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docking
ocladock-fpga
Commits
03e0ba14
Commit
03e0ba14
authored
Oct 30, 2018
by
Leonardo Solis
Browse files
#28, replaced krnl refs: from k3,k4 to krnl_intere, krnl_intrae
parent
2d758e37
Changes
2
Hide whitespace changes
Inline
Side-by-side
common_xilinx/utility/boards.mk
View file @
03e0ba14
...
...
@@ -22,8 +22,8 @@ CXXFLAGS:=-Wall -O0 -g -std=c++14 $(OTHER_FLAGS)
# =============================
ENABLE_KRNL_GA
=
YES
ENABLE_KRNL_CONFORM
=
YES
ENABLE_K
3
=
YES
ENABLE_K
4
=
YES
ENABLE_K
RNL_INTERE
=
YES
ENABLE_K
RNL_INTRAE
=
YES
# Prng kernels
ENABLE_K6
=
YES
...
...
@@ -88,16 +88,16 @@ else
KRNL_CONFORM
=
endif
ifeq
($(ENABLE_K
3
),YES)
K
3
=
-DENABLE_K
E
RN
EL3
ifeq
($(ENABLE_K
RNL_INTERE
),YES)
K
RNL_INTERE
=
-DENABLE_KRN
L_INTERE
else
K
3
=
K
RNL_INTERE
=
endif
ifeq
($(ENABLE_K
4
),YES)
K
4
=
-DENABLE_K
E
RN
EL4
ifeq
($(ENABLE_K
RNL_INTRAE
),YES)
K
RNL_INTRAE
=
-DENABLE_KRN
L_INTRAE
else
K
4
=
K
RNL_INTRAE
=
endif
ifeq
($(ENABLE_K6),YES)
...
...
@@ -249,7 +249,9 @@ else
endif
ENABLE_KERNELS
=
$(KRNL_GA)
\
$(KRNL_CONFORM)
\
$(K3)
$(K4)
$(K6)
$(K7)
$(K10)
\
$(KRNL_INTERE)
\
$(KRNL_INTRAE)
\
$(K6)
$(K7)
$(K10)
\
$(K12)
$(K14)
$(K15)
$(K20)
\
$(K21)
$(K27)
\
$(K35)
$(K36)
$(K37)
$(K38)
$(K39)
$(K40)
\
...
...
ofdock_taskpar_xl/host/src/performdocking.cpp
View file @
03e0ba14
...
...
@@ -53,16 +53,16 @@ static cl_kernel kernel_conform = NULL;
static
const
char
*
name_krnl_conform
=
"Krnl_Conform"
;
#endif
#ifdef ENABLE_K
E
RN
EL3
static
cl_command_queue
command_queue
3
=
NULL
;
static
cl_kernel
kernel
3
=
NULL
;
static
const
char
*
name_k
3
=
"Krnl_InterE"
;
#ifdef ENABLE_KRN
L_INTERE
static
cl_command_queue
command_queue
_intere
=
NULL
;
static
cl_kernel
kernel
_intere
=
NULL
;
static
const
char
*
name_k
rnl_intere
=
"Krnl_InterE"
;
#endif
#ifdef ENABLE_K
E
RN
EL4
static
cl_command_queue
command_queue
4
=
NULL
;
static
cl_kernel
kernel
4
=
NULL
;
static
const
char
*
name_k
4
=
"Krnl_IntraE"
;
#ifdef ENABLE_KRN
L_INTRAE
static
cl_command_queue
command_queue
_intrae
=
NULL
;
static
cl_kernel
kernel
_intrae
=
NULL
;
static
const
char
*
name_k
rnl_intrae
=
"Krnl_IntraE"
;
#endif
#ifdef ENABLE_KERNEL10
...
...
