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 #ifdef __cplusplus
 116 extern "C" {
 117 #endif
 118
 119
 120 /*! \brief Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation */
 121 typedef enum
 122 {
 123     nbnxnkNotSet = 0,
 124     nbnxnk4x4_PlainC,
 125     nbnxnk4xN_SIMD_4xN,
 126     nbnxnk4xN_SIMD_2xNN,
 127     nbnxnk8x8x8_GPU,
 128     nbnxnk8x8x8_PlainC,
 129     nbnxnkNR
 130 } nbnxn_kernel_type;
 131
 132 /*! \brief Return a string identifying the kernel type.
 133  *
 134  * \param [in] kernel_type   nonbonded kernel types, takes values from the nbnxn_kernel_type enum
 135  * \returns                  a string identifying the kernel corresponding to the type passed as argument
 136  */
 137 const char *lookup_nbnxn_kernel_name(int kernel_type);
 138
 139 /*! \brief Ewald exclusion types */
 140 enum {
 141     ewaldexclTable, ewaldexclAnalytical
 142 };
 143
 144 /*! \brief Atom locality indicator: local, non-local, all.
 145  *
 146  * Used for calls to:
 147  * gridding, pair-search, force calculation, x/f buffer operations
 148  * */
 149 enum {
 150     eatLocal = 0, eatNonlocal = 1, eatAll
 151 };
 152
 153 /*! \brief Tests for local atom range */
 154 #define LOCAL_A(x)               ((x) == eatLocal)
 155 /*! \brief Tests for non-local atom range */
 156 #define NONLOCAL_A(x)            ((x) == eatNonlocal)
 157 /*! \brief Tests for either local or non-local atom range */
 158 #define LOCAL_OR_NONLOCAL_A(x)   (LOCAL_A(x) || NONLOCAL_A(x))
 159
 160 /*! \brief Interaction locality indicator
 161  *
 162  * Used in pair-list search/calculations in the following manner:
 163  *  - local interactions require local atom data and affect local output only;
 164  *  - non-local interactions require both local and non-local atom data and
 165  *    affect both local- and non-local output.
 166  */
 167 enum {
 168     eintLocal = 0, eintNonlocal = 1
 169 };
 170
 171 /*! \brief Tests for local interaction indicator */
 172 #define LOCAL_I(x)               ((x) == eintLocal)
 173 /*! \brief Tests for non-local interaction indicator */
 174 #define NONLOCAL_I(x)            ((x) == eintNonlocal)
 175
 176 /*! \brief Flag to tell the nonbonded kernels whether to clear the force output buffers */
 177 enum {
 178     enbvClearFNo, enbvClearFYes
 179 };
 180
 181 /*! \libinternal
 182  *  \brief Non-bonded interaction group data structure. */
 183 typedef struct nonbonded_verlet_group_t {
 184     nbnxn_pairlist_set_t  nbl_lists;   /**< pair list(s)                       */
 185     nbnxn_atomdata_t     *nbat;        /**< atom data                          */
 186     int                   kernel_type; /**< non-bonded kernel - see enum above */
 187     int                   ewald_excl;  /**< Ewald exclusion - see enum above   */
 188 } nonbonded_verlet_group_t;
 189
 190 /*! \libinternal
 191  *  \brief Top-level non-bonded data structure for the Verlet-type cut-off scheme. */
 192 typedef struct nonbonded_verlet_t {
 193     std::unique_ptr<NbnxnListParameters> listParams;      /**< Parameters for the search and list pruning setup */
 194     nbnxn_search_t                       nbs;             /**< n vs n atom pair searching data       */
 195     int                                  ngrp;            /**< number of interaction groups          */
 196     nonbonded_verlet_group_t             grp[2];          /**< local and non-local interaction group */
 197
 198     gmx_bool                             bUseGPU;         /**< TRUE when non-bonded interactions are computed on a physical GPU */
 199     EmulateGpuNonbonded                  emulateGpu;      /**< true when non-bonded interactions are computed on the CPU using GPU-style pair lists */
 200     gmx_nbnxn_gpu_t                     *gpu_nbv;         /**< pointer to GPU nb verlet data     */
 201     int                                  min_ci_balanced; /**< pair list balancing parameter
 202                                                                used for the 8x8x8 GPU kernels    */
 203 } nonbonded_verlet_t;
 204
 205 /*! \brief Getter for bUseGPU */
 206 gmx_bool
 207 usingGpu(nonbonded_verlet_t *nbv);
 208
 209 #ifdef __cplusplus
 210 }
 211 #endif
 212
 213 #endif /* NB_VERLET_H */