Commit 9c153df7 authored by Leonardo Solis's avatar Leonardo Solis
Browse files

LS9 blocks + added comments + corrections

parent 3938e557

ofdock_taskpar_alt/Makefile

+66 −47
Original line number Diff line number Diff line
@@ -532,7 +532,11 @@ else 
endif





ENABLE_KERNELS = $(K1) $(K2) $(K3) $(K4) $(K5) $(K6) $(K7) $(K8) $(K9) $(K10) $(K11) $(K12) $(K13) $(K14) $(K15) $(K16) $(K17) $(K18) $(K19) $(K20) $(K21) $(K22) $(K23) $(K24) $(K25) $(K26) $(K27) $(K28) $(K29) $(K30) $(K31) $(K32) $(K33) $(K34) $(K35) $(K36) $(K37) $(K38) $(K39) $(K40) $(K41) $(K42) $(K43) $(K44) $(K45) $(K46) $(K47) $(K48)

ENABLE_KERNELS = $(K1)  $(K2)  $(K3)  $(K4)  $(K5)  $(K6)  $(K7)  $(K8)  $(K9)  $(K10) \

		 $(K11) $(K12) $(K13) $(K14) $(K15) $(K16) $(K17) $(K18) $(K19) $(K20) \

		 $(K21) $(K22) $(K23) $(K24) $(K25) $(K26) $(K27) $(K28) $(K29) $(K30) \

		 $(K31) $(K32) $(K33) $(K34) $(K35) $(K36) $(K37) $(K38) $(K39) $(K40) \

		 $(K41) $(K42) $(K43) $(K44) $(K45) $(K46) $(K47) $(K48)



# =============================

# Reproduce result (remove randomness)
@@ -666,7 +670,18 @@ else 
	SEP_FGRID_FLAG=

endif



FIPO_FLAG = $(FIPOCO_FLAG) $(FIPOIE_FLAG) $(FIPOIA_FLAG) $(FIPOLS1_FLAG) $(FIPOLS2_FLAG) $(FIPOLS3_FLAG) $(FIPOLS4_FLAG) $(FIPOLS5_FLAG) $(FIPOLS6_FLAG) $(FIPOLS7_FLAG) $(FIPOLS8_FLAG) $(FIPOLS9_FLAG) $(COPYPOPENE_FLAG) $(SEP_FGRID_FLAG) 

FIPO_FLAG = $(FIPOCO_FLAG) \

	    $(FIPOIE_FLAG) $(FIPOIA_FLAG) \

	    $(FIPOLS1_FLAG) \

	    $(FIPOLS2_FLAG) \

	    $(FIPOLS3_FLAG) \

	    $(FIPOLS4_FLAG) \

	    $(FIPOLS5_FLAG) \

	    $(FIPOLS6_FLAG) \

	    $(FIPOLS7_FLAG) \

	    $(FIPOLS8_FLAG) \

	    $(FIPOLS9_FLAG) \

	    $(COPYPOPENE_FLAG) $(SEP_FGRID_FLAG) 



# =============================

# AOC flags
@@ -716,18 +731,19 @@ $(TARGET_DIR)/$(TARGET) : Makefile $(SRCS) $(INCS) $(TARGET_DIR) 
			$(foreach L,$(LIBS),-l$L) \

			-o $(TARGET_DIR)/$(TARGET) $(DOCK_DEBUG_FLAG) $(DEV) $(DOCK_PROG) $(ENABLE_KERNELS) $(REP) $(FIPO_FLAG)

	@echo " "

	@echo "================================"

	@echo "INFO: host binary is under: bin/"

	@echo "================================"

	@echo "==================================================="

	@echo "INFO: host binary is under: $(TARGET_DIR)/$(TARGET)"

	@echo "==================================================="

	@echo " "



# Docking parameters 

# NEV was usually set to 100000

# that directly determine the execution time

# Following values are used only for emulation

# to have a short but still a representative test

PDB  := 1stp

NRUN := 10

NEV  := 50000 





# Project name

PROJECT_NAME := ofdock_taskpar_alt
@@ -753,9 +769,9 @@ BOARD := Proc10A_X115 
keremu: $(DEV_SRC)

	aoc -march=emulator -v --board $(BOARD) $(DEV_SRC) -o $(TARGET_DIR)/$(KRNL_NAME).aocx $(REP) $(FIPO_FLAG) $(AOC_FLAG) -g

