src/gromacs/domdec/domdec.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2005 - 2014, The GROMACS development team.
   5  * Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team.
   6  * Copyright (c) 2020, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 /*! \defgroup module_domdec Spatial domain decomposition (for parallelization over MPI)
  38  * \ingroup group_mdrun
  39  *
  40  * \brief Manages the decomposition of the simulation volume over MPI
  41  * ranks to try to distribute work evenly with minimal communication
  42  * overheads.
  43  *
  44  * \todo Get domdec stuff out of mdtypes/commrec.h
  45  *
  46  * \author Berk Hess <hess@kth.se>
  47  *
  48  */
  49
  50 /*! \libinternal \file
  51  *
  52  * \brief This file declares functions for mdrun to call to manage the
  53  * details of its domain decomposition.
  54  *
  55  * \author Berk Hess <hess@kth.se>
  56  * \inlibraryapi
  57  * \ingroup module_domdec
  58  */
  59
  60 #ifndef GMX_DOMDEC_DOMDEC_H
  61 #define GMX_DOMDEC_DOMDEC_H
  62
  63 #include <vector>
  64
  65 #include "gromacs/math/vectypes.h"
  66 #include "gromacs/utility/arrayref.h"
  67 #include "gromacs/utility/basedefinitions.h"
  68 #include "gromacs/utility/real.h"
  69
  70 struct cginfo_mb_t;
  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 RangePartitioning;
  92 } // namespace gmx
  93
  94 /*! \brief Returns the global topology atom number belonging to local atom index i.
  95  *
  96  * This function is intended for writing ASCII output
  97  * and returns atom numbers starting at 1.
  98  * When dd=NULL returns i+1.
  99  */
 100 int ddglatnr(const gmx_domdec_t* dd, int i);
 101
 102 /*! \brief Returns a list of update group partitioning for each molecule type or empty when update groups are not used */
 103 gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingPerMoleculetype(const gmx_domdec_t& dd);
 104
 105 /*! \brief Store the global cg indices of the home cgs in state,
 106  *
 107  * This means it can be reset, even after a new DD partitioning.
 108  */
 109 void dd_store_state(struct gmx_domdec_t* dd, t_state* state);
 110
 111 /*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
 112 struct gmx_domdec_zones_t* domdec_zones(struct gmx_domdec_t* dd);
 113
 114 /*! \brief Returns the range for atoms in zones*/
 115 int dd_numAtomsZones(const gmx_domdec_t& dd);
 116
 117 /*! \brief Returns the number of home atoms */
 118 int dd_numHomeAtoms(const gmx_domdec_t& dd);
 119
 120 /*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
 121 int dd_natoms_mdatoms(const gmx_domdec_t* dd);
 122
 123 /*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
 124 int dd_natoms_vsite(const gmx_domdec_t* dd);
 125
 126 /*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
 127 void dd_get_constraint_range(const gmx_domdec_t* dd, int* at_start, int* at_end);
 128
 129 /*! \libinternal \brief Struct for passing around the number of PME domains */
 130 struct NumPmeDomains
 131 {
 132     int x; //!< The number of PME domains along dimension x
 133     int y; //!< The number of PME domains along dimension y
 134 };
 135
 136 /*! \brief Returns the number of PME domains, can be called with dd=NULL */
 137 NumPmeDomains getNumPmeDomains(const gmx_domdec_t* dd);
 138
 139 /*! \brief Returns the set of DD ranks that communicate with pme node cr->nodeid */
 140 std::vector<int> get_pme_ddranks(const t_commrec* cr, int pmenodeid);
 141
 142 /*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
