Local atom set handling during simulations.

[gromacs.git] / src / gromacs / domdec / domdec.h

/*
 * This file is part of the GROMACS molecular simulation package.
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 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
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/*! \defgroup module_domdec Spatial domain decomposition (for parallelization over MPI)
 * \ingroup group_mdrun
 *
 * \brief Manages the decomposition of the simulation volume over MPI
 * ranks to try to distribute work evenly with minimal communication
 * overheads.
 *
 * \todo Get domdec stuff out of mdtypes/commrec.h
 *
 * \author Berk Hess <hess@kth.se>
 *
 */

/*! \libinternal \file
 *
 * \brief This file declares functions for mdrun to call to manage the
 * details of its domain decomposition.
 *
 * \author Berk Hess <hess@kth.se>
 * \inlibraryapi
 * \ingroup module_domdec
 */

#ifndef GMX_DOMDEC_DOMDEC_H
#define GMX_DOMDEC_DOMDEC_H

#include <vector>

#include "gromacs/math/paddedvector.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

struct cginfo_mb_t;
struct gmx_domdec_t;
struct gmx_ddbox_t;
struct gmx_domdec_zones_t;
struct gmx_localtop_t;
struct gmx_mtop_t;
struct gmx_vsite_t;
struct MdrunOptions;
struct t_block;
struct t_blocka;
struct t_commrec;
struct t_forcerec;
struct t_inputrec;
struct t_mdatoms;
struct t_nrnb;
struct gmx_wallcycle;
class t_state;

namespace gmx
{
class Constraints;
class MDAtoms;
class LocalAtomSetManager;
} // namespace

/*! \brief Returns the global topology atom number belonging to local atom index i.
 *
 * This function is intended for writing ASCII output
 * and returns atom numbers starting at 1.
 * When dd=NULL returns i+1.
 */
int ddglatnr(const gmx_domdec_t *dd, int i);

/*! \brief Return a block struct for the charge groups of the whole system */
t_block *dd_charge_groups_global(struct gmx_domdec_t *dd);

/*! \brief Store the global cg indices of the home cgs in state,
 *
 * This means it can be reset, even after a new DD partitioning.
 */
void dd_store_state(struct gmx_domdec_t *dd, t_state *state);

/*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
struct gmx_domdec_zones_t *domdec_zones(struct gmx_domdec_t *dd);

/*! \brief Sets the j-charge-group range for i-charge-group \p icg */
void dd_get_ns_ranges(const gmx_domdec_t *dd, int icg,
                      int *jcg0, int *jcg1, ivec shift0, ivec shift1);

/*! \brief Returns the number of home atoms */
int dd_numHomeAtoms(const gmx_domdec_t &dd);

/*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
int dd_natoms_mdatoms(const gmx_domdec_t *dd);

/*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
int dd_natoms_vsite(const gmx_domdec_t *dd);

/*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
void dd_get_constraint_range(const gmx_domdec_t *dd,
                             int *at_start, int *at_end);

/*! \libinternal \brief Struct for passing around the number of PME domains */
struct NumPmeDomains
{
    int x; //!< The number of PME domains along dimension x
    int y; //!< The number of PME domains along dimension y
};

/*! \brief Returns the number of PME domains, can be called with dd=NULL */
NumPmeDomains getNumPmeDomains(const gmx_domdec_t *dd);

/*! \brief Returns the set of DD ranks that communicate with pme node cr->nodeid */
std::vector<int> get_pme_ddranks(const t_commrec *cr, int pmenodeid);

/*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
int dd_pme_maxshift_x(const gmx_domdec_t *dd);

/*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
int dd_pme_maxshift_y(const gmx_domdec_t *dd);

/*! \brief The options for the domain decomposition MPI task ordering. */
enum class DdRankOrder
{
    select,     //!< First value (needed to cope with command-line parsing)
    interleave, //!< Interleave the PP and PME ranks
    pp_pme,     //!< First all PP ranks, all PME rank at the end
    cartesian,  //!< Use Cartesian communicators for PP, PME and PP-PME
    nr          //!< The number of options
};

/*! \brief The options for the dynamic load balancing. */
enum class DlbOption
{
    select,           //!< First value (needed to cope with command-line parsing)
    turnOnWhenUseful, //!< Turn on DLB when we think it would improve performance
    no,               //!< Never turn on DLB
    yes,              //!< Turn on DLB from the start and keep it on
    nr                //!< The number of options
};