	@echo " "

	@echo "==============================================================="

	@echo "INFO: emulation files are under: bin/$(KRNL_NAME)(.aoco)(.aocx)"

	@echo "==============================================================="

	@echo "========================================================================="

	@echo "INFO: emulation files are under: $(TARGET_DIR)/$(KRNL_NAME)(.aoco)(.aocx)"

	@echo "========================================================================="

	@echo " "



# Run emulation
@@ -766,9 +782,9 @@ emu: $(TARGET_DIR)/$(TARGET) keremu 
	cd $(TARGET_DIR) && \

	CL_CONTEXT_EMULATOR_DEVICE_ALTERA=1 ./$(TARGET) -ffile ../input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ../input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nev $(NEV) -nrun $(NRUN) -gfpop 1

	@echo " "

	@echo "========================================"

	@echo "INFO: log file is under: bin/docking.dlg"

	@echo "========================================"

	@echo "=================================================="

	@echo "INFO: log file is under: $(TARGET_DIR)/docking.dlg"

	@echo "=================================================="

	@echo " "
@@ -781,13 +797,13 @@ emu: $(TARGET_DIR)/$(TARGET) keremu 
kerrpt: $(DEV_SRC)

	aoc --board $(BOARD) $(DEV_SRC) -o $(TARGET_DIR)/$(KRNL_NAME).aoco $(REP) $(FIPO_FLAG) $(AOC_FLAG) -c --report -g

	@echo " "

	@echo "=================================================================="

	@echo "INFO: report files are under: bin/$(KRNL_NAME)/reports/report.html"

	@echo "============================================================================"

	@echo "INFO: report files are under: $(TARGET_DIR)/$(KRNL_NAME)/reports/report.html"

	@echo "INFO: THIS WORKS ONLY FROM V16.1 ON                                         "

	@echo "                                        		                           "

	@echo "INFO: report file is under: bin/$(KRNL_NAME).log                  "

	@echo "INFO: report file is under: $(TARGET_DIR)/$(KRNL_NAME).log                  "

	@echo "INFO: THIS WORKS IN V16.0 AND OLDER.                                        "

	@echo "=================================================================="

	@echo "============================================================================"

	@echo " "



# Build hw (FPGA bitstream)
@@ -799,17 +815,17 @@ kerrpt: $(DEV_SRC) 
hw: 	

	aoc --board $(BOARD) $(DEV_SRC) -o $(TARGET_DIR_HW)/$(KRNL_NAME).aocx $(FIPO_FLAG) $(AOC_FLAG)

	@echo " "

	@echo "================================================================"

	@echo "INFO: FPGA bitstream is under: bin_hw/$(KRNL_NAME)(.aoco)(.aocx)"

	@echo "================================================================"

	@echo "=========================================================================="

	@echo "INFO: FPGA bitstream is under: $(TARGET_DIR_HW)/$(KRNL_NAME)(.aoco)(.aocx)"

	@echo "=========================================================================="

	@echo " "



hw-he:

	aoc --high-effort --board $(BOARD) $(DEV_SRC) -o $(TARGET_DIR_HW)/$(KRNL_NAME).aocx $(FIPO_FLAG) $(AOC_FLAG)

	@echo " "

	@echo "================================================================"

	@echo "INFO: FPGA bitstream is under: bin_hw/$(KRNL_NAME)(.aoco)(.aocx)"

	@echo "================================================================"

	@echo "=========================================================================="

	@echo "INFO: FPGA bitstream is under: $(TARGET_DIR_HW)/$(KRNL_NAME)(.aoco)(.aocx)"

	@echo "=========================================================================="

	@echo " "



# Build hw (FPGA bitstream) instrumented with performance counters
@@ -821,13 +837,13 @@ hw-he: 
hw-prof:

	aoc --profile --board $(BOARD) $(DEV_SRC) -o $(TARGET_DIR_HW_PROF)/$(KRNL_NAME).aocx $(FIPO_FLAG) $(AOC_FLAG)

	@echo " "

	@echo "====================================================================================="

