diff --git a/Makefile b/Makefile index 3535aa5..df99a25 100644 --- a/Makefile +++ b/Makefile @@ -15,6 +15,9 @@ INCLUDES += -I./$(SRC_DIR)/includes ifeq ($(strip $(DATA_LAYOUT)),AOS) DEFINES += -DAOS endif +ifeq ($(strip $(CLUSTER_LAYOUT)),AOS) +DEFINES += -DCLUSTER_AOS +endif ifeq ($(strip $(DATA_TYPE)),SP) DEFINES += -DPRECISION=1 else @@ -49,6 +52,10 @@ ifeq ($(strip $(COMPUTE_STATS)),true) DEFINES += -DCOMPUTE_STATS endif +ifeq ($(strip $(USE_REFERENCE_VERSION)),true) + DEFINES += -DUSE_REFERENCE_VERSION +endif + ifneq ($(VECTOR_WIDTH),) DEFINES += -DVECTOR_WIDTH=$(VECTOR_WIDTH) endif diff --git a/config.mk b/config.mk index 90c619b..2f16422 100644 --- a/config.mk +++ b/config.mk @@ -1,7 +1,7 @@ # Compiler tag (GCC/CLANG/ICC) TAG ?= ICC # Optimization scheme (lammps/gromacs/clusters_per_bin) -OPT_SCHEME = lammps +OPT_SCHEME = gromacs # Enable likwid (true or false) ENABLE_LIKWID ?= false # SP or DP @@ -26,6 +26,12 @@ VECTOR_WIDTH ?= 8 # Compute statistics COMPUTE_STATS ?= true +# Configurations for gromacs optimization scheme +# AOS or SOA +CLUSTER_LAYOUT ?= SOA +# Use reference version +USE_REFERENCE_VERSION ?= true + #Feature options OPTIONS = -DALIGNMENT=64 #OPTIONS += More options diff --git a/gromacs/atom.c b/gromacs/atom.c index 9e0e830..74afc7a 100644 --- a/gromacs/atom.c +++ b/gromacs/atom.c @@ -284,7 +284,7 @@ void growClusters(Atom *atom) int nold = atom->Nclusters_max; atom->Nclusters_max += DELTA; atom->clusters = (Cluster*) reallocate(atom->clusters, ALIGNMENT, atom->Nclusters_max * sizeof(Cluster), nold * sizeof(Cluster)); - atom->cl_x = (MD_FLOAT*) reallocate(atom->cl_x, ALIGNMENT, atom->Nclusters_max * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT), nold * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT)); - atom->cl_f = (MD_FLOAT*) reallocate(atom->cl_f, ALIGNMENT, atom->Nclusters_max * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT), nold * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT)); - atom->cl_v = (MD_FLOAT*) reallocate(atom->cl_v, ALIGNMENT, atom->Nclusters_max * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT), nold * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT)); + atom->cl_x = (MD_FLOAT*) reallocate(atom->cl_x, ALIGNMENT, atom->Nclusters_max * CLUSTER_DIM_M * 3 * sizeof(MD_FLOAT), nold * CLUSTER_DIM_M * 3 * sizeof(MD_FLOAT)); + atom->cl_f = (MD_FLOAT*) reallocate(atom->cl_f, ALIGNMENT, atom->Nclusters_max * CLUSTER_DIM_M * 3 * sizeof(MD_FLOAT), nold * CLUSTER_DIM_M * 3 * sizeof(MD_FLOAT)); + atom->cl_v = (MD_FLOAT*) reallocate(atom->cl_v, ALIGNMENT, atom->Nclusters_max * CLUSTER_DIM_M * 3 * sizeof(MD_FLOAT), nold * CLUSTER_DIM_M * 3 * sizeof(MD_FLOAT)); } diff --git a/gromacs/force_lj.c b/gromacs/force_lj.c index 1392731..cfc3029 100644 --- a/gromacs/force_lj.c +++ b/gromacs/force_lj.c @@ -29,9 +29,10 @@ #include #include #include +#include -double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) { +double computeForceLJ_ref(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) { DEBUG_MESSAGE("computeForceLJ begin\n"); int Nlocal = atom->Nlocal; int* neighs; @@ -69,7 +70,7 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s MD_FLOAT fiy = 0; MD_FLOAT fiz = 0; - for(int cjj = 0; cjj < CLUSTER_DIM_N; cjj++) { + for(int cjj = 0; cjj < CLUSTER_DIM_M; cjj++) { if(ci != cj || cii != cjj) { MD_FLOAT delx = xtmp - cluster_x(cjptr, cjj); MD_FLOAT dely = ytmp - cluster_y(cjptr, cjj); @@ -101,3 +102,153 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s DEBUG_MESSAGE("computeForceLJ end\n"); return E-S; } + + +double computeForceLJ_4xn(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 epsilon_vec = simd_broadcast(epsilon); + MD_SIMD_FLOAT c48_vec = simd_broadcast(48.0); + MD_SIMD_FLOAT c05_vec = simd_broadcast(0.5); + const int unroll_j = CLUSTER_DIM_N / CLUSTER_DIM_M; + + for(int ci = 0; ci < atom->Nclusters_local; ci++) { + MD_FLOAT *fptr = cluster_force_ptr(ci); + for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) { + cluster_x(fptr, cii) = 0.0; + cluster_y(fptr, cii) = 0.0; + cluster_z(fptr, cii) = 0.0; + } + } + + double S = getTimeStamp(); + LIKWID_MARKER_START("force"); + + #pragma omp parallel for + for(int ci = 0; ci < atom->Nclusters_local; ci++) { + MD_FLOAT *ciptr = cluster_pos_ptr(ci); + MD_FLOAT *cifptr = cluster_force_ptr(ci); + neighs = &neighbor->neighbors[ci * neighbor->maxneighs]; + int numneighs = neighbor->numneigh[ci]; + + MD_SIMD_FLOAT xi0_tmp = simd_broadcast(cluster_x(ciptr, 0)); + MD_SIMD_FLOAT yi0_tmp = simd_broadcast(cluster_y(ciptr, 0)); + MD_SIMD_FLOAT zi0_tmp = simd_broadcast(cluster_z(ciptr, 0)); + MD_SIMD_FLOAT xi1_tmp = simd_broadcast(cluster_x(ciptr, 1)); + MD_SIMD_FLOAT yi1_tmp = simd_broadcast(cluster_y(ciptr, 1)); + MD_SIMD_FLOAT zi1_tmp = simd_broadcast(cluster_z(ciptr, 1)); + MD_SIMD_FLOAT xi2_tmp = simd_broadcast(cluster_x(ciptr, 2)); + MD_SIMD_FLOAT yi2_tmp = simd_broadcast(cluster_y(ciptr, 2)); + MD_SIMD_FLOAT zi2_tmp = simd_broadcast(cluster_z(ciptr, 2)); + MD_SIMD_FLOAT xi3_tmp = simd_broadcast(cluster_x(ciptr, 3)); + MD_SIMD_FLOAT yi3_tmp = simd_broadcast(cluster_y(ciptr, 3)); + MD_SIMD_FLOAT zi3_tmp = simd_broadcast(cluster_z(ciptr, 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 += unroll_j) { + int cj0 = neighs[k + 0]; + int cj1 = neighs[k + 1]; + unsigned int cond0 = (unsigned int)(ci == cj0); + unsigned int cond1 = (unsigned int)(ci == cj1); + MD_FLOAT *cj0_ptr = cluster_pos_ptr(cj0); + MD_FLOAT *cj1_ptr = cluster_pos_ptr(cj1); + MD_SIMD_FLOAT xj_tmp = simd_gather2(cj0_ptr, cj1_ptr, 0); + MD_SIMD_FLOAT yj_tmp = simd_gather2(cj0_ptr, cj1_ptr, 1); + MD_SIMD_FLOAT zj_tmp = simd_gather2(cj0_ptr, cj1_ptr, 2); + + 