 143 int dd_pme_maxshift_x(const gmx_domdec_t* dd);
 144
 145 /*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
 146 int dd_pme_maxshift_y(const gmx_domdec_t* dd);
 147
 148 /*! \brief Return whether constraints, not including settles, cross domain boundaries */
 149 bool ddHaveSplitConstraints(const gmx_domdec_t& dd);
 150
 151 /*! \brief Return whether update groups are used */
 152 bool ddUsesUpdateGroups(const gmx_domdec_t& dd);
 153
 154 /*! \brief Return whether the DD has a single dimension with a single pulse
 155  *
 156  * The GPU halo exchange code requires a 1D single-pulse DD, and its
 157  * setup code can use the returned value to understand what it should
 158  * do. */
 159 bool is1DAnd1PulseDD(const gmx_domdec_t& dd);
 160
 161 /*! \brief Initialize data structures for bonded interactions */
 162 void dd_init_bondeds(FILE*                      fplog,
 163                      gmx_domdec_t*              dd,
 164                      const gmx_mtop_t&          mtop,
 165                      const gmx_vsite_t*         vsite,
 166                      const t_inputrec*          ir,
 167                      gmx_bool                   bBCheck,
 168                      gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
 169
 170 /*! \brief Returns whether molecules are always whole, i.e. not broken by PBC */
 171 bool dd_moleculesAreAlwaysWhole(const gmx_domdec_t& dd);
 172
 173 /*! \brief Returns if we need to do pbc for calculating bonded interactions */
 174 gmx_bool dd_bonded_molpbc(const gmx_domdec_t* dd, int ePBC);
 175
 176 /*! \brief Change the DD non-bonded communication cut-off.
 177  *
 178  * This could fail when trying to increase the cut-off,
 179  * then FALSE will be returned and the cut-off is not modified.
 180  *
 181  * \param[in] cr               Communication recrod
 182  * \param[in] box              Box matrix, used for computing the dimensions of the system
 183  * \param[in] x                Position vector, used for computing the dimensions of the system
 184  * \param[in] cutoffRequested  The requested atom to atom cut-off distance, usually the pair-list cutoff distance
 185  */
 186 gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested);
 187
 188 /*! \brief Set up communication for averaging GPU wait times over domains
 189  *
 190  * When domains (PP MPI ranks) share a GPU, the individual GPU wait times
 191  * are meaningless, as it depends on the order in which tasks on the same
 192  * GPU finish. Therefore there wait times need to be averaged over the ranks
 193  * sharing the same GPU. This function sets up the communication for that.
 194  */
 195 void dd_setup_dlb_resource_sharing(const t_commrec* cr, int gpu_id);
 196
 197 /*! \brief Cycle counter indices used internally in the domain decomposition */
 198 enum
 199 {
 200     ddCyclStep,
 201     ddCyclPPduringPME,
 202     ddCyclF,
 203     ddCyclWaitGPU,
 204     ddCyclPME,
 205     ddCyclNr
 206 };
 207
 208 /*! \brief Add the wallcycle count to the DD counter */
 209 void dd_cycles_add(const gmx_domdec_t* dd, float cycles, int ddCycl);
 210
 211 /*! \brief Communicate the coordinates to the neighboring cells and do pbc. */
 212 void dd_move_x(struct gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle);
 213
 214 /*! \brief Sum the forces over the neighboring cells.
 215  *
 216  * When fshift!=NULL the shift forces are updated to obtain
 217  * the correct virial from the single sum including f.
