif
838

839
		#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
840
841
842
843
844
845
846
847
848
		kernel_prng_ls123_ushort.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 4]);
		kernel_prng_ls123_ushort.setArg(1, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 5]);
		kernel_prng_ls123_ushort.setArg(2, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 6]);
		kernel_prng_ls123_ushort.setArg(3, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 7]);
		kernel_prng_ls123_ushort.setArg(4, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 8]);
		kernel_prng_ls123_ushort.setArg(5, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 9]);
		kernel_prng_ls123_ushort.setArg(6, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 10]);
		kernel_prng_ls123_ushort.setArg(7, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 11]);
		kernel_prng_ls123_ushort.setArg(8, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 12]);
849
		#endif
850

851
		#ifdef ENABLE_KRNL_PRNG_LS_FLOAT
852
		kernel_prng_ls_float.setArg (0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 13]);
853
854
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS2_FLOAT
855
		kernel_prng_ls2_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 14]);
856
857
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS3_FLOAT
858
		kernel_prng_ls3_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 15]);
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS4_FLOAT
		kernel_prng_ls4_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 16]);
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS5_FLOAT
		kernel_prng_ls5_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 17]);
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS6_FLOAT
		kernel_prng_ls6_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 18]);
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS7_FLOAT
		kernel_prng_ls7_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 19]);
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS8_FLOAT
		kernel_prng_ls8_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 20]);
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS9_FLOAT
		kernel_prng_ls9_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 21]);
		#endif
lvs's avatar
lvs committed
878

879
		#ifdef ENABLE_KRNL_GA
880
		command_queue_ga.enqueueTask(kernel_ga);
881
		#endif
882
883
		#ifdef ENABLE_KRNL_CONFORM
		command_queue_conform.enqueueTask(kernel_conform);
884
		#endif
885
886
		#ifdef ENABLE_KRNL_INTERE
		command_queue_intere.enqueueTask(kernel_intere);
887
		#endif
888
889
		#ifdef ENABLE_KRNL_INTRAE
		command_queue_intrae.enqueueTask(kernel_intrae);
890
		#endif
891
892
		#ifdef ENABLE_KRNL_PRNG_BT_USHORT_FLOAT
		command_queue_prng_bt_ushort_float.enqueueTask(kernel_prng_bt_ushort_float);
893
		#endif
894
895
896
897
898
		#ifdef ENABLE_KRNL_PRNG_GG_UCHAR
		command_queue_prng_gg_uchar.enqueueTask(kernel_prng_gg_uchar);
		#endif
		#ifdef ENABLE_KRNL_PRNG_GG_FLOAT
		command_queue_prng_gg_float.enqueueTask(kernel_prng_gg_float);
899
		#endif
900
901
902
903
904
		#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
		command_queue_prng_ls123_ushort.enqueueTask(kernel_prng_ls123_ushort);
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS_FLOAT
		command_queue_prng_ls_float.enqueueTask(kernel_prng_ls_float);
905
		#endif
906
907
		#ifdef ENABLE_KRNL_PRNG_LS2_FLOAT
		command_queue_prng_ls2_float.enqueueTask(kernel_prng_ls2_float);
908
		#endif
909
910
		#ifdef ENABLE_KRNL_PRNG_LS3_FLOAT
		command_queue_prng_ls3_float.enqueueTask(kernel_prng_ls3_float);
911
		#endif
912
913
		#ifdef ENABLE_KRNL_PRNG_LS4_FLOAT
		command_queue_prng_ls4_float.enqueueTask(kernel_prng_ls4_float);
914
		#endif
915
916
		#ifdef ENABLE_KRNL_PRNG_LS5_FLOAT
		command_queue_prng_ls5_float.enqueueTask(kernel_prng_ls5_float);
917
		#endif
918
919
		#ifdef ENABLE_KRNL_PRNG_LS6_FLOAT
		command_queue_prng_ls6_float.enqueueTask(kernel_prng_ls6_float);
920
		#endif
921
922
		#ifdef ENABLE_KRNL_PRNG_LS7_FLOAT
		command_queue_prng_ls7_float.enqueueTask(kernel_prng_ls7_float);
923
		#endif
924
925
		#ifdef ENABLE_KRNL_PRNG_LS8_FLOAT
		command_queue_prng_ls8_float.enqueueTask(kernel_prng_ls8_float);
926
		#endif
927
928
		#ifdef ENABLE_KRNL_PRNG_LS9_FLOAT
		command_queue_prng_ls9_float.enqueueTask(kernel_prng_ls9_float);
929
		#endif
930
931
		#ifdef ENABLE_KRNL_LS
		command_queue_ls.enqueueTask(kernel_ls);
932
		#endif
933
934
935
936
937
		#ifdef ENABLE_KRNL_LS2
		command_queue_ls2.enqueueTask(kernel_ls2);
		#endif
		#ifdef ENABLE_KRNL_LS3
		command_queue_ls3.enqueueTask(kernel_ls3);
938
		#endif
939
940
		#ifdef ENABLE_KRNL_LS4
		command_queue_ls4.enqueueTask(kernel_ls4);
941
		#endif
942
943
		#ifdef ENABLE_KRNL_LS5
		command_queue_ls5.enqueueTask(kernel_ls5);
944
		#endif
945
946
		#ifdef ENABLE_KRNL_LS6
		command_queue_ls6.enqueueTask(kernel_ls6);
947
		#endif
948
949
		#ifdef ENABLE_KRNL_LS7
		command_queue_ls7.enqueueTask(kernel_ls7);
950
		#endif
951
952
		#ifdef ENABLE_KRNL_LS8
		command_queue_ls8.enqueueTask(kernel_ls8);
953
		#endif
954
955
		#ifdef ENABLE_KRNL_LS9
		command_queue_ls9.enqueueTask(kernel_ls9);
956
		#endif
957
958
		#ifdef ENABLE_KRNL_IGL_ARBITER
		command_queue_igl_arbiter.enqueueTask(kernel_igl_arbiter);
959
		#endif
lvs's avatar
lvs committed
960