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); + + MD_SIMD_MASK excl_mask0 = simd_mask_from_u32((unsigned int)(0xff - 0x80 * cond0 - 0x8 * cond1)); + MD_SIMD_MASK excl_mask1 = simd_mask_from_u32((unsigned int)(0xff - 0x40 * cond0 - 0x4 * cond1)); + MD_SIMD_MASK excl_mask2 = simd_mask_from_u32((unsigned int)(0xff - 0x20 * cond0 - 0x2 * cond1)); + MD_SIMD_MASK excl_mask3 = simd_mask_from_u32((unsigned int)(0xff - 0x10 * cond0 - 0x1 * cond1)); + + 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, epsilon_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, epsilon_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, epsilon_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, epsilon_vec)))); + + simd_masked_add(fix0, simd_mul(delx0, force0), cutoff_mask0); + simd_masked_add(fiy0, simd_mul(dely0, force0), cutoff_mask0); + simd_masked_add(fiz0, simd_mul(delz0, force0), cutoff_mask0); + simd_masked_add(fix1, simd_mul(delx1, force1), cutoff_mask1); + simd_masked_add(fiy1, simd_mul(dely1, force1), cutoff_mask1); + simd_masked_add(fiz1, simd_mul(delz1, force1), cutoff_mask1); + simd_masked_add(fix2, simd_mul(delx2, force2), cutoff_mask2); + simd_masked_add(fiy2, simd_mul(dely2, force2), cutoff_mask2); + simd_masked_add(fiz2, simd_mul(delz2, force2), cutoff_mask2); + simd_masked_add(fix3, simd_mul(delx3, force3), cutoff_mask3); + simd_masked_add(fiy3, simd_mul(dely3, force3), cutoff_mask3); + simd_masked_add(fiz3, simd_mul(delz3, force3), cutoff_mask3); + } + + cluster_x(cifptr, 0) = simd_horizontal_sum(fix0); + cluster_y(cifptr, 0) = simd_horizontal_sum(fiy0); + cluster_z(cifptr, 0) = simd_horizontal_sum(fiz0); + cluster_x(cifptr, 1) = simd_horizontal_sum(fix1); + cluster_y(cifptr, 1) = simd_horizontal_sum(fiy1); + cluster_z(cifptr, 1) = simd_horizontal_sum(fiz1); + cluster_x(cifptr, 2) = simd_horizontal_sum(fix2); + cluster_y(cifptr, 2) = simd_horizontal_sum(fiy2); + cluster_z(cifptr, 2) = simd_horizontal_sum(fiz2); + cluster_x(cifptr, 3) = simd_horizontal_sum(fix3); + cluster_y(cifptr, 3) = simd_horizontal_sum(fiy3); + cluster_z(cifptr, 3) = simd_horizontal_sum(fiz3); + + addStat(stats->total_force_neighs, numneighs); + addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH); + } + + LIKWID_MARKER_STOP("force"); + double E = getTimeStamp(); + DEBUG_MESSAGE("computeForceLJ_4xn end\n"); + return E-S; +} diff --git a/gromacs/includes/atom.h b/gromacs/includes/atom.h index 4b04fda..87cf71f 100644 --- a/gromacs/includes/atom.h +++ b/gromacs/includes/atom.h @@ -26,12 +26,12 @@ #define __ATOM_H_ #define CLUSTER_DIM_M 4 -#define CLUSTER_DIM_N 4 +#define CLUSTER_DIM_N 8 typedef struct { int bin; int natoms; - int type[CLUSTER_DIM_N]; + int type[CLUSTER_DIM_M]; MD_FLOAT bbminx, bbmaxx; MD_FLOAT bbminy, bbmaxy; MD_FLOAT bbminz, bbmaxz; @@ -62,26 +62,30 @@ extern int