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Add first version for half neighbor lists in GROMACS variant

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-03-22 23:47:05 +01:00
parent 2a555a7deb
commit 8709bc2a06
7 changed files with 379 additions and 24 deletions
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327
gromacs/force_lj.c
View File

@ -68,6 +68,7 @@ double computeForceLJ_ref(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
int cj_vec_base = CJ_VECTOR_BASE_INDEX(cj);
int any = 0;
MD_FLOAT *cj_x = &atom->cl_x[cj_vec_base];
MD_FLOAT *cj_f = &atom->cl_f[cj_vec_base];
for(int cii = 0; cii < CLUSTER_M; cii++) {
MD_FLOAT xtmp = ci_x[CL_X_OFFSET + cii];
@ -93,6 +94,13 @@ double computeForceLJ_ref(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
if(neighbor->half_neigh) {
cj_f[CL_X_OFFSET + cjj] -= delx * force;
cj_f[CL_Y_OFFSET + cjj] -= dely * force;
cj_f[CL_Z_OFFSET + cjj] -= delz * force;
}
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
@ -127,7 +135,148 @@ double computeForceLJ_ref(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
return E-S;
}
double computeForceLJ_2xnn(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
double computeForceLJ_2xnn_half(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
DEBUG_MESSAGE("computeForceLJ_2xnn begin\n");
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
MD_SIMD_FLOAT cutforcesq_vec = simd_broadcast(cutforcesq);
MD_SIMD_FLOAT sigma6_vec = simd_broadcast(sigma6);
MD_SIMD_FLOAT eps_vec = simd_broadcast(epsilon);
MD_SIMD_FLOAT c48_vec = simd_broadcast(48.0);
MD_SIMD_FLOAT c05_vec = simd_broadcast(0.5);
const unsigned int half_mask_bits = VECTOR_WIDTH >> 1;
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_f = &atom->cl_f[ci_vec_base];
for(int cii = 0; cii < atom->iclusters[ci].natoms; cii++) {
ci_f[CL_X_OFFSET + cii] = 0.0;
ci_f[CL_Y_OFFSET + cii] = 0.0;
ci_f[CL_Z_OFFSET + cii] = 0.0;
}
}
double S = getTimeStamp();
LIKWID_MARKER_START("force");
#pragma omp parallel for
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_cj0 = CJ0_FROM_CI(ci);
#if CLUSTER_M > CLUSTER_N
int ci_cj1 = CJ1_FROM_CI(ci);
#endif
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
MD_FLOAT *ci_f = &atom->cl_f[ci_vec_base];
neighs = &neighbor->neighbors[ci * neighbor->maxneighs];
int numneighs = neighbor->numneigh[ci];
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 yi0_tmp = simd_load_h_dual(&ci_x[CL_Y_OFFSET + 0]);
MD_SIMD_FLOAT yi2_tmp = simd_load_h_dual(&ci_x[CL_Y_OFFSET + 2]);
MD_SIMD_FLOAT zi0_tmp = simd_load_h_dual(&ci_x[CL_Z_OFFSET + 0]);
MD_SIMD_FLOAT zi2_tmp = simd_load_h_dual(&ci_x[CL_Z_OFFSET + 2]);
MD_SIMD_FLOAT fix0 = simd_zero();
MD_SIMD_FLOAT fiy0 = simd_zero();
MD_SIMD_FLOAT fiz0 = simd_zero();
MD_SIMD_FLOAT fix2 = simd_zero();
MD_SIMD_FLOAT fiy2 = simd_zero();
MD_SIMD_FLOAT fiz2 = simd_zero();
for(int k = 0; k < numneighs; k++) {
