kernel3.cl 12.8 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.

*/


Leonardo Solis's avatar
Leonardo Solis committed
25
__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))
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
perform_LS(		
			char   dockpars_num_of_atoms,
			char   dockpars_num_of_atypes,
			int    dockpars_num_of_intraE_contributors,
			char   dockpars_gridsize_x,
			char   dockpars_gridsize_y,
			char   dockpars_gridsize_z,
			float  dockpars_grid_spacing,
         __global const float* restrict dockpars_fgrids, // This is too large to be allocated in __constant 
	        	int    dockpars_rotbondlist_length,
			float  dockpars_coeff_elec,
			float  dockpars_coeff_desolv,
  	 __global       float* restrict dockpars_conformations_next,
  	 __global 	float* restrict dockpars_energies_next,
  	 __global 	int*   restrict dockpars_evals_of_new_entities,
  	 __global 	uint*  restrict dockpars_prng_states,
			int    dockpars_pop_size,
			int    dockpars_num_of_genes,
			float  dockpars_lsearch_rate,
			uint   dockpars_num_of_lsentities,
			float  dockpars_rho_lower_bound,
			float  dockpars_base_dmov_mul_sqrt3,
			float  dockpars_base_dang_mul_sqrt3,
			uint   dockpars_cons_limit,
			uint   dockpars_max_num_of_iters,
			float  dockpars_qasp,
	     __constant float* atom_charges_const,
             __constant char*  atom_types_const,
	     __constant char*  intraE_contributors_const,
             __constant float* VWpars_AC_const,
             __constant float* VWpars_BD_const,
             __constant float* dspars_S_const,
             __constant float* dspars_V_const,
             __constant int*   rotlist_const,
             __constant float* ref_coords_x_const,
             __constant float* ref_coords_y_const,
             __constant float* ref_coords_z_const,
             __constant float* rotbonds_moving_vectors_const,
             __constant float* rotbonds_unit_vectors_const,
             __constant float* ref_orientation_quats_const
Leonardo Solis's avatar
Leonardo Solis committed
66
67
68
69
70
71
72
73
74
)
//The GPU global function performs local search on the pre-defined entities of conformations_next.
//The number of blocks which should be started equals to num_of_lsentities*num_of_runs.
//This way the first num_of_lsentities entity of each population will be subjected to local search
//(and each block carries out the algorithm for one entity).
//Since the first entity is always the best one in the current population,
//it is always tested according to the ls probability, and if it not to be
//subjected to local search, the entity with ID num_of_lsentities is selected instead of the first one (with ID 0).
{
75
76
77
78
	// Some OpenCL compilers don't allow declaring 
	// local variables within non-kernel functions.
	// These local variables must be declared in a kernel, 
	// and then passed to non-kernel functions.
Leonardo Solis's avatar
Leonardo Solis committed
79
80
81
	__local float genotype_candidate[ACTUAL_GENOTYPE_LENGTH];
	__local float genotype_deviate  [ACTUAL_GENOTYPE_LENGTH];
	__local float genotype_bias     [ACTUAL_GENOTYPE_LENGTH];
Leonardo Solis's avatar
Leonardo Solis committed
82
        __local float rho;
Leonardo Solis's avatar
Leonardo Solis committed
83
84
85
86
87
88
89
90
91
92
93
94
	__local int   cons_succ;
	__local int   cons_fail;
	__local int   iteration_cnt;
	__local float candidate_energy;
	__local int   evaluation_cnt;
	int gene_counter;

	__local float offspring_genotype[ACTUAL_GENOTYPE_LENGTH];
	__local int run_id;
	__local int entity_id;
	__local float offspring_energy;

Leonardo Solis's avatar
Leonardo Solis committed
95
96
97
98
99
	__local float calc_coords_x[MAX_NUM_OF_ATOMS];
	__local float calc_coords_y[MAX_NUM_OF_ATOMS];
	__local float calc_coords_z[MAX_NUM_OF_ATOMS];
	__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];

100
101
	// Determining run ID and entity ID
	// Initializing offspring genotype
Leonardo Solis's avatar
Leonardo Solis committed
102
103
104
105
106
	if (get_local_id(0) == 0)
	{
		run_id = get_group_id(0) / dockpars_num_of_lsentities;
		entity_id = get_group_id(0) % dockpars_num_of_lsentities;

