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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!
84 * \defgroup module_nbnxm Non-bonded pair interactions
85 * \ingroup group_mdrun
87 * Implements non-bonded pair interaction functionality for NxM atom clusters.
89 * This module provides methods to, very efficiently, compute non-bonded
90 * pair interactions on CPUs as well as accelerators. It also provides
91 * a method to construct the NxM atom-cluster pair-list required for
92 * computing these non-bonded iteractions.
95 /*! \libinternal \file
97 * \brief This file contains the public interface of the nbnxm module
98 * that implements the NxM atom cluster non-bonded algorithm to efficiently
99 * compute pair forces.
102 * \author Berk Hess <hess@kth.se>
103 * \author Szilárd Páll <pall.szilard@gmail.com>
106 * \ingroup module_nbnxm
110 #ifndef GMX_NBNXM_NBNXM_H
111 #define GMX_NBNXM_NBNXM_H
115 #include "gromacs/gpu_utils/devicebuffer_datatype.h"
116 #include "gromacs/math/vectypes.h"
117 #include "gromacs/utility/arrayref.h"
118 #include "gromacs/utility/enumerationhelpers.h"
119 #include "gromacs/utility/real.h"
121 #include "locality.h"
123 // TODO: Remove this include and the two nbnxm includes above
124 #include "nbnxm_gpu.h"
126 struct gmx_device_info_t
;
127 struct gmx_domdec_zones_t
;
128 struct gmx_enerdata_t
;
129 struct gmx_hw_info_t
;
131 struct gmx_wallcycle
;
132 struct interaction_const_t
;
133 struct nonbonded_verlet_t
;
144 /*! \brief Switch for whether to use GPU for buffer ops*/
145 enum class BufferOpsUseGpu
151 class GpuEventSynchronizer
;
155 class ForceWithShiftForces
;
157 class UpdateGroupsCog
;
162 enum class KernelType
;
168 /*! \brief Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation */
169 enum class KernelType
: int
180 /*! \brief Ewald exclusion types */
181 enum class EwaldExclusionType
: int
189 /* \brief The non-bonded setup, also affects the pairlist construction kernel */
192 //! The non-bonded type, also affects the pairlist construction kernel
193 KernelType kernelType
= KernelType::NotSet
;
194 //! Ewald exclusion computation handling type, currently only used for CPU
195 EwaldExclusionType ewaldExclusionType
= EwaldExclusionType::NotSet
;
198 /*! \brief Return a string identifying the kernel type.
200 * \param [in] kernelType nonbonded kernel type, takes values from the nbnxn_kernel_type enum
201 * \returns a string identifying the kernel corresponding to the type passed as argument
203 const char *lookup_kernel_name(Nbnxm::KernelType kernelType
);
207 /*! \brief Flag to tell the nonbonded kernels whether to clear the force output buffers */
209 enbvClearFNo
, enbvClearFYes
213 * \brief Top-level non-bonded data structure for the Verlet-type cut-off scheme. */
214 struct nonbonded_verlet_t
217 //! Constructs an object from its components
218 nonbonded_verlet_t(std::unique_ptr
<PairlistSets
> pairlistSets
,
219 std::unique_ptr
<PairSearch
> pairSearch
,
220 std::unique_ptr
<nbnxn_atomdata_t
> nbat
,
221 const Nbnxm::KernelSetup
&kernelSetup
,
222 gmx_nbnxn_gpu_t
*gpu_nbv
,
223 gmx_wallcycle
*wcycle
);
225 ~nonbonded_verlet_t();
227 //! Returns whether a GPU is use for the non-bonded calculations
230 return kernelSetup_
.kernelType
== Nbnxm::KernelType::Gpu8x8x8
;
233 //! Returns whether a GPU is emulated for the non-bonded calculations
234 bool emulateGpu() const
236 return kernelSetup_
.kernelType
== Nbnxm::KernelType::Cpu8x8x8_PlainC
;
239 //! Return whether the pairlist is of simple, CPU type
240 bool pairlistIsSimple() const
242 return !useGpu() && !emulateGpu();
245 //! Initialize the pair list sets, TODO this should be private
246 void initPairlistSets(bool haveMultipleDomains
);
248 //! Returns the order of the local atoms on the grid
249 gmx::ArrayRef
<const int> getLocalAtomOrder() const;
251 //! Sets the order of the local atoms to the order grid atom ordering
252 void setLocalAtomOrder();
254 //! Returns the index position of the atoms on the search grid
255 gmx::ArrayRef
<const int> getGridIndices() const;
257 //! Constructs the pairlist for the given locality
258 void constructPairlist(Nbnxm::InteractionLocality iLocality
,
259 const t_blocka
*excl
,
263 //! Updates all the atom properties in Nbnxm
264 void setAtomProperties(const t_mdatoms
&mdatoms
,
265 gmx::ArrayRef
<const int> atomInfo
);
267 /*!\brief Convert the coordinates to NBNXM format for the given locality.
