2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2012,2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
36 // FIXME: remove the "__" prefix in front of the group def when we move the
37 // nonbonded code into separate dir.
39 /*! \libinternal \defgroup __module_nbnxm Short-range non-bonded interaction module
40 * \ingroup group_mdrun
42 * \brief Computes forces and energies for short-range pair-interactions
43 * based on the Verlet algorithm. The algorithm uses pair-lists generated
44 * at fixed intervals as well as various flavors of pair interaction kernels
45 * implemented for a wide range of CPU and GPU architectures.
47 * The module includes support for flavors of Coulomb and Lennard-Jones interaction
48 * treatment implemented for a large range of SIMD instruction sets for CPU
49 * architectures as well as in CUDA and OpenCL for GPU architectures.
50 * Additionally there is a reference CPU non-SIMD and a reference CPU
51 * for GPU pair-list setup interaction kernel.
53 * The implementation of the kernels is based on the cluster non-bonded algorithm
54 * which in the code is referred to as the NxM algorithms ("nbnxm_" prefix);
55 * for details of the algorithm see DOI:10.1016/j.cpc.2013.06.003.
57 * Algorithmically, the non-bonded computation has two different modes:
58 * A "classical" mode: generate a list every nstlist steps containing at least
59 * all atom pairs up to a distance of rlistOuter and compute pair interactions
60 * for all pairs that are within the interaction cut-off.
61 * A "dynamic pruning" mode: generate an "outer-list" up to cut-off rlistOuter
62 * every nstlist steps and prune the outer-list using a cut-off of rlistInner
63 * every nstlistPrune steps to obtain a, smaller, "inner-list". This
64 * results in fewer interaction computations and allows for a larger nstlist.
65 * On a GPU, this dynamic pruning is performed in a rolling fashion, pruning
66 * only a sub-part of the list each (second) step. This way it can often
67 * overlap with integration and constraints on the CPU.
68 * Currently a simple heuristic determines which mode will be used.
70 * TODO: add a summary list and brief descriptions of the different submodules:
71 * search, CPU kernels, GPU glue code + kernels.
73 * \author Berk Hess <hess@kth.se>
74 * \author Szilárd Páll <pall.szilard@gmail.com>
75 * \author Mark Abraham <mark.j.abraham@gmail.com>
76 * \author Anca Hamuraru <anca@streamcomputing.eu>
77 * \author Teemu Virolainen <teemu@streamcomputing.eu>
78 * \author Dimitrios Karkoulis <dimitris.karkoulis@gmail.com>
80 * TODO: add more authors!
83 /*! \libinternal \file
85 * \brief This file contains the public interface of the nbnxm module
86 * that implements the NxM atom cluster non-bonded algorithm to efficiently
87 * compute pair forces.
90 * \author Berk Hess <hess@kth.se>
91 * \author Szilárd Páll <pall.szilard@gmail.com>
94 * \ingroup __module_nbnxm
98 #ifndef GMX_NBNXM_NBNXM_H
99 #define GMX_NBNXM_NBNXM_H
103 #include "gromacs/math/vectypes.h"
104 #include "gromacs/utility/arrayref.h"
105 #include "gromacs/utility/enumerationhelpers.h"
106 #include "gromacs/utility/real.h"
108 #include "locality.h"
110 // TODO: Remove this include and the two nbnxm includes above
111 #include "nbnxm_gpu.h"
113 struct gmx_device_info_t;
114 struct gmx_domdec_zones_t;
115 struct gmx_enerdata_t;
116 struct gmx_hw_info_t;
118 struct gmx_wallcycle;
119 struct interaction_const_t;
120 struct nonbonded_verlet_t;
134 class UpdateGroupsCog;
139 enum class KernelType;
145 /*! \brief Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation */
146 enum class KernelType : int
157 /*! \brief Ewald exclusion types */
158 enum class EwaldExclusionType : int
166 /* \brief The non-bonded setup, also affects the pairlist construction kernel */
169 //! The non-bonded type, also affects the pairlist construction kernel
170 KernelType kernelType = KernelType::NotSet;
171 //! Ewald exclusion computation handling type, currently only used for CPU
172 EwaldExclusionType ewaldExclusionType = EwaldExclusionType::NotSet;
175 /*! \brief Return a string identifying the kernel type.