	@echo "INFO: instrumented FPGA bitstream is under: bin_hw_profile/$(KRNL_NAME)(.aoco)(.aocx)"

	@echo "====================================================================================="

	@echo "============================================================================================"

	@echo "INFO: instrumented FPGA bitstream is under: $(TARGET_DIR_HW_PROF)/$(KRNL_NAME)(.aoco)(.aocx)"

	@echo "============================================================================================"

	@echo " "





# Execute on sauron server

# Execute on remote server

# Host-recompilation

# Copy of host to $(TARGET_DIR_HW)

# The working directory is changed
@@ -835,15 +851,15 @@ hw-prof: 
exe: $(TARGET_DIR)/$(TARGET)

	cp $(TARGET_DIR)/$(TARGET) $(TARGET_DIR_HW)/ && \

	cd $(TARGET_DIR_HW) && \

	./$(TARGET) -ffile ../input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ../input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun 10

	./$(TARGET) -ffile ../input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ../input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -resnam docking_$(PDB)_$(NRUN)

	@echo " "

	@echo "==========================================="

	@echo "INFO: log file is under: bin_hw/docking.dlg"

	@echo "==========================================="

	@echo "===================================================================="

	@echo "INFO: log file is under: $(TARGET_DIR_HW)/docking_$(PDB)_$(NRUN).dlg"

	@echo "===================================================================="

	@echo " "





# Execute and profile on sauron server

# Execute and profile on remote server

# Host-recompilation

# Copy of host to $(TARGET_DIR_HW_PROF)

# The working directory is changed
@@ -851,20 +867,23 @@ exe: $(TARGET_DIR)/$(TARGET) 
exe-prof: $(TARGET_DIR)/$(TARGET)

	cp $(TARGET_DIR)/$(TARGET) $(TARGET_DIR_HW_PROF)/ && \

	cd $(TARGET_DIR_HW_PROF) && \

	./$(TARGET) -ffile ../input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ../input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun 10

	./$(TARGET) -ffile ../input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ../input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -resnam docking_$(PDB)_$(NRUN)

	@echo " "

	@echo "==================================================="

	@echo "INFO: log file is under: bin_hw_profile/docking.dlg"

	@echo "==================================================="

	@echo "========================================================================="

	@echo "INFO: log file is under: $(TARGET_DIR_HW_PROF)/docking_$(PDB)_$(NRUN).dlg"

	@echo "========================================================================="

	@echo " "



COPY_DIR := copy_$(PROJECT_NAME)

COPY_DIR_DOCK := $(PROJECT_NAME)



# Make sure this remote-server alias exists (in ~/.ssh/config)

SERVER := sauron



# Delete an existing folder if previously created

# Create a folder $(COPY_DIR) in the parent directory

# Copy binaries into $(COPY_DIR) folder, avoiding the (innecesary) compilation intermediate files

# Copy source files into $(COPY_DIR) as host is built in the HARP2 front-end

# Copy source files into $(COPY_DIR) as host is built in the remote $(SERVER)

# Create a zip file out of the $(COPY_DIR) folder

copy: clean-copy

	mkdir ../$(COPY_DIR)
@@ -882,16 +901,16 @@ copy: clean-copy 
	cp -r input/ ../$(COPY_DIR)/$(COPY_DIR_DOCK)/

	cp -r wrapcl/ ../$(COPY_DIR)/$(COPY_DIR_DOCK)/

	cp -r ../common ../$(COPY_DIR)/

	cp ../conf_aoc160_sauron.sh ../$(COPY_DIR)/

	cp ../conf_aoc160_$(SERVER).sh ../$(COPY_DIR)/

	cd ../;	zip -r $(COPY_DIR).zip $(COPY_DIR)

	@echo " "

	@echo "Transfer the $(COPY_DIR).zip file to sauron server: "

	@echo "Transfer the $(COPY_DIR).zip file to $(SERVER) server: "

	@echo " "

	cd ../ && scp $(COPY_DIR).zip sauron:~/

	cd ../ && scp $(COPY_DIR).zip $(SERVER):~/

	@echo " "

	@echo "================="

	@echo "Transfer finished"

	@echo "================="

	@echo "=========================================="

	@echo "Files listed were transferred to $(SERVER)"

	@echo "=========================================="

	@echo " "



clean-copy:

ofdock_taskpar_alt/device/Krnl_Conform.cl

+41 −113
Original line number Diff line number Diff line 
// --------------------------------------------------------------------------

// The function changes the conformation of myligand according to 

// the genotype given by the second parameter.

