Commit 809fc997 authored by Leonardo Solis's avatar Leonardo Solis
Browse files

removed unneeded kernels files

parent fc53c03e

ofdock_taskpar_alt/device/Krnl_Conf_Arbiter.cl

deleted100644 → 0
+0 −98
Original line number Diff line number Diff line 
channel bool  chan_IGL_active;

channel char  chan_IGL_mode;

channel float chan_IGL_genotype __attribute__((depth(ACTUAL_GENOTYPE_LENGTH)));



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

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

__kernel __attribute__ ((max_global_work_dim(0)))

void Krnl_Conf_Arbiter(unsigned int DockConst_num_of_genes) {



	__local float genotype[ACTUAL_GENOTYPE_LENGTH];



	bool active = true;



while(active) {



	//printf("BEFORE In Conf_Arbiter CHANNEL\n");

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

	// Wait for genotypes in channel

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

	bool IC_valid     = false;

	bool GG_valid     = false;

	bool LS_valid     = false;

	bool Off_valid    = false;



	float IC_active;

	float GG_active;

	float LS_active;

	bool Off_active;



	uchar pipe_cnt = 0;



	while (

	       (Off_valid == false) && (pipe_cnt < DockConst_num_of_genes) 

	) {

		IC_active  = read_channel_nb_altera(chan_IC2Conf_genotype, &IC_valid);

		GG_active  = read_channel_nb_altera(chan_GG2Conf_genotype, &GG_valid);

		LS_active  = read_channel_nb_altera(chan_LS2Conf_genotype, &LS_valid);

		Off_active = read_channel_nb_altera(chan_Off2Conf_active,  &Off_valid);



		if (IC_valid || GG_valid || LS_valid) {

			genotype[pipe_cnt] = (IC_valid)  ?  IC_active :

	       			    	     (GG_valid)  ?  GG_active : 

				     	     (LS_valid)  ?  LS_active :

                                     	     (Off_valid) ?  0.0f:

				     	     0.0f; // last case should never occur, otherwise above while would be still running

			

			if (pipe_cnt > 2) {

				genotype [pipe_cnt] = genotype [pipe_cnt]*DEG_TO_RAD;

			}

			

			pipe_cnt++;

		}	

	}



	char mode;



	/*

	active = (IC_valid)     ? true :

		 (GG_valid)     ? true :

		 (LS_valid)     ? true :

		 (Off_valid)    ? Off_active :

		 false; // last case should never occur, otherwise above while would be still running

	*/

	active = (Off_valid) ? Off_active : true; 



	/*

	mode = (IC_valid)  ? 0x01 :

	       (GG_valid)  ? 0x02 :

	       (LS_valid)  ? 0x03 :

	       (Off_valid) ? 0x05 :

	       0x05; // last case should never occur, otherwise above while would be still running

	*/

	mode = (Off_valid) ? 0x05 : (IC_valid) ? 0x01 : (GG_valid) ? 0x02 : 0x03 ; // last case is LS (0x03)

	       

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

	//printf("AFTER In Conf_Arbiter CHANNEL\n");





	// communicate to Krnl_Conform

	for (uchar i=0; i<DockConst_num_of_genes; i++) {

		if (i == 0) {

			write_channel_altera(chan_IGL_active, active);

			mem_fence(CLK_CHANNEL_MEM_FENCE);



			write_channel_altera(chan_IGL_mode,   mode);

			mem_fence(CLK_CHANNEL_MEM_FENCE);

		}



		write_channel_altera(chan_IGL_genotype, genotype[i]);

	}



	



} // End of while (active)



}

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

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

ofdock_taskpar_alt/device/Krnl_Conf_Arbiter2.cl

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Original line number Diff line number Diff line 
//channel bool  chan_Conf2LS_LS2_token;

//channel bool  chan_Conf2LS_LS3_token;



channel bool  chan_LS23_active;

channel char  chan_LS23_mode;

channel float chan_LS23_genotype     __attribute__((depth(ACTUAL_GENOTYPE_LENGTH)));



//channel bool chan_LS2Arbiter_LS2_end;

//channel bool chan_LS2Arbiter_LS3_end;



