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Commit 0f21ae28 authored by Leonardo Solis's avatar Leonardo Solis
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removed unneeded kernels files 


Former-commit-id: 809fc997
parent be4dc487
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ofdock_taskpar_alt/device/Krnl_Conf_Arbiter.cl deleted 100644 → 0
View file @ be4dc487
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 deleted 100644 → 0
View file @ be4dc487
//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 deleted 100644 → 0
View file @ be4dc487
// --------------------------------------------------------------------------
// 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++) {