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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/arrayref.h"
68 #include "gromacs/utility/basedefinitions.h"
69 #include "gromacs/utility/real.h"
74 struct gmx_domdec_zones_t;
75 struct gmx_localtop_t;
86 enum class PbcType : int;
89 class GpuEventSynchronizer;
93 class ForceWithShiftForces;
95 class RangePartitioning;
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 Returns a list of update group partitioning for each molecule type or empty when update groups are not used */
107 gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingPerMoleculetype(const gmx_domdec_t& dd);
109 /*! \brief Store the global cg indices of the home cgs in state,
111 * This means it can be reset, even after a new DD partitioning.
113 void dd_store_state(struct gmx_domdec_t* dd, t_state* state);
115 /*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
116 struct gmx_domdec_zones_t* domdec_zones(struct gmx_domdec_t* dd);
118 /*! \brief Returns the range for atoms in zones*/
119 int dd_numAtomsZones(const gmx_domdec_t& dd);
121 /*! \brief Returns the number of home atoms */
122 int dd_numHomeAtoms(const gmx_domdec_t& dd);
124 /*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
125 int dd_natoms_mdatoms(const gmx_domdec_t* dd);
127 /*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
128 int dd_natoms_vsite(const gmx_domdec_t* dd);
130 /*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
131 void dd_get_constraint_range(const gmx_domdec_t* dd, int* at_start, int* at_end);
133 /*! \libinternal \brief Struct for passing around the number of PME domains */
136 int x; //!< The number of PME domains along dimension x
137 int y; //!< The number of PME domains along dimension y
140 /*! \brief Returns the number of PME domains, can be called with dd=NULL */
141 NumPmeDomains getNumPmeDomains(const gmx_domdec_t* dd);
143 /*! \brief Returns the set of DD ranks that communicate with pme node cr->nodeid */
144 std::vector<int> get_pme_ddranks(const t_commrec* cr, int pmenodeid);
146 /*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
147 int dd_pme_maxshift_x(const gmx_domdec_t* dd);
149 /*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
150 int dd_pme_maxshift_y(const gmx_domdec_t* dd);
152 /*! \brief Return whether constraints, not including settles, cross domain boundaries */
153 bool ddHaveSplitConstraints(const gmx_domdec_t& dd);
155 /*! \brief Return whether update groups are used */
156 bool ddUsesUpdateGroups(const gmx_domdec_t& dd);
158 /*! \brief Return whether the DD has a single dimension
160 * The GPU halo exchange code requires a 1D DD, and its setup code can
161 * use the returned value to understand what it should do.
163 bool is1D(const gmx_domdec_t& dd);
165 /*! \brief Initialize data structures for bonded interactions */
166 void dd_init_bondeds(FILE* fplog,
168 const gmx_mtop_t& mtop,
169 const gmx_vsite_t* vsite,
170 const t_inputrec* ir,
172 gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
174 /*! \brief Returns whether molecules are always whole, i.e. not broken by PBC */
175 bool dd_moleculesAreAlwaysWhole(const gmx_domdec_t& dd);
177 /*! \brief Returns if we need to do pbc for calculating bonded interactions */
178 gmx_bool dd_bonded_molpbc(const gmx_domdec_t* dd, PbcType pbcType);
180 /*! \brief Change the DD non-bonded communication cut-off.
182 * This could fail when trying to increase the cut-off,
183 * then FALSE will be returned and the cut-off is not modified.
185 * \param[in] cr Communication recrod
186 * \param[in] box Box matrix, used for computing the dimensions of the system
187 * \param[in] x Position vector, used for computing the dimensions of the system
188 * \param[in] cutoffRequested The requested atom to atom cut-off distance, usually the pair-list cutoff distance
190 gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested);
192 /*! \brief Set up communication for averaging GPU wait times over domains
194 * When domains (PP MPI ranks) share a GPU, the individual GPU wait times
195 * are meaningless, as it depends on the order in which tasks on the same
196 * GPU finish. Therefore there wait times need to be averaged over the ranks
197 * sharing the same GPU. This function sets up the communication for that.
199 void dd_setup_dlb_resource_sharing(const t_commrec* cr, int gpu_id);
201 /*! \brief Cycle counter indices used internally in the domain decomposition */
212 /*! \brief Add the wallcycle count to the DD counter */
213 void dd_cycles_add(const gmx_domdec_t* dd, float cycles, int ddCycl);
215 /*! \brief Communicate the coordinates to the neighboring cells and do pbc. */
216 void dd_move_x(struct gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle);
218 /*! \brief Sum the forces over the neighboring cells.