269 * The API function for the transformation of the coordinates from one layout to another.
271 * \param[in] locality Whether coordinates for local or non-local atoms should be transformed.
272 * \param[in] fillLocal If the coordinates for filler particles should be zeroed.
273 * \param[in] coordinates Coordinates in plain rvec format to be transformed.
275 void convertCoordinates(Nbnxm::AtomLocality locality
,
277 gmx::ArrayRef
<const gmx::RVec
> coordinates
);
279 /*!\brief Convert the coordinates to NBNXM format on the GPU for the given locality
281 * The API function for the transformation of the coordinates from one layout to another in the GPU memory.
283 * \param[in] locality Whether coordinates for local or non-local atoms should be transformed.
284 * \param[in] fillLocal If the coordinates for filler particles should be zeroed.
285 * \param[in] d_x GPU coordinates buffer in plain rvec format to be transformed.
287 void convertCoordinatesGpu(Nbnxm::AtomLocality locality
,
289 DeviceBuffer
<float> d_x
);
291 //! Init for GPU version of setup coordinates in Nbnxm
292 void atomdata_init_copy_x_to_nbat_x_gpu();
294 //! Sync the nonlocal GPU stream with dependent tasks in the local queue.
295 void insertNonlocalGpuDependency(Nbnxm::InteractionLocality interactionLocality
);
297 //! Returns a reference to the pairlist sets
298 const PairlistSets
&pairlistSets() const
300 return *pairlistSets_
;
303 //! Returns whether step is a dynamic list pruning step, for CPU lists
304 bool isDynamicPruningStepCpu(int64_t step
) const;
306 //! Returns whether step is a dynamic list pruning step, for GPU lists
307 bool isDynamicPruningStepGpu(int64_t step
) const;
309 //! Dispatches the dynamic pruning kernel for the given locality, for CPU lists
310 void dispatchPruneKernelCpu(Nbnxm::InteractionLocality iLocality
,
311 const rvec
*shift_vec
);
313 //! Dispatches the dynamic pruning kernel for GPU lists
314 void dispatchPruneKernelGpu(int64_t step
);
316 //! \brief Executes the non-bonded kernel of the GPU or launches it on the GPU
317 void dispatchNonbondedKernel(Nbnxm::InteractionLocality iLocality
,
318 const interaction_const_t
&ic
,
319 const gmx::StepWorkload
&stepWork
,
321 const t_forcerec
&fr
,
322 gmx_enerdata_t
*enerd
,
325 //! Executes the non-bonded free-energy kernel, always runs on the CPU
326 void dispatchFreeEnergyKernel(Nbnxm::InteractionLocality iLocality
,
327 const t_forcerec
*fr
,
329 gmx::ForceWithShiftForces
*forceWithShiftForces
,
330 const t_mdatoms
&mdatoms
,
333 gmx_enerdata_t
*enerd
,
334 const gmx::StepWorkload
&stepWork
,
337 /*! \brief Add the forces stored in nbat to f, zeros the forces in nbat
338 * \param [in] locality Local or non-local
339 * \param [inout] force Force to be added to
341 void atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality locality
,
342 gmx::ArrayRef
<gmx::RVec
> force
);
344 /*! \brief Add the forces stored in nbat to total force using GPU buffer opse
346 * \param [in] locality Local or non-local
347 * \param [in,out] totalForcesDevice Force to be added to
348 * \param [in] forcesPmeDevice Device buffer with PME forces
349 * \param [in] pmeForcesReady Event triggered when PME force calculation has completed
350 * \param [in] useGpuFPmeReduction Whether PME forces should be added
351 * \param [in] accumulateForce If the total force buffer already contains data
353 void atomdata_add_nbat_f_to_f_gpu(Nbnxm::AtomLocality locality
,
354 DeviceBuffer
<float> totalForcesDevice
,
355 void *forcesPmeDevice
,
356 GpuEventSynchronizer
*pmeForcesReady
,
357 bool useGpuFPmeReduction
,
358 bool accumulateForce
);
360 /*! \brief Outer body of function to perform initialization for F buffer operations on GPU. */
361 void atomdata_init_add_nbat_f_to_f_gpu();
363 /*! \brief Wait for GPU force reduction task and D2H transfer of its results to complete
365 * FIXME: need more details: when should be called / after which operation, etc.
