[alexxy/gromacs.git] / src / gromacs / nbnxm / nbnxm.h

/*
 * This file is part of the GROMACS molecular simulation package.
 *
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 * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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// FIXME: remove the "__" prefix in front of the group def when we move the
//        nonbonded code into separate dir.

/*! \libinternal \defgroup __module_nbnxm Short-range non-bonded interaction module
 * \ingroup group_mdrun
 *
 * \brief Computes forces and energies for short-range pair-interactions
 * based on the Verlet algorithm. The algorithm uses pair-lists generated
 * at fixed intervals as well as various flavors of pair interaction kernels
 * implemented for a wide range of CPU and GPU architectures.
 *
 * The module includes support for flavors of Coulomb and Lennard-Jones interaction
 * treatment implemented for a large range of SIMD instruction sets for CPU
 * architectures as well as in CUDA and OpenCL for GPU architectures.
 * Additionally there is a reference CPU non-SIMD and a reference CPU
 * for GPU pair-list setup interaction kernel.
 *
 * The implementation of the kernels is based on the cluster non-bonded algorithm
 * which in the code is referred to as the NxM algorithms ("nbnxm_" prefix);
 * for details of the algorithm see DOI:10.1016/j.cpc.2013.06.003.
 *
 * Algorithmically, the non-bonded computation has two different modes:
 * A "classical" mode: generate a list every nstlist steps containing at least
 * all atom pairs up to a distance of rlistOuter and compute pair interactions
 * for all pairs that are within the interaction cut-off.
 * A "dynamic pruning" mode: generate an "outer-list" up to cut-off rlistOuter
 * every nstlist steps and prune the outer-list using a cut-off of rlistInner
 * every nstlistPrune steps to obtain a, smaller, "inner-list". This
 * results in fewer interaction computations and allows for a larger nstlist.
 * On a GPU, this dynamic pruning is performed in a rolling fashion, pruning
 * only a sub-part of the list each (second) step. This way it can often
 * overlap with integration and constraints on the CPU.
 * Currently a simple heuristic determines which mode will be used.
 *
 * TODO: add a summary list and brief descriptions of the different submodules:
 * search, CPU kernels, GPU glue code + kernels.
 *
 * \author Berk Hess <hess@kth.se>
 * \author Szilárd Páll <pall.szilard@gmail.com>
 * \author Mark Abraham <mark.j.abraham@gmail.com>
 * \author Anca Hamuraru <anca@streamcomputing.eu>
 * \author Teemu Virolainen <teemu@streamcomputing.eu>
 * \author Dimitrios Karkoulis <dimitris.karkoulis@gmail.com>
 *
 * TODO: add more authors!
 */

/*! \libinternal
 * \defgroup module_nbnxm Non-bonded pair interactions
 * \ingroup group_mdrun
 * \brief
 * Implements non-bonded pair interaction functionality for NxM atom clusters.
 *
 * This module provides methods to, very efficiently, compute non-bonded
 * pair interactions on CPUs as well as accelerators. It also provides
 * a method to construct the NxM atom-cluster pair-list required for
 * computing these non-bonded iteractions.
 */

/*! \libinternal \file
 *
 * \brief This file contains the public interface of the nbnxm module
 * that implements the NxM atom cluster non-bonded algorithm to efficiently
 * compute pair forces.
 *
 *
 * \author Berk Hess <hess@kth.se>
 * \author Szilárd Páll <pall.szilard@gmail.com>
 *
 * \inlibraryapi
 * \ingroup module_nbnxm
 */


#ifndef GMX_NBNXM_NBNXM_H
#define GMX_NBNXM_NBNXM_H

#include <memory>

#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/locality.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"

struct DeviceInformation;
struct gmx_domdec_zones_t;
struct gmx_enerdata_t;
struct gmx_hw_info_t;
struct gmx_mtop_t;
struct NbnxmGpu;
struct gmx_wallcycle;
struct interaction_const_t;
struct nbnxn_atomdata_t;
struct nonbonded_verlet_t;
class PairSearch;
class PairlistSets;
struct t_commrec;
struct t_lambda;
struct t_mdatoms;
struct t_nrnb;
struct t_forcerec;
struct t_inputrec;

class GpuEventSynchronizer;

namespace gmx
{
class DeviceStreamManager;
class ForceWithShiftForces;
class GpuBonded;
template<typename>
class ListOfLists;
class MDLogger;
template<typename>
class Range;
class StepWorkload;
class UpdateGroupsCog;
} // namespace gmx

namespace Nbnxm
{
enum class KernelType;
}

namespace Nbnxm
{

/*! \brief Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation */
enum class KernelType : int
{
    NotSet = 0,
    Cpu4x4_PlainC,
    Cpu4xN_Simd_4xN,
    Cpu4xN_Simd_2xNN,
    Gpu8x8x8,
    Cpu8x8x8_PlainC,
    Count
};