// Conform changes the conformation of the ligand according to 

// the genotype fed by any producer logic/kernel (IC, GG, LSs).

// Originally from: processligand.c

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

__kernel __attribute__ ((max_global_work_dim(0)))
@@ -18,9 +18,7 @@ void Krnl_Conform( 
			      unsigned int          DockConst_rotbondlist_length,

			      unsigned char         DockConst_num_of_atoms,

			      unsigned char         DockConst_num_of_genes,

/*

			      unsigned char         Host_num_of_rotbonds,

*/



	     #if defined (FIXED_POINT_CONFORM)

	     __constant fixedpt4* restrict KerConstStatic_ref_orientation_quats_const,

	     #else
@@ -36,17 +34,13 @@ void Krnl_Conform( 
	printf("%-40s %u\n", "DockConst_num_of_genes: ",        DockConst_num_of_genes);	

	#endif



/*

	// check best practices guide

	// 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];

*/

	// 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];



/*

	bool active = true;

*/

	char active = 0x01;	



	__local int rotlist_localcache [MAX_NUM_OF_ROTATIONS];
@@ -62,10 +56,6 @@ while(active) { 
	fixedpt  phi;

	fixedpt  theta;

	fixedpt  genrotangle;

/*

	fixedpt  sin_theta, cos_theta;

	fixedpt3 genrot_unitvec;

*/

	fixedpt3 genotype_xyz;

	fixedpt3 __attribute__ ((

			      memory,
@@ -79,10 +69,6 @@ while(active) { 
	float  phi;

	float  theta;

	float  genrotangle;

/*

	float  sin_theta, cos_theta;

	float3 genrot_unitvec;

*/

	float3 genotype_xyz;

	float3 __attribute__ ((

			      memory,
@@ -94,10 +80,6 @@ while(active) { 
			    )) loc_coords [MAX_NUM_OF_ATOMS];

	#endif



/*

	active = read_channel_altera(chan_IGL2Conform_active);

	mem_fence(CLK_CHANNEL_MEM_FENCE);

*/

	char2 actmode = read_channel_altera(chan_IGL2Conform_actmode);

	mem_fence(CLK_CHANNEL_MEM_FENCE);
@@ -113,52 +95,19 @@ while(active) { 
	#endif



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

		/*float fl_tmp = read_channel_altera(chan_IGL2Conform_genotype);*/

		float fl_tmp;

		switch (mode) {

			case 'I':

				fl_tmp = read_channel_altera(chan_IC2Conf_genotype);

			break;



			case 'G':

				fl_tmp = read_channel_altera(chan_GG2Conf_genotype);

			break;



			case 0x01:

				fl_tmp = read_channel_altera(chan_LS2Conf_LS1_genotype);

			break;



			case 0x02:

				fl_tmp = read_channel_altera(chan_LS2Conf_LS2_genotype);

			break;



			case 0x03:

				fl_tmp = read_channel_altera(chan_LS2Conf_LS3_genotype);

			break;



			case 0x04:

				fl_tmp = read_channel_altera(chan_LS2Conf_LS4_genotype);

			break;



			case 0x05:

				fl_tmp = read_channel_altera(chan_LS2Conf_LS5_genotype);

			break;



			case 0x06:

				fl_tmp = read_channel_altera(chan_LS2Conf_LS6_genotype);

			break;



			case 0x07:

				fl_tmp = read_channel_altera(chan_LS2Conf_LS7_genotype);

			break;



			case 0x08:

				fl_tmp = read_channel_altera(chan_LS2Conf_LS8_genotype);

			break;



			case 0x09:

				fl_tmp = read_channel_altera(chan_LS2Conf_LS9_genotype);

			break;

			case 'I':  fl_tmp = read_channel_altera(chan_IC2Conf_genotype);     break;

			case 'G':  fl_tmp = read_channel_altera(chan_GG2Conf_genotype);     break;

