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CUDAVolMapCreateILS.cu File Reference

CUDA kernels for calculating implicit ligand sampling occupancy maps. More...

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <cuda.h>
#include "WKFThreads.h"
#include "WKFUtils.h"
#include "CUDAKernels.h"
#include "utilities.h"

Go to the source code of this file.


Compounds

union flint_t
struct occthrparms_t

Defines

#define CUERR
#define USE_ENERGY_EXCL
#define TEST_MBLOCK_EXCL
#define TEST_SHIFT_EXCL
#define MAX_THREADBLOCKS 65536
#define BIN_DEPTH 8
#define BIN_SLOTSIZE 4
#define BIN_SIZE (BIN_DEPTH * BIN_SLOTSIZE)
#define BIN_SHIFT 5
#define BIN_SLOTSHIFT 2
#define MAX_VDWPARMS 160
#define MAX_PROBES 8
#define MAX_EXTRAS 50
#define MAX_BINOFFSETS 1467
#define MAX_EXCLOFFSETS 27
#define MAX_CONFORMERS 586
#define DO_ONE_PLANE
#define THBLEN 4
#define NTHREADSPERBLOCK (THBLEN*THBLEN*THBLEN)
#define BSHIFT 2
#define NTPBSHIFT 6
#define NCONFPERLOOP 5
#define NTPB_TIMES_NCPL (NTHREADSPERBLOCK * NCONFPERLOOP)
#define PADMASK (THBLEN-1)
#define MAX_ALLOWABLE_ENERGY 87.f
#define TIME_PER_MONOATOM_WORKUNIT 1.24553913519431e-10
#define TIME_PER_MULTIATOM_WORKUNIT 5.24559386973180e-09
#define MAX_TIME_PER_KERNEL 1.f
#define DEFAULT_EXCL_DIST 1.f

Typedefs

typedef flint_t flint
typedef occthrparms_t occthrparms

Functions

__global__ void cuda_find_energy_exclusions (int *excl, const flint *bin_zero, int nbx, int nby, int mzblocks, int mzblockoffset)
__global__ void cuda_occupancy_monoatom (float *map, const int *excl, const flint *bin_zero, int nbx, int nby, int mzblocks, int mzblockoffset)
__global__ void cuda_occupancy_multiatom (float *map, const int *excl, const flint *bin_zero, int nbx, int nby, int mzblocks, int mzblockoffset)
void * cuda_occupancy_thread (void *voidparms)
int vmd_cuda_evaluate_occupancy_map (int mx, int my, int mz, float *map, float max_energy, float cutoff, float hx, float hy, float hz, float x0, float y0, float z0, float bx_1, float by_1, float bz_1, int nbx, int nby, int nbz, const float *bin, const float *bin_zero, int num_binoffsets, const char *binoffsets, int num_extras, const float *extra, int num_vdwparms, const float *vdwparms, int num_probes, const float *probevdwparms, int num_conformers, const float *conformers)

Variables

__constant__ float const_max_energy
__constant__ float const_min_occupancy
__constant__ float const_cutoff
__constant__ float const_min_excldist
__constant__ float const_hx
__constant__ float const_hy
__constant__ float const_hz
__constant__ float const_x0
__constant__ float const_y0
__constant__ float const_z0
__constant__ float const_bx_1
__constant__ float const_by_1
__constant__ float const_bz_1
__constant__ float const_inv_numconf
__constant__ int const_num_binoffsets
__constant__ int const_num_extras
__constant__ int const_num_probes
__constant__ int const_num_conformers
__constant__ float const_vdwparms [2 *MAX_VDWPARMS]
__constant__ float const_probevdwparms [2 *MAX_PROBES]
__constant__ flint const_extra [BIN_SLOTSIZE *MAX_EXTRAS]
__constant__ int const_binoffsets [MAX_BINOFFSETS]
__constant__ int const_excloffsets [MAX_EXCLOFFSETS]
__constant__ float const_conformers [3 *MAX_PROBES *MAX_CONFORMERS]

Detailed Description

CUDA kernels for calculating implicit ligand sampling occupancy maps.

Definition in file CUDAVolMapCreateILS.cu.

Define Documentation

#define BIN_DEPTH 8

Definition at line 86 of file CUDAVolMapCreateILS.cu.

#define BIN_SHIFT 5

Definition at line 89 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, and cuda_occupancy_multiatom.

#define BIN_SIZE (BIN_DEPTH * BIN_SLOTSIZE)

Definition at line 88 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

#define BIN_SLOTSHIFT 2

Definition at line 90 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, and cuda_occupancy_multiatom.

#define BIN_SLOTSIZE 4

Definition at line 87 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

#define BSHIFT 2

Definition at line 182 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

#define CUERR

Value:

do { \
 cudaError_t err; \
 if ((err = cudaGetLastError()) != cudaSuccess) { \
 printf("CUDA error: %s, %s line %d\n", cudaGetErrorString(err), __FILE__, __LINE__); \
 printf("Thread aborting...\n"); \
 return NULL; \
 } \
 } while (0)

Definition at line 38 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_thread.

