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Specialize force kernel when there are no masks to be checked

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2023-03-28 18:04:18 +02:00
parent 965fda3879
commit 85f1484449
3 changed files with 75 additions and 4 deletions
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55
gromacs/force_lj.c
View File

@ -220,6 +220,7 @@ double computeForceLJ_2xnn_half(Parameter *param, Atom *atom, Neighbor *neighbor
MD_FLOAT *ci_f = &atom->cl_f[ci_vec_base]; MD_FLOAT *ci_f = &atom->cl_f[ci_vec_base];
neighs = &neighbor->neighbors[ci * neighbor->maxneighs]; neighs = &neighbor->neighbors[ci * neighbor->maxneighs];
int numneighs = neighbor->numneigh[ci]; int numneighs = neighbor->numneigh[ci];
int numneighs_masked = neighbor->numneigh_masked[ci];
MD_SIMD_FLOAT xi0_tmp = simd_load_h_dual(&ci_x[CL_X_OFFSET + 0]); MD_SIMD_FLOAT xi0_tmp = simd_load_h_dual(&ci_x[CL_X_OFFSET + 0]);
MD_SIMD_FLOAT xi2_tmp = simd_load_h_dual(&ci_x[CL_X_OFFSET + 2]); MD_SIMD_FLOAT xi2_tmp = simd_load_h_dual(&ci_x[CL_X_OFFSET + 2]);
@ -234,7 +235,7 @@ double computeForceLJ_2xnn_half(Parameter *param, Atom *atom, Neighbor *neighbor
MD_SIMD_FLOAT fiy2 = simd_zero(); MD_SIMD_FLOAT fiy2 = simd_zero();
MD_SIMD_FLOAT fiz2 = simd_zero(); MD_SIMD_FLOAT fiz2 = simd_zero();
for(int k = 0; k < numneighs; k++) { for(int k = 0; k < numneighs_masked; k++) {
int cj = neighs[k].cj; int cj = neighs[k].cj;
int cj_vec_base = CJ_VECTOR_BASE_INDEX(cj); int cj_vec_base = CJ_VECTOR_BASE_INDEX(cj);
int imask = neighs[k].imask; int imask = neighs[k].imask;
@ -328,6 +329,58 @@ double computeForceLJ_2xnn_half(Parameter *param, Atom *atom, Neighbor *neighbor
#endif #endif
} }
for(int k = numneighs_masked; k < numneighs; k++) {
int cj = neighs[k].cj;
int cj_vec_base = CJ_VECTOR_BASE_INDEX(cj);
MD_FLOAT *cj_x = &atom->cl_x[cj_vec_base];
MD_FLOAT *cj_f = &atom->cl_f[cj_vec_base];
MD_SIMD_FLOAT xj_tmp = simd_load_h_duplicate(&cj_x[CL_X_OFFSET]);
MD_SIMD_FLOAT yj_tmp = simd_load_h_duplicate(&cj_x[CL_Y_OFFSET]);