			case 0x01: fl_tmp = read_channel_altera(chan_LS2Conf_LS1_genotype); break;

			case 0x02: fl_tmp = read_channel_altera(chan_LS2Conf_LS2_genotype); break;

			case 0x03: fl_tmp = read_channel_altera(chan_LS2Conf_LS3_genotype); break;

			case 0x04: fl_tmp = read_channel_altera(chan_LS2Conf_LS4_genotype); break;

			case 0x05: fl_tmp = read_channel_altera(chan_LS2Conf_LS5_genotype); break;

			case 0x06: fl_tmp = read_channel_altera(chan_LS2Conf_LS6_genotype); break;

			case 0x07: fl_tmp = read_channel_altera(chan_LS2Conf_LS7_genotype); break;

			case 0x08: fl_tmp = read_channel_altera(chan_LS2Conf_LS8_genotype); break;

			case 0x09: fl_tmp = read_channel_altera(chan_LS2Conf_LS9_genotype); break;

		}

		

		if (i > 2) {
@@ -168,7 +117,7 @@ while(active) { 
//printf("Conform: %u %u\n", mode, i);



		#if defined (FIXED_POINT_CONFORM)

		// convert float to fixedpt

		// Convert float to fixedpt

		fixedpt fx_tmp = fixedpt_fromfloat(fl_tmp);

		switch (i) {

			case 0: genotype_xyz.x = fx_tmp; break;
@@ -196,40 +145,23 @@ while(active) { 
	if (active == 0x00) {printf("	%-20s: %s\n", "Krnl_Conform", "must be disabled");}

	#endif



/*

	#if defined (FIXED_POINT_CONFORM)

	sin_theta = fixedpt_sin(theta);

	cos_theta = fixedpt_cos(theta);

	genrot_unitvec.x = fixedpt_mul(sin_theta, fixedpt_cos(phi));

	genrot_unitvec.y = fixedpt_mul(sin_theta, fixedpt_sin(phi));

	genrot_unitvec.z = cos_theta;

	#else

	sin_theta = native_sin(theta);

	cos_theta = native_cos(theta);

	genrot_unitvec.x = sin_theta*native_cos(phi);

	genrot_unitvec.y = sin_theta*native_sin(phi);

	genrot_unitvec.z = cos_theta;

	#endif

*/



	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

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

		{

			uint atom_id = rotation_list_element & RLIST_ATOMID_MASK;



			//capturing atom coordinates

			// Capturing atom coordinates

			#if defined (FIXED_POINT_CONFORM)

			fixedpt3 atom_to_rotate;

			#else

			float3 atom_to_rotate;

			#endif



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

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

			{	

				/*atom_to_rotate = ref_coords_localcache [atom_id];*/

				atom_to_rotate = KerConstStatic_ref_coords_const [atom_id];

			}

			else
@@ -237,7 +169,7 @@ while(active) { 
				atom_to_rotate = loc_coords[atom_id];

			}



			//capturing rotation vectors and angle

			// Capturing rotation vectors and angle

			#if defined (FIXED_POINT_CONFORM)

			fixedpt3 rotation_unitvec;

			fixedpt3 rotation_movingvec;
@@ -248,7 +180,7 @@ while(active) { 
			float    rotation_angle;

			#endif



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

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

			{

				#if defined (FIXED_POINT_CONFORM)

				fixedpt  sin_theta, cos_theta;
@@ -274,19 +206,17 @@ while(active) { 


				rotation_movingvec = genotype_xyz;

			}

			else	//if rotating around rotatable bond

			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_unitvec = KerConstStatic_rotbonds_unit_vectors_const [rotbond_id];

				

				rotation_angle = genotype [6+rotbond_id];



				/*rotation_movingvec = rotbonds_moving_vectors_localcache [rotbond_id];*/

				rotation_movingvec = KerConstStatic_rotbonds_moving_vectors_const [rotbond_id];



				//in addition performing the first movement 

				// In addition performing the first movement 

				// which is needed only if rotating around rotatable bond



				#if defined (FIXED_POINT_CONFORM)
@@ -298,7 +228,7 @@ while(active) { 
				#endif