/*! \brief Ewald exclusion types */
enum class EwaldExclusionType : int
{
    NotSet = 0,
    Table,
    Analytical,
    DecidedByGpuModule
};

/* \brief The non-bonded setup, also affects the pairlist construction kernel */
struct KernelSetup
{
    //! The non-bonded type, also affects the pairlist construction kernel
    KernelType kernelType = KernelType::NotSet;
    //! Ewald exclusion computation handling type, currently only used for CPU
    EwaldExclusionType ewaldExclusionType = EwaldExclusionType::NotSet;
};

/*! \brief Return a string identifying the kernel type.
 *
 * \param [in] kernelType   nonbonded kernel type, takes values from the nbnxn_kernel_type enum
 * \returns                 a string identifying the kernel corresponding to the type passed as argument
 */
const char* lookup_kernel_name(Nbnxm::KernelType kernelType);

} // namespace Nbnxm

/*! \brief Flag to tell the nonbonded kernels whether to clear the force output buffers */
enum
{
    enbvClearFNo,
    enbvClearFYes
};

/*! \libinternal
 *  \brief Top-level non-bonded data structure for the Verlet-type cut-off scheme. */
struct nonbonded_verlet_t
{
public:
    //! Constructs an object from its components
    nonbonded_verlet_t(std::unique_ptr<PairlistSets>     pairlistSets,
                       std::unique_ptr<PairSearch>       pairSearch,
                       std::unique_ptr<nbnxn_atomdata_t> nbat,
                       const Nbnxm::KernelSetup&         kernelSetup,
                       NbnxmGpu*                         gpu_nbv,
                       gmx_wallcycle*                    wcycle);

    ~nonbonded_verlet_t();

    //! Returns whether a GPU is use for the non-bonded calculations
    bool useGpu() const { return kernelSetup_.kernelType == Nbnxm::KernelType::Gpu8x8x8; }

    //! Returns whether a GPU is emulated for the non-bonded calculations
    bool emulateGpu() const
    {
        return kernelSetup_.kernelType == Nbnxm::KernelType::Cpu8x8x8_PlainC;
    }

    //! Return whether the pairlist is of simple, CPU type
    bool pairlistIsSimple() const { return !useGpu() && !emulateGpu(); }

    //! Initialize the pair list sets, TODO this should be private
    void initPairlistSets(bool haveMultipleDomains);

    //! Returns the order of the local atoms on the grid
    gmx::ArrayRef<const int> getLocalAtomOrder() const;

    //! Sets the order of the local atoms to the order grid atom ordering
    void setLocalAtomOrder();

    //! Returns the index position of the atoms on the search grid
    gmx::ArrayRef<const int> getGridIndices() const;

    /*! \brief Constructs the pairlist for the given locality
     *
     * When there are no non-self exclusions, \p exclusions can be empty.
     * Otherwise the number of lists in \p exclusions should match the number
     * of atoms when not using DD, or the total number of atoms in the i-zones
     * when using DD.
     *
     * \param[in] iLocality   The interaction locality: local or non-local
     * \param[in] exclusions  Lists of exclusions for every atom.
     * \param[in] step        Used to set the list creation step
     * \param[in,out] nrnb    Flop accounting struct, can be nullptr
     */
    void constructPairlist(gmx::InteractionLocality     iLocality,
                           const gmx::ListOfLists<int>& exclusions,
                           int64_t                      step,
                           t_nrnb*                      nrnb);

    //! Updates all the atom properties in Nbnxm
    void setAtomProperties(gmx::ArrayRef<const int>  atomTypes,
                           gmx::ArrayRef<const real> atomCharges,
                           gmx::ArrayRef<const int>  atomInfo);

    /*!\brief Convert the coordinates to NBNXM format for the given locality.
     *
     * The API function for the transformation of the coordinates from one layout to another.
     *
     * \param[in] locality     Whether coordinates for local or non-local atoms should be
     * transformed. \param[in] fillLocal    If the coordinates for filler particles should be
     * zeroed. \param[in] coordinates  Coordinates in plain rvec format to be transformed.
     */
    void convertCoordinates(gmx::AtomLocality locality, bool fillLocal, gmx::ArrayRef<const gmx::RVec> coordinates);