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

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

__kernel __attribute__ ((max_global_work_dim(0)))

void Krnl_Conf_Arbiter2(unsigned int DockConst_num_of_genes) {



	__local float genotype2 [ACTUAL_GENOTYPE_LENGTH];

	__local float genotype3 [ACTUAL_GENOTYPE_LENGTH];

	__local float genotype_if_bound_1 [ACTUAL_GENOTYPE_LENGTH];

	__local float genotype [2][ACTUAL_GENOTYPE_LENGTH];



	bool active = true;

	bool LS2_last_geno = false;

	bool LS3_last_geno = false;

	bool bothLS_last_geno = false;



	uint LS2_eval = 0;

	uint LS3_eval = 0;



while(active) {

	bool Off_valid     = false;

	bool LS2_end_valid = false;

	bool LS3_end_valid = false;

	bool Off_active;

	bool LS2_end_active;

	bool LS3_end_active;



	while (

		(Off_valid == false) && (LS2_end_valid == false) && (LS3_end_valid == false)

	){

		Off_active     = read_channel_nb_altera(chan_ConfArbiter_Off,    &Off_valid);

		LS2_end_active = read_channel_nb_altera(chan_LS2Arbiter_LS2_end, &LS2_end_valid);

		LS3_end_active = read_channel_nb_altera(chan_LS2Arbiter_LS3_end, &LS3_end_valid);



		/*

		printf("%-15s %5s",   "Off_valid: ",     Off_valid?"true":"false");

		printf("%-15s %5s ",  "LS2_end_valid: ", LS2_end_valid?"true":"false");

		printf("%-15s %5s\n", "LS3_end_valid: ", LS3_end_valid?"true":"false");

		*/

	}

	

	/*

	if ((LS2_end_valid == true) &&  (LS3_end_valid == true)){

		printf("BOTH LS WANT TO PROCESS DATA!!!!!!\n");

	}

	*/



	uchar bound_tmp = 0;



	/*

	active = Off_valid?Off_active:

		 LS2_end_valid?true:

		 LS3_end_valid?true:

		 false; // last case should never occur, otherwise above while would be still running

	*/

	active = Off_valid ? Off_active : true;



	// get genos from LS2 and LS3

/*

	if (active == true) {



		// if LS2 sent geno

		if (LS2_end_valid == true) {

			bound_tmp++;

			for (uchar i=0; i<DockConst_num_of_genes; i++) {

				genotype2 [i] = read_channel_altera(chan_LS2Conf_LS2_genotype);

			}

			LS2_eval++;



			#if defined (DEBUG_KRNL_CONF_ARBITER)

			printf("LS2 genotype: %u\n", LS2_eval);

			#endif

		}



		// if LS3 sent geno

		if (LS3_end_valid == true) {

			bound_tmp++;

			for (uchar i=0; i<DockConst_num_of_genes; i++) {

				genotype3 [i] = read_channel_altera(chan_LS2Conf_LS3_genotype);

			}

			LS3_eval++;



			#if defined (DEBUG_KRNL_CONF_ARBITER)

			printf("LS3 genotype: %u\n", LS3_eval);

			#endif

		}

	} // End if (active == true)

*/







	if (active == true) {

		for (uchar i=0; i<DockConst_num_of_genes; i++) {

			// if LS2 sent geno

			if (LS2_end_valid == true) {

				genotype2 [i] = read_channel_altera(chan_LS2Conf_LS2_genotype);

			}



			// if LS3 sent geno

			if (LS3_end_valid == true) {

				genotype3 [i] = read_channel_altera(chan_LS2Conf_LS3_genotype);

			}

		}

		

		// if LS2 sent geno

		if (LS2_end_valid == true) {

			bound_tmp++;

			LS2_eval++;

		}



		// if LS3 sent geno

		if (LS3_end_valid == true) {

			bound_tmp++;

			LS3_eval++;

		}

	} // End if (active == true)





























	

	uchar bound = (active)?bound_tmp:1;



