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38 * \brief Declares the PairSearch class and helper structs
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.
45 * \author Berk Hess <hess@kth.se>
47 * \ingroup module_nbnxm
50 #ifndef GMX_NBNXM_PAIRSEARCH_H
51 #define GMX_NBNXM_PAIRSEARCH_H
56 #include "gromacs/domdec/domdec.h"
57 #include "gromacs/math/vectypes.h"
58 #include "gromacs/timing/cyclecounter.h"
59 #include "gromacs/utility/alignedallocator.h"
60 #include "gromacs/utility/arrayref.h"
61 #include "gromacs/utility/real.h"
67 struct gmx_domdec_zones_t;
68 struct PairsearchWork;
71 /*! \brief Convenience declaration for an std::vector with aligned memory */
73 using AlignedVector = std::vector<T, gmx::AlignedAllocator<T>>;
76 /* Local cycle count struct for profiling */
80 void start() { start_ = gmx_cycles_read(); }
84 cycles_ += gmx_cycles_read() - start_;
88 int count() const { return count_; }
90 double averageMCycles() const
94 return static_cast<double>(cycles_) * 1e-6 / count_;
104 gmx_cycles_t cycles_ = 0;
105 gmx_cycles_t start_ = 0;
108 //! Local cycle count enum for profiling different parts of search
118 * \brief Struct for collecting detailed cycle counts for the search
120 struct SearchCycleCounting
122 //! Start a pair search cycle counter
123 void start(const int enbsCC) { cc_[enbsCC].start(); }
125 //! Stop a pair search cycle counter
126 void stop(const int enbsCC) { cc_[enbsCC].stop(); }
128 //! Print the cycle counts to \p fp
129 void printCycles(FILE* fp, gmx::ArrayRef<const PairsearchWork> work) const;
131 //! Tells whether we record cycles
132 bool recordCycles_ = false;
133 //! The number of times pairsearching has been performed, local+non-local count as 1
134 int searchCount_ = 0;
135 //! The set of cycle counters
136 nbnxn_cycle_t cc_[enbsCCnr];
139 // TODO: Move nbnxn_search_work_t definition to its own file
141 /* Thread-local work struct, contains working data for Grid */
142 struct PairsearchWork
148 gmx_cache_protect_t cp0; /* Buffer to avoid cache polution */
150 std::vector<int> sortBuffer; /* Temporary buffer for sorting atoms within a grid column */
152 nbnxn_buffer_flags_t buffer_flags; /* Flags for force buffer access */
154 int ndistc; /* Number of distance checks for flop counting */
157 std::unique_ptr<t_nblist> nbl_fep; /* Temporary FEP list for load balancing */
159 nbnxn_cycle_t cycleCounter; /* Counter for thread-local cycles */
161 gmx_cache_protect_t cp1; /* Buffer to avoid cache polution */
164 /* Main pair-search struct, contains the grid(s), not the pair-list(s) */
168 //! Puts the atoms in \p ddZone on the grid and copies the coordinates to \p nbat
169 void putOnGrid(const matrix box,
171 const rvec lowerCorner,
172 const rvec upperCorner,
173 const gmx::UpdateGroupsCog* updateGroupsCog,
174 gmx::Range<int> atomRange,
176 gmx::ArrayRef<const int> atomInfo,
177 gmx::ArrayRef<const gmx::RVec> x,
180 nbnxn_atomdata_t* nbat)
182 cycleCounting_.start(enbsCCgrid);
184 gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
185 atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
187 cycleCounting_.stop(enbsCCgrid);
190 /* \brief Constructor
192 * \param[in] ePBC The periodic boundary conditions
193 * \param[in] numDDCells The number of domain decomposition cells per dimension, without DD nullptr should be passed
194 * \param[in] zones The domain decomposition zone setup, without DD nullptr should be passed
195 * \param[in] haveFep Tells whether non-bonded interactions are perturbed
196 * \param[in] maxNumThreads The maximum number of threads used in the search
199 bool doTestParticleInsertion,
200 const ivec* numDDCells,
201 const gmx_domdec_zones_t* zones,
202 PairlistType pairlistType,
205 gmx::PinningPolicy pinningPolicy);
207 //! Sets the order of the local atoms to the order grid atom ordering
208 void setLocalAtomOrder() { gridSet_.setLocalAtomOrder(); }
210 //! Returns the set of search grids
211 const Nbnxm::GridSet& gridSet() const { return gridSet_; }
213 //! Returns the list of thread-local work objects
214 gmx::ArrayRef<const PairsearchWork> work() const { return work_; }
216 //! Returns the list of thread-local work objects
217 gmx::ArrayRef<PairsearchWork> work() { return work_; }
220 //! The set of search grids
221 Nbnxm::GridSet gridSet_;
222 //! Work objects, one entry for each thread
223 std::vector<PairsearchWork> work_;
226 //! Cycle counting for measuring components of the search
227 SearchCycleCounting cycleCounting_;