performdocking.cpp 45.2 KB
Newer Older
lvs's avatar
lvs committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
//// ------------------------
//// Correct time measurement
//// Moved from main.cpp to performdocking.cpp
//// to skip measuring build time
//#include <sys/time.h>
//// ------------------------
#include "performdocking.h"

//// --------------------------------
//// Altera OpenCL Helper Variables
//// --------------------------------
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <cstring>
17

lvs's avatar
lvs committed
18
19
20
21

//// --------------------------------
//// Device memory buffers
//// --------------------------------
Leonardo Solis's avatar
Leonardo Solis committed
22

lvs's avatar
lvs committed
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
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67

/*								                  // 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() */
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
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
{
	// 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
253

254
255
256
	clock_t clock_start_docking;
	clock_t	clock_stop_docking;
	clock_t clock_stop_program_before_clustering;
lvs's avatar
lvs committed
257

258
259
260
	Liganddata myligand_reference;

 	//allocating GPU memory for floatgrids,
261
262
	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
263

264
265
	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
266

267
268
	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
269

270
271
272
273
274
	//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
275

276
277
278
279
280
281
282
283
	//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
284
285
286
287

	//generating initial populations and random orientation angles of reference ligand
	//(ligand will be moved to origo and scaled as well)
	myligand_reference = *myligand_init;
288
	gen_initpop_and_reflig(mypars, cpu_init_populations.data(), cpu_ref_ori_angles.data(), &myligand_reference, mygrid);
289
290
291
292
293
294
295
296
297
298
299

	//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
300
301
		cpu_prng_seeds[i] = genseed(0u);
	}
302
303
304
305

	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
306
	// allocating memory in CPU for evaluation counters
307
308
309
310
	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
311

312
313
	//preparing the constant data fields for the FPGA
	// -----------------------------------------------------------------------------------------------------
lvs's avatar
lvs committed
314
315
316
317
	// 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.
318
319
320
	// -----------------------------------------------------------------------------------------------------
	kernelconstant_static  KerConstStatic;
	if (prepare_conststatic_fields_for_gpu(&myligand_reference, mypars, cpu_ref_ori_angles.data(), &KerConstStatic) == 1)
lvs's avatar
lvs committed
321
322
		return 1;

323
324
325
326
327
	//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);
328
329
330
331
332
333
334
	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);
335
	dockpars.rotbondlist_length 		= ((unsigned int) myligand_reference.num_of_rotcyc);
336
	dockpars.coeff_elec    			= ((float) mypars->coeffs.scaled_AD4_coeff_elec);
337
	dockpars.coeff_desolv  			= ((float) mypars->coeffs.AD4_coeff_desolv);
338
339
340
	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;
341
	dockpars.num_of_genes  			= (unsigned char)(myligand_reference.num_of_rotbonds + 6);
342
343
344
345
346
347
348
349
350
351
352
353
354
355
	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
356
357
358
359
360
361
362
363
364
365

	// 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;
366

367
	// -----------------------------------------------------------------------------------------------------
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
	#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
	// -----------------------------------------------------------------------------------------------------
384

385
386
387
388
389
390
        // 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
391
392
	cl::Buffer mem_dockpars_conformations_current_Initial
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY, 
393
							size_populations_nbytes,	cpu_init_populations.data());
394
395
396
	cl::Buffer mem_dockpars_conformations_current_Final
							(context, CL_MEM_USE_HOST_PTR | CL_MEM_WRITE_ONLY, 
							size_populations_nbytes,	cpu_final_populations.data());
397
	cl::Buffer mem_dockpars_energies_current     	(context, CL_MEM_USE_HOST_PTR | CL_MEM_WRITE_ONLY, 
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
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
							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);	
459

460
461
	// 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
462
	cl::Buffer mem_dummy				(context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY, sizeof(int), cpu_dummy.data());
463
	#endif
464

465
	// -----------------------------------------------------------------------------------------------------
466
467
468
469
	//Separate Read/write Buffer vector is needed to migrate data between host/device
	std::vector<cl::Memory> inBufVec, outBufVec;

	// Krnl_GA
470
	inBufVec.push_back(mem_dockpars_conformations_current_Initial);
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
	// 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
495
496
        outBufVec.push_back(mem_dockpars_conformations_current_Final);
	outBufVec.push_back(mem_dockpars_energies_current);
497
498
	outBufVec.push_back(mem_evals_performed);
	outBufVec.push_back(mem_gens_performed);
Leonardo Solis's avatar
Leonardo Solis committed
499

