src/gromacs/mdlib/nb_verlet.h

   1 /*
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  35
  36 // FIXME: remove the "__" prefix in front of the group def when we move the
  37 //        nonbonded code into separate dir.
  38
  39 /*! \libinternal \defgroup __module_nb_verlet Short-range non-bonded interaction module
  40  * \ingroup group_mdrun
  41  *
  42  * \brief Computes forces and energies for short-range pair-interactions
  43  * based on the Verlet algorithm. The algorithm uses pair-lists generated
  44  * at fixed intervals as well as various flavors of pair interaction kernels
  45  * implemented for a wide range of CPU and GPU architectures.
  46  *
  47  * The module includes support for flavors of Coulomb and Lennard-Jones interaction
  48  * treatment implemented for a large range of SIMD instruction sets for CPU
  49  * architectures as well as in CUDA and OpenCL for GPU architectures.
  50  * Additionally there is a reference CPU non-SIMD and a reference CPU
  51  * for GPU pair-list setup interaction kernel.
  52  *
  53  * The implementation of the kernels is based on the cluster non-bonded algorithm
  54  * which in the code is referred to as the NxN algorithms ("nbnxn_" prefix);
  55  * for details of the algorithm see DOI:10.1016/j.cpc.2013.06.003.
  56  *
  57  * Algorithmically, the non-bonded computation has two different modes:
  58  * A "classical" mode: generate a list every nstlist steps containing at least
  59  * all atom pairs up to a distance of rlistOuter and compute pair interactions
  60  * for all pairs that are within the interaction cut-off.
  61  * A "dynamic pruning" mode: generate an "outer-list" up to cut-off rlistOuter
  62  * every nstlist steps and prune the outer-list using a cut-off of rlistInner
  63  * every nstlistPrune steps to obtain a, smaller, "inner-list". This
  64  * results in fewer interaction computations and allows for a larger nstlist.
  65  * On a GPU, this dynamic pruning is performed in a rolling fashion, pruning
  66  * only a sub-part of the list each (second) step. This way it can often
  67  * overlap with integration and constraints on the CPU.
  68  * Currently a simple heuristic determines which mode will be used.
  69  *
  70  * TODO: add a summary list and brief descriptions of the different submodules:
  71  * search, CPU kernels, GPU glue code + kernels.
  72  *
  73  * \author Berk Hess <hess@kth.se>
  74  * \author Szilárd Páll <pall.szilard@gmail.com>
  75  * \author Mark Abraham <mark.j.abraham@gmail.com>
  76  * \author Anca Hamuraru <anca@streamcomputing.eu>
  77  * \author Teemu Virolainen <teemu@streamcomputing.eu>
  78  * \author Dimitrios Karkoulis <dimitris.karkoulis@gmail.com>
  79  *
  80  * TODO: add more authors!
  81  */
  82
  83 /*! \libinternal \file
  84  *
  85  * \brief This file contains the public interface of the non-bonded Verlet module
  86  * that implements the NxN cluster non-bonded algorithm to efficiently compute
  87  * pair forces.
  88  *
  89  *
  90  * \author Berk Hess <hess@kth.se>
  91  * \author Szilárd Páll <pall.szilard@gmail.com>
  92  *
  93  * \inlibraryapi
  94  * \ingroup __module_nb_verlet
  95  */
  96
  97
  98 #ifndef NB_VERLET_H
  99 #define NB_VERLET_H
 100
 101 #include <memory>
 102
 103 #include "gromacs/mdlib/nbnxn_gpu_types.h"
 104 #include "gromacs/mdlib/nbnxn_pairlist.h"
 105
 106 //! Help pass GPU-emulation parameters with type safety.
 107 enum class EmulateGpuNonbonded : bool
 108 {
 109     //! Do not emulate GPUs.
 110     No,
 111     //! Do emulate GPUs.
 112     Yes
 113 };
 114
 115
 116 /*! \brief Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation */
 117 typedef enum
 118 {
 119     nbnxnkNotSet = 0,
 120     nbnxnk4x4_PlainC,
 121     nbnxnk4xN_SIMD_4xN,
 122     nbnxnk4xN_SIMD_2xNN,
 123     nbnxnk8x8x8_GPU,
 124     nbnxnk8x8x8_PlainC,
 125     nbnxnkNR
 126 } nbnxn_kernel_type;
 127
 128 /*! \brief Return a string identifying the kernel type.