			}



			//performing rotation

			// Performing rotation

			#if defined (FIXED_POINT_CONFORM)

			fixedpt quatrot_left_x, quatrot_left_y, quatrot_left_z, quatrot_left_q;

			fixedpt quatrot_temp_x, quatrot_temp_y, quatrot_temp_z, quatrot_temp_q;
@@ -331,7 +261,7 @@ while(active) { 
			quatrot_left.w = cos_angle;

			#endif



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

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

										// two rotations should be performed 

										// (multiplying the quaternions)

			{
@@ -349,7 +279,7 @@ while(active) { 
				const float  ref_orientation_quats_const_3 = ref_orientation_quats_const.w;

				#endif



				//calculating quatrot_left*ref_orientation_quats_const, 

				// Calculating quatrot_left*ref_orientation_quats_const, 

				// which means that reference orientation rotation is the first

				#if defined (FIXED_POINT_CONFORM)

				quatrot_temp_q = quatrot_left_q;
@@ -360,7 +290,7 @@ while(active) { 
				quatrot_temp = quatrot_left;

				#endif



				//taking the first element of ref_orientation_quats_const member

				// Taking the first element of ref_orientation_quats_const member

				#if defined (FIXED_POINT_CONFORM)

				quatrot_left_q =   fixedpt_mul(quatrot_temp_q, ref_orientation_quats_const_0) 

						 - fixedpt_mul(quatrot_temp_x, ref_orientation_quats_const_1)
@@ -445,7 +375,7 @@ while(active) { 
			atom_to_rotate.z = dot(quatrot_temp, left4z);

			#endif



			//performing final movement and storing values

			// Performing final movement and storing values

			loc_coords[atom_id] = atom_to_rotate + rotation_movingvec;



		} // End if-statement not dummy rotation
@@ -501,8 +431,6 @@ while(active) { 
	}

	*/







	for (uchar pipe_cnt=0; pipe_cnt<DockConst_num_of_atoms; pipe_cnt+=2) {

		if (pipe_cnt == 0) {

			char  active_tmp = active;
@@ -528,7 +456,7 @@ while(active) { 
		float8 tmp;



		#if defined (FIXED_POINT_CONFORM)

		// convert fixedpt3 to float3

		// Convert fixedpt3 to float3

		float tmp_x1 = fixedpt_tofloat(tmp_coords[0].x);

		float tmp_y1 = fixedpt_tofloat(tmp_coords[0].y);

		float tmp_z1 = fixedpt_tofloat(tmp_coords[0].z);
@@ -551,7 +479,7 @@ while(active) { 
	printf("AFTER Out CONFORM CHANNEL\n");

	#endif



} // End of while(1)

} // End of while(active)



#if defined (DEBUG_ACTIVE_KERNEL)

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

ofdock_taskpar_alt/device/Krnl_GA.cl

+104 −119

File changed.

Preview size limit exceeded, changes collapsed.

ofdock_taskpar_alt/device/Krnl_IGL_Arbiter.cl

+26 −38
Original line number Diff line number Diff line 
// --------------------------------------------------------------------------

// IGL_Arbiter keeps checking whether any kernel (GA or any LSs) 

// is sending genotypes to Conform, as well as whether 

// GA sent the "turn-off" signal.

// Its name references the logic that is producing genotypes: 

// IC, GG and any LS.

// IC and GG are two logic blocks inside the GA kernel,

// while any LS logic is a kernel itself.



// It uses the valid signals to determine the "mode" value,

// used as a mux selector signal (of genotype logic-producers) in Conform.



// Initially genotypes passed through this kernel getting reordered and 

// synchronized with "mode".

// This has been later optimized, so now genotypes go directly 

// from producer logic/kernel (IC, GG, LSs) to the consumer (Conform) kernel.

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

__kernel __attribute__ ((max_global_work_dim(0)))

void Krnl_IGL_Arbiter(/*unsigned char DockConst_num_of_genes*/) {
@@ -71,12 +86,11 @@ while(active) { 
	active = Off_valid ? 0x00 : 0x01;

	char mode [9];	// mode for all LS



/*

	float genotypeICGG  [ACTUAL_GENOTYPE_LENGTH]; 

	float genotype   [3][ACTUAL_GENOTYPE_LENGTH];

*/



	// get genotype from IC, GG, LS1, LS2, LS3

	// Determine "mode" value

	// This considers all possible cases as all LS could be 

	// potentially producing genotypes simultaneously.