int cj = neighs[k];
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];
unsigned int mask0, mask1, mask2, mask3;
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);
#if CLUSTER_M == CLUSTER_N
unsigned int cond0 = (unsigned int)(cj == ci_cj0);
mask0 = (unsigned int)(0xf - 0x1 * cond0);
mask1 = (unsigned int)(0xf - 0x3 * cond0);
mask2 = (unsigned int)(0xf - 0x7 * cond0);
mask3 = (unsigned int)(0xf - 0xf * cond0);
#elif CLUSTER_M < CLUSTER_N
unsigned int cond0 = (unsigned int)((cj << 1) + 0 == ci);
unsigned int cond1 = (unsigned int)((cj << 1) + 1 == ci);
mask0 = (unsigned int)(0xff - 0x1 * cond0 - 0x1f * cond1);
mask1 = (unsigned int)(0xff - 0x3 * cond0 - 0x3f * cond1);
mask2 = (unsigned int)(0xff - 0x7 * cond0 - 0x7f * cond1);
mask3 = (unsigned int)(0xff - 0xf * cond0 - 0xff * cond1);
#else
unsigned int cond0 = (unsigned int)(cj == ci_cj0);
unsigned int cond1 = (unsigned int)(cj == ci_cj1);
mask0 = (unsigned int)(0x3 - 0x1 * cond0);
mask1 = (unsigned int)(0x3 - 0x3 * cond0);
mask2 = (unsigned int)(0x3 - cond0 * 0x3 - 0x1 * cond1);
mask3 = (unsigned int)(0x3 - cond0 * 0x3 - 0x3 * cond1);
#endif
MD_SIMD_MASK excl_mask0 = simd_mask_from_u32((mask1 << half_mask_bits) | mask0);
MD_SIMD_MASK excl_mask2 = simd_mask_from_u32((mask3 << half_mask_bits) | mask2);
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_and(excl_mask0, simd_mask_cond_lt(rsq0, cutforcesq_vec));
MD_SIMD_MASK cutoff_mask2 = simd_mask_and(excl_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 = simd_mul(sr2_0, simd_mul(sr2_0, simd_mul(sr2_0, sigma6_vec)));
MD_SIMD_FLOAT sr6_2 = simd_mul(sr2_2, simd_mul(sr2_2, simd_mul(sr2_2, sigma6_vec)));
MD_SIMD_FLOAT force0 = simd_mul(c48_vec, simd_mul(sr6_0, simd_mul(simd_sub(sr6_0, c05_vec), simd_mul(sr2_0, eps_vec))));
MD_SIMD_FLOAT force2 = simd_mul(c48_vec, simd_mul(sr6_2, simd_mul(simd_sub(sr6_2, c05_vec), simd_mul(sr2_2, eps_vec))));
MD_SIMD_FLOAT tx0 = select_by_mask(simd_mul(delx0, force0), cutoff_mask0);
MD_SIMD_FLOAT ty0 = select_by_mask(simd_mul(dely0, force0), cutoff_mask0);
MD_SIMD_FLOAT tz0 = select_by_mask(simd_mul(delz0, force0), cutoff_mask0);
MD_SIMD_FLOAT tx2 = select_by_mask(simd_mul(delx2, force2), cutoff_mask2);
MD_SIMD_FLOAT ty2 = select_by_mask(simd_mul(dely2, force2), cutoff_mask2);
MD_SIMD_FLOAT tz2 = select_by_mask(simd_mul(delz2, force2), cutoff_mask2);
fix0 = simd_add(fix0, tx0);
fiy0 = simd_add(fiy0, ty0);
fiz0 = simd_add(fiz0, tz0);
fix2 = simd_add(fix2, tx2);
fiy2 = simd_add(fiy2, ty2);
fiz2 = simd_add(fiz2, tz2);
simd_h_decr3(cj_f, tx0 + tx2, ty0 + ty2, tz0 + tz2);
}
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_Z_OFFSET], fiz0, fiz2);
addStat(stats->calculated_forces, 1);
addStat(stats->num_neighs, numneighs);
addStat(stats->force_iters, (long long int)((double)numneighs * CLUSTER_M / CLUSTER_N));
}
LIKWID_MARKER_STOP("force");
double E = getTimeStamp();
