corrections + code-restructure in grad

Makefile

@@ -198,8 +198,8 @@ odock: check-env-all stringify $(SRC)
 
 # Example
 PDB     := 3ce3
-NRUN    := 100
-POPSIZE := 500
+NRUN    := 200
+POPSIZE := 2048
 TESTNAME:= test
 
 test: odock

device/auxiliary_genetic.cl

@@ -172,7 +172,6 @@ void gpu_perform_elitist_selection(
 	for (gene_counter = get_local_id(0);
 	     gene_counter < dockpars_num_of_genes;
 	     gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
-	     dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0) + 
-																   GENOTYPE_LENGTH_IN_GLOBMEM*best_ID[0]+gene_counter];
+	     dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0) + GENOTYPE_LENGTH_IN_GLOBMEM*best_ID[0]+gene_counter];
 	}
 }

device/auxiliary_gradient.cl

@@ -2,11 +2,7 @@
 // Implementation of auxiliary functions 
 // for the gradient-based minimizer
 bool is_gradDescent_enabled(
-			    __local    bool* 	is_gNorm_gt_gMin,
-			    __local    bool* 	is_nIter_lt_maxIter,
 			    __local    bool* 	is_perturb_gt_gene_min,
-		            __local    bool* 	is_perturb_gt_genotype,
-
 			    __local    float*   local_gNorm,
                                        float    gradMin_tol,
                             __local    uint*    local_nIter,
@@ -16,10 +12,14 @@ bool is_gradDescent_enabled(
                             __local    bool*    is_gradDescentEn,
 				       uint     gradMin_numElements)
 {
+	bool is_gNorm_gt_gMin;
+	bool is_nIter_lt_maxIter;
+	bool is_perturb_gt_genotype;
+	
 	if (get_local_id(0) == 0) {
-		*is_gNorm_gt_gMin    = (local_gNorm[0] >= gradMin_tol);
-		*is_nIter_lt_maxIter = (local_nIter[0] <= gradMin_maxiter);
-		*is_perturb_gt_genotype = true;
+		is_gNorm_gt_gMin    = (local_gNorm[0] >= gradMin_tol);
+		is_nIter_lt_maxIter = (local_nIter[0] <= gradMin_maxiter);
+		is_perturb_gt_genotype = true;
 	}
 
 	// For every gene, let's determine 
@@ -35,153 +35,35 @@ bool is_gradDescent_enabled(
 	if (get_local_id(0) == 0) {
 		// Reduce all is_perturb_gt_gene_min's 
 		// into their corresponding genotype
+
+
 	  	for(uint i = 0; 
 			 i < gradMin_numElements;
 			 i++) {
-	    		*is_perturb_gt_genotype = *is_perturb_gt_genotype && is_perturb_gt_gene_min[i];
+	    		is_perturb_gt_genotype = is_perturb_gt_genotype && is_perturb_gt_gene_min[i];
+/*
+			printf("is_perturb_gt_gene_min[%u]?: %s\n", i, (is_perturb_gt_gene_min[i] == true)?"yes":"no");
+*/
 	  	}
 
 		// Reduce all three previous 
 		// partial evaluations (gNorm, nIter, perturb) into a final one
-		is_gradDescentEn[0] = *is_gNorm_gt_gMin && *is_nIter_lt_maxIter && *is_perturb_gt_genotype;
+
+		*is_gradDescentEn = is_gNorm_gt_gMin && is_nIter_lt_maxIter && is_perturb_gt_genotype;
+/*
+		if (get_local_id(0) == 0) {
+			printf("is_gNorm_gt_gMin?: %s\n", (is_gNorm_gt_gMin == true)?"yes":"no");
+			printf("is_nIter_lt_maxIter?: %s\n", (is_nIter_lt_maxIter == true)?"yes":"no");
+			printf("is_perturb_gt_genotype?: %s\n", (is_perturb_gt_genotype == true)?"yes":"no");
+			printf("Continue gradient iteration?: %s\n", (*is_gradDescentEn == true)?"yes":"no");
+		}
+*/
 	}
 
   	barrier(CLK_LOCAL_MEM_FENCE);
 