	// Be careful modifying the nested conditional-statements below,

	// as even a litle mistake may be undetectable in emulation.

	if (active == 0x01) {



		if (IC_valid == true) {
@@ -86,7 +100,7 @@ while(active) { 
			bound_tmp++;

		}	

		else{

			// Reorder the mode & genotype coming from LS

			// Reorder the mode & from LS



			// **************************************************************************************

			// LS1: yes
@@ -1292,39 +1306,14 @@ while(active) { 


	uchar bound = active ? bound_tmp : 1;



/*

	if ((LS1_end_valid || LS2_end_valid || LS3_end_valid)) {

		printf("bound_tmp: %-5u, LS1: %-5s, LS2: %-5s, LS3: %-5s\n", bound_tmp, LS1_end_valid?"yes":"no", LS2_end_valid?"yes":"no", LS3_end_valid?"yes":"no");

	}

*/



	// send data to Krnl_Conform

	// Send "mode" to Conform

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



		char mode_tmp = Off_valid? 0x00: IC_valid? 'I': GG_valid? 'G': mode[j];



//printf("IGL: %u\n", mode_tmp);



		char2 actmode = {active, mode_tmp};



		write_channel_altera(chan_IGL2Conform_actmode, actmode);

/*

		mem_fence(CLK_CHANNEL_MEM_FENCE);

*/



/*

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



			float gene_tmp = (IC_valid || GG_valid)? genotypeICGG[i]: genotype[j][i & MASK_GENOTYPE];



			if (i > 2) {

				gene_tmp = gene_tmp * DEG_TO_RAD;

			}



			write_channel_altera(chan_IGL2Conform_genotype, gene_tmp);

		}

*/

		#if defined (DEBUG_KRNL_CONF_ARBITER)

		#if defined (DEBUG_KRNL_IGL_ARBITER)

		printf("bound: %u, mode: %u\n", bound, mode_tmp);

		#endif

	}
@@ -1344,7 +1333,6 @@ while(active) { 
	}

	*/

	



} // End of while (active)



}

ofdock_taskpar_alt/device/Krnl_InterE.cl

+18 −52
Original line number Diff line number Diff line 
// --------------------------------------------------------------------------

// The function calculates the intermolecular energy of a ligand given by 

// myligand parameter, and a receptor represented as a grid. 

// The grid point values must be stored at the location which starts at GlobFgrids, 

// the memory content can be generated with get_gridvalues function.

// The mygrid parameter must be the corresponding grid informtaion. 

// If an atom is outside the grid, the coordinates will be changed with 

// the value of outofgrid_tolerance, 

// if it remains outside, a very high value will be added to the current energy as a penalty. 

// InterE calculates the intermolecular energy of a ligand given by 

// ligand xyz-positions, and a receptor represented as a grid. 

// The grid point values must be stored at the location which starts at GlobFgrids. 

// If an atom is remains outside the grid, 

// a very high value will be added to the current energy as a penalty. 

// Originally from: processligand.c

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

__kernel __attribute__ ((max_global_work_dim(0)))
@@ -47,9 +44,6 @@ void Krnl_InterE( 
*/

)

{

/*

	bool active = true;

*/	

	char active = 0x01;



	__global const float* GlobFgrids2 = & GlobFgrids [Host_mul_tmp2];
@@ -80,12 +74,6 @@ while(active) { 
	active = actmode.x;

	mode   = actmode.y;



/*

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

		loc_coords[pipe_cnt] = read_channel_altera(chan_Conf2Intere_xyz);

	}

*/



	for (uchar pipe_cnt=0; pipe_cnt<DockConst_num_of_atoms; pipe_cnt+=2) {

		float8 tmp = read_channel_altera(chan_Conf2Intere_xyz);

		float3 tmp1 = {tmp.s0, tmp.s1, tmp.s2};
@@ -94,7 +82,6 @@ while(active) { 
		loc_coords[pipe_cnt+1] = tmp2;

	}





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

	//printf("AFTER In INTER CHANNEL\n");
@@ -108,7 +95,7 @@ while(active) { 
	float interE = 0.0f;