DEBUG_MESSAGE("computeForceLJ_2xnn end\n");
return E-S;
}
double computeForceLJ_2xnn_full(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
DEBUG_MESSAGE("computeForceLJ_2xnn begin\n");
int Nlocal = atom->Nlocal;
int* neighs;
@ -258,7 +407,173 @@ double computeForceLJ_2xnn(Parameter *param, Atom *atom, Neighbor *neighbor, Sta
return E-S;
}
double computeForceLJ_4xn(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
double computeForceLJ_2xnn(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
if(neighbor->half_neigh) {
return computeForceLJ_2xnn_half(param, atom, neighbor, stats);
}
return computeForceLJ_2xnn_full(param, atom, neighbor, stats);
}
double computeForceLJ_4xn_half(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
DEBUG_MESSAGE("computeForceLJ_4xn begin\n");
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
MD_SIMD_FLOAT cutforcesq_vec = simd_broadcast(cutforcesq);
MD_SIMD_FLOAT sigma6_vec = simd_broadcast(sigma6);
MD_SIMD_FLOAT eps_vec = simd_broadcast(epsilon);
MD_SIMD_FLOAT c48_vec = simd_broadcast(48.0);
MD_SIMD_FLOAT c05_vec = simd_broadcast(0.5);
double S = getTimeStamp();
LIKWID_MARKER_START("force");
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_f = &atom->cl_f[ci_vec_base];
for(int cii = 0; cii < atom->iclusters[ci].natoms; cii++) {
ci_f[CL_X_OFFSET + cii] = 0.0;
ci_f[CL_Y_OFFSET + cii] = 0.0;
ci_f[CL_Z_OFFSET + cii] = 0.0;
}
}
#pragma omp parallel for
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_cj0 = CJ0_FROM_CI(ci);
#if CLUSTER_M > CLUSTER_N
int ci_cj1 = CJ1_FROM_CI(ci);
#endif
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
MD_FLOAT *ci_f = &atom->cl_f[ci_vec_base];
neighs = &neighbor->neighbors[ci * neighbor->maxneighs];
int numneighs = neighbor->numneigh[ci];
MD_SIMD_FLOAT xi0_tmp = simd_broadcast(ci_x[CL_X_OFFSET + 0]);
MD_SIMD_FLOAT xi1_tmp = simd_broadcast(ci_x[CL_X_OFFSET + 1]);
MD_SIMD_FLOAT xi2_tmp = simd_broadcast(ci_x[CL_X_OFFSET + 2]);
MD_SIMD_FLOAT xi3_tmp = simd_broadcast(ci_x[CL_X_OFFSET + 3]);
MD_SIMD_FLOAT yi0_tmp = simd_broadcast(ci_x[CL_Y_OFFSET + 0]);
MD_SIMD_FLOAT yi1_tmp = simd_broadcast(ci_x[CL_Y_OFFSET + 1]);
MD_SIMD_FLOAT yi2_tmp = simd_broadcast(ci_x[CL_Y_OFFSET + 2]);
MD_SIMD_FLOAT yi3_tmp = simd_broadcast(ci_x[CL_Y_OFFSET + 3]);
MD_SIMD_FLOAT zi0_tmp = simd_broadcast(ci_x[CL_Z_OFFSET + 0]);
MD_SIMD_FLOAT zi1_tmp = simd_broadcast(ci_x[CL_Z_OFFSET + 1]);
MD_SIMD_FLOAT zi2_tmp = simd_broadcast(ci_x[CL_Z_OFFSET + 2]);
MD_SIMD_FLOAT zi3_tmp = simd_broadcast(ci_x[CL_Z_OFFSET + 3]);
MD_SIMD_FLOAT fix0 = simd_zero();
MD_SIMD_FLOAT fiy0 = simd_zero();
MD_SIMD_FLOAT fiz0 = simd_zero();
MD_SIMD_FLOAT fix1 = simd_zero();
MD_SIMD_FLOAT fiy1 = simd_zero();
MD_SIMD_FLOAT fiz1 = simd_zero();
MD_SIMD_FLOAT fix2 = simd_zero();
MD_SIMD_FLOAT fiy2 = simd_zero();
MD_SIMD_FLOAT fiz2 = simd_zero();
MD_SIMD_FLOAT fix3 = simd_zero();