#define DEFAULT_EXCL_DIST 1.f

#define DO_ONE_PLANE

Definition at line 176 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, and cuda_occupancy_multiatom.

#define MAX_ALLOWABLE_ENERGY 87.f

Definition at line 199 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_multiatom.

#define MAX_BINOFFSETS 1467

Definition at line 160 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_thread.

#define MAX_CONFORMERS 586

Definition at line 172 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_thread.

#define MAX_EXCLOFFSETS 27

Definition at line 164 of file CUDAVolMapCreateILS.cu.

#define MAX_EXTRAS 50

Definition at line 156 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_thread.

#define MAX_PROBES 8

Definition at line 153 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_multiatom, and cuda_occupancy_thread.

#define MAX_THREADBLOCKS 65536

Definition at line 84 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_thread.

#define MAX_TIME_PER_KERNEL 1.f

#define MAX_VDWPARMS 160

Definition at line 150 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_thread.

#define NCONFPERLOOP 5

Definition at line 190 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_multiatom.

#define NTHREADSPERBLOCK (THBLEN*THBLEN*THBLEN)

Definition at line 180 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, and cuda_occupancy_multiatom.

#define NTPB_TIMES_NCPL (NTHREADSPERBLOCK * NCONFPERLOOP)

Definition at line 195 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_multiatom.

#define NTPBSHIFT 6

Definition at line 184 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, and cuda_occupancy_multiatom.

#define PADMASK (THBLEN-1)

Definition at line 197 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_multiatom, and cuda_occupancy_thread.

#define TEST_MBLOCK_EXCL

Definition at line 75 of file CUDAVolMapCreateILS.cu.

#define TEST_SHIFT_EXCL

Definition at line 76 of file CUDAVolMapCreateILS.cu.

#define THBLEN 4

Definition at line 179 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_thread.

#define TIME_PER_MONOATOM_WORKUNIT 1.24553913519431e-10

#define TIME_PER_MULTIATOM_WORKUNIT 5.24559386973180e-09

#define USE_ENERGY_EXCL

Definition at line 67 of file CUDAVolMapCreateILS.cu.

Typedef Documentation

typedef union flint_t flint

typedef struct occthrparms_t occthrparms

Function Documentation

__global__ void cuda_find_energy_exclusions ( int * excl,
const flint * bin_zero,
int nbx,
int nby,
int mzblocks,
int mzblockoffset
) [static]

Definition at line 320 of file CUDAVolMapCreateILS.cu.

References BIN_SHIFT, BIN_SIZE, BIN_SLOTSHIFT, BIN_SLOTSIZE, BSHIFT, const_binoffsets, const_bx_1, const_by_1, const_bz_1, const_cutoff, const_extra, const_hx, const_hy, const_hz, const_max_energy, const_num_binoffsets, const_num_extras, const_probevdwparms, const_vdwparms, const_x0, const_y0, const_z0, DO_ONE_PLANE, n, NTHREADSPERBLOCK, and NTPBSHIFT.

__global__ void cuda_occupancy_monoatom ( float * map,
const int * excl,
const flint * bin_zero,
int nbx,
int nby,
int mzblocks,
int mzblockoffset
) [static]

Definition at line 495 of file CUDAVolMapCreateILS.cu.

References BIN_SHIFT, BIN_SIZE, BIN_SLOTSHIFT, BIN_SLOTSIZE, BSHIFT, const_binoffsets, const_bx_1, const_by_1, const_bz_1, const_cutoff, const_extra, const_hx, const_hy, const_hz, const_max_energy, const_num_binoffsets, const_num_extras, const_probevdwparms, const_vdwparms, const_x0, const_y0, const_z0, DO_ONE_PLANE, n, NTHREADSPERBLOCK, and NTPBSHIFT.

__global__ void cuda_occupancy_multiatom ( float * map,
const int * excl,
const flint * bin_zero,
int nbx,
int nby,
int mzblocks,
int mzblockoffset
) [static]

Definition at line 667 of file CUDAVolMapCreateILS.cu.

References BIN_SHIFT, BIN_SIZE, BIN_SLOTSHIFT, BIN_SLOTSIZE, BSHIFT, conf, const_binoffsets, const_bx_1, const_by_1, const_bz_1, const_conformers, const_cutoff, const_extra, const_hx, const_hy, const_hz, const_inv_numconf, const_min_occupancy, const_num_binoffsets, const_num_conformers, const_num_extras, const_num_probes, const_probevdwparms, const_vdwparms, const_x0, const_y0, const_z0, DO_ONE_PLANE, MAX_ALLOWABLE_ENERGY, MAX_PROBES, n, NCONFPERLOOP, NTHREADSPERBLOCK, NTPB_TIMES_NCPL, NTPBSHIFT, and PADMASK.

void* cuda_occupancy_thread ( void * voidparms ) [static]

Definition at line 1036 of file CUDAVolMapCreateILS.cu.