-  	return is_gradDescentEn[0];
-}
-
-void stepGPU (// Args for minimization
-	      __local float* local_genotype,         // originally as "d_x"
-              __local float* local_genotype_new,     // originally as "d_xnew"
-              __local float* local_genotype_diff,    // originally as "d_xdiff"
-              __local float* local_gradient,         // originally as "d_g"
-                      float  gradMin_alpha,          // originally as "alpha"
-                      float  gradMin_h,              // originally as "h"
-                      uint   gradMin_inputSize,      // originally as "M". initially labelled as "gradMin_M"
-
-	       // Args for energy and gradient calculation
-		      int    dockpars_rotbondlist_length,
-		      char   dockpars_num_of_atoms,
-		      char   dockpars_gridsize_x,
-		      char   dockpars_gridsize_y,
-		      char   dockpars_gridsize_z,
-       __global const float* restrict dockpars_fgrids, // This is too large to be allocated in __constant 
-	              char   dockpars_num_of_atypes,
-		      int    dockpars_num_of_intraE_contributors,
-		      float  dockpars_grid_spacing,
-	              float  dockpars_coeff_elec,
-	              float  dockpars_qasp,
-		      float  dockpars_coeff_desolv,
-
-              __local float* genotype,
-	      __local float* energy,
-              __local int*   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.
-	      __local float* calc_coords_x,
-	      __local float* calc_coords_y,
-	      __local float* calc_coords_z,
-	      __local float* partial_energies,
-
-	   __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
-
-	      // Gradient-related arguments
-	      // Calculate gradients (forces) for intermolecular energy
-	      // Derived from autodockdev/maps.py
-		
-	      // "is_enabled_gradient_calc": enables gradient calculation.
-	      // In Genetic-Generation: no need for gradients
-	      // In Gradient-Minimizer: must calculate gradients
-	      ,
-	      __local bool*  is_enabled_gradient_calc,
-	      __local float* gradient_inter_x,
-	      __local float* gradient_inter_y,
-	      __local float* gradient_inter_z,
-	      __local float* gradient_genotype
-)
-{
-	// Calculate gradient
-	// =============================================================
-	gpu_calc_energy(dockpars_rotbondlist_length,
-			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,
-			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,
-
-	                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,
-			ref_orientation_quats_const
-		 	// Gradient-related arguments
-		 	// Calculate gradients (forces) for intermolecular energy
-		 	// Derived from autodockdev/maps.py
-			,
-			is_enabled_gradient_calc,
-			gradient_inter_x,
-			gradient_inter_y,
-			gradient_inter_z,
-			gradient_genotype
-			);
-	// =============================================================
-
-	for(uint i = get_local_id(0); 
-	         i < gradMin_inputSize; 
-	         i+= NUM_OF_THREADS_PER_BLOCK) {
-
-     		// Taking step
-     		local_genotype_new[i]  = local_genotype[i] - gradMin_alpha * local_gradient[i];
 
-     		// Updating termination metrics
-     		local_genotype_diff[i] = local_genotype_new[i] - local_genotype[i];
-
-     		// Updating current solution
-     		local_genotype[i] = local_genotype_new[i];
-   	}
+  	return *is_gradDescentEn;
 }
 
 float inner_product(__local float*	vector1,

device/kernel1.cl

@@ -59,7 +59,7 @@ gpu_calc_initpop(
 	// local variables within non-kernel functions.
 	// These local variables must be declared in a kernel, 
 	// and then passed to non-kernel functions.
-	__local float  genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
+	__local float  genotype[ACTUAL_GENOTYPE_LENGTH];
 	__local float  energy;
 	__local int    run_id;
 
@@ -80,27 +80,6 @@ gpu_calc_initpop(
 		run_id = get_group_id(0) / dockpars_pop_size;
 	}
 