    /*!\brief Convert the coordinates to NBNXM format on the GPU for the given locality
     *
     * The API function for the transformation of the coordinates from one layout to another in the GPU memory.
     *
     * \param[in] locality        Whether coordinates for local or non-local atoms should be transformed.
     * \param[in] fillLocal       If the coordinates for filler particles should be zeroed.
     * \param[in] d_x             GPU coordinates buffer in plain rvec format to be transformed.
     * \param[in] xReadyOnDevice  Event synchronizer indicating that the coordinates are ready in the device memory.
     */
    void convertCoordinatesGpu(gmx::AtomLocality       locality,
                               bool                    fillLocal,
                               DeviceBuffer<gmx::RVec> d_x,
                               GpuEventSynchronizer*   xReadyOnDevice);

    //! Init for GPU version of setup coordinates in Nbnxm
    void atomdata_init_copy_x_to_nbat_x_gpu();

    //! Sync the nonlocal GPU stream with dependent tasks in the local queue.
    void insertNonlocalGpuDependency(gmx::InteractionLocality interactionLocality);

    //! Returns a reference to the pairlist sets
    const PairlistSets& pairlistSets() const { return *pairlistSets_; }

    //! Returns whether step is a dynamic list pruning step, for CPU lists
    bool isDynamicPruningStepCpu(int64_t step) const;

    //! Returns whether step is a dynamic list pruning step, for GPU lists
    bool isDynamicPruningStepGpu(int64_t step) const;

    //! Dispatches the dynamic pruning kernel for the given locality, for CPU lists
    void dispatchPruneKernelCpu(gmx::InteractionLocality iLocality, const rvec* shift_vec);

    //! Dispatches the dynamic pruning kernel for GPU lists
    void dispatchPruneKernelGpu(int64_t step);

    //! \brief Executes the non-bonded kernel of the GPU or launches it on the GPU
    void dispatchNonbondedKernel(gmx::InteractionLocality   iLocality,
                                 const interaction_const_t& ic,
                                 const gmx::StepWorkload&   stepWork,
                                 int                        clearF,
                                 const t_forcerec&          fr,
                                 gmx_enerdata_t*            enerd,
                                 t_nrnb*                    nrnb);

    //! Executes the non-bonded free-energy kernel, always runs on the CPU
    void dispatchFreeEnergyKernel(gmx::InteractionLocality   iLocality,
                                  const t_forcerec*          fr,
                                  rvec                       x[],
                                  gmx::ForceWithShiftForces* forceWithShiftForces,
                                  const t_mdatoms&           mdatoms,
                                  t_lambda*                  fepvals,
                                  gmx::ArrayRef<const real>  lambda,
                                  gmx_enerdata_t*            enerd,
                                  const gmx::StepWorkload&   stepWork,
                                  t_nrnb*                    nrnb);

    /*! \brief Add the forces stored in nbat to f, zeros the forces in nbat
     * \param [in] locality         Local or non-local
     * \param [inout] force         Force to be added to
     */
    void atomdata_add_nbat_f_to_f(gmx::AtomLocality locality, gmx::ArrayRef<gmx::RVec> force);

    /*! \brief Add the forces stored in nbat to total force using GPU buffer opse
     *
     * \param [in]     locality             Local or non-local
     * \param [in,out] totalForcesDevice    Force to be added to
     * \param [in]     forcesPmeDevice      Device buffer with PME forces
     * \param[in]      dependencyList       List of synchronizers that represent the dependencies the reduction task needs to sync on.
     * \param [in]     useGpuFPmeReduction  Whether PME forces should be added
     * \param [in]     accumulateForce      If the total force buffer already contains data
     */
    void atomdata_add_nbat_f_to_f_gpu(gmx::AtomLocality                          locality,
                                      DeviceBuffer<gmx::RVec>                    totalForcesDevice,
                                      void*                                      forcesPmeDevice,
                                      gmx::ArrayRef<GpuEventSynchronizer* const> dependencyList,
                                      bool useGpuFPmeReduction,
                                      bool accumulateForce);

    /*! \brief Outer body of function to perform initialization for F buffer operations on GPU.
     *
     * \param localReductionDone     Pointer to an event synchronizer that marks the completion of the local f buffer ops kernel.
     */
    void atomdata_init_add_nbat_f_to_f_gpu(GpuEventSynchronizer* localReductionDone);

    /*! \brief return GPU pointer to f in rvec format */
    void* get_gpu_frvec();

    //! Return the kernel setup
    const Nbnxm::KernelSetup& kernelSetup() const { return kernelSetup_; }

