src/gromacs/domdec/domdec.h

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  36 /*! \defgroup module_domdec Spatial domain decomposition (for parallelization over MPI)
  37  * \ingroup group_mdrun
  38  *
  39  * \brief Manages the decomposition of the simulation volume over MPI
  40  * ranks to try to distribute work evenly with minimal communication
  41  * overheads.
  42  *
  43  * \todo Get domdec stuff out of mdtypes/commrec.h
  44  *
  45  * \author Berk Hess <hess@kth.se>
  46  *
  47  */
  48
  49 /*! \libinternal \file
  50  *
  51  * \brief This file declares functions for mdrun to call to manage the
  52  * details of its domain decomposition.
  53  *
  54  * \author Berk Hess <hess@kth.se>
  55  * \inlibraryapi
  56  * \ingroup module_domdec
  57  */
  58
  59 #ifndef GMX_DOMDEC_DOMDEC_H
  60 #define GMX_DOMDEC_DOMDEC_H
  61
  62 #include <vector>
  63
  64 #include "gromacs/math/vectypes.h"
  65 #include "gromacs/utility/arrayref.h"
  66 #include "gromacs/utility/basedefinitions.h"
  67 #include "gromacs/utility/real.h"
  68
  69 struct cginfo_mb_t;
  70 struct DDSystemInfo;
  71 struct gmx_domdec_t;
  72 struct gmx_ddbox_t;
  73 struct gmx_domdec_zones_t;
  74 struct gmx_localtop_t;
  75 struct gmx_mtop_t;
  76 struct gmx_vsite_t;
  77 struct t_block;
  78 struct t_blocka;
  79 struct t_commrec;
  80 struct t_forcerec;
  81 struct t_inputrec;
  82 struct t_mdatoms;
  83 struct t_nrnb;
  84 struct gmx_wallcycle;
  85 class t_state;
  86
  87 namespace gmx
  88 {
  89 class ForceWithShiftForces;
  90 class MDLogger;
  91 class LocalAtomSetManager;
  92 class RangePartitioning;
  93 struct DomdecOptions;
  94 struct MdrunOptions;
  95 } // namespace
  96
  97 /*! \brief Returns the global topology atom number belonging to local atom index i.
  98  *
  99  * This function is intended for writing ASCII output
 100  * and returns atom numbers starting at 1.
 101  * When dd=NULL returns i+1.
 102  */
 103 int ddglatnr(const gmx_domdec_t *dd, int i);
 104
 105 /*! \brief Return a block struct for the charge groups of the whole system */
 106 t_block *dd_charge_groups_global(struct gmx_domdec_t *dd);
 107
 108 /*! \brief Returns a list of update group partitioning for each molecule type or empty when update groups are not used */
 109 gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingPerMoleculetype(const gmx_domdec_t &dd);
 110
 111 /*! \brief Store the global cg indices of the home cgs in state,
 112  *
 113  * This means it can be reset, even after a new DD partitioning.
 114  */
 115 void dd_store_state(struct gmx_domdec_t *dd, t_state *state);
 116
 117 /*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
 118 struct gmx_domdec_zones_t *domdec_zones(struct gmx_domdec_t *dd);
 119
 120 /*! \brief Sets the j-charge-group range for i-charge-group \p icg */
 121 void dd_get_ns_ranges(const gmx_domdec_t *dd, int icg,
 122                       int *jcg0, int *jcg1, ivec shift0, ivec shift1);
 123
 124 /*! \brief Returns the number of home atoms */
 125 int dd_numHomeAtoms(const gmx_domdec_t &dd);
 126
 127 /*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
 128 int dd_natoms_mdatoms(const gmx_domdec_t *dd);
 129
 130 /*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
 131 int dd_natoms_vsite(const gmx_domdec_t *dd);
 132
 133 /*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
 134 void dd_get_constraint_range(const gmx_domdec_t *dd,
 135                              int *at_start, int *at_end);
 136
 137 /*! \libinternal \brief Struct for passing around the number of PME domains */
 138 struct NumPmeDomains
 139 {
 140     int x; //!< The number of PME domains along dimension x
 141     int y; //!< The number of PME domains along dimension y
 142 };
 143
 144 /*! \brief Returns the number of PME domains, can be called with dd=NULL */
 145 NumPmeDomains getNumPmeDomains(const gmx_domdec_t *dd);
 146
 147 /*! \brief Returns the set of DD ranks that communicate with pme node cr->nodeid */
 148 std::vector<int> get_pme_ddranks(const t_commrec *cr, int pmenodeid);
 149
 150 /*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
 151 int dd_pme_maxshift_x(const gmx_domdec_t *dd);
 152
 153 /*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
 154 int dd_pme_maxshift_y(const gmx_domdec_t *dd);
 155
 156 /*! \brief Return whether constraints, not including settles, cross domain boundaries */
 157 bool ddHaveSplitConstraints(const gmx_domdec_t &dd);
 158
 159 /*! \brief Initialized the domain decomposition, chooses the DD grid and PME ranks, return the DD struct */
 160 gmx_domdec_t *
 161 init_domain_decomposition(const gmx::MDLogger            &mdlog,
 162                           t_commrec                      *cr,
