class ForceWithShiftForces;
class MDLogger;
class UpdateGroupsCog;
-}
+} // namespace gmx
namespace Nbnxm
{
struct KernelSetup
{
//! The non-bonded type, also affects the pairlist construction kernel
- KernelType kernelType = KernelType::NotSet;
+ KernelType kernelType = KernelType::NotSet;
//! Ewald exclusion computation handling type, currently only used for CPU
EwaldExclusionType ewaldExclusionType = EwaldExclusionType::NotSet;
};
* \param [in] kernelType nonbonded kernel type, takes values from the nbnxn_kernel_type enum
* \returns a string identifying the kernel corresponding to the type passed as argument
*/
-const char *lookup_kernel_name(Nbnxm::KernelType kernelType);
+const char* lookup_kernel_name(Nbnxm::KernelType kernelType);
} // namespace Nbnxm
/*! \brief Flag to tell the nonbonded kernels whether to clear the force output buffers */
-enum {
- enbvClearFNo, enbvClearFYes
+enum
+{
+ enbvClearFNo,
+ enbvClearFYes
};
/*! \libinternal
* \brief Top-level non-bonded data structure for the Verlet-type cut-off scheme. */
struct nonbonded_verlet_t
{
- public:
- //! Constructs an object from its components
- nonbonded_verlet_t(std::unique_ptr<PairlistSets> pairlistSets,
- std::unique_ptr<PairSearch> pairSearch,
- std::unique_ptr<nbnxn_atomdata_t> nbat,
- const Nbnxm::KernelSetup &kernelSetup,
- gmx_nbnxn_gpu_t *gpu_nbv,
- gmx_wallcycle *wcycle);
-
- ~nonbonded_verlet_t();
-
- //! Returns whether a GPU is use for the non-bonded calculations
- bool useGpu() const
- {
- return kernelSetup_.kernelType == Nbnxm::KernelType::Gpu8x8x8;
- }
-
- //! Returns whether a GPU is emulated for the non-bonded calculations
- bool emulateGpu() const
- {
- return kernelSetup_.kernelType == Nbnxm::KernelType::Cpu8x8x8_PlainC;
- }
-
- //! Return whether the pairlist is of simple, CPU type
- bool pairlistIsSimple() const
- {
- return !useGpu() && !emulateGpu();
- }
-
- //! Initialize the pair list sets, TODO this should be private
- void initPairlistSets(bool haveMultipleDomains);
-
- //! Returns the order of the local atoms on the grid
- gmx::ArrayRef<const int> getLocalAtomOrder() const;
-
- //! Sets the order of the local atoms to the order grid atom ordering
- void setLocalAtomOrder();
-
- //! Returns the index position of the atoms on the search grid
- gmx::ArrayRef<const int> getGridIndices() const;
-
- //! Constructs the pairlist for the given locality
- void constructPairlist(gmx::InteractionLocality iLocality,
- const t_blocka *excl,
- int64_t step,
- t_nrnb *nrnb);
-
- //! Updates all the atom properties in Nbnxm
- void setAtomProperties(const t_mdatoms &mdatoms,
- gmx::ArrayRef<const int> atomInfo);
-
- /*!\brief Convert the coordinates to NBNXM format for the given locality.
- *
- * The API function for the transformation of the coordinates from one layout to another.
- *
- * \param[in] locality Whether coordinates for local or non-local atoms should be transformed.
- * \param[in] fillLocal If the coordinates for filler particles should be zeroed.
- * \param[in] coordinates Coordinates in plain rvec format to be transformed.
- */
- void convertCoordinates(gmx::AtomLocality locality,
- bool fillLocal,
- gmx::ArrayRef<const gmx::RVec> coordinates);
-
- /*!\brief Convert the coordinates to NBNXM format on the GPU for the given locality
- *
- * The API function for the transformation of the coordinates from one layout to another in the GPU memory.
- *
- * \param[in] locality Whether coordinates for local or non-local atoms should be transformed.
- * \param[in] fillLocal If the coordinates for filler particles should be zeroed.
- * \param[in] d_x GPU coordinates buffer in plain rvec format to be transformed.
- * \param[in] xReadyOnDevice Event synchronizer indicating that the coordinates are ready in the device memory.
