src/mdlib/nbnxn_internal.h

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  35
  36 #ifndef _nbnxn_internal_h
  37 #define _nsnxn_internal_h
  38
  39 #include "typedefs.h"
  40 #include "domdec.h"
  41 #include "gmx_cyclecounter.h"
  42
  43 #ifdef __cplusplus
  44 extern "C" {
  45 #endif
  46
  47
  48 #ifdef GMX_X86_SSE2
  49 #define NBNXN_SEARCH_SSE
  50 #endif
  51
  52
  53 /* Block size for the non-bonded thread force-buffer reduction,
  54  * should be a multiple of 2 in case of AVX256.
  55  */
  56 #define NBNXN_CELLBLOCK_SIZE       4
  57 #define NBNXN_CELLBLOCK_SIZE_2LOG  2
  58
  59 /* We currently store the reduction flags as bits in an unsigned int.
  60  * In most cases this limits the number of flags to 32.
  61  * The reduction will automatically disable the flagging and do a full
  62  * reduction when the flags won't fit, but this will lead to very slow
  63  * reduction. As we anyhow don't expect reasonable performance with
  64  * more than 32 threads, we put in this hard limit.
  65  * You can increase this number, but the reduction will be very slow.
  66  */
  67 #define NBNXN_CELLBLOCK_MAX_THREADS  32
  68
  69 /* Flags for telling if threads write to force output buffers */
  70 typedef struct {
  71     int ncb;         /* The number of cell blocks                         */
  72     gmx_bool bUse;   /* Should we use these flags?                        */
  73     unsigned *flag;  /* Bit i is set when thread i writes to a cell-block */
  74     int flag_nalloc; /* Allocation size of cxy_flag                       */
  75 } nbnxn_cellblock_flags;
  76
  77 /* A pair-search grid struct for one domain decomposition zone */
  78 typedef struct {
  79     rvec c0;             /* The lower corner of the (local) grid        */
  80     rvec c1;             /* The upper corner of the (local) grid        */
  81     real atom_density;   /* The atom number density for the local grid  */
  82
  83     gmx_bool bSimple;    /* Is this grid simple or super/sub            */
  84     int  na_c;           /* Number of atoms per cluster                 */
  85     int  na_cj;          /* Number of atoms for list j-clusters         */
  86     int  na_sc;          /* Number of atoms per super-cluster           */
  87     int  na_c_2log;      /* 2log of na_c                                */
  88
  89     int  ncx;            /* Number of (super-)cells along x             */
  90     int  ncy;            /* Number of (super-)cells along y             */
  91     int  nc;             /* Total number of (super-)cells               */
  92
  93     real sx;             /* x-size of a (super-)cell                    */
  94     real sy;             /* y-size of a (super-)cell                    */
  95     real inv_sx;         /* 1/sx                                        */
  96     real inv_sy;         /* 1/sy                                        */
  97
  98     int  cell0;          /* Index in nbs->cell corresponding to cell 0  */
  99
 100     int  *cxy_na;        /* The number of atoms for each column in x,y  */
 101     int  *cxy_ind;       /* Grid (super)cell index, offset from cell0   */
 102     int  cxy_nalloc;     /* Allocation size for cxy_na and cxy_ind      */
 103
 104     int   *nsubc;        /* The number of sub cells for each super cell */
 105     float *bbcz;         /* Bounding boxes in z for the super cells     */
 106     float *bb;           /* 3D bounding boxes for the sub cells         */
 107     float *bbj;          /* 3D j-b.boxes for SSE-double or AVX-single   */
 108     int   *flags;        /* Flag for the super cells                    */
 109     int   nc_nalloc;     /* Allocation size for the pointers above      */
 110
 111     float *bbcz_simple;  /* bbcz for simple grid converted from super   */
 112     float *bb_simple;    /* bb for simple grid converted from super     */
 113     int   *flags_simple; /* flags for simple grid converted from super  */
 114     int   nc_nalloc_simple; /* Allocation size for the pointers above   */
 115
 116     nbnxn_cellblock_flags cellblock_flags; /* Flags for F output buffers */
 117
 118     int  nsubc_tot;      /* Total number of subcell, used for printing  */
 119 } nbnxn_grid_t;
 120
 121 #ifdef NBNXN_SEARCH_SSE
 122 #define GMX_MM128_HERE
 123 #include "gmx_x86_simd_macros.h"
 124 typedef struct nbnxn_x_ci_x86_simd128 {
 125     /* The i-cluster coordinates for simple search */
 126     gmx_mm_pr ix_SSE0,iy_SSE0,iz_SSE0;
 127     gmx_mm_pr ix_SSE1,iy_SSE1,iz_SSE1;
 128     gmx_mm_pr ix_SSE2,iy_SSE2,iz_SSE2;
 129     gmx_mm_pr ix_SSE3,iy_SSE3,iz_SSE3;
 130 } nbnxn_x_ci_x86_simd128_t;
 131 #undef GMX_MM128_HERE
 132 #ifdef GMX_X86_AVX_256
 133 #define GMX_MM256_HERE
 134 #include "gmx_x86_simd_macros.h"
 135 typedef struct nbnxn_x_ci_x86_simd256 {
 136     /* The i-cluster coordinates for simple search */
 137     gmx_mm_pr ix_SSE0,iy_SSE0,iz_SSE0;
 138     gmx_mm_pr ix_SSE1,iy_SSE1,iz_SSE1;
