kernel_ad.cl 18.3 KB
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// Gradient-based adadelta minimizer
// https://arxiv.org/pdf/1212.5701.pdf
// Alternative to Solis-Wets / Steepest-Descent / FIRE

// "rho": controls degree of memory of previous gradients
//        ranges between [0, 1[
//        "rho" = 0.9 most popular value
// "epsilon":  to better condition the square root

// Adadelta parameters (TODO: to be moved to header file?)
#define RHO		0.9f
#define EPSILON 	1e-6

//#define DEBUG_ENERGY_ADADELTA
	//#define PRINT_ADADELTA_ENERGIES
	//#define PRINT_ADADELTA_GENES_AND_GRADS
	//#define PRINT_ADADELTA_ATOMIC_COORDS

// Enable DEBUG_ADADELTA_MINIMIZER for a seeing a detailed ADADELTA evolution
// If only PRINT_ADADELTA_MINIMIZER_ENERGY_EVOLUTION is enabled,
// then a only a simplified ADADELTA evolution will be shown
//#define DEBUG_ADADELTA_MINIMIZER
//	#define PRINT_ADADELTA_MINIMIZER_ENERGY_EVOLUTION

// Enable this for debugging ADADELTA from a defined initial genotype
//#define DEBUG_ADADELTA_INITIAL_2BRT

__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))
gradient_minAD(	
			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,
							    		// g1 = gridsize_x
			uint   dockpars_gridsize_x_times_y, 		// g2 = gridsize_x * gridsize_y
			uint   dockpars_gridsize_x_times_y_times_z,	// g3 = gridsize_x * gridsize_y * 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,
			uint   dockpars_max_num_of_iters,
			float  dockpars_qasp,
                        float  dockpars_smooth,

      __constant        kernelconstant_interintra* 	kerconst_interintra,
      __global const    kernelconstant_intracontrib* 	kerconst_intracontrib,
      __constant        kernelconstant_intra*	 	kerconst_intra,
      __constant        kernelconstant_rotlist*   	kerconst_rotlist,
      __constant        kernelconstant_conform*	 	kerconst_conform
		,
      __constant int*         rotbonds_const,
      __global   const int*   rotbonds_atoms_const,
      __constant int*         num_rotating_atoms_per_rotbond_const
		,
      __global   const float* angle_const,
      __constant       float* dependence_on_theta_const,
      __constant       float* dependence_on_rotangle_const
)
//The GPU global function performs gradient-based minimization on (some) entities of conformations_next.
//The number of OpenCL compute units (CU) which should be started equals to num_of_minEntities*num_of_runs.
//This way the first num_of_lsentities entity of each population will be subjected to local search
//(and each CU 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).
{


	// -----------------------------------------------------------------------------
	// -----------------------------------------------------------------------------
	// -----------------------------------------------------------------------------

	// Determining entity, and its run, energy, and genotype
	__local int   entity_id;
	__local int   run_id;
  	__local float energy;
	__local float genotype[ACTUAL_GENOTYPE_LENGTH];
  
	// Iteration counter fot the minimizer
  	__local uint iteration_cnt;  	

	if (get_local_id(0) == 0)
	{
		// Choosing a random entity out of the entire population
		/*
		run_id = get_group_id(0);
		//entity_id = (uint)(dockpars_pop_size * gpu_randf(dockpars_prng_states));
		entity_id = 0;
		*/

		run_id = get_group_id(0) / dockpars_num_of_lsentities;
		entity_id = get_group_id(0) % dockpars_num_of_lsentities;

		// 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;					
			}
		}
		
		energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];

		// Initializing gradient-minimizer counters and flags
    		iteration_cnt  = 0;