/*! \libinternal \brief Structure containing all (command line) options for the domain decomposition */
struct DomdecOptions
{
    /*! \brief Constructor */
    DomdecOptions();

    //! If true, check that all bonded interactions have been assigned to exactly one domain/rank.
    gmx_bool          checkBondedInteractions;
    //! If true, don't communicate all atoms between the non-bonded cut-off and the larger bonded cut-off, but only those that have non-local bonded interactions. This significantly reduces the communication volume.
    gmx_bool          useBondedCommunication;
    //! The domain decomposition grid cell count, 0 means let domdec choose based on the number of ranks.
    ivec              numCells;
    //! The number of separate PME ranks requested, -1 = auto.
    int               numPmeRanks;
    //! Ordering of the PP and PME ranks, values from enum above.
    DdRankOrder       rankOrder;
    //! The minimum communication range, used for extended the communication range for bonded interactions (nm).
    real              minimumCommunicationRange;
    //! Communication range for atom involved in constraints (P-LINCS) (nm).
    real              constraintCommunicationRange;
    //! Dynamic load balancing option, values from enum above.
    DlbOption         dlbOption;
    /*! \brief Fraction in (0,1) by whose reciprocal the initial
     * DD cell size will be increased in order to provide a margin
     * in which dynamic load balancing can act, while preserving
     * the minimum cell size. */
    real              dlbScaling;
    //! String containing a vector of the relative sizes in the x direction of the corresponding DD cells.
    const char       *cellSizeX;
    //! String containing a vector of the relative sizes in the y direction of the corresponding DD cells.
    const char       *cellSizeY;
    //! String containing a vector of the relative sizes in the z direction of the corresponding DD cells.
    const char       *cellSizeZ;
};

/*! \brief Initialized the domain decomposition, chooses the DD grid and PME ranks, return the DD struct */
gmx_domdec_t *
init_domain_decomposition(FILE                           *fplog,
                          t_commrec                      *cr,
                          const DomdecOptions            &options,
                          const MdrunOptions             &mdrunOptions,
                          const gmx_mtop_t               *mtop,
                          const t_inputrec               *ir,
                          const matrix                    box,
                          gmx::ArrayRef<const gmx::RVec>  xGlobal,
                          gmx::LocalAtomSetManager       *atomSets);

/*! \brief Initialize data structures for bonded interactions */
void dd_init_bondeds(FILE              *fplog,
                     gmx_domdec_t      *dd,
                     const gmx_mtop_t  *mtop,
                     const gmx_vsite_t *vsite,
                     const t_inputrec  *ir,
                     gmx_bool           bBCheck,
                     cginfo_mb_t       *cginfo_mb);

/*! \brief Returns if we need to do pbc for calculating bonded interactions */
gmx_bool dd_bonded_molpbc(const gmx_domdec_t *dd, int ePBC);

/*! \brief Change the DD non-bonded communication cut-off.
 *
 * This could fail when trying to increase the cut-off,
 * then FALSE will be returned and the cut-off is not modified.
 */
gmx_bool change_dd_cutoff(struct t_commrec *cr,
                          t_state *state, const t_inputrec *ir,
                          real cutoff_req );

/*! \brief 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.
 */
void set_dd_dlb_max_cutoff(struct t_commrec *cr, real cutoff);

/*! \brief Return if we are currently using dynamic load balancing */
gmx_bool dd_dlb_is_on(const struct gmx_domdec_t *dd);

/*! \brief Return if the DLB lock is set */
gmx_bool dd_dlb_is_locked(const struct gmx_domdec_t *dd);

/*! \brief Set a lock such that with DLB=auto DLB cannot get turned on */
void dd_dlb_lock(struct gmx_domdec_t *dd);

/*! \brief Clear a lock such that with DLB=auto DLB may get turned on later */
void dd_dlb_unlock(struct gmx_domdec_t *dd);

/*! \brief Set up communication for averaging GPU wait times over domains
 *
 * When domains (PP MPI ranks) share a GPU, the individual GPU wait times
 * are meaningless, as it depends on the order in which tasks on the same
 * GPU finish. Therefore there wait times need to be averaged over the ranks
 * sharing the same GPU. This function sets up the communication for that.
 */
void dd_setup_dlb_resource_sharing(t_commrec           *cr,
                                   int                  gpu_id);

/*! \brief Cycle counter indices used internally in the domain decomposition */
enum {
    ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclWaitGPU, ddCyclPME, ddCyclNr
};

