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Commit 3ee08f63 authored by Leonardo Solis's avatar Leonardo Solis
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#31, clean code based on SINGLE_COPY_POP_ENE=yes 


Former-commit-id: 647ff479
parent e0f6511a
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ofdock_taskpar_xl/Makefile
View file @ 3ee08f63
......@@ -91,23 +91,10 @@ FIPO_FLAG = $(FIPOCO_FLAG) \
$(FIPOLS9_FLAG)
# Other configs
SINGLE_COPY_POP_ENE=YES
SEPARATE_FGRID_INTERE=NO
ifeq ($(SINGLE_COPY_POP_ENE), YES)
COPYPOPENE_FLAG=-DSINGLE_COPY_POP_ENE
else
COPYPOPENE_FLAG=
endif
ifeq ($(SEPARATE_FGRID_INTERE), YES)
SEP_FGRID_FLAG=-DSEPARATE_FGRID_INTERE
else
SEP_FGRID_FLAG=
endif
# Overall custom configs
CONFIG_FLAG = $(FIPO_FLAG) $(COPYPOPENE_FLAG) $(SEP_FGRID_FLAG)
CONFIG_FLAG = $(FIPO_FLAG)
CXXFLAGS:=-Wall -O0 -g -std=c++14 $(OTHER_FLAGS)
......
ofdock_taskpar_xl/device/Krnl_GA.cl
View file @ 3ee08f63
......@@ -224,12 +224,8 @@ __kernel __attribute__ ((reqd_work_group_size(1,1,1)))
void Krnl_GA(
__global float* restrict GlobPopulationCurrent,
__global float* restrict GlobEnergyCurrent,
#if defined(SINGLE_COPY_POP_ENE)
__global unsigned int* restrict GlobEvals_performed,
__global unsigned int* restrict GlobGens_performed,
#else
__global unsigned int* restrict GlobEvalsGenerations_performed,
#endif
unsigned int DockConst_pop_size,
unsigned int DockConst_num_of_energy_evals,
unsigned int DockConst_num_of_generations,
......@@ -241,13 +237,10 @@ void Krnl_GA(
float Host_two_absmaxdang,
float DockConst_crossover_rate,
unsigned int DockConst_num_of_lsentities,
unsigned char DockConst_num_of_genes
#if defined(SINGLE_COPY_POP_ENE)
,
unsigned char DockConst_num_of_genes,
unsigned short Host_RunId,
unsigned int Host_Offset_Pop,
unsigned int Host_Offset_Ene
#endif
)
{
#if defined (DEBUG_KRNL_GA)
......@@ -271,10 +264,8 @@ void Krnl_GA(
__local float LocalPopCurr[MAX_POPSIZE][ACTUAL_GENOTYPE_LENGTH];
__local float LocalEneCurr[MAX_POPSIZE];
#if defined(SINGLE_COPY_POP_ENE)
__global float* GlobPopCurr = & GlobPopulationCurrent [Host_Offset_Pop];
__global float* GlobEneCurr = & GlobEnergyCurrent [Host_Offset_Ene];
#endif
// ------------------------------------------------------------------
// Initial Calculation (IC) of scores
......@@ -292,11 +283,7 @@ void Krnl_GA(
LOOP_FOR_GA_IC_INNER_WRITE_GENOTYPE:
for (uchar gene_cnt=0; gene_cnt<DockConst_num_of_genes; gene_cnt++) {
float tmp_ic;
#if defined(SINGLE_COPY_POP_ENE)
tmp_ic = GlobPopCurr[pop_cnt*ACTUAL_GENOTYPE_LENGTH + gene_cnt];
#else
tmp_ic = GlobPopulationCurrent[pop_cnt*ACTUAL_GENOTYPE_LENGTH + gene_cnt];
#endif
LocalPopCurr[pop_cnt][gene_cnt & MASK_GENOTYPE] = tmp_ic;
write_pipe_block(chan_IC2Conf_genotype, &tmp_ic);
......@@ -869,18 +856,10 @@ void Krnl_GA(
__attribute__((xcl_pipeline_loop))
LOOP_GA_WRITEPOP2DDR_INNER:
for (uchar gene_cnt=0; gene_cnt<DockConst_num_of_genes; gene_cnt++) {
#if defined(SINGLE_COPY_POP_ENE)
GlobPopCurr[pop_cnt*ACTUAL_GENOTYPE_LENGTH + gene_cnt] = LocalPopCurr[pop_cnt][gene_cnt & MASK_GENOTYPE];
#else
GlobPopulationCurrent[pop_cnt*ACTUAL_GENOTYPE_LENGTH + gene_cnt] = LocalPopCurr[pop_cnt][gene_cnt & MASK_GENOTYPE];
#endif
}
#if defined(SINGLE_COPY_POP_ENE)
GlobEneCurr[pop_cnt] = LocalEneCurr[pop_cnt];
#else
GlobEnergyCurrent[pop_cnt] = LocalEneCurr[pop_cnt];
#endif
}
#if defined (DEBUG_KRNL_GA)
......@@ -892,13 +871,8 @@ void Krnl_GA(
#endif
// Write final evals & generation counts to FPGA-board DDRs
#if defined(SINGLE_COPY_POP_ENE)
GlobEvals_performed[Host_RunId] = eval_cnt;
GlobGens_performed [Host_RunId] = generation_cnt;
#else
GlobEvalsGenerations_performed[0] = eval_cnt;
GlobEvalsGenerations_performed[1] = generation_cnt;
#endif
}
// --------------------------------------------------------------------------
......