MD_SIMD_FLOAT fiy3 = simd_zero();
MD_SIMD_FLOAT fiz3 = simd_zero();
for(int k = 0; k < numneighs; k++) {
int cj = neighs[k];
int cj_vec_base = CJ_VECTOR_BASE_INDEX(cj);
MD_FLOAT *cj_x = &atom->cl_x[cj_vec_base];
MD_SIMD_FLOAT xj_tmp = simd_load(&cj_x[CL_X_OFFSET]);
MD_SIMD_FLOAT yj_tmp = simd_load(&cj_x[CL_Y_OFFSET]);
MD_SIMD_FLOAT zj_tmp = simd_load(&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 delx1 = simd_sub(xi1_tmp, xj_tmp);
MD_SIMD_FLOAT dely1 = simd_sub(yi1_tmp, yj_tmp);
MD_SIMD_FLOAT delz1 = simd_sub(zi1_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 delx3 = simd_sub(xi3_tmp, xj_tmp);
MD_SIMD_FLOAT dely3 = simd_sub(yi3_tmp, yj_tmp);
MD_SIMD_FLOAT delz3 = simd_sub(zi3_tmp, zj_tmp);
#if CLUSTER_M == CLUSTER_N
unsigned int cond0 = (unsigned int)(cj == ci_cj0);
MD_SIMD_MASK excl_mask0 = simd_mask_from_u32((unsigned int)(0xf - 0x1 * cond0));
MD_SIMD_MASK excl_mask1 = simd_mask_from_u32((unsigned int)(0xf - 0x3 * cond0));
MD_SIMD_MASK excl_mask2 = simd_mask_from_u32((unsigned int)(0xf - 0x7 * cond0));
MD_SIMD_MASK excl_mask3 = simd_mask_from_u32((unsigned int)(0xf - 0xf * cond0));
#elif CLUSTER_M < CLUSTER_N
unsigned int cond0 = (unsigned int)((cj << 1) + 0 == ci);
unsigned int cond1 = (unsigned int)((cj << 1) + 1 == ci);
MD_SIMD_MASK excl_mask0 = simd_mask_from_u32((unsigned int)(0xff - 0x1 * cond0 - 0x1f * cond1));
MD_SIMD_MASK excl_mask1 = simd_mask_from_u32((unsigned int)(0xff - 0x3 * cond0 - 0x3f * cond1));
MD_SIMD_MASK excl_mask2 = simd_mask_from_u32((unsigned int)(0xff - 0x7 * cond0 - 0x7f * cond1));
MD_SIMD_MASK excl_mask3 = simd_mask_from_u32((unsigned int)(0xff - 0xf * cond0 - 0xff * cond1));
#else
unsigned int cond0 = (unsigned int)(cj == ci_cj0);
unsigned int cond1 = (unsigned int)(cj == ci_cj1);
MD_SIMD_MASK excl_mask0 = simd_mask_from_u32((unsigned int)(0x3 - 0x1 * cond0));
MD_SIMD_MASK excl_mask1 = simd_mask_from_u32((unsigned int)(0x3 - 0x3 * cond0));
MD_SIMD_MASK excl_mask2 = simd_mask_from_u32((unsigned int)(0x3 - 0x3 * cond0 - 0x1 * cond1));
MD_SIMD_MASK excl_mask3 = simd_mask_from_u32((unsigned int)(0x3 - 0x3 * cond0 - 0x3 * cond1));
#endif
MD_SIMD_FLOAT rsq0 = simd_fma(delx0, delx0, simd_fma(dely0, dely0, simd_mul(delz0, delz0)));
MD_SIMD_FLOAT rsq1 = simd_fma(delx1, delx1, simd_fma(dely1, dely1, simd_mul(delz1, delz1)));
MD_SIMD_FLOAT rsq2 = simd_fma(delx2, delx2, simd_fma(dely2, dely2, simd_mul(delz2, delz2)));
MD_SIMD_FLOAT rsq3 = simd_fma(delx3, delx3, simd_fma(dely3, dely3, simd_mul(delz3, delz3)));
MD_SIMD_MASK cutoff_mask0 = simd_mask_and(excl_mask0, simd_mask_cond_lt(rsq0, cutforcesq_vec));
MD_SIMD_MASK cutoff_mask1 = simd_mask_and(excl_mask1, simd_mask_cond_lt(rsq1, cutforcesq_vec));
MD_SIMD_MASK cutoff_mask2 = simd_mask_and(excl_mask2, simd_mask_cond_lt(rsq2, cutforcesq_vec));
MD_SIMD_MASK cutoff_mask3 = simd_mask_and(excl_mask3, simd_mask_cond_lt(rsq3, cutforcesq_vec));