- */
- void convertCoordinatesGpu(gmx::AtomLocality locality,
- bool fillLocal,
- DeviceBuffer<float> d_x,
- GpuEventSynchronizer *xReadyOnDevice);
-
- //! Init for GPU version of setup coordinates in Nbnxm
- void atomdata_init_copy_x_to_nbat_x_gpu();
-
- //! Sync the nonlocal GPU stream with dependent tasks in the local queue.
- void insertNonlocalGpuDependency(gmx::InteractionLocality interactionLocality);
-
- //! Returns a reference to the pairlist sets
- const PairlistSets &pairlistSets() const
- {
- return *pairlistSets_;
- }
-
- //! Returns whether step is a dynamic list pruning step, for CPU lists
- bool isDynamicPruningStepCpu(int64_t step) const;
-
- //! Returns whether step is a dynamic list pruning step, for GPU lists
- bool isDynamicPruningStepGpu(int64_t step) const;
-
- //! Dispatches the dynamic pruning kernel for the given locality, for CPU lists
- void dispatchPruneKernelCpu(gmx::InteractionLocality iLocality,
- const rvec *shift_vec);
-
- //! Dispatches the dynamic pruning kernel for GPU lists
- void dispatchPruneKernelGpu(int64_t step);
-
- //! \brief Executes the non-bonded kernel of the GPU or launches it on the GPU
- void dispatchNonbondedKernel(gmx::InteractionLocality iLocality,
- const interaction_const_t &ic,
- const gmx::StepWorkload &stepWork,
- int clearF,
- const t_forcerec &fr,
- gmx_enerdata_t *enerd,
- t_nrnb *nrnb);
-
- //! Executes the non-bonded free-energy kernel, always runs on the CPU
- void dispatchFreeEnergyKernel(gmx::InteractionLocality iLocality,
- const t_forcerec *fr,
- rvec x[],
- gmx::ForceWithShiftForces *forceWithShiftForces,
- const t_mdatoms &mdatoms,
- t_lambda *fepvals,
- real *lambda,
- gmx_enerdata_t *enerd,
- const gmx::StepWorkload &stepWork,
- t_nrnb *nrnb);
-
- /*! \brief Add the forces stored in nbat to f, zeros the forces in nbat
- * \param [in] locality Local or non-local
- * \param [inout] force Force to be added to
- */
- void atomdata_add_nbat_f_to_f(gmx::AtomLocality locality,
- gmx::ArrayRef<gmx::RVec> force);
-
- /*! \brief Add the forces stored in nbat to total force using GPU buffer opse
- *
- * \param [in] locality Local or non-local
- * \param [in,out] totalForcesDevice Force to be added to
- * \param [in] forcesPmeDevice Device buffer with PME forces
- * \param[in] dependencyList List of synchronizers that represent the dependencies the reduction task needs to sync on.
- * \param [in] useGpuFPmeReduction Whether PME forces should be added
- * \param [in] accumulateForce If the total force buffer already contains data
- */
- void atomdata_add_nbat_f_to_f_gpu(gmx::AtomLocality locality,
- DeviceBuffer<float> totalForcesDevice,
- void *forcesPmeDevice,
- gmx::ArrayRef<GpuEventSynchronizer* const> dependencyList,
- bool useGpuFPmeReduction,
- bool accumulateForce);
-
- /*! \brief Outer body of function to perform initialization for F buffer operations on GPU.
- *
- * \param localReductionDone Pointer to an event synchronizer that marks the completion of the local f buffer ops kernel.
- */
- void atomdata_init_add_nbat_f_to_f_gpu(GpuEventSynchronizer* localReductionDone);
-
- /*! \brief Wait for non-local copy of coordinate buffer from device to host */
- void wait_nonlocal_x_copy_D2H_done();
-
- /*! \brief return GPU pointer to f in rvec format */
- void* get_gpu_frvec();
-
- /*! \brief Ensure local stream waits for non-local stream */
- void stream_local_wait_for_nonlocal();
-
- //! Return the kernel setup
- const Nbnxm::KernelSetup &kernelSetup() const
- {
- return kernelSetup_;
- }
-
- //! Returns the outer radius for the pair list
- real pairlistInnerRadius() const;
-
- //! Returns the outer radius for the pair list
- real pairlistOuterRadius() const;
-
- //! Changes the pair-list outer and inner radius
- void changePairlistRadii(real rlistOuter,
- real rlistInner);
-
- //! Set up internal flags that indicate what type of short-range work there is.