	// mode for both LS

	char mode [2];

	mode [0] = (LS2_end_valid)? 0x02: 0x00; 

	mode [1] = (LS3_end_valid)? 0x03: 0x00;

	char mode_if_bound_1 = LS2_end_valid?0x02:(LS3_end_valid?0x03:0x00);



	// genotype for both LS

	#pragma ivdep

	for (uchar i=0; i<DockConst_num_of_genes; i++) {

		genotype[0][i & 0x3F] = (LS2_end_valid)?genotype2[i]:0.0f;

		genotype[1][i & 0x3F] = (LS3_end_valid)?genotype3[i]:0.0f;

		genotype_if_bound_1[i] = LS2_end_valid?genotype2[i]:(LS3_end_valid?genotype3[i]:0.0f);

	}



	// Send data to Krnl_Conform2

	for (uchar j=0; j<bound; j++) {

		write_channel_altera(chan_LS23_active, active);

		mem_fence(CLK_CHANNEL_MEM_FENCE);



		write_channel_altera(chan_LS23_mode,(bound==1)?mode_if_bound_1:mode[j]);

		mem_fence(CLK_CHANNEL_MEM_FENCE);



		/*

		for (uchar i=0; i<DockConst_num_of_genes; i++) {

			write_channel_altera(chan_LS23_genotype, (bound==1)?genotype_if_bound_1[i]:genotype[j][i & 0x3F]);

		}

		*/



		for (uchar i=0; i<DockConst_num_of_genes; i++) {

/*

			float tmp;

			

			if (i > 2) {

				tmp = ((bound==1)?genotype_if_bound_1[i]:genotype[j][i & 0x3F]) * DEG_TO_RAD;

			}

*/

			float tmp = (bound==1)?genotype_if_bound_1[i]:genotype[j][i & 0x3F];

			

			if (i > 2) {

				tmp =  tmp * DEG_TO_RAD;

			}



			write_channel_altera(chan_LS23_genotype, tmp);

		}



		#if defined (DEBUG_KRNL_CONF_ARBITER)

		printf("bound: %u, mode: %u\n", bound, (bound==1)?mode_if_bound_1:mode[j]);

		#endif

	}



	if (LS2_end_active == true) {

		LS2_eval = 0;

	}



	if (LS3_end_active == true) {

		LS3_eval = 0;

	}



} // End of while (active)



}

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

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

ofdock_taskpar_alt/device/Krnl_Conform2.cl

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Original line number Diff line number Diff line 
// --------------------------------------------------------------------------

// The function changes the conformation of myligand according to 

// the genotype given by the second parameter.

// Originally from: processligand.c

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

__kernel __attribute__ ((max_global_work_dim(0)))

void Krnl_Conform2(

	     __constant int*    restrict KerConstStatic_rotlist_const,

	     __constant float3* restrict KerConstDynamic_ref_coords_const,

	     __constant float3* restrict KerConstDynamic_rotbonds_moving_vectors_const,

	     __constant float3* restrict KerConstDynamic_rotbonds_unit_vectors_const,

	    

			      unsigned int                     DockConst_rotbondlist_length,

			      unsigned char                    DockConst_num_of_atoms,

			      unsigned int                     DockConst_num_of_genes,



			      float                            ref_orientation_quats_const_0,

			      float                            ref_orientation_quats_const_1,

			      float                            ref_orientation_quats_const_2,

			      float                            ref_orientation_quats_const_3

)

{

	#if defined (DEBUG_KRNL_Conform) 

	printf("\n");

	printf("%-40s %u\n", "DockConst->rotbondlist_length: ",	DockConst_rotbondlist_length);

	printf("%-40s %u\n", "DockConst->num_of_atoms: ",  	DockConst_num_of_atoms);

	printf("%-40s %u\n", "DockConst_num_of_genes: ",        DockConst_num_of_genes);	

	#endif



/*

	// check best practices guide

	// Table 11. Effects of numbanks and bankwidth on the Bank Geometry ...

