added 23_run_harp2 (2b7760ca) · Commits · docking / ocladock-fpga

ofdock_taskpar_alt/Makefile

+34 −1

Original line number	Diff line number	Diff line
		@@ -142,6 +142,7 @@ ENABLE_K2 = YES
		ENABLE_K3 = YES
		ENABLE_K4 = YES

		# Prng kernels
		ENABLE_K5 = YES
		ENABLE_K6 = YES
		ENABLE_K7 = YES
		@@ -150,6 +151,13 @@ ENABLE_K9 = YES
		ENABLE_K10 = YES
		ENABLE_K11 = YES

		# LS kernels
		ENABLE_K12 = YES
		ENABLE_K13 = YES

		#ENABLE_K14 = YES
		#ENABLE_K15 = YES

		ifeq ($(ENABLE_K1),YES)
		K1 =-DENABLE_KERNEL1
		else
		@@ -216,7 +224,32 @@ else
		K11 =
		endif

		ENABLE_KERNELS = $(K1) $(K2) $(K3) $(K4) $(K5) $(K6) $(K7) $(K8) $(K9) $(K10) $(K11)

		ifeq ($(ENABLE_K12),YES)
		K12 =-DENABLE_KERNEL12
		else
		K12 =
		endif

		ifeq ($(ENABLE_K13),YES)
		K13 =-DENABLE_KERNEL13
		else
		K13 =
		endif

		ifeq ($(ENABLE_K14),YES)
		K14 =-DENABLE_KERNEL14
		else
		K14 =
		endif

		ifeq ($(ENABLE_K15),YES)
		K15 =-DENABLE_KERNEL15
		else
		K15 =
		endif

		ENABLE_KERNELS = $(K1) $(K2) $(K3) $(K4) $(K5) $(K6) $(K7) $(K8) $(K9) $(K10) $(K11) $(K12) $(K13) $(K14) $(K15)

		# =============================
		# Reproduce result (remove randomness)

ofdock_taskpar_alt/device/Krnl_Conform.cl

+18 −24

Original line number	Diff line number	Diff line
		@@ -63,11 +63,7 @@ while(active) {
		bool GG_valid = false;
		bool LS_valid = false;
		bool Off_valid = false;
		/*
		bool IC_active;
		bool GG_active;
		bool LS_active;
		*/

		float IC_active;
		float GG_active;
		float LS_active;
		@@ -99,37 +95,23 @@ while(active) {
		}

		char mode;
		/*
		float genotype[ACTUAL_GENOTYPE_LENGTH];
		*/

		/*
		active = (IC_valid) ? IC_active :
		(GG_valid) ? GG_active :
		(LS_valid) ? LS_active :
		*/

		//printf("LS_valid: %u, LS2_valid: %u\n", LS_valid, LS2_valid);

		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


		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


		/*
		for (uchar pipe_cnt=0; pipe_cnt<DockConst_num_of_genes; pipe_cnt++) {
		genotype[pipe_cnt] = (IC_valid) ? read_channel_altera(chan_IC2Conf_genotype) :
		(GG_valid) ? read_channel_altera(chan_GG2Conf_genotype) :
		(LS_valid) ? read_channel_altera(chan_LS2Conf_genotype) :
		(Off_valid) ? 0.0f:
		0.0f; // last case should never occur, otherwise above while would be still running
		}
		*/
		// --------------------------------------------------------------
		//printf("AFTER In CONFORM CHANNEL\n");
		/*
		@@ -317,6 +299,13 @@ while(active) {
		printf("BEFORE Out CONFORM CHANNEL\n");
		#endif

		/*
		if (mode == 0x04) {
		printf("Krnl_Conform after loop\n");
		}
		*/


		// --------------------------------------------------------------
		// Send ligand atomic coordinates to channel
		// --------------------------------------------------------------
		@@ -333,6 +322,11 @@ while(active) {
		write_channel_altera(chan_Conf2Intere_xyz, loc_coords[pipe_cnt]);
		write_channel_altera(chan_Conf2Intrae_xyz, loc_coords[pipe_cnt]);
		}
		/*
		if (mode == 0x04) {
		printf("Krnl_Conform sent\n");
		}
		*/

