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36 /*! \defgroup module_domdec Spatial domain decomposition (for parallelization over MPI)
37 * \ingroup group_mdrun
39 * \brief Manages the decomposition of the simulation volume over MPI
40 * ranks to try to distribute work evenly with minimal communication
43 * \todo Get domdec stuff out of mdtypes/commrec.h
45 * \author Berk Hess <hess@kth.se>
49 /*! \libinternal \file
51 * \brief This file declares functions for mdrun to call to manage the
52 * details of its domain decomposition.
54 * \author Berk Hess <hess@kth.se>
56 * \ingroup module_domdec
59 #ifndef GMX_DOMDEC_DOMDEC_H
60 #define GMX_DOMDEC_DOMDEC_H
64 #include "gromacs/math/vectypes.h"
65 #include "gromacs/utility/arrayref.h"
66 #include "gromacs/utility/basedefinitions.h"
67 #include "gromacs/utility/real.h"
73 struct gmx_domdec_zones_t;
74 struct gmx_localtop_t;
89 class ForceWithShiftForces;
91 class LocalAtomSetManager;
92 class RangePartitioning;
97 /*! \brief Returns the global topology atom number belonging to local atom index i.
99 * This function is intended for writing ASCII output
100 * and returns atom numbers starting at 1.
101 * When dd=NULL returns i+1.
103 int ddglatnr(const gmx_domdec_t *dd, int i);
105 /*! \brief Return a block struct for the charge groups of the whole system */
106 t_block *dd_charge_groups_global(struct gmx_domdec_t *dd);
108 /*! \brief Returns a list of update group partitioning for each molecule type or empty when update groups are not used */
109 gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingPerMoleculetype(const gmx_domdec_t &dd);
111 /*! \brief Store the global cg indices of the home cgs in state,
113 * This means it can be reset, even after a new DD partitioning.
115 void dd_store_state(struct gmx_domdec_t *dd, t_state *state);
117 /*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
118 struct gmx_domdec_zones_t *domdec_zones(struct gmx_domdec_t *dd);
120 /*! \brief Sets the j-charge-group range for i-charge-group \p icg */
121 void dd_get_ns_ranges(const gmx_domdec_t *dd, int icg,
122 int *jcg0, int *jcg1, ivec shift0, ivec shift1);
124 /*! \brief Returns the number of home atoms */
125 int dd_numHomeAtoms(const gmx_domdec_t &dd);
127 /*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
128 int dd_natoms_mdatoms(const gmx_domdec_t *dd);
130 /*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
131 int dd_natoms_vsite(const gmx_domdec_t *dd);
133 /*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
134 void dd_get_constraint_range(const gmx_domdec_t *dd,
135 int *at_start, int *at_end);
137 /*! \libinternal \brief Struct for passing around the number of PME domains */
140 int x; //!< The number of PME domains along dimension x
141 int y; //!< The number of PME domains along dimension y
144 /*! \brief Returns the number of PME domains, can be called with dd=NULL */
145 NumPmeDomains getNumPmeDomains(const gmx_domdec_t *dd);
147 /*! \brief Returns the set of DD ranks that communicate with pme node cr->nodeid */
148 std::vector<int> get_pme_ddranks(const t_commrec *cr, int pmenodeid);
150 /*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
151 int dd_pme_maxshift_x(const gmx_domdec_t *dd);
153 /*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
154 int dd_pme_maxshift_y(const gmx_domdec_t *dd);
156 /*! \brief Return whether constraints, not including settles, cross domain boundaries */
157 bool ddHaveSplitConstraints(const gmx_domdec_t &dd);
159 /*! \brief Initialized the domain decomposition, chooses the DD grid and PME ranks, return the DD struct */
161 init_domain_decomposition(const gmx::MDLogger &mdlog,
163 const gmx::DomdecOptions &options,
164 const gmx::MdrunOptions &mdrunOptions,
165 const gmx_mtop_t *mtop,
166 const t_inputrec *ir,
168 gmx::ArrayRef<const gmx::RVec> xGlobal,
169 gmx::LocalAtomSetManager *atomSets);
171 /*! \brief Initialize data structures for bonded interactions */
172 void dd_init_bondeds(FILE *fplog,
174 const gmx_mtop_t *mtop,
175 const gmx_vsite_t *vsite,
176 const t_inputrec *ir,
178 cginfo_mb_t *cginfo_mb);
180 /*! \brief Returns if we need to do pbc for calculating bonded interactions */
181 gmx_bool dd_bonded_molpbc(const gmx_domdec_t *dd, int ePBC);
183 /*! \brief Change the DD non-bonded communication cut-off.
185 * This could fail when trying to increase the cut-off,
186 * then FALSE will be returned and the cut-off is not modified.
188 * \param[in] cr Communication recrod
189 * \param[in] box Box matrix, used for computing the dimensions of the system
190 * \param[in] x Position vector, used for computing the dimensions of the system
191 * \param[in] cutoffRequested The requested atom to atom cut-off distance, usually the pair-list cutoff distance
193 gmx_bool change_dd_cutoff(t_commrec *cr,
195 gmx::ArrayRef<const gmx::RVec> x,
196 real cutoffRequested);
198 /*! \brief Set up communication for averaging GPU wait times over domains
200 * When domains (PP MPI ranks) share a GPU, the individual GPU wait times
201 * are meaningless, as it depends on the order in which tasks on the same
202 * GPU finish. Therefore there wait times need to be averaged over the ranks
203 * sharing the same GPU. This function sets up the communication for that.
