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36 #ifndef _nbnxn_internal_h
37 #define _nbnxn_internal_h
41 #include "gromacs/timing/cyclecounter.h"
44 /* The include below sets the SIMD instruction type (precision+width)
45 * for all nbnxn SIMD search and non-bonded kernel code.
47 #ifdef GMX_NBNXN_HALF_WIDTH_SIMD
48 #define GMX_USE_HALF_WIDTH_SIMD_HERE
50 #include "gromacs/simd/macros.h"
54 /* Bounding box calculations are (currently) always in single precision.
55 * This uses less (cache-)memory and SIMD is faster, at least on x86.
57 #define GMX_SIMD4_SINGLE
58 /* Include the 4-wide SIMD macro file */
59 #include "gromacs/simd/four_wide_macros.h"
60 /* Check if we have 4-wide SIMD macro support */
61 #ifdef GMX_HAVE_SIMD4_MACROS
62 #define NBNXN_SEARCH_BB_SIMD4
72 /* Memory alignment in bytes as required by SIMD aligned loads/stores */
73 #define NBNXN_MEM_ALIGN (GMX_SIMD_REAL_WIDTH*sizeof(real))
75 /* No alignment required, but set it so we can call the same routines */
76 #define NBNXN_MEM_ALIGN 32
80 #ifdef NBNXN_SEARCH_BB_SIMD4
81 /* Memory alignment in bytes as required by SIMD aligned loads/stores */
82 #define NBNXN_SEARCH_BB_MEM_ALIGN (GMX_SIMD4_WIDTH*sizeof(float))
84 /* No alignment required, but set it so we can call the same routines */
85 #define NBNXN_SEARCH_BB_MEM_ALIGN 32
89 /* Pair search box lower and upper corner in x,y,z.
90 * Store this in 4 iso 3 reals, which is useful with 4-wide SIMD.
91 * To avoid complicating the code we also use 4 without 4-wide SIMD.
94 /* Pair search box lower and upper bound in z only. */
96 /* Pair search box lower and upper corner x,y,z indices, entry 3 is unused */
101 /* Bounding box for a nbnxn atom cluster */
103 float lower[NNBSBB_C];
104 float upper[NNBSBB_C];
108 /* A pair-search grid struct for one domain decomposition zone */
110 rvec c0; /* The lower corner of the (local) grid */
111 rvec c1; /* The upper corner of the (local) grid */
112 real atom_density; /* The atom number density for the local grid */
114 gmx_bool bSimple; /* Is this grid simple or super/sub */
115 int na_c; /* Number of atoms per cluster */
116 int na_cj; /* Number of atoms for list j-clusters */
117 int na_sc; /* Number of atoms per super-cluster */
118 int na_c_2log; /* 2log of na_c */
120 int ncx; /* Number of (super-)cells along x */
121 int ncy; /* Number of (super-)cells along y */
122 int nc; /* Total number of (super-)cells */
124 real sx; /* x-size of a (super-)cell */
125 real sy; /* y-size of a (super-)cell */
126 real inv_sx; /* 1/sx */
127 real inv_sy; /* 1/sy */
129 int cell0; /* Index in nbs->cell corresponding to cell 0 */
131 int *cxy_na; /* The number of atoms for each column in x,y */
132 int *cxy_ind; /* Grid (super)cell index, offset from cell0 */
133 int cxy_nalloc; /* Allocation size for cxy_na and cxy_ind */
135 int *nsubc; /* The number of sub cells for each super cell */
136 float *bbcz; /* Bounding boxes in z for the super cells */
137 nbnxn_bb_t *bb; /* 3D bounding boxes for the sub cells */
138 nbnxn_bb_t *bbj; /* 3D j-bounding boxes for the case where *
139 * the i- and j-cluster sizes are different */
140 float *pbb; /* 3D b. boxes in xxxx format per super cell */
141 int *flags; /* Flag for the super cells */
142 int nc_nalloc; /* Allocation size for the pointers above */
144 float *bbcz_simple; /* bbcz for simple grid converted from super */
145 nbnxn_bb_t *bb_simple; /* bb for simple grid converted from super */
146 int *flags_simple; /* flags for simple grid converted from super */
147 int nc_nalloc_simple; /* Allocation size for the pointers above */
149 int nsubc_tot; /* Total number of subcell, used for printing */
152 #ifdef GMX_NBNXN_SIMD
154 typedef struct nbnxn_x_ci_simd_4xn {
155 /* The i-cluster coordinates for simple search */
156 gmx_simd_real_t ix_S0, iy_S0, iz_S0;
157 gmx_simd_real_t ix_S1, iy_S1, iz_S1;