		#if defined (DEBUG_ADADELTA_MINIMIZER) || defined (PRINT_ADADELTA_MINIMIZER_ENERGY_EVOLUTION)
		printf("\n");
		printf("-------> Start of ADADELTA minimization cycle\n");
		printf("%20s %6u\n", "run_id: ", run_id);
		printf("%20s %6u\n", "entity_id: ", entity_id);
		printf("\n");
		printf("%20s \n", "LGA genotype: ");
		printf("%20s %.6f\n", "initial energy: ", energy);
		#endif
	}
	barrier(CLK_LOCAL_MEM_FENCE);

  	event_t ev = async_work_group_copy(genotype,
  			      		   dockpars_conformations_next+(run_id*dockpars_pop_size+entity_id)*GENOTYPE_LENGTH_IN_GLOBMEM,
                              		   dockpars_num_of_genes, 0);

	// Asynchronous copy should be finished by here
	wait_group_events(1, &ev);

  	// -----------------------------------------------------------------------------
	// -----------------------------------------------------------------------------
	// -----------------------------------------------------------------------------
         
	// Partial results of the gradient step
	__local float gradient[ACTUAL_GENOTYPE_LENGTH];

	// Energy may go up, so we keep track of the best energy ever calculated.
	// Then, we return the genotype corresponding 
	// to the best observed energy, i.e. "best_genotype"
	__local float best_energy;
	__local float best_genotype[ACTUAL_GENOTYPE_LENGTH];

	// -------------------------------------------------------------------
	// Calculate gradients (forces) for intermolecular energy
	// Derived from autodockdev/maps.py
	// -------------------------------------------------------------------
	// Gradient of the intermolecular energy per each ligand atom
	// Also used to store the accummulated gradient per each ligand atom
	__local float gradient_inter_x[MAX_NUM_OF_ATOMS];
	__local float gradient_inter_y[MAX_NUM_OF_ATOMS];
	__local float gradient_inter_z[MAX_NUM_OF_ATOMS];

	// Gradient of the intramolecular energy per each ligand atom
	__local float gradient_intra_x[MAX_NUM_OF_ATOMS];
	__local float gradient_intra_y[MAX_NUM_OF_ATOMS];
	__local float gradient_intra_z[MAX_NUM_OF_ATOMS];

	// Ligand-atom position and partial energies
	__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];

	#if defined (DEBUG_ENERGY_KERNEL)
	__local float partial_interE[NUM_OF_THREADS_PER_BLOCK];
	__local float partial_intraE[NUM_OF_THREADS_PER_BLOCK];
	#endif

	// Enable this for debugging ADADELTA from a defined initial genotype
	#if defined (DEBUG_ADADELTA_INITIAL_2BRT)
	if (get_local_id(0) == 0) {
		// 2brt
		genotype[0]  = 24.093334;
		genotype[1]  = 24.658667;
		genotype[2]  = 24.210667;
		genotype[3]  = 50.0;
		genotype[4]  = 50.0;
		genotype[5]  = 50.0;
		genotype[6]  = 0.0f;
		genotype[7]  = 0.0f;
		genotype[8]  = 0.0f;
		genotype[9]  = 0.0f;
		genotype[10] = 0.0f;
		genotype[11] = 0.0f;
		genotype[12] = 0.0f;
		genotype[13] = 0.0f;
		genotype[14] = 0.0f;
		genotype[15] = 0.0f;
		genotype[16] = 0.0f;
		genotype[17] = 0.0f;
		genotype[18] = 0.0f;
		genotype[19] = 0.0f;
		genotype[20] = 0.0f;
	}
	barrier(CLK_LOCAL_MEM_FENCE);
	#endif

	// Vector for storing squared gradients E[g^2]
	__local float square_gradient[ACTUAL_GENOTYPE_LENGTH];

	// Update vector, i.e., "delta".
	// It is added to the genotype to create the next genotype.
	// E.g. in steepest descent "delta" is -1.0 * stepsize * gradient
	__local float delta[ACTUAL_GENOTYPE_LENGTH];

	// Squared updates E[dx^2]
	__local float square_delta[ACTUAL_GENOTYPE_LENGTH];

	// Initializing best energy
	if (get_local_id(0) == 0) {
		best_energy = INFINITY;
	}