-	// -------------------------------------------------------------------
-	// Calculate gradients (forces) for intermolecular energy
-	// Derived from autodockdev/maps.py
-	// -------------------------------------------------------------------
-
-	// Disabling gradient calculation for this kernel
-	__local bool  is_enabled_gradient_calc;
-	if (get_local_id(0) == 0) {
-		is_enabled_gradient_calc = false;
-	}
-
-	// Variables to store gradient of 
-	// the intermolecular energy 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];
-	
-	// Final gradient resulting out of gradient calculation
-	__local float gradient_genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
-	// -------------------------------------------------------------------
-
 	// =============================================================
 	// WARNING: only energy of work-item=0 will be valid
 	gpu_calc_energy(dockpars_rotbondlist_length,
@@ -141,15 +120,6 @@ gpu_calc_initpop(
 			rotbonds_moving_vectors_const,
 			rotbonds_unit_vectors_const,
 			ref_orientation_quats_const
-		 	// Gradient-related arguments
-		 	// Calculate gradients (forces) for intermolecular energy
-		 	// Derived from autodockdev/maps.py
-			,
-			&is_enabled_gradient_calc,
-			gradient_inter_x,
-			gradient_inter_y,
-			gradient_inter_z,
-			gradient_genotype
 			);
 	// =============================================================
 

device/kernel3.cl

@@ -97,27 +97,6 @@ perform_LS(
 	__local float calc_coords_z[MAX_NUM_OF_ATOMS];
 	__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
 
-	// -------------------------------------------------------------------
-	// Calculate gradients (forces) for intermolecular energy
-	// Derived from autodockdev/maps.py
-	// -------------------------------------------------------------------
-
-	// Disabling gradient calculation for this kernel
-	__local bool  is_enabled_gradient_calc;
-	if (get_local_id(0) == 0) {
-		is_enabled_gradient_calc = false;
-	}
-
-	// Variables to store gradient of 
-	// the intermolecular energy 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];
-
-	// Final gradient resulting out of gradient calculation
-	__local float gradient_genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
-	// -------------------------------------------------------------------
-
 	// Determining run ID and entity ID
 	// Initializing offspring genotype
 	if (get_local_id(0) == 0)
@@ -240,15 +219,6 @@ perform_LS(
 				rotbonds_moving_vectors_const,
 				rotbonds_unit_vectors_const,
 				ref_orientation_quats_const
-			 	// Gradient-related arguments
-			 	// Calculate gradients (forces) for intermolecular energy
-			 	// Derived from autodockdev/maps.py
-				,
-				&is_enabled_gradient_calc,
-				gradient_inter_x,
-				gradient_inter_y,
-				gradient_inter_z,
-				gradient_genotype
 				);
 		// =================================================================
 
@@ -343,15 +313,6 @@ perform_LS(
 					rotbonds_moving_vectors_const,
 					rotbonds_unit_vectors_const,
 					ref_orientation_quats_const
-				 	// Gradient-related arguments
-				 	// Calculate gradients (forces) for intermolecular energy
-				 	// Derived from autodockdev/maps.py
-					,
-					&is_enabled_gradient_calc,
-					gradient_inter_x,
-					gradient_inter_y,
-					gradient_inter_z,
-					gradient_genotype
 					);
 			// =================================================================
 

device/kernel4.cl

@@ -90,27 +90,6 @@ gpu_gen_and_eval_newpops(
 	__local float calc_coords_z[MAX_NUM_OF_ATOMS];
 	__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
 
-	// -------------------------------------------------------------------
-	// Calculate gradients (forces) for intermolecular energy
-	// Derived from autodockdev/maps.py
-	// -------------------------------------------------------------------
-
-	// Disabling gradient calculation for this kernel
-	__local bool  is_enabled_gradient_calc;
-	if (get_local_id(0) == 0) {
-		is_enabled_gradient_calc = false;
-	}
-
-	// Variables to store gradient of 
-	// the intermolecular energy 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];
-
-	// Final gradient resulting out of gradient calculation
-	__local float gradient_genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
-	// -------------------------------------------------------------------
-
 	// In this case this compute-unit is responsible for elitist selection
 	if ((get_group_id(0) % dockpars_pop_size) == 0) {
 		gpu_perform_elitist_selection(dockpars_pop_size,
@@ -291,16 +270,6 @@ gpu_gen_and_eval_newpops(
 				rotbonds_moving_vectors_const,
 				rotbonds_unit_vectors_const,
 				ref_orientation_quats_const
-
-		 		// Gradient-related arguments
-		 		// Calculate gradients (forces) for intermolecular energy
-		 		// Derived from autodockdev/maps.py
-				,
-				&is_enabled_gradient_calc,
-				gradient_inter_x,
-				gradient_inter_y,
-				gradient_inter_z,
-				gradient_genotype
 				);
 		// =============================================================
 