 139     gmx_mm_pr ix_SSE2,iy_SSE2,iz_SSE2;
 140     gmx_mm_pr ix_SSE3,iy_SSE3,iz_SSE3;
 141 } nbnxn_x_ci_x86_simd256_t;
 142 #undef GMX_MM256_HERE
 143 #endif
 144 #endif
 145
 146 /* Working data for the actual i-supercell during pair search */
 147 typedef struct nbnxn_list_work {
 148     gmx_cache_protect_t cp0; /* Protect cache between threads               */
 149
 150     float *bb_ci;      /* The bounding boxes, pbc shifted, for each cluster */
 151     real  *x_ci;       /* The coordinates, pbc shifted, for each atom       */
 152 #ifdef NBNXN_SEARCH_SSE
 153     nbnxn_x_ci_x86_simd128_t *x_ci_x86_simd128;
 154 #ifdef GMX_X86_AVX_256
 155     nbnxn_x_ci_x86_simd256_t *x_ci_x86_simd256;
 156 #endif
 157 #endif
 158     int  cj_ind;       /* The current cj_ind index for the current list     */
 159     int  cj4_init;     /* The first unitialized cj4 block                   */
 160
 161     float *d2;         /* Bounding box distance work array                  */
 162
 163     nbnxn_cj_t *cj;    /* The j-cell list                                   */
 164     int  cj_nalloc;    /* Allocation size of cj                             */
 165
 166     int ncj_noq;       /* Nr. of cluster pairs without Coul for flop count  */
 167     int ncj_hlj;       /* Nr. of cluster pairs with 1/2 LJ for flop count   */
 168
 169     gmx_cache_protect_t cp1; /* Protect cache between threads               */
 170 } nbnxn_list_work_t;
 171
 172 /* Function type for setting the i-atom coordinate working data */
 173 typedef void
 174 gmx_icell_set_x_t(int ci,
 175                   real shx,real shy,real shz,
 176                   int na_c,
 177                   int stride,const real *x,
 178                   nbnxn_list_work_t *work);
 179
 180 static gmx_icell_set_x_t icell_set_x_simple;
 181 #ifdef NBNXN_SEARCH_SSE
 182 static gmx_icell_set_x_t icell_set_x_simple_x86_simd128;
 183 #ifdef GMX_X86_AVX_256
 184 static gmx_icell_set_x_t icell_set_x_simple_x86_simd256;
 185 #endif
 186 #endif
 187 static gmx_icell_set_x_t icell_set_x_supersub;
 188 #ifdef NBNXN_SEARCH_SSE
 189 static gmx_icell_set_x_t icell_set_x_supersub_sse8;
 190 #endif
 191
 192 /* Local cycle count struct for profiling */
 193 typedef struct {
 194     int          count;
 195     gmx_cycles_t c;
 196     gmx_cycles_t start;
 197 } nbnxn_cycle_t;
 198
 199 /* Local cycle count enum for profiling */
 200 enum { enbsCCgrid, enbsCCsearch, enbsCCcombine, enbsCCreducef, enbsCCnr };
 201
 202 /* Thread-local work struct, contains part of nbnxn_grid_t */
 203 typedef struct {
 204     gmx_cache_protect_t cp0;
 205
 206     int *cxy_na;
 207     int cxy_na_nalloc;
 208
 209     int  *sort_work;
 210     int  sort_work_nalloc;
 211
 212     nbnxn_cellblock_flags gridi_flags; /* Flags for i-grid f buffer     */
 213     nbnxn_cellblock_flags gridj_flags; /* Flags for j-grid f buffer     */
 214
 215     int  ndistc;         /* Number of distance checks for flop counting */
 216
 217     nbnxn_cycle_t cc[enbsCCnr];
 218
 219     gmx_cache_protect_t cp1;
 220 } nbnxn_search_work_t;
 221
 222 /* Main pair-search struct, contains the grid(s), not the pair-list(s) */
 223 typedef struct nbnxn_search {
 224     int  ePBC;            /* PBC type enum                              */
 225     matrix box;           /* The periodic unit-cell                     */
 226
 227     gmx_bool DomDec;      /* Are we doing domain decomposition?         */
 228     ivec dd_dim;          /* Are we doing DD in x,y,z?                  */
 229     gmx_domdec_zones_t *zones; /* The domain decomposition zones        */
 230
 231     int  ngrid;           /* The number of grids, equal to #DD-zones    */
 232     nbnxn_grid_t *grid;   /* Array of grids, size ngrid                 */
 233     int  *cell;           /* Actual allocated cell array for all grids  */
 234     int  cell_nalloc;     /* Allocation size of cell                    */
 235     int  *a;              /* Atom index for grid, the inverse of cell   */
 236     int  a_nalloc;        /* Allocation size of a                       */
 237
 238     int  natoms_local;    /* The local atoms run from 0 to natoms_local */
 239     int  natoms_nonlocal; /* The non-local atoms run from natoms_local
 240                            * to natoms_nonlocal */
 241
 242     gmx_bool print_cycles;
 243     int      search_count;
 244     nbnxn_cycle_t cc[enbsCCnr];
 245
 246     gmx_icell_set_x_t *icell_set_x; /* Function for setting i-coords    */
 247
 248     int  nthread_max;     /* Maximum number of threads for pair-search  */
 249     nbnxn_search_work_t *work; /* Work array, size nthread_max          */
 250 } nbnxn_search_t_t;
 251
 252
 253 static void nbs_cycle_start(nbnxn_cycle_t *cc)
 254 {
 255     cc->start = gmx_cycles_read();
 256 }
 257
 258 static void nbs_cycle_stop(nbnxn_cycle_t *cc)
 259 {
 260     cc->c += gmx_cycles_read() - cc->start;
 261     cc->count++;
 262 }
 263
 264
 265 #ifdef __cplusplus
 266 }
 267 #endif
 268
 269 #endif