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Add first draft version of GROMACS method separating i-clusters and j-clusters

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-03-09 02:25:39 +01:00
parent cecb31d6a9
commit c7360305c8
9 changed files with 411 additions and 247 deletions
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79
gromacs/includes/atom.h
View File

@@ -27,13 +27,60 @@
#define DELTA 20000
#define CLUSTER_DIM_M 4
#define CLUSTER_DIM_N VECTOR_WIDTH
#define CLUSTER_M 4
// Nbnxn layouts (as of GROMACS):
// Simd4xN: M=4, N=VECTOR_WIDTH
// Simd2xNN: M=4, N=(VECTOR_WIDTH/2)
// Simd2XNN (here used for single-precision)
#if VECTOR_WIDTH > CLUSTER_M * 2
# define CLUSTER_N (VECTOR_WIDTH / 2)
// Simd4xN
#else
# define CLUSTER_N VECTOR_WIDTH
#endif
#if CLUSTER_M == CLUSTER_N
# define CJ0_FROM_CI(a) (a)
# define CJ1_FROM_CI(a) (a)
# define CI_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
# define CJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
#elif CLUSTER_M == CLUSTER_N * 2 // M > N
# define CJ0_FROM_CI(a) ((a) << 1)
# define CJ1_FROM_CI(a) (((a) << 1) | 0x1)
# define CI_BASE_INDEX(a,b) ((a) * CLUSTER_M * (b))
# define CJ_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_M * (b) + ((a) & 0x1) * (CLUSTER_M >> 1))
#elif CLUSTER_M == CLUSTER_N / 2 // M < N
# define CJ0_FROM_CI(a) ((a) >> 1)
# define CJ1_FROM_CI(a) ((a) >> 1)
# define CI_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_N * (b) + ((a) & 0x1) * (CLUSTER_N >> 1))
# define CJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
#else
# error "Invalid cluster configuration!"
#endif
#if CLUSTER_N != 2 && CLUSTER_N != 4 && CLUSTER_N != 8
# error "Cluster N dimension can be only 2, 4 and 8"
#endif
#define CI_SCALAR_BASE_INDEX(a) (CI_BASE_INDEX(a, 1))
#define CI_VECTOR_BASE_INDEX(a) (CI_BASE_INDEX(a, 3))
#define CJ_SCALAR_BASE_INDEX(a) (CJ_BASE_INDEX(a, 1))
#define CJ_VECTOR_BASE_INDEX(a) (CJ_BASE_INDEX(a, 3))
#if CLUSTER_M >= CLUSTER_N
# define CL_X_OFFSET (0 * CLUSTER_M)
# define CL_Y_OFFSET (1 * CLUSTER_M)
# define CL_Z_OFFSET (2 * CLUSTER_M)
#else
# define CL_X_OFFSET (0 * CLUSTER_N)
# define CL_Y_OFFSET (1 * CLUSTER_N)
# define CL_Z_OFFSET (2 * CLUSTER_N)
#endif
typedef struct {
int bin;
int natoms;
int type[CLUSTER_DIM_M];
MD_FLOAT bbminx, bbmaxx;
MD_FLOAT bbminy, bbmaxy;
MD_FLOAT bbminz, bbmaxz;
@@ -44,9 +91,6 @@ typedef struct {
int Nclusters, Nclusters_local, Nclusters_ghost, Nclusters_max;
MD_FLOAT *x, *y, *z;
MD_FLOAT *vx, *vy, *vz;
MD_FLOAT *cl_x;
MD_FLOAT *cl_v;
MD_FLOAT *cl_f;
int *border_map;
int *type;
int ntypes;
@@ -54,8 +98,13 @@ typedef struct {
MD_FLOAT *sigma6;
MD_FLOAT *cutforcesq;
MD_FLOAT *cutneighsq;
Cluster *clusters;
int *PBCx, *PBCy, *PBCz;
// Data in cluster format
MD_FLOAT *cl_x;
MD_FLOAT *cl_v;
MD_FLOAT *cl_f;
int *cl_type;
Cluster *iclusters, *jclusters;
} Atom;
extern void initAtom(Atom*);
@@ -67,10 +116,6 @@ extern int readAtom_dmp(Atom*, Parameter*);
extern void growAtom(Atom*);
extern void growClusters(Atom*);
#define cluster_pos_ptr(ci) &(atom->cl_x[(ci) * CLUSTER_DIM_M * 3])
#define cluster_velocity_ptr(ci) &(atom->cl_v[(ci) * CLUSTER_DIM_M * 3])
#define cluster_force_ptr(ci) &(atom->cl_f[(ci) * CLUSTER_DIM_M * 3])
#ifdef AOS
#define POS_DATA_LAYOUT "AoS"
#define atom_x(i) atom->x[(i) * 3 + 0]
@@ -83,14 +128,4 @@ extern void growClusters(Atom*);
#define atom_z(i) atom->z[i]
#endif
#ifdef CLUSTER_AOS
#define cluster_x(cptr, i) cptr[(i) * 3 + 0]
#define cluster_y(cptr, i) cptr[(i) * 3 + 1]
#define cluster_z(cptr, i) cptr[(i) * 3 + 2]
#else
#define cluster_x(cptr, i) cptr[0 * CLUSTER_DIM_M + (i)]
#define cluster_y(cptr, i) cptr[1 * CLUSTER_DIM_M + (i)]
#define cluster_z(cptr, i) cptr[2 * CLUSTER_DIM_M + (i)]
#endif
#endif

6
gromacs/includes/simd.h
View File

@@ -54,8 +54,8 @@ static MD_SIMD_FLOAT simd_load2(MD_FLOAT *c0, MD_FLOAT *c1, int d) {
x = _mm512_mask_i32gather_pd(simd_zero(), simd_mask_from_u32(0x0f), vindex, c0, sizeof(double));
x = _mm512_mask_i32gather_pd(x, simd_mask_from_u32(0xf0), vindex, c1, sizeof(double));
#else
x = _mm512_load_pd(&c0[d * CLUSTER_DIM_M]);
x = _mm512_insertf64x4(x, _mm256_load_pd(&c1[d * CLUSTER_DIM_M]), 1);
x = _mm512_load_pd(&c0[d * CLUSTER_M]);
x = _mm512_insertf64x4(x, _mm256_load_pd(&c1[d * CLUSTER_M]), 1);
#endif
return x;
}
@@ -134,7 +134,7 @@ static MD_SIMD_FLOAT simd_load(MD_FLOAT *c0, int d) {
__m128i vindex = _mm128_add_epi32(aos_gather_vindex, _mm128_set1_epi32(d));
x = _mm256_i32gather_pd(c0, vindex, sizeof(double));
#else
x = _mm256_load_pd(&c0[d * CLUSTER_DIM_M]);
x = _mm256_load_pd(&c0[d * CLUSTER_M]);
#endif
return x;
}