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Gromacs
2025.3
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Gromacs
2025.3
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#include "gmxpre.h"#include "partition.h"#include "config.h"#include <cinttypes>#include <cmath>#include <cstdio>#include <cstdlib>#include <cstring>#include <algorithm>#include <array>#include <filesystem>#include <memory>#include <string>#include <vector>#include "gromacs/domdec/collect.h"#include "gromacs/domdec/dlb.h"#include "gromacs/domdec/dlbtiming.h"#include "gromacs/domdec/domdec.h"#include "gromacs/domdec/domdec_network.h"#include "gromacs/domdec/domdec_struct.h"#include "gromacs/domdec/ga2la.h"#include "gromacs/domdec/localatomsetmanager.h"#include "gromacs/domdec/localtopology.h"#include "gromacs/domdec/localtopologychecker.h"#include "gromacs/domdec/mdsetup.h"#include "gromacs/domdec/nsgrid.h"#include "gromacs/ewald/pme_pp.h"#include "gromacs/gmxlib/network.h"#include "gromacs/gmxlib/nrnb.h"#include "gromacs/imd/imd.h"#include "gromacs/math/functions.h"#include "gromacs/math/vec.h"#include "gromacs/mdlib/forcerec.h"#include "gromacs/mdlib/gmx_omp_nthreads.h"#include "gromacs/mdlib/mdatoms.h"#include "gromacs/mdlib/updategroupscog.h"#include "gromacs/mdlib/vsite.h"#include "gromacs/mdrunutility/mdmodulesnotifiers.h"#include "gromacs/mdtypes/atominfo.h"#include "gromacs/mdtypes/commrec.h"#include "gromacs/mdtypes/forcerec.h"#include "gromacs/mdtypes/inputrec.h"#include "gromacs/mdtypes/md_enums.h"#include "gromacs/mdtypes/mdatom.h"#include "gromacs/mdtypes/state.h"#include "gromacs/nbnxm/nbnxm.h"#include "gromacs/pulling/pull.h"#include "gromacs/timing/wallcycle.h"#include "gromacs/topology/idef.h"#include "gromacs/topology/mtop_util.h"#include "gromacs/topology/topology.h"#include "gromacs/utility/arrayref.h"#include "gromacs/utility/basedefinitions.h"#include "gromacs/utility/cstringutil.h"#include "gromacs/utility/exceptions.h"#include "gromacs/utility/fatalerror.h"#include "gromacs/utility/gmxassert.h"#include "gromacs/utility/listoflists.h"#include "gromacs/utility/logger.h"#include "gromacs/utility/range.h"#include "gromacs/utility/real.h"#include "gromacs/utility/strconvert.h"#include "gromacs/utility/stringstream.h"#include "gromacs/utility/stringutil.h"#include "gromacs/utility/textwriter.h"#include "box.h"#include "cellsizes.h"#include "distribute.h"#include "domdec_constraints.h"#include "domdec_internal.h"#include "domdec_vsite.h"#include "dump.h"#include "haloexchange.h"#include "redistribute.h"#include "utility.h"This file defines functions for mdrun to call to make a new domain decomposition, and check it.
Classes | |
| struct | dd_corners_t |
| Domain corners for communication, a maximum of 4 i-zones see a j domain. More... | |
Macros | |
| #define | DD_PERF_LOSS_DLB_ON 0.02 |
| Turn on DLB when the load imbalance causes this amount of total loss. More... | |
| #define | DD_PERF_LOSS_WARN 0.05 |
| Warn about imbalance due to PP or PP/PME load imbalance at this loss. | |
Functions | |
| static void | print_ddzone (FILE *fp, int d, int i, int j, gmx_ddzone_t *zone) |
| Debug helper printing a DD zone. | |
| 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. | |
| static void | set_zones_numHomeAtoms (gmx_domdec_t *dd) |
Sets the atom-range for the home zone to dd->numHomeAtoms and all other zones empty. | |
| static void | restoreAtomGroups (gmx_domdec_t *dd, const t_state *state) |
| Restore atom groups for the charge groups. | |
| static void | ddSetAtominfo (gmx::ArrayRef< const int > index_gl, const gmx::Range< int > &atomRange, t_forcerec *fr) |
| Sets the atom info structures. | |
| static int | make_dd_indices (gmx_domdec_t *dd, const int atomStart) |
| Makes the mappings between global and local atom indices during DD repartitioning. More... | |
| 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. | |
| static void | clearDDStateIndices (gmx_domdec_t *dd, const bool keepLocalAtomIndices) |
| Clear all DD global state indices. | |
| static float | dd_force_load (gmx_domdec_comm_t *comm) |
| Return the duration of force calculations on this rank. | |
| 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. | |
| static void | get_load_distribution (gmx_domdec_t *dd, gmx_wallcycle *wcycle) |
| Compute and communicate to determine the load distribution across PP ranks. | |
| 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. | |
| 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. | |
| static void | print_dd_load_av (FILE *fplog, gmx_domdec_t *dd) |
| Print load-balance report e.g. at the end of a run. | |
| static float | dd_vol_min (gmx_domdec_t *dd) |
| Return the minimum communication volume. | |
| static int | dd_load_flags (gmx_domdec_t *dd) |
| Return the DD load flags. | |
| static float | dd_f_imbal (gmx_domdec_t *dd) |
| Return the reported load imbalance in force calculations. | |
| static std::string | dd_print_load (gmx_domdec_t *dd, int64_t step) |
| Returns DD load balance report. | |
| static void | dd_print_load_verbose (gmx_domdec_t *dd) |
| Prints DD load balance report in mdrun verbose mode. | |
| 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. | |
| 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). | |