500
501
502
503
504
505
506
	// -----------------------------------------------------------------------------------------------------
    	// 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
507
508

	clock_start_docking = clock();
509
510
511
512

	int narg;
	#ifdef ENABLE_KRNL_GA
	narg = 0;
513
514
	kernel_ga.setArg(narg++, mem_dockpars_conformations_current_Initial);
	kernel_ga.setArg(narg++, mem_dockpars_conformations_current_Final);
515
516
517
518
519
520
521
522
523
524
525
526
527
528
	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);
529
530
	kernel_ga.setArg(narg++, dockpars.num_of_genes);
	// Other kernel args are configured at every docking run
lvs's avatar
lvs committed
531
532
	#endif

533
534
535
536
537
538
539
540
541
542
	#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);
543
	// Other kernel args are configured at every docking run
lvs's avatar
lvs committed
544
545
546
547
	#endif

	unsigned char gridsizex_minus1 = dockpars.gridsize_x - 1;
	unsigned char gridsizey_minus1 = dockpars.gridsize_y - 1;
lvs's avatar
lvs committed
548
	unsigned char gridsizez_minus1 = dockpars.gridsize_z - 1;
lvs's avatar
lvs committed
549
550
	float fgridsizex_minus1 = (float) gridsizex_minus1;
	float fgridsizey_minus1 = (float) gridsizey_minus1;
lvs's avatar
lvs committed
551
552
	float fgridsizez_minus1 = (float) gridsizez_minus1;

553
554
555
556
557
558
559
560
561
562
563
564
565
566
	#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
567
	#endif
lvs's avatar
lvs committed
568

569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
	#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

592
593
594
	#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);
595
	#if !defined(SW_EMU)
596
	kernel_prng_bt_ushort_float.setArg(3, mem_dummy);
597
	#endif
598
	#endif
599

600
601
602
	#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);
603
	#if !defined(SW_EMU)
604
	kernel_prng_gg_uchar.setArg(2, mem_dummy);
605
	#endif
606
	#endif
lvs's avatar
lvs committed
607

608
609
610
	#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
611
	#if !defined(SW_EMU)
612
	kernel_prng_gg_float.setArg(2, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
613
	#endif
614
	#endif
615

616
617
618
	#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
	// Other kernel args are configured at every docking run
	kernel_prng_ls123_ushort.setArg(9, dockpars.pop_size);
619
	#if !defined(SW_EMU)
620
	kernel_prng_ls123_ushort.setArg(10, mem_dummy);
621
	#endif
622
	#endif
623

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

632
633
634
	#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);
635
	#if !defined(SW_EMU)
636
	kernel_prng_ls2_float.setArg(2, mem_dummy);
637
	#endif
638
	#endif
639

640
641
642
	#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);
643
	#if !defined(SW_EMU)
644
	kernel_prng_ls3_float.setArg(2, mem_dummy);
645
	#endif
646
	#endif
647

648
649
650
	#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);
651
	#if !defined(SW_EMU)
652
	kernel_prng_ls4_float.setArg(2, mem_dummy);
653
	#endif
654
	#endif
655

656
657
658
	#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);
659
	#if !defined(SW_EMU)
660
	kernel_prng_ls5_float.setArg(2, mem_dummy);
661
	#endif
662
	#endif
663

664
665
666
	#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);
667
	#if !defined(SW_EMU)
668
	kernel_prng_ls6_float.setArg(2, mem_dummy);
669
	#endif
670
	#endif
671

672
673
674
	#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);
675
	#if !defined(SW_EMU)
676
	kernel_prng_ls7_float.setArg(2, mem_dummy);
677
	#endif
678
	#endif
679

680
681
682
	#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);
683
	#if !defined(SW_EMU)
684
	kernel_prng_ls8_float.setArg(2, mem_dummy);
685
	#endif
686
	#endif
687

688
689
690
	#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);
691
	#if !defined(SW_EMU)
692
	kernel_prng_ls9_float.setArg(2, mem_dummy);
693
	#endif
694
	#endif
695

696
697
	unsigned short Host_max_num_of_iters = (unsigned short)dockpars.max_num_of_iters;
	unsigned char  Host_cons_limit       = (unsigned char) dockpars.cons_limit;
698

699
700
701
702
703
704
705
706
	#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
707
	#if !defined(SW_EMU)
708
	kernel_ls.setArg(narg++, mem_dummy);
lvs's avatar
lvs committed
709
	#endif
710
	#endif
711

712
713
714
715
716
717
718
719
	#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
720
	#if !defined(SW_EMU)
721
722
	kernel_ls2.setArg(narg++, mem_dummy);
	#endif
Leonardo Solis's avatar
Leonardo Solis committed
723
	#endif
724