- void setupGpuShortRangeWork(const gmx::GpuBonded *gpuBonded,
- const gmx::InteractionLocality iLocality)
- {
- if (useGpu() && !emulateGpu())
- {
- Nbnxm::setupGpuShortRangeWork(gpu_nbv, gpuBonded, iLocality);
- }
- }
-
- //! Returns true if there is GPU short-range work for the given atom locality.
- bool haveGpuShortRangeWork(const gmx::AtomLocality aLocality)
+public:
+ //! Constructs an object from its components
+ nonbonded_verlet_t(std::unique_ptr<PairlistSets> pairlistSets,
+ std::unique_ptr<PairSearch> pairSearch,
+ std::unique_ptr<nbnxn_atomdata_t> nbat,
+ const Nbnxm::KernelSetup& kernelSetup,
+ gmx_nbnxn_gpu_t* gpu_nbv,
+ gmx_wallcycle* wcycle);
+
+ ~nonbonded_verlet_t();
+
+ //! Returns whether a GPU is use for the non-bonded calculations
+ bool useGpu() const { return kernelSetup_.kernelType == Nbnxm::KernelType::Gpu8x8x8; }
+
+ //! Returns whether a GPU is emulated for the non-bonded calculations
+ bool emulateGpu() const
+ {
+ return kernelSetup_.kernelType == Nbnxm::KernelType::Cpu8x8x8_PlainC;
+ }
+
+ //! Return whether the pairlist is of simple, CPU type
+ bool pairlistIsSimple() const { return !useGpu() && !emulateGpu(); }
+
+ //! Initialize the pair list sets, TODO this should be private
+ void initPairlistSets(bool haveMultipleDomains);
+
+ //! Returns the order of the local atoms on the grid
+ gmx::ArrayRef<const int> getLocalAtomOrder() const;
+
+ //! Sets the order of the local atoms to the order grid atom ordering
+ void setLocalAtomOrder();
+
+ //! Returns the index position of the atoms on the search grid
+ gmx::ArrayRef<const int> getGridIndices() const;
+
+ //! Constructs the pairlist for the given locality
+ void constructPairlist(gmx::InteractionLocality iLocality, const t_blocka* excl, int64_t step, t_nrnb* nrnb);
+
+ //! Updates all the atom properties in Nbnxm
+ void setAtomProperties(const t_mdatoms& mdatoms, gmx::ArrayRef<const int> atomInfo);
+
+ /*!\brief Convert the coordinates to NBNXM format for the given locality.
+ *
+ * The API function for the transformation of the coordinates from one layout to another.
+ *
+ * \param[in] locality Whether coordinates for local or non-local atoms should be
+ * transformed. \param[in] fillLocal If the coordinates for filler particles should be
+ * zeroed. \param[in] coordinates Coordinates in plain rvec format to be transformed.
+ */
+ void convertCoordinates(gmx::AtomLocality locality, bool fillLocal, gmx::ArrayRef<const gmx::RVec> coordinates);
+
+ /*!\brief Convert the coordinates to NBNXM format on the GPU for the given locality
+ *
+ * The API function for the transformation of the coordinates from one layout to another in the GPU memory.
+ *
+ * \param[in] locality Whether coordinates for local or non-local atoms should be transformed.
+ * \param[in] fillLocal If the coordinates for filler particles should be zeroed.
+ * \param[in] d_x GPU coordinates buffer in plain rvec format to be transformed.
+ * \param[in] xReadyOnDevice Event synchronizer indicating that the coordinates are ready in the device memory.
+ */
+ void convertCoordinatesGpu(gmx::AtomLocality locality,
+ bool fillLocal,
+ DeviceBuffer<float> d_x,
+ GpuEventSynchronizer* xReadyOnDevice);
+
+ //! Init for GPU version of setup coordinates in Nbnxm
+ void atomdata_init_copy_x_to_nbat_x_gpu();
+
+ //! Sync the nonlocal GPU stream with dependent tasks in the local queue.