ofdock_taskpar_xl/host/inc/calcenergy.h
View file @ 3ee08f63
......@@ -124,11 +124,7 @@ typedef struct
cl_float3 ref_coords_const[MAX_NUM_OF_ATOMS] __attribute__ ((aligned (2048)));
cl_float3 rotbonds_moving_vectors_const[MAX_NUM_OF_ROTBONDS] __attribute__ ((aligned (512)));
cl_float3 rotbonds_unit_vectors_const [MAX_NUM_OF_ROTBONDS] __attribute__ ((aligned (512)));
#if defined(SINGLE_COPY_POP_ENE)
cl_float4 ref_orientation_quats_const [MAX_NUM_OF_RUNS] __attribute__ ((aligned (512)));
#endif
} kernelconstant_static;
// As struct members are used as host buffers
......@@ -136,14 +132,6 @@ typedef struct
// This is added for the sake of completion
// cl_float3 is made of 4 floats, its size is 16 bytes
#if defined(SINGLE_COPY_POP_ENE)
#else
typedef struct
{
float ref_orientation_quats_const [4] __attribute__ ((aligned (64)));
} kernelconstant_dynamic;
#endif
/*
......@@ -153,20 +141,9 @@ int prepare_const_fields_for_gpu(Liganddata* myligand_reference,
kernelconstant* KerConst);
*/
int prepare_conststatic_fields_for_gpu(Liganddata* myligand_reference,
Dockpars* mypars,
#if defined(SINGLE_COPY_POP_ENE)
float* cpu_ref_ori_angles,
#endif
Dockpars* mypars,
float* cpu_ref_ori_angles,
kernelconstant_static* KerConstStatic);
#if defined(SINGLE_COPY_POP_ENE)
#else
int prepare_constdynamic_fields_for_gpu(Liganddata* myligand_reference,
Dockpars* mypars,
float* cpu_ref_ori_angles,
kernelconstant_dynamic* KerConstDynamic);
#endif
void make_reqrot_ordering(char number_of_req_rotations[MAX_NUM_OF_ATOMS],
char atom_id_of_numrots[MAX_NUM_OF_ATOMS],
......
ofdock_taskpar_xl/host/src/calcenergy.cpp
View file @ 3ee08f63
......@@ -232,20 +232,9 @@ int prepare_const_fields_for_gpu(Liganddata* myligand_reference,
}
*/
int prepare_conststatic_fields_for_gpu(Liganddata* myligand_reference,
Dockpars* mypars,
#if defined(SINGLE_COPY_POP_ENE)
float* cpu_ref_ori_angles,
#endif
Dockpars* mypars,
float* cpu_ref_ori_angles,
kernelconstant_static* KerConstStatic)
{
int i, j;
......@@ -441,9 +430,6 @@ int prepare_conststatic_fields_for_gpu(Liganddata* myligand_reference,
KerConstStatic->rotbonds_unit_vectors_const[i].z = myligand_reference->rotbonds_unit_vectors[i][2];
}
#if defined(SINGLE_COPY_POP_ENE)
float phi, theta, genrotangle;
//reference orientation quaternions
......@@ -465,167 +451,10 @@ int prepare_conststatic_fields_for_gpu(Liganddata* myligand_reference,
KerConstStatic->ref_orientation_quats_const[i].z = sinf(genrotangle/2.0f)*sinf(theta)*sinf(phi); //y
KerConstStatic->ref_orientation_quats_const[i].w = sinf(genrotangle/2.0f)*cosf(theta); //z
}
#endif
return 0;
}
#if defined(SINGLE_COPY_POP_ENE)
#else
int prepare_constdynamic_fields_for_gpu(Liganddata* myligand_reference,
Dockpars* mypars,
float* cpu_ref_ori_angles,
kernelconstant_dynamic* KerConstDynamic)
{
int i, j;
//int type_id1, type_id2;
//float* floatpoi;
//char* charpoi;
float phi, theta, genrotangle;
/*
// ------------------------------
cl_float3 ref_coords[MAX_NUM_OF_ATOMS];
cl_float3 rotbonds_moving_vectors[MAX_NUM_OF_ROTBONDS];
cl_float3 rotbonds_unit_vectors[MAX_NUM_OF_ROTBONDS];
float ref_orientation_quats[4];
// ------------------------------
*/
#if 0
//coordinates of reference ligand
for (i=0; i < myligand_reference->num_of_atoms; i++)
{
/*