 163                           const gmx::DomdecOptions       &options,
 164                           const gmx::MdrunOptions        &mdrunOptions,
 165                           const gmx_mtop_t               *mtop,
 166                           const t_inputrec               *ir,
 167                           const matrix                    box,
 168                           gmx::ArrayRef<const gmx::RVec>  xGlobal,
 169                           gmx::LocalAtomSetManager       *atomSets);
 170
 171 /*! \brief Initialize data structures for bonded interactions */
 172 void dd_init_bondeds(FILE              *fplog,
 173                      gmx_domdec_t      *dd,
 174                      const gmx_mtop_t  *mtop,
 175                      const gmx_vsite_t *vsite,
 176                      const t_inputrec  *ir,
 177                      gmx_bool           bBCheck,
 178                      cginfo_mb_t       *cginfo_mb);
 179
 180 /*! \brief Returns if we need to do pbc for calculating bonded interactions */
 181 gmx_bool dd_bonded_molpbc(const gmx_domdec_t *dd, int ePBC);
 182
 183 /*! \brief Change the DD non-bonded communication cut-off.
 184  *
 185  * This could fail when trying to increase the cut-off,
 186  * then FALSE will be returned and the cut-off is not modified.
 187  *
 188  * \param[in] cr               Communication recrod
 189  * \param[in] state            State, used for computing the dimensions of the system
 190  * \param[in] cutoffRequested  The requested atom to atom cut-off distance, usually the pair-list cutoff distance
 191  */
 192 gmx_bool change_dd_cutoff(t_commrec     *cr,
 193                           const t_state &state,
 194                           real           cutoffRequested);
 195
 196 /*! \brief Set up communication for averaging GPU wait times over domains
 197  *
 198  * When domains (PP MPI ranks) share a GPU, the individual GPU wait times
 199  * are meaningless, as it depends on the order in which tasks on the same
 200  * GPU finish. Therefore there wait times need to be averaged over the ranks
 201  * sharing the same GPU. This function sets up the communication for that.
 202  */
 203 void dd_setup_dlb_resource_sharing(t_commrec           *cr,
 204                                    int                  gpu_id);
 205
 206 /*! \brief Cycle counter indices used internally in the domain decomposition */
 207 enum {
 208     ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclWaitGPU, ddCyclPME, ddCyclNr
 209 };
 210
 211 /*! \brief Add the wallcycle count to the DD counter */
 212 void dd_cycles_add(const gmx_domdec_t *dd, float cycles, int ddCycl);
 213
 214 /*! \brief Communicate the coordinates to the neighboring cells and do pbc. */
 215 void dd_move_x(struct gmx_domdec_t      *dd,
 216                const matrix              box,
 217                gmx::ArrayRef<gmx::RVec>  x,
 218                gmx_wallcycle            *wcycle);
 219
 220 /*! \brief Sum the forces over the neighboring cells.
 221  *
 222  * When fshift!=NULL the shift forces are updated to obtain
 223  * the correct virial from the single sum including f.
 224  */
 225 void dd_move_f(struct gmx_domdec_t       *dd,
 226                gmx::ForceWithShiftForces *forceWithShiftForces,
 227                gmx_wallcycle             *wcycle);
 228
 229 /*! \brief Communicate a real for each atom to the neighboring cells. */
 230 void dd_atom_spread_real(struct gmx_domdec_t *dd, real v[]);
 231
 232 /*! \brief Sum the contributions to a real for each atom over the neighboring cells. */
 233 void dd_atom_sum_real(struct gmx_domdec_t *dd, real v[]);
 234
 235 /*! \brief Reset all the statistics and counters for total run counting */
 236 void reset_dd_statistics_counters(struct gmx_domdec_t *dd);
 237
 238 /* In domdec_con.c */
 239
 240 /*! \brief Communicates the virtual site forces, reduces the shift forces when \p fshift != NULL */
 241 void dd_move_f_vsites(struct gmx_domdec_t *dd, rvec *f, rvec *fshift);
 242
 243 /*! \brief Clears the forces for virtual sites */
 244 void dd_clear_f_vsites(struct gmx_domdec_t *dd, rvec *f);
 245
 246 /*! \brief Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
 247 void dd_move_x_constraints(struct gmx_domdec_t *dd, matrix box,
 248                            rvec *x0, rvec *x1, gmx_bool bX1IsCoord);
 249
 250 /*! \brief Communicates the coordinates involved in virtual sites */
 251 void dd_move_x_vsites(struct gmx_domdec_t *dd, const matrix box, rvec *x);
 252
 253 /*! \brief Returns the local atom count array for all constraints
 254  *
 255  * The local atom count for a constraint, possible values 2/1/0, is needed
 256  * to avoid not/double-counting contributions linked to the Lagrange
 257  * multiplier, such as the virial and free-energy derivatives.