+ void insertNonlocalGpuDependency(gmx::InteractionLocality interactionLocality);
+
+ //! Returns a reference to the pairlist sets
+ const PairlistSets& pairlistSets() const { return *pairlistSets_; }
+
+ //! Returns whether step is a dynamic list pruning step, for CPU lists
+ bool isDynamicPruningStepCpu(int64_t step) const;
+
+ //! Returns whether step is a dynamic list pruning step, for GPU lists
+ bool isDynamicPruningStepGpu(int64_t step) const;
+
+ //! Dispatches the dynamic pruning kernel for the given locality, for CPU lists
+ void dispatchPruneKernelCpu(gmx::InteractionLocality iLocality, const rvec* shift_vec);
+
+ //! Dispatches the dynamic pruning kernel for GPU lists
+ void dispatchPruneKernelGpu(int64_t step);
+
+ //! \brief Executes the non-bonded kernel of the GPU or launches it on the GPU
+ void dispatchNonbondedKernel(gmx::InteractionLocality iLocality,
+ const interaction_const_t& ic,
+ const gmx::StepWorkload& stepWork,
+ int clearF,
+ const t_forcerec& fr,
+ gmx_enerdata_t* enerd,
+ t_nrnb* nrnb);
+
+ //! Executes the non-bonded free-energy kernel, always runs on the CPU
+ void dispatchFreeEnergyKernel(gmx::InteractionLocality iLocality,
+ const t_forcerec* fr,
+ rvec x[],
+ gmx::ForceWithShiftForces* forceWithShiftForces,
+ const t_mdatoms& mdatoms,
+ t_lambda* fepvals,
+ real* lambda,
+ gmx_enerdata_t* enerd,
+ const gmx::StepWorkload& stepWork,
+ t_nrnb* nrnb);
+
+ /*! \brief Add the forces stored in nbat to f, zeros the forces in nbat
+ * \param [in] locality Local or non-local
+ * \param [inout] force Force to be added to
+ */
+ void atomdata_add_nbat_f_to_f(gmx::AtomLocality locality, gmx::ArrayRef<gmx::RVec> force);
+
+ /*! \brief Add the forces stored in nbat to total force using GPU buffer opse
+ *
+ * \param [in] locality Local or non-local
+ * \param [in,out] totalForcesDevice Force to be added to
+ * \param [in] forcesPmeDevice Device buffer with PME forces
+ * \param[in] dependencyList List of synchronizers that represent the dependencies the reduction task needs to sync on.
+ * \param [in] useGpuFPmeReduction Whether PME forces should be added
+ * \param [in] accumulateForce If the total force buffer already contains data
+ */
+ void atomdata_add_nbat_f_to_f_gpu(gmx::AtomLocality locality,
+ DeviceBuffer<float> totalForcesDevice,
+ void* forcesPmeDevice,
+ gmx::ArrayRef<GpuEventSynchronizer* const> dependencyList,
+ bool useGpuFPmeReduction,
+ bool accumulateForce);
+
+ /*! \brief Outer body of function to perform initialization for F buffer operations on GPU.
+ *
+ * \param localReductionDone Pointer to an event synchronizer that marks the completion of the local f buffer ops kernel.
+ */
+ void atomdata_init_add_nbat_f_to_f_gpu(GpuEventSynchronizer* localReductionDone);
+
+ /*! \brief Wait for non-local copy of coordinate buffer from device to host */
+ void wait_nonlocal_x_copy_D2H_done();
+
+ /*! \brief return GPU pointer to f in rvec format */
+ void* get_gpu_frvec();
+
+ /*! \brief Ensure local stream waits for non-local stream */
+ void stream_local_wait_for_nonlocal();
+
+ //! Return the kernel setup
+ const Nbnxm::KernelSetup& kernelSetup() const { return kernelSetup_; }
+
+ //! Returns the outer radius for the pair list
+ real pairlistInnerRadius() const;
+
+ //! Returns the outer radius for the pair list
+ real pairlistOuterRadius() const;
+
+ //! Changes the pair-list outer and inner radius
+ void changePairlistRadii(real rlistOuter, real rlistInner);
+
+ //! Set up internal flags that indicate what type of short-range work there is.
+ void setupGpuShortRangeWork(const gmx::GpuBonded* gpuBonded, const gmx::InteractionLocality iLocality)
+ {
+ if (useGpu() && !emulateGpu())
{
- return ((useGpu() && !emulateGpu()) &&
- Nbnxm::haveGpuShortRangeWork(gpu_nbv, aLocality));
+ Nbnxm::setupGpuShortRangeWork(gpu_nbv, gpuBonded, iLocality);
}
-
- // TODO: Make all data members private
- public:
- //! All data related to the pair lists
- std::unique_ptr<PairlistSets> pairlistSets_;
- //! Working data for constructing the pairlists
- std::unique_ptr<PairSearch> pairSearch_;
- //! Atom data
- std::unique_ptr<nbnxn_atomdata_t> nbat;
- private:
- //! The non-bonded setup, also affects the pairlist construction kernel
- Nbnxm::KernelSetup kernelSetup_;
- //! \brief Pointer to wallcycle structure.