		// --------------------------------------------------------------
		#if defined (DEBUG_KRNL_CONFORM)

ofdock_taskpar_alt/device/Krnl_GA.cl

+128 −214

Original line number	Diff line number	Diff line
		@@ -24,10 +24,21 @@
		channel float chan_IC2Conf_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));
		channel float chan_GG2Conf_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));
		channel float chan_LS2Conf_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));
		/*
		channel float chan_LS2Conf_LS2_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));
		channel float chan_LS2Conf_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));
		*/

		// To turn off Conform, InterE, IntraE
		/*
		channel bool chan_IC2Conf_active;
		channel bool chan_GG2Conf_active;
		channel bool chan_LS2Conf_LS1_active;
		channel bool chan_LS2Conf_LS2_active;
		*/
		channel bool chan_Off2Conf_active;


		channel float3 chan_Conf2Intere_xyz __attribute__((depth(MAX_NUM_OF_ATOMS)));
		channel bool chan_Conf2Intere_active;
		channel char chan_Conf2Intere_mode;
		@@ -39,10 +50,19 @@ channel char chan_Conf2Intrae_mode;
		channel float chan_Intere2StoreIC_intere __attribute__((depth(MAX_POPSIZE)));
		channel float chan_Intere2StoreGG_intere __attribute__((depth(MAX_POPSIZE)));
		channel float chan_Intere2StoreLS_intere __attribute__((depth(20))); // it requires 6% MAX_POPSIZE
		channel float chan_Intere2StoreLS_LS2_intere __attribute__((depth(20))); // it requires 6% MAX_POPSIZE
		/*
		channel float chan_Intere2StoreLS_LS3_intere __attribute__((depth(20))); // it requires 6% MAX_POPSIZE
		*/

		channel float chan_Intrae2StoreIC_intrae __attribute__((depth(MAX_POPSIZE)));
		channel float chan_Intrae2StoreGG_intrae __attribute__((depth(MAX_POPSIZE)));
		channel float chan_Intrae2StoreLS_intrae __attribute__((depth(20))); // it requires 6% MAX_POPSIZE
		channel float chan_Intrae2StoreLS_LS2_intrae __attribute__((depth(20))); // it requires 6% MAX_POPSIZE
		/*
		channel float chan_Intrae2StoreLS_LS3_intrae __attribute__((depth(20))); // it requires 6% MAX_POPSIZE
		*/


		// PRNG kernerls
		channel bool chan_GA2PRNG_BT_ushort_active;
		@@ -62,9 +82,44 @@ channel ushort chan_PRNG2GA_LS_ushort_prng;

		channel bool chan_GA2PRNG_LS_float_active;
		channel float chan_PRNG2GA_LS_float_prng;

		/*
		channel bool chan_GA2PRNG_LS2_float_active;
		channel float chan_PRNG2GA_LS2_float_prng;
		*/
		/*
		channel bool chan_GA2PRNG_LS23_float_active;
		channel float chan_PRNG2GA_LS3_float_prng;
		*/
		channel bool chan_GA2PRNG_Off_active;


		channel bool chan_GA2LS_LS1_active;
		channel float chan_GA2LS_LS1_energy;
		channel float chan_GA2LS_LS1_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));

		channel uint chan_LS2GA_LS1_eval;
		channel float chan_LS2GA_LS1_energy;
		channel float chan_LS2GA_LS1_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));

		channel bool chan_GA2LS_LS2_active;
		channel float chan_GA2LS_LS2_energy;
		channel float chan_GA2LS_LS2_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));

		channel uint chan_LS2GA_LS2_eval;
		channel float chan_LS2GA_LS2_energy;
		channel float chan_LS2GA_LS2_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));