@@ -926,66 +926,66 @@ printf("%i %i\n", dockpars.num_of_intraE_contributors, myligand_reference.num_of
#endif
#ifdef ENABLE_K
E
RN
EL3
// Krnl_InterE
setKernelArg
(
kernel
3
,
0
,
sizeof
(
mem_dockpars_fgrids
),
&
mem_dockpars_fgrids
);
#ifdef ENABLE_KRN
L_INTERE
// Krnl_InterE
setKernelArg
(
kernel
_intere
,
0
,
sizeof
(
mem_dockpars_fgrids
),
&
mem_dockpars_fgrids
);
#if defined (FIXED_POINT_INTERE)
setKernelArg
(
kernel
3
,
1
,
sizeof
(
mem_KerConstStatic_fixpt64_atom_charges_const
),
&
mem_KerConstStatic_fixpt64_atom_charges_const
);
setKernelArg
(
kernel
_intere
,
1
,
sizeof
(
mem_KerConstStatic_fixpt64_atom_charges_const
),
&
mem_KerConstStatic_fixpt64_atom_charges_const
);
#else
setKernelArg
(
kernel
3
,
1
,
sizeof
(
mem_KerConstStatic_InterE_atom_charges_const
),
&
mem_KerConstStatic_InterE_atom_charges_const
);
setKernelArg
(
kernel
_intere
,
1
,
sizeof
(
mem_KerConstStatic_InterE_atom_charges_const
),
&
mem_KerConstStatic_InterE_atom_charges_const
);
#endif
setKernelArg
(
kernel
3
,
2
,
sizeof
(
mem_KerConstStatic_InterE_atom_types_const
),
&
mem_KerConstStatic_InterE_atom_types_const
);
setKernelArg
(
kernel
3
,
3
,
sizeof
(
unsigned
char
),
&
dockpars
.
g1
);
setKernelArg
(
kernel
3
,
4
,
sizeof
(
unsigned
int
),
&
dockpars
.
g2
);
setKernelArg
(
kernel
3
,
5
,
sizeof
(
unsigned
int
),
&
dockpars
.
g3
);
setKernelArg
(
kernel
3
,
6
,
sizeof
(
unsigned
char
),
&
dockpars
.
num_of_atoms
);
setKernelArg
(
kernel
_intere
,
2
,
sizeof
(
mem_KerConstStatic_InterE_atom_types_const
),
&
mem_KerConstStatic_InterE_atom_types_const
);
setKernelArg
(
kernel
_intere
,
3
,
sizeof
(
unsigned
char
),
&
dockpars
.
g1
);
setKernelArg
(
kernel
_intere
,
4
,
sizeof
(
unsigned
int
),
&
dockpars
.
g2
);
setKernelArg
(
kernel
_intere
,
5
,
sizeof
(
unsigned
int
),
&
dockpars
.
g3
);
setKernelArg
(
kernel
_intere
,
6
,
sizeof
(
unsigned
char
),
&
dockpars
.
num_of_atoms
);
#if defined (FIXED_POINT_INTERE)
setKernelArg
(
kernel
3
,
7
,
sizeof
(
unsigned
char
),
&
gridsizex_minus1
);
setKernelArg
(
kernel
3
,
8
,
sizeof
(
unsigned
char
),
&
gridsizey_minus1
);
setKernelArg
(
kernel
3
,
9
,
sizeof
(
unsigned
char
),
&
gridsizez_minus1
);
setKernelArg
(
kernel
_intere
,
7
,
sizeof
(
unsigned
char
),
&
gridsizex_minus1
);
setKernelArg
(
kernel
_intere
,
8
,
sizeof
(
unsigned
char
),
&
gridsizey_minus1
);
setKernelArg
(
kernel
_intere
,
9
,
sizeof
(
unsigned
char
),
&
gridsizez_minus1
);
#else
setKernelArg
(
kernel
3
,
7
,
sizeof
(
float
),
&
fgridsizex_minus1
);
setKernelArg
(
kernel
3
,
8
,
sizeof
(
float
),
&
fgridsizey_minus1
);
setKernelArg
(
kernel
3
,
9
,
sizeof
(
float
),
&
fgridsizez_minus1
);
setKernelArg
(
kernel
_intere
,
7
,
sizeof
(
float
),
&
fgridsizex_minus1
);
setKernelArg
(
kernel
_intere
,
8
,
sizeof
(
float
),
&
fgridsizey_minus1
);
setKernelArg
(
kernel
_intere
,
9
,
sizeof