device/kernel_gradient.cl

@@ -45,7 +45,6 @@ gradient_minimizer(
     	     __constant float* rotbonds_moving_vectors_const,
              __constant float* rotbonds_unit_vectors_const,
              __constant float* ref_orientation_quats_const,
-
     			// Specific gradient-minimizer args
     //  __global float* restrict dockpars_conformations_next,   // initial population
                                                                 // whose (some) entities (genotypes) are to be minimized
@@ -97,6 +96,15 @@ gradient_minimizer(
 		}
 
 		local_energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
+
+/*
+		printf("run_id: %u, entity_id: %u, local_energy: %f\n", run_id, entity_id, local_energy);
+*/
+
+/*
+		printf("BEFORE GRADIENT - local_energy: %f\n", local_energy);
+*/
+
 	}
 
 	barrier(CLK_LOCAL_MEM_FENCE);
@@ -106,7 +114,7 @@ gradient_minimizer(
   	__local float   local_gNorm;                                  // gradient norm (shared in the CU), originally as "gnorm"
   	__local uint 	local_nIter;                                  // iteration counter, originally as "niter"
   	__local float   local_perturbation [ACTUAL_GENOTYPE_LENGTH];  // perturbation, originally as "dx"
-  	__local float   local_genotype[ACTUAL_GENOTYPE_LENGTH];       // optimization vector, originally as "d_x"
+  	__local float   local_genotype     [ACTUAL_GENOTYPE_LENGTH];  // optimization vector, originally as "d_x"
 
 	if (get_local_id(0) == 0) {
 		local_gNorm = FLT_MAX;
@@ -132,13 +140,10 @@ gradient_minimizer(
 	// and then passed to non-kernel functions.
 	
 	// Partial results in "is_gradDescent_enabled()"
-	__local bool is_gNorm_gt_gMin;
-	__local bool is_nIter_lt_maxIter;
 	__local bool is_perturb_gt_gene_min [ACTUAL_GENOTYPE_LENGTH];
-	__local bool is_perturb_gt_genotype;
   	__local bool is_gradDescentEn;                
 
-	// Partial results in "stepGPU()"
+	// Partial results of the gradient step
 	__local float local_gradient      [ACTUAL_GENOTYPE_LENGTH]; // gradient, originally as "d_g"
 	__local float local_genotype_new  [ACTUAL_GENOTYPE_LENGTH]; // new actual solution, originally as "d_xnew"
 	__local float local_genotype_diff [ACTUAL_GENOTYPE_LENGTH]; // difference between actual and old solution, originally as "d_xdiff"
@@ -155,15 +160,6 @@ gradient_minimizer(
 	__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];
-
-	// Enable gradient calculation for this kernel
-	__local bool  is_enabled_gradient_calc;
-	if (get_local_id(0) == 0) {
-		is_enabled_gradient_calc = true;
-	}
-
-	// Final gradient resulting out of gradient calculation
-	__local float gradient_genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
 	// -------------------------------------------------------------------
 
 	// Variables to store partial energies
@@ -175,10 +171,7 @@ gradient_minimizer(
 	// -----------------------------------------------------------------------------
 	// Perform gradient-descent iterations
 	while (is_gradDescent_enabled(
-				      &is_gNorm_gt_gMin,
-				      &is_nIter_lt_maxIter,
 				      is_perturb_gt_gene_min,
-				      &is_perturb_gt_genotype,
 				      &local_gNorm,
     				      gradMin_tol,
     				      &local_nIter,
@@ -188,16 +181,9 @@ gradient_minimizer(
     				      &is_gradDescentEn,
 				      dockpars_num_of_genes) == true) {
 		
