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Pre-compute masks in the same way as in the master branch

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2023-03-28 17:32:42 +02:00
parent a86d214c73
commit 965fda3879
4 changed files with 67 additions and 35 deletions
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1
Makefile
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@ -152,6 +152,7 @@ $(BUILD_DIR)/%.o: %.s
clean: clean:
$(info ===> CLEAN) $(info ===> CLEAN)
@rm -rf $(BUILD_DIR) @rm -rf $(BUILD_DIR)
@rm -rf MDBench-$(IDENTIFIER)
@rm -f tags @rm -f tags
cleanall: cleanall:

70
gromacs/atom.c
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@ -37,6 +37,7 @@ void initAtom(Atom *atom) {
atom->iclusters = NULL; atom->iclusters = NULL;
atom->jclusters = NULL; atom->jclusters = NULL;
atom->icluster_bin = NULL; atom->icluster_bin = NULL;
initMasks(atom);
} }
void createAtom(Atom *atom, Parameter *param) { void createAtom(Atom *atom, Parameter *param) {
@ -50,9 +51,6 @@ void createAtom(Atom *atom, Parameter *param) {
atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT)); atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT)); atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT)); atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->exclusion_filter = allocate(ALIGNMENT, CLUSTER_M * VECTOR_WIDTH * sizeof(MD_UINT));
atom->diagonal_4xn_j_minus_i = allocate(ALIGNMENT, MAX(CLUSTER_M, VECTOR_WIDTH) * sizeof(MD_UINT));
atom->diagonal_2xnn_j_minus_i = allocate(ALIGNMENT, VECTOR_WIDTH * sizeof(MD_UINT));
for(int i = 0; i < atom->ntypes * atom->ntypes; i++) { for(int i = 0; i < atom->ntypes * atom->ntypes; i++) {
atom->epsilon[i] = param->epsilon; atom->epsilon[i] = param->epsilon;
@ -61,19 +59,6 @@ void createAtom(Atom *atom, Parameter *param) {
atom->cutforcesq[i] = param->cutforce * param->cutforce; atom->cutforcesq[i] = param->cutforce * param->cutforce;
} }
for(int j = 0; j < MAX(CLUSTER_M, VECTOR_WIDTH); j++) {
atom->diagonal_4xn_j_minus_i[j] = (MD_FLOAT)(j) - 0.5;
}
for(int j = 0; j < VECTOR_WIDTH / 2; j++) {
atom->diagonal_2xnn_j_minus_i[j] = (MD_FLOAT)(j) - 0.5;
atom->diagonal_2xnn_j_minus_i[VECTOR_WIDTH / 2 + j] = (MD_FLOAT)(j - 1) - 0.5;
}
for(int i = 0; i < CLUSTER_M * VECTOR_WIDTH; i++) {
atom->exclusion_filter[i] = (1U << i);
}
MD_FLOAT alat = pow((4.0 / param->rho), (1.0 / 3.0)); MD_FLOAT alat = pow((4.0 / param->rho), (1.0 / 3.0));
int ilo = (int) (xlo / (0.5 * alat) - 1); int ilo = (int) (xlo / (0.5 * alat) - 1);
int ihi = (int) (xhi / (0.5 * alat) + 1); int ihi = (int) (xhi / (0.5 * alat) + 1);
@ -409,6 +394,59 @@ int readAtom_dmp(Atom* atom, Parameter* param) {
return natoms; return natoms;
} }
void initMasks(Atom *atom) {
const unsigned int half_mask_bits = VECTOR_WIDTH >> 1;
unsigned int mask0, mask1, mask2, mask3;
