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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"
71 struct gmx_domdec_zones_t;
72 struct gmx_localtop_t;
80 enum class PbcType : int;
83 class GpuEventSynchronizer;
87 struct AtomInfoWithinMoleculeBlock;
88 class DeviceStreamManager;
89 class ForceWithShiftForces;
90 class LocalTopologyChecker;
92 class RangePartitioning;
93 class VirtualSitesHandler;
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 /*! Const getter for the local topology checker
244 * \returns Const handle to local topology checker */
245 const gmx::LocalTopologyChecker& dd_localTopologyChecker(const gmx_domdec_t& dd);
247 /*! Getter for the local topology checker
249 * \returns Handle to local topology checker */
250 gmx::LocalTopologyChecker* dd_localTopologyChecker(gmx_domdec_t* dd);
252 /*! \brief Construct local state */
253 void dd_init_local_state(const gmx_domdec_t& dd, const t_state* state_global, t_state* local_state);
255 /*! \brief Construct the GPU halo exchange object(s).
257 * \param[in] mdlog The logger object.
258 * \param[in] cr The commrec object.
259 * \param[in] deviceStreamManager Manager of the GPU context and streams.
260 * \param[in] wcycle The wallclock counter.
262 void constructGpuHaloExchange(const gmx::MDLogger& mdlog,
264 const gmx::DeviceStreamManager& deviceStreamManager,
265 gmx_wallcycle* wcycle);
268 * (Re-) Initialization for GPU halo exchange
269 * \param [in] cr The commrec object
270 * \param [in] d_coordinatesBuffer pointer to coordinates buffer in GPU memory
271 * \param [in] d_forcesBuffer pointer to forces buffer in GPU memory
273 void reinitGpuHaloExchange(const t_commrec& cr,
274 DeviceBuffer<gmx::RVec> d_coordinatesBuffer,
275 DeviceBuffer<gmx::RVec> d_forcesBuffer);
278 /*! \brief GPU halo exchange of coordinates buffer.
279 * \param [in] cr The commrec object
280 * \param [in] box Coordinate box (from which shifts will be constructed)
281 * \param [in] coordinatesReadyOnDeviceEvent event recorded when coordinates have been copied to device
283 void communicateGpuHaloCoordinates(const t_commrec& cr,
285 GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
288 /*! \brief GPU halo exchange of force buffer.
289 * \param [in] cr The commrec object
290 * \param [in] accumulateForces True if forces should accumulate, otherwise they are set
292 void communicateGpuHaloForces(const t_commrec& cr, bool accumulateForces);
294 /*! \brief Wraps the \c positions so that atoms from the same
295 * update group share the same periodic image wrt \c box.
297 * When DD and update groups are in use, the simulation master rank
298 * should call this to ensure that e.g. when restarting a simulation
299 * that did not use update groups that the coordinates satisfy the new
302 * This function can probably be removed when even single-rank
303 * simulations use domain decomposition, because then the choice of
304 * whether update groups are used is probably going to be the same
305 * regardless of the rank count.
307 * \param[in] dd The DD manager
308 * \param[in] mtop The system topology
309 * \param[in] box The global system box
310 * \param[in] positions The global system positions
312 void putUpdateGroupAtomsInSamePeriodicImage(const gmx_domdec_t& dd,
313 const gmx_mtop_t& mtop,
315 gmx::ArrayRef<gmx::RVec> positions);