readAtom(Atom*, Parameter*); extern void growAtom(Atom*); extern void growClusters(Atom*); -#define cluster_pos_ptr(ci) &(atom->cl_x[(ci) * CLUSTER_DIM_N * 3]) -#define cluster_velocity_ptr(ci) &(atom->cl_v[(ci) * CLUSTER_DIM_N * 3]) -#define cluster_force_ptr(ci) &(atom->cl_f[(ci) * CLUSTER_DIM_N * 3]) +#define cluster_pos_ptr(ci) &(atom->cl_x[(ci) * CLUSTER_DIM_M * 3]) +#define cluster_velocity_ptr(ci) &(atom->cl_v[(ci) * CLUSTER_DIM_M * 3]) +#define cluster_force_ptr(ci) &(atom->cl_f[(ci) * CLUSTER_DIM_M * 3]) #ifdef AOS #define POS_DATA_LAYOUT "AoS" #define atom_x(i) atom->x[(i) * 3 + 0] #define atom_y(i) atom->x[(i) * 3 + 1] #define atom_z(i) atom->x[(i) * 3 + 2] -#define cluster_x(cptr, i) cptr[(i) * 3 + 0] -#define cluster_y(cptr, i) cptr[(i) * 3 + 1] -#define cluster_z(cptr, i) cptr[(i) * 3 + 2] #else #define POS_DATA_LAYOUT "SoA" #define atom_x(i) atom->x[i] #define atom_y(i) atom->y[i] #define atom_z(i) atom->z[i] -#define cluster_x(cptr, i) cptr[0 * CLUSTER_DIM_N + (i)] -#define cluster_y(cptr, i) cptr[1 * CLUSTER_DIM_N + (i)] -#define cluster_z(cptr, i) cptr[2 * CLUSTER_DIM_N + (i)] +#endif + +#ifdef CLUSTER_AOS +#define cluster_x(cptr, i) cptr[(i) * 3 + 0] +#define cluster_y(cptr, i) cptr[(i) * 3 + 1] +#define cluster_z(cptr, i) cptr[(i) * 3 + 2] +#else +#define cluster_x(cptr, i) cptr[0 * CLUSTER_DIM_M + (i)] +#define cluster_y(cptr, i) cptr[1 * CLUSTER_DIM_M + (i)] +#define cluster_z(cptr, i) cptr[2 * CLUSTER_DIM_M + (i)] #endif #endif diff --git a/gromacs/includes/simd.h b/gromacs/includes/simd.h new file mode 100644 index 0000000..1c867df --- /dev/null +++ b/gromacs/includes/simd.h @@ -0,0 +1,61 @@ +/* + * ======================================================================================= + * + * Author: Jan Eitzinger (je), jan.eitzinger@fau.de + * Copyright (c) 2020 RRZE, University Erlangen-Nuremberg + * + * This file is part of MD-Bench. + * + * MD-Bench is free software: you can redistribute it and/or modify it + * under the terms of the GNU Lesser General Public License as published + * by the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY + * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A + * PARTICULAR PURPOSE. See the GNU Lesser General Public License for more + * details. + * + * You should have received a copy of the GNU Lesser General Public License along + * with MD-Bench. If not, see . + * ======================================================================================= + */ + +#include +#include + +#define MD_SIMD_FLOAT __m512d +#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_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_sub(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b) { return _mm512_sub_pd(a, b); } +static inline MD_SIMD_FLOAT simd_mul(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b) { return _mm512_mul_pd(a, b); } +static inline MD_SIMD_FLOAT simd_fma(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b, MD_SIMD_FLOAT c) { return _mm512_fmadd_pd(a, b, c); } +static inline MD_SIMD_FLOAT simd_reciprocal(MD_SIMD_FLOAT a) { return _mm512_rcp14_pd(a); } +static inline MD_SIMD_FLOAT simd_masked_add(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b, MD_SIMD_MASK m) { return _mm512_mask_add_pd(a, m, a, b); } +static inline MD_SIMD_MASK simd_mask_from_u32(unsigned int m) { return _cvtu32_mask8(m); } +static inline MD_SIMD_MASK simd_mask_and(MD_SIMD_MASK a, MD_SIMD_MASK b) { return _kand_mask8(a, b); } +static inline MD_SIMD_MASK simd_mask_cond_lt(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b) { return _mm512_cmp_pd_mask(a, b, _CMP_LT_OQ); } + +static MD_SIMD_FLOAT simd_gather2(MD_FLOAT *c0, MD_FLOAT *c1, int d) { + MD_SIMD_FLOAT x; +#ifdef CLUSTER_AOS + __m256i aos_gather_vindex = _mm256_set_epi32(9, 6, 3, 0, 9, 6, 3, 0); + __m256i vindex = _mm256_add_epi32(aos_gather_vindex, _mm256_set1_epi32(d)); + x = _mm512_mask_i32gather_pd(simd_zero(), simd_mask_from_u32(0x0f), vindex, c0, sizeof(double)); + x = _mm512_mask_i32gather_pd(x, simd_mask_from_u32(0xf0), vindex, c1, sizeof(double)); +#else + x = _mm512_loadu_pd(&c0[d * CLUSTER_DIM_M]); + x = _mm512_insertf64x4(x, _mm256_loadu_pd(&c1[d * CLUSTER_DIM_M]), 1); +#endif + return x; +} + +static inline MD_FLOAT simd_horizontal_sum(MD_SIMD_FLOAT a) { + MD_SIMD_FLOAT x = _mm512_add_pd(a, _mm512_shuffle_f64x2(a, a, 0xee)); + x = _mm512_add_pd(x, _mm512_shuffle_f64x2(x, x, 0x11)); + x = _mm512_add_pd(x, _mm512_permute_pd(x, 0x01)); + return *((double *) &x); +} diff --git a/gromacs/main.c b/gromacs/main.c index 27cb50e..4694741 100644 --- a/gromacs/main.c +++ b/gromacs/main.c @@ -45,9 +45,16 @@ #define HLINE "----------------------------------------------------------------------------\n" -extern double computeForceLJ(Parameter*, Atom*, Neighbor*, Stats*); +extern double computeForceLJ_ref(Parameter*, Atom*, Neighbor*, Stats*); +extern double computeForceLJ_4xn(Parameter*, Atom*, Neighbor*, Stats*); extern double computeForceEam(Eam*, Parameter*, Atom*, Neighbor*, Stats*); +#ifdef USE_REFERENCE_VERSION +# define computeForceLJ computeForceLJ_ref +#else +# define computeForceLJ computeForceLJ_4xn +#endif + void init(Parameter *param) { param->input_file = NULL; param->vtk_file = NULL; diff --git a/gromacs/neighbor.c b/gromacs/neighbor.c index e5e2118..593eac3 100644 --- a/gromacs/neighbor.c +++ b/gromacs/neighbor.c @@ -63,7 +63,7 @@ void initNeighbor(Neighbor *neighbor, Parameter *param) { cutneigh = param->cutneigh; nmax = 0; atoms_per_bin = 8; - clusters_per_bin = (atoms_per_bin / CLUSTER_DIM_N) + 4; + clusters_per_bin = (atoms_per_bin / CLUSTER_DIM_M) + 4; stencil = NULL; bins = NULL; bincount = NULL; @@ -91,7 +91,8 @@ void setupNeighbor(Parameter *param, Atom *atom) { MD_FLOAT zlo = 0.0; MD_FLOAT zhi = zprd; MD_FLOAT atom_density = ((MD_FLOAT)(atom->Nlocal)) / ((xhi - xlo) * (yhi - ylo) * (zhi - zlo)); - MD_FLOAT atoms_in_cell = MAX(CLUSTER_DIM_M, CLUSTER_DIM_N); + //MD_FLOAT atoms_in_cell = MAX(CLUSTER_DIM_M, CLUSTER_DIM_N); + MD_FLOAT atoms_in_cell = CLUSTER_DIM_M; binsizex = cbrt(atoms_in_cell / atom_density); binsizey = cbrt(atoms_in_cell / atom_density); cutneighsq = cutneigh * cutneigh; @@ -269,6 +270,12 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) { } } + if(CLUSTER_DIM_N > CLUSTER_DIM_M) { + while(n % (CLUSTER_DIM_N / CLUSTER_DIM_M)) { + neighptr[n++] = nall - 1; // Last cluster is always a dummy cluster + } + } + neighbor->numneigh[ci] = n; if(n >= neighbor->maxneighs) { resize = 1; @@ -302,7 +309,7 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) { atom->clusters[ci].bbminz, atom->clusters[ci].bbmaxz); - for(int cii = 0; cii < CLUSTER_DIM_N; cii++) { + for(int cii = 0; cii < CLUSTER_DIM_M; cii++) { DEBUG_MESSAGE("%f, %f, %f\n", cluster_x(ciptr, cii), cluster_y(ciptr, cii), cluster_z(ciptr, cii)); } @@ -320,7 +327,7 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) { atom->clusters[cj].bbminz, atom->clusters[cj].bbmaxz); - for(int cjj = 0; cjj < CLUSTER_DIM_N; cjj++) { + for(int cjj = 0; cjj < CLUSTER_DIM_M; cjj++) { DEBUG_MESSAGE(" %f, %f, %f\n", cluster_x(cjptr, cjj), cluster_y(cjptr, cjj), cluster_z(cjptr, cjj)); } } @@ -481,7 +488,7 @@ void buildClusters(Atom *atom) { MD_FLOAT bbminz = INFINITY, bbmaxz = -INFINITY; atom->clusters[ci].natoms = 0; - for(int cii = 0; cii < CLUSTER_DIM_N; cii++) { + for(int cii = 0; cii < CLUSTER_DIM_M; cii++) { if(ac < c) { int i = bins[bin * atoms_per_bin + ac]; MD_FLOAT xtmp = atom_x(i); @@ -546,7 +553,7 @@ void binClusters(Atom *atom) { atom->clusters[ci].bbminz, atom->clusters[ci].bbmaxz); - for(int cii = 0; cii < CLUSTER_DIM_N; cii++) { + for(int cii = 0; cii < CLUSTER_DIM_M; cii++) { DEBUG_MESSAGE("%f, %f, %f\n", cluster_x(cptr, cii), cluster_y(cptr, cii), cluster_z(cptr, cii)); } } diff --git a/gromacs/pbc.c b/gromacs/pbc.c index 5a303c3..acb203e 100644 --- a/gromacs/pbc.c +++ b/gromacs/pbc.c @@ -210,6 +210,18 @@ void setupPbc(Atom *atom, Parameter *param) { if (bbmaxy >= (yprd-Cutneigh) && bbmaxx >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); } } + if(atom->Nclusters_local + Nghost + 1 >= atom->Nclusters_max) { + growClusters(atom); + } + + // Add dummy cluster at the end + MD_FLOAT *cptr = cluster_pos_ptr(atom->Nclusters_local + Nghost + 1); + for(int cii = 0; cii < CLUSTER_DIM_M; cii++) { + cluster_x(cptr, cii) = INFINITY; + cluster_y(cptr, cii) = INFINITY; + cluster_z(cptr, cii) = INFINITY; + } + // increase by one to make it the ghost atom count atom->Nghost = Nghost_atoms; atom->Nclusters_ghost = Nghost + 1;