220 * When fshift!=NULL the shift forces are updated to obtain
221 * the correct virial from the single sum including f.
223 void dd_move_f(struct gmx_domdec_t* dd, gmx::ForceWithShiftForces* forceWithShiftForces, gmx_wallcycle* wcycle);
225 /*! \brief Communicate a real for each atom to the neighboring cells. */
226 void dd_atom_spread_real(struct gmx_domdec_t* dd, real v[]);
228 /*! \brief Sum the contributions to a real for each atom over the neighboring cells. */
229 void dd_atom_sum_real(struct gmx_domdec_t* dd, real v[]);
231 /*! \brief Reset all the statistics and counters for total run counting */
232 void reset_dd_statistics_counters(struct gmx_domdec_t* dd);
234 /* In domdec_con.c */
236 /*! \brief Communicates the virtual site forces, reduces the shift forces when \p fshift != NULL */
237 void dd_move_f_vsites(struct gmx_domdec_t* dd, rvec* f, rvec* fshift);
239 /*! \brief Clears the forces for virtual sites */
240 void dd_clear_f_vsites(struct gmx_domdec_t* dd, rvec* f);
242 /*! \brief Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
243 void dd_move_x_constraints(struct gmx_domdec_t* dd,
245 gmx::ArrayRef<gmx::RVec> x0,
246 gmx::ArrayRef<gmx::RVec> x1,
247 gmx_bool bX1IsCoord);
249 /*! \brief Communicates the coordinates involved in virtual sites */
250 void dd_move_x_vsites(struct gmx_domdec_t* dd, const matrix box, rvec* x);
252 /*! \brief Returns the local atom count array for all constraints
254 * The local atom count for a constraint, possible values 2/1/0, is needed
255 * to avoid not/double-counting contributions linked to the Lagrange
256 * multiplier, such as the virial and free-energy derivatives.
258 * \note When \p dd = nullptr, an empty reference is returned.
260 gmx::ArrayRef<const int> dd_constraints_nlocalatoms(const gmx_domdec_t* dd);
262 /* In domdec_top.c */
264 /*! \brief Print error output when interactions are missing */
265 [[noreturn]] void dd_print_missing_interactions(const gmx::MDLogger& mdlog,
268 const gmx_mtop_t* top_global,
269 const gmx_localtop_t* top_local,
270 gmx::ArrayRef<const gmx::RVec> x,
273 /*! \brief Generate and store the reverse topology */
274 void dd_make_reverse_top(FILE* fplog,
276 const gmx_mtop_t* mtop,
277 const gmx_vsite_t* vsite,
278 const t_inputrec* ir,
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,
290 const gmx_mtop_t& top,
291 gmx_localtop_t* ltop);
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, gmx_localtop_t* ltop);
296 /*! \brief Construct local state */
297 void dd_init_local_state(struct gmx_domdec_t* dd, const t_state* state_global, t_state* local_state);
299 /*! \brief Generate a list of links between atoms that are linked by bonded interactions
301 * Also stores whether atoms are linked in \p cginfo_mb.
303 t_blocka* makeBondedLinks(const gmx_mtop_t& mtop, gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
305 /*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
306 void dd_bonded_cg_distance(const gmx::MDLogger& mdlog,
307 const gmx_mtop_t* mtop,
308 const t_inputrec* ir,
315 /*! \brief Construct the GPU halo exchange object(s)
316 * \param[in] mdlog The logger object
317 * \param[in] cr The commrec object
318 * \param[in] deviceContext GPU device context
319 * \param[in] streamLocal The local GPU stream
320 * \param[in] streamNonLocal The non-local GPU stream
322 void constructGpuHaloExchange(const gmx::MDLogger& mdlog,
324 const DeviceContext& deviceContext,
326 void* streamNonLocal);
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
334 void reinitGpuHaloExchange(const t_commrec& cr,
335 DeviceBuffer<gmx::RVec> d_coordinatesBuffer,
336 DeviceBuffer<gmx::RVec> d_forcesBuffer);
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
344 void communicateGpuHaloCoordinates(const t_commrec& cr,
346 GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
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
353 void communicateGpuHaloForces(const t_commrec& cr, bool accumulateForces);