performdocking.cpp 58.5 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
/*

OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.

AutoDock is a Trade Mark of the Scripps Research Institute.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

*/


25
26
27
28
29
30
31
32
33
34
#ifndef _WIN32
#define STRINGIZE2(s) #s
#define STRINGIZE(s)	STRINGIZE2(s)
#define KRNL_FILE STRINGIZE(KRNL_SOURCE)
#define KRNL_FOLDER STRINGIZE(KRNL_DIRECTORY)
#define KRNL_COMMON STRINGIZE(KCMN_DIRECTORY)
#define KRNL1 STRINGIZE(K1)
#define KRNL2 STRINGIZE(K2)
#define KRNL3 STRINGIZE(K3)
#define KRNL4 STRINGIZE(K4)
35
#define KRNL5 STRINGIZE(K5)
lvs's avatar
lvs committed
36
#define KRNL6 STRINGIZE(K6)
37
38
39
40
41
42
43
44
45

#else
#define KRNL_FILE KRNL_SOURCE
#define KRNL_FOLDER KRNL_DIRECTORY
#define KRNL_COMMON KCMN_DIRECTORY
#define KRNL1 K1
#define KRNL2 K2
#define KRNL3 K3
#define KRNL4 K4
46
#define KRNL5 K5
lvs's avatar
lvs committed
47
#define KRNL6 K6
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
#endif

#define INC " -I " KRNL_FOLDER " -I " KRNL_COMMON

#if defined (N16WI)
	#define KNWI " -DN16WI "
#elif defined (N32WI)
	#define KNWI " -DN32WI "
#elif defined (N64WI)
	#define KNWI " -DN64WI "
#elif defined (N128WI)
	#define KNWI " -DN128WI "
#elif defined (N256WI)
		#define KNWI " -DN256WI "
#else
	#define KNWI	" -DN64WI "
#endif

#if defined (REPRO)
	#define REP " -DREPRO "
#else
	#define REP " "
#endif

72

73
74
75
#define KGDB_AMD 		" -g -O0 "
#define KGDB_INTEL	" -g -s " KRNL_FILE

76

77
78
79
80
81
82
83
84
85
86
#if defined (DOCK_DEBUG)
	#if defined (CPU_DEVICE)
		#define KGDB KGDB_INTEL
	#elif defined (GPU_DEVICE)
		#define KGDB KGDB_AMD
	#endif
#else
	#define KGDB " "
#endif

87

88
89
90
91
#define OPT_PROG INC KNWI REP KGDB

#include "performdocking.h"
#include "stringify.h"
92
#include "correct_grad_axisangle.h"
93
94

int docking_with_gpu(const Gridinfo*   mygrid,
95
	         /*const*/ float*      cpu_floatgrids,
96
                           Dockpars*   mypars,
97
98
99
100
		     const Liganddata* myligand_init,
		     const int*        argc,
		           char**      argv,
		           clock_t     clock_start_program)
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
/* The function performs the docking algorithm and generates the corresponding result files.
parameter mygrid:
		describes the grid
		filled with get_gridinfo()
parameter cpu_floatgrids:
		points to the memory region containing the grids
		filled with get_gridvalues_f()
parameter mypars:
		describes the docking parameters
		filled with get_commandpars()
parameter myligand_init:
		describes the ligands
		filled with get_liganddata()
parameters argc and argv:
		are the corresponding command line arguments parameter clock_start_program:
		contains the state of the clock tick counter at the beginning of the program
filled with clock() */
{
// =======================================================================
// OpenCL Host Setup
// =======================================================================
lvs's avatar
lvs committed
122
123
124
	cl_platform_id*  platform_id;
	cl_device_id*    device_id;
	cl_context       context;
125
	cl_command_queue command_queue;
lvs's avatar
lvs committed
126
	cl_program       program;
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150

#ifdef _WIN32
	const char *filename = KRNL_FILE;
	printf("\n%-40s %-40s\n", "Kernel source file: ", filename);  fflush(stdout);
#else
	printf("\n%-40s %-40s\n", "Kernel source used for development: ", "./device/calcenergy.cl");  fflush(stdout);
	printf(  "%-40s %-40s\n", "Kernel string used for building: ",    "./host/inc/stringify.h");  fflush(stdout);
#endif

	const char* options_program = OPT_PROG;
	printf("%-40s %-40s\n", "Kernel compilation flags: ", options_program); fflush(stdout);

	cl_kernel kernel1; const char *name_k1 = KRNL1;
	size_t kernel1_gxsize, kernel1_lxsize;

	cl_kernel kernel2; const char *name_k2 = KRNL2;
	size_t kernel2_gxsize, kernel2_lxsize;

	cl_kernel kernel3; const char *name_k3 = KRNL3;
	size_t kernel3_gxsize, kernel3_lxsize;

	cl_kernel kernel4; const char *name_k4 = KRNL4;
	size_t kernel4_gxsize, kernel4_lxsize;

151
152
153
	cl_kernel kernel5; const char *name_k5 = KRNL5;
	size_t kernel5_gxsize, kernel5_lxsize;

lvs's avatar
lvs committed
154
155
156
	cl_kernel kernel6; const char *name_k6 = KRNL6;
	size_t kernel6_gxsize, kernel6_lxsize;

157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
	cl_uint platformCount;
	cl_uint deviceCount;

	// Times
	cl_ulong time_start_kernel;
	cl_ulong time_end_kernel;

	// Get all available platforms
	if (getPlatforms(&platform_id,&platformCount) != 0) return 1;

	// Get all devices of first platform
	if (getDevices(platform_id[0],platformCount,&device_id,&deviceCount) != 0) return 1;

	// Create context from first platform
	if (createContext(platform_id[0],1,device_id,&context) != 0) return 1;

	// Create command queue for first device
	if (createCommandQueue(context,device_id[0],&command_queue) != 0) return 1;

lvs's avatar
lvs committed
176
	// Create program from source 
177
178
179
180
181
#ifdef _WIN32
	if (ImportSource(filename, name_k1, device_id, context, options_program, &kernel1) != 0) return 1;
	if (ImportSource(filename, name_k2, device_id, context, options_program, &kernel2) != 0) return 1;
	if (ImportSource(filename, name_k3, device_id, context, options_program, &kernel3) != 0) return 1;
	if (ImportSource(filename, name_k4, device_id, context, options_program, &kernel4) != 0) return 1;
182
	if (ImportSource(filename, name_k5, device_id, context, options_program, &kernel5) != 0) return 1;
lvs's avatar
lvs committed
183
	if (ImportSource(filename, name_k6, device_id, context, options_program, &kernel6) != 0) return 1;
184
#else
lvs's avatar
lvs committed
185
	if (ImportSourceToProgram(calcenergy_ocl, device_id, context, &program, options_program) != 0) return 1;
186
187
#endif

lvs's avatar
lvs committed
188
189
190
191
192
193
	// Create kernels
	if (createKernel(device_id, &program, name_k1, &kernel1) != 0) return 1;
	if (createKernel(device_id, &program, name_k2, &kernel2) != 0) return 1;
	if (createKernel(device_id, &program, name_k3, &kernel3) != 0) return 1;
	if (createKernel(device_id, &program, name_k4, &kernel4) != 0) return 1;
	if (createKernel(device_id, &program, name_k5, &kernel5) != 0) return 1;
lvs's avatar
lvs committed
194
	if (createKernel(device_id, &program, name_k6, &kernel6) != 0) return 1;
lvs's avatar
lvs committed
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
// End of OpenCL Host Setup
// =======================================================================

	Liganddata myligand_reference;

	float* cpu_init_populations;
	float* cpu_final_populations;
	float* cpu_energies;
	Ligandresult* cpu_result_ligands;
	unsigned int* cpu_prng_seeds;
	int* cpu_evals_of_runs;
	float* cpu_ref_ori_angles;