367 void wait_for_gpu_force_reduction(Nbnxm::AtomLocality locality
);
369 /*! \brief return pointer to GPU event recorded when coordinates have been copied to device */
370 void* get_x_on_device_event();
372 /*! \brief Wait for non-local copy of coordinate buffer from device to host */
373 void wait_nonlocal_x_copy_D2H_done();
375 /*! \brief return GPU pointer to f in rvec format */
376 void* get_gpu_frvec();
378 /*! \brief Ensure local stream waits for non-local stream */
379 void stream_local_wait_for_nonlocal();
381 //! Return the kernel setup
382 const Nbnxm::KernelSetup
&kernelSetup() const
387 //! Returns the outer radius for the pair list
388 real
pairlistInnerRadius() const;
390 //! Returns the outer radius for the pair list
391 real
pairlistOuterRadius() const;
393 //! Changes the pair-list outer and inner radius
394 void changePairlistRadii(real rlistOuter
,
397 //! Set up internal flags that indicate what type of short-range work there is.
398 void setupGpuShortRangeWork(const gmx::GpuBonded
*gpuBonded
,
399 const Nbnxm::InteractionLocality iLocality
)
401 if (useGpu() && !emulateGpu())
403 Nbnxm::setupGpuShortRangeWork(gpu_nbv
, gpuBonded
, iLocality
);
407 //! Returns true if there is GPU short-range work for the given atom locality.
408 bool haveGpuShortRangeWork(const Nbnxm::AtomLocality aLocality
)
410 return ((useGpu() && !emulateGpu()) &&
411 Nbnxm::haveGpuShortRangeWork(gpu_nbv
, aLocality
));
414 // TODO: Make all data members private
416 //! All data related to the pair lists
417 std::unique_ptr
<PairlistSets
> pairlistSets_
;
418 //! Working data for constructing the pairlists
419 std::unique_ptr
<PairSearch
> pairSearch_
;
421 std::unique_ptr
<nbnxn_atomdata_t
> nbat
;
423 //! The non-bonded setup, also affects the pairlist construction kernel
424 Nbnxm::KernelSetup kernelSetup_
;
425 //! \brief Pointer to wallcycle structure.
426 gmx_wallcycle
*wcycle_
;
428 //! GPU Nbnxm data, only used with a physical GPU (TODO: use unique_ptr)
429 gmx_nbnxn_gpu_t
*gpu_nbv
;
435 /*! \brief Creates an Nbnxm object */
436 std::unique_ptr
<nonbonded_verlet_t
>
437 init_nb_verlet(const gmx::MDLogger
&mdlog
,
438 gmx_bool bFEP_NonBonded
,
439 const t_inputrec
*ir
,
440 const t_forcerec
*fr
,
442 const gmx_hw_info_t
&hardwareInfo
,
443 const gmx_device_info_t
*deviceInfo
,
444 const gmx_mtop_t
*mtop
,
446 gmx_wallcycle
*wcycle
);
450 /*! \brief Put the atoms on the pair search grid.
452 * Only atoms atomStart to atomEnd in x are put on the grid.
453 * The atom_density is used to determine the grid size.
454 * When atomDensity<=0, the density is determined from atomEnd-atomStart and the corners.
455 * With domain decomposition part of the n particles might have migrated,
456 * but have not been removed yet. This count is given by nmoved.
457 * When move[i] < 0 particle i has migrated and will not be put on the grid.
458 * Without domain decomposition move will be NULL.
460 void nbnxn_put_on_grid(nonbonded_verlet_t
*nb_verlet
,
463 const rvec lowerCorner
,
464 const rvec upperCorner
,
465 const gmx::UpdateGroupsCog
*updateGroupsCog
,
469 gmx::ArrayRef
<const int> atomInfo
,
470 gmx::ArrayRef
<const gmx::RVec
> x
,
474 /*! \brief As nbnxn_put_on_grid, but for the non-local atoms
476 * with domain decomposition. Should be called after calling
477 * nbnxn_search_put_on_grid for the local atoms / home zone.
479 void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t
*nb_verlet
,
480 const struct gmx_domdec_zones_t
*zones
,
481 gmx::ArrayRef
<const int> atomInfo
,
482 gmx::ArrayRef
<const gmx::RVec
> x
);
484 #endif // GMX_NBNXN_NBNXM_H