ref_coords[i].x = myligand_reference->atom_idxyzq[i][1];
ref_coords[i].y = myligand_reference->atom_idxyzq[i][2];
ref_coords[i].z = myligand_reference->atom_idxyzq[i][3];
*/
KerConstDynamic->ref_coords_const[i].x = myligand_reference->atom_idxyzq[i][1];
KerConstDynamic->ref_coords_const[i].y = myligand_reference->atom_idxyzq[i][2];
KerConstDynamic->ref_coords_const[i].z = myligand_reference->atom_idxyzq[i][3];
}
//rotatable bond vectors
for (i=0; i < myligand_reference->num_of_rotbonds; i++) {
/*
rotbonds_moving_vectors[i].x = myligand_reference->rotbonds_moving_vectors[i][0];
rotbonds_moving_vectors[i].y = myligand_reference->rotbonds_moving_vectors[i][1];
rotbonds_moving_vectors[i].z = myligand_reference->rotbonds_moving_vectors[i][2];
rotbonds_unit_vectors[i].x = myligand_reference->rotbonds_unit_vectors[i][0];
rotbonds_unit_vectors[i].y = myligand_reference->rotbonds_unit_vectors[i][1];
rotbonds_unit_vectors[i].z = myligand_reference->rotbonds_unit_vectors[i][2];
*/
KerConstDynamic->rotbonds_moving_vectors_const[i].x = myligand_reference->rotbonds_moving_vectors[i][0];
KerConstDynamic->rotbonds_moving_vectors_const[i].y = myligand_reference->rotbonds_moving_vectors[i][1];
KerConstDynamic->rotbonds_moving_vectors_const[i].z = myligand_reference->rotbonds_moving_vectors[i][2];
KerConstDynamic->rotbonds_unit_vectors_const[i].x = myligand_reference->rotbonds_unit_vectors[i][0];
KerConstDynamic->rotbonds_unit_vectors_const[i].y = myligand_reference->rotbonds_unit_vectors[i][1];
KerConstDynamic->rotbonds_unit_vectors_const[i].z = myligand_reference->rotbonds_unit_vectors[i][2];
}
#endif
//reference orientation quaternions
// for (i=0; i<mypars->num_of_runs; i++)
// {
// //printf("Pregenerated angles for run %d: %f %f %f\n", i, cpu_ref_ori_angles[3*i], cpu_ref_ori_angles[3*i+1], cpu_ref_ori_angles[3*i+2]);
// phi = cpu_ref_ori_angles[3*i]*DEG_TO_RAD;
// theta = cpu_ref_ori_angles[3*i+1]*DEG_TO_RAD;
// genrotangle = cpu_ref_ori_angles[3*i+2]*DEG_TO_RAD;
// ref_orientation_quats[4*i] = cosf(genrotangle/2.0f); //q
// ref_orientation_quats[4*i+1] = sinf(genrotangle/2.0f)*sinf(theta)*cosf(phi); //x
// ref_orientation_quats[4*i+2] = sinf(genrotangle/2.0f)*sinf(theta)*sinf(phi); //y
// ref_orientation_quats[4*i+3] = sinf(genrotangle/2.0f)*cosf(theta); //z
// //printf("Precalculated quaternion for run %d: %f %f %f %f\n", i, ref_orientation_quats[4*i], ref_orientation_quats[4*i+1], ref_orientation_quats[4*i+2], ref_orientation_quats[4*i+3]);
// }
phi = cpu_ref_ori_angles[0]*DEG_TO_RAD;
theta = cpu_ref_ori_angles[1]*DEG_TO_RAD;
genrotangle = cpu_ref_ori_angles[2]*DEG_TO_RAD;
/*
ref_orientation_quats[0] = cosf(genrotangle/2.0f); //q
ref_orientation_quats[1] = sinf(genrotangle/2.0f)*sinf(theta)*cosf(phi); //x
ref_orientation_quats[2] = sinf(genrotangle/2.0f)*sinf(theta)*sinf(phi); //y
ref_orientation_quats[3] = sinf(genrotangle/2.0f)*cosf(theta); //z
*/
KerConstDynamic->ref_orientation_quats_const[0] = cosf(genrotangle/2.0f); //q
KerConstDynamic->ref_orientation_quats_const[1] = sinf(genrotangle/2.0f)*sinf(theta)*cosf(phi); //x
KerConstDynamic->ref_orientation_quats_const[2] = sinf(genrotangle/2.0f)*sinf(theta)*sinf(phi); //y
KerConstDynamic->ref_orientation_quats_const[3] = sinf(genrotangle/2.0f)*cosf(theta); //z
