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37 /*! \defgroup module_domdec Spatial domain decomposition (for parallelization over MPI)
38 * \ingroup group_mdrun
40 * \brief Manages the decomposition of the simulation volume over MPI
41 * ranks to try to distribute work evenly with minimal communication
44 * \todo Get domdec stuff out of mdtypes/commrec.h
46 * \author Berk Hess <hess@kth.se>
50 /*! \libinternal \file
52 * \brief This file declares functions for mdrun to call to manage the
53 * details of its domain decomposition.
55 * \author Berk Hess <hess@kth.se>
57 * \ingroup module_domdec
60 #ifndef GMX_DOMDEC_DOMDEC_H
61 #define GMX_DOMDEC_DOMDEC_H
65 #include "gromacs/gpu_utils/devicebuffer_datatype.h"
66 #include "gromacs/math/vectypes.h"
67 #include "gromacs/utility/real.h"
72 struct gmx_domdec_zones_t;
73 struct gmx_localtop_t;
81 enum class PbcType : int;
84 class GpuEventSynchronizer;
88 class DeviceStreamManager;
89 class ForceWithShiftForces;
91 class RangePartitioning;
92 class VirtualSitesHandler;
95 enum class DDBondedChecking : bool;
98 /*! \brief Returns the global topology atom number belonging to local atom index i.
100 * This function is intended for writing ASCII output
101 * and returns atom numbers starting at 1.
102 * When dd=NULL returns i+1.
104 int ddglatnr(const gmx_domdec_t* dd, int i);
106 /*! \brief Store the global cg indices of the home cgs in state,
108 * This means it can be reset, even after a new DD partitioning.
110 void dd_store_state(const gmx_domdec_t& dd, t_state* state);
112 /*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
113 struct gmx_domdec_zones_t* domdec_zones(struct gmx_domdec_t* dd);
115 /*! \brief Returns the range for atoms in zones*/
116 int dd_numAtomsZones(const gmx_domdec_t& dd);
118 /*! \brief Returns the number of home atoms */
119 int dd_numHomeAtoms(const gmx_domdec_t& dd);
121 /*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
122 int dd_natoms_mdatoms(const gmx_domdec_t& dd);
124 /*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
125 int dd_natoms_vsite(const gmx_domdec_t& dd);
127 /*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
128 void dd_get_constraint_range(const gmx_domdec_t& dd, int* at_start, int* at_end);
130 /*! \libinternal \brief Struct for passing around the number of PME domains */
133 int x; //!< The number of PME domains along dimension x
134 int y; //!< The number of PME domains along dimension y
137 /*! \brief Returns the number of PME domains, can be called with dd=NULL */
138 NumPmeDomains getNumPmeDomains(const gmx_domdec_t* dd);
140 /*! \brief Returns the set of DD ranks that communicate with pme node cr->nodeid */
141 std::vector<int> get_pme_ddranks(const t_commrec* cr, int pmenodeid);
143 /*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
144 int dd_pme_maxshift_x(const gmx_domdec_t& dd);
146 /*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
147 int dd_pme_maxshift_y(const gmx_domdec_t& dd);
149 /*! \brief Return whether update groups are used */
150 bool ddUsesUpdateGroups(const gmx_domdec_t& dd);
152 /*! \brief Returns whether molecules are always whole, i.e. not broken by PBC */
153 bool dd_moleculesAreAlwaysWhole(const gmx_domdec_t& dd);
155 /*! \brief Returns if we need to do pbc for calculating bonded interactions */
156 bool dd_bonded_molpbc(const gmx_domdec_t& dd, PbcType pbcType);
158 /*! \brief Change the DD non-bonded communication cut-off.
160 * This could fail when trying to increase the cut-off,
161 * then FALSE will be returned and the cut-off is not modified.
163 * \param[in] cr Communication recrod
164 * \param[in] box Box matrix, used for computing the dimensions of the system
165 * \param[in] x Position vector, used for computing the dimensions of the system
166 * \param[in] cutoffRequested The requested atom to atom cut-off distance, usually the pair-list cutoff distance
168 bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested);
170 /*! \brief Set up communication for averaging GPU wait times over domains
172 * When domains (PP MPI ranks) share a GPU, the individual GPU wait times
173 * are meaningless, as it depends on the order in which tasks on the same
174 * GPU finish. Therefore there wait times need to be averaged over the ranks
175 * sharing the same GPU. This function sets up the communication for that.
177 void dd_setup_dlb_resource_sharing(const t_commrec* cr, int gpu_id);
179 /*! \brief Cycle counter indices used internally in the domain decomposition */
190 /*! \brief Add the wallcycle count to the DD counter */
191 void dd_cycles_add(const gmx_domdec_t* dd, float cycles, int ddCycl);
193 /*! \brief Communicate the coordinates to the neighboring cells and do pbc. */
194 void dd_move_x(struct gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle);
196 /*! \brief Sum the forces over the neighboring cells.
198 * When fshift!=NULL the shift forces are updated to obtain
199 * the correct virial from the single sum including f.