 129  *
 130  * \param [in] kernel_type   nonbonded kernel types, takes values from the nbnxn_kernel_type enum
 131  * \returns                  a string identifying the kernel corresponding to the type passed as argument
 132  */
 133 const char *lookup_nbnxn_kernel_name(int kernel_type);
 134
 135 /*! \brief Ewald exclusion types */
 136 enum {
 137     ewaldexclTable, ewaldexclAnalytical
 138 };
 139
 140 /*! \brief Atom locality indicator: local, non-local, all.
 141  *
 142  * Used for calls to:
 143  * gridding, pair-search, force calculation, x/f buffer operations
 144  * */
 145 enum {
 146     eatLocal = 0, eatNonlocal = 1, eatAll
 147 };
 148
 149 /*! \brief Tests for local atom range */
 150 #define LOCAL_A(x)               ((x) == eatLocal)
 151 /*! \brief Tests for non-local atom range */
 152 #define NONLOCAL_A(x)            ((x) == eatNonlocal)
 153 /*! \brief Tests for either local or non-local atom range */
 154 #define LOCAL_OR_NONLOCAL_A(x)   (LOCAL_A(x) || NONLOCAL_A(x))
 155
 156 /*! \brief Interaction locality indicator
 157  *
 158  * Used in pair-list search/calculations in the following manner:
 159  *  - local interactions require local atom data and affect local output only;
 160  *  - non-local interactions require both local and non-local atom data and
 161  *    affect both local- and non-local output.
 162  */
 163 enum {
 164     eintLocal = 0, eintNonlocal = 1
 165 };
 166
 167 /*! \brief Tests for local interaction indicator */
 168 #define LOCAL_I(x)               ((x) == eintLocal)
 169 /*! \brief Tests for non-local interaction indicator */
 170 #define NONLOCAL_I(x)            ((x) == eintNonlocal)
 171
 172 /*! \brief Flag to tell the nonbonded kernels whether to clear the force output buffers */
 173 enum {
 174     enbvClearFNo, enbvClearFYes
 175 };
 176
 177 /*! \libinternal
 178  *  \brief Non-bonded interaction group data structure. */
 179 typedef struct nonbonded_verlet_group_t {
 180     nbnxn_pairlist_set_t  nbl_lists;   /**< pair list(s)                       */
 181     int                   kernel_type; /**< non-bonded kernel - see enum above */
 182     int                   ewald_excl;  /**< Ewald exclusion - see enum above   */
 183 } nonbonded_verlet_group_t;
 184
 185 /*! \libinternal
 186  *  \brief Top-level non-bonded data structure for the Verlet-type cut-off scheme. */
 187 typedef struct nonbonded_verlet_t {
 188     std::unique_ptr<NbnxnListParameters> listParams;      /**< Parameters for the search and list pruning setup */
 189     std::unique_ptr<nbnxn_search>        nbs;             /**< n vs n atom pair searching data       */
 190     int                                  ngrp;            /**< number of interaction groups          */
 191     nonbonded_verlet_group_t             grp[2];          /**< local and non-local interaction group */
 192     nbnxn_atomdata_t                    *nbat;            /**< atom data                             */
 193
 194     gmx_bool                             bUseGPU;         /**< TRUE when non-bonded interactions are computed on a physical GPU */
 195     EmulateGpuNonbonded                  emulateGpu;      /**< true when non-bonded interactions are computed on the CPU using GPU-style pair lists */
 196     gmx_nbnxn_gpu_t                     *gpu_nbv;         /**< pointer to GPU nb verlet data     */
 197     int                                  min_ci_balanced; /**< pair list balancing parameter
 198                                                                used for the 8x8x8 GPU kernels    */
 199 } nonbonded_verlet_t;
 200
 201 /*! \brief Getter for bUseGPU */
 202 gmx_bool
 203 usingGpu(nonbonded_verlet_t *nbv);
 204
 205 #endif /* NB_VERLET_H */