	// Initializing vectors
	for(uint i = get_local_id(0); 
		 i < dockpars_num_of_genes; 
		 i+= NUM_OF_THREADS_PER_BLOCK) {
		gradient[i]        = 0.0f;
		square_gradient[i] = 0.0f;
		delta[i]           = 0.0f;
		square_delta[i]    = 0.0f;
	}
	barrier(CLK_LOCAL_MEM_FENCE);

	// Perform adadelta iterations

	// The termination criteria is based on 
	// a maximum number of iterations, and
	// the minimum step size allowed for single-floating point numbers 
	// (IEEE-754 single float has a precision of about 6 decimal digits)
	do {
		// Printing number of ADADELTA iterations
		#if defined (DEBUG_ADADELTA_MINIMIZER) 
		if (get_local_id(0) == 0) {
			printf("%s\n", "----------------------------------------------------------");	
		}
		#endif
		
		#if defined (DEBUG_ADADELTA_MINIMIZER) || defined (PRINT_ADADELTA_MINIMIZER_ENERGY_EVOLUTION)
		if (get_local_id(0) == 0) {
			printf("%-15s %-3u ", "# ADADELTA iteration: ", iteration_cnt);
		}
		#endif

		// =============================================================
		// Calculating gradient
		barrier(CLK_LOCAL_MEM_FENCE);

		gpu_calc_gradient(
				dockpars_rotbondlist_length,
				dockpars_num_of_atoms,
				dockpars_gridsize_x,
				dockpars_gridsize_y,
				dockpars_gridsize_z,
								    	// g1 = gridsize_x
				dockpars_gridsize_x_times_y, 		// g2 = gridsize_x * gridsize_y
				dockpars_gridsize_x_times_y_times_z,	// g3 = gridsize_x * gridsize_y * gridsize_z
				dockpars_fgrids,
				dockpars_num_of_atypes,
				dockpars_num_of_intraE_contributors,
				dockpars_grid_spacing,
				dockpars_coeff_elec,
				dockpars_qasp,
				dockpars_coeff_desolv,
				dockpars_smooth,

				// 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.
				genotype,
				&energy,
				&run_id,

				calc_coords_x,
				calc_coords_y,
				calc_coords_z,

				kerconst_interintra,
				kerconst_intracontrib,
				kerconst_intra,
				kerconst_rotlist,
				kerconst_conform
				,
				rotbonds_const,
				rotbonds_atoms_const,
				num_rotating_atoms_per_rotbond_const
				,
	     			angle_const,
	     			dependence_on_theta_const,
	     			dependence_on_rotangle_const
			 	// Gradient-related arguments
			 	// Calculate gradients (forces) for intermolecular energy
			 	// Derived from autodockdev/maps.py
				,
				dockpars_num_of_genes,
				gradient_inter_x,
				gradient_inter_y,
				gradient_inter_z,
				gradient_intra_x,
				gradient_intra_y,
				gradient_intra_z,
				gradient
				);

		// =============================================================

		// This could be enabled back for double checking
		#if 0
		#if defined (DEBUG_ENERGY_ADADELTA)
		if (/*(get_group_id(0) == 0) &&*/ (get_local_id(0) == 0)) {

			#if defined (PRINT_ADADELTA_GENES_AND_GRADS)
			for(uint i = 0; i < dockpars_num_of_genes; i++) {
				if (i == 0) {
					printf("\n%s\n", "----------------------------------------------------------");
					printf("%13s %13s %5s %15s %15s\n", "gene_id", "gene.value", "|", "gene.grad", "(autodockdevpy units)");
				}
				printf("%13u %13.6f %5s %15.6f %15.6f\n", i, genotype[i], "|", gradient[i], (i<3)? (gradient[i]/0.375f):(gradient[i]*180.0f/PI_FLOAT));
			}
			#endif

			#if defined (PRINT_ADADELTA_ATOMIC_COORDS)
			for(uint i = 0; i < dockpars_num_of_atoms; i++) {
				if (i == 0) {
					printf("\n%s\n", "----------------------------------------------------------");
					printf("%s\n", "Coordinates calculated by calcenergy.cl");
					printf("%12s %12s %12s %12s\n", "atom_id", "coords.x", "coords.y", "coords.z");
				}
				printf("%12u %12.6f %12.6f %12.6f\n", i, calc_coords_x[i], calc_coords_y[i], calc_coords_z[i]);
			}
			printf("\n");
			#endif
		}
		barrier(CLK_LOCAL_MEM_FENCE);
		#endif
		#endif

