solved segfault by limiting value of u1 into 0.1-0.9

Makefile

@@ -196,9 +196,9 @@ odock: check-env-all stringify $(SRC)
 
 
 # Example
-PDB     := 1stp
-NRUN    := 1
-POPSIZE := 50
+PDB     := 3ce3
+NRUN    := 100
+POPSIZE := 150
 TESTNAME:= test
 
 test: odock

device/calcenergy.cl

@@ -289,16 +289,33 @@ void gpu_calc_energy(	    int    dockpars_rotbondlist_length,
 				rotation_unitvec[0] = genrot_unitvec[0];
 				rotation_unitvec[1] = genrot_unitvec[1];
 				rotation_unitvec[2] = genrot_unitvec[2];
-				rotation_angle = genrotangle;rotation_unitvec
+				rotation_angle = genrotangle;
 */
 				// Moved back in here
 				// Transforming Shoemake (u1, u2, u3) into quaternions
 				// FIXME: add precision choices with preprocessor directives: 
 				// NATIVE_PRECISION, HALF_PRECISION, Full precision
-				quatrot_left_q = sqrt(1 - u1) * sin(u2);
-				quatrot_left_x = sqrt(1 - u1) * cos(u2);
-				quatrot_left_y = sqrt(u1) * sin(u3);
-				quatrot_left_z = sqrt(u1) * cos(u3);
+
+				if (u1 > 1) {
+					u1 = 0.9f;
+				}
+
+				if (u1 < 0) {
+					u1 = 0.1f;
+				}
+
+
+				quatrot_left_q = native_sqrt(1 - u1) * native_sin(u2); 
+				quatrot_left_x = native_sqrt(1 - u1) * native_cos(u2);
+				quatrot_left_y = native_sqrt(u1)     * native_sin(u3);
+				quatrot_left_z = native_sqrt(u1)     * native_cos(u3);
+
+/*
+				if ((1-u1) < 0) {
+					printf("u1:%f 1-u1:%f sqrt(1-u1):%f\n", u1, (1-u1), sqrt(1-u1));
+				}
+*/
+
 
 				// Kept as the original
 				rotation_movingvec[0] = genotype[0];
@@ -342,8 +359,8 @@ void gpu_calc_energy(	    int    dockpars_rotbondlist_length,
 				// FIXME: add precision choices with preprocessor directives: 
 				// NATIVE_PRECISION, HALF_PRECISION, Full precision
 				rotation_angle = rotation_angle/2;
-				quatrot_left_q = cos(rotation_angle);
-				sin_angle      = sin(rotation_angle);
+				quatrot_left_q = native_cos(rotation_angle);
+				sin_angle      = native_sin(rotation_angle);
 				quatrot_left_x = sin_angle*rotation_unitvec[0];
 				quatrot_left_y = sin_angle*rotation_unitvec[1];
 				quatrot_left_z = sin_angle*rotation_unitvec[2];

device/kernel3.cl

@@ -199,9 +199,24 @@ perform_LS(	char   dockpars_num_of_atoms,
 		//generating new genotype candidate
 		for (gene_counter=get_local_id(0);
 		     gene_counter<dockpars_num_of_genes;
-		     gene_counter += NUM_OF_THREADS_PER_BLOCK)
+		     gene_counter += NUM_OF_THREADS_PER_BLOCK) {
 			   genotype_candidate[gene_counter] = offspring_genotype[gene_counter] + genotype_deviate[gene_counter] + genotype_bias[gene_counter];
 
+///*
+			if (gene_counter == 3) {// u1, FIXME: hardcoded
+				if (genotype_candidate[gene_counter] > 1.0f) { // clamp it
+					offspring_genotype[gene_counter] = 0.9f;
+				}
+				if (genotype_candidate[gene_counter] < 0.0f) { // clamp it
+					offspring_genotype[gene_counter] = 0.1f;
+				}
+				//printf("LS positive - genotype_candidate[gene_counter]: %f\n", genotype_candidate[gene_counter]);
+			}
+//*/
+
+		}
+
+
 		//evaluating candidate
 		barrier(CLK_LOCAL_MEM_FENCE);
 
@@ -279,9 +294,23 @@ perform_LS(	char   dockpars_num_of_atoms,
 			//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)
+			     gene_counter += NUM_OF_THREADS_PER_BLOCK) {
 				   genotype_candidate[gene_counter] = offspring_genotype[gene_counter] - genotype_deviate[gene_counter] - genotype_bias[gene_counter];
 