		/*
		channel bool chan_GA2LS_LS3_active;
		channel float chan_GA2LS_LS3_energy;
		channel float chan_GA2LS_LS3_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));

		channel uint chan_LS2GA_LS3_eval;
		channel float chan_LS2GA_LS3_energy;
		channel float chan_LS2GA_LS3_genotype __attribute__((depth(MAX_NUM_OF_ROTBONDS+6)));
		*/
		channel bool chan_GA2LS_Off_active;

		// --------------------------------------------------------------------------
		// These functions map the argument into the interval 0 - 180, or 0 - 360
		// by adding/subtracting n*ang_max to/from it.
		@@ -110,12 +165,12 @@ void Krnl_GA(__global float* restrict GlobPopulationCurrent,
		float DockConst_abs_max_dang,
		float DockConst_crossover_rate,
		unsigned int DockConst_num_of_lsentities,
		unsigned int DockConst_max_num_of_iters,
		float DockConst_rho_lower_bound,
		float DockConst_base_dmov_mul_sqrt3,
		unsigned int DockConst_num_of_genes,
		float DockConst_base_dang_mul_sqrt3,
		unsigned int DockConst_cons_limit
		//unsigned int DockConst_max_num_of_iters,
		//float DockConst_rho_lower_bound,
		//float DockConst_base_dmov_mul_sqrt3,
		unsigned int DockConst_num_of_genes //,
		//float DockConst_base_dang_mul_sqrt3,
		//unsigned int DockConst_cons_limit
		)
		{
		//Print algorithm parameters
		@@ -188,9 +243,14 @@ void Krnl_GA(__global float* restrict GlobPopulationCurrent,
		// Binary tournament
		ushort parent1, parent2;

		/*
		__local float genotype_deviate [ACTUAL_GENOTYPE_LENGTH];
		__local float genotype_bias [ACTUAL_GENOTYPE_LENGTH];
		__local float entity_possible_new_genotype [ACTUAL_GENOTYPE_LENGTH];
		*/

		__local ushort entity_ls[20];


		__local float LocalPopNext[MAX_POPSIZE][ACTUAL_GENOTYPE_LENGTH];
		/*
		@@ -419,11 +479,16 @@ void Krnl_GA(__global float* restrict GlobPopulationCurrent,








		// choose all random entities
		// without checking if it has already been subjected to LS in this cycle
		write_channel_altera(chan_GA2PRNG_LS_ushort_active, true);
		mem_fence(CLK_CHANNEL_MEM_FENCE);
		for(uchar i=0; i<DockConst_num_of_lsentities; i++) {
		entity_ls [i] = read_channel_altera(chan_PRNG2GA_LS_ushort_prng);
		/*
		printf("LS entities idx: %u\n", entity_ls [i]);
		*/
		}


		// ------------------------------------------------------------------
		@@ -431,231 +496,75 @@ void Krnl_GA(__global float* restrict GlobPopulationCurrent,
		// ------------------------------------------------------------------
		tmp_eval_cnt = 0;


		// subject num_of_entity_for_ls pieces of offsprings to LS
		for (ushort ls_ent_cnt=0; ls_ent_cnt<DockConst_num_of_lsentities; ls_ent_cnt++) {

		//float genotype_bias [ACTUAL_GENOTYPE_LENGTH];
		for (ushort ls_ent_cnt=0; ls_ent_cnt<DockConst_num_of_lsentities; ls_ent_cnt++) {
		/*
		float __attribute__ ((
		memory,
		numbanks(1),
		bankwidth(64),
		singlepump,
		numreadports(2),
		numwriteports(1)
		)) genotype_bias [ACTUAL_GENOTYPE_LENGTH];
		for (ushort ls_ent_cnt=0; ls_ent_cnt<DockConst_num_of_lsentities; ls_ent_cnt+=2) {
		*/

		//float entity_possible_new_genotype [ACTUAL_GENOTYPE_LENGTH];