| static void | turn_off_dlb_forever (const gmx::MDLogger &mdlog, gmx_domdec_t *dd, int64_t step) |
| Turns off dynamic load balancing permanently. | |
| 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... | |
| static void | mergeAtomBuffers (const int numZones, gmx_domdec_comm_dim_t *cd, const int pulse, gmx::DomdecZones *zones, 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< int32_t > atomInfo) |
| Merge received atoms for one pulse and zone into the atom buffers. More... | |
| 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. | |
| static bool | missing_link (const gmx::ListOfLists< int > &link, const int globalAtomIndex, const gmx_ga2la_t &ga2la) |
| Returns whether a link is missing. | |
| 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. | |
| static void | get_zone_pulse_groups (gmx_domdec_t *dd, int zonei, int zone, int cg0, int cg1, gmx::ArrayRef< const int > globalAtomIndices, 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 int32_t > atomInfo, gmx::FastVector< 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. | |
| static void | clearCommSetupData (dd_comm_setup_work_t *work) |
| Clear data. | |
| static void | setup_dd_communication (gmx_domdec_t *dd, matrix box, gmx_ddbox_t *ddbox, t_forcerec *fr, t_state *state) |
| Prepare DD communication. | |
| static bool | isValidLocalAtom (const int localAtomIndex) |
Returns whether localAtomIndex is a valid local atom index, i.e. >= 0. | |
| template<typename T > | |
| static void | orderVector (gmx::ArrayRef< const gmx_cgsort_t > sort, gmx::ArrayRef< T > dataToSort, const T fillerValue, gmx::ArrayRef< T > sortBuffer) |
Order data in dataToSort according to sort. More... | |
| 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... | |
| template<typename T > | |
| static void | orderVector (gmx::ArrayRef< const gmx_cgsort_t > sort, gmx::ArrayRef< T > vectorToSort, const T &fillerValue, gmx::FastVector< T > *workVector) |
Order data in dataToSort according to sort. More... | |
| static void | dd_sort_order_nbnxn (const gmx::nonbonded_verlet_t &nbv, gmx::FastVector< gmx_cgsort_t > *sort) |
| Returns the sorting order for atoms based on the nbnxn grid order in sort. | |
| static void | dd_sort_state (gmx_domdec_t *dd, t_forcerec *fr, t_state *state) |
| Returns the sorting state for DD. | |
| static void | add_dd_statistics (gmx_domdec_t *dd) |
| Accumulates load statistics. | |
| void | reset_dd_statistics_counters (gmx_domdec_t *dd) |
| Reset all the statistics and counters for total run counting. | |
| 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. | |
| void | gmx::print_dd_statistics (const t_commrec *cr, const t_inputrec &inputrec, FILE *fplog) |
| Print statistics for domain decomposition communication. | |
| void | gmx::dd_partition_system (FILE *fplog, const gmx::MDLogger &mdlog, int64_t step, const t_commrec *cr, bool bMainState, t_state *state_global, const gmx_mtop_t &top_global, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, 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... | |
| #define DD_PERF_LOSS_DLB_ON 0.02 |
Turn on DLB when the load imbalance causes this amount of total loss.
There is a bit of overhead with DLB and it's difficult to achieve a load imbalance of less than 2% with DLB.
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Makes the mappings between global and local atom indices during DD repartitioning.
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Merge received atoms for one pulse and zone into the atom buffers.
| [in] | numZones | The number of zones to apply the merging to |
| [in,out] | cd | The communication setup for the pulses along the current dimension |
| [in] | pulse | The index of the current pulse |
| [in,out] | zones | The DD zone information in which the atom ranges will be updated |
| [in,out] | index_gl | The global atom indices |
| [in] | recv_i | List of received atom indices for this pulse |
| [in,out] | x | The home + halo coordinate buffer |
| [in] | recv_vr | Buffer with received coordinates |
| [in] | atomInfoForEachMoleculeBlock | List of atom information for molecule blocks |
| [in,out] | atomInfo | List of home + halo atom information |
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Order data in dataToSort according to sort.
Uses fillerValue for filler particles
Note: both buffers should have at least sort.size() elements.
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Order data in dataToSort according to sort.
For filler particles the value for the last real atom is used
Note: both buffers should have at least sort.size() elements.
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Order data in dataToSort according to sort.
Uses fillerValue for filler particles
Note: vectorToSort should have at least sort.size() elements, workVector is resized when it is too small.
| void set_dd_dlb_max_cutoff | ( | struct t_commrec * | cr, |
| real | cutoff | ||
| ) |
Limit DLB to preserve the option of returning to the current cut-off.
Domain boundary changes due to the DD dynamic load balancing can limit the cut-off distance that can be set in change_dd_cutoff. This function sets/changes the DLB limit such that using the passed (pair-list) cut-off should still be possible after subsequently setting a shorter cut-off with change_dd_cutoff.
1.8.5