 218  */
 219 void dd_move_f(struct gmx_domdec_t* dd, gmx::ForceWithShiftForces* forceWithShiftForces, gmx_wallcycle* wcycle);
 220
 221 /*! \brief Communicate a real for each atom to the neighboring cells. */
 222 void dd_atom_spread_real(struct gmx_domdec_t* dd, real v[]);
 223
 224 /*! \brief Sum the contributions to a real for each atom over the neighboring cells. */
 225 void dd_atom_sum_real(struct gmx_domdec_t* dd, real v[]);
 226
 227 /*! \brief Reset all the statistics and counters for total run counting */
 228 void reset_dd_statistics_counters(struct gmx_domdec_t* dd);
 229
 230 /* In domdec_con.c */
 231
 232 /*! \brief Communicates the virtual site forces, reduces the shift forces when \p fshift != NULL */
 233 void dd_move_f_vsites(struct gmx_domdec_t* dd, rvec* f, rvec* fshift);
 234
 235 /*! \brief Clears the forces for virtual sites */
 236 void dd_clear_f_vsites(struct gmx_domdec_t* dd, rvec* f);
 237
 238 /*! \brief Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
 239 void dd_move_x_constraints(struct gmx_domdec_t* dd, const matrix box, rvec* x0, rvec* x1, gmx_bool bX1IsCoord);
 240
 241 /*! \brief Communicates the coordinates involved in virtual sites */
 242 void dd_move_x_vsites(struct gmx_domdec_t* dd, const matrix box, rvec* x);
 243
 244 /*! \brief Returns the local atom count array for all constraints
 245  *
 246  * The local atom count for a constraint, possible values 2/1/0, is needed
 247  * to avoid not/double-counting contributions linked to the Lagrange
 248  * multiplier, such as the virial and free-energy derivatives.
 249  *
 250  * \note When \p dd = nullptr, an empty reference is returned.
 251  */
 252 gmx::ArrayRef<const int> dd_constraints_nlocalatoms(const gmx_domdec_t* dd);
 253
 254 /* In domdec_top.c */
 255
 256 /*! \brief Print error output when interactions are missing */
 257 [[noreturn]] void dd_print_missing_interactions(const gmx::MDLogger&  mdlog,
 258                                                 t_commrec*            cr,
 259                                                 int                   local_count,
 260                                                 const gmx_mtop_t*     top_global,
 261                                                 const gmx_localtop_t* top_local,
 262                                                 const rvec*           x,
 263                                                 const matrix          box);
 264
 265 /*! \brief Generate and store the reverse topology */
 266 void dd_make_reverse_top(FILE*              fplog,
 267                          gmx_domdec_t*      dd,
 268                          const gmx_mtop_t*  mtop,
 269                          const gmx_vsite_t* vsite,
 270                          const t_inputrec*  ir,
 271                          gmx_bool           bBCheck);
 272
 273 /*! \brief Generate the local topology and virtual site data */
 274 void dd_make_local_top(struct gmx_domdec_t*       dd,
 275                        struct gmx_domdec_zones_t* zones,
 276                        int                        npbcdim,
 277                        matrix                     box,
 278                        rvec                       cellsize_min,
 279                        const ivec                 npulse,
 280                        t_forcerec*                fr,
 281                        rvec*                      cgcm_or_x,
 282                        const gmx_mtop_t&          top,
 283                        gmx_localtop_t*            ltop);
 284
 285 /*! \brief Sort ltop->ilist when we are doing free energy. */
 286 void dd_sort_local_top(gmx_domdec_t* dd, const t_mdatoms* mdatoms, gmx_localtop_t* ltop);
 287
 288 /*! \brief Initialize local topology
 289  *
 290  * \param[in] top_global Reference to global topology.
 291  * \param[in,out] top Pointer to new local topology
 292  */
 293 void dd_init_local_top(const gmx_mtop_t& top_global, gmx_localtop_t* top);
 294
 295 /*! \brief Construct local state */
 296 void dd_init_local_state(struct gmx_domdec_t* dd, const t_state* state_global, t_state* local_state);
 297
 298 /*! \brief Generate a list of links between atoms that are linked by bonded interactions
 299  *
 300  * Also stores whether atoms are linked in \p cginfo_mb.
 301  */
 302 t_blocka* makeBondedLinks(const gmx_mtop_t& mtop, gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
 303
 304 /*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
 305 void dd_bonded_cg_distance(const gmx::MDLogger& mdlog,
 306                            const gmx_mtop_t*    mtop,
 307                            const t_inputrec*    ir,
 308                            const rvec*          x,
 309                            const matrix         box,
 310                            gmx_bool             bBCheck,
 311                            real*                r_2b,
 312                            real*                r_mb);
 313
 314 #endif