	Dockparameters dockpars;
	size_t size_floatgrids;
	size_t size_populations;
	size_t size_energies;
	size_t size_prng_seeds;
	size_t size_evals_of_runs;

	int threadsPerBlock;
	int blocksPerGridForEachEntity;
	int blocksPerGridForEachRun;
	int blocksPerGridForEachLSEntity;
220
	int blocksPerGridForEachGradMinimizerEntity;
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
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284

	unsigned long run_cnt;	/* int run_cnt; */
	int generation_cnt;
	int i;
	double progress;

	int curr_progress_cnt;
	int new_progress_cnt;

	clock_t clock_start_docking;
	clock_t	clock_stop_docking;
	clock_t clock_stop_program_before_clustering;

	//setting number of blocks and threads
	threadsPerBlock = NUM_OF_THREADS_PER_BLOCK;
	blocksPerGridForEachEntity = mypars->pop_size * mypars->num_of_runs;
	blocksPerGridForEachRun = mypars->num_of_runs;

	//allocating CPU memory for initial populations
	size_populations = mypars->num_of_runs * mypars->pop_size * GENOTYPE_LENGTH_IN_GLOBMEM*sizeof(float);
	cpu_init_populations = (float*) malloc(size_populations);
	memset(cpu_init_populations, 0, size_populations);

	//allocating CPU memory for results
	size_energies = mypars->pop_size * mypars->num_of_runs * sizeof(float);
	cpu_energies = (float*) malloc(size_energies);
	cpu_result_ligands = (Ligandresult*) malloc(sizeof(Ligandresult)*(mypars->num_of_runs));
	cpu_final_populations = cpu_init_populations;

	//allocating memory in CPU for reference orientation angles
	cpu_ref_ori_angles = (float*) malloc(mypars->num_of_runs*3*sizeof(float));

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

	//allocating memory in CPU for pseudorandom number generator seeds and
	//generating them (seed for each thread during GA)
	size_prng_seeds = blocksPerGridForEachEntity * threadsPerBlock * sizeof(unsigned int);
	cpu_prng_seeds = (unsigned int*) malloc(size_prng_seeds);

	genseed(time(NULL));	//initializing seed generator

	for (i=0; i<blocksPerGridForEachEntity*threadsPerBlock; i++)
#if defined (REPRO)
		cpu_prng_seeds[i] = 1u;
#else
		cpu_prng_seeds[i] = genseed(0u);
#endif

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

	//preparing the constant data fields for the GPU
	// ----------------------------------------------------------------------
	// The original function does CUDA calls initializing const Kernel data.
	// We create a struct to hold those constants
	// and return them <here> (<here> = where prepare_const_fields_for_gpu() is called),
	// so we can send them to Kernels from <here>, instead of from calcenergy.cpp as originally.
	// ----------------------------------------------------------------------
	// Constant struct
lvs's avatar
lvs committed
285
286

/*
287
288
289
290
	kernelconstant KerConst;

	if (prepare_const_fields_for_gpu(&myligand_reference, mypars, cpu_ref_ori_angles, &KerConst) == 1)
		return 1;
lvs's avatar
lvs committed
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
*/

	kernelconstant_interintra	KerConst_interintra;
	kernelconstant_intracontrib	KerConst_intracontrib;
	kernelconstant_intra		KerConst_intra;
	kernelconstant_rotlist		KerConst_rotlist;
	kernelconstant_conform		KerConst_conform;
	kernelconstant_grads		KerConst_grads;

	if (prepare_const_fields_for_gpu(&myligand_reference, mypars, cpu_ref_ori_angles, 
					 &KerConst_interintra, 
					 &KerConst_intracontrib, 
					 &KerConst_intra, 
					 &KerConst_rotlist, 
					 &KerConst_conform,
					 &KerConst_grads) == 1) {
		return 1;
	}
309
310
311
312

	// Constant data holding struct data
	// Created because structs containing array
	// are not supported as OpenCL kernel args
lvs's avatar
lvs committed
313
/*
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
  	cl_mem mem_atom_charges_const;
	cl_mem mem_atom_types_const;
  	cl_mem mem_intraE_contributors_const;
  	cl_mem mem_reqm_const;
  	cl_mem mem_reqm_hbond_const;
  	cl_mem mem_atom1_types_reqm_const;
  	cl_mem mem_atom2_types_reqm_const;
  	cl_mem mem_VWpars_AC_const;
  	cl_mem mem_VWpars_BD_const;
  	cl_mem mem_dspars_S_const;
  	cl_mem mem_dspars_V_const;
  	cl_mem mem_rotlist_const;
  	cl_mem mem_ref_coords_x_const;
  	cl_mem mem_ref_coords_y_const;
  	cl_mem mem_ref_coords_z_const;
  	cl_mem mem_rotbonds_moving_vectors_const;
  	cl_mem mem_rotbonds_unit_vectors_const;
  	cl_mem mem_ref_orientation_quats_const;
lvs's avatar
lvs committed
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
*/

	cl_mem mem_interintra_const;
	cl_mem mem_intracontrib_const;
	cl_mem mem_intra_const;
	cl_mem mem_rotlist_const;
	cl_mem mem_conform_const;

	size_t sz_interintra_const	= MAX_NUM_OF_ATOMS*sizeof(float) + 
					  MAX_NUM_OF_ATOMS*sizeof(char);

	size_t sz_intracontrib_const	= 3*MAX_INTRAE_CONTRIBUTORS*sizeof(char);

	size_t sz_intra_const		= ATYPE_NUM*sizeof(float) + 
					  ATYPE_NUM*sizeof(float) + 
					  ATYPE_NUM*sizeof(unsigned int) + 
					  ATYPE_NUM*sizeof(unsigned int) + 
				          MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float) + 
					  MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float) + 
					  MAX_NUM_OF_ATYPES*sizeof(float) + 
					  MAX_NUM_OF_ATYPES*sizeof(float);

	size_t sz_rotlist_const		= MAX_NUM_OF_ROTATIONS*sizeof(int);

	size_t sz_conform_const		= MAX_NUM_OF_ATOMS*sizeof(float) + 
					  MAX_NUM_OF_ATOMS*sizeof(float) + 
					  MAX_NUM_OF_ATOMS*sizeof(float) + 
					  3*MAX_NUM_OF_ROTBONDS*sizeof(float) + 
					  3*MAX_NUM_OF_ROTBONDS*sizeof(float) + 
					  4*MAX_NUM_OF_RUNS*sizeof(float);

363
364
365
366
367
368
369
370
  	cl_mem mem_rotbonds_const;
  	cl_mem mem_rotbonds_atoms_const;
  	cl_mem mem_num_rotating_atoms_per_rotbond_const;

	// Constant data for correcting axisangle gradients
	cl_mem mem_angle_const;
	cl_mem mem_dependence_on_theta_const;
	cl_mem mem_dependence_on_rotangle_const;
371
372
373
374

	// These constants are allocated in global memory since
	// there is a limited number of constants that can be passed
	// as arguments to kernel
lvs's avatar
lvs committed
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
/*
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ATOMS*sizeof(float),                         &mem_atom_charges_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ATOMS*sizeof(char),                          &mem_atom_types_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,3*MAX_INTRAE_CONTRIBUTORS*sizeof(char),                 &mem_intraE_contributors_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,ATYPE_NUM*sizeof(float),				    &mem_reqm_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,ATYPE_NUM*sizeof(float),				    &mem_reqm_hbond_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,ATYPE_NUM*sizeof(unsigned int),			    &mem_atom1_types_reqm_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,ATYPE_NUM*sizeof(unsigned int),                         &mem_atom2_types_reqm_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float),      &mem_VWpars_AC_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float),      &mem_VWpars_BD_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ATYPES*sizeof(float),                        &mem_dspars_S_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ATYPES*sizeof(float),                        &mem_dspars_V_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ROTATIONS*sizeof(int),                       &mem_rotlist_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ATOMS*sizeof(float),                         &mem_ref_coords_x_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ATOMS*sizeof(float),                         &mem_ref_coords_y_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ATOMS*sizeof(float),                         &mem_ref_coords_z_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,3*MAX_NUM_OF_ROTBONDS*sizeof(float),                    &mem_rotbonds_moving_vectors_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,3*MAX_NUM_OF_ROTBONDS*sizeof(float),                    &mem_rotbonds_unit_vectors_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,4*MAX_NUM_OF_RUNS*sizeof(float),                        &mem_ref_orientation_quats_const);
*/

	mallocBufferObject(context,CL_MEM_READ_ONLY,sz_interintra_const,	&mem_interintra_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,sz_intracontrib_const,   	&mem_intracontrib_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,sz_intra_const,             &mem_intra_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,sz_rotlist_const,           &mem_rotlist_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,sz_conform_const,           &mem_conform_const);

	mallocBufferObject(context,CL_MEM_READ_ONLY,2*MAX_NUM_OF_ROTBONDS*sizeof(int),                      &mem_rotbonds_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ATOMS*MAX_NUM_OF_ROTBONDS*sizeof(int),       &mem_rotbonds_atoms_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,MAX_NUM_OF_ROTBONDS*sizeof(int),      		    &mem_num_rotating_atoms_per_rotbond_const);
405