205 void dd_setup_dlb_resource_sharing(t_commrec *cr,
208 /*! \brief Cycle counter indices used internally in the domain decomposition */
210 ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclWaitGPU, ddCyclPME, ddCyclNr
213 /*! \brief Add the wallcycle count to the DD counter */
214 void dd_cycles_add(const gmx_domdec_t *dd, float cycles, int ddCycl);
216 /*! \brief Communicate the coordinates to the neighboring cells and do pbc. */
217 void dd_move_x(struct gmx_domdec_t *dd,
219 gmx::ArrayRef<gmx::RVec> x,
220 gmx_wallcycle *wcycle);
222 /*! \brief Sum the forces over the neighboring cells.
224 * When fshift!=NULL the shift forces are updated to obtain
225 * the correct virial from the single sum including f.
227 void dd_move_f(struct gmx_domdec_t *dd,
228 gmx::ForceWithShiftForces *forceWithShiftForces,
229 gmx_wallcycle *wcycle);
231 /*! \brief Communicate a real for each atom to the neighboring cells. */
232 void dd_atom_spread_real(struct gmx_domdec_t *dd, real v[]);
234 /*! \brief Sum the contributions to a real for each atom over the neighboring cells. */
235 void dd_atom_sum_real(struct gmx_domdec_t *dd, real v[]);
237 /*! \brief Reset all the statistics and counters for total run counting */
238 void reset_dd_statistics_counters(struct gmx_domdec_t *dd);
240 /* In domdec_con.c */
242 /*! \brief Communicates the virtual site forces, reduces the shift forces when \p fshift != NULL */
243 void dd_move_f_vsites(struct gmx_domdec_t *dd, rvec *f, rvec *fshift);
245 /*! \brief Clears the forces for virtual sites */
246 void dd_clear_f_vsites(struct gmx_domdec_t *dd, rvec *f);
248 /*! \brief Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
249 void dd_move_x_constraints(struct gmx_domdec_t *dd, const matrix box,
250 rvec *x0, rvec *x1, gmx_bool bX1IsCoord);
252 /*! \brief Communicates the coordinates involved in virtual sites */
253 void dd_move_x_vsites(struct gmx_domdec_t *dd, const matrix box, rvec *x);
255 /*! \brief Returns the local atom count array for all constraints
257 * The local atom count for a constraint, possible values 2/1/0, is needed
258 * to avoid not/double-counting contributions linked to the Lagrange
259 * multiplier, such as the virial and free-energy derivatives.
261 * \note When \p dd = nullptr, an empty reference is returned.
263 gmx::ArrayRef<const int> dd_constraints_nlocalatoms(const gmx_domdec_t *dd);
265 /* In domdec_top.c */
267 /*! \brief Print error output when interactions are missing */
269 void dd_print_missing_interactions(const gmx::MDLogger &mdlog,
272 const gmx_mtop_t *top_global,
273 const gmx_localtop_t *top_local,
277 /*! \brief Generate and store the reverse topology */
278 void dd_make_reverse_top(FILE *fplog,
279 gmx_domdec_t *dd, const gmx_mtop_t *mtop,
280 const gmx_vsite_t *vsite,
281 const t_inputrec *ir, gmx_bool bBCheck);
283 /*! \brief Generate the local topology and virtual site data */
284 void dd_make_local_top(struct gmx_domdec_t *dd,
285 struct gmx_domdec_zones_t *zones,
292 const gmx_mtop_t &top,
293 gmx_localtop_t *ltop);
295 /*! \brief Sort ltop->ilist when we are doing free energy. */
296 void dd_sort_local_top(gmx_domdec_t *dd, const t_mdatoms *mdatoms,
297 gmx_localtop_t *ltop);
299 /*! \brief Initialize local topology
301 * \param[in] top_global Reference to global topology.
302 * \param[in,out] top Pointer to new local topology
304 void dd_init_local_top(const gmx_mtop_t &top_global,
305 gmx_localtop_t *top);
307 /*! \brief Construct local state */
308 void dd_init_local_state(struct gmx_domdec_t *dd,
309 const t_state *state_global, t_state *local_state);
311 /*! \brief Generate a list of links between charge groups that are linked by bonded interactions */
312 t_blocka *make_charge_group_links(const gmx_mtop_t *mtop, gmx_domdec_t *dd,
313 cginfo_mb_t *cginfo_mb);
315 /*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
316 void dd_bonded_cg_distance(const gmx::MDLogger &mdlog,
317 const gmx_mtop_t *mtop,
318 const t_inputrec *ir,
319 const rvec *x, const matrix box,
321 real *r_2b, real *r_mb);
324 /* In domdec_setup.c */
326 /*! \brief Returns the volume fraction of the system that is communicated */
327 real comm_box_frac(const ivec dd_nc, real cutoff, const gmx_ddbox_t *ddbox);
331 int numPmeOnlyRanks = 0;
332 ivec numDomains = { 0, 0, 0 };
333 real cellsizeLimit = 0;
334 int numDDDimensions = 0;
335 ivec ddDimensions = { -1, -1, -1 };
338 /*! \brief Determines the optimal DD cell setup dd->nc and possibly npmenodes
342 dd_choose_grid(const gmx::MDLogger &mdlog,
344 const t_inputrec *ir,
345 const gmx_mtop_t *mtop,
346 const matrix box, const gmx_ddbox_t *ddbox,
347 int numPmeRanksRequested,
348 gmx_bool bDynLoadBal, real dlb_scale,
349 const DDSystemInfo &systemInfo);