		// =============================================================
		// Evaluating candidate
		gpu_calc_energy(
				dockpars_rotbondlist_length,
				dockpars_num_of_atoms,
				dockpars_gridsize_x,
				dockpars_gridsize_y,
				dockpars_gridsize_z,
								    	// g1 = gridsize_x
				dockpars_gridsize_x_times_y, 		// g2 = gridsize_x * gridsize_y
				dockpars_gridsize_x_times_y_times_z,	// g3 = gridsize_x * gridsize_y * gridsize_z
				dockpars_fgrids,
				dockpars_num_of_atypes,
				dockpars_num_of_intraE_contributors,
				dockpars_grid_spacing,
				dockpars_coeff_elec,
				dockpars_qasp,
				dockpars_coeff_desolv,
				dockpars_smooth,

				genotype,
				&energy,
				&run_id,
				// 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.
				calc_coords_x,
				calc_coords_y,
				calc_coords_z,
				partial_energies,
				#if defined (DEBUG_ENERGY_KERNEL)
				partial_interE,
				partial_intraE,
				#endif
#if 0
				true,
#endif
				kerconst_interintra,
				kerconst_intracontrib,
				kerconst_intra,
				kerconst_rotlist,
				kerconst_conform
				);
		// =============================================================

		#if defined (DEBUG_ENERGY_ADADELTA)
		if (/*(get_group_id(0) == 0) &&*/ (get_local_id(0) == 0)) {
			#if defined (PRINT_ADADELTA_ENERGIES)
			printf("\n");
			printf("%-10s %-10.6f \n", "intra: ",  partial_intraE[0]);
			printf("%-10s %-10.6f \n", "grids: ",  partial_interE[0]);
			printf("%-10s %-10.6f \n", "Energy: ", (partial_intraE[0] + partial_interE[0]));
			#endif

			#if defined (PRINT_ADADELTA_GENES_AND_GRADS)
			for(uint i = 0; i < dockpars_num_of_genes; i++) {
				if (i == 0) {
					printf("\n%s\n", "----------------------------------------------------------");
					printf("%13s %13s %5s %15s %15s\n", "gene_id", "gene.value", "|", "gene.grad", "(autodockdevpy units)");
				}
				printf("%13u %13.6f %5s %15.6f %15.6f\n", i, genotype[i], "|", gradient[i], (i<3)? (gradient[i]/0.375f):(gradient[i]*180.0f/PI_FLOAT));
			}
			#endif

			#if defined (PRINT_ADADELTA_ATOMIC_COORDS)
			for(uint i = 0; i < dockpars_num_of_atoms; i++) {
				if (i == 0) {
					printf("\n%s\n", "----------------------------------------------------------");
					printf("%s\n", "Coordinates calculated by calcenergy.cl");
					printf("%12s %12s %12s %12s\n", "atom_id", "coords.x", "coords.y", "coords.z");
				}
				printf("%12u %12.6f %12.6f %12.6f\n", i, calc_coords_x[i], calc_coords_y[i], calc_coords_z[i]);
			}
			printf("\n");
			#endif
		}
		barrier(CLK_LOCAL_MEM_FENCE);
		#endif

		// If this energy is the best so far, save the genotype
		if (energy < best_energy){
			
			for(uint i = get_local_id(0); 
			 	 i < dockpars_num_of_genes; 
		 	 	 i+= NUM_OF_THREADS_PER_BLOCK) {

				#if defined (DEBUG_ADADELTA_MINIMIZER)
				if (i == 0) {
					printf("%s\n", "Energy IMPROVED! ... then update genotype:");
					printf("%13s %13s %13s\n", "gene_id", "old.gene", "new.gene");
				}
				printf("%13u %13.6f %13.6f\n", i, best_genotype[i], genotype[i]);
				#endif

				if (i == 0) {
					#if defined (DEBUG_ADADELTA_MINIMIZER)
					printf("\n%s\n", "Energy IMPROVED! ... then update energy:");
					#endif

