include/types/commrec.h

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  38 #ifndef _commrec_h
  39 #define _commrec_h
  40
  41 #ifdef GMX_LIB_MPI
  42 #include <mpi.h>
  43 #else
  44 #ifdef GMX_THREAD_MPI
  45 #include "../thread_mpi/tmpi.h"
  46 #include "../thread_mpi/mpi_bindings.h"
  47 #else
  48 typedef void* MPI_Comm;
  49 typedef void* MPI_Request;
  50 typedef void* MPI_Group;
  51 #endif
  52 #endif
  53
  54 #include "idef.h"
  55
  56 #ifdef __cplusplus
  57 extern "C" {
  58 #endif
  59
  60
  61 #define DD_MAXZONE  8
  62 #define DD_MAXIZONE 4
  63
  64 typedef struct gmx_domdec_master *gmx_domdec_master_p_t;
  65
  66 typedef struct {
  67     int  j0;     /* j-zone start               */
  68     int  j1;     /* j-zone end                 */
  69     int  cg1;    /* i-charge-group end         */
  70     int  jcg0;   /* j-charge-group start       */
  71     int  jcg1;   /* j-charge-group end         */
  72     ivec shift0; /* Minimum shifts to consider */
  73     ivec shift1; /* Maximum shifts to consider */
  74 } gmx_domdec_ns_ranges_t;
  75
  76 typedef struct {
  77     rvec x0;     /* Zone lower corner in triclinic coordinates         */
  78     rvec x1;     /* Zone upper corner in triclinic coordinates         */
  79     rvec bb_x0;  /* Zone bounding box lower corner in Cartesian coords */
  80     rvec bb_x1;  /* Zone bounding box upper corner in Cartesian coords */
  81 } gmx_domdec_zone_size_t;
  82
  83 typedef struct {
  84     /* The number of zones including the home zone */
  85     int                    n;
  86     /* The shift of the zones with respect to the home zone */
  87     ivec                   shift[DD_MAXZONE];
  88     /* The charge group boundaries for the zones */
  89     int                    cg_range[DD_MAXZONE+1];
  90     /* The number of neighbor search zones with i-particles */
  91     int                    nizone;
  92     /* The neighbor search charge group ranges for each i-zone */
  93     gmx_domdec_ns_ranges_t izone[DD_MAXIZONE];
  94     /* Boundaries of the zones */
  95     gmx_domdec_zone_size_t size[DD_MAXZONE];
  96     /* The cg density of the home zone */
  97     real                   dens_zone0;
  98 } gmx_domdec_zones_t;
  99
 100 typedef struct gmx_ga2la *gmx_ga2la_t;
 101
 102 typedef struct gmx_hash *gmx_hash_t;
 103
 104 typedef struct gmx_reverse_top *gmx_reverse_top_p_t;
 105
 106 typedef struct gmx_domdec_constraints *gmx_domdec_constraints_p_t;
 107
 108 typedef struct gmx_domdec_specat_comm *gmx_domdec_specat_comm_p_t;
 109
 110 typedef struct gmx_domdec_comm *gmx_domdec_comm_p_t;
 111
 112 typedef struct gmx_pme_comm_n_box *gmx_pme_comm_n_box_p_t;
 113
 114 typedef struct {
 115     int  npbcdim;
 116     int  nboundeddim;
 117     rvec box0;
 118     rvec box_size;
 119     /* Tells if the box is skewed for each of the three cartesian directions */
 120     ivec tric_dir;
 121     rvec skew_fac;
 122     /* Orthogonal vectors for triclinic cells, Cartesian index */
 123     rvec v[DIM][DIM];
 124     /* Normal vectors for the cells walls */
 125     rvec normal[DIM];
 126 } gmx_ddbox_t;
 127
 128
 129 typedef struct {
 130     /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
 131        supported.*/
 132     int             *ibuf; /* for ints */
 133     int              ibuf_alloc;
 134
 135     gmx_large_int_t *libuf;
 136     int              libuf_alloc;
 137
 138     float           *fbuf; /* for floats */
 139     int              fbuf_alloc;
 140
 141     double          *dbuf; /* for doubles */
 142     int              dbuf_alloc;
 143 } mpi_in_place_buf_t;
 144
 145
 146 typedef struct {
 147     /* The DD particle-particle nodes only */
 148     /* The communication setup within the communicator all
 149      * defined in dd->comm in domdec.c
 150      */
 151     int                    nnodes;
 152     MPI_Comm               mpi_comm_all;
 153     /* Use MPI_Sendrecv communication instead of non-blocking calls */
 154     gmx_bool               bSendRecv2;
 155     /* The local DD cell index and rank */
 156     ivec                   ci;
 157     int                    rank;
 158     ivec                   master_ci;
 159     int                    masterrank;
 160     /* Communication with the PME only nodes */
 161     int                    pme_nodeid;
 162     gmx_bool               pme_receive_vir_ener;
 163     gmx_pme_comm_n_box_p_t cnb;
 164     int                    nreq_pme;
 165     MPI_Request            req_pme[4];
 166
 167
 168     /* The communication setup, identical for each cell, cartesian index */
 169     ivec     nc;
 170     int      ndim;
 171     ivec     dim; /* indexed by 0 to ndim */
 172     gmx_bool bGridJump;
 173
 174     /* PBC from dim 0 to npbcdim */
 175     int npbcdim;
 176
 177     /* Screw PBC? */
 178     gmx_bool bScrewPBC;
 179
 180     /* Forward and backward neighboring cells, indexed by 0 to ndim */
 181     int  neighbor[DIM][2];