atom->exclusion_filter = allocate(ALIGNMENT, CLUSTER_M * VECTOR_WIDTH * sizeof(MD_UINT));
atom->diagonal_4xn_j_minus_i = allocate(ALIGNMENT, MAX(CLUSTER_M, VECTOR_WIDTH) * sizeof(MD_UINT));
atom->diagonal_2xnn_j_minus_i = allocate(ALIGNMENT, VECTOR_WIDTH * sizeof(MD_UINT));
//atom->masks_2xnn = allocate(ALIGNMENT, 8 * sizeof(unsigned int));
for(int j = 0; j < MAX(CLUSTER_M, VECTOR_WIDTH); j++) {
atom->diagonal_4xn_j_minus_i[j] = (MD_FLOAT)(j) - 0.5;
}
for(int j = 0; j < VECTOR_WIDTH / 2; j++) {
atom->diagonal_2xnn_j_minus_i[j] = (MD_FLOAT)(j) - 0.5;
atom->diagonal_2xnn_j_minus_i[VECTOR_WIDTH / 2 + j] = (MD_FLOAT)(j - 1) - 0.5;
}
for(int i = 0; i < CLUSTER_M * VECTOR_WIDTH; i++) {
atom->exclusion_filter[i] = (1U << i);
}
#if CLUSTER_M == CLUSTER_N
for(unsigned int cond0 = 0; cond0 < 2; cond0++) {
mask0 = (unsigned int)(0xf - 0x1 * cond0);
mask1 = (unsigned int)(0xf - 0x3 * cond0);
mask2 = (unsigned int)(0xf - 0x7 * cond0);
mask3 = (unsigned int)(0xf - 0xf * cond0);
atom->masks_2xnn[cond0 * 2 + 0] = (mask1 << half_mask_bits) | mask0;
atom->masks_2xnn[cond0 * 2 + 1] = (mask3 << half_mask_bits) | mask2;
}
#else
for(unsigned int cond0 = 0; cond0 < 2; cond0++) {
for(unsigned int cond1 = 0; cond1 < 2; cond1++) {
#if CLUSTER_M < CLUSTER_N
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
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
atom->masks_2xnn[cond0 * 4 + cond1 * 2 + 0] = (mask1 << half_mask_bits) | mask0;
atom->masks_2xnn[cond0 * 4 + cond1 * 2 + 1] = (mask3 << half_mask_bits) | mask2;
}
}
#endif
}
void growAtom(Atom *atom) { void growAtom(Atom *atom) {
int nold = atom->Nmax; int nold = atom->Nmax;
atom->Nmax += DELTA; atom->Nmax += DELTA;

29
gromacs/force_lj.c
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@ -165,7 +165,6 @@ double computeForceLJ_2xnn_half(Parameter *param, Atom *atom, Neighbor *neighbor
MD_SIMD_FLOAT eps_vec = simd_broadcast(epsilon); MD_SIMD_FLOAT eps_vec = simd_broadcast(epsilon);
MD_SIMD_FLOAT c48_vec = simd_broadcast(48.0); MD_SIMD_FLOAT c48_vec = simd_broadcast(48.0);
MD_SIMD_FLOAT c05_vec = simd_broadcast(0.5); 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++) { for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci); int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
@ -236,7 +235,6 @@ double computeForceLJ_2xnn_half(Parameter *param, Atom *atom, Neighbor *neighbor
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; k++) {
unsigned int mask0, mask1, mask2, mask3;
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;
@ -261,30 +259,23 @@ double computeForceLJ_2xnn_half(Parameter *param, Atom *atom, Neighbor *neighbor
#if CLUSTER_M == CLUSTER_N #if CLUSTER_M == CLUSTER_N
unsigned int cond0 = (unsigned int)(cj == ci_cj0); unsigned int cond0 = (unsigned int)(cj == ci_cj0);
mask0 = (unsigned int)(0xf - 0x1 * cond0); MD_SIMD_MASK excl_mask0 = simd_mask_from_u32(atom->masks_2xnn[cond0 * 2 + 0]);
