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/gpu_utils/devicebuffer_datatype.h"
  66 #include "gromacs/math/vectypes.h"
  67 #include "gromacs/utility/arrayref.h"
  68 #include "gromacs/utility/basedefinitions.h"
  69 #include "gromacs/utility/real.h"
  70
  71 struct cginfo_mb_t;
  72 struct gmx_domdec_t;
  73 struct gmx_ddbox_t;
  74 struct gmx_domdec_zones_t;
  75 struct gmx_localtop_t;
  76 struct gmx_mtop_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 enum class PbcType : int;
  86 class t_state;
  87 class DeviceContext;
  88 class GpuEventSynchronizer;
  89
  90 namespace gmx
  91 {
  92 class DeviceStreamManager;
  93 class ForceWithShiftForces;
  94 class MDLogger;
  95 class RangePartitioning;
  96 class VirtualSitesHandler;
  97 } // namespace gmx
  98
  99 /*! \brief Returns the global topology atom number belonging to local atom index i.
 100  *
 101  * This function is intended for writing ASCII output
 102  * and returns atom numbers starting at 1.
 103  * When dd=NULL returns i+1.
 104  */
 105 int ddglatnr(const gmx_domdec_t* dd, int i);
 106
 107 /*! \brief Returns a list of update group partitioning for each molecule type or empty when update groups are not used */
 108 gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingPerMoleculetype(const gmx_domdec_t& dd);
 109
 110 /*! \brief Store the global cg indices of the home cgs in state,
 111  *
 112  * This means it can be reset, even after a new DD partitioning.
 113  */
 114 void dd_store_state(struct gmx_domdec_t* dd, t_state* state);
 115
 116 /*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
 117 struct gmx_domdec_zones_t* domdec_zones(struct gmx_domdec_t* dd);
 118
 119 /*! \brief Returns the range for atoms in zones*/
 120 int dd_numAtomsZones(const gmx_domdec_t& dd);
 121
 122 /*! \brief Returns the number of home atoms */
 123 int dd_numHomeAtoms(const gmx_domdec_t& dd);
 124
 125 /*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
 126 int dd_natoms_mdatoms(const gmx_domdec_t* dd);
 127
 128 /*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
 129 int dd_natoms_vsite(const gmx_domdec_t* dd);
 130
 131 /*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
 132 void dd_get_constraint_range(const gmx_domdec_t* dd, int* at_start, int* at_end);
 133
 134 /*! \libinternal \brief Struct for passing around the number of PME domains */
 135 struct NumPmeDomains
 136 {
 137     int x; //!< The number of PME domains along dimension x
 138     int y; //!< The number of PME domains along dimension y
 139 };
 140
 141 /*! \brief Returns the number of PME domains, can be called with dd=NULL */
 142 NumPmeDomains getNumPmeDomains(const gmx_domdec_t* dd);
 143
 144 /*! \brief Returns the set of DD ranks that communicate with pme node cr->nodeid */
 145 std::vector<int> get_pme_ddranks(const t_commrec* cr, int pmenodeid);
 146
 147 /*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
 148 int dd_pme_maxshift_x(const gmx_domdec_t* dd);
 149
 150 /*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
 151 int dd_pme_maxshift_y(const gmx_domdec_t* dd);
 152
 153 /*! \brief Return whether constraints, not including settles, cross domain boundaries */
 154 bool ddHaveSplitConstraints(const gmx_domdec_t& dd);
 155
 156 /*! \brief Return whether update groups are used */
 157 bool ddUsesUpdateGroups(const gmx_domdec_t& dd);
 158
 159 /*! \brief Return whether the DD has a single dimension
 160  *
 161  * The GPU halo exchange code requires a 1D DD, and its setup code can
 162  * use the returned value to understand what it should do.