MD_SIMD_FLOAT zj_tmp = simd_load_h_duplicate(&cj_x[CL_Z_OFFSET]);
MD_SIMD_FLOAT delx0 = simd_sub(xi0_tmp, xj_tmp);
MD_SIMD_FLOAT dely0 = simd_sub(yi0_tmp, yj_tmp);
MD_SIMD_FLOAT delz0 = simd_sub(zi0_tmp, zj_tmp);
MD_SIMD_FLOAT delx2 = simd_sub(xi2_tmp, xj_tmp);
MD_SIMD_FLOAT dely2 = simd_sub(yi2_tmp, yj_tmp);
MD_SIMD_FLOAT delz2 = simd_sub(zi2_tmp, zj_tmp);
MD_SIMD_FLOAT rsq0 = simd_fma(delx0, delx0, simd_fma(dely0, dely0, simd_mul(delz0, delz0)));
MD_SIMD_FLOAT rsq2 = simd_fma(delx2, delx2, simd_fma(dely2, dely2, simd_mul(delz2, delz2)));
MD_SIMD_MASK cutoff_mask0 = simd_mask_cond_lt(rsq0, cutforcesq_vec);
MD_SIMD_MASK cutoff_mask2 = simd_mask_cond_lt(rsq2, cutforcesq_vec);
MD_SIMD_FLOAT sr2_0 = simd_reciprocal(rsq0);
MD_SIMD_FLOAT sr2_2 = simd_reciprocal(rsq2);
MD_SIMD_FLOAT sr6_0 = sr2_0 * sr2_0 * sr2_0 * sigma6_vec;
MD_SIMD_FLOAT sr6_2 = sr2_2 * sr2_2 * sr2_2 * sigma6_vec;
MD_SIMD_FLOAT force0 = c48_vec * sr6_0 * (sr6_0 - c05_vec) * sr2_0 * eps_vec;
MD_SIMD_FLOAT force2 = c48_vec * sr6_2 * (sr6_2 - c05_vec) * sr2_2 * eps_vec;
MD_SIMD_FLOAT tx0 = select_by_mask(delx0 * force0, cutoff_mask0);
MD_SIMD_FLOAT ty0 = select_by_mask(dely0 * force0, cutoff_mask0);
MD_SIMD_FLOAT tz0 = select_by_mask(delz0 * force0, cutoff_mask0);
MD_SIMD_FLOAT tx2 = select_by_mask(delx2 * force2, cutoff_mask2);
MD_SIMD_FLOAT ty2 = select_by_mask(dely2 * force2, cutoff_mask2);
MD_SIMD_FLOAT tz2 = select_by_mask(delz2 * force2, cutoff_mask2);
fix0 += tx0;
fiy0 += ty0;
fiz0 += tz0;
fix2 += tx2;
fiy2 += ty2;
fiz2 += tz2;
#ifdef HALF_NEIGHBOR_LISTS_CHECK_CJ
if(cj < CJ1_FROM_CI(atom->Nlocal)) {
simd_h_decr3(cj_f, tx0 + tx2, ty0 + ty2, tz0 + tz2);
}
#else
simd_h_decr3(cj_f, tx0 + tx2, ty0 + ty2, tz0 + tz2);
#endif
}
simd_h_dual_incr_reduced_sum(&ci_f[CL_X_OFFSET], fix0, fix2); simd_h_dual_incr_reduced_sum(&ci_f[CL_X_OFFSET], fix0, fix2);
simd_h_dual_incr_reduced_sum(&ci_f[CL_Y_OFFSET], fiy0, fiy2); simd_h_dual_incr_reduced_sum(&ci_f[CL_Y_OFFSET], fiy0, fiy2);
simd_h_dual_incr_reduced_sum(&ci_f[CL_Z_OFFSET], fiz0, fiz2); simd_h_dual_incr_reduced_sum(&ci_f[CL_Z_OFFSET], fiz0, fiz2);

