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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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1
gromacs/includes/neighbor.h
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@@ -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
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@@ -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);
}