+///*
+				if (gene_counter == 3) {// u1, FIXME: hardcoded
+					if (genotype_candidate[gene_counter] > 1.0f) { // clamp it
+						offspring_genotype[gene_counter] = 0.9f;
+					}
+					if (genotype_candidate[gene_counter] < 0.0f) { // clamp it
+						offspring_genotype[gene_counter] = 0.1f;
+					}
+					//printf("LS negative - genotype_candidate[gene_counter]: %f\n", genotype_candidate[gene_counter]);
+				}
+//*/
+
+			}
+
 			//evaluating candidate
 			barrier(CLK_LOCAL_MEM_FENCE);
 

device/kernel4.cl

@@ -250,8 +250,20 @@ gpu_gen_and_eval_newpops(char   dockpars_num_of_atoms,
 */
 				if (gene_counter < 3)
 					offspring_genotype[gene_counter] += dockpars_abs_max_dmov*(2*gpu_randf(dockpars_prng_states)-1);
-				else if (gene_counter == 3) // u1, FIXME: hardcoded
+				else if (gene_counter == 3) {// u1, FIXME: hardcoded
 					offspring_genotype[gene_counter] +=  0.2f*(2*gpu_randf(dockpars_prng_states)-1);
+					
+///*
+					if (offspring_genotype[gene_counter] > 1.0f) { // clamp it
+						offspring_genotype[gene_counter] = 0.9f;
+					}
+					if (offspring_genotype[gene_counter] < 0.0f) { // clamp it
+						offspring_genotype[gene_counter] = 0.1f;
+					}
+					//printf("mutation - offspring_genotype[gene_counter]: %f\n", offspring_genotype[gene_counter]);
+//*/
+
+				}
 				else if (gene_counter < 6) { // u2&3, FIXME: hardcoded
 					offspring_genotype[gene_counter] += 90.0f*(2*gpu_randf(dockpars_prng_states)-1);
 					map_angle(&(offspring_genotype[gene_counter]));

host/src/performdocking.cpp

@@ -722,10 +722,10 @@ filled with clock() */
 #if defined (DOCK_DEBUG)
 	for (int cnt_pop=0;cnt_pop<size_populations/sizeof(float);cnt_pop++)
 		printf("total_num_pop: %u, cpu_final_populations[%u]: %f\n",(unsigned int)(size_populations/sizeof(float)),cnt_pop,cpu_final_populations[cnt_pop]);
-
+#endif
 	for (int cnt_pop=0;cnt_pop<size_energies/sizeof(float);cnt_pop++)
 		printf("total_num_energies: %u, cpu_energies[%u]: %f\n",    (unsigned int)(size_energies/sizeof(float)),cnt_pop,cpu_energies[cnt_pop]);
-#endif
+
 
 	// ===============================================================================
 

host/src/processligand.cpp

@@ -1240,6 +1240,7 @@ void change_conform_f(Liganddata* myligand,
 }
 #endif // End of original change_conform_f()
 
+#if 1
 void change_conform_f(Liganddata* myligand,
 		      const float genotype_f [],
 		      float* cpu_ref_ori_angles,
@@ -1322,12 +1323,12 @@ void change_conform_f(Liganddata* myligand,
 
 		rotate_shoemake(&(myligand->atom_idxyzq[atom_id][1]),
 	  		        genrot_movvec,
-		       		&refori_shoemake [0],
+		       		refori_shoemake,
 		       		debug);		//rotating to reference oritentation
 
 		rotate_shoemake(&(myligand->atom_idxyzq[atom_id][1]),
 			       genrot_movvec,
-			       &shoemake [0],
+			       shoemake,
 			       debug);		//general rotation
 	}
 
@@ -1338,6 +1339,7 @@ void change_conform_f(Liganddata* myligand,
 			printf("Moved point (final values) (x,y,z): %lf, %lf, %lf\n", myligand->atom_idxyzq [atom_id][1], myligand->atom_idxyzq [atom_id][2], myligand->atom_idxyzq [atom_id][3]);
 
 }
+#endif
 
 float calc_interE_f(const Gridinfo*   mygrid,
 		    const Liganddata* myligand,