177 * \param [in] kernelType nonbonded kernel type, takes values from the nbnxn_kernel_type enum
178 * \returns a string identifying the kernel corresponding to the type passed as argument
180 const char *lookup_kernel_name(Nbnxm::KernelType kernelType);
184 /*! \brief Flag to tell the nonbonded kernels whether to clear the force output buffers */
186 enbvClearFNo, enbvClearFYes
190 * \brief Top-level non-bonded data structure for the Verlet-type cut-off scheme. */
191 struct nonbonded_verlet_t
194 //! Constructs an object from its components
195 nonbonded_verlet_t(std::unique_ptr<PairlistSets> pairlistSets,
196 std::unique_ptr<PairSearch> pairSearch,
197 std::unique_ptr<nbnxn_atomdata_t> nbat,
198 const Nbnxm::KernelSetup &kernelSetup,
199 gmx_nbnxn_gpu_t *gpu_nbv);
201 ~nonbonded_verlet_t();
203 //! Returns whether a GPU is use for the non-bonded calculations
206 return kernelSetup_.kernelType == Nbnxm::KernelType::Gpu8x8x8;
209 //! Returns whether a GPU is emulated for the non-bonded calculations
210 bool emulateGpu() const
212 return kernelSetup_.kernelType == Nbnxm::KernelType::Cpu8x8x8_PlainC;
215 //! Return whether the pairlist is of simple, CPU type
216 bool pairlistIsSimple() const
218 return !useGpu() && !emulateGpu();
221 //! Initialize the pair list sets, TODO this should be private
222 void initPairlistSets(bool haveMultipleDomains);
224 //! Returns the order of the local atoms on the grid
225 gmx::ArrayRef<const int> getLocalAtomOrder() const;
227 //! Sets the order of the local atoms to the order grid atom ordering
228 void setLocalAtomOrder();
230 //! Returns the index position of the atoms on the search grid
231 gmx::ArrayRef<const int> getGridIndices() const;
233 //! Constructs the pairlist for the given locality
234 void constructPairlist(Nbnxm::InteractionLocality iLocality,
235 const t_blocka *excl,
239 //! Updates all the atom properties in Nbnxm
240 void setAtomProperties(const t_mdatoms &mdatoms,
241 gmx::ArrayRef<const int> atomInfo);
243 //! Updates the coordinates in Nbnxm for the given locality
244 void setCoordinates(Nbnxm::AtomLocality locality,
246 gmx::ArrayRef<const gmx::RVec> x,
249 gmx_wallcycle *wcycle);
251 //! Init for GPU version of setup coordinates in Nbnxm, for the given locality
252 void atomdata_init_copy_x_to_nbat_x_gpu(Nbnxm::AtomLocality locality);
255 //! Returns a reference to the pairlist sets
256 const PairlistSets &pairlistSets() const
258 return *pairlistSets_;
261 //! Returns whether step is a dynamic list pruning step, for CPU lists
262 bool isDynamicPruningStepCpu(int64_t step) const;
264 //! Returns whether step is a dynamic list pruning step, for GPU lists
265 bool isDynamicPruningStepGpu(int64_t step) const;
267 //! Dispatches the dynamic pruning kernel for the given locality, for CPU lists
268 void dispatchPruneKernelCpu(Nbnxm::InteractionLocality iLocality,
269 const rvec *shift_vec);
271 //! Dispatches the dynamic pruning kernel for GPU lists
272 void dispatchPruneKernelGpu(int64_t step);
274 //! \brief Executes the non-bonded kernel of the GPU or launches it on the GPU
275 void dispatchNonbondedKernel(Nbnxm::InteractionLocality iLocality,
276 const interaction_const_t &ic,
279 const t_forcerec &fr,
280 gmx_enerdata_t *enerd,
283 //! Executes the non-bonded free-energy kernel, always runs on the CPU
284 void dispatchFreeEnergyKernel(Nbnxm::InteractionLocality iLocality,
288 const t_mdatoms &mdatoms,
291 gmx_enerdata_t *enerd,
295 //! Add the forces stored in nbat to f, zeros the forces in nbat */
296 void atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality locality,
298 gmx_wallcycle *wcycle);
300 //! Return the kernel setup
301 const Nbnxm::KernelSetup &kernelSetup() const
306 //! Returns the outer radius for the pair list
307 real pairlistInnerRadius() const;
309 //! Returns the outer radius for the pair list
310 real pairlistOuterRadius() const;
312 //! Changes the pair-list outer and inner radius
313 void changePairlistRadii(real rlistOuter,
316 // TODO: Make all data members private
318 //! All data related to the pair lists
319 std::unique_ptr<PairlistSets> pairlistSets_;
320 //! Working data for constructing the pairlists
321 std::unique_ptr<PairSearch> pairSearch_;
323 std::unique_ptr<nbnxn_atomdata_t> nbat;
325 //! The non-bonded setup, also affects the pairlist construction kernel
326 Nbnxm::KernelSetup kernelSetup_;
328 //! GPU Nbnxm data, only used with a physical GPU (TODO: use unique_ptr)
329 gmx_nbnxn_gpu_t *gpu_nbv;
335 /*! \brief Creates an Nbnxm object */
336 std::unique_ptr<nonbonded_verlet_t>
337 init_nb_verlet(const gmx::MDLogger &mdlog,
338 gmx_bool bFEP_NonBonded,
339 const t_inputrec *ir,
340 const t_forcerec *fr,
342 const gmx_hw_info_t &hardwareInfo,
343 const gmx_device_info_t *deviceInfo,
344 const gmx_mtop_t *mtop,
349 /*! \brief Put the atoms on the pair search grid.
351 * Only atoms atomStart to atomEnd in x are put on the grid.
352 * The atom_density is used to determine the grid size.
353 * When atomDensity<=0, the density is determined from atomEnd-atomStart and the corners.
354 * With domain decomposition part of the n particles might have migrated,
355 * but have not been removed yet. This count is given by nmoved.
356 * When move[i] < 0 particle i has migrated and will not be put on the grid.
357 * Without domain decomposition move will be NULL.
359 void nbnxn_put_on_grid(nonbonded_verlet_t *nb_verlet,
362 const rvec lowerCorner,
363 const rvec upperCorner,
364 const gmx::UpdateGroupsCog *updateGroupsCog,
368 gmx::ArrayRef<const int> atomInfo,
369 gmx::ArrayRef<const gmx::RVec> x,
373 /*! \brief As nbnxn_put_on_grid, but for the non-local atoms
375 * with domain decomposition. Should be called after calling
376 * nbnxn_search_put_on_grid for the local atoms / home zone.
378 void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t *nb_verlet,
379 const struct gmx_domdec_zones_t *zones,
380 gmx::ArrayRef<const int> atomInfo,
381 gmx::ArrayRef<const gmx::RVec> x);
383 #endif // GMX_NBNXN_NBNXM_H