 163  */
 164 bool is1D(const gmx_domdec_t& dd);
 165
 166 /*! \brief Initialize data structures for bonded interactions */
 167 void dd_init_bondeds(FILE*                           fplog,
 168                      gmx_domdec_t*                   dd,
 169                      const gmx_mtop_t&               mtop,
 170                      const gmx::VirtualSitesHandler* vsite,
 171                      const t_inputrec*               ir,
 172                      gmx_bool                        bBCheck,
 173                      gmx::ArrayRef<cginfo_mb_t>      cginfo_mb);
 174
 175 /*! \brief Returns whether molecules are always whole, i.e. not broken by PBC */
 176 bool dd_moleculesAreAlwaysWhole(const gmx_domdec_t& dd);
 177
 178 /*! \brief Returns if we need to do pbc for calculating bonded interactions */
 179 gmx_bool dd_bonded_molpbc(const gmx_domdec_t* dd, PbcType pbcType);
 180
 181 /*! \brief Change the DD non-bonded communication cut-off.
 182  *
 183  * This could fail when trying to increase the cut-off,
 184  * then FALSE will be returned and the cut-off is not modified.
 185  *
 186  * \param[in] cr               Communication recrod
 187  * \param[in] box              Box matrix, used for computing the dimensions of the system
 188  * \param[in] x                Position vector, used for computing the dimensions of the system
 189  * \param[in] cutoffRequested  The requested atom to atom cut-off distance, usually the pair-list cutoff distance
 190  */
 191 gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested);
 192
 193 /*! \brief Set up communication for averaging GPU wait times over domains
 194  *
 195  * When domains (PP MPI ranks) share a GPU, the individual GPU wait times
 196  * are meaningless, as it depends on the order in which tasks on the same
 197  * GPU finish. Therefore there wait times need to be averaged over the ranks
 198  * sharing the same GPU. This function sets up the communication for that.
 199  */
 200 void dd_setup_dlb_resource_sharing(const t_commrec* cr, int gpu_id);
 201
 202 /*! \brief Cycle counter indices used internally in the domain decomposition */
 203 enum
 204 {
 205     ddCyclStep,
 206     ddCyclPPduringPME,
 207     ddCyclF,
 208     ddCyclWaitGPU,
 209     ddCyclPME,
 210     ddCyclNr
 211 };
 212
 213 /*! \brief Add the wallcycle count to the DD counter */
 214 void dd_cycles_add(const gmx_domdec_t* dd, float cycles, int ddCycl);
 215
 216 /*! \brief Communicate the coordinates to the neighboring cells and do pbc. */
 217 void dd_move_x(struct gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle);
 218
 219 /*! \brief Sum the forces over the neighboring cells.
 220  *
 221  * When fshift!=NULL the shift forces are updated to obtain
 222  * the correct virial from the single sum including f.
 223  */
 224 void dd_move_f(struct gmx_domdec_t* dd, gmx::ForceWithShiftForces* forceWithShiftForces, gmx_wallcycle* wcycle);
 225
 226 /*! \brief Communicate a real for each atom to the neighboring cells. */
 227 void dd_atom_spread_real(struct gmx_domdec_t* dd, real v[]);
 228
 229 /*! \brief Sum the contributions to a real for each atom over the neighboring cells. */
 230 void dd_atom_sum_real(struct gmx_domdec_t* dd, real v[]);
 231
 232 /*! \brief Reset all the statistics and counters for total run counting */
 233 void reset_dd_statistics_counters(struct gmx_domdec_t* dd);
 234
 235 /* In domdec_con.c */
 236
 237 /*! \brief Communicates the virtual site forces, reduces the shift forces when \p fshift != NULL */
 238 void dd_move_f_vsites(const gmx_domdec_t& dd, gmx::ArrayRef<gmx::RVec> f, gmx::ArrayRef<gmx::RVec> fshift);
 239
 240 /*! \brief Clears the forces for virtual sites */
 241 void dd_clear_f_vsites(const gmx_domdec_t& dd, gmx::ArrayRef<gmx::RVec> f);
 242
 243 /*! \brief Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
 244 void dd_move_x_constraints(struct gmx_domdec_t*     dd,
 245                            const matrix             box,
 246                            gmx::ArrayRef<gmx::RVec> x0,
 247                            gmx::ArrayRef<gmx::RVec> x1,
 248                            gmx_bool                 bX1IsCoord);
 249
 250 /*! \brief Communicates the coordinates involved in virtual sites */
 251 void dd_move_x_vsites(const 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]] void dd_print_missing_interactions(const gmx::MDLogger&           mdlog,
 267                                                 t_commrec*                     cr,
 268                                                 int                            local_count,
 269                                                 const gmx_mtop_t*              top_global,