107
108
109
110
111
112
113
114
115
		// Since entity 0 is the best one due to elitism,
		// it should be subjected to random selection
		if (entity_id == 0) {
			// If entity 0 is not selected according to LS-rate,
			// choosing an other entity
			if (100.0f*gpu_randf(dockpars_prng_states) > dockpars_lsearch_rate) {
				entity_id = dockpars_num_of_lsentities;					
			}
		}
Leonardo Solis's avatar
Leonardo Solis committed
116
117
118
119
120
121

		offspring_energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
	}

	barrier(CLK_LOCAL_MEM_FENCE);

122
123
124
125
126
127
128
  	async_work_group_copy(offspring_genotype,
			      dockpars_conformations_next+(run_id*dockpars_pop_size+entity_id)*GENOTYPE_LENGTH_IN_GLOBMEM,
                              dockpars_num_of_genes, 0);

	for (gene_counter = get_local_id(0);
	     gene_counter < dockpars_num_of_genes;
	     gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
Leonardo Solis's avatar
Leonardo Solis committed
129
		   genotype_bias[gene_counter] = 0.0f;
130
	}
Leonardo Solis's avatar
Leonardo Solis committed
131
132
133
134
135
136
137
138
139
140
141
142
143

	if (get_local_id(0) == 0) {
		rho = 1.0f;
		cons_succ = 0;
		cons_fail = 0;
		iteration_cnt = 0;
		evaluation_cnt = 0;
	}

	barrier(CLK_LOCAL_MEM_FENCE);

	while ((iteration_cnt < dockpars_max_num_of_iters) && (rho > dockpars_rho_lower_bound))
	{
144
145
146
147
		// New random deviate
		for (gene_counter = get_local_id(0);
		     gene_counter < dockpars_num_of_genes;
		     gene_counter+= NUM_OF_THREADS_PER_BLOCK)
Leonardo Solis's avatar
Leonardo Solis committed
148
149
150
		{
			genotype_deviate[gene_counter] = rho*(2*gpu_randf(dockpars_prng_states)-1);

151
152
			// Translation genes
			if (gene_counter <= 2)
153
				genotype_deviate[gene_counter] *= dockpars_base_dmov_mul_sqrt3;
154
155
			
			// Shoemake orientation-genes do not use initial deviation
156

157
158
			// Torsion genes
			else if (gene_counter >= 6) 
Leonardo Solis's avatar
Leonardo Solis committed
159
				genotype_deviate[gene_counter] *= dockpars_base_dang_mul_sqrt3;
160

Leonardo Solis's avatar
Leonardo Solis committed
161
162
		}

163
164
165
166
167
168
169
		// Generating new genotype candidate
		for (gene_counter = get_local_id(0);
		     gene_counter < dockpars_num_of_genes;
		     gene_counter+= NUM_OF_THREADS_PER_BLOCK) {

			// Shoemake genes (u1, u2, u3) ranges between [0,1]
			if ((gene_counter >= 3) && (gene_counter <= 5)) { 
170
			   genotype_candidate[gene_counter] = gpu_randf(dockpars_prng_states);
171
			}
172
			// Other genes: translation and torsions
173
			else {
174
175
176
			   genotype_candidate[gene_counter] = offspring_genotype[gene_counter] + 
							      genotype_deviate[gene_counter]   + 
							      genotype_bias[gene_counter];
177
			}
178
179
		}

180
		// Evaluating candidate
Leonardo Solis's avatar
Leonardo Solis committed
181
182
183
184
		barrier(CLK_LOCAL_MEM_FENCE);

		// ==================================================================
		gpu_calc_energy(dockpars_rotbondlist_length,
Leonardo Solis's avatar
Leonardo Solis committed
185
186
187
188
189
190
191
192
193
194
195
196
197
198
				dockpars_num_of_atoms,
				dockpars_gridsize_x,
				dockpars_gridsize_y,
				dockpars_gridsize_z,
				dockpars_fgrids,
				dockpars_num_of_atypes,
				dockpars_num_of_intraE_contributors,
				dockpars_grid_spacing,
				dockpars_coeff_elec,
				dockpars_qasp,
				dockpars_coeff_desolv,
				genotype_candidate,
				&candidate_energy,
				&run_id,
199
200
201
202
				// Some OpenCL compilers don't allow declaring 
				// local variables within non-kernel functions.
				// These local variables must be declared in a kernel, 
				// and then passed to non-kernel functions.
Leonardo Solis's avatar
Leonardo Solis committed
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
				calc_coords_x,
				calc_coords_y,
				calc_coords_z,
				partial_energies,

				atom_charges_const,
				atom_types_const,
				intraE_contributors_const,
				VWpars_AC_const,
				VWpars_BD_const,
				dspars_S_const,
				dspars_V_const,
				rotlist_const,
				ref_coords_x_const,
				ref_coords_y_const,
				ref_coords_z_const,
				rotbonds_moving_vectors_const,
				rotbonds_unit_vectors_const,
221
222
				ref_orientation_quats_const
				);
Leonardo Solis's avatar
Leonardo Solis committed
223
224
		// =================================================================