	// only first three indexes of the lower array are used

	// however size of lower array was declared as 4, just to keep sizes equal to power of 2

	__local float  __attribute__((numbanks(8), bankwidth(16))) loc_coords[MAX_NUM_OF_ATOMS][4];

*/



	__local float genotype[ACTUAL_GENOTYPE_LENGTH];



	bool active = true;



	// local mem to cache KerConstStatic->rotlist_const[], marked as bottleneck by profiler

	__local int rotlist_localcache [MAX_NUM_OF_ROTATIONS];

	for (ushort c = 0; c < DockConst_rotbondlist_length; c++) {

		rotlist_localcache [c] = KerConstStatic_rotlist_const [c];

	}



	__local float3 ref_coords_localcache [MAX_NUM_OF_ATOMS];

	for (uchar c = 0; c < DockConst_num_of_atoms; c++) {

		ref_coords_localcache [c] = KerConstDynamic_ref_coords_const [c];

	}



	__local float3 rotbonds_moving_vectors_localcache[MAX_NUM_OF_ROTBONDS];

	__local float3 rotbonds_unit_vectors_localcache[MAX_NUM_OF_ROTBONDS];

	for (uchar c = 0; c < MAX_NUM_OF_ROTBONDS; c++) {

		rotbonds_moving_vectors_localcache [c] = KerConstDynamic_rotbonds_moving_vectors_const[c];

		rotbonds_unit_vectors_localcache   [c] = KerConstDynamic_rotbonds_unit_vectors_const [c];

	}





while(active) {



	//printf("BEFORE In CONFORM CHANNEL\n");

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

	// Wait for genotypes in channel

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

/*

	bool LS2_valid  = false;

	bool Off2_valid = false;



	float LS2_active;

	bool  Off2_active;



	uchar pipe_cnt = 0;



	while (

		(Off2_valid == false) && (pipe_cnt < DockConst_num_of_genes)

	) {

		LS2_active = read_channel_nb_altera(chan_LS2Conf_LS2_genotype, &LS2_valid);

		Off2_active = read_channel_nb_altera(chan_LS2Conf_Off, &Off2_valid);



		if (LS2_valid) {

			genotype [pipe_cnt] = (LS2_valid)? LS2_active:

					      (Off2_valid)? 0.0f:

					      0.0f; // last case should never occur, otherwise above while would be still running

			if (pipe_cnt > 2) {

				genotype [pipe_cnt] = genotype [pipe_cnt]*DEG_TO_RAD;

			}



			pipe_cnt++;

		}

	}



	char mode;



	active = (LS2_valid) ? true :

		 (Off2_valid)? Off2_active :

		 false;	// last case should never occur, otherwise above while would be still running

*/

	char mode;



	active = read_channel_altera(chan_LS23_active);

	mem_fence(CLK_CHANNEL_MEM_FENCE);



	for (uchar i=0; i<DockConst_num_of_genes; i++) {

		if (i == 0) {

			mode = read_channel_altera(chan_LS23_mode);

			mem_fence(CLK_CHANNEL_MEM_FENCE);

		}



		genotype [i] = read_channel_altera(chan_LS23_genotype);

		/*

		if (i > 2) {

			genotype [i] = genotype [i]*DEG_TO_RAD;

		}

		*/

	}

	

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

	//printf("AFTER In CONFORM 2 CHANNEL\n");



	/*

	float3 __attribute__ ((

			      memory,

			      numbanks(2),

			      bankwidth(16),

			      singlepump,

			      numreadports(2),

			      numwriteports(1)

			    )) loc_coords[MAX_NUM_OF_ATOMS];

	*/

	float3 loc_coords[MAX_NUM_OF_ATOMS];



	#if defined (DEBUG_ACTIVE_KERNEL)

	if (active == 0) {printf("	%-20s: %s\n", "Krnl_Conform", "must be disabled");}

	#endif



	

	float3 genotype_xyz = {genotype[0], genotype[1], genotype[2]};



	float phi         = genotype [3];

	float theta       = genotype [4];

	float genrotangle = genotype [5];



	float sin_theta, cos_theta;

	sin_theta = native_sin(theta);

	cos_theta = native_cos(theta);



	float3 genrot_unitvec;

	genrot_unitvec.x = sin_theta*native_cos(phi);

	genrot_unitvec.y = sin_theta*native_sin(phi);

	genrot_unitvec.z = cos_theta;



	for (ushort rotation_counter = 0; rotation_counter < DockConst_rotbondlist_length; rotation_counter++)