MD_SIMD_FLOAT sr2_0 = simd_reciprocal(rsq0);
MD_SIMD_FLOAT sr2_1 = simd_reciprocal(rsq1);
MD_SIMD_FLOAT sr2_2 = simd_reciprocal(rsq2);
MD_SIMD_FLOAT sr2_3 = simd_reciprocal(rsq3);
MD_SIMD_FLOAT sr6_0 = simd_mul(sr2_0, simd_mul(sr2_0, simd_mul(sr2_0, sigma6_vec)));
MD_SIMD_FLOAT sr6_1 = simd_mul(sr2_1, simd_mul(sr2_1, simd_mul(sr2_1, sigma6_vec)));
MD_SIMD_FLOAT sr6_2 = simd_mul(sr2_2, simd_mul(sr2_2, simd_mul(sr2_2, sigma6_vec)));
MD_SIMD_FLOAT sr6_3 = simd_mul(sr2_3, simd_mul(sr2_3, simd_mul(sr2_3, sigma6_vec)));
MD_SIMD_FLOAT force0 = simd_mul(c48_vec, simd_mul(sr6_0, simd_mul(simd_sub(sr6_0, c05_vec), simd_mul(sr2_0, eps_vec))));
MD_SIMD_FLOAT force1 = simd_mul(c48_vec, simd_mul(sr6_1, simd_mul(simd_sub(sr6_1, c05_vec), simd_mul(sr2_1, eps_vec))));
MD_SIMD_FLOAT force2 = simd_mul(c48_vec, simd_mul(sr6_2, simd_mul(simd_sub(sr6_2, c05_vec), simd_mul(sr2_2, eps_vec))));
MD_SIMD_FLOAT force3 = simd_mul(c48_vec, simd_mul(sr6_3, simd_mul(simd_sub(sr6_3, c05_vec), simd_mul(sr2_3, eps_vec))));
fix0 = simd_masked_add(fix0, simd_mul(delx0, force0), cutoff_mask0);
fiy0 = simd_masked_add(fiy0, simd_mul(dely0, force0), cutoff_mask0);
fiz0 = simd_masked_add(fiz0, simd_mul(delz0, force0), cutoff_mask0);
fix1 = simd_masked_add(fix1, simd_mul(delx1, force1), cutoff_mask1);
fiy1 = simd_masked_add(fiy1, simd_mul(dely1, force1), cutoff_mask1);
fiz1 = simd_masked_add(fiz1, simd_mul(delz1, force1), cutoff_mask1);
fix2 = simd_masked_add(fix2, simd_mul(delx2, force2), cutoff_mask2);
fiy2 = simd_masked_add(fiy2, simd_mul(dely2, force2), cutoff_mask2);
fiz2 = simd_masked_add(fiz2, simd_mul(delz2, force2), cutoff_mask2);
fix3 = simd_masked_add(fix3, simd_mul(delx3, force3), cutoff_mask3);
fiy3 = simd_masked_add(fiy3, simd_mul(dely3, force3), cutoff_mask3);
fiz3 = simd_masked_add(fiz3, simd_mul(delz3, force3), cutoff_mask3);
}
simd_incr_reduced_sum(&ci_f[CL_X_OFFSET], fix0, fix1, fix2, fix3);
simd_incr_reduced_sum(&ci_f[CL_Y_OFFSET], fiy0, fiy1, fiy2, fiy3);
simd_incr_reduced_sum(&ci_f[CL_Z_OFFSET], fiz0, fiz1, fiz2, fiz3);
addStat(stats->calculated_forces, 1);
addStat(stats->num_neighs, numneighs);
addStat(stats->force_iters, (long long int)((double)numneighs * CLUSTER_M / CLUSTER_N));
}
LIKWID_MARKER_STOP("force");
double E = getTimeStamp();
DEBUG_MESSAGE("computeForceLJ_4xn end\n");
return E-S;
}
double computeForceLJ_4xn_full(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
DEBUG_MESSAGE("computeForceLJ_4xn begin\n");
int Nlocal = atom->Nlocal;
int* neighs;
@ -415,3 +730,11 @@ double computeForceLJ_4xn(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
DEBUG_MESSAGE("computeForceLJ_4xn end\n");
return E-S;
}
double computeForceLJ_4xn(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
if(neighbor->half_neigh) {
return computeForceLJ_4xn_half(param, atom, neighbor, stats);
}
return computeForceLJ_4xn_full(param, atom, neighbor, stats);
}

