src/gromacs/nbnxm/pairsearch.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
   5  * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
   6  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   7  * and including many others, as listed in the AUTHORS file in the
   8  * top-level source directory and at http://www.gromacs.org.
   9  *
  10  * GROMACS is free software; you can redistribute it and/or
  11  * modify it under the terms of the GNU Lesser General Public License
  12  * as published by the Free Software Foundation; either version 2.1
  13  * of the License, or (at your option) any later version.
  14  *
  15  * GROMACS is distributed in the hope that it will be useful,
  16  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  17  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  18  * Lesser General Public License for more details.
  19  *
  20  * You should have received a copy of the GNU Lesser General Public
  21  * License along with GROMACS; if not, see
  22  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  23  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  24  *
  25  * If you want to redistribute modifications to GROMACS, please
  26  * consider that scientific software is very special. Version
  27  * control is crucial - bugs must be traceable. We will be happy to
  28  * consider code for inclusion in the official distribution, but
  29  * derived work must not be called official GROMACS. Details are found
  30  * in the README & COPYING files - if they are missing, get the
  31  * official version at http://www.gromacs.org.
  32  *
  33  * To help us fund GROMACS development, we humbly ask that you cite
  34  * the research papers on the package. Check out http://www.gromacs.org.
  35  */
  36
  37 /*! \internal \file
  38  *
  39  * \brief Declares the PairSearch class and helper structs
  40  *
  41  * The PairSearch class holds the domain setup, the search grids
  42  * and helper object for the pair search. It manages the search work.
  43  * The actual gridding and pairlist generation is performeed by the
  44  * GridSet/Grid and PairlistSet/Pairlist classes, respectively.
  45  *
  46  * \author Berk Hess <hess@kth.se>
  47  *
  48  * \ingroup module_nbnxm
  49  */
  50
  51 #ifndef GMX_NBNXM_PAIRSEARCH_H
  52 #define GMX_NBNXM_PAIRSEARCH_H
  53
  54 #include <memory>
  55 #include <vector>
  56
  57 #include "gromacs/domdec/domdec.h"
  58 #include "gromacs/math/vectypes.h"
  59 #include "gromacs/nbnxm/atomdata.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 #include "pairlist.h"
  67
  68 struct gmx_domdec_zones_t;
  69 struct PairsearchWork;
  70
  71
  72 /*! \brief Convenience declaration for an std::vector with aligned memory */
  73 template<class T>
  74 using AlignedVector = std::vector<T, gmx::AlignedAllocator<T>>;
  75
  76
  77 //! Local cycle count struct for profiling \internal
  78 class nbnxn_cycle_t
  79 {
  80 public:
  81     //! Start counting cycles
  82     void start() { start_ = gmx_cycles_read(); }
  83     //! Stop counting cycles
  84     void stop()
  85     {
  86         cycles_ += gmx_cycles_read() - start_;
  87         count_++;
  88     }
  89     //! Return the number of periods of cycle counting
  90     int count() const { return count_; }
  91
  92     //! Return the average number of million cycles per counting period
  93     double averageMCycles() const
  94     {
  95         if (count_ > 0)
  96         {
  97             return static_cast<double>(cycles_) * 1e-6 / count_;
  98         }
  99         else
 100         {
 101             return 0;
 102         }
 103     }
 104
 105 private:
 106     //! Number of counting periods
 107     int count_ = 0;
 108     //! Total cycles in all counting periods
 109     gmx_cycles_t cycles_ = 0;
 110     //! Cycle count at the most recent start
 111     gmx_cycles_t start_ = 0;
 112 };
 113
 114 //! Local cycle count enum for profiling different parts of search
 115 enum
 116 {
 117     enbsCCgrid,
 118     enbsCCsearch,
 119     enbsCCcombine,
 120     enbsCCnr
 121 };
 122
 123 /*! \internal
 124  * \brief Struct for collecting detailed cycle counts for the search
 125  */
 126 struct SearchCycleCounting
 127 {
 128     //! Start a pair search cycle counter
 129     void start(const int enbsCC) { cc_[enbsCC].start(); }
 130
 131     //! Stop a pair search cycle counter
 132     void stop(const int enbsCC) { cc_[enbsCC].stop(); }
 133
 134     //! Print the cycle counts to \p fp
 135     void printCycles(FILE* fp, gmx::ArrayRef<const PairsearchWork> work) const;
 136
 137     //! Tells whether we record cycles
