src/gromacs/nbnxm/pairlistwork.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35
  36 /*! \internal \file
  37  *
  38  * \brief Declares working data structures for the CPU and GPU pairlists
  39  *
  40  * \author Berk Hess <hess@kth.se>
  41  *
  42  * \ingroup module_nbnxn
  43  */
  44
  45 #ifndef GMX_NBNXM_PAIRLISTWORK_H
  46 #define GMX_NBNXM_PAIRLISTWORK_H
  47
  48 #include <memory>
  49 #include <vector>
  50
  51 #include "gromacs/nbnxm/pairlist.h"
  52 #include "gromacs/simd/simd.h"
  53
  54 #include "grid.h"
  55
  56 /* Working data for the actual i-supercell during pair search */
  57 struct NbnxnPairlistCpuWork
  58 {
  59     // Struct for storing coordinats and bounding box for an i-entry during search
  60     struct IClusterData
  61     {
  62         IClusterData() :
  63             bb(1),
  64             x(c_nbnxnCpuIClusterSize*DIM),
  65             xSimd(c_nbnxnCpuIClusterSize*DIM*GMX_REAL_MAX_SIMD_WIDTH)
  66         {
  67         }
  68
  69         // The bounding boxes, pbc shifted, for each cluster
  70         AlignedVector<Nbnxm::BoundingBox> bb;
  71         // The coordinates, pbc shifted, for each atom
  72         std::vector<real>                 x;
  73         // Aligned list for storing 4*DIM*GMX_SIMD_REAL_WIDTH reals
  74         AlignedVector<real>               xSimd;
  75     };
  76
  77     // Protect data from cache pollution between threads
  78     gmx_cache_protect_t       cp0;
  79
  80     // Work data for generating an IEntry in the pairlist
  81     IClusterData              iClusterData;
  82     // The current cj_ind index for the current list
  83     int                       cj_ind;
  84     // Temporary j-cluster list, used for sorting on exclusions
  85     std::vector<nbnxn_cj_t>   cj;
  86
  87     // Nr. of cluster pairs without Coulomb for flop counting
  88     int                       ncj_noq;
  89     // Nr. of cluster pairs with 1/2 LJ for flop count
  90     int                       ncj_hlj;
  91
  92     // Protect data from cache pollution between threads
  93     gmx_cache_protect_t       cp1;
  94 };
  95
  96 /* Working data for the actual i-supercell during pair search */
  97 struct NbnxnPairlistGpuWork
  98 {
  99     struct ISuperClusterData
 100     {
 101         ISuperClusterData() :
 102             bb(c_gpuNumClusterPerCell),
 103 #if NBNXN_SEARCH_BB_SIMD4
 104             bbPacked(c_gpuNumClusterPerCell/c_packedBoundingBoxesDimSize*c_packedBoundingBoxesSize),
 105 #endif
 106             x(c_gpuNumClusterPerCell*c_nbnxnGpuClusterSize*DIM),
 107             xSimd(c_gpuNumClusterPerCell*c_nbnxnGpuClusterSize*DIM)
 108         {
 109         }
 110
 111         // The bounding boxes, pbc shifted, for each cluster
 112         AlignedVector<Nbnxm::BoundingBox> bb;
 113         // As bb, but in packed xxxx format
 114         AlignedVector<float>              bbPacked;
 115         // The coordinates, pbc shifted, for each atom
 116         AlignedVector<real>               x;
 117         // Aligned coordinate list used for 4*DIM*GMX_SIMD_REAL_WIDTH floats
 118         AlignedVector<real>               xSimd;
 119     };
 120
 121     NbnxnPairlistGpuWork() :
 122         distanceBuffer(c_gpuNumClusterPerCell),
 123         sci_sort({}, {gmx::PinningPolicy::PinnedIfSupported})
 124     {
 125     }
 126
 127     // Protect data from cache pollution between threads
 128     gmx_cache_protect_t       cp0;
 129
 130     // Work data for generating an i-entry in the pairlist
 131     ISuperClusterData         iSuperClusterData;
 132     // The current j-cluster index for the current list
 133     int                       cj_ind;
 134     // Bounding box distance work array
 135     AlignedVector<float>      distanceBuffer;
 136
 137     // Buffer for sorting list entries
 138     std::vector<int>          sortBuffer;
 139
 140     // Second sci array, for sorting
 141     gmx::HostVector<nbnxn_sci_t> sci_sort;
 142
 143     // Protect data from cache pollution between threads
 144     gmx_cache_protect_t       cp1;
 145 };
 146
 147 #endif