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Optimize partial forces reduction for compute_4xn kernel

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-03-16 17:54:52 +01:00
parent f3263a2d48
commit 4090f43095
2 changed files with 44 additions and 7 deletions
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21
gromacs/force_lj.c
View File

@ -239,9 +239,9 @@ double computeForceLJ_2xnn(Parameter *param, Atom *atom, Neighbor *neighbor, Sta
fiz2 = simd_masked_add(fiz2, simd_mul(delz2, force2), cutoff_mask2); fiz2 = simd_masked_add(fiz2, simd_mul(delz2, force2), cutoff_mask2);
} }
simd_h_dual_reduce_sum(&ci_f[CL_X_OFFSET], fix0, fix2); simd_h_dual_incr_reduced_sum(&ci_f[CL_X_OFFSET], fix0, fix2);
simd_h_dual_reduce_sum(&ci_f[CL_Y_OFFSET], fiy0, fiy2); simd_h_dual_incr_reduced_sum(&ci_f[CL_Y_OFFSET], fiy0, fiy2);
simd_h_dual_reduce_sum(&ci_f[CL_Z_OFFSET], fiz0, fiz2); simd_h_dual_incr_reduced_sum(&ci_f[CL_Z_OFFSET], fiz0, fiz2);
addStat(stats->calculated_forces, 1); addStat(stats->calculated_forces, 1);
addStat(stats->num_neighs, numneighs); addStat(stats->num_neighs, numneighs);
@ -269,6 +269,16 @@ double computeForceLJ_4xn(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
double S = getTimeStamp(); double S = getTimeStamp();
LIKWID_MARKER_START("force"); 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 #pragma omp parallel for
for(int ci = 0; ci < atom->Nclusters_local; ci++) { for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_cj0 = CJ0_FROM_CI(ci); int ci_cj0 = CJ0_FROM_CI(ci);
@ -387,6 +397,10 @@ double computeForceLJ_4xn(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
fiz3 = simd_masked_add(fiz3, simd_mul(delz3, 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);
/*
ci_f[CL_X_OFFSET + 0] = simd_h_reduce_sum(fix0); ci_f[CL_X_OFFSET + 0] = simd_h_reduce_sum(fix0);
ci_f[CL_X_OFFSET + 1] = simd_h_reduce_sum(fix1); ci_f[CL_X_OFFSET + 1] = simd_h_reduce_sum(fix1);
ci_f[CL_X_OFFSET + 2] = simd_h_reduce_sum(fix2); ci_f[CL_X_OFFSET + 2] = simd_h_reduce_sum(fix2);
@ -399,6 +413,7 @@ double computeForceLJ_4xn(Parameter *param, Atom *atom, Neighbor *neighbor, Stat
ci_f[CL_Z_OFFSET + 1] = simd_h_reduce_sum(fiz1); ci_f[CL_Z_OFFSET + 1] = simd_h_reduce_sum(fiz1);
ci_f[CL_Z_OFFSET + 2] = simd_h_reduce_sum(fiz2); ci_f[CL_Z_OFFSET + 2] = simd_h_reduce_sum(fiz2);
ci_f[CL_Z_OFFSET + 3] = simd_h_reduce_sum(fiz3); ci_f[CL_Z_OFFSET + 3] = simd_h_reduce_sum(fiz3);
*/
addStat(stats->calculated_forces, 1); addStat(stats->calculated_forces, 1);
addStat(stats->num_neighs, numneighs); addStat(stats->num_neighs, numneighs);