(
float
),
&
fgridsizez_minus1
);
#endif
#if defined(SEPARATE_FGRID_INTERE)
setKernelArg
(
kernel
3
,
10
,
sizeof
(
mem_dockpars_fgrids2
),
&
mem_dockpars_fgrids2
);
setKernelArg
(
kernel
3
,
11
,
sizeof
(
mem_dockpars_fgrids3
),
&
mem_dockpars_fgrids3
);
setKernelArg
(
kernel
_intere
,
10
,
sizeof
(
mem_dockpars_fgrids2
),
&
mem_dockpars_fgrids2
);
setKernelArg
(
kernel
_intere
,
11
,
sizeof
(
mem_dockpars_fgrids3
),
&
mem_dockpars_fgrids3
);
#else
setKernelArg
(
kernel
3
,
10
,
sizeof
(
unsigned
int
),
&
mul_tmp2
);
setKernelArg
(
kernel
3
,
11
,
sizeof
(
unsigned
int
),
&
mul_tmp3
);
setKernelArg
(
kernel
_intere
,
10
,
sizeof
(
unsigned
int
),
&
mul_tmp2
);
setKernelArg
(
kernel
_intere
,
11
,
sizeof
(
unsigned
int
),
&
mul_tmp3
);
#endif
#endif // End of ENABLE_K
E
RN
EL3
#ifdef ENABLE_K
E
RN
EL4
// Krnl_IntraE
setKernelArg
(
kernel
4
,
0
,
sizeof
(
mem_KerConstStatic_IntraE_atom_charges_const
),
&
mem_KerConstStatic_IntraE_atom_charges_const
);
setKernelArg
(
kernel
4
,
1
,
sizeof
(
mem_KerConstStatic_IntraE_atom_types_const
),
&
mem_KerConstStatic_IntraE_atom_types_const
);
setKernelArg
(
kernel
4
,
2
,
sizeof
(
mem_KerConstStatic_intraE_contributors_const
),
&
mem_KerConstStatic_intraE_contributors_const
);
setKernelArg
(
kernel
4
,
3
,
sizeof
(
dockpars
.
smooth
),
&
dockpars
.
smooth
);
setKernelArg
(
kernel
4
,
4
,
sizeof
(
mem_KerConstStatic_reqm_const
),
&
mem_KerConstStatic_reqm_const
);
setKernelArg
(
kernel
4
,
5
,
sizeof
(
mem_KerConstStatic_reqm_hbond_const
),
&
mem_KerConstStatic_reqm_hbond_const
);
setKernelArg
(
kernel
4
,
6
,
sizeof
(
mem_KerConstStatic_atom1_types_reqm_const
),
&
mem_KerConstStatic_atom1_types_reqm_const
);
setKernelArg
(
kernel
4
,
7
,
sizeof
(
mem_KerConstStatic_atom2_types_reqm_const
),
&
mem_KerConstStatic_atom2_types_reqm_const
);
setKernelArg
(
kernel
4
,
8
,
sizeof
(
mem_KerConstStatic_VWpars_AC_const
),
&
mem_KerConstStatic_VWpars_AC_const
);
setKernelArg
(
kernel
4
,
9
,
sizeof
(
mem_KerConstStatic_VWpars_BD_const
),
&
mem_KerConstStatic_VWpars_BD_const
);
setKernelArg
(
kernel
4
,
10
,
sizeof
(
mem_KerConstStatic_dspars_S_const
),
&
mem_KerConstStatic_dspars_S_const
);
setKernelArg
(
kernel
4
,
11
,
sizeof
(
mem_KerConstStatic_dspars_V_const
),
&
mem_KerConstStatic_dspars_V_const
);
setKernelArg
(
kernel
4
,
12
,
sizeof
(
unsigned
char
),
&
dockpars
.
num_of_atoms
);
setKernelArg
(
kernel
4
,
13
,
sizeof
(
unsigned
int
),
&
dockpars
.
num_of_intraE_contributors
);
setKernelArg
(
kernel
4
,
14
,
sizeof
(
float
),
&
dockpars
.
grid_spacing
);
setKernelArg
(
kernel
4
,
15
,
sizeof
(
unsigned
char
),
&
dockpars
.
num_of_atypes
);
setKernelArg
(
kernel
4
,
16
,
sizeof
(
float
),
&
dockpars
.
coeff_elec
);
setKernelArg
(
kernel
4
,
17
,
sizeof
(
float
),
&
dockpars
.
qasp
);
setKernelArg
(
kernel
4
,
18
,
sizeof
(
float
),
&
dockpars
.