					// Updating energy
					best_energy = energy;
				}

				// Updating genotype
				best_genotype[i] = genotype[i];
			}
		}
		else { 
			#if defined (DEBUG_ADADELTA_MINIMIZER)
			if (get_local_id(0) == 0) {
				printf("%s\n", "NO energy improvement!");
			}
			#endif
		}
		barrier(CLK_LOCAL_MEM_FENCE);

		for(uint i = get_local_id(0); 
			 i < dockpars_num_of_genes; 
			 i+= NUM_OF_THREADS_PER_BLOCK) {

			// Accummulating gradient^2 (eq.8 in the paper)
			// square_gradient corresponds to E[g^2]
			square_gradient[i] = RHO * square_gradient[i] + (1.0f - RHO) * gradient[i] * gradient[i];

			// Computing update (eq.9 in the paper)
			float tmp_num = native_sqrt((float)(square_delta[i] + EPSILON));
			float tmp_den = native_sqrt((float)(square_gradient[i] + EPSILON));

			delta[i] = -1.0f * gradient[i] * native_divide(tmp_num, tmp_den);

			// Accummulating update^2
			// square_delta corresponds to E[dx^2]
			square_delta[i] = RHO * square_delta[i] + (1.0f - RHO) * delta[i] * delta [i];

			// Applying update
			genotype[i] = genotype[i] + delta[i];
	   	}
		barrier(CLK_LOCAL_MEM_FENCE);

		// Updating number of ADADELTA iterations (energy evaluations)
		if (get_local_id(0) == 0) {
	    		iteration_cnt = iteration_cnt + 1;

			#if defined (DEBUG_ADADELTA_MINIMIZER) || defined (PRINT_ADADELTA_MINIMIZER_ENERGY_EVOLUTION)
			printf("%20s %10.6f\n", "new.energy: ", energy);
			#endif

			#if defined (DEBUG_ENERGY_ADADELTA)
			printf("%-18s [%-5s]---{%-5s}   [%-10.7f]---{%-10.7f}\n", "-ENERGY-KERNEL7-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
			#endif
		}
		barrier(CLK_LOCAL_MEM_FENCE);

  	} while (iteration_cnt < dockpars_max_num_of_iters);
	// -----------------------------------------------------------------------------
	// -----------------------------------------------------------------------------
	// -----------------------------------------------------------------------------

  	// Updating eval counter and energy
	if (get_local_id(0) == 0) {
		dockpars_evals_of_new_entities[run_id*dockpars_pop_size+entity_id] += iteration_cnt;
		dockpars_energies_next[run_id*dockpars_pop_size+entity_id] = best_energy;

		#if defined (DEBUG_ADADELTA_MINIMIZER) || defined (PRINT_ADADELTA_MINIMIZER_ENERGY_EVOLUTION)
		printf("\n");
		printf("Termination criteria: ( #adadelta-iters >= %-3u )\n", dockpars_max_num_of_iters);
		printf("-------> End of ADADELTA minimization cycle, num of energy evals: %u, final energy: %.6f\n", iteration_cnt, best_energy);
		#endif
	}

	// Mapping torsion angles
	for (uint gene_counter = get_local_id(0);
	     	  gene_counter < dockpars_num_of_genes;
	          gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
		   if (gene_counter >= 3) {
			    map_angle(&(best_genotype[gene_counter]));
		   }
	}

	// Updating old offspring in population
	barrier(CLK_LOCAL_MEM_FENCE);

	event_t ev2 = async_work_group_copy(dockpars_conformations_next+(run_id*dockpars_pop_size+entity_id)*GENOTYPE_LENGTH_IN_GLOBMEM,
			      		    best_genotype,
			      		    dockpars_num_of_genes, 0);

	// Asynchronous copy should be finished by here
	wait_group_events(1, &ev2);
}