201 void dd_move_f(struct gmx_domdec_t* dd, gmx::ForceWithShiftForces* forceWithShiftForces, gmx_wallcycle* wcycle);
203 /*! \brief Communicate a real for each atom to the neighboring cells. */
204 void dd_atom_spread_real(struct gmx_domdec_t* dd, real v[]);
206 /*! \brief Sum the contributions to a real for each atom over the neighboring cells. */
207 void dd_atom_sum_real(struct gmx_domdec_t* dd, real v[]);
209 /*! \brief Reset all the statistics and counters for total run counting */
210 void reset_dd_statistics_counters(struct gmx_domdec_t* dd);
212 /* In domdec_con.c */
214 /*! \brief Communicates the virtual site forces, reduces the shift forces when \p fshift != NULL */
215 void dd_move_f_vsites(const gmx_domdec_t& dd, gmx::ArrayRef<gmx::RVec> f, gmx::ArrayRef<gmx::RVec> fshift);
217 /*! \brief Clears the forces for virtual sites */
218 void dd_clear_f_vsites(const gmx_domdec_t& dd, gmx::ArrayRef<gmx::RVec> f);
220 /*! \brief Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
221 void dd_move_x_constraints(struct gmx_domdec_t* dd,
223 gmx::ArrayRef<gmx::RVec> x0,
224 gmx::ArrayRef<gmx::RVec> x1,
227 /*! \brief Communicates the coordinates involved in virtual sites */
228 void dd_move_x_vsites(const gmx_domdec_t& dd, const matrix box, rvec* x);
229 /*! \brief Communicates the positions and velocities involved in virtual sites */
230 void dd_move_x_and_v_vsites(const gmx_domdec_t& dd, const matrix box, rvec* x, rvec* v);
232 /*! \brief Returns the local atom count array for all constraints
234 * The local atom count for a constraint, possible values 2/1/0, is needed
235 * to avoid not/double-counting contributions linked to the Lagrange
236 * multiplier, such as the virial and free-energy derivatives.
238 * \note When \p dd = nullptr, an empty reference is returned.
240 gmx::ArrayRef<const int> dd_constraints_nlocalatoms(const gmx_domdec_t* dd);
242 /* In domdec_top.c */
244 /*! \brief Generate the local topology and virtual site data
246 * \returns Total count of bonded interactions in the local topology on this domain */
247 int dd_make_local_top(struct gmx_domdec_t* dd,
248 struct gmx_domdec_zones_t* zones,
254 gmx::ArrayRef<const gmx::RVec> coordinates,
255 const gmx_mtop_t& top,
256 gmx_localtop_t* ltop);
258 /*! \brief Sort ltop->ilist when we are doing free energy. */
259 void dd_sort_local_top(const gmx_domdec_t& dd, const t_mdatoms* mdatoms, gmx_localtop_t* ltop);
261 /*! \brief Construct local state */
262 void dd_init_local_state(const gmx_domdec_t& dd, const t_state* state_global, t_state* local_state);
264 /*! \brief Generate a list of links between atoms that are linked by bonded interactions
266 * Also stores whether atoms are linked in \p cginfo_mb.
268 void makeBondedLinks(gmx_domdec_t* dd, const gmx_mtop_t& mtop, gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
270 /*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
271 void dd_bonded_cg_distance(const gmx::MDLogger& mdlog,
272 const gmx_mtop_t& mtop,
273 const t_inputrec& ir,
274 gmx::ArrayRef<const gmx::RVec> x,
276 gmx::DDBondedChecking ddBondedChecking,
280 /*! \brief Construct the GPU halo exchange object(s).
282 * \param[in] mdlog The logger object.
283 * \param[in] cr The commrec object.
284 * \param[in] deviceStreamManager Manager of the GPU context and streams.
285 * \param[in] wcycle The wallclock counter.
287 void constructGpuHaloExchange(const gmx::MDLogger& mdlog,
289 const gmx::DeviceStreamManager& deviceStreamManager,
290 gmx_wallcycle* wcycle);
293 * (Re-) Initialization for GPU halo exchange
294 * \param [in] cr The commrec object
295 * \param [in] d_coordinatesBuffer pointer to coordinates buffer in GPU memory
296 * \param [in] d_forcesBuffer pointer to forces buffer in GPU memory
298 void reinitGpuHaloExchange(const t_commrec& cr,
299 DeviceBuffer<gmx::RVec> d_coordinatesBuffer,
300 DeviceBuffer<gmx::RVec> d_forcesBuffer);
303 /*! \brief GPU halo exchange of coordinates buffer.
304 * \param [in] cr The commrec object
305 * \param [in] box Coordinate box (from which shifts will be constructed)
306 * \param [in] coordinatesReadyOnDeviceEvent event recorded when coordinates have been copied to device
308 void communicateGpuHaloCoordinates(const t_commrec& cr,
310 GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
313 /*! \brief GPU halo exchange of force buffer.
314 * \param [in] cr The commrec object
315 * \param [in] accumulateForces True if forces should accumulate, otherwise they are set
317 void communicateGpuHaloForces(const t_commrec& cr, bool accumulateForces);