725
726
727
728
729
730
731
732
	#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
733
	#if !defined(SW_EMU)
734
	kernel_ls3.setArg(narg++, mem_dummy);
lvs's avatar
lvs committed
735
	#endif
736
	#endif
737

738
739
740
741
742
743
744
745
	#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
746
	#if !defined(SW_EMU)
747
	kernel_ls4.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
748
	#endif
749
	#endif
750

751
752
753
754
755
756
757
758
	#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
759
	#if !defined(SW_EMU)
760
	kernel_ls5.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
761
	#endif
762
	#endif
763

764
765
766
767
768
769
770
771
	#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
772
	#if !defined(SW_EMU)
773
	kernel_ls6.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
774
	#endif
775
	#endif
776

777
778
779
780
781
782
783
784
	#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
785
	#if !defined(SW_EMU)
786
	kernel_ls7.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
787
	#endif
788
	#endif
789

790
791
792
793
794
795
796
797
	#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
798
	#if !defined(SW_EMU)
799
	kernel_ls8.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
800
	#endif
801
	#endif
802

803
804
805
806
807
808
809
810
	#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
811
	#if !defined(SW_EMU)
812
	kernel_ls9.setArg(narg++, mem_dummy);
Leonardo Solis's avatar
Leonardo Solis committed
813
	#endif
814
	#endif
815

816
	#ifdef ENABLE_KRNL_IGL_ARBITER
817
	#if !defined(SW_EMU)
818
819
	kernel_igl_arbiter.setArg(0, mem_dummy);
	#endif
820
	#endif
lvs's avatar
lvs committed
821
822
823

	printf("Docking runs to be executed: %u\n", mypars->num_of_runs); 
	printf("Execution run: ");
lvs's avatar
lvs committed
824

825
	for (unsigned int run_cnt = 0; run_cnt < mypars->num_of_runs; run_cnt++) {
lvs's avatar
lvs committed
826
		printf(" %u", run_cnt+1); 
lvs's avatar
lvs committed
827
		fflush(stdout);
lvs's avatar
lvs committed
828

829
830
831
832
		#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;
833
834
835
		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
836
		#endif
837

838
		#ifdef ENABLE_KRNL_CONFORM
Leonardo Solis's avatar
Leonardo Solis committed
839
		kernel_conform.setArg(8, ushort_run_cnt);
840
		#endif
841

842
843
844
845
		#ifdef ENABLE_KRNL_PRNG_BT_USHORT_FLOAT
		kernel_prng_bt_ushort_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 14]);
		kernel_prng_bt_ushort_float.setArg(1, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 15]);
		#endif
846

847
848
849
		#ifdef ENABLE_KRNL_PRNG_GG_UCHAR
		kernel_prng_gg_uchar.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 2]);
		#endif
850

851
852
853
		#ifdef ENABLE_KRNL_PRNG_GG_FLOAT
		kernel_prng_gg_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt]);
		#endif
854

855
856
857
858
859
860
861
862
863
864
865
		#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
		kernel_prng_ls123_ushort.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 5]);
		kernel_prng_ls123_ushort.setArg(1, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 6]);
		kernel_prng_ls123_ushort.setArg(2, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 7]);
		kernel_prng_ls123_ushort.setArg(3, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 8]);
		kernel_prng_ls123_ushort.setArg(4, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 9]);
		kernel_prng_ls123_ushort.setArg(5, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 10]);
		kernel_prng_ls123_ushort.setArg(6, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 11]);
		kernel_prng_ls123_ushort.setArg(7, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 12]);
		kernel_prng_ls123_ushort.setArg(8, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 13]);
		#endif
866

867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
		#ifdef ENABLE_KRNL_PRNG_LS_FLOAT
		kernel_prng_ls_float.setArg (0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 1]);
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS2_FLOAT
		kernel_prng_ls2_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 3]);
		#endif
		#ifdef ENABLE_KRNL_PRNG_LS3_FLOAT
		kernel_prng_ls3_float.setArg(0, cpu_prng_seeds[num_of_prng_blocks * run_cnt + 4]);
		#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
894