- gmx_wallcycle *wcycle_;
- public:
- //! GPU Nbnxm data, only used with a physical GPU (TODO: use unique_ptr)
- gmx_nbnxn_gpu_t *gpu_nbv;
+ }
+
+ //! Returns true if there is GPU short-range work for the given atom locality.
+ bool haveGpuShortRangeWork(const gmx::AtomLocality aLocality)
+ {
+ return ((useGpu() && !emulateGpu()) && Nbnxm::haveGpuShortRangeWork(gpu_nbv, aLocality));
+ }
+
+ // TODO: Make all data members private
+public:
+ //! All data related to the pair lists
+ std::unique_ptr<PairlistSets> pairlistSets_;
+ //! Working data for constructing the pairlists
+ std::unique_ptr<PairSearch> pairSearch_;
+ //! Atom data
+ std::unique_ptr<nbnxn_atomdata_t> nbat;
+
+private:
+ //! The non-bonded setup, also affects the pairlist construction kernel
+ Nbnxm::KernelSetup kernelSetup_;
+ //! \brief Pointer to wallcycle structure.
+ gmx_wallcycle* wcycle_;
+
+public:
+ //! GPU Nbnxm data, only used with a physical GPU (TODO: use unique_ptr)
+ gmx_nbnxn_gpu_t* gpu_nbv;
};
namespace Nbnxm
{
/*! \brief Creates an Nbnxm object */
-std::unique_ptr<nonbonded_verlet_t>
-init_nb_verlet(const gmx::MDLogger &mdlog,
- gmx_bool bFEP_NonBonded,
- const t_inputrec *ir,
- const t_forcerec *fr,
- const t_commrec *cr,
- const gmx_hw_info_t &hardwareInfo,
- const gmx_device_info_t *deviceInfo,
- const gmx_mtop_t *mtop,
- matrix box,
- gmx_wallcycle *wcycle);
+std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger& mdlog,
+ gmx_bool bFEP_NonBonded,
+ const t_inputrec* ir,
+ const t_forcerec* fr,
+ const t_commrec* cr,
+ const gmx_hw_info_t& hardwareInfo,
+ const gmx_device_info_t* deviceInfo,
+ const gmx_mtop_t* mtop,
+ matrix box,
+ gmx_wallcycle* wcycle);
} // namespace Nbnxm
* \param[in] numAtomsMoved The number of atoms that will move to another domain, pass 0 without DD
* \param[in] move Move flags for atoms, pass nullptr without DD
*/
-void nbnxn_put_on_grid(nonbonded_verlet_t *nb_verlet,
- const matrix box,
- int gridIndex,
- const rvec lowerCorner,
- const rvec upperCorner,
- const gmx::UpdateGroupsCog *updateGroupsCog,
- gmx::Range<int> atomRange,
- real atomDensity,
- gmx::ArrayRef<const int> atomInfo,
- gmx::ArrayRef<const gmx::RVec> x,
- int numAtomsMoved,
- const int *move);
+void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
+ const matrix box,
+ int gridIndex,
+ const rvec lowerCorner,
+ const rvec upperCorner,
+ const gmx::UpdateGroupsCog* updateGroupsCog,
+ gmx::Range<int> atomRange,
+ real atomDensity,
+ gmx::ArrayRef<const int> atomInfo,
+ gmx::ArrayRef<const gmx::RVec> x,
+ int numAtomsMoved,
+ const int* move);
/*! \brief As nbnxn_put_on_grid, but for the non-local atoms
*
* with domain decomposition. Should be called after calling
* nbnxn_search_put_on_grid for the local atoms / home zone.
*/
-void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t *nb_verlet,
- const struct gmx_domdec_zones_t *zones,
+void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nb_verlet,
+ const struct gmx_domdec_zones_t* zones,
gmx::ArrayRef<const int> atomInfo,
gmx::ArrayRef<const gmx::RVec> x);
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