/*! \brief Add the wallcycle count to the DD counter */
void dd_cycles_add(const gmx_domdec_t *dd, float cycles, int ddCycl);

/*! \brief Start the force flop count */
void dd_force_flop_start(struct gmx_domdec_t *dd, t_nrnb *nrnb);

/*! \brief Stop the force flop count */
void dd_force_flop_stop(struct gmx_domdec_t *dd, t_nrnb *nrnb);

/*! \brief Return the PME/PP force load ratio, or -1 if nothing was measured.
 *
 * Should only be called on the DD master node.
 */
float dd_pme_f_ratio(struct gmx_domdec_t *dd);

/*! \brief Communicate the coordinates to the neighboring cells and do pbc. */
void dd_move_x(struct gmx_domdec_t      *dd,
               matrix                    box,
               gmx::ArrayRef<gmx::RVec>  x,
               gmx_wallcycle            *wcycle);

/*! \brief Sum the forces over the neighboring cells.
 *
 * When fshift!=NULL the shift forces are updated to obtain
 * the correct virial from the single sum including f.
 */
void dd_move_f(struct gmx_domdec_t      *dd,
               gmx::ArrayRef<gmx::RVec>  f,
               rvec                     *fshift,
               gmx_wallcycle            *wcycle);

/*! \brief Communicate a real for each atom to the neighboring cells. */
void dd_atom_spread_real(struct gmx_domdec_t *dd, real v[]);

/*! \brief Sum the contributions to a real for each atom over the neighboring cells. */
void dd_atom_sum_real(struct gmx_domdec_t *dd, real v[]);

/*! \brief Partition the system over the nodes.
 *
 * step is only used for printing error messages.
 * If bMasterState==TRUE then state_global from the master node is used,
 * else state_local is redistributed between the nodes.
 * When f!=NULL, *f will be reallocated to the size of state_local.
 */
void dd_partition_system(FILE                *fplog,
                         gmx_int64_t          step,
                         const t_commrec     *cr,
                         gmx_bool             bMasterState,
                         int                  nstglobalcomm,
                         t_state             *state_global,
                         const gmx_mtop_t    *top_global,
                         const t_inputrec    *ir,
                         t_state             *state_local,
                         PaddedRVecVector    *f,
                         gmx::MDAtoms        *mdatoms,
                         gmx_localtop_t      *top_local,
                         t_forcerec          *fr,
                         gmx_vsite_t         *vsite,
                         gmx::Constraints    *constr,
                         t_nrnb              *nrnb,
                         gmx_wallcycle       *wcycle,
                         gmx_bool             bVerbose);

/*! \brief Reset all the statistics and counters for total run counting */
void reset_dd_statistics_counters(struct gmx_domdec_t *dd);

/*! \brief Print statistics for domain decomposition communication */
void print_dd_statistics(const t_commrec *cr, const t_inputrec *ir, FILE *fplog);

/*! \brief Check whether bonded interactions are missing, if appropriate
 *
 * \param[in]    fplog                                  Log file pointer
 * \param[in]    cr                                     Communication object
 * \param[in]    totalNumberOfBondedInteractions        Result of the global reduction over the number of bonds treated in each domain
 * \param[in]    top_global                             Global topology for the error message
 * \param[in]    top_local                              Local topology for the error message
 * \param[in]    state                                  Global state for the error message
 * \param[in,out] shouldCheckNumberOfBondedInteractions Whether we should do the check. Always set to false.
 */
void checkNumberOfBondedInteractions(FILE                 *fplog,
                                     t_commrec            *cr,
                                     int                   totalNumberOfBondedInteractions,
                                     const gmx_mtop_t     *top_global,
                                     const gmx_localtop_t *top_local,
                                     const t_state        *state,
                                     bool                 *shouldCheckNumberOfBondedInteractions);

/* In domdec_con.c */

/*! \brief Communicates the virtual site forces, reduces the shift forces when \p fshift != NULL */
void dd_move_f_vsites(struct gmx_domdec_t *dd, rvec *f, rvec *fshift);

/*! \brief Clears the forces for virtual sites */
void dd_clear_f_vsites(struct gmx_domdec_t *dd, rvec *f);

/*! \brief Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
void dd_move_x_constraints(struct gmx_domdec_t *dd, matrix box,
                           rvec *x0, rvec *x1, gmx_bool bX1IsCoord);

/*! \brief Communicates the coordinates involved in virtual sites */
void dd_move_x_vsites(struct gmx_domdec_t *dd, const matrix box, rvec *x);