30
gromacs/includes/simd/avx512_double.h
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@ -29,7 +29,7 @@
#define MD_SIMD_FLOAT __m512d #define MD_SIMD_FLOAT __m512d
#define MD_SIMD_MASK __mmask8 #define MD_SIMD_MASK __mmask8
static inline MD_SIMD_FLOAT simd_broadcast(double scalar) { return _mm512_set1_pd(scalar); } static inline MD_SIMD_FLOAT simd_broadcast(MD_FLOAT scalar) { return _mm512_set1_pd(scalar); }
static inline MD_SIMD_FLOAT simd_zero() { return _mm512_set1_pd(0.0); } static inline MD_SIMD_FLOAT simd_zero() { return _mm512_set1_pd(0.0); }
static inline MD_SIMD_FLOAT simd_add(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b) { return _mm512_add_pd(a, b); } static inline MD_SIMD_FLOAT simd_add(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b) { return _mm512_add_pd(a, b); }
static inline MD_SIMD_FLOAT simd_sub(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b) { return _mm512_sub_pd(a, b); } static inline MD_SIMD_FLOAT simd_sub(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b) { return _mm512_sub_pd(a, b); }
@ -50,15 +50,37 @@ static inline MD_FLOAT simd_h_reduce_sum(MD_SIMD_FLOAT a) {
return *((MD_FLOAT *) &x); return *((MD_FLOAT *) &x);
} }
static inline MD_SIMD_FLOAT simd_load_h_duplicate(const double* m) { static inline MD_FLOAT simd_incr_reduced_sum(MD_FLOAT *m, MD_SIMD_FLOAT v0, MD_SIMD_FLOAT v1, MD_SIMD_FLOAT v2, MD_SIMD_FLOAT v3) {
__m512d t0, t2;
__m256d t3, t4;
t0 = _mm512_add_pd(v0, _mm512_permute_pd(v0, 0x55));
t2 = _mm512_add_pd(v2, _mm512_permute_pd(v2, 0x55));
t0 = _mm512_mask_add_pd(t0, simd_mask_from_u32(0xaa), v1, _mm512_permute_pd(v1, 0x55));
t2 = _mm512_mask_add_pd(t2, simd_mask_from_u32(0xaa), v3, _mm512_permute_pd(v3, 0x55));
t0 = _mm512_add_pd(t0, _mm512_shuffle_f64x2(t0, t0, 0x4e));
t0 = _mm512_mask_add_pd(t0, simd_mask_from_u32(0xF0), t2, _mm512_shuffle_f64x2(t2, t2, 0x4e));
t0 = _mm512_add_pd(t0, _mm512_shuffle_f64x2(t0, t0, 0xb1));
t0 = _mm512_mask_shuffle_f64x2(t0, simd_mask_from_u32(0x0C), t0, t0, 0xee);
t3 = _mm512_castpd512_pd256(t0);
t4 = _mm256_load_pd(m);
t4 = _mm256_add_pd(t4, t3);
_mm256_store_pd(m, t4);
t0 = _mm512_add_pd(t0, _mm512_permutex_pd(t0, 0x4e));
t0 = _mm512_add_pd(t0, _mm512_permutex_pd(t0, 0xb1));
return _mm_cvtsd_f64(_mm512_castpd512_pd128(t0));
}
static inline MD_SIMD_FLOAT simd_load_h_duplicate(const MD_FLOAT *m) {
return _mm512_broadcast_f64x4(_mm256_load_pd(m)); return _mm512_broadcast_f64x4(_mm256_load_pd(m));
} }
static inline MD_SIMD_FLOAT simd_load_h_dual(const double* m) { static inline MD_SIMD_FLOAT simd_load_h_dual(const MD_FLOAT *m) {
return _mm512_insertf64x4(_mm512_broadcastsd_pd(_mm_load_sd(m)), _mm256_broadcastsd_pd(_mm_load_sd(m + 1)), 1); return _mm512_insertf64x4(_mm512_broadcastsd_pd(_mm_load_sd(m)), _mm256_broadcastsd_pd(_mm_load_sd(m + 1)), 1);
} }
static inline double simd_h_dual_reduce_sum(double* m, MD_SIMD_FLOAT v0, MD_SIMD_FLOAT v1) { static inline MD_FLOAT simd_h_dual_incr_reduced_sum(MD_FLOAT *m, MD_SIMD_FLOAT v0, MD_SIMD_FLOAT v1) {
__m512d t0; __m512d t0;
__m256d t2, t3; __m256d t2, t3;