	{

		int rotation_list_element = rotlist_localcache [rotation_counter];



		if ((rotation_list_element & RLIST_DUMMY_MASK) == 0)	//if not dummy rotation

		{

			uint atom_id = rotation_list_element & RLIST_ATOMID_MASK;



			//capturing atom coordinates

			float3 atom_to_rotate;



			if ((rotation_list_element & RLIST_FIRSTROT_MASK) != 0)	//if first rotation of this atom

			{	

				atom_to_rotate = ref_coords_localcache [atom_id];

			}

			else

			{	

				atom_to_rotate = loc_coords[atom_id];

			}



			//capturing rotation vectors and angle

			float3 rotation_unitvec;

			float3 rotation_movingvec;

			float rotation_angle;



			if ((rotation_list_element & RLIST_GENROT_MASK) != 0)	//if general rotation

			{

				rotation_unitvec = genrot_unitvec;



				rotation_angle = genrotangle;



				rotation_movingvec = genotype_xyz;

			}

			else	//if rotating around rotatable bond

			{

				uint rotbond_id = (rotation_list_element & RLIST_RBONDID_MASK) >> RLIST_RBONDID_SHIFT;

				rotation_unitvec = rotbonds_unit_vectors_localcache [rotbond_id];

				

				rotation_angle = genotype[6+rotbond_id];



				rotation_movingvec = rotbonds_moving_vectors_localcache [rotbond_id];



				//in addition performing the first movement 

				//which is needed only if rotating around rotatable bond

				atom_to_rotate -= rotation_movingvec;

			}



			//performing rotation

			float quatrot_left_x, quatrot_left_y, quatrot_left_z, quatrot_left_q;

			float quatrot_temp_x, quatrot_temp_y, quatrot_temp_z, quatrot_temp_q;



			rotation_angle = rotation_angle*0.5f;



			float sin_angle, cos_angle;

			sin_angle = native_sin(rotation_angle);

			cos_angle = native_cos(rotation_angle);

			quatrot_left_x = sin_angle*rotation_unitvec.x;

			quatrot_left_y = sin_angle*rotation_unitvec.y;

			quatrot_left_z = sin_angle*rotation_unitvec.z;

			quatrot_left_q = cos_angle;



			if ((rotation_list_element & RLIST_GENROT_MASK) != 0)	//if general rotation, 

										//two rotations should be performed 

										//(multiplying the quaternions)

			{

				//calculating quatrot_left*ref_orientation_quats_const, 

				//which means that reference orientation rotation is the first

				quatrot_temp_q = quatrot_left_q;

				quatrot_temp_x = quatrot_left_x;

				quatrot_temp_y = quatrot_left_y;

				quatrot_temp_z = quatrot_left_z;



				// L30nardoSV: taking the first element of ref_orientation_quats_const member

				quatrot_left_q = quatrot_temp_q*ref_orientation_quats_const_0-

						 quatrot_temp_x*ref_orientation_quats_const_1-

						 quatrot_temp_y*ref_orientation_quats_const_2-

						 quatrot_temp_z*ref_orientation_quats_const_3;

				quatrot_left_x = quatrot_temp_q*ref_orientation_quats_const_1+

						 ref_orientation_quats_const_0*quatrot_temp_x+

						 quatrot_temp_y*ref_orientation_quats_const_3-

						 ref_orientation_quats_const_2*quatrot_temp_z;

				quatrot_left_y = quatrot_temp_q*ref_orientation_quats_const_2+

						 ref_orientation_quats_const_0*quatrot_temp_y+

						 ref_orientation_quats_const_1*quatrot_temp_z-

						 quatrot_temp_x*ref_orientation_quats_const_3;

				quatrot_left_z = quatrot_temp_q*ref_orientation_quats_const_3+

						 ref_orientation_quats_const_0*quatrot_temp_z+

						 quatrot_temp_x*ref_orientation_quats_const_2-

						 ref_orientation_quats_const_1*quatrot_temp_y;