 182
 183     /* Only available on the master node */
 184     gmx_domdec_master_p_t ma;
 185
 186     /* Are there inter charge group constraints */
 187     gmx_bool bInterCGcons;
 188     gmx_bool bInterCGsettles;
 189
 190     /* Global atom number to interaction list */
 191     gmx_reverse_top_p_t reverse_top;
 192     int                 nbonded_global;
 193     int                 nbonded_local;
 194
 195     /* The number of inter charge-group exclusions */
 196     int  n_intercg_excl;
 197
 198     /* Vsite stuff */
 199     gmx_hash_t                 ga2la_vsite;
 200     gmx_domdec_specat_comm_p_t vsite_comm;
 201
 202     /* Constraint stuff */
 203     gmx_domdec_constraints_p_t constraints;
 204     gmx_domdec_specat_comm_p_t constraint_comm;
 205
 206     /* The local to gobal charge group index and local cg to local atom index */
 207     int   ncg_home;
 208     int   ncg_tot;
 209     int  *index_gl;
 210     int  *cgindex;
 211     int   cg_nalloc;
 212     /* Local atom to local cg index, only for special cases */
 213     int  *la2lc;
 214     int   la2lc_nalloc;
 215
 216     /* The number of home atoms */
 217     int   nat_home;
 218     /* The total number of atoms: home and received zones */
 219     int   nat_tot;
 220     /* Index from the local atoms to the global atoms */
 221     int  *gatindex;
 222     int   gatindex_nalloc;
 223
 224     /* Global atom number to local atom number list */
 225     gmx_ga2la_t ga2la;
 226
 227     /* Communication stuff */
 228     gmx_domdec_comm_p_t comm;
 229
 230     /* The partioning count, to keep track of the state */
 231     gmx_large_int_t ddp_count;
 232
 233
 234     /* gmx_pme_recv_f buffer */
 235     int   pme_recv_f_alloc;
 236     rvec *pme_recv_f_buf;
 237
 238 } gmx_domdec_t;
 239
 240 typedef struct gmx_partdec *gmx_partdec_p_t;
 241
 242 typedef struct {
 243     int       nsim;
 244     int       sim;
 245     MPI_Group mpi_group_masters;
 246     MPI_Comm  mpi_comm_masters;
 247     /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
 248        supported.*/
 249     mpi_in_place_buf_t *mpb;
 250 } gmx_multisim_t;
 251
 252 #define DUTY_PP  (1<<0)
 253 #define DUTY_PME (1<<1)
 254
 255 typedef struct {
 256     int      bUse;
 257     MPI_Comm comm_intra;
 258     int      rank_intra;
 259     MPI_Comm comm_inter;
 260
 261 } gmx_nodecomm_t;
 262
 263 typedef struct {
 264     /* The nodeids in one sim are numbered sequentially from 0.
 265      * All communication within some simulation should happen
 266      * in mpi_comm_mysim, or its subset mpi_comm_mygroup.
 267      */
 268     int sim_nodeid, nnodes, npmenodes;
 269
 270     /* thread numbers: */
 271     /* Not used yet: int threadid, nthreads; */
 272     /* The nodeid in the PP/PME, PP or PME group */
 273     int      nodeid;
 274     MPI_Comm mpi_comm_mysim;
 275     MPI_Comm mpi_comm_mygroup;
 276
 277     /* MPI ranks within a physical node for hardware access */
 278     int            nrank_intranode;    /* nr of ranks on this physical node */
 279     int            rank_intranode;     /* our rank on this physical node */
 280     int            nrank_pp_intranode; /* as nrank_intranode, for particle-particle only */
 281     int            rank_pp_intranode;  /* as rank_intranode, for particle-particle only */
 282
 283     gmx_nodecomm_t nc;
 284
 285     /* For domain decomposition */
 286     gmx_domdec_t *dd;
 287
 288     /* For particle decomposition */
 289     gmx_partdec_p_t pd;
 290
 291     /* The duties of this node, see the defines above */
 292     int             duty;
 293
 294     gmx_multisim_t *ms;
 295
 296     /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
 297        supported.*/
 298     mpi_in_place_buf_t *mpb;
 299 } t_commrec;
 300
 301 #define MASTERNODE(cr)     (((cr)->nodeid == 0) || !PAR(cr))
 302 /* #define MASTERTHREAD(cr)   ((cr)->threadid == 0) */
 303 /* #define MASTER(cr)         (MASTERNODE(cr) && MASTERTHREAD(cr)) */
 304 #define MASTER(cr)         MASTERNODE(cr)
 305 #define SIMMASTER(cr)      ((MASTER(cr) && ((cr)->duty & DUTY_PP)) || !PAR(cr))
 306 #define NODEPAR(cr)        ((cr)->nnodes > 1)
 307 /* #define THREADPAR(cr)      ((cr)->nthreads > 1) */
 308 /* #define PAR(cr)            (NODEPAR(cr) || THREADPAR(cr)) */
 309 #define PAR(cr)            NODEPAR(cr)
 310 #define RANK(cr, nodeid)    (nodeid)
 311 #define MASTERRANK(cr)     (0)
 312
 313 #define DOMAINDECOMP(cr)   (((cr)->dd != NULL) && PAR(cr))
 314 #define DDMASTER(dd)       ((dd)->rank == (dd)->masterrank)
 315
 316 #define PARTDECOMP(cr)     ((cr)->pd != NULL)
 317
 318 #define MULTISIM(cr)       ((cr)->ms)
 319 #define MSRANK(ms, nodeid)  (nodeid)
 320 #define MASTERSIM(ms)      ((ms)->sim == 0)
 321
 322 /* The master of all (the node that prints the remaining run time etc.) */
 323 #define MULTIMASTER(cr)    (SIMMASTER(cr) && (!MULTISIM(cr) || MASTERSIM((cr)->ms)))
 324
 325 #ifdef __cplusplus
 326 }
 327 #endif
 328 #endif