961
		#ifdef ENABLE_KRNL_GA	
962
		command_queue_ga.finish(); 
lvs's avatar
lvs committed
963
		#endif
964
		#ifdef ENABLE_KRNL_CONFORM	
965
		command_queue_conform.finish(); 
lvs's avatar
lvs committed
966
		#endif
967
		#ifdef ENABLE_KRNL_INTERE	
968
		command_queue_intere.finish(); 
lvs's avatar
lvs committed
969
		#endif
970
		#ifdef ENABLE_KRNL_INTRAE	
971
		command_queue_intrae.finish(); 
972
973
		#endif
		#ifdef ENABLE_KRNL_PRNG_BT_USHORT_FLOAT
974
		command_queue_prng_bt_ushort_float.finish();
975
976
		#endif
		#ifdef ENABLE_KRNL_PRNG_GG_UCHAR
977
		command_queue_prng_gg_uchar.finish();
lvs's avatar
lvs committed
978
		#endif
979
		#ifdef ENABLE_KRNL_PRNG_GG_FLOAT
980
		command_queue_prng_gg_float.finish(); 
981
		#endif
982
		#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
983
		command_queue_prng_ls123_ushort.finish();
984
985
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS_FLOAT
986
987
		command_queue_prng_ls_float.finish();
		#endif
988
		#ifdef ENABLE_KRNL_PRNG_LS2_FLOAT
989
		command_queue_prng_ls2_float.finish();
990
991
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS3_FLOAT
992
		command_queue_prng_ls3_float.finish();
993
		#endif
994
		#ifdef ENABLE_KRNL_PRNG_LS4_FLOAT
995
		command_queue_prng_ls4_float.finish();
996
997
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS5_FLOAT
998
		command_queue_prng_ls5_float.finish();
999
1000
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS6_FLOAT
For faster browsing, not all history is shown. View entire blame