coeff_desolv
);
#endif // End of ENABLE_KRN
L_INTERE
#ifdef ENABLE_KRN
L_INTRAE
// Krnl_IntraE
setKernelArg
(
kernel
_intrae
,
0
,
sizeof
(
mem_KerConstStatic_IntraE_atom_charges_const
),
&
mem_KerConstStatic_IntraE_atom_charges_const
);
setKernelArg
(
kernel
_intrae
,
1
,
sizeof
(
mem_KerConstStatic_IntraE_atom_types_const
),
&
mem_KerConstStatic_IntraE_atom_types_const
);
setKernelArg
(
kernel
_intrae
,
2
,
sizeof
(
mem_KerConstStatic_intraE_contributors_const
),
&
mem_KerConstStatic_intraE_contributors_const
);
setKernelArg
(
kernel
_intrae
,
3
,
sizeof
(
dockpars
.
smooth
),
&
dockpars
.
smooth
);
setKernelArg
(
kernel
_intrae
,
4
,
sizeof
(
mem_KerConstStatic_reqm_const
),
&
mem_KerConstStatic_reqm_const
);
setKernelArg
(
kernel
_intrae
,
5
,
sizeof
(
mem_KerConstStatic_reqm_hbond_const
),
&
mem_KerConstStatic_reqm_hbond_const
);
setKernelArg
(
kernel
_intrae
,
6
,
sizeof
(
mem_KerConstStatic_atom1_types_reqm_const
),
&
mem_KerConstStatic_atom1_types_reqm_const
);
setKernelArg
(
kernel
_intrae
,
7
,
sizeof
(
mem_KerConstStatic_atom2_types_reqm_const
),
&
mem_KerConstStatic_atom2_types_reqm_const
);
setKernelArg
(
kernel
_intrae
,
8
,
sizeof
(
mem_KerConstStatic_VWpars_AC_const
),
&
mem_KerConstStatic_VWpars_AC_const
);
setKernelArg
(
kernel
_intrae
,
9
,
sizeof
(
mem_KerConstStatic_VWpars_BD_const
),
&
mem_KerConstStatic_VWpars_BD_const
);
setKernelArg
(
kernel
_intrae
,
10
,
sizeof
(
mem_KerConstStatic_dspars_S_const
),
&
mem_KerConstStatic_dspars_S_const
);
setKernelArg
(
kernel
_intrae
,
11
,
sizeof
(
mem_KerConstStatic_dspars_V_const
),
&
mem_KerConstStatic_dspars_V_const
);
setKernelArg
(
kernel
_intrae
,
12
,
sizeof
(
unsigned
char
),
&
dockpars
.
num_of_atoms
);
setKernelArg
(
kernel
_intrae
,
13
,
sizeof
(
unsigned
int
),
&
dockpars
.
num_of_intraE_contributors
);
setKernelArg
(
kernel
_intrae
,
14
,
sizeof
(
float
),
&
dockpars
.
grid_spacing
);
setKernelArg
(
kernel
_intrae
,
15
,
sizeof
(
unsigned
char
),
&
dockpars
.
num_of_atypes
);
setKernelArg
(
kernel
_intrae
,
16
,
sizeof
(
float
),
&
dockpars
.
coeff_elec
);
setKernelArg
(
kernel
_intrae
,
17
,
sizeof
(
float
),
&
dockpars
.
qasp
);
setKernelArg
(
kernel
_intrae
,
18
,
sizeof
(
float
),
&
dockpars
.
coeff_desolv
);
/*
setKernelArg(kernel
4
,14, sizeof(unsigned int), &square_num_of_atypes);
setKernelArg(kernel
_intrae
,14, sizeof(unsigned int), &square_num_of_atypes);
*/
#endif // End of ENABLE_K
E
RN
EL4
#endif // End of ENABLE_KRN
L_INTRAE
#ifdef ENABLE_KERNEL6 // Krnl_PRNG_GG_float
setKernelArg
(
kernel6
,
1
,
sizeof
(
unsigned
char
),
&
dockpars
.
num_of_genes
);
...
...
@@ -1474,13 +1474,13 @@ unsigned char Host_cons_limit = (unsigned char) dockpars.cons_limit;
runKernelTask
(
command_queue_conform
,
kernel_conform
,
NULL
,
NULL
);
#endif // ENABLE_KRNL_CONFORM
#ifdef ENABLE_K
E
RN
EL3
runKernelTask
(
command_queue
3
,
kernel3
,
NULL
,
NULL
);
#endif // ENABLE_K
E
RN
EL3
#ifdef ENABLE_KRN
L_INTERE
runKernelTask
(
command_queue
_intere
,
kernel_intere
,
NULL
,
NULL
);
#endif // ENABLE_KRN
L_INTERE
#ifdef ENABLE_K
E
RN
EL4
runKernelTask
(
command_queue
4
,
kernel4
,
NULL
,
NULL
);
#endif // ENABLE_K
E
RN
EL4
#ifdef ENABLE_KRN
L_INTRAE
runKernelTask
(
command_queue
_intrae
,
kernel_intrae
,
NULL
,
NULL
);
#endif // ENABLE_KRN
L_INTRAE
#ifdef ENABLE_KERNEL6
runKernelTask
(
command_queue6
,
kernel6
,
NULL
,
NULL
);
...