		//float genotype_deviate [ACTUAL_GENOTYPE_LENGTH];
		/*
		float __attribute__ ((
		memory,
		numbanks(1),
		bankwidth(64),
		singlepump,
		numreadports(1),
		numwriteports(1)
		)) genotype_deviate [ACTUAL_GENOTYPE_LENGTH];
		*/
		float rho = 1.0f;
		ushort iteration_cnt = 0;
		uchar cons_succ = 0;
		uchar cons_fail = 0;
		uint LS_eval = 0;
		bool positive_direction = true;

		// choose a random entity without checking if it has already been subjected to LS in this cycle
		write_channel_altera(chan_GA2PRNG_LS_ushort_active, true);
		mem_fence(CLK_CHANNEL_MEM_FENCE);
		ushort entity_for_ls = read_channel_altera(chan_PRNG2GA_LS_ushort_prng);

		//__local float offspring_genotype [ACTUAL_GENOTYPE_LENGTH];
		/*
		float __attribute__ ((
		memory,
		numbanks(1),
		bankwidth(64),
		singlepump,
		numreadports(2),
		numwriteports(1)
		)) offspring_genotype [ACTUAL_GENOTYPE_LENGTH];
		*/

		// performing local search
		while ((iteration_cnt < DockConst_max_num_of_iters) && (rho > DockConst_rho_lower_bound)) {
		// LS1

		write_channel_altera(chan_GA2LS_LS1_active, true);
		mem_fence(CLK_CHANNEL_MEM_FENCE);
		write_channel_altera(chan_GA2LS_LS1_energy, LocalEneNext[entity_ls[ls_ent_cnt]]);
		mem_fence(CLK_CHANNEL_MEM_FENCE);

		// -----------------------------------------------
		// Exit condition is groups here. It allows pipelining
		if (positive_direction == true) {
		if (cons_succ >= DockConst_cons_limit) {
		rho = LS_EXP_FACTOR*rho;
		cons_fail = 0;
		cons_succ = 0;
		}
		else {
		if (cons_fail >= DockConst_cons_limit) {
		rho = LS_CONT_FACTOR*rho;
		cons_fail = 0;
		cons_succ = 0;
		}
		}
		iteration_cnt++;
		for (uchar i=0; i<DockConst_num_of_genes; i++) {
		write_channel_altera(chan_GA2LS_LS1_genotype, LocalPopNext[entity_ls[ls_ent_cnt]][i & 0x3F]);
		}

		//printf("positive?: %u, iteration_cnt: %u, rho: %f, limit rho: %f\n", positive_direction, iteration_cnt, rho, DockConst_rho_lower_bound);
		// -----------------------------------------------
		/*
		float __attribute__ ((
		memory,
		numbanks(1),
		bankwidth(64),
		singlepump,
		numreadports(2),
		numwriteports(1)
		)) entity_possible_new_genotype [ACTUAL_GENOTYPE_LENGTH];
		*/

		// new random deviate
		// rho is the deviation of the uniform distribution
		for (uchar i=0; i<DockConst_num_of_genes; i++) {
		write_channel_altera(chan_GA2PRNG_LS_float_active, true);
		// LS2
		write_channel_altera(chan_GA2LS_LS2_active, true);
		mem_fence(CLK_CHANNEL_MEM_FENCE);
		float tmp_prng = read_channel_altera(chan_PRNG2GA_LS_float_prng);


		// tmp1 is genotype_deviate
		float tmp1 = rho * (2.0f*tmp_prng - 1.0f);
		write_channel_altera(chan_GA2LS_LS2_energy, LocalEneNext[entity_ls[ls_ent_cnt+1]]);
		mem_fence(CLK_CHANNEL_MEM_FENCE);

		if (i<3) {
		tmp1 = tmp1 * DockConst_base_dmov_mul_sqrt3;
		}
		else {
		tmp1 = tmp1 * DockConst_base_dang_mul_sqrt3;
		for (uchar i=0; i<DockConst_num_of_genes; i++) {
		write_channel_altera(chan_GA2LS_LS2_genotype, LocalPopNext[entity_ls[ls_ent_cnt+1]][i & 0x3F]);
		}