 270                                                 const gmx_localtop_t*          top_local,
 271                                                 gmx::ArrayRef<const gmx::RVec> x,
 272                                                 const matrix                   box);
 273
 274 /*! \brief Generate and store the reverse topology */
 275 void dd_make_reverse_top(FILE*                           fplog,
 276                          gmx_domdec_t*                   dd,
 277                          const gmx_mtop_t*               mtop,
 278                          const gmx::VirtualSitesHandler* vsite,
 279                          const t_inputrec*               ir,
 280                          gmx_bool                        bBCheck);
 281
 282 /*! \brief Generate the local topology and virtual site data */
 283 void dd_make_local_top(struct gmx_domdec_t*       dd,
 284                        struct gmx_domdec_zones_t* zones,
 285                        int                        npbcdim,
 286                        matrix                     box,
 287                        rvec                       cellsize_min,
 288                        const ivec                 npulse,
 289                        t_forcerec*                fr,
 290                        rvec*                      cgcm_or_x,
 291                        const gmx_mtop_t&          top,
 292                        gmx_localtop_t*            ltop);
 293
 294 /*! \brief Sort ltop->ilist when we are doing free energy. */
 295 void dd_sort_local_top(gmx_domdec_t* dd, const t_mdatoms* mdatoms, gmx_localtop_t* ltop);
 296
 297 /*! \brief Construct local state */
 298 void dd_init_local_state(struct gmx_domdec_t* dd, const t_state* state_global, t_state* local_state);
 299
 300 /*! \brief Generate a list of links between atoms that are linked by bonded interactions
 301  *
 302  * Also stores whether atoms are linked in \p cginfo_mb.
 303  */
 304 t_blocka* makeBondedLinks(const gmx_mtop_t& mtop, gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
 305
 306 /*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
 307 void dd_bonded_cg_distance(const gmx::MDLogger&           mdlog,
 308                            const gmx_mtop_t*              mtop,
 309                            const t_inputrec*              ir,
 310                            gmx::ArrayRef<const gmx::RVec> x,
 311                            const matrix                   box,
 312                            gmx_bool                       bBCheck,
 313                            real*                          r_2b,
 314                            real*                          r_mb);
 315
 316 /*! \brief Construct the GPU halo exchange object(s).
 317  *
 318  * \param[in] mdlog               The logger object.
 319  * \param[in] cr                  The commrec object.
 320  * \param[in] deviceStreamManager Manager of the GPU context and streams.
 321  * \param[in] wcycle              The wallclock counter.
 322  */
 323 void constructGpuHaloExchange(const gmx::MDLogger&            mdlog,
 324                               const t_commrec&                cr,
 325                               const gmx::DeviceStreamManager& deviceStreamManager,
 326                               gmx_wallcycle*                  wcycle);
 327
 328 /*! \brief
 329  * (Re-) Initialization for GPU halo exchange
 330  * \param [in] cr                   The commrec object
 331  * \param [in] d_coordinatesBuffer  pointer to coordinates buffer in GPU memory
 332  * \param [in] d_forcesBuffer       pointer to forces buffer in GPU memory
 333  */
 334 void reinitGpuHaloExchange(const t_commrec&        cr,
 335                            DeviceBuffer<gmx::RVec> d_coordinatesBuffer,
 336                            DeviceBuffer<gmx::RVec> d_forcesBuffer);
 337
 338
 339 /*! \brief GPU halo exchange of coordinates buffer.
 340  * \param [in] cr                             The commrec object
 341  * \param [in] box                            Coordinate box (from which shifts will be constructed)
 342  * \param [in] coordinatesReadyOnDeviceEvent  event recorded when coordinates have been copied to device
 343  */
 344 void communicateGpuHaloCoordinates(const t_commrec&      cr,
 345                                    const matrix          box,
 346                                    GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
 347
 348
 349 /*! \brief GPU halo exchange of force buffer.
 350  * \param [in] cr                The commrec object
 351  * \param [in] accumulateForces  True if forces should accumulate, otherwise they are set
 352  */
 353 void communicateGpuHaloForces(const t_commrec& cr, bool accumulateForces);
 354
 355 #endif