406
407
408
409
	mallocBufferObject(context,CL_MEM_READ_ONLY,1000*sizeof(float),&mem_angle_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,1000*sizeof(float),&mem_dependence_on_theta_const);
	mallocBufferObject(context,CL_MEM_READ_ONLY,1000*sizeof(float),&mem_dependence_on_rotangle_const);
   	
lvs's avatar
lvs committed
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
/*
	memcopyBufferObjectToDevice(command_queue,mem_atom_charges_const,			false,  &KerConst.atom_charges_const,           MAX_NUM_OF_ATOMS*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_atom_types_const,           		false,	&KerConst.atom_types_const,             MAX_NUM_OF_ATOMS*sizeof(char));
	memcopyBufferObjectToDevice(command_queue,mem_intraE_contributors_const,  		false,  &KerConst.intraE_contributors_const,    3*MAX_INTRAE_CONTRIBUTORS*sizeof(char));
	memcopyBufferObjectToDevice(command_queue,mem_reqm_const,         			false,  &KerConst.reqm_const,           	ATYPE_NUM*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_reqm_hbond_const,         		false,	&KerConst.reqm_hbond_const,           	ATYPE_NUM*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_atom1_types_reqm_const,         		false,  &KerConst.atom1_types_reqm_const,       ATYPE_NUM*sizeof(unsigned int));
	memcopyBufferObjectToDevice(command_queue,mem_atom2_types_reqm_const,         		false,	&KerConst.atom2_types_reqm_const,       ATYPE_NUM*sizeof(unsigned int));
	memcopyBufferObjectToDevice(command_queue,mem_VWpars_AC_const,            		false,	&KerConst.VWpars_AC_const,              MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_VWpars_BD_const,            		false,	&KerConst.VWpars_BD_const,              MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_dspars_S_const,             		false,	&KerConst.dspars_S_const,               MAX_NUM_OF_ATYPES*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_dspars_V_const,             		false,	&KerConst.dspars_V_const,               MAX_NUM_OF_ATYPES*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_rotlist_const,              		false,	&KerConst.rotlist_const,                MAX_NUM_OF_ROTATIONS*sizeof(int));
	memcopyBufferObjectToDevice(command_queue,mem_ref_coords_x_const,         		false,	&KerConst.ref_coords_x_const,           MAX_NUM_OF_ATOMS*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_ref_coords_y_const,         		false,	&KerConst.ref_coords_y_const,           MAX_NUM_OF_ATOMS*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_ref_coords_z_const,         		false,	&KerConst.ref_coords_z_const,           MAX_NUM_OF_ATOMS*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_rotbonds_moving_vectors_const,		false,	&KerConst.rotbonds_moving_vectors_const,3*MAX_NUM_OF_ROTBONDS*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_rotbonds_unit_vectors_const,  		false,	&KerConst.rotbonds_unit_vectors_const,  3*MAX_NUM_OF_ROTBONDS*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_ref_orientation_quats_const, 		false,	&KerConst.ref_orientation_quats_const,  4*MAX_NUM_OF_RUNS*sizeof(float));
*/
	
	memcopyBufferObjectToDevice(command_queue,mem_interintra_const,		false,	&KerConst_interintra,	sz_interintra_const);
	memcopyBufferObjectToDevice(command_queue,mem_intracontrib_const,      	false,	&KerConst_intracontrib, sz_intracontrib_const);
	memcopyBufferObjectToDevice(command_queue,mem_intra_const,       	false,	&KerConst_intra,       	sz_intra_const);
	memcopyBufferObjectToDevice(command_queue,mem_rotlist_const,     	false,	&KerConst_rotlist,     	sz_rotlist_const);
	memcopyBufferObjectToDevice(command_queue,mem_conform_const,     	false,	&KerConst_conform,     	sz_conform_const);

	memcopyBufferObjectToDevice(command_queue,mem_rotbonds_const,  	      			false,	&KerConst_grads.rotbonds,  			2*MAX_NUM_OF_ROTBONDS*sizeof(int));
	memcopyBufferObjectToDevice(command_queue,mem_rotbonds_atoms_const,  	      		false,	&KerConst_grads.rotbonds_atoms,  		MAX_NUM_OF_ATOMS*MAX_NUM_OF_ROTBONDS*sizeof(int));
	memcopyBufferObjectToDevice(command_queue,mem_num_rotating_atoms_per_rotbond_const, 	false,	&KerConst_grads.num_rotating_atoms_per_rotbond, MAX_NUM_OF_ROTBONDS*sizeof(int));

  	memcopyBufferObjectToDevice(command_queue,mem_angle_const,				false,  &angle,           		1000*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_dependence_on_theta_const,		false,  &dependence_on_theta,           1000*sizeof(float));
	memcopyBufferObjectToDevice(command_queue,mem_dependence_on_rotangle_const,		false,  &dependence_on_rotangle,        1000*sizeof(float));
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
	// ----------------------------------------------------------------------

 	//allocating GPU memory for populations, floatgirds,
	//energies, evaluation counters and random number generator states
	size_floatgrids = (sizeof(float)) * (mygrid->num_of_atypes+2) * (mygrid->size_xyz[0]) * (mygrid->size_xyz[1]) * (mygrid->size_xyz[2]);

	cl_mem mem_dockpars_fgrids;
	cl_mem mem_dockpars_conformations_current;
	cl_mem mem_dockpars_energies_current;
	cl_mem mem_dockpars_conformations_next;
	cl_mem mem_dockpars_energies_next;
	cl_mem mem_dockpars_evals_of_new_entities;
	cl_mem mem_gpu_evals_of_runs;
	cl_mem mem_dockpars_prng_states;

lvs's avatar
lvs committed
459
460
	mallocBufferObject(context,CL_MEM_READ_ONLY,size_floatgrids,         			&mem_dockpars_fgrids);
	mallocBufferObject(context,CL_MEM_READ_WRITE,size_populations,        			&mem_dockpars_conformations_current);
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
	mallocBufferObject(context,CL_MEM_READ_WRITE,size_energies,           			&mem_dockpars_energies_current);
	mallocBufferObject(context,CL_MEM_READ_WRITE,size_populations,        			&mem_dockpars_conformations_next);
	mallocBufferObject(context,CL_MEM_READ_WRITE,size_energies,    	      			&mem_dockpars_energies_next);
	mallocBufferObject(context,CL_MEM_READ_WRITE,mypars->pop_size*mypars->num_of_runs*sizeof(int), 	&mem_dockpars_evals_of_new_entities);

	// -------- Replacing with memory maps! ------------
#if defined (MAPPED_COPY)
	mallocBufferObject(context,CL_MEM_READ_WRITE | CL_MEM_ALLOC_HOST_PTR ,size_evals_of_runs,	  			&mem_gpu_evals_of_runs);
#else
	mallocBufferObject(context,CL_MEM_READ_WRITE,size_evals_of_runs,	  			&mem_gpu_evals_of_runs);
#endif
	// -------- Replacing with memory maps! ------------

	mallocBufferObject(context,CL_MEM_READ_WRITE,size_prng_seeds,  	      				&mem_dockpars_prng_states);

