#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/nblist.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 "redistribute.h"
#include "utility.h"

Description

This file defines functions for mdrun to call to make a new domain decomposition, and check it.

Author: Berk Hess hess@.nosp@m.kth..nosp@m.se

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 void	make_dd_indices (gmx_domdec_t *dd, const int atomStart)
	Makes the mappings between global and local atom indices during DD repartioning.

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.

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 > 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...

Macro Definition Documentation

#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.

Function Documentation

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
	)

static

Merge received atoms for one pulse and zone into the atom buffers.

Parameters

[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

template<typename T >

static void orderVector	(	gmx::ArrayRef< const gmx_cgsort_t >	sort,
		gmx::ArrayRef< T >	dataToSort,
		const T	fillerValue,
		gmx::ArrayRef< T >	sortBuffer
	)

static

Order data in dataToSort according to sort.

Note: both buffers should have at least sort.size() elements.

template<typename T >

static void orderVector	(	gmx::ArrayRef< const gmx_cgsort_t >	sort,
		gmx::ArrayRef< T >	vectorToSort,
		const T	fillerValue,
		gmx::FastVector< T > *	workVector
	)

static

Order data in dataToSort according to sort.

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.

Description

Classes

Macros

Functions

Macro Definition Documentation

Function Documentation