src/gromacs/nbnxm/pairlist.h

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  35
  36 #ifndef GMX_NBNXM_PAIRLIST_H
  37 #define GMX_NBNXM_PAIRLIST_H
  38
  39 #include <cstddef>
  40
  41 #include "gromacs/gpu_utils/hostallocator.h"
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/mdtypes/nblist.h"
  44 #include "gromacs/utility/basedefinitions.h"
  45 #include "gromacs/utility/defaultinitializationallocator.h"
  46 #include "gromacs/utility/enumerationhelpers.h"
  47 #include "gromacs/utility/real.h"
  48
  49 // This file with constants is separate from this file to be able
  50 // to include it during OpenCL jitting without including config.h
  51 #include "gromacs/nbnxm/constants.h"
  52
  53 #include "locality.h"
  54 #include "pairlistparams.h"
  55
  56 struct NbnxnPairlistCpuWork;
  57 struct NbnxnPairlistGpuWork;
  58
  59
  60 /* Convenience type for vector with aligned memory */
  61 template<typename T>
  62 using AlignedVector = std::vector < T, gmx::AlignedAllocator < T>>;
  63
  64 /* Convenience type for vector that avoids initialization at resize() */
  65 template<typename T>
  66 using FastVector = std::vector < T, gmx::DefaultInitializationAllocator < T>>;
  67
  68 /* A buffer data structure of 64 bytes
  69  * to be placed at the beginning and end of structs
  70  * to avoid cache invalidation of the real contents
  71  * of the struct by writes to neighboring memory.
  72  */
  73 typedef struct {
  74     int dummy[16];
  75 } gmx_cache_protect_t;
  76
  77 /* This is the actual cluster-pair list j-entry.
  78  * cj is the j-cluster.
  79  * The interaction bits in excl are indexed i-major, j-minor.
  80  * The cj entries are sorted such that ones with exclusions come first.
  81  * This means that once a full mask (=NBNXN_INTERACTION_MASK_ALL)
  82  * is found, all subsequent j-entries in the i-entry also have full masks.
  83  */
  84 struct nbnxn_cj_t
  85 {
  86     int          cj;    /* The j-cluster                    */
  87     unsigned int excl;  /* The exclusion (interaction) bits */
  88 };
  89
  90 /* In nbnxn_ci_t the integer shift contains the shift in the lower 7 bits.
  91  * The upper bits contain information for non-bonded kernel optimization.
  92  * Simply calculating LJ and Coulomb for all pairs in a cluster pair is fine.
  93  * But three flags can be used to skip interactions, currently only for subc=0
  94  * !(shift & NBNXN_CI_DO_LJ(subc))   => we can skip LJ for all pairs
  95  * shift & NBNXN_CI_HALF_LJ(subc)    => we can skip LJ for the second half of i
  96  * !(shift & NBNXN_CI_DO_COUL(subc)) => we can skip Coulomb for all pairs
  97  */
  98 #define NBNXN_CI_SHIFT          127
  99 #define NBNXN_CI_DO_LJ(subc)    (1<<(7+3*(subc)))
 100 #define NBNXN_CI_HALF_LJ(subc)  (1<<(8+3*(subc)))
 101 #define NBNXN_CI_DO_COUL(subc)  (1<<(9+3*(subc)))
 102
 103 /* Cluster-pair Interaction masks
 104  * Bit i*j-cluster-size + j tells if atom i and j interact.