 138     bool recordCycles_ = false;
 139     //! The number of times pairsearching has been performed, local+non-local count as 1
 140     int searchCount_ = 0;
 141     //! The set of cycle counters
 142     nbnxn_cycle_t cc_[enbsCCnr];
 143 };
 144
 145 // TODO: Move nbnxn_search_work_t definition to its own file
 146
 147 //! Thread-local work struct, contains working data for Grid \internal
 148 struct PairsearchWork
 149 {
 150     PairsearchWork();
 151
 152     ~PairsearchWork();
 153
 154     //! Buffer to avoid cache polution
 155     gmx_cache_protect_t cp0;
 156
 157     //! Temporary buffer for sorting atoms within a grid column
 158     std::vector<int> sortBuffer;
 159
 160     //! Flags for force buffer access
 161     std::vector<gmx_bitmask_t> buffer_flags;
 162
 163     //! Number of distance checks for flop counting
 164     int ndistc;
 165
 166
 167     //! Temporary FEP list for load balancing
 168     std::unique_ptr<t_nblist> nbl_fep;
 169
 170     //! Counter for thread-local cycles
 171     nbnxn_cycle_t cycleCounter;
 172
 173     //! Buffer to avoid cache polution
 174     gmx_cache_protect_t cp1;
 175 };
 176
 177 //! Main pair-search struct, contains the grid(s), not the pair-list(s) \internal
 178 class PairSearch
 179 {
 180 public:
 181     //! Puts the atoms in \p ddZone on the grid and copies the coordinates to \p nbat
 182     void putOnGrid(const matrix                   box,
 183                    int                            ddZone,
 184                    const rvec                     lowerCorner,
 185                    const rvec                     upperCorner,
 186                    const gmx::UpdateGroupsCog*    updateGroupsCog,
 187                    gmx::Range<int>                atomRange,
 188                    real                           atomDensity,
 189                    gmx::ArrayRef<const int>       atomInfo,
 190                    gmx::ArrayRef<const gmx::RVec> x,
 191                    int                            numAtomsMoved,
 192                    const int*                     move,
 193                    nbnxn_atomdata_t*              nbat)
 194     {
 195         cycleCounting_.start(enbsCCgrid);
 196
 197         gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
 198                            atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
 199
 200         cycleCounting_.stop(enbsCCgrid);
 201     }
 202
 203     /*! \brief Constructor
 204      *
 205      * \param[in] pbcType                  The periodic boundary conditions
 206      * \param[in] doTestParticleInsertion  Whether test-particle insertion is active
 207      * \param[in] numDDCells               The number of domain decomposition cells per dimension, without DD nullptr should be passed
 208      * \param[in] zones                    The domain decomposition zone setup, without DD nullptr should be passed
 209      * \param[in] pairlistType             The type of tte pair list
 210      * \param[in] haveFep                  Tells whether non-bonded interactions are perturbed
 211      * \param[in] maxNumThreads            The maximum number of threads used in the search
 212      * \param[in] pinningPolicy            Sets the pinning policy for all buffers used on the GPU
 213      */
 214     PairSearch(PbcType                   pbcType,
 215                bool                      doTestParticleInsertion,
 216                const ivec*               numDDCells,
 217                const gmx_domdec_zones_t* zones,
 218                PairlistType              pairlistType,
 219                bool                      haveFep,
 220                int                       maxNumThreads,
 221                gmx::PinningPolicy        pinningPolicy);
 222
 223     //! Sets the order of the local atoms to the order grid atom ordering
 224     void setLocalAtomOrder() { gridSet_.setLocalAtomOrder(); }
 225
 226     //! Returns the set of search grids
 227     const Nbnxm::GridSet& gridSet() const { return gridSet_; }
 228
 229     //! Returns the list of thread-local work objects
 230     gmx::ArrayRef<const PairsearchWork> work() const { return work_; }
 231
 232     //! Returns the list of thread-local work objects
 233     gmx::ArrayRef<PairsearchWork> work() { return work_; }
 234
 235 private:
 236     //! The set of search grids
 237     Nbnxm::GridSet gridSet_;
 238     //! Work objects, one entry for each thread
 239     std::vector<PairsearchWork> work_;
 240
 241 public:
 242     //! Cycle counting for measuring components of the search
 243     SearchCycleCounting cycleCounting_;
 244 };
 245
 246 #endif