		/*
		genotype_deviate [i] = tmp1;
		*/
		genotype_deviate [i] = 0.4f*tmp1;


		// tmp2 is the addition: genotype_deviate + genotype_bias
		float tmp2 = tmp1 + ((iteration_cnt == 1)? 0.0f:genotype_bias[i]);

		// tmp3 is entity_possible_new_genotype
		float tmp3;
		tmp3 = (positive_direction == true)?
		(LocalPopNext[entity_for_ls][i & 0x3F] + tmp2):
		(LocalPopNext[entity_for_ls][i & 0x3F] - tmp2);

		if (i>3) {
		if (i==4) {
		tmp3 = map_angle_180(tmp3);
		}
		else {
		tmp3 = map_angle_360(tmp3);
		}
		}

		entity_possible_new_genotype [i] = tmp3;
		write_channel_altera(chan_LS2Conf_genotype, tmp3);
		}

		// calculate energy of genotype
		float energyIA_LS_rx = read_channel_altera(chan_Intrae2StoreLS_intrae);
		float energyIE_LS_rx = read_channel_altera(chan_Intere2StoreLS_intere);
		float candidate_energy = energyIA_LS_rx + energyIE_LS_rx;
		// LS1
		uint LS_eval = read_channel_altera(chan_LS2GA_LS1_eval);
		mem_fence(CLK_CHANNEL_MEM_FENCE);

		// update LS energy-evaluation count
		LS_eval++;
		LocalEneNext[entity_ls[ls_ent_cnt]] = read_channel_altera(chan_LS2GA_LS1_energy);
		mem_fence(CLK_CHANNEL_MEM_FENCE);

		#if 1
		for (uchar i=0; i<DockConst_num_of_genes; i++) {
		// updating offspring_genotype
		// updating genotype_bias
		float tmp;
		float a = ((iteration_cnt == 1)? 0.0f:genotype_bias[i]);
		/*
		float b = 0.4f*genotype_deviate[i];
		*/
		float b = genotype_deviate[i];

		if (candidate_energy < LocalEneNext[entity_for_ls]) {
		LocalPopNext[entity_for_ls][i & 0x3F] = entity_possible_new_genotype [i];
		float c = 0.6f*a;
		tmp = (positive_direction == true) ? (c + b): (c - b);
		}
		else {
		// updating (halving) genotype_bias
		tmp = 0.5f*a;
		}

		genotype_bias[i] = tmp;
		}


		// if the new entity is better
		if (candidate_energy < LocalEneNext[entity_for_ls])
		{
		LocalEneNext[entity_for_ls] = candidate_energy;
		cons_succ++;
		cons_fail = 0;
		positive_direction = true;
		}
		else {
		if (positive_direction == false) {
		cons_fail++;
		cons_succ = 0;
		LocalPopNext[entity_ls[ls_ent_cnt]][i & 0x3F] = read_channel_altera(chan_LS2GA_LS1_genotype);
		}
		positive_direction = !positive_direction;
		}
		#endif
		//printf("After LS1 comes back in GA: %u\n", ls_ent_cnt);

		/*
		// if the new entity is better
		if (candidate_energy < LocalEneNext[entity_for_ls])
		{
		#pragma unroll
		for (uchar i=0; i<ACTUAL_GENOTYPE_LENGTH; i++) {
		LocalPopNext[entity_for_ls][i & 0x3F] = entity_possible_new_genotype [i];
		float c = 0.6f*((iteration_cnt == 1)? 0.0f:genotype_bias[i]);
		float b = genotype_deviate[i];
		genotype_bias[i] = (positive_direction == true) ? (c + b): (c - b);
		}
		// LS2
		uint eval_tmp = read_channel_altera(chan_LS2GA_LS2_eval);
		LS_eval += eval_tmp;
		mem_fence(CLK_CHANNEL_MEM_FENCE);