476
477
478
479
	memcopyBufferObjectToDevice(command_queue,mem_dockpars_fgrids,                	false, cpu_floatgrids,  	size_floatgrids);
 	memcopyBufferObjectToDevice(command_queue,mem_dockpars_conformations_current, 	false, cpu_init_populations, 	size_populations);
	memcopyBufferObjectToDevice(command_queue,mem_gpu_evals_of_runs, 		false, cpu_evals_of_runs, 	size_evals_of_runs);
	memcopyBufferObjectToDevice(command_queue,mem_dockpars_prng_states,     	false, cpu_prng_seeds,      	size_prng_seeds);
480
481
482
483
484
485
486
487
488
489
490
491
492
493

	//preparing parameter struct
	dockpars.num_of_atoms  = ((char)  myligand_reference.num_of_atoms);
	dockpars.num_of_atypes = ((char)  myligand_reference.num_of_atypes);
	dockpars.num_of_intraE_contributors = ((int) myligand_reference.num_of_intraE_contributors);
	dockpars.gridsize_x    = ((char)  mygrid->size_xyz[0]);
	dockpars.gridsize_y    = ((char)  mygrid->size_xyz[1]);
	dockpars.gridsize_z    = ((char)  mygrid->size_xyz[2]);
	dockpars.grid_spacing  = ((float) mygrid->spacing);
	dockpars.rotbondlist_length = ((int) NUM_OF_THREADS_PER_BLOCK*(myligand_reference.num_of_rotcyc));
	dockpars.coeff_elec    = ((float) mypars->coeffs.scaled_AD4_coeff_elec);
	dockpars.coeff_desolv  = ((float) mypars->coeffs.AD4_coeff_desolv);
	dockpars.pop_size      = mypars->pop_size;
	dockpars.num_of_genes  = myligand_reference.num_of_rotbonds + 6;
lvs's avatar
lvs committed
494
495
496
497
498
	// Notice: dockpars.tournament_rate, dockpars.crossover_rate, dockpars.mutation_rate
	// were scaled down to [0,1] in host to reduce number of operations in device
	dockpars.tournament_rate = mypars->tournament_rate/100.0f; 
	dockpars.crossover_rate  = mypars->crossover_rate/100.0f;
	dockpars.mutation_rate   = mypars->mutation_rate/100.f;
499
500
	dockpars.abs_max_dang    = mypars->abs_max_dang;
	dockpars.abs_max_dmov    = mypars->abs_max_dmov;
lvs's avatar
lvs committed
501
502
	dockpars.qasp 		 = mypars->qasp;
	dockpars.smooth 	 = mypars->smooth;
503
504
505
	unsigned int g2 = dockpars.gridsize_x * dockpars.gridsize_y;
	unsigned int g3 = dockpars.gridsize_x * dockpars.gridsize_y * dockpars.gridsize_z;

lvs's avatar
lvs committed
506
	dockpars.lsearch_rate    = mypars->lsearch_rate;
507

lvs's avatar
lvs committed
508
509
510
511
512
513
514
515
516
517
518
519
520
521
	if (dockpars.lsearch_rate != 0.0f) 
	{
		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;

		// The number of entities that undergo Solis-Wets minimization,
		blocksPerGridForEachLSEntity = dockpars.num_of_lsentities*mypars->num_of_runs;

		// The number of entities that undergo any gradient-based minimization,
		// by default, it is the same as the number of entities that undergo the Solis-Wets minimizer
lvs's avatar
lvs committed
522
		blocksPerGridForEachGradMinimizerEntity = dockpars.num_of_lsentities*mypars->num_of_runs;
lvs's avatar
lvs committed
523

lvs's avatar
lvs committed
524
525
526
		// Enable only for debugging.
		// Only one entity per reach run, undergoes gradient minimization
		//blocksPerGridForEachGradMinimizerEntity = mypars->num_of_runs;
lvs's avatar
lvs committed
527
528
529
530
531
532
533
534
	}
	
	printf("Local-search chosen method is: %s\n", (dockpars.lsearch_rate == 0.0f)? "GA" :
						      (
						      (strcmp(mypars->ls_method, "sw")   == 0)?"Solis-Wets":
						      (strcmp(mypars->ls_method, "sd")   == 0)?"Steepest descent": 
						      (strcmp(mypars->ls_method, "fire") == 0)?"Fire": "Unknown")
						      );
535

Leonardo Solis's avatar
Leonardo Solis committed
536
	/*
Leonardo Solis's avatar
Leonardo Solis committed
537
	printf("dockpars.num_of_intraE_contributors:%u\n", dockpars.num_of_intraE_contributors);
538
	printf("dockpars.rotbondlist_length:%u\n", dockpars.rotbondlist_length);
Leonardo Solis's avatar
Leonardo Solis committed
539
	*/
540

541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
	clock_start_docking = clock();

	//print progress bar
#ifndef DOCK_DEBUG
	printf("\nExecuting docking runs:\n");
	printf("        20%%        40%%       60%%       80%%       100%%\n");
	printf("---------+---------+---------+---------+---------+\n");
#else
	printf("\n");
#endif
	curr_progress_cnt = 0;

#ifdef DOCK_DEBUG
	// Main while-loop iterarion counter
	unsigned int ite_cnt = 0;
#endif

Leonardo Solis's avatar
Leonardo Solis committed
558
	/*
Leonardo Solis's avatar
Leonardo Solis committed
559
560
561
562
563
564
565
566
567
568
569
570
	// Addded for printing intracontributor_pairs (autodockdevpy)
	for (unsigned int intrapair_cnt=0; 
			  intrapair_cnt<dockpars.num_of_intraE_contributors;
			  intrapair_cnt++) {
		if (intrapair_cnt == 0) {
			printf("%-10s %-10s %-10s\n", "#pair", "#atom1", "#atom2");
		}

		printf ("%-10u %-10u %-10u\n", intrapair_cnt,
					    KerConst.intraE_contributors_const[3*intrapair_cnt],
					    KerConst.intraE_contributors_const[3*intrapair_cnt+1]);
	}
Leonardo Solis's avatar
Leonardo Solis committed
571
	*/
Leonardo Solis's avatar
Leonardo Solis committed
572

lvs's avatar
lvs committed
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
	// Kernel1
	setKernelArg(kernel1,0, sizeof(dockpars.num_of_atoms),                  &dockpars.num_of_atoms);
	setKernelArg(kernel1,1, sizeof(dockpars.num_of_atypes),                 &dockpars.num_of_atypes);
	setKernelArg(kernel1,2, sizeof(dockpars.num_of_intraE_contributors),    &dockpars.num_of_intraE_contributors);
	setKernelArg(kernel1,3, sizeof(dockpars.gridsize_x),                    &dockpars.gridsize_x);
	setKernelArg(kernel1,4, sizeof(dockpars.gridsize_y),                    &dockpars.gridsize_y);
	setKernelArg(kernel1,5, sizeof(dockpars.gridsize_z),                    &dockpars.gridsize_z);
	setKernelArg(kernel1,6, sizeof(g2),                    		  	&g2);
	setKernelArg(kernel1,7, sizeof(g3),                    		  	&g3);
	setKernelArg(kernel1,8, sizeof(dockpars.grid_spacing),                  &dockpars.grid_spacing);
	setKernelArg(kernel1,9, sizeof(mem_dockpars_fgrids),                    &mem_dockpars_fgrids);
	setKernelArg(kernel1,10,sizeof(dockpars.rotbondlist_length),            &dockpars.rotbondlist_length);
	setKernelArg(kernel1,11,sizeof(dockpars.coeff_elec),                    &dockpars.coeff_elec);
	setKernelArg(kernel1,12,sizeof(dockpars.coeff_desolv),                  &dockpars.coeff_desolv);
	setKernelArg(kernel1,13,sizeof(mem_dockpars_conformations_current),     &mem_dockpars_conformations_current);
	setKernelArg(kernel1,14,sizeof(mem_dockpars_energies_current),          &mem_dockpars_energies_current);
	setKernelArg(kernel1,15,sizeof(mem_dockpars_evals_of_new_entities),     &mem_dockpars_evals_of_new_entities);
	setKernelArg(kernel1,16,sizeof(dockpars.pop_size),                      &dockpars.pop_size);
	setKernelArg(kernel1,17,sizeof(dockpars.qasp),                          &dockpars.qasp);
lvs's avatar
lvs committed
592
593
594
595
596
597
598
	setKernelArg(kernel1,18,sizeof(dockpars.smooth),                        &dockpars.smooth);
	
	setKernelArg(kernel1,19,sizeof(mem_interintra_const),                 	&mem_interintra_const);
  	setKernelArg(kernel1,20,sizeof(mem_intracontrib_const),          	&mem_intracontrib_const);
  	setKernelArg(kernel1,21,sizeof(mem_intra_const),                        &mem_intra_const);
  	setKernelArg(kernel1,22,sizeof(mem_rotlist_const),                      &mem_rotlist_const);
  	setKernelArg(kernel1,23,sizeof(mem_conform_const),                 	&mem_conform_const);
lvs's avatar
lvs committed
599
600
	kernel1_gxsize = blocksPerGridForEachEntity * threadsPerBlock;
	kernel1_lxsize = threadsPerBlock;
601
602
603
#ifdef DOCK_DEBUG
	printf("%-25s %10s %8u %10s %4u\n", "Kernel1: ", "gSize: ", kernel1_gxsize, "lSize: ", kernel1_lxsize); fflush(stdout);
#endif
lvs's avatar
lvs committed
604
605
606
607
608
609
610
611
	// End of Kernel1