895
		#ifdef ENABLE_KRNL_GA
896
		command_queue_ga.enqueueTask(kernel_ga);
897
		#endif
898
899
		#ifdef ENABLE_KRNL_CONFORM
		command_queue_conform.enqueueTask(kernel_conform);
900
		#endif
901
902
		#ifdef ENABLE_KRNL_INTERE
		command_queue_intere.enqueueTask(kernel_intere);
903
		#endif
904
905
		#ifdef ENABLE_KRNL_INTRAE
		command_queue_intrae.enqueueTask(kernel_intrae);
906
		#endif
907
908
		#ifdef ENABLE_KRNL_PRNG_BT_USHORT_FLOAT
		command_queue_prng_bt_ushort_float.enqueueTask(kernel_prng_bt_ushort_float);
909
		#endif
910
911
912
913
914
		#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);
915
		#endif
916
917
918
919
920
		#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);
921
		#endif
922
923
		#ifdef ENABLE_KRNL_PRNG_LS2_FLOAT
		command_queue_prng_ls2_float.enqueueTask(kernel_prng_ls2_float);
924
		#endif
925
926
		#ifdef ENABLE_KRNL_PRNG_LS3_FLOAT
		command_queue_prng_ls3_float.enqueueTask(kernel_prng_ls3_float);
927
		#endif
928
929
		#ifdef ENABLE_KRNL_PRNG_LS4_FLOAT
		command_queue_prng_ls4_float.enqueueTask(kernel_prng_ls4_float);
930
		#endif
931
932
		#ifdef ENABLE_KRNL_PRNG_LS5_FLOAT
		command_queue_prng_ls5_float.enqueueTask(kernel_prng_ls5_float);
933
		#endif
934
935
		#ifdef ENABLE_KRNL_PRNG_LS6_FLOAT
		command_queue_prng_ls6_float.enqueueTask(kernel_prng_ls6_float);
936
		#endif
937
938
		#ifdef ENABLE_KRNL_PRNG_LS7_FLOAT
		command_queue_prng_ls7_float.enqueueTask(kernel_prng_ls7_float);
939
		#endif
940
941
		#ifdef ENABLE_KRNL_PRNG_LS8_FLOAT
		command_queue_prng_ls8_float.enqueueTask(kernel_prng_ls8_float);
942
		#endif
943
944
		#ifdef ENABLE_KRNL_PRNG_LS9_FLOAT
		command_queue_prng_ls9_float.enqueueTask(kernel_prng_ls9_float);
945
		#endif
946
947
		#ifdef ENABLE_KRNL_LS
		command_queue_ls.enqueueTask(kernel_ls);
948
		#endif
949
950
951
952
953
		#ifdef ENABLE_KRNL_LS2
		command_queue_ls2.enqueueTask(kernel_ls2);
		#endif
		#ifdef ENABLE_KRNL_LS3
		command_queue_ls3.enqueueTask(kernel_ls3);
954
		#endif
955
956
		#ifdef ENABLE_KRNL_LS4
		command_queue_ls4.enqueueTask(kernel_ls4);
957
		#endif
958
959
		#ifdef ENABLE_KRNL_LS5
		command_queue_ls5.enqueueTask(kernel_ls5);
960
		#endif
961
962
		#ifdef ENABLE_KRNL_LS6
		command_queue_ls6.enqueueTask(kernel_ls6);
963
		#endif
964
965
		#ifdef ENABLE_KRNL_LS7
		command_queue_ls7.enqueueTask(kernel_ls7);
966
		#endif
967
968
		#ifdef ENABLE_KRNL_LS8
		command_queue_ls8.enqueueTask(kernel_ls8);
969
		#endif
970
971
		#ifdef ENABLE_KRNL_LS9
		command_queue_ls9.enqueueTask(kernel_ls9);
972
		#endif
973
974
		#ifdef ENABLE_KRNL_IGL_ARBITER
		command_queue_igl_arbiter.enqueueTask(kernel_igl_arbiter);
975
		#endif
lvs's avatar
lvs committed
976

977
		#ifdef ENABLE_KRNL_GA	
978
		command_queue_ga.finish(); 
lvs's avatar
lvs committed
979
		#endif
980
		#ifdef ENABLE_KRNL_CONFORM	
981
		command_queue_conform.finish(); 
lvs's avatar
lvs committed
982
		#endif
983
		#ifdef ENABLE_KRNL_INTERE	
984
		command_queue_intere.finish(); 
lvs's avatar
lvs committed
985
		#endif
986
		#ifdef ENABLE_KRNL_INTRAE	
987
		command_queue_intrae.finish(); 
988
989
		#endif
		#ifdef ENABLE_KRNL_PRNG_BT_USHORT_FLOAT
990
		command_queue_prng_bt_ushort_float.finish();
991
992
		#endif
		#ifdef ENABLE_KRNL_PRNG_GG_UCHAR
993
		command_queue_prng_gg_uchar.finish();
lvs's avatar
lvs committed
994
		#endif
995
		#ifdef ENABLE_KRNL_PRNG_GG_FLOAT
996
		command_queue_prng_gg_float.finish(); 
997
		#endif
998
		#ifdef ENABLE_KRNL_PRNG_LS123_USHORT
999
		command_queue_prng_ls123_ushort.finish();
1000
		#endif
For faster browsing, not all history is shown. View entire blame