 258  *
 259  * \note When \p dd = nullptr, an empty reference is returned.
 260  */
 261 gmx::ArrayRef<const int> dd_constraints_nlocalatoms(const gmx_domdec_t *dd);
 262
 263 /* In domdec_top.c */
 264
 265 /*! \brief Print error output when interactions are missing */
 266 [[ noreturn ]]
 267 void dd_print_missing_interactions(const gmx::MDLogger  &mdlog,
 268                                    t_commrec            *cr,
 269                                    int                   local_count,
 270                                    const gmx_mtop_t     *top_global,
 271                                    const gmx_localtop_t *top_local,
 272                                    const rvec           *x,
 273                                    const matrix          box);
 274
 275 /*! \brief Generate and store the reverse topology */
 276 void dd_make_reverse_top(FILE *fplog,
 277                          gmx_domdec_t *dd, const gmx_mtop_t *mtop,
 278                          const gmx_vsite_t *vsite,
 279                          const t_inputrec *ir, gmx_bool bBCheck);
 280
 281 /*! \brief Generate the local topology and virtual site data */
 282 void dd_make_local_top(struct gmx_domdec_t       *dd,
 283                        struct gmx_domdec_zones_t *zones,
 284                        int                        npbcdim,
 285                        matrix                     box,
 286                        rvec                       cellsize_min,
 287                        const ivec                 npulse,
 288                        t_forcerec                *fr,
 289                        rvec                      *cgcm_or_x,
 290                        const gmx_mtop_t          &top,
 291                        gmx_localtop_t            *ltop);
 292
 293 /*! \brief Sort ltop->ilist when we are doing free energy. */
 294 void dd_sort_local_top(gmx_domdec_t *dd, const t_mdatoms *mdatoms,
 295                        gmx_localtop_t *ltop);
 296
 297 /*! \brief Initialize local topology
 298  *
 299  * \param[in] top_global Reference to global topology.
 300  * \param[in,out] top Pointer to new local topology
 301  */
 302 void dd_init_local_top(const gmx_mtop_t &top_global,
 303                        gmx_localtop_t   *top);
 304
 305 /*! \brief Construct local state */
 306 void dd_init_local_state(struct gmx_domdec_t *dd,
 307                          const t_state *state_global, t_state *local_state);
 308
 309 /*! \brief Generate a list of links between charge groups that are linked by bonded interactions */
 310 t_blocka *make_charge_group_links(const gmx_mtop_t *mtop, gmx_domdec_t *dd,
 311                                   cginfo_mb_t *cginfo_mb);
 312
 313 /*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
 314 void dd_bonded_cg_distance(const gmx::MDLogger &mdlog,
 315                            const gmx_mtop_t *mtop,
 316                            const t_inputrec *ir,
 317                            const rvec *x, const matrix box,
 318                            gmx_bool bBCheck,
 319                            real *r_2b, real *r_mb);
 320
 321
 322 /* In domdec_setup.c */
 323
 324 /*! \brief Returns the volume fraction of the system that is communicated */
 325 real comm_box_frac(const ivec dd_nc, real cutoff, const gmx_ddbox_t *ddbox);
 326
 327 struct DDSetup
 328 {
 329     int  numPmeRanks   = 0;
 330     ivec numDomains    = { 0, 0, 0 };
 331     real cellsizeLimit = 0;
 332 };
 333
 334 /*! \brief Determines the optimal DD cell setup dd->nc and possibly npmenodes
 335  * for the system.
 336  */
 337 DDSetup
 338 dd_choose_grid(const gmx::MDLogger &mdlog,
 339                const t_commrec *cr,
 340                const t_inputrec *ir,
 341                const gmx_mtop_t *mtop,
 342                const matrix box, const gmx_ddbox_t *ddbox,
 343                int numPmeRanksRequested,
 344                gmx_bool bDynLoadBal, real dlb_scale,
 345                const DDSystemInfo &systemInfo);
 346
 347 #endif