...
@@ -1587,12 +1587,12 @@ unsigned char Host_cons_limit = (unsigned char) dockpars.cons_limit;
clFinish
(
command_queue_conform
);
#endif
#ifdef ENABLE_K
E
RN
EL3
clFinish
(
command_queue
3
);
#ifdef ENABLE_KRN
L_INTERE
clFinish
(
command_queue
_intere
);
#endif
#ifdef ENABLE_K
E
RN
EL4
clFinish
(
command_queue
4
);
#ifdef ENABLE_KRN
L_INTRAE
clFinish
(
command_queue
_intrae
);
#endif
#ifdef ENABLE_KERNEL6
...
...
@@ -1982,18 +1982,18 @@ bool init() {
checkError
(
status
,
"Failed to create kernel conform"
);
#endif
#ifdef ENABLE_K
E
RN
EL3
command_queue
3
=
clCreateCommandQueue
(
context
,
device
,
0
,
&
status
);
checkError
(
status
,
"Failed to create command queue
3
"
);
kernel
3
=
clCreateKernel
(
program
,
name_k
3
,
&
status
);
checkError
(
status
,
"Failed to create kernel"
);
#ifdef ENABLE_KRN
L_INTERE
command_queue
_intere
=
clCreateCommandQueue
(
context
,
device
,
0
,
&
status
);
checkError
(
status
,
"Failed to create command queue
intere
"
);
kernel
_intere
=
clCreateKernel
(
program
,
name_k
rnl_intere
,
&
status
);
checkError
(
status
,
"Failed to create kernel
intere
"
);
#endif
#ifdef ENABLE_K
E
RN
EL4
command_queue
4
=
clCreateCommandQueue
(
context
,
device
,
0
,
&
status
);
checkError
(
status
,
"Failed to create command queue
4
"
);
kernel
4
=
clCreateKernel
(
program
,
name_k
4
,
&
status
);
checkError
(
status
,
"Failed to create kernel"
);
#ifdef ENABLE_KRN
L_INTRAE
command_queue
_intrae
=
clCreateCommandQueue
(
context
,
device
,
0
,
&
status
);
checkError
(
status
,
"Failed to create command queue
intrae
"
);
kernel
_intrae
=
clCreateKernel
(
program
,
name_k
rnl_intrae
,
&
status
);
checkError
(
status
,
"Failed to create kernel
intrae
"
);
#endif
#ifdef ENABLE_KERNEL6
...
...
@@ -2172,14 +2172,14 @@ void cleanup() {
if
(
command_queue_conform
)
{
clReleaseCommandQueue
(
command_queue_conform
);}
#endif
#ifdef ENABLE_K
E
RN
EL3
if
(
kernel
3
)
{
clReleaseKernel
(
kernel
3
);}
if
(
command_queue
3
)
{
clReleaseCommandQueue
(
command_queue
3
);}
#ifdef ENABLE_KRN
L_INTERE
if
(
kernel
_intere
)
{
clReleaseKernel
(
kernel
_intere
);}
if
(
command_queue
_intere
)
{
clReleaseCommandQueue
(
command_queue
_intere
);}
#endif
#ifdef ENABLE_K
E
RN
EL4
if
(
kernel
4
)
{
clReleaseKernel
(
kernel
4
);}
if
(
command_queue
4
)
{
clReleaseCommandQueue
(
command_queue
4
);}
#ifdef ENABLE_KRN
L_INTRAE
if
(
kernel
_intrae
)
{
clReleaseKernel
(
kernel
_intrae
);}
if
(
command_queue
_intrae
)
{
clReleaseCommandQueue
(
command_queue
_intrae
);}
#endif
#ifdef ENABLE_KERNEL6
...
...
Leonardo Solis
@solis
mentioned in commit
f1098976
·
Jan 04, 2021
mentioned in commit
f1098976
mentioned in commit f1098976aaa5b4611c01c685d2e5de3948a95f9e
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