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static void | print_ddzone (FILE *fp, int d, int i, int j, gmx_ddzone_t *zone) |
| Debug helper printing a DD zone.
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static void | dd_move_cellx (gmx_domdec_t *dd, const gmx_ddbox_t *ddbox, rvec cell_ns_x0, rvec cell_ns_x1) |
| Using the home grid size as input in cell_ns_x0 and cell_ns_x1 takes the extremes over all home and remote zones in the halo and returns the results in cell_ns_x0 and cell_ns_x1. Note: only used with the group cut-off scheme.
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static void | set_zones_numHomeAtoms (gmx_domdec_t *dd) |
| Sets the charge-group zones to be equal to the home zone.
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static void | restoreAtomGroups (gmx_domdec_t *dd, const t_state *state) |
| Restore atom groups for the charge groups.
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static void | dd_set_atominfo (gmx::ArrayRef< const int > index_gl, int cg0, int cg1, t_forcerec *fr) |
| Sets the atom info structures.
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static void | make_dd_indices (gmx_domdec_t *dd, const int atomStart) |
| Makes the mappings between global and local atom indices during DD repartioning.
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static void | check_index_consistency (const gmx_domdec_t *dd, int natoms_sys, const char *where) |
| Checks whether global and local atom indices are consistent.
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static void | clearDDStateIndices (gmx_domdec_t *dd, const bool keepLocalAtomIndices) |
| Clear all DD global state indices.
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static float | dd_force_load (gmx_domdec_comm_t *comm) |
| Return the duration of force calculations on this rank.
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static void | comm_dd_ns_cell_sizes (gmx_domdec_t *dd, gmx_ddbox_t *ddbox, rvec cell_ns_x0, rvec cell_ns_x1, int64_t step) |
| Runs cell size checks and communicates the boundaries.
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static void | get_load_distribution (gmx_domdec_t *dd, gmx_wallcycle *wcycle) |
| Compute and communicate to determine the load distribution across PP ranks.
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static float | dd_force_load_fraction (gmx_domdec_t *dd) |
| Return the relative performance loss on the total run time due to the force calculation load imbalance.
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static float | dd_force_imb_perf_loss (gmx_domdec_t *dd) |
| Return the relative performance loss on the total run time due to the force calculation load imbalance.
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static void | print_dd_load_av (FILE *fplog, gmx_domdec_t *dd) |
| Print load-balance report e.g. at the end of a run.
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static float | dd_vol_min (gmx_domdec_t *dd) |
| Return the minimum communication volume.
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static int | dd_load_flags (gmx_domdec_t *dd) |
| Return the DD load flags.
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static float | dd_f_imbal (gmx_domdec_t *dd) |
| Return the reported load imbalance in force calculations.
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static std::string | dd_print_load (gmx_domdec_t *dd, int64_t step) |
| Returns DD load balance report.
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static void | dd_print_load_verbose (gmx_domdec_t *dd) |
| Prints DD load balance report in mdrun verbose mode.
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static void | turn_on_dlb (const gmx::MDLogger &mdlog, gmx_domdec_t *dd, int64_t step) |
| Turns on dynamic load balancing if possible and needed.
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static void | turn_off_dlb (const gmx::MDLogger &mdlog, gmx_domdec_t *dd, int64_t step) |
| Turns off dynamic load balancing (but leave it able to turn back on).
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static void | turn_off_dlb_forever (const gmx::MDLogger &mdlog, gmx_domdec_t *dd, int64_t step) |
| Turns off dynamic load balancing permanently.
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void | set_dd_dlb_max_cutoff (t_commrec *cr, real cutoff) |
| Limit DLB to preserve the option of returning to the current cut-off. More...
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static void | merge_cg_buffers (int ncell, gmx_domdec_comm_dim_t *cd, int pulse, int *ncg_cell, gmx::ArrayRef< int > index_gl, const int *recv_i, gmx::ArrayRef< gmx::RVec > x, gmx::ArrayRef< const gmx::RVec > recv_vr, gmx::ArrayRef< gmx::AtomInfoWithinMoleculeBlock > atomInfoForEachMoleculeBlock, gmx::ArrayRef< int64_t > atomInfo) |
| Merge atom buffers.
