2 * This file is part of the GROMACS molecular simulation package.
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.
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.
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.
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.
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.
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.
39 * \brief Declares the PairSearch class and helper structs
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.
46 * \author Berk Hess <hess@kth.se>
48 * \ingroup module_nbnxm
51 #ifndef GMX_NBNXM_PAIRSEARCH_H
52 #define GMX_NBNXM_PAIRSEARCH_H
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"
68 struct gmx_domdec_zones_t;
69 struct PairsearchWork;
72 /*! \brief Convenience declaration for an std::vector with aligned memory */
74 using AlignedVector = std::vector<T, gmx::AlignedAllocator<T>>;
77 //! Local cycle count struct for profiling \internal
81 //! Start counting cycles
82 void start() { start_ = gmx_cycles_read(); }
83 //! Stop counting cycles
86 cycles_ += gmx_cycles_read() - start_;
89 //! Return the number of periods of cycle counting
90 int count() const { return count_; }
92 //! Return the average number of million cycles per counting period
93 double averageMCycles() const
97 return static_cast<double>(cycles_) * 1e-6 / count_;
106 //! Number of counting periods
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;
114 //! Local cycle count enum for profiling different parts of search
124 * \brief Struct for collecting detailed cycle counts for the search
126 struct SearchCycleCounting
128 //! Start a pair search cycle counter
129 void start(const int enbsCC) { cc_[enbsCC].start(); }
131 //! Stop a pair search cycle counter
132 void stop(const int enbsCC) { cc_[enbsCC].stop(); }
134 //! Print the cycle counts to \p fp
135 void printCycles(FILE* fp, gmx::ArrayRef<const PairsearchWork> work) const;
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];
145 // TODO: Move nbnxn_search_work_t definition to its own file
147 //! Thread-local work struct, contains working data for Grid \internal
148 struct PairsearchWork
154 //! Buffer to avoid cache polution
155 gmx_cache_protect_t cp0;
157 //! Temporary buffer for sorting atoms within a grid column
158 std::vector<int> sortBuffer;
160 //! Flags for force buffer access
161 std::vector<gmx_bitmask_t> buffer_flags;
163 //! Number of distance checks for flop counting
167 //! Temporary FEP list for load balancing
168 std::unique_ptr<t_nblist> nbl_fep;
170 //! Counter for thread-local cycles
171 nbnxn_cycle_t cycleCounter;
173 //! Buffer to avoid cache polution
174 gmx_cache_protect_t cp1;
177 //! Main pair-search struct, contains the grid(s), not the pair-list(s) \internal
181 //! Puts the atoms in \p ddZone on the grid and copies the coordinates to \p nbat
182 void putOnGrid(const matrix box,
184 const rvec lowerCorner,
185 const rvec upperCorner,
186 const gmx::UpdateGroupsCog* updateGroupsCog,
187 gmx::Range<int> atomRange,
189 gmx::ArrayRef<const int> atomInfo,
190 gmx::ArrayRef<const gmx::RVec> x,
193 nbnxn_atomdata_t* nbat)
195 cycleCounting_.start(enbsCCgrid);
197 gridSet_.putOnGrid(box,
210 cycleCounting_.stop(enbsCCgrid);
213 /*! \brief Constructor
215 * \param[in] pbcType The periodic boundary conditions
216 * \param[in] doTestParticleInsertion Whether test-particle insertion is active
217 * \param[in] numDDCells The number of domain decomposition cells per dimension, without DD nullptr should be passed
218 * \param[in] zones The domain decomposition zone setup, without DD nullptr should be passed
219 * \param[in] pairlistType The type of tte pair list
220 * \param[in] haveFep Tells whether non-bonded interactions are perturbed
221 * \param[in] maxNumThreads The maximum number of threads used in the search
222 * \param[in] pinningPolicy Sets the pinning policy for all buffers used on the GPU
224 PairSearch(PbcType pbcType,
225 bool doTestParticleInsertion,
226 const ivec* numDDCells,
227 const gmx_domdec_zones_t* zones,
228 PairlistType pairlistType,
231 gmx::PinningPolicy pinningPolicy);
233 //! Sets the order of the local atoms to the order grid atom ordering
234 void setLocalAtomOrder() { gridSet_.setLocalAtomOrder(); }
236 //! Returns the set of search grids
237 const Nbnxm::GridSet& gridSet() const { return gridSet_; }
239 //! Returns the list of thread-local work objects
240 gmx::ArrayRef<const PairsearchWork> work() const { return work_; }
242 //! Returns the list of thread-local work objects
243 gmx::ArrayRef<PairsearchWork> work() { return work_; }
246 //! The set of search grids
247 Nbnxm::GridSet gridSet_;
248 //! Work objects, one entry for each thread
249 std::vector<PairsearchWork> work_;
252 //! Cycle counting for measuring components of the search
253 SearchCycleCounting cycleCounting_;