/*
int m;
for (m=0;m<MAX_NUM_OF_ATOMS;m++) { KerConstDynamic->ref_coords_const[m]= ref_coords[m]; }
for (m=0;m<MAX_NUM_OF_ROTBONDS;m++){ KerConstDynamic->rotbonds_moving_vectors_const[m]= rotbonds_moving_vectors[m]; }
for (m=0;m<MAX_NUM_OF_ROTBONDS;m++){ KerConstDynamic->rotbonds_unit_vectors_const[m] = rotbonds_unit_vectors[m]; }
for (m=0;m<4;m++) { KerConstDynamic->ref_orientation_quats_const[m] = ref_orientation_quats[m]; }
*/
return 0;
}
#endif
void make_reqrot_ordering(char number_of_req_rotations[MAX_NUM_OF_ATOMS],
char atom_id_of_numrots[MAX_NUM_OF_ATOMS],
int num_of_atoms)
......
ofdock_taskpar_xl/host/src/getparameters.cpp
View file @ 3ee08f63
......@@ -598,11 +598,7 @@ void gen_initpop_and_reflig(Dockpars* mypars,
//Generating initial population
if (gen_pop == 1)
{
#if defined(SINGLE_COPY_POP_ENE)
for (entity_id=0; entity_id<pop_size*mypars->num_of_runs; entity_id++)
#else
for (entity_id=0; entity_id<pop_size; entity_id++)
#endif
for (gene_id=0; gene_id<3; gene_id++)
#if defined (REPRO)
//init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = 30.1186;
......@@ -612,11 +608,7 @@ void gen_initpop_and_reflig(Dockpars* mypars,
init_populations[entity_id*ACTUAL_GENOTYPE_LENGTH+gene_id] = (float) myrand()*(mygrid->size_xyz_angstr[gene_id]);
#endif
#if defined(SINGLE_COPY_POP_ENE)
for (entity_id=0; entity_id<pop_size*mypars->num_of_runs; entity_id++)
#else
for (entity_id=0; entity_id<pop_size; entity_id++)
#endif
for (gene_id=3; gene_id<MAX_NUM_OF_ROTBONDS+6; gene_id++)
if (gene_id == 4)
#if defined (REPRO)
......@@ -668,12 +660,7 @@ void gen_initpop_and_reflig(Dockpars* mypars,
//genotypes should contain x, y and z genes in grid spacing instead of Angstroms
//(but was previously generated in Angstroms since fdock does the same)
#if defined(SINGLE_COPY_POP_ENE)
for (entity_id=0; entity_id<pop_size*mypars->num_of_runs; entity_id++)
#else
for (entity_id=0; entity_id<pop_size; entity_id++)
#endif
for (gene_id=0; gene_id<3; gene_id++)
//init_populations [entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = init_populations [entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id]/mygrid->spacing;
init_populations [entity_id*ACTUAL_GENOTYPE_LENGTH+gene_id] = init_populations [entity_id*ACTUAL_GENOTYPE_LENGTH+gene_id]/mygrid->spacing;
......@@ -699,7 +686,6 @@ void gen_initpop_and_reflig(Dockpars* mypars,
//initial orientation will be calculated during docking,
//only the required angles are generated here,
//but the angles possibly read from file are ignored
#if defined(SINGLE_COPY_POP_ENE)
for (int i=0; i<mypars->num_of_runs; i++)
{
#if defined (REPRO)
......@@ -712,17 +698,7 @@ void gen_initpop_and_reflig(Dockpars* mypars,
ref_ori_angles[3*i+2] = (float) (myrand()*360.0); //angle
#endif
}
#else
#if defined (REPRO)
ref_ori_angles[0] = 190.279;
ref_ori_angles[1] = 90.279;
ref_ori_angles[2] = 190.279;
#else
ref_ori_angles[0] = (float) (myrand()*360.0); //phi
ref_ori_angles[1] = (float) (myrand()*180.0); //theta
ref_ori_angles[2] = (float) (myrand()*360.0); //angle
#endif
#endif
get_movvec_to_origo(myligand, movvec_to_origo);
move_ligand(myligand, movvec_to_origo);
scale_ligand(myligand, 1.0/mygrid->spacing);
......
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