	// Kernel2
  	setKernelArg(kernel2,0,sizeof(dockpars.pop_size),       		&dockpars.pop_size);
  	setKernelArg(kernel2,1,sizeof(mem_dockpars_evals_of_new_entities),      &mem_dockpars_evals_of_new_entities);
  	setKernelArg(kernel2,2,sizeof(mem_gpu_evals_of_runs),                   &mem_gpu_evals_of_runs);
  	kernel2_gxsize = blocksPerGridForEachRun * threadsPerBlock;
  	kernel2_lxsize = threadsPerBlock;
612
613
614
#ifdef DOCK_DEBUG
	printf("%-25s %10s %8u %10s %4u\n", "Kernel2: ", "gSize: ", kernel2_gxsize, "lSize: ",  kernel2_lxsize); fflush(stdout);
#endif
lvs's avatar
lvs committed
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
	// End of Kernel2

	// Kernel4
  	setKernelArg(kernel4,0, sizeof(dockpars.num_of_atoms),                  &dockpars.num_of_atoms);
  	setKernelArg(kernel4,1, sizeof(dockpars.num_of_atypes),                 &dockpars.num_of_atypes);
  	setKernelArg(kernel4,2, sizeof(dockpars.num_of_intraE_contributors),    &dockpars.num_of_intraE_contributors);
  	setKernelArg(kernel4,3, sizeof(dockpars.gridsize_x),                    &dockpars.gridsize_x);
  	setKernelArg(kernel4,4, sizeof(dockpars.gridsize_y),                    &dockpars.gridsize_y);
  	setKernelArg(kernel4,5, sizeof(dockpars.gridsize_z),                    &dockpars.gridsize_z);
  	setKernelArg(kernel4,6, sizeof(g2),                    		  	&g2);
  	setKernelArg(kernel4,7, sizeof(g3),                    		  	&g3);
  	setKernelArg(kernel4,8, sizeof(dockpars.grid_spacing),                  &dockpars.grid_spacing);
  	setKernelArg(kernel4,9, sizeof(mem_dockpars_fgrids),                    &mem_dockpars_fgrids);
  	setKernelArg(kernel4,10,sizeof(dockpars.rotbondlist_length),            &dockpars.rotbondlist_length);
  	setKernelArg(kernel4,11,sizeof(dockpars.coeff_elec),                    &dockpars.coeff_elec);
  	setKernelArg(kernel4,12,sizeof(dockpars.coeff_desolv),                  &dockpars.coeff_desolv);
  	setKernelArg(kernel4,13,sizeof(mem_dockpars_conformations_current),     &mem_dockpars_conformations_current);
  	setKernelArg(kernel4,14,sizeof(mem_dockpars_energies_current),          &mem_dockpars_energies_current);
  	setKernelArg(kernel4,15,sizeof(mem_dockpars_conformations_next),        &mem_dockpars_conformations_next);
  	setKernelArg(kernel4,16,sizeof(mem_dockpars_energies_next),             &mem_dockpars_energies_next);
  	setKernelArg(kernel4,17,sizeof(mem_dockpars_evals_of_new_entities),     &mem_dockpars_evals_of_new_entities);
  	setKernelArg(kernel4,18,sizeof(mem_dockpars_prng_states),               &mem_dockpars_prng_states);
  	setKernelArg(kernel4,19,sizeof(dockpars.pop_size),                      &dockpars.pop_size);
  	setKernelArg(kernel4,20,sizeof(dockpars.num_of_genes),                  &dockpars.num_of_genes);
  	setKernelArg(kernel4,21,sizeof(dockpars.tournament_rate),               &dockpars.tournament_rate);
  	setKernelArg(kernel4,22,sizeof(dockpars.crossover_rate),                &dockpars.crossover_rate);
  	setKernelArg(kernel4,23,sizeof(dockpars.mutation_rate),                 &dockpars.mutation_rate);
  	setKernelArg(kernel4,24,sizeof(dockpars.abs_max_dmov),                  &dockpars.abs_max_dmov);
  	setKernelArg(kernel4,25,sizeof(dockpars.abs_max_dang),                  &dockpars.abs_max_dang);
  	setKernelArg(kernel4,26,sizeof(dockpars.qasp),                          &dockpars.qasp);
lvs's avatar
lvs committed
645
646
647
648
649
650
651
  	setKernelArg(kernel4,27,sizeof(dockpars.smooth),                        &dockpars.smooth);

  	setKernelArg(kernel4,28,sizeof(mem_interintra_const),                 	&mem_interintra_const);
  	setKernelArg(kernel4,29,sizeof(mem_intracontrib_const),          	&mem_intracontrib_const);
  	setKernelArg(kernel4,30,sizeof(mem_intra_const),                        &mem_intra_const);
  	setKernelArg(kernel4,31,sizeof(mem_rotlist_const),                      &mem_rotlist_const);
  	setKernelArg(kernel4,32,sizeof(mem_conform_const),                 	&mem_conform_const);
lvs's avatar
lvs committed
652
653
  	kernel4_gxsize = blocksPerGridForEachEntity * threadsPerBlock;
  	kernel4_lxsize = threadsPerBlock;
654
655
656
#ifdef DOCK_DEBUG
	printf("%-25s %10s %8u %10s %4u\n", "K_GENETIC_GENERATION: ", "gSize: ",  kernel4_gxsize, "lSize: ", kernel4_lxsize); fflush(stdout);
#endif
lvs's avatar
lvs committed
657
	// End of Kernel4
658
659


