src/gromacs/nbnxm/pairsearch.h

   1 /*
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   4  * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, 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 the PairSearch class and helper structs
  39  *
  40  * The PairSearch class holds the domain setup, the search grids
  41  * and helper object for the pair search. It manages the search work.
  42  * The actual gridding and pairlist generation is performeed by the
  43  * GridSet/Grid and PairlistSet/Pairlist classes, respectively.
  44  *
  45  * \author Berk Hess <hess@kth.se>
  46  *
  47  * \ingroup module_nbnxm
  48  */
  49
  50 #ifndef GMX_NBNXM_PAIRSEARCH_H
  51 #define GMX_NBNXM_PAIRSEARCH_H
  52
  53 #include <memory>
  54 #include <vector>
  55
  56 #include "gromacs/domdec/domdec.h"
  57 #include "gromacs/math/vectypes.h"
  58 #include "gromacs/nbnxm/atomdata.h"
  59 #include "gromacs/nbnxm/pairlist.h"
  60 #include "gromacs/timing/cyclecounter.h"
  61 #include "gromacs/utility/alignedallocator.h"
  62 #include "gromacs/utility/arrayref.h"
  63 #include "gromacs/utility/real.h"
  64
  65 #include "gridset.h"
  66
  67 struct gmx_domdec_zones_t;
  68 struct PairsearchWork;
  69
  70
  71 /*! \brief Convenience declaration for an std::vector with aligned memory */
  72 template <class T>
  73 using AlignedVector = std::vector < T, gmx::AlignedAllocator < T>>;
  74
  75
  76 /* Local cycle count struct for profiling */
  77 class nbnxn_cycle_t
  78 {
  79     public:
  80         void start()
  81         {
  82             start_ = gmx_cycles_read();
  83         }
  84
  85         void stop()
  86         {
  87             cycles_ += gmx_cycles_read() - start_;
  88             count_++;
  89         }
  90
  91         int count() const
  92         {
  93             return count_;
  94         }
  95
  96         double averageMCycles() const
  97         {
  98             if (count_ > 0)
  99             {
 100                 return static_cast<double>(cycles_)*1e-6/count_;
 101             }
 102             else
 103             {
 104                 return 0;
 105             }
 106         }
 107
 108     private:
 109         int          count_  = 0;
 110         gmx_cycles_t cycles_ = 0;
 111         gmx_cycles_t start_  = 0;
 112 };
 113
 114 //! Local cycle count enum for profiling different parts of search
 115 enum {
 116     enbsCCgrid, enbsCCsearch, enbsCCcombine, enbsCCnr
 117 };
 118
 119 /*! \internal
 120  * \brief Struct for collecting detailed cycle counts for the search
 121  */
 122 struct SearchCycleCounting
 123 {
 124     //! Start a pair search cycle counter
 125     void start(const int enbsCC)
 126     {
 127         cc_[enbsCC].start();
 128     }
 129
 130     //! Stop a pair search cycle counter
 131     void stop(const int enbsCC)
 132     {
 133         cc_[enbsCC].stop();
 134     }
 135
 136     //! Print the cycle counts to \p fp
 137     void printCycles(FILE                               *fp,
 138                      gmx::ArrayRef<const PairsearchWork> work) const;
 139
 140     //! Tells whether we record cycles
 141     bool          recordCycles_ = false;
 142     //! The number of times pairsearching has been performed, local+non-local count as 1
 143     int           searchCount_  = 0;
 144     //! The set of cycle counters
 145     nbnxn_cycle_t cc_[enbsCCnr];
 146 };
 147
 148 // TODO: Move nbnxn_search_work_t definition to its own file
 149
 150 /* Thread-local work struct, contains working data for Grid */
 151 struct PairsearchWork
 152 {
 153     PairsearchWork();
 154
 155     ~PairsearchWork();
 156
 157     gmx_cache_protect_t       cp0;          /* Buffer to avoid cache polution */
 158
 159     std::vector<int>          sortBuffer;   /* Temporary buffer for sorting atoms within a grid column */
 160
 161     nbnxn_buffer_flags_t      buffer_flags; /* Flags for force buffer access */
 162
 163     int                       ndistc;       /* Number of distance checks for flop counting */
 164
 165
 166     std::unique_ptr<t_nblist> nbl_fep;      /* Temporary FEP list for load balancing */
 167
 168     nbnxn_cycle_t             cycleCounter; /* Counter for thread-local cycles */
 169
 170     gmx_cache_protect_t       cp1;          /* Buffer to avoid cache polution */
 171 };
 172
 173 /* Main pair-search struct, contains the grid(s), not the pair-list(s) */
 174 class PairSearch
 175 {
 176     public:
 177         //! Puts the atoms in \p ddZone on the grid and copies the coordinates to \p nbat
 178         void putOnGrid(const matrix                    box,
 179                        int                             ddZone,
 180                        const rvec                      lowerCorner,
 181                        const rvec                      upperCorner,
 182                        const gmx::UpdateGroupsCog     *updateGroupsCog,
 183                        int                             atomStart,
 184                        int                             atomEnd,
 185                        real                            atomDensity,
 186                        gmx::ArrayRef<const int>        atomInfo,
 187                        gmx::ArrayRef<const gmx::RVec>  x,
 188                        int                             numAtomsMoved,
 189                        const int                      *move,
 190                        nbnxn_atomdata_t               *nbat)
 191         {
 192             cycleCounting_.start(enbsCCgrid);
 193
 194             gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner,
 195                                updateGroupsCog, atomStart, atomEnd, atomDensity,
 196                                atomInfo, x, numAtomsMoved, move, nbat);
 197
 198             cycleCounting_.stop(enbsCCgrid);
 199         }
 200
 201         /* \brief Constructor
 202          *
 203          * \param[in] ePBC            The periodic boundary conditions
 204          * \param[in] numDDCells      The number of domain decomposition cells per dimension, without DD nullptr should be passed
 205          * \param[in] zones           The domain decomposition zone setup, without DD nullptr should be passed
 206          * \param[in] haveFep         Tells whether non-bonded interactions are perturbed
 207          * \param[in] maxNumThreads   The maximum number of threads used in the search
 208          */
 209         PairSearch(int                       ePBC,
 210                    const ivec               *numDDCells,
 211                    const gmx_domdec_zones_t *zones,
 212                    PairlistType              pairlistType,
 213                    bool                      haveFep,
 214                    int                       maxNumthreads,
 215                    gmx::PinningPolicy        pinningPolicy);
 216
 217         //! Sets the order of the local atoms to the order grid atom ordering
 218         void setLocalAtomOrder()
 219         {
 220             gridSet_.setLocalAtomOrder();
 221         }
 222
 223         //! Returns the set of search grids
 224         const Nbnxm::GridSet &gridSet() const
 225         {
 226             return gridSet_;
 227         }
 228
 229         //! Returns the list of thread-local work objects
 230         gmx::ArrayRef<const PairsearchWork> work() const
 231         {
 232             return work_;
 233         }
 234
 235         //! Returns the list of thread-local work objects
 236         gmx::ArrayRef<PairsearchWork> work()
 237         {
 238             return work_;
 239         }
 240
 241     private:
 242         //! The set of search grids
 243         Nbnxm::GridSet              gridSet_;
 244         //! Work objects, one entry for each thread
 245         std::vector<PairsearchWork> work_;
 246
 247     public:
 248         //! Cycle counting for measuring components of the search
 249         SearchCycleCounting         cycleCounting_;
 250 };
 251
 252 #endif