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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 bool prefer1DAnd1Pulse
,
166 const gmx_mtop_t
*mtop
,
167 const t_inputrec
*ir
,
169 gmx::ArrayRef
<const gmx::RVec
> xGlobal
,
170 gmx::LocalAtomSetManager
*atomSets
);
172 /*! \brief Return whether the DD has a single dimension with a single pulse
174 * The GPU halo exchange code requires a 1D single-pulse DD, and its
175 * setup code can use the returned value to understand what it should
177 bool is1DAnd1PulseDD(const gmx_domdec_t
&dd
);
179 /*! \brief Initialize data structures for bonded interactions */
180 void dd_init_bondeds(FILE *fplog
,
182 const gmx_mtop_t
*mtop
,
183 const gmx_vsite_t
*vsite
,
184 const t_inputrec
*ir
,
186 cginfo_mb_t
*cginfo_mb
);
188 /*! \brief Returns whether molecules are always whole, i.e. not broken by PBC */
189 bool dd_moleculesAreAlwaysWhole(const gmx_domdec_t
&dd
);
191 /*! \brief Returns if we need to do pbc for calculating bonded interactions */
192 gmx_bool
dd_bonded_molpbc(const gmx_domdec_t
*dd
, int ePBC
);
194 /*! \brief Change the DD non-bonded communication cut-off.
196 * This could fail when trying to increase the cut-off,
197 * then FALSE will be returned and the cut-off is not modified.
199 * \param[in] cr Communication recrod
200 * \param[in] box Box matrix, used for computing the dimensions of the system
201 * \param[in] x Position vector, used for computing the dimensions of the system
202 * \param[in] cutoffRequested The requested atom to atom cut-off distance, usually the pair-list cutoff distance
204 gmx_bool
change_dd_cutoff(t_commrec
*cr
,
206 gmx::ArrayRef
<const gmx::RVec
> x
,
207 real cutoffRequested
);
209 /*! \brief Set up communication for averaging GPU wait times over domains
211 * When domains (PP MPI ranks) share a GPU, the individual GPU wait times
212 * are meaningless, as it depends on the order in which tasks on the same
213 * GPU finish. Therefore there wait times need to be averaged over the ranks
214 * sharing the same GPU. This function sets up the communication for that.
216 void dd_setup_dlb_resource_sharing(t_commrec
*cr
,
219 /*! \brief Cycle counter indices used internally in the domain decomposition */
221 ddCyclStep
, ddCyclPPduringPME
, ddCyclF
, ddCyclWaitGPU
, ddCyclPME
, ddCyclNr
224 /*! \brief Add the wallcycle count to the DD counter */
225 void dd_cycles_add(const gmx_domdec_t
*dd
, float cycles
, int ddCycl
);
227 /*! \brief Communicate the coordinates to the neighboring cells and do pbc. */
228 void dd_move_x(struct gmx_domdec_t
*dd
,
230 gmx::ArrayRef
<gmx::RVec
> x
,
231 gmx_wallcycle
*wcycle
);
233 /*! \brief Sum the forces over the neighboring cells.
235 * When fshift!=NULL the shift forces are updated to obtain
236 * the correct virial from the single sum including f.
238 void dd_move_f(struct gmx_domdec_t
*dd
,
239 gmx::ForceWithShiftForces
*forceWithShiftForces
,
240 gmx_wallcycle
*wcycle
);
242 /*! \brief Communicate a real for each atom to the neighboring cells. */
243 void dd_atom_spread_real(struct gmx_domdec_t
*dd
, real v
[]);
245 /*! \brief Sum the contributions to a real for each atom over the neighboring cells. */
246 void dd_atom_sum_real(struct gmx_domdec_t
*dd
, real v
[]);
248 /*! \brief Reset all the statistics and counters for total run counting */
249 void reset_dd_statistics_counters(struct gmx_domdec_t
*dd
);
251 /* In domdec_con.c */
253 /*! \brief Communicates the virtual site forces, reduces the shift forces when \p fshift != NULL */
254 void dd_move_f_vsites(struct gmx_domdec_t
*dd
, rvec
*f
, rvec
*fshift
);
256 /*! \brief Clears the forces for virtual sites */
257 void dd_clear_f_vsites(struct gmx_domdec_t
*dd
, rvec
*f
);
259 /*! \brief Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
260 void dd_move_x_constraints(struct gmx_domdec_t
*dd
, const matrix box
,
261 rvec
*x0
, rvec
*x1
, gmx_bool bX1IsCoord
);
263 /*! \brief Communicates the coordinates involved in virtual sites */
264 void dd_move_x_vsites(struct gmx_domdec_t
*dd
, const matrix box
, rvec
*x
);
266 /*! \brief Returns the local atom count array for all constraints
268 * The local atom count for a constraint, possible values 2/1/0, is needed
269 * to avoid not/double-counting contributions linked to the Lagrange
270 * multiplier, such as the virial and free-energy derivatives.
272 * \note When \p dd = nullptr, an empty reference is returned.
274 gmx::ArrayRef
<const int> dd_constraints_nlocalatoms(const gmx_domdec_t
*dd
);
276 /* In domdec_top.c */
278 /*! \brief Print error output when interactions are missing */
280 void dd_print_missing_interactions(const gmx::MDLogger
&mdlog
,
283 const gmx_mtop_t
*top_global
,
284 const gmx_localtop_t
*top_local
,
288 /*! \brief Generate and store the reverse topology */
289 void dd_make_reverse_top(FILE *fplog
,
290 gmx_domdec_t
*dd
, const gmx_mtop_t
*mtop
,
291 const gmx_vsite_t
*vsite
,
292 const t_inputrec
*ir
, gmx_bool bBCheck
);
294 /*! \brief Generate the local topology and virtual site data */
295 void dd_make_local_top(struct gmx_domdec_t
*dd
,
296 struct gmx_domdec_zones_t
*zones
,
303 const gmx_mtop_t
&top
,
304 gmx_localtop_t
*ltop
);
306 /*! \brief Sort ltop->ilist when we are doing free energy. */
307 void dd_sort_local_top(gmx_domdec_t
*dd
, const t_mdatoms
*mdatoms
,
308 gmx_localtop_t
*ltop
);
310 /*! \brief Initialize local topology
312 * \param[in] top_global Reference to global topology.
313 * \param[in,out] top Pointer to new local topology
315 void dd_init_local_top(const gmx_mtop_t
&top_global
,
316 gmx_localtop_t
*top
);
318 /*! \brief Construct local state */
319 void dd_init_local_state(struct gmx_domdec_t
*dd
,
320 const t_state
*state_global
, t_state
*local_state
);
322 /*! \brief Generate a list of links between charge groups that are linked by bonded interactions */
323 t_blocka
*make_charge_group_links(const gmx_mtop_t
*mtop
, gmx_domdec_t
*dd
,
324 cginfo_mb_t
*cginfo_mb
);
326 /*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
327 void dd_bonded_cg_distance(const gmx::MDLogger
&mdlog
,
328 const gmx_mtop_t
*mtop
,
329 const t_inputrec
*ir
,
330 const rvec
*x
, const matrix box
,
332 real
*r_2b
, real
*r_mb
);