lvs's avatar
lvs committed
660
	if (dockpars.lsearch_rate != 0.0f) {
661

lvs's avatar
lvs committed
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
		if (strcmp(mypars->ls_method, "sw") == 0) {
			// Kernel3
  			setKernelArg(kernel3,0, sizeof(dockpars.num_of_atoms),                  &dockpars.num_of_atoms);
  			setKernelArg(kernel3,1, sizeof(dockpars.num_of_atypes),                 &dockpars.num_of_atypes);
  			setKernelArg(kernel3,2, sizeof(dockpars.num_of_intraE_contributors),    &dockpars.num_of_intraE_contributors);
	 	 	setKernelArg(kernel3,3, sizeof(dockpars.gridsize_x),                    &dockpars.gridsize_x);
  			setKernelArg(kernel3,4, sizeof(dockpars.gridsize_y),                    &dockpars.gridsize_y);
  			setKernelArg(kernel3,5, sizeof(dockpars.gridsize_z),                    &dockpars.gridsize_z);
  			setKernelArg(kernel3,6, sizeof(g2),                    		  	&g2);
  			setKernelArg(kernel3,7, sizeof(g3),                    		  	&g3);
  			setKernelArg(kernel3,8, sizeof(dockpars.grid_spacing),                  &dockpars.grid_spacing);
  			setKernelArg(kernel3,9, sizeof(mem_dockpars_fgrids),                    &mem_dockpars_fgrids);
  			setKernelArg(kernel3,10,sizeof(dockpars.rotbondlist_length),            &dockpars.rotbondlist_length);
			setKernelArg(kernel3,11,sizeof(dockpars.coeff_elec),                    &dockpars.coeff_elec);
			setKernelArg(kernel3,12,sizeof(dockpars.coeff_desolv),                  &dockpars.coeff_desolv);
			setKernelArg(kernel3,13,sizeof(mem_dockpars_conformations_next),        &mem_dockpars_conformations_next);
			setKernelArg(kernel3,14,sizeof(mem_dockpars_energies_next),             &mem_dockpars_energies_next);
			setKernelArg(kernel3,15,sizeof(mem_dockpars_evals_of_new_entities),     &mem_dockpars_evals_of_new_entities);
			setKernelArg(kernel3,16,sizeof(mem_dockpars_prng_states),               &mem_dockpars_prng_states);
			setKernelArg(kernel3,17,sizeof(dockpars.pop_size),                      &dockpars.pop_size);
			setKernelArg(kernel3,18,sizeof(dockpars.num_of_genes),                  &dockpars.num_of_genes);
			setKernelArg(kernel3,19,sizeof(dockpars.lsearch_rate),                  &dockpars.lsearch_rate);
			setKernelArg(kernel3,20,sizeof(dockpars.num_of_lsentities),             &dockpars.num_of_lsentities);
			setKernelArg(kernel3,21,sizeof(dockpars.rho_lower_bound),               &dockpars.rho_lower_bound);
			setKernelArg(kernel3,22,sizeof(dockpars.base_dmov_mul_sqrt3),           &dockpars.base_dmov_mul_sqrt3);
			setKernelArg(kernel3,23,sizeof(dockpars.base_dang_mul_sqrt3),           &dockpars.base_dang_mul_sqrt3);
			setKernelArg(kernel3,24,sizeof(dockpars.cons_limit),                    &dockpars.cons_limit);
			setKernelArg(kernel3,25,sizeof(dockpars.max_num_of_iters),              &dockpars.max_num_of_iters);
			setKernelArg(kernel3,26,sizeof(dockpars.qasp),                          &dockpars.qasp);
lvs's avatar
lvs committed
691
692
693
694
695
696
697
			setKernelArg(kernel3,27,sizeof(dockpars.smooth),                        &dockpars.smooth);

	  		setKernelArg(kernel3,28,sizeof(mem_interintra_const),                 	&mem_interintra_const);
		  	setKernelArg(kernel3,29,sizeof(mem_intracontrib_const),          	&mem_intracontrib_const);
	  		setKernelArg(kernel3,30,sizeof(mem_intra_const),                        &mem_intra_const);
	  		setKernelArg(kernel3,31,sizeof(mem_rotlist_const),                      &mem_rotlist_const);
	  		setKernelArg(kernel3,32,sizeof(mem_conform_const),                 	&mem_conform_const);
lvs's avatar
lvs committed
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
			kernel3_gxsize = blocksPerGridForEachLSEntity * threadsPerBlock;
			kernel3_lxsize = threadsPerBlock;
  			#ifdef DOCK_DEBUG
	  		printf("%-25s %10s %8u %10s %4u\n", "K_LOCAL_SEARCH: ", "gSize: ", kernel3_gxsize, "lSize: ", kernel3_lxsize); fflush(stdout);
  			#endif
			// End of Kernel3
		} else if (strcmp(mypars->ls_method, "sd") == 0) {
			// Kernel5
  			setKernelArg(kernel5,0, sizeof(dockpars.num_of_atoms),                   &dockpars.num_of_atoms);
  			setKernelArg(kernel5,1, sizeof(dockpars.num_of_atypes),                  &dockpars.num_of_atypes);
  			setKernelArg(kernel5,2, sizeof(dockpars.num_of_intraE_contributors),     &dockpars.num_of_intraE_contributors);
  			setKernelArg(kernel5,3, sizeof(dockpars.gridsize_x),                     &dockpars.gridsize_x);
  			setKernelArg(kernel5,4, sizeof(dockpars.gridsize_y),                     &dockpars.gridsize_y);
  			setKernelArg(kernel5,5, sizeof(dockpars.gridsize_z),                     &dockpars.gridsize_z);
  			setKernelArg(kernel5,6, sizeof(g2),                    		   	 &g2);
  			setKernelArg(kernel5,7, sizeof(g3),                    		   	 &g3);
  			setKernelArg(kernel5,8, sizeof(dockpars.grid_spacing),                   &dockpars.grid_spacing);
  			setKernelArg(kernel5,9, sizeof(mem_dockpars_fgrids),                     &mem_dockpars_fgrids);
  			setKernelArg(kernel5,10,sizeof(dockpars.rotbondlist_length),             &dockpars.rotbondlist_length);
  			setKernelArg(kernel5,11,sizeof(dockpars.coeff_elec),                     &dockpars.coeff_elec);
  			setKernelArg(kernel5,12,sizeof(dockpars.coeff_desolv),                   &dockpars.coeff_desolv);
  			setKernelArg(kernel5,13,sizeof(mem_dockpars_conformations_next),         &mem_dockpars_conformations_next);
  			setKernelArg(kernel5,14,sizeof(mem_dockpars_energies_next),              &mem_dockpars_energies_next);
  			setKernelArg(kernel5,15,sizeof(mem_dockpars_evals_of_new_entities),      &mem_dockpars_evals_of_new_entities);
  			setKernelArg(kernel5,16,sizeof(mem_dockpars_prng_states),                &mem_dockpars_prng_states);
  			setKernelArg(kernel5,17,sizeof(dockpars.pop_size),                       &dockpars.pop_size);
  			setKernelArg(kernel5,18,sizeof(dockpars.num_of_genes),                   &dockpars.num_of_genes);
  			setKernelArg(kernel5,19,sizeof(dockpars.lsearch_rate),                   &dockpars.lsearch_rate);
  			setKernelArg(kernel5,20,sizeof(dockpars.num_of_lsentities),              &dockpars.num_of_lsentities);
  			setKernelArg(kernel5,21,sizeof(dockpars.max_num_of_iters),               &dockpars.max_num_of_iters);
  			setKernelArg(kernel5,22,sizeof(dockpars.qasp),                           &dockpars.qasp);
lvs's avatar
lvs committed
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
			setKernelArg(kernel5,23,sizeof(dockpars.smooth),                         &dockpars.smooth);

	  		setKernelArg(kernel5,24,sizeof(mem_interintra_const),                 	 &mem_interintra_const);
		  	setKernelArg(kernel5,25,sizeof(mem_intracontrib_const),          	 &mem_intracontrib_const);
	  		setKernelArg(kernel5,26,sizeof(mem_intra_const),                         &mem_intra_const);
	  		setKernelArg(kernel5,27,sizeof(mem_rotlist_const),                       &mem_rotlist_const);
	  		setKernelArg(kernel5,28,sizeof(mem_conform_const),                 	 &mem_conform_const);

  			setKernelArg(kernel5,29,sizeof(mem_rotbonds_const),         		 &mem_rotbonds_const);
  			setKernelArg(kernel5,30,sizeof(mem_rotbonds_atoms_const),   		 &mem_rotbonds_atoms_const);
  			setKernelArg(kernel5,31,sizeof(mem_num_rotating_atoms_per_rotbond_const),&mem_num_rotating_atoms_per_rotbond_const);
  			setKernelArg(kernel5,32,sizeof(mem_angle_const),			 &mem_angle_const);
  			setKernelArg(kernel5,33,sizeof(mem_dependence_on_theta_const),		 &mem_dependence_on_theta_const);
  			setKernelArg(kernel5,34,sizeof(mem_dependence_on_rotangle_const),  	 &mem_dependence_on_rotangle_const);