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static void | make_cell2at_index (gmx_domdec_comm_dim_t *cd, int nzone, int atomGroupStart) |
| Makes a range partitioning for the atom groups wthin a cell.
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static gmx_bool | missing_link (const t_blocka &link, const int globalAtomIndex, const gmx_ga2la_t &ga2la) |
| Returns whether a link is missing.
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static void | set_dd_corners (const gmx_domdec_t *dd, int dim0, int dim1, int dim2, gmx_bool bDistMB, dd_corners_t *c) |
| Determine the corners of the domain(s) we are communicating with.
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static void | get_zone_pulse_groups (gmx_domdec_t *dd, int zonei, int zone, int cg0, int cg1, gmx::ArrayRef< const int > globalAtomGroupIndices, int dim, int dim_ind, int dim0, int dim1, int dim2, real r_comm2, real r_bcomm2, matrix box, bool distanceIsTriclinic, rvec *normal, real skew_fac2_d, real skew_fac_01, rvec *v_d, rvec *v_0, rvec *v_1, const dd_corners_t *c, const rvec sf2_round, gmx_bool bDistBonded, gmx_bool bBondComm, gmx_bool bDist2B, gmx_bool bDistMB, gmx::ArrayRef< const gmx::RVec > coordinates, gmx::ArrayRef< const int64_t > atomInfo, std::vector< int > *localAtomGroups, dd_comm_setup_work_t *work) |
| Add the atom groups and coordinates we need to send in this pulse from this zone to localAtomGroups and work .
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static void | clearCommSetupData (dd_comm_setup_work_t *work) |
| Clear data.
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static void | setup_dd_communication (gmx_domdec_t *dd, matrix box, gmx_ddbox_t *ddbox, t_forcerec *fr, t_state *state) |
| Prepare DD communication.
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static void | set_cg_boundaries (gmx_domdec_zones_t *zones) |
| Set boundaries for the charge group range.
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static void | set_zones_size (gmx_domdec_t *dd, matrix box, const gmx_ddbox_t *ddbox, int zone_start, int zone_end, int numMovedChargeGroupsInHomeZone) |
| Set zone dimensions for zones zone_start to zone_end-1 . More...
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template<typename T > |
static void | orderVector (gmx::ArrayRef< const gmx_cgsort_t > sort, gmx::ArrayRef< T > dataToSort, gmx::ArrayRef< T > sortBuffer) |
| Order data in dataToSort according to sort . More...
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template<typename T > |
static void | orderVector (gmx::ArrayRef< const gmx_cgsort_t > sort, gmx::ArrayRef< T > vectorToSort, std::vector< T > *workVector) |
| Order data in dataToSort according to sort . More...
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static void | dd_sort_order_nbnxn (const t_forcerec *fr, std::vector< gmx_cgsort_t > *sort) |
| Returns the sorting order for atoms based on the nbnxn grid order in sort.
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static void | dd_sort_state (gmx_domdec_t *dd, t_forcerec *fr, t_state *state) |
| Returns the sorting state for DD.
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static void | add_dd_statistics (gmx_domdec_t *dd) |
| Accumulates load statistics.
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void | reset_dd_statistics_counters (gmx_domdec_t *dd) |
| Reset all the statistics and counters for total run counting.
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bool | gmx::check_grid_jump (int64_t step, const gmx_domdec_t *dd, real cutoff, const gmx_ddbox_t *ddbox, bool bFatal) |
| Check whether the DD grid has moved too far for correctness.
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void | gmx::print_dd_statistics (const t_commrec *cr, const t_inputrec &inputrec, FILE *fplog) |
| Print statistics for domain decomposition communication.
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void | gmx::dd_partition_system (FILE *fplog, const gmx::MDLogger &mdlog, int64_t step, const t_commrec *cr, bool bMasterState, int nstglobalcomm, t_state *state_global, const gmx_mtop_t &top_global, const t_inputrec &inputrec, gmx::ImdSession *imdSession, pull_t *pull_work, t_state *state_local, gmx::ForceBuffers *f, gmx::MDAtoms *mdAtoms, gmx_localtop_t *top_local, t_forcerec *fr, gmx::VirtualSitesHandler *vsite, gmx::Constraints *constr, t_nrnb *nrnb, gmx_wallcycle *wcycle, bool bVerbose) |
| TODO Remove fplog when group scheme and charge groups are gone. More...
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