225
		if (get_local_id(0) == 0) {
Leonardo Solis's avatar
Leonardo Solis committed
226
			evaluation_cnt++;
227
		}
Leonardo Solis's avatar
Leonardo Solis committed
228
229
230

		barrier(CLK_LOCAL_MEM_FENCE);

231
		if (candidate_energy < offspring_energy)	// If candidate is better, success
Leonardo Solis's avatar
Leonardo Solis committed
232
		{
233
234
235
			for (gene_counter = get_local_id(0);
			     gene_counter < dockpars_num_of_genes;
			     gene_counter+= NUM_OF_THREADS_PER_BLOCK)
Leonardo Solis's avatar
Leonardo Solis committed
236
			{
237
				// Updating offspring_genotype
Leonardo Solis's avatar
Leonardo Solis committed
238
239
				offspring_genotype[gene_counter] = genotype_candidate[gene_counter];

240
				// Updating genotype_bias
Leonardo Solis's avatar
Leonardo Solis committed
241
242
243
				genotype_bias[gene_counter] = 0.6f*genotype_bias[gene_counter] + 0.4f*genotype_deviate[gene_counter];
			}

244
245
			// Work-item 0 will overwrite the shared variables
			// used in the previous if condition
Leonardo Solis's avatar
Leonardo Solis committed
246
247
248
249
250
251
252
253
254
			barrier(CLK_LOCAL_MEM_FENCE);

			if (get_local_id(0) == 0)
			{
				offspring_energy = candidate_energy;
				cons_succ++;
				cons_fail = 0;
			}
		}
255
		else	// If candidate is worser, check the opposite direction
Leonardo Solis's avatar
Leonardo Solis committed
256
		{
257
258
259
260
			// Generating the other genotype candidate
			for (gene_counter = get_local_id(0);
			     gene_counter < dockpars_num_of_genes;
			     gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
261

262
263
				// Shoemake genes (u1, u2, u3) ranges between [0,1]
				if ((gene_counter >= 3) && (gene_counter <= 5)) {
264
				   genotype_candidate[gene_counter] = gpu_randf(dockpars_prng_states);
265
				}
266
				// Other genes: translation and torsions
267
				else {
268
269
270
				   genotype_candidate[gene_counter] = offspring_genotype[gene_counter] - 
								      genotype_deviate[gene_counter] - 
								      genotype_bias[gene_counter];
271
272
273
				}
			}

Leonardo Solis's avatar
Leonardo Solis committed
274
275
276
277
278
			//evaluating candidate
			barrier(CLK_LOCAL_MEM_FENCE);

			// =================================================================
			gpu_calc_energy(dockpars_rotbondlist_length,
Leonardo Solis's avatar
Leonardo Solis committed
279
280
281
282
283
284
285
286
287
288
289
290
291
292
					dockpars_num_of_atoms,
					dockpars_gridsize_x,
					dockpars_gridsize_y,
					dockpars_gridsize_z,
					dockpars_fgrids,
					dockpars_num_of_atypes,
					dockpars_num_of_intraE_contributors,
					dockpars_grid_spacing,
					dockpars_coeff_elec,
				        dockpars_qasp,
					dockpars_coeff_desolv,
					genotype_candidate,
					&candidate_energy,
					&run_id,
293
294
295
296
					// Some OpenCL compilers don't allow declaring 
					// local variables within non-kernel functions.
					// These local variables must be declared in a kernel, 
					// and then passed to non-kernel functions.
Leonardo Solis's avatar
Leonardo Solis committed
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
					calc_coords_x,
					calc_coords_y,
					calc_coords_z,
					partial_energies,

					atom_charges_const,
					atom_types_const,
					intraE_contributors_const,
					VWpars_AC_const,
					VWpars_BD_const,
					dspars_S_const,
					dspars_V_const,
					rotlist_const,
					ref_coords_x_const,
					ref_coords_y_const,
					ref_coords_z_const,
					rotbonds_moving_vectors_const,
					rotbonds_unit_vectors_const,
315
316
					ref_orientation_quats_const
					);
Leonardo Solis's avatar
Leonardo Solis committed
317
318
			// =================================================================