	#endif



	// for each atom

	// For each ligand atom

	for (uchar atom1_id=0; atom1_id<DockConst_num_of_atoms; atom1_id++)

	{

		char atom1_typeid = KerConstStatic_atom_types_const [atom1_id];
@@ -143,7 +130,7 @@ while(active) { 
		float partialE3;

		#endif



		// if the atom is outside of the grid

		// If the atom is outside of the grid

		#if defined (FIXED_POINT_INTERE)

		if ((fixpt_x < 0) || (fixpt_x >= fixedpt64_fromint(DockConst_gridsize_x_minus1)) || 

		    (fixpt_y < 0) || (fixpt_y >= fixedpt64_fromint(DockConst_gridsize_y_minus1)) ||
@@ -154,7 +141,7 @@ while(active) { 
		    (z < 0.0f) || (z >= DockConst_gridsize_z_minus1))	{

		#endif



			//penalty is 2^24 for each atom outside the grid

			// Penalty is 2^24 for each atom outside the grid

			/*

			interE += 16777216.0f; 

			*/
@@ -235,7 +222,7 @@ while(active) { 
			printf("coeff(1,1,1) = %f\n", weights [1][1][1]);

			#endif



			// lvs added temporal variables

			// Added temporal variables

			uint cube_000, cube_100, cube_010, cube_110, cube_001, cube_101, cube_011, cube_111;



			uint ylow_times_g1  = y_low  * DockConst_g1;
@@ -254,7 +241,7 @@ while(active) { 


			uint mul_tmp = atom1_typeid * DockConst_g3;



			//energy contribution of the current grid type

			// Energy contribution of the current grid type

			#if defined (FIXED_POINT_INTERE)

			fixedpt64 fixpt_cube [2][2][2];

	                fixpt_cube [0][0][0] = fixedpt64_fromfloat(GlobFgrids[cube_000 + mul_tmp]);
@@ -314,7 +301,7 @@ while(active) { 
			printf("interpolated value = %f\n\n", TRILININTERPOL(cube, weights));

			#endif



			//energy contribution of the electrostatic grid

			// Energy contribution of the electrostatic grid

			/*

			#if defined(SEPARATE_FGRID_INTERE)

			#else
@@ -383,7 +370,7 @@ while(active) { 
			printf("interpolated value = %f, multiplied by q = %f\n\n", TRILININTERPOL(cube, weights), q*TRILININTERPOL(cube, weights));

			#endif



			//energy contribution of the desolvation grid

			// Energy contribution of the desolvation grid

			/*

			#if defined(SEPARATE_FGRID_INTERE)

			#else
@@ -471,42 +458,21 @@ while(active) { 
	#endif



	switch (mode) {

		// IC

		case 'I':  write_channel_altera(chan_Intere2StoreIC_intere, final_interE);     break;



		// GG

		case 'G':  write_channel_altera(chan_Intere2StoreGG_intere, final_interE);     break;



		// LS 1

		case 0x01: write_channel_altera(chan_Intere2StoreLS_LS1_intere, final_interE); break;



		// LS 2

		case 0x02: write_channel_altera(chan_Intere2StoreLS_LS2_intere, final_interE); break;



		// LS 3

		case 0x03: write_channel_altera(chan_Intere2StoreLS_LS3_intere, final_interE); break;



		// LS 4

		case 0x04: write_channel_altera(chan_Intere2StoreLS_LS4_intere, final_interE); break;



		// LS 5

		case 0x05: write_channel_altera(chan_Intere2StoreLS_LS5_intere, final_interE); break;



		// LS 6

		case 0x06: write_channel_altera(chan_Intere2StoreLS_LS6_intere, final_interE); break;



		// LS 7

		case 0x07: write_channel_altera(chan_Intere2StoreLS_LS7_intere, final_interE); break;



		// LS 8

		case 0x08: write_channel_altera(chan_Intere2StoreLS_LS8_intere, final_interE); break;



		// LS 9

		case 0x09: write_channel_altera(chan_Intere2StoreLS_LS9_intere, final_interE); break;

	}

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

 	

} // End of while(1)

} // End of while(active)



	#if defined (DEBUG_ACTIVE_KERNEL)

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