lvs's avatar
lvs committed
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
  			kernel5_gxsize = blocksPerGridForEachGradMinimizerEntity * threadsPerBlock;
  			kernel5_lxsize = threadsPerBlock;
			#ifdef DOCK_DEBUG
			printf("%-25s %10s %8u %10s %4u\n", "K_GRAD_MINIMIZER: ", "gSize: ", kernel5_gxsize, "lSize: ", kernel5_lxsize); fflush(stdout);
			#endif
			// End of Kernel5
		} else if (strcmp(mypars->ls_method, "fire") == 0) {
			// Kernel6
  			setKernelArg(kernel6,0, sizeof(dockpars.num_of_atoms),                   &dockpars.num_of_atoms);
  			setKernelArg(kernel6,1, sizeof(dockpars.num_of_atypes),                  &dockpars.num_of_atypes);
  			setKernelArg(kernel6,2, sizeof(dockpars.num_of_intraE_contributors),     &dockpars.num_of_intraE_contributors);
  			setKernelArg(kernel6,3, sizeof(dockpars.gridsize_x),                     &dockpars.gridsize_x);
  			setKernelArg(kernel6,4, sizeof(dockpars.gridsize_y),                     &dockpars.gridsize_y);
  			setKernelArg(kernel6,5, sizeof(dockpars.gridsize_z),                     &dockpars.gridsize_z);
  			setKernelArg(kernel6,6, sizeof(g2),                    		   	 &g2);
  			setKernelArg(kernel6,7, sizeof(g3),                    		   	 &g3);
  			setKernelArg(kernel6,8, sizeof(dockpars.grid_spacing),                   &dockpars.grid_spacing);
  			setKernelArg(kernel6,9, sizeof(mem_dockpars_fgrids),                     &mem_dockpars_fgrids);
  			setKernelArg(kernel6,10,sizeof(dockpars.rotbondlist_length),             &dockpars.rotbondlist_length);
  			setKernelArg(kernel6,11,sizeof(dockpars.coeff_elec),                     &dockpars.coeff_elec);
  			setKernelArg(kernel6,12,sizeof(dockpars.coeff_desolv),                   &dockpars.coeff_desolv);
  			setKernelArg(kernel6,13,sizeof(mem_dockpars_conformations_next),         &mem_dockpars_conformations_next);
  			setKernelArg(kernel6,14,sizeof(mem_dockpars_energies_next),              &mem_dockpars_energies_next);
  			setKernelArg(kernel6,15,sizeof(mem_dockpars_evals_of_new_entities),      &mem_dockpars_evals_of_new_entities);
  			setKernelArg(kernel6,16,sizeof(mem_dockpars_prng_states),                &mem_dockpars_prng_states);
  			setKernelArg(kernel6,17,sizeof(dockpars.pop_size),                       &dockpars.pop_size);
  			setKernelArg(kernel6,18,sizeof(dockpars.num_of_genes),                   &dockpars.num_of_genes);
  			setKernelArg(kernel6,19,sizeof(dockpars.lsearch_rate),                   &dockpars.lsearch_rate);
  			setKernelArg(kernel6,20,sizeof(dockpars.num_of_lsentities),              &dockpars.num_of_lsentities);
  			setKernelArg(kernel6,21,sizeof(dockpars.max_num_of_iters),               &dockpars.max_num_of_iters);
  			setKernelArg(kernel6,22,sizeof(dockpars.qasp),                           &dockpars.qasp);
lvs's avatar
lvs committed
775
776
777
778
779
780
781
782
783
784
785
786
787
788
  			setKernelArg(kernel6,23,sizeof(dockpars.smooth),                         &dockpars.smooth);

	  		setKernelArg(kernel6,24,sizeof(mem_interintra_const),                 	 &mem_interintra_const);
		  	setKernelArg(kernel6,25,sizeof(mem_intracontrib_const),          	 &mem_intracontrib_const);
	  		setKernelArg(kernel6,26,sizeof(mem_intra_const),                         &mem_intra_const);
	  		setKernelArg(kernel6,27,sizeof(mem_rotlist_const),                       &mem_rotlist_const);
	  		setKernelArg(kernel6,28,sizeof(mem_conform_const),                 	 &mem_conform_const);

  			setKernelArg(kernel6,29,sizeof(mem_rotbonds_const),         		 &mem_rotbonds_const);
  			setKernelArg(kernel6,30,sizeof(mem_rotbonds_atoms_const),   		 &mem_rotbonds_atoms_const);
  			setKernelArg(kernel6,31,sizeof(mem_num_rotating_atoms_per_rotbond_const),&mem_num_rotating_atoms_per_rotbond_const);
  			setKernelArg(kernel6,32,sizeof(mem_angle_const),			 &mem_angle_const);
  			setKernelArg(kernel6,33,sizeof(mem_dependence_on_theta_const),		 &mem_dependence_on_theta_const);
  			setKernelArg(kernel6,34,sizeof(mem_dependence_on_rotangle_const),	 &mem_dependence_on_rotangle_const);
lvs's avatar
lvs committed
789
790
791
792
793
794
795
796
  			kernel6_gxsize = blocksPerGridForEachGradMinimizerEntity * threadsPerBlock;
  			kernel6_lxsize = threadsPerBlock;
			#ifdef DOCK_DEBUG
			printf("%-25s %10s %8u %10s %4u\n", "K_GRAD_MINFIRE: ", "gSize: ", kernel6_gxsize, "lSize: ", kernel6_lxsize); fflush(stdout);
			#endif
			// End of Kernel6
		}
	} // End if (dockpars.lsearch_rate != 0.0f)
797

lvs's avatar
lvs committed
798
	// Kernel1
799
800
801
	#ifdef DOCK_DEBUG
		printf("Start Kernel1 ... ");fflush(stdout);
	#endif
802
	runKernel1D(command_queue,kernel1,kernel1_gxsize,kernel1_lxsize,&time_start_kernel,&time_end_kernel);
803
804
805
	#ifdef DOCK_DEBUG
		printf(" ... Finish Kernel1\n");fflush(stdout);
	#endif
lvs's avatar
lvs committed
806
	// End of Kernel1
807

lvs's avatar
lvs committed
808
	// Kernel2
809
810
811
	#ifdef DOCK_DEBUG
		printf("Start Kernel2 ... ");fflush(stdout);
	#endif
812
	runKernel1D(command_queue,kernel2,kernel2_gxsize,kernel2_lxsize,&time_start_kernel,&time_end_kernel);
813
814
815
	#ifdef DOCK_DEBUG
		printf(" ... Finish Kernel2\n");fflush(stdout);
	#endif
lvs's avatar
lvs committed
816
	// End of Kernel2
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
	// ===============================================================================


	// -------- Replacing with memory maps! ------------
#if defined (MAPPED_COPY)
	int* map_cpu_evals_of_runs;
	map_cpu_evals_of_runs = (int*) memMap(command_queue, mem_gpu_evals_of_runs, CL_MAP_READ, size_evals_of_runs);
#else
	memcopyBufferObjectFromDevice(command_queue,cpu_evals_of_runs,mem_gpu_evals_of_runs,size_evals_of_runs);
#endif
	// -------- Replacing with memory maps! ------------


	generation_cnt = 1;


	// -------- Replacing with memory maps! ------------
#if defined (MAPPED_COPY)
	while ((progress = check_progress(map_cpu_evals_of_runs, generation_cnt, mypars->num_of_energy_evals, mypars->num_of_generations, mypars->num_of_runs)) < 100.0)
#else
	while ((progress = check_progress(cpu_evals_of_runs, generation_cnt, mypars->num_of_energy_evals, mypars->num_of_generations, mypars->num_of_runs)) < 100.0)
#endif
	// -------- Replacing with memory maps! ------------

	{
#ifdef DOCK_DEBUG
    ite_cnt++;
    printf("\nIteration # %u\n", ite_cnt);
    fflush(stdout);
#endif