/*! \brief Returns the local atom count array for all constraints
 *
 * The local atom count for a constraint, possible values 2/1/0, is needed
 * to avoid not/double-counting contributions linked to the Lagrange
 * multiplier, such as the virial and free-energy derivatives.
 *
 * \note When \p dd = nullptr, an empty reference is returned.
 */
gmx::ArrayRef<const int> dd_constraints_nlocalatoms(const gmx_domdec_t *dd);

/* In domdec_top.c */

/*! \brief Print error output when interactions are missing */
[[ noreturn ]]
void dd_print_missing_interactions(FILE *fplog, struct t_commrec *cr,
                                   int local_count,
                                   const gmx_mtop_t *top_global,
                                   const gmx_localtop_t *top_local,
                                   const t_state *state_local);

/*! \brief Generate and store the reverse topology */
void dd_make_reverse_top(FILE *fplog,
                         gmx_domdec_t *dd, const gmx_mtop_t *mtop,
                         const gmx_vsite_t *vsite,
                         const t_inputrec *ir, gmx_bool bBCheck);

/*! \brief Store the local charge group index in \p lcgs */
void dd_make_local_cgs(struct gmx_domdec_t *dd, t_block *lcgs);

/*! \brief Generate the local topology and virtual site data */
void dd_make_local_top(struct gmx_domdec_t *dd, struct gmx_domdec_zones_t *zones,
                       int npbcdim, matrix box,
                       rvec cellsize_min, const ivec npulse,
                       t_forcerec *fr,
                       rvec *cgcm_or_x,
                       gmx_vsite_t *vsite,
                       const gmx_mtop_t *top, gmx_localtop_t *ltop);

/*! \brief Sort ltop->ilist when we are doing free energy. */
void dd_sort_local_top(gmx_domdec_t *dd, const t_mdatoms *mdatoms,
                       gmx_localtop_t *ltop);

/*! \brief Construct local topology */
gmx_localtop_t *dd_init_local_top(const gmx_mtop_t *top_global);

/*! \brief Construct local state */
void dd_init_local_state(struct gmx_domdec_t *dd,
                         t_state *state_global, t_state *local_state);

/*! \brief Generate a list of links between charge groups that are linked by bonded interactions */
t_blocka *make_charge_group_links(const gmx_mtop_t *mtop, gmx_domdec_t *dd,
                                  cginfo_mb_t *cginfo_mb);

/*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
void dd_bonded_cg_distance(FILE *fplog, const gmx_mtop_t *mtop,
                           const t_inputrec *ir,
                           const rvec *x, const matrix box,
                           gmx_bool bBCheck,
                           real *r_2b, real *r_mb);

/*! \brief Dump a pdb file with the current DD home + communicated atoms.
 *
 * When natoms=-1, dump all known atoms.
 */
void write_dd_pdb(const char *fn, gmx_int64_t step, const char *title,
                  const gmx_mtop_t *mtop,
                  const t_commrec *cr,
                  int natoms, const rvec x[], const matrix box);


/* In domdec_setup.c */

/*! \brief Returns the volume fraction of the system that is communicated */
real comm_box_frac(const ivec dd_nc, real cutoff, const gmx_ddbox_t *ddbox);

/*! \brief Determines the optimal DD cell setup dd->nc and possibly npmenodes
 * for the system.
 *
 * On the master node returns the actual cellsize limit used.
 */
real dd_choose_grid(FILE *fplog,
                    t_commrec *cr, gmx_domdec_t *dd,
                    const t_inputrec *ir,
                    const gmx_mtop_t *mtop,
                    const matrix box, const gmx_ddbox_t *ddbox,
                    int nPmeRanks,
                    gmx_bool bDynLoadBal, real dlb_scale,
                    real cellsize_limit, real cutoff_dd,
                    gmx_bool bInterCGBondeds);


/* In domdec_box.c */

/*! \brief Set the box and PBC data in \p ddbox */
void set_ddbox(gmx_domdec_t *dd, bool masterRankHasTheSystemState,
               const t_inputrec *ir, const matrix box,
               bool calculateUnboundedSize,
               gmx::ArrayRef<const gmx::RVec> x,
               gmx_ddbox_t *ddbox);

/*! \brief Set the box and PBC data in \p ddbox */
void set_ddbox_cr(const t_commrec *cr, const ivec *dd_nc,
                  const t_inputrec *ir, const matrix box,
                  gmx::ArrayRef<const gmx::RVec> x,
                  gmx_ddbox_t *ddbox);

#endif