References occthrparms_t::bin, BIN_SIZE, BIN_SLOTSIZE, occthrparms_t::bin_zero, occthrparms_t::binoffsets, BSHIFT, occthrparms_t::bx_1, occthrparms_t::by_1, occthrparms_t::bz_1, occthrparms_t::conformers, const_binoffsets, const_bx_1, const_by_1, const_bz_1, const_conformers, const_cutoff, const_excloffsets, const_extra, const_hx, const_hy, const_hz, const_inv_numconf, const_max_energy, const_min_excldist, const_min_occupancy, const_num_binoffsets, const_num_conformers, const_num_extras, const_num_probes, const_probevdwparms, const_vdwparms, const_x0, const_y0, const_z0, CUERR, occthrparms_t::cutoff, occthrparms_t::errcode, occthrparms_t::extra, occthrparms_t::hx, occthrparms_t::hy, occthrparms_t::hz, occthrparms_t::map, MAX_BINOFFSETS, MAX_CONFORMERS, occthrparms_t::max_energy, MAX_EXTRAS, MAX_PROBES, MAX_THREADBLOCKS, MAX_VDWPARMS, occthrparms_t::min_excldist, occthrparms_t::mx, occthrparms_t::my, occthrparms_t::mz, n, occthrparms_t::nbx, occthrparms_t::nby, occthrparms_t::nbz, NULL, occthrparms_t::num_binoffsets, occthrparms_t::num_conformers, occthrparms_t::num_extras, occthrparms_t::num_probes, occthrparms_t::num_vdwparms, PADMASK, occthrparms_t::probevdwparms, THBLEN, occthrparms_t::vdwparms, vmd_cuda_num_devices, VMDCUDA_ERR_NONE, wkf_timer_create, wkf_timer_destroy, wkf_timer_start, wkf_timer_timenow, wkf_timerhandle, occthrparms_t::x0, occthrparms_t::y0, and occthrparms_t::z0.

Referenced by vmd_cuda_evaluate_occupancy_map.

int vmd_cuda_evaluate_occupancy_map ( int mx,
int my,
int mz,
float * map,
float max_energy,
float cutoff,
float hx,
float hy,
float hz,
float x0,
float y0,
float z0,
float bx_1,
float by_1,
float bz_1,
int nbx,
int nby,
int nbz,
const float * bin,
const float * bin_zero,
int num_binoffsets,
const char * binoffsets,
int num_extras,
const float * extra,
int num_vdwparms,
const float * vdwparms,
int num_probes,
const float * probevdwparms,
int num_conformers,
const float * conformers
)

Definition at line 1601 of file CUDAVolMapCreateILS.cu.

References occthrparms_t::bin, bin, occthrparms_t::bin_zero, occthrparms_t::binoffsets, occthrparms_t::bx_1, occthrparms_t::by_1, occthrparms_t::bz_1, occthrparms_t::conformers, cuda_occupancy_thread, occthrparms_t::cutoff, occthrparms_t::errcode, occthrparms_t::extra, occthrparms_t::hx, occthrparms_t::hy, occthrparms_t::hz, occthrparms_t::map, occthrparms_t::max_energy, occthrparms_t::min_excldist, occthrparms_t::mx, occthrparms_t::my, occthrparms_t::mz, occthrparms_t::nbx, occthrparms_t::nby, occthrparms_t::nbz, occthrparms_t::num_binoffsets, occthrparms_t::num_conformers, occthrparms_t::num_extras, occthrparms_t::num_probes, occthrparms_t::num_vdwparms, occthrparms_t::probevdwparms, occthrparms_t::vdwparms, occthrparms_t::x0, occthrparms_t::y0, and occthrparms_t::z0.

Variable Documentation

__constant__ int const_binoffsets[MAX_BINOFFSETS] [static]

Definition at line 161 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_bx_1 [static]

Definition at line 141 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_by_1 [static]

Definition at line 141 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_bz_1 [static]

Definition at line 141 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_conformers[3*MAX_PROBES*MAX_CONFORMERS] [static]

Definition at line 173 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_cutoff [static]

Definition at line 137 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ int const_excloffsets[MAX_EXCLOFFSETS] [static]

Definition at line 165 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_thread.

__constant__ flint const_extra[BIN_SLOTSIZE * MAX_EXTRAS] [static]

Definition at line 157 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_hx [static]

Definition at line 139 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_hy [static]

Definition at line 139 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_hz [static]

Definition at line 139 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_inv_numconf [static]

Definition at line 143 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_max_energy [static]

Definition at line 135 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, and cuda_occupancy_thread.

__constant__ float const_min_excldist [static]

Definition at line 138 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_thread.

__constant__ float const_min_occupancy [static]

Definition at line 136 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ int const_num_binoffsets [static]

Definition at line 145 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ int const_num_conformers [static]

Definition at line 148 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ int const_num_extras [static]

Definition at line 146 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ int const_num_probes [static]

Definition at line 147 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_probevdwparms[2 * MAX_PROBES] [static]

Definition at line 154 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_vdwparms[2 * MAX_VDWPARMS] [static]

Definition at line 151 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_x0 [static]

Definition at line 140 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_y0 [static]

Definition at line 140 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

__constant__ float const_z0 [static]

Definition at line 140 of file CUDAVolMapCreateILS.cu.

Referenced by cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, and cuda_occupancy_thread.

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