158 gmx_simd_real_t ix_S2, iy_S2, iz_S2;
159 gmx_simd_real_t ix_S3, iy_S3, iz_S3;
160 } nbnxn_x_ci_simd_4xn_t;
162 typedef struct nbnxn_x_ci_simd_2xnn {
163 /* The i-cluster coordinates for simple search */
164 gmx_simd_real_t ix_S0, iy_S0, iz_S0;
165 gmx_simd_real_t ix_S2, iy_S2, iz_S2;
166 } nbnxn_x_ci_simd_2xnn_t;
170 /* Working data for the actual i-supercell during pair search */
171 typedef struct nbnxn_list_work {
172 gmx_cache_protect_t cp0; /* Protect cache between threads */
174 nbnxn_bb_t *bb_ci; /* The bounding boxes, pbc shifted, for each cluster */
175 float *pbb_ci; /* As bb_ci, but in xxxx packed format */
176 real *x_ci; /* The coordinates, pbc shifted, for each atom */
177 #ifdef GMX_NBNXN_SIMD
178 nbnxn_x_ci_simd_4xn_t *x_ci_simd_4xn;
179 nbnxn_x_ci_simd_2xnn_t *x_ci_simd_2xnn;
181 int cj_ind; /* The current cj_ind index for the current list */
182 int cj4_init; /* The first unitialized cj4 block */
184 float *d2; /* Bounding box distance work array */
186 nbnxn_cj_t *cj; /* The j-cell list */
187 int cj_nalloc; /* Allocation size of cj */
189 int ncj_noq; /* Nr. of cluster pairs without Coul for flop count */
190 int ncj_hlj; /* Nr. of cluster pairs with 1/2 LJ for flop count */
192 int *sort; /* Sort index */
193 int sort_nalloc; /* Allocation size of sort */
195 nbnxn_sci_t *sci_sort; /* Second sci array, for sorting */
196 int sci_sort_nalloc; /* Allocation size of sci_sort */
198 gmx_cache_protect_t cp1; /* Protect cache between threads */
201 /* Function type for setting the i-atom coordinate working data */
203 gmx_icell_set_x_t (int ci,
204 real shx, real shy, real shz,
206 int stride, const real *x,
207 nbnxn_list_work_t *work);
209 static gmx_icell_set_x_t icell_set_x_simple;
210 #ifdef GMX_NBNXN_SIMD
211 static gmx_icell_set_x_t icell_set_x_simple_simd_4xn;
212 static gmx_icell_set_x_t icell_set_x_simple_simd_2xnn;
214 static gmx_icell_set_x_t icell_set_x_supersub;
215 #ifdef NBNXN_SEARCH_SSE
216 static gmx_icell_set_x_t icell_set_x_supersub_sse8;
219 /* Local cycle count struct for profiling */
226 /* Local cycle count enum for profiling */
228 enbsCCgrid, enbsCCsearch, enbsCCcombine, enbsCCreducef, enbsCCnr
231 /* Thread-local work struct, contains part of nbnxn_grid_t */
233 gmx_cache_protect_t cp0;
239 int sort_work_nalloc;
241 nbnxn_buffer_flags_t buffer_flags; /* Flags for force buffer access */
243 int ndistc; /* Number of distance checks for flop counting */
245 nbnxn_cycle_t cc[enbsCCnr];
247 gmx_cache_protect_t cp1;
248 } nbnxn_search_work_t;
250 /* Main pair-search struct, contains the grid(s), not the pair-list(s) */
251 typedef struct nbnxn_search {
252 int ePBC; /* PBC type enum */
253 matrix box; /* The periodic unit-cell */
255 gmx_bool DomDec; /* Are we doing domain decomposition? */
256 ivec dd_dim; /* Are we doing DD in x,y,z? */
257 gmx_domdec_zones_t *zones; /* The domain decomposition zones */
259 int ngrid; /* The number of grids, equal to #DD-zones */
260 nbnxn_grid_t *grid; /* Array of grids, size ngrid */
261 int *cell; /* Actual allocated cell array for all grids */
262 int cell_nalloc; /* Allocation size of cell */
263 int *a; /* Atom index for grid, the inverse of cell */
264 int a_nalloc; /* Allocation size of a */
266 int natoms_local; /* The local atoms run from 0 to natoms_local */
267 int natoms_nonlocal; /* The non-local atoms run from natoms_local
268 * to natoms_nonlocal */
270 gmx_bool print_cycles;
272 nbnxn_cycle_t cc[enbsCCnr];
274 gmx_icell_set_x_t *icell_set_x; /* Function for setting i-coords */
276 int nthread_max; /* Maximum number of threads for pair-search */
277 nbnxn_search_work_t *work; /* Work array, size nthread_max */
281 static void nbs_cycle_start(nbnxn_cycle_t *cc)
283 cc->start = gmx_cycles_read();
286 static void nbs_cycle_stop(nbnxn_cycle_t *cc)
288 cc->c += gmx_cycles_read() - cc->start;