-    		stepGPU(// Args for minimization
-			local_genotype,
-		        local_genotype_new,
-      			local_genotype_diff,
-      			local_gradient,
-      			gradMin_alpha,
-      			gradMin_h,
-      			dockpars_num_of_genes, //gradMin_M
-
-			// Args for energy and gradient calculation
+		// Calculating gradient
+		// =============================================================
+		gpu_calc_gradient(
 				dockpars_rotbondlist_length,
 				dockpars_num_of_atoms,
 				dockpars_gridsize_x,
@@ -211,7 +197,9 @@ gradient_minimizer(
 				dockpars_qasp,
 				dockpars_coeff_desolv,
 				local_genotype,
+/*
 				&local_energy,
+*/
 				&run_id,
 				// Some OpenCL compilers don't allow declaring 
 				// local variables within non-kernel functions.
@@ -220,7 +208,6 @@ gradient_minimizer(
 				calc_coords_x,
 				calc_coords_y,
 				calc_coords_z,
-			partial_energies,
 
 			        atom_charges_const,
 				atom_types_const,
@@ -240,14 +227,27 @@ gradient_minimizer(
 			 	// Calculate gradients (forces) for intermolecular energy
 			 	// Derived from autodockdev/maps.py
 				,
-			&is_enabled_gradient_calc,
+				dockpars_num_of_genes,
 				gradient_inter_x,
 				gradient_inter_y,
 				gradient_inter_z,
-			gradient_genotype
+				local_gradient
 				);
-			// -------------------------------------------------------------------
+		// =============================================================
 
+		for(uint i = get_local_id(0); 
+			 i < dockpars_num_of_genes; 
+			 i+= NUM_OF_THREADS_PER_BLOCK) {
+
+	     		// Taking step
+	     		local_genotype_new[i]  = local_genotype[i] - gradMin_alpha * local_gradient[i];
+
+	     		// Updating terminatiodockpars_num_of_genesn metrics
+	     		local_genotype_diff[i] = local_genotype_new[i] - local_genotype[i];
+
+	     		// Updating current solution
+	     		local_genotype[i] = local_genotype_new[i];
+	   	}
 
 		// Updating number of stepest-descent iterations
 		if (get_local_id(0) == 0) {
@@ -255,13 +255,6 @@ gradient_minimizer(
 		}
 
 	    	// Storing the norm of all gradients
-/*
-	    	local_gNorm = native_sqrt(inner_product(local_gradient, 
-							local_gradient,
-		                                        dockpars_num_of_genes,
-		                                        dotProduct));
-*/
-		
 		local_gNorm = inner_product(local_gradient, local_gradient, dockpars_num_of_genes, dotProduct);
 
 		if (get_local_id(0) == 0) {
@@ -282,17 +275,63 @@ gradient_minimizer(
 			printf("Entity: %u, Run: %u, minimized E: %f\n", entity_id, run_id, local_energy);
 		}		
 */
+
 /*
-		if ((get_group_id(0) == 0) && (get_local_id(0) == 0)) {
+		if (get_local_id(0) == 0) {
 			printf("Number of gradient iterations: %u\n", local_nIter);
 		}
 */
   	}
 	// -----------------------------------------------------------------------------
 
-  	// Functional calculation
-	// stepGPU () calls gpu_calc_energy ()
-	// the former calculates energy + gradients
+  	// Calculating energy
+	// =============================================================
+	gpu_calc_energy(dockpars_rotbondlist_length,
+			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,
+			local_genotype,
+			&local_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,
+
+	                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,
+			ref_orientation_quats_const
+			);
+	// =============================================================
+
+/*
+	if (get_local_id(0) == 0) {
+		printf("AFTER- GRADIENT - local_energy: %f\n\n", local_energy);
+	}
+*/
 
   	// Copying final genotype and energy into global memory
 	if (get_local_id(0) == 0) {

host/src/performdocking.cpp

@@ -67,9 +67,11 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 	#define REP " "
 #endif
 
+
 #define KGDB_AMD 		" -g -O0 "
 #define KGDB_INTEL	" -g -s " KRNL_FILE
 
+
 #if defined (DOCK_DEBUG)
 	#if defined (CPU_DEVICE)
 		#define KGDB KGDB_INTEL
@@ -80,6 +82,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 	#define KGDB " "
 #endif
 
+
 #define OPT_PROG INC KNWI REP KGDB
 
 #include "performdocking.h"
@@ -396,7 +399,7 @@ filled with clock() */
 	Gradientparameters gradientpars;
 	gradientpars.tolerance = 1.e-6;
 	gradientpars.max_num_of_iters = 10000;