319
			if (get_local_id(0) == 0) {
Leonardo Solis's avatar
Leonardo Solis committed
320
				evaluation_cnt++;
321
			}
Leonardo Solis's avatar
Leonardo Solis committed
322
323
324

			barrier(CLK_LOCAL_MEM_FENCE);

325
			if (candidate_energy < offspring_energy) // If candidate is better, success
Leonardo Solis's avatar
Leonardo Solis committed
326
			{
327
328
329
				for (gene_counter = get_local_id(0);
				     gene_counter < dockpars_num_of_genes;
			       	     gene_counter+= NUM_OF_THREADS_PER_BLOCK)
Leonardo Solis's avatar
Leonardo Solis committed
330
				{
331
					// Updating offspring_genotype
Leonardo Solis's avatar
Leonardo Solis committed
332
333
					offspring_genotype[gene_counter] = genotype_candidate[gene_counter];

334
					// Updating genotype_bias
Leonardo Solis's avatar
Leonardo Solis committed
335
336
337
					genotype_bias[gene_counter] = 0.6f*genotype_bias[gene_counter] - 0.4f*genotype_deviate[gene_counter];
				}

338
339
				// Work-item 0 will overwrite the shared variables
				// used in the previous if condition
Leonardo Solis's avatar
Leonardo Solis committed
340
341
342
343
344
345
346
347
348
				barrier(CLK_LOCAL_MEM_FENCE);

				if (get_local_id(0) == 0)
				{
					offspring_energy = candidate_energy;
					cons_succ++;
					cons_fail = 0;
				}
			}
349
			else	// Failure in both directions
Leonardo Solis's avatar
Leonardo Solis committed
350
			{
351
352
353
354
				for (gene_counter = get_local_id(0);
				     gene_counter < dockpars_num_of_genes;
				     gene_counter+= NUM_OF_THREADS_PER_BLOCK)
					   // Updating genotype_bias
Leonardo Solis's avatar
Leonardo Solis committed
355
356
357
358
359
360
361
362
363
364
					   genotype_bias[gene_counter] = 0.5f*genotype_bias[gene_counter];

				if (get_local_id(0) == 0)
				{
					cons_succ = 0;
					cons_fail++;
				}
			}
		}

365
		// Changing rho if needed
Leonardo Solis's avatar
Leonardo Solis committed
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
		if (get_local_id(0) == 0)
		{
			iteration_cnt++;

			if (cons_succ >= dockpars_cons_limit)
			{
				rho *= LS_EXP_FACTOR;
				cons_succ = 0;
			}
			else
				if (cons_fail >= dockpars_cons_limit)
				{
					rho *= LS_CONT_FACTOR;
					cons_fail = 0;
				}
		}
		barrier(CLK_LOCAL_MEM_FENCE);
	}

385
386
	// Updating eval counter and energy
	if (get_local_id(0) == 0) {
Leonardo Solis's avatar
Leonardo Solis committed
387
388
389
390
		dockpars_evals_of_new_entities[run_id*dockpars_pop_size+entity_id] += evaluation_cnt;
		dockpars_energies_next[run_id*dockpars_pop_size+entity_id] = offspring_energy;
	}

391
392
393
394
395
	// Mapping torsion angles
	for (gene_counter = get_local_id(0);
	     gene_counter < dockpars_num_of_genes;
	     gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
		   if (gene_counter >= 6) {
Leonardo Solis's avatar
Leonardo Solis committed
396
			    map_angle(&(offspring_genotype[gene_counter]));
397
398
		   }
	}
Leonardo Solis's avatar
Leonardo Solis committed
399

400
	// Updating old offspring in population
Leonardo Solis's avatar
Leonardo Solis committed
401
402
	barrier(CLK_LOCAL_MEM_FENCE);

403
404
405
  	async_work_group_copy(dockpars_conformations_next+(run_id*dockpars_pop_size+entity_id)*GENOTYPE_LENGTH_IN_GLOBMEM,
        	              offspring_genotype,
        	              dockpars_num_of_genes,0);
Leonardo Solis's avatar
Leonardo Solis committed
406
}