1
gromacs/includes/neighbor.h
View File

@ -35,6 +35,7 @@ typedef struct {
int ncalls; int ncalls;
int maxneighs; int maxneighs;
int* numneigh; int* numneigh;
int* numneigh_masked;
int half_neigh; int half_neigh;
NeighborCluster* neighbors; NeighborCluster* neighbors;
} Neighbor; } Neighbor;

19
gromacs/neighbor.c
View File

@ -56,6 +56,7 @@ void initNeighbor(Neighbor *neighbor, Parameter *param) {
neighbor->half_neigh = param->half_neigh; neighbor->half_neigh = param->half_neigh;
neighbor->maxneighs = 100; neighbor->maxneighs = 100;
neighbor->numneigh = NULL; neighbor->numneigh = NULL;
neighbor->numneigh_masked = NULL;
neighbor->neighbors = NULL; neighbor->neighbors = NULL;
} }
@ -230,6 +231,7 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
if(neighbor->numneigh) free(neighbor->numneigh); if(neighbor->numneigh) free(neighbor->numneigh);
if(neighbor->neighbors) free(neighbor->neighbors); if(neighbor->neighbors) free(neighbor->neighbors);
neighbor->numneigh = (int*) malloc(nmax * sizeof(int)); neighbor->numneigh = (int*) malloc(nmax * sizeof(int));
neighbor->numneigh_masked = (int*) malloc(nmax * sizeof(int));
neighbor->neighbors = (NeighborCluster*) malloc(nmax * neighbor->maxneighs * sizeof(NeighborCluster)); neighbor->neighbors = (NeighborCluster*) malloc(nmax * neighbor->maxneighs * sizeof(NeighborCluster));
} }
@ -247,7 +249,7 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
for(int ci = 0; ci < atom->Nclusters_local; ci++) { for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_cj1 = CJ1_FROM_CI(ci); int ci_cj1 = CJ1_FROM_CI(ci);
NeighborCluster *neighptr = &(neighbor->neighbors[ci * neighbor->maxneighs]); NeighborCluster *neighptr = &(neighbor->neighbors[ci * neighbor->maxneighs]);
int n = 0; int n = 0, nmasked = 0;
int ibin = atom->icluster_bin[ci]; int ibin = atom->icluster_bin[ci];
MD_FLOAT ibb_xmin = atom->iclusters[ci].bbminx; MD_FLOAT ibb_xmin = atom->iclusters[ci].bbminx;
MD_FLOAT ibb_xmax = atom->iclusters[ci].bbmaxx; MD_FLOAT ibb_xmax = atom->iclusters[ci].bbmaxx;
@ -319,8 +321,17 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
imask = get_imask_simd_4xn(neighbor->half_neigh, ci, cj); imask = get_imask_simd_4xn(neighbor->half_neigh, ci, cj);
#endif #endif
if(imask == NBNXN_INTERACTION_MASK_ALL) {
neighptr[n].cj = cj; neighptr[n].cj = cj;
neighptr[n].imask = imask; neighptr[n].imask = imask;
} else {
neighptr[n].cj = neighptr[nmasked].cj;
neighptr[n].imask = neighptr[nmasked].imask;
neighptr[nmasked].cj = cj;
neighptr[nmasked].imask = imask;
nmasked++;
}
n++; n++;
} }
} }
@ -350,6 +361,7 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
} }
neighbor->numneigh[ci] = n; neighbor->numneigh[ci] = n;
neighbor->numneigh_masked[ci] = nmasked;
if(n >= neighbor->maxneighs) { if(n >= neighbor->maxneighs) {
resize = 1; resize = 1;
@ -420,6 +432,7 @@ void pruneNeighbor(Parameter *param, Atom *atom, Neighbor *neighbor) {
for(int ci = 0; ci < atom->Nclusters_local; ci++) { for(int ci = 0; ci < atom->Nclusters_local; ci++) {
NeighborCluster *neighs = &neighbor->neighbors[ci * neighbor->maxneighs]; NeighborCluster *neighs = &neighbor->neighbors[ci * neighbor->maxneighs];
int numneighs = neighbor->numneigh[ci]; int numneighs = neighbor->numneigh[ci];
int numneighs_masked = neighbor->numneigh_masked[ci];
int k = 0; int k = 0;
// Remove dummy clusters if necessary // Remove dummy clusters if necessary
@ -435,6 +448,9 @@ void pruneNeighbor(Parameter *param, Atom *atom, Neighbor *neighbor) {
k++; k++;
} else { } else {
numneighs--; numneighs--;
if(k < numneighs_masked) {
numneighs_masked--;
}
neighs[k] = neighs[numneighs]; neighs[k] = neighs[numneighs];
} }
} }
@ -449,6 +465,7 @@ void pruneNeighbor(Parameter *param, Atom *atom, Neighbor *neighbor) {
} }
neighbor->numneigh[ci] = numneighs; neighbor->numneigh[ci] = numneighs;
neighbor->numneigh_masked[ci] = numneighs_masked;
} }
DEBUG_MESSAGE("pruneNeighbor end\n"); DEBUG_MESSAGE("pruneNeighbor end\n");