		LocalEneNext[entity_for_ls] = candidate_energy;
		cons_succ++;
		cons_fail = 0;
		positive_direction = true;
		}
		else {
		#pragma unroll
		for (uchar i=0; i<ACTUAL_GENOTYPE_LENGTH; i++) {
		genotype_bias[i] = 0.5f*genotype_bias[i];
		}
		LocalEneNext[entity_ls[ls_ent_cnt+1]] = read_channel_altera(chan_LS2GA_LS2_energy);
		mem_fence(CLK_CHANNEL_MEM_FENCE);

		if (positive_direction == false) {
		cons_fail++;
		cons_succ = 0;
		}
		positive_direction = !positive_direction;
		for (uchar i=0; i<DockConst_num_of_genes; i++) {
		LocalPopNext[entity_ls[ls_ent_cnt+1]][i & 0x3F] = read_channel_altera(chan_LS2GA_LS2_genotype);
		}
		*/
		//printf("AFTER LS2 comes back in GA: %u\n", ls_ent_cnt);





		} // end of while (iteration_cnt)
		//------------------------------------------------------------------------------------------------------------

		tmp_eval_cnt += LS_eval;
		} // End of for-loop ls_ent_cnt
		// ------------------------------------------------------------------



		// update current pops & energies
		for (ushort pop_cnt=0;pop_cnt<DockConst_pop_size; pop_cnt++) {

		@@ -677,8 +586,12 @@ void Krnl_GA(__global float* restrict GlobPopulationCurrent,
		// ------------------------------------------------------------------
		// Off: turn off Conform, InterE, IntraE
		// ------------------------------------------------------------------
		write_channel_altera(chan_Off2Conf_active, false);
		write_channel_altera(chan_GA2LS_Off_active, false);
		write_channel_altera(chan_GA2PRNG_Off_active, false);
		write_channel_altera(chan_Off2Conf_active, false);



		//mem_fence(CLK_CHANNEL_MEM_FENCE);

		for (ushort pop_cnt=0;pop_cnt<DockConst_pop_size; pop_cnt++) {
		@@ -704,6 +617,7 @@ void Krnl_GA(__global float* restrict GlobPopulationCurrent,
		// --------------------------------------------------------------------------
		// --------------------------------------------------------------------------

		#include "Krnl_LS.cl"
		#include "Krnl_PRNG.cl"
		#include "Krnl_Conform.cl"
		#include "Krnl_InterE.cl"

ofdock_taskpar_alt/device/Krnl_InterE.cl

+8 −0

Original line number	Diff line number	Diff line
		@@ -276,7 +276,15 @@ while(active) {
		case 0x03: // LS
		write_channel_altera(chan_Intere2StoreLS_intere, interE);
		break;
		/*
		case 0x04: // LS 2
		write_channel_altera(chan_Intere2StoreLS_LS2_intere, interE);
		break;

		case 0x06: // LS 2
		write_channel_altera(chan_Intere2StoreLS_LS2_intere, interE);
		break;
		*/
		//case 5: // Off
		// write_channel_altera(chan_Intere2StoreOff_intere, interE);
		//break;

ofdock_taskpar_alt/device/Krnl_IntraE.cl

+9 −1

Original line number	Diff line number	Diff line
		@@ -164,10 +164,18 @@ while(active) {
		write_channel_altera(chan_Intrae2StoreGG_intrae, intraE);
		break;

		case 0x03: // LS
		case 0x03: // LS 1
		write_channel_altera(chan_Intrae2StoreLS_intrae, intraE);
		break;
		/*
		case 0x04: // LS 2
		write_channel_altera(chan_Intrae2StoreLS_LS2_intrae, intraE);
		break;

		case 0x06: // LS 3
		write_channel_altera(chan_Intrae2StoreLS_LS3_intrae, intraE);
		break;
		*/
		//case 5: // Off
		// write_channel_altera(chan_Intrae2StoreOff_intrae, intraE);
		//break;