mask1 = (unsigned int)(0xf - 0x3 * cond0); MD_SIMD_MASK excl_mask2 = simd_mask_from_u32(atom->masks_2xnn[cond0 * 2 + 1]);
mask2 = (unsigned int)(0xf - 0x7 * cond0); #else
mask3 = (unsigned int)(0xf - 0xf * cond0); #if CLUSTER_M < CLUSTER_N
#elif CLUSTER_M < CLUSTER_N
unsigned int cond0 = (unsigned int)((cj << 1) + 0 == ci); unsigned int cond0 = (unsigned int)((cj << 1) + 0 == ci);
unsigned int cond1 = (unsigned int)((cj << 1) + 1 == 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 #else
unsigned int cond0 = (unsigned int)(cj == ci_cj0); unsigned int cond0 = (unsigned int)(cj == ci_cj0);
unsigned int cond1 = (unsigned int)(cj == ci_cj1); unsigned int cond1 = (unsigned int)(cj == ci_cj1);
mask0 = (unsigned int)(0x3 - 0x1 * cond0); #endif
mask1 = (unsigned int)(0x3 - 0x3 * cond0); MD_SIMD_MASK excl_mask0 = simd_mask_from_u32(atom->masks_2xnn[cond0 * 4 + cond1 * 2 + 0]);
mask2 = (unsigned int)(0x3 - cond0 * 0x3 - 0x1 * cond1); MD_SIMD_MASK excl_mask2 = simd_mask_from_u32(atom->masks_2xnn[cond0 * 4 + cond1 * 2 + 1]);
mask3 = (unsigned int)(0x3 - cond0 * 0x3 - 0x3 * cond1);
#endif #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_MASK cutoff_mask0 = simd_mask_cond_lt(rsq0, cutforcesq_vec); 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_MASK cutoff_mask2 = simd_mask_cond_lt(rsq2, cutforcesq_vec);
cutoff_mask0 = simd_mask_and(cutoff_mask0, excl_mask0); cutoff_mask0 = simd_mask_and(cutoff_mask0, excl_mask0);
cutoff_mask2 = simd_mask_and(cutoff_mask2, excl_mask2); cutoff_mask2 = simd_mask_and(cutoff_mask2, excl_mask2);
@ -308,8 +299,8 @@ double computeForceLJ_2xnn_half(Parameter *param, Atom *atom, Neighbor *neighbor
MD_SIMD_FLOAT sr2_0 = simd_reciprocal(rsq0); MD_SIMD_FLOAT sr2_0 = simd_reciprocal(rsq0);
MD_SIMD_FLOAT sr2_2 = simd_reciprocal(rsq2); MD_SIMD_FLOAT sr2_2 = simd_reciprocal(rsq2);
MD_SIMD_FLOAT sr6_0 = sr2_0 * sr2_0 * sr2_0; MD_SIMD_FLOAT sr6_0 = sr2_0 * sr2_0 * sr2_0 * sigma6_vec;
MD_SIMD_FLOAT sr6_2 = sr2_2 * sr2_2 * sr2_2; 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 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 force2 = c48_vec * sr6_2 * (sr6_2 - c05_vec) * sr2_2 * eps_vec;

2
gromacs/includes/atom.h
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@ -124,9 +124,11 @@ typedef struct {
MD_UINT *exclusion_filter; MD_UINT *exclusion_filter;
MD_FLOAT *diagonal_4xn_j_minus_i; MD_FLOAT *diagonal_4xn_j_minus_i;
MD_FLOAT *diagonal_2xnn_j_minus_i; MD_FLOAT *diagonal_2xnn_j_minus_i;
unsigned int masks_2xnn[8];
} Atom; } Atom;
extern void initAtom(Atom*); extern void initAtom(Atom*);
extern void initMasks(Atom*);
extern void createAtom(Atom*, Parameter*); extern void createAtom(Atom*, Parameter*);
extern int readAtom(Atom*, Parameter*); extern int readAtom(Atom*, Parameter*);
extern int readAtom_pdb(Atom*, Parameter*); extern int readAtom_pdb(Atom*, Parameter*);