 105  */
 106 // TODO: Rename according to convention when moving into Nbnxn namespace
 107 /* All interaction mask is the same for all kernels */
 108 constexpr unsigned int NBNXN_INTERACTION_MASK_ALL       = 0xffffffffU;
 109 /* 4x4 kernel diagonal mask */
 110 constexpr unsigned int NBNXN_INTERACTION_MASK_DIAG      = 0x08ceU;
 111 /* 4x2 kernel diagonal masks */
 112 constexpr unsigned int NBNXN_INTERACTION_MASK_DIAG_J2_0 = 0x0002U;
 113 constexpr unsigned int NBNXN_INTERACTION_MASK_DIAG_J2_1 = 0x002fU;
 114 /* 4x8 kernel diagonal masks */
 115 constexpr unsigned int NBNXN_INTERACTION_MASK_DIAG_J8_0 = 0xf0f8fcfeU;
 116 constexpr unsigned int NBNXN_INTERACTION_MASK_DIAG_J8_1 = 0x0080c0e0U;
 117
 118 /* Simple pair-list i-unit */
 119 struct nbnxn_ci_t
 120 {
 121     int ci;             /* i-cluster             */
 122     int shift;          /* Shift vector index plus possible flags, see above */
 123     int cj_ind_start;   /* Start index into cj   */
 124     int cj_ind_end;     /* End index into cj     */
 125 };
 126
 127 /* Grouped pair-list i-unit */
 128 typedef struct {
 129     /* Returns the number of j-cluster groups in this entry */
 130     int numJClusterGroups() const
 131     {
 132         return cj4_ind_end - cj4_ind_start;
 133     }
 134
 135     int sci;            /* i-super-cluster       */
 136     int shift;          /* Shift vector index plus possible flags */
 137     int cj4_ind_start;  /* Start index into cj4  */
 138     int cj4_ind_end;    /* End index into cj4    */
 139 } nbnxn_sci_t;
 140
 141 /* Interaction data for a j-group for one warp */
 142 struct nbnxn_im_ei_t
 143 {
 144     // The i-cluster interactions mask for 1 warp
 145     unsigned int imask    = 0U;
 146     // Index into the exclusion array for 1 warp, default index 0 which means no exclusions
 147     int          excl_ind = 0;
 148 };
 149
 150 typedef struct {
 151     int           cj[c_nbnxnGpuJgroupSize];         /* The 4 j-clusters */
 152     nbnxn_im_ei_t imei[c_nbnxnGpuClusterpairSplit]; /* The i-cluster mask data       for 2 warps   */
 153 } nbnxn_cj4_t;
 154
 155 /* Struct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist */
 156 struct nbnxn_excl_t
 157 {
 158     /* Constructor, sets no exclusions, so all atom pairs interacting */
 159     nbnxn_excl_t()
 160     {
 161         for (unsigned int &pairEntry : pair)
 162         {
 163             pairEntry = NBNXN_INTERACTION_MASK_ALL;
 164         }
 165     }
 166
 167     /* Topology exclusion interaction bits per warp */
 168     unsigned int pair[c_nbnxnGpuExclSize];
 169 };
 170
 171 /* Cluster pairlist type for use on CPUs */
 172 struct NbnxnPairlistCpu
 173 {
 174     NbnxnPairlistCpu();
 175
 176     gmx_cache_protect_t     cp0;
 177
 178     int                     na_ci;       /* The number of atoms per i-cluster        */
 179     int                     na_cj;       /* The number of atoms per j-cluster        */
 180     real                    rlist;       /* The radius for constructing the list     */
 181     FastVector<nbnxn_ci_t>  ci;          /* The i-cluster list                       */
 182     FastVector<nbnxn_ci_t>  ciOuter;     /* The outer, unpruned i-cluster list       */
 183
 184     FastVector<nbnxn_cj_t>  cj;          /* The j-cluster list, size ncj             */
 185     FastVector<nbnxn_cj_t>  cjOuter;     /* The outer, unpruned j-cluster list       */
 186     int                     ncjInUse;    /* The number of j-clusters that are used by ci entries in this list, will be <= cj.size() */
 187
 188     int                     nci_tot;     /* The total number of i clusters           */
 189
 190     /* Working data storage for list construction */
 191     std::unique_ptr<NbnxnPairlistCpuWork> work;
 192
 193     gmx_cache_protect_t                   cp1;
 194 };
 195
 196 /* Cluster pairlist type, with extra hierarchies, for on the GPU
 197  *
 198  * NOTE: for better performance when combining lists over threads,
 199  *       all vectors should use default initialization. But when
 200  *       changing this, excl should be intialized when adding entries.
 201  */
 202 struct NbnxnPairlistGpu
 203 {
 204     /* Constructor
 205      *
 206      * \param[in] pinningPolicy  Sets the pinning policy for all buffers used on the GPU
 207      */
 208     NbnxnPairlistGpu(gmx::PinningPolicy pinningPolicy);
 209
 210     gmx_cache_protect_t            cp0;
 211
 212     int                            na_ci; /* The number of atoms per i-cluster        */
 213     int                            na_cj; /* The number of atoms per j-cluster        */
 214     int                            na_sc; /* The number of atoms per super cluster    */
 215     real                           rlist; /* The radius for constructing the list     */
 216     // The i-super-cluster list, indexes into cj4;
 217     gmx::HostVector<nbnxn_sci_t>   sci;
 218     // The list of 4*j-cluster groups
 219     gmx::HostVector<nbnxn_cj4_t>   cj4;
 220     // Atom interaction bits (non-exclusions)
 221     gmx::HostVector<nbnxn_excl_t>  excl;
 222     // The total number of i-clusters
 223     int                            nci_tot;
 224
 225     /* Working data storage for list construction */
 226     std::unique_ptr<NbnxnPairlistGpuWork> work;
 227
 228     gmx_cache_protect_t                   cp1;
 229 };
 230
 231 //! Initializes a free-energy pair-list
 232 void nbnxn_init_pairlist_fep(t_nblist *nl);
 233
 234 #endif