	 //update progress bar (bar length is 50)
	 new_progress_cnt = (int) (progress/2.0+0.5);
	 if (new_progress_cnt > 50)
	 	new_progress_cnt = 50;

	 while (curr_progress_cnt < new_progress_cnt) {
		curr_progress_cnt++;
#ifndef DOCK_DEBUG
		printf("*");
#endif
		fflush(stdout);
	}

lvs's avatar
lvs committed
861
	// Kernel4
862
863
864
865
866
867
868
	#ifdef DOCK_DEBUG
		printf("%-25s", "K_GENETIC_GENERATION: ");fflush(stdout);
	#endif
		runKernel1D(command_queue,kernel4,kernel4_gxsize,kernel4_lxsize,&time_start_kernel,&time_end_kernel);
	#ifdef DOCK_DEBUG
		printf("%15s", " ... Finished\n");fflush(stdout);
	#endif
lvs's avatar
lvs committed
869
	// End of Kernel4
lvs's avatar
lvs committed
870

lvs's avatar
lvs committed
871
872
873
874
875
876
877
878
879
880
881
	if (dockpars.lsearch_rate != 0.0f) {
		if (strcmp(mypars->ls_method, "sw") == 0) {
			// Kernel3
			#ifdef DOCK_DEBUG
				printf("%-25s", "K_LOCAL_SEARCH: ");fflush(stdout);
			#endif
				runKernel1D(command_queue,kernel3,kernel3_gxsize,kernel3_lxsize,&time_start_kernel,&time_end_kernel);
			#ifdef DOCK_DEBUG
				printf("%15s" ," ... Finished\n");fflush(stdout);
			#endif
			// End of Kernel3
lvs's avatar
lvs committed
882

lvs's avatar
lvs committed
883
884
885
886
887
888
889
890
891
892
		} else if (strcmp(mypars->ls_method, "sd") == 0) {
			// Kernel5
			#ifdef DOCK_DEBUG
				printf("%-25s", "K_GRAD_MINIMIZER: ");fflush(stdout);
			#endif
				runKernel1D(command_queue,kernel5,kernel5_gxsize,kernel5_lxsize,&time_start_kernel,&time_end_kernel);
			#ifdef DOCK_DEBUG
				printf("%15s" ," ... Finished\n");fflush(stdout);
			#endif
			// End of Kernel5
893

lvs's avatar
lvs committed
894
895
896
897
898
899
900
901
902
903
904
905
		} else if (strcmp(mypars->ls_method, "fire") == 0) {
			// Kernel6
			#ifdef DOCK_DEBUG
				printf("%-25s", "K_GRAD_MINFIRE: ");fflush(stdout);
			#endif
				runKernel1D(command_queue,kernel6,kernel6_gxsize,kernel6_lxsize,&time_start_kernel,&time_end_kernel);
			#ifdef DOCK_DEBUG
				printf("%15s" ," ... Finished\n");fflush(stdout);
			#endif
			// End of Kernel6
		}
	} // End if (dockpars.lsearch_rate != 0.0f)
906

907
908
909
910
911
912
	// -------- Replacing with memory maps! ------------
	#if defined (MAPPED_COPY)
	unmemMap(command_queue,mem_gpu_evals_of_runs,map_cpu_evals_of_runs);
	#endif
	// -------- Replacing with memory maps! ------------

lvs's avatar
lvs committed
913
	// Kernel2
914
915
916
	#ifdef DOCK_DEBUG
		printf("Start Kernel2 ... ");fflush(stdout);
	#endif
917
		runKernel1D(command_queue,kernel2,kernel2_gxsize,kernel2_lxsize,&time_start_kernel,&time_end_kernel);
918
919
920
	#ifdef DOCK_DEBUG
		printf(" ... Finish Kernel2\n");fflush(stdout);
	#endif
lvs's avatar
lvs committed
921
	// End of Kernel2
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
		// ===============================================================================


		// -------- Replacing with memory maps! ------------
#if defined (MAPPED_COPY)
		map_cpu_evals_of_runs = (int*) memMap(command_queue, mem_gpu_evals_of_runs, CL_MAP_READ, size_evals_of_runs);
#else
		memcopyBufferObjectFromDevice(command_queue,cpu_evals_of_runs,mem_gpu_evals_of_runs,size_evals_of_runs);
#endif
		// -------- Replacing with memory maps! ------------

		generation_cnt++;

		// ----------------------------------------------------------------------
		// ORIGINAL APPROACH: switching conformation and energy pointers
		// CURRENT APPROACH:  copy data from one buffer to another, pointers are kept the same
		// IMPROVED CURRENT APPROACH
		// Kernel arguments are changed on every iteration
		// No copy from dev glob memory to dev glob memory occurs
		// Use generation_cnt as it evolves with the main loop
		// No need to use tempfloat
		// No performance improvement wrt to "CURRENT APPROACH"

		// Kernel args exchange regions they point to
		// But never two args point to the same region of dev memory
		// NO ALIASING -> use restrict in Kernel
		if (generation_cnt % 2 == 0) {
			// Kernel 4
950
951
952
953
			setKernelArg(kernel4,13,sizeof(mem_dockpars_conformations_next),                &mem_dockpars_conformations_next);
			setKernelArg(kernel4,14,sizeof(mem_dockpars_energies_next),                     &mem_dockpars_energies_next);
      			setKernelArg(kernel4,15,sizeof(mem_dockpars_conformations_current),             &mem_dockpars_conformations_current);
			setKernelArg(kernel4,16,sizeof(mem_dockpars_energies_current),                  &mem_dockpars_energies_current);
lvs's avatar
lvs committed
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969

			if (dockpars.lsearch_rate != 0.0f) {
				if (strcmp(mypars->ls_method, "sw") == 0) {
						// Kernel 3
			     			setKernelArg(kernel3,13,sizeof(mem_dockpars_conformations_current),	&mem_dockpars_conformations_current);
			      			setKernelArg(kernel3,14,sizeof(mem_dockpars_energies_current),		&mem_dockpars_energies_current);
				} else if (strcmp(mypars->ls_method, "sd") == 0) {
						// Kernel 5
			     			setKernelArg(kernel5,13,sizeof(mem_dockpars_conformations_current),	&mem_dockpars_conformations_current);
			      			setKernelArg(kernel5,14,sizeof(mem_dockpars_energies_current),		&mem_dockpars_energies_current);
				} else if (strcmp(mypars->ls_method, "fire") == 0) {
						// Kernel 6
			     			setKernelArg(kernel6,13,sizeof(mem_dockpars_conformations_current),	&mem_dockpars_conformations_current);
			      			setKernelArg(kernel6,14,sizeof(mem_dockpars_energies_current),		&mem_dockpars_energies_current);
				}
			} // End if (dockpars.lsearch_rate != 0.0f)
970
971
972
		}
		else { // In this configuration, the program starts
			// Kernel 4
973
974
975
976
			setKernelArg(kernel4,13,sizeof(mem_dockpars_conformations_current),             &mem_dockpars_conformations_current);
			setKernelArg(kernel4,14,sizeof(mem_dockpars_energies_current),                  &mem_dockpars_energies_current);
      			setKernelArg(kernel4,15,sizeof(mem_dockpars_conformations_next),                &mem_dockpars_conformations_next);
			setKernelArg(kernel4,16,sizeof(mem_dockpars_energies_next),                     &mem_dockpars_energies_next);
977

lvs's avatar
lvs committed
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
			if (dockpars.lsearch_rate != 0.0f) {
				if (strcmp(mypars->ls_method, "sw") == 0) {
					// Kernel 3
					setKernelArg(kernel3,13,sizeof(mem_dockpars_conformations_next),		&mem_dockpars_conformations_next);
		      			setKernelArg(kernel3,14,sizeof(mem_dockpars_energies_next),			&mem_dockpars_energies_next);
				} else if (strcmp(mypars->ls_method, "sd") == 0) {
					// Kernel 5
					setKernelArg(kernel5,13,sizeof(mem_dockpars_conformations_next),                &mem_dockpars_conformations_next);
		      			setKernelArg(kernel5,14,sizeof(mem_dockpars_energies_next),                     &mem_dockpars_energies_next);
				} else if (strcmp(mypars->ls_method, "fire") == 0) {
					// Kernel 6
					setKernelArg(kernel6,13,sizeof(mem_dockpars_conformations_next),                &mem_dockpars_conformations_next);
		      			setKernelArg(kernel6,14,sizeof(mem_dockpars_energies_next),                     &mem_dockpars_energies_next);
				}
			} // End if (dockpars.lsearch_rate != 0.0f)
993
994
995
996
997
998
999
1000
		}
		// ----------------------------------------------------------------------

#ifdef DOCK_DEBUG
        printf("Progress %.3f %%\n", progress);
        fflush(stdout);
#endif
	} // End of while-loop