			}



			quatrot_temp_q = - 

					(quatrot_left_x*atom_to_rotate.x +

					 quatrot_left_y*atom_to_rotate.y +

					 quatrot_left_z*atom_to_rotate.z);



			quatrot_temp_x = quatrot_left_q*atom_to_rotate.x +

					 quatrot_left_y*atom_to_rotate.z -

					 quatrot_left_z*atom_to_rotate.y;

			quatrot_temp_y = quatrot_left_q*atom_to_rotate.y -

					 quatrot_left_x*atom_to_rotate.z +

					 quatrot_left_z*atom_to_rotate.x;

			quatrot_temp_z = quatrot_left_q*atom_to_rotate.z +

					 quatrot_left_x*atom_to_rotate.y -

					 quatrot_left_y*atom_to_rotate.x;



			atom_to_rotate.x = quatrot_temp_x*quatrot_left_q - quatrot_temp_q*quatrot_left_x - 

					     quatrot_temp_y*quatrot_left_z + quatrot_temp_z*quatrot_left_y;

			atom_to_rotate.y = quatrot_temp_x*quatrot_left_z + quatrot_temp_y*quatrot_left_q - 

					     quatrot_temp_z*quatrot_left_x - quatrot_temp_q*quatrot_left_y ;

			atom_to_rotate.z = quatrot_temp_y*quatrot_left_x - quatrot_temp_x*quatrot_left_y - 

					     quatrot_temp_q*quatrot_left_z + quatrot_temp_z*quatrot_left_q;



			//performing final movement and storing values

			loc_coords[atom_id] = atom_to_rotate + rotation_movingvec;



		} // End if-statement not dummy rotation

	} // End rotation_counter for-loop



	#if defined (DEBUG_KRNL_CONFORM)

	printf("BEFORE Out CONFORM CHANNEL\n");

	#endif



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

	// Send ligand atomic coordinates to channel 

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

	/*

	write_channel_altera(chan_Conf2Intere_LS2_active, active);

	write_channel_altera(chan_Conf2Intrae_LS2_active, active);

	mem_fence(CLK_CHANNEL_MEM_FENCE);



	write_channel_altera(chan_Conf2Intere_LS2_mode,   mode);

	write_channel_altera(chan_Conf2Intrae_LS2_mode,   mode);

	mem_fence(CLK_CHANNEL_MEM_FENCE);



	//float3 position_xyz;

	for (uchar pipe_cnt=0; pipe_cnt<DockConst_num_of_atoms; pipe_cnt++) {

		write_channel_altera(chan_Conf2Intere_LS2_xyz, loc_coords[pipe_cnt]);

		write_channel_altera(chan_Conf2Intrae_LS2_xyz, loc_coords[pipe_cnt]);

	}

	mem_fence(CLK_CHANNEL_MEM_FENCE);

	*/



	for (uchar pipe_cnt=0; pipe_cnt<DockConst_num_of_atoms; pipe_cnt++) {

		if (pipe_cnt == 0) {

			write_channel_altera(chan_Conf2Intere_LS2_active, active);

			write_channel_altera(chan_Conf2Intrae_LS2_active, active);

			mem_fence(CLK_CHANNEL_MEM_FENCE);



			write_channel_altera(chan_Conf2Intere_LS2_mode,   mode);

			write_channel_altera(chan_Conf2Intrae_LS2_mode,   mode);

			mem_fence(CLK_CHANNEL_MEM_FENCE);

		}



		write_channel_altera(chan_Conf2Intere_LS2_xyz, loc_coords[pipe_cnt]);

		write_channel_altera(chan_Conf2Intrae_LS2_xyz, loc_coords[pipe_cnt]);

	}



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

	#if defined (DEBUG_KRNL_CONFORM)

	printf("AFTER Out CONFORM CHANNEL\n");

	#endif



} // End of while(1)



#if defined (DEBUG_ACTIVE_KERNEL)

printf("	%-20s: %s\n", "Krnl_Conform", "disabled");

#endif



}

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

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

ofdock_taskpar_alt/device/Krnl_Conform2_fixedpt.cl

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ofdock_taskpar_alt/device/Krnl_Conform_fixedpt.cl

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