1
gromacs/includes/neighbor.h
View File

@ -31,6 +31,7 @@ typedef struct {
int* neighbors;
int maxneighs;
int* numneigh;
int half_neigh;
} Neighbor;
extern void initNeighbor(Neighbor*, Parameter*);

3
gromacs/includes/parameter.h
View File

@ -48,12 +48,13 @@ typedef struct {
int prune_every;
int x_out_every;
int v_out_every;
int half_neigh;
int nx, ny, nz;
MD_FLOAT dt;
MD_FLOAT dtforce;
MD_FLOAT cutforce;
MD_FLOAT skin;
MD_FLOAT cutneigh;
int nx, ny, nz;
MD_FLOAT lattice;
MD_FLOAT xlo, xhi, ylo, yhi, zlo, zhi;
MD_FLOAT xprd, yprd, zprd;

16
gromacs/includes/simd/avx512_float.h
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@ -42,6 +42,7 @@ static inline MD_SIMD_MASK simd_mask_cond_lt(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b) {
static inline MD_SIMD_MASK simd_mask_from_u32(unsigned int a) { return _cvtu32_mask16(a); }
static inline unsigned int simd_mask_to_u32(MD_SIMD_MASK a) { return _cvtmask16_u32(a); }
static inline MD_SIMD_FLOAT simd_load(MD_FLOAT *p) { return _mm512_load_ps(p); }
static inline MD_SIMD_FLOAT select_by_mask(MD_SIMD_FLOAT a, MD_SIMD_MASK m) { return _mm512_mask_mov_ps(_mm512_setzero_ps(), m, a); }
static inline MD_FLOAT simd_h_reduce_sum(MD_SIMD_FLOAT a) {
// This would only be called in a Mx16 configuration, which is not valid in GROMACS
fprintf(stderr, "simd_h_reduce_sum(): Called with AVX512 intrinsics and single-precision which is not valid!\n");
@ -83,3 +84,18 @@ static inline MD_FLOAT simd_h_dual_incr_reduced_sum(float* m, MD_SIMD_FLOAT v0,
t3 = _mm_add_ps(t3, _mm_permute_ps(t3, 0xb1));
return _mm_cvtss_f32(t3);
}
inline void simd_h_decr(MD_FLOAT *m, MD_SIMD_FLOAT a) {
__m256 t;
a = _mm512_add_ps(a, _mm512_shuffle_f32x4(a, a, 0xee));
t = _mm256_load_ps(m);
t = _mm256_sub_ps(t, _mm512_castps512_ps256(a));
_mm256_store_ps(m, t);
}
static inline void simd_h_decr3(MD_FLOAT *m, MD_SIMD_FLOAT a0, MD_SIMD_FLOAT a1, MD_SIMD_FLOAT a2) {
simd_h_decr(m, a0);
simd_h_decr(m + CLUSTER_M, a1);
simd_h_decr(m + CLUSTER_M * 2, a2);
}

4
gromacs/main.c
View File

@ -198,6 +198,10 @@ int main(int argc, char** argv) {
param.nz = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-half") == 0)) {
param.half_neigh = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-m") == 0) || (strcmp(argv[i], "--mass") == 0)) {
param.mass = atof(argv[++i]);
continue;