    //! Returns the outer radius for the pair list
    real pairlistInnerRadius() const;

    //! Returns the outer radius for the pair list
    real pairlistOuterRadius() const;

    //! Changes the pair-list outer and inner radius
    void changePairlistRadii(real rlistOuter, real rlistInner);

    //! Set up internal flags that indicate what type of short-range work there is.
    void setupGpuShortRangeWork(const gmx::GpuBonded* gpuBonded, gmx::InteractionLocality iLocality);

    // TODO: Make all data members private
public:
    //! All data related to the pair lists
    std::unique_ptr<PairlistSets> pairlistSets_;
    //! Working data for constructing the pairlists
    std::unique_ptr<PairSearch> pairSearch_;
    //! Atom data
    std::unique_ptr<nbnxn_atomdata_t> nbat;

private:
    //! The non-bonded setup, also affects the pairlist construction kernel
    Nbnxm::KernelSetup kernelSetup_;
    //! \brief Pointer to wallcycle structure.
    gmx_wallcycle* wcycle_;

public:
    //! GPU Nbnxm data, only used with a physical GPU (TODO: use unique_ptr)
    NbnxmGpu* gpu_nbv;
};

namespace Nbnxm
{

/*! \brief Creates an Nbnxm object */
std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger& mdlog,
                                                   const t_inputrec*    ir,
                                                   const t_forcerec*    fr,
                                                   const t_commrec*     cr,
                                                   const gmx_hw_info_t& hardwareInfo,
                                                   bool                 useGpuForNonbonded,
                                                   const gmx::DeviceStreamManager* deviceStreamManager,
                                                   const gmx_mtop_t*               mtop,
                                                   matrix                          box,
                                                   gmx_wallcycle*                  wcycle);

} // namespace Nbnxm

/*! \brief Put the atoms on the pair search grid.
 *
 * Only atoms with indices wihtin \p atomRange in x are put on the grid.
 * When \p updateGroupsCog != nullptr, atoms are put on the grid
 * based on the center of geometry of the group they belong to.
 * Atoms or COGs of groups should be within the bounding box provided,
 * this is checked in debug builds when not using update groups.
 * The atom density is used to determine the grid size when \p gridIndex = 0.
 * When \p atomDensity <= 0, the density is determined from atomEnd-atomStart
 * and the bounding box corners.
 * With domain decomposition, part of the atoms might have migrated,
 * but have not been removed yet. This count is given by \p numAtomsMoved.
 * When \p move[i] < 0 particle i has migrated and will not be put on the grid.
 *
 * \param[in,out] nb_verlet    The non-bonded object
 * \param[in]     box          Box used for periodic distance calculations
 * \param[in]     gridIndex    The index of the grid to spread to, always 0 except with test particle insertion
 * \param[in]     lowerCorner  Atom groups to be gridded should have coordinates >= this corner
 * \param[in]     upperCorner  Atom groups to be gridded should have coordinates <= this corner
 * \param[in]     updateGroupsCog  Centers of geometry for update groups, pass nullptr when not using update groups
 * \param[in]     atomRange    Range of atoms to grid
 * \param[in]     atomDensity  An estimate of the atom density, used for peformance optimization and only with \p gridIndex = 0
 * \param[in]     atomInfo     Atom information flags
 * \param[in]     x            Coordinates for atoms to grid
 * \param[in]     numAtomsMoved  The number of atoms that will move to another domain, pass 0 without DD
 * \param[in]     move         Move flags for atoms, pass nullptr without DD
 */
void nbnxn_put_on_grid(nonbonded_verlet_t*            nb_verlet,
                       const matrix                   box,
                       int                            gridIndex,
                       const rvec                     lowerCorner,
                       const rvec                     upperCorner,
                       const gmx::UpdateGroupsCog*    updateGroupsCog,
                       gmx::Range<int>                atomRange,
                       real                           atomDensity,
                       gmx::ArrayRef<const int>       atomInfo,
                       gmx::ArrayRef<const gmx::RVec> x,
                       int                            numAtomsMoved,
                       const int*                     move);

/*! \brief As nbnxn_put_on_grid, but for the non-local atoms
 *
 * with domain decomposition. Should be called after calling
 * nbnxn_search_put_on_grid for the local atoms / home zone.
 */
void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*              nb_verlet,
                                const struct gmx_domdec_zones_t* zones,
                                gmx::ArrayRef<const int>         atomInfo,
                                gmx::ArrayRef<const gmx::RVec>   x);

#endif // GMX_NBNXN_NBNXM_H