49
gromacs/neighbor.c
View File

@ -69,6 +69,7 @@ void initNeighbor(Neighbor *neighbor, Parameter *param) {
bincount = NULL;
bin_clusters = NULL;
bin_nclusters = NULL;
neighbor->half_neigh = param->half_neigh;
neighbor->maxneighs = 100;
neighbor->numneigh = NULL;
neighbor->neighbors = NULL;
@ -223,6 +224,7 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
resize = 0;
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_cj1 = CJ1_FROM_CI(ci);
int *neighptr = &(neighbor->neighbors[ci * neighbor->maxneighs]);
int n = 0;
int ibin = atom->icluster_bin[ci];
@ -246,6 +248,9 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
do {
m++;
cj = loc_bin[m];
if(neighbor->half_neigh && ci_cj1 > cj) {
continue;
}
jbb_zmin = atom->jclusters[cj].bbminz;
jbb_zmax = atom->jclusters[cj].bbmaxz;
dl = ibb_zmin - jbb_zmax;
@ -261,31 +266,33 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
jbb_ymax = atom->jclusters[cj].bbmaxy;
while(m < c) {
dl = ibb_zmin - jbb_zmax;
dh = jbb_zmin - ibb_zmax;
dm = MAX(dl, dh);
dm0 = MAX(dm, 0.0);
d_bb_sq = dm0 * dm0;
if(!neighbor->half_neigh || ci_cj1 <= cj) {
dl = ibb_zmin - jbb_zmax;
dh = jbb_zmin - ibb_zmax;
dm = MAX(dl, dh);
dm0 = MAX(dm, 0.0);
d_bb_sq = dm0 * dm0;
/*if(d_bb_sq > cutneighsq) {
break;
}*/
/*if(d_bb_sq > cutneighsq) {
break;
}*/
dl = ibb_ymin - jbb_ymax;
dh = jbb_ymin - ibb_ymax;
dm = MAX(dl, dh);
dm0 = MAX(dm, 0.0);
d_bb_sq += dm0 * dm0;
dl = ibb_ymin - jbb_ymax;
dh = jbb_ymin - ibb_ymax;
dm = MAX(dl, dh);
dm0 = MAX(dm, 0.0);
d_bb_sq += dm0 * dm0;
dl = ibb_xmin - jbb_xmax;
dh = jbb_xmin - ibb_xmax;
dm = MAX(dl, dh);
dm0 = MAX(dm, 0.0);
d_bb_sq += dm0 * dm0;
dl = ibb_xmin - jbb_xmax;
dh = jbb_xmin - ibb_xmax;
dm = MAX(dl, dh);
dm0 = MAX(dm, 0.0);
d_bb_sq += dm0 * dm0;
if(d_bb_sq < cutneighsq) {
if(d_bb_sq < rbb_sq || atomDistanceInRange(atom, ci, cj, cutneighsq)) {
neighptr[n++] = cj;
if(d_bb_sq < cutneighsq) {
if(d_bb_sq < rbb_sq || atomDistanceInRange(atom, ci, cj, cutneighsq)) {
neighptr[n++] = cj;
}
}
}

3
gromacs/parameter.c
View File

@ -43,6 +43,7 @@ void initParameter(Parameter *param) {
param->nx = 32;
param->ny = 32;
param->nz = 32;
param->half_neigh = 0;
param->cutforce = 2.5;
param->skin = 0.3;
param->cutneigh = param->cutforce + param->skin;
@ -101,6 +102,7 @@ void readParameter(Parameter *param, const char *filename) {
PARSE_INT(nx);
PARSE_INT(ny);
PARSE_INT(nz);
PARSE_INT(half_neigh);
PARSE_INT(nstat);
PARSE_INT(reneigh_every);
PARSE_INT(prune_every);
@ -152,5 +154,6 @@ void printParameter(Parameter *param) {
printf("\tDelta time (dt): %e\n", param->dt);
printf("\tCutoff radius: %e\n", param->cutforce);
printf("\tSkin: %e\n", param->skin);
printf("\tHalf neighbor lists: %d\n", param->half_neigh);
printf("\tProcessor frequency (GHz): %.4f\n\n", param->proc_freq);
}