* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/real.h"
struct DeviceInformation;
+class FreeEnergyDispatch;
struct gmx_domdec_zones_t;
struct gmx_enerdata_t;
struct gmx_hw_info_t;
struct NbnxmGpu;
struct gmx_wallcycle;
struct interaction_const_t;
+enum class LJCombinationRule;
struct nbnxn_atomdata_t;
struct nonbonded_verlet_t;
class PairSearch;
class PairlistSets;
struct t_commrec;
struct t_lambda;
-struct t_mdatoms;
struct t_nrnb;
struct t_forcerec;
struct t_inputrec;
+struct gmx_grppairener_t;
class GpuEventSynchronizer;
namespace gmx
{
+template<typename>
+class ArrayRefWithPadding;
class DeviceStreamManager;
class ForceWithShiftForces;
-class GpuBonded;
+class ListedForcesGpu;
template<typename>
class ListOfLists;
class MDLogger;
class UpdateGroupsCog;
} // namespace gmx
+//! Namespace for non-bonded kernels
namespace Nbnxm
{
enum class KernelType;
-}
-namespace Nbnxm
+/*! \brief Nbnxm electrostatic GPU kernel flavors.
+ *
+ * Types of electrostatics implementations available in the GPU non-bonded
+ * force kernels. These represent both the electrostatics types implemented
+ * by the kernels (cut-off, RF, and Ewald - a subset of what's defined in
+ * enums.h) as well as encode implementation details analytical/tabulated
+ * and single or twin cut-off (for Ewald kernels).
+ * Note that the cut-off and RF kernels have only analytical flavor and unlike
+ * in the CPU kernels, the tabulated kernels are ATM Ewald-only.
+ *
+ * The row-order of pointers to different electrostatic kernels defined in
+ * nbnxn_cuda.cu by the nb_*_kfunc_ptr function pointer table
+ * should match the order of enumerated types below.
+ */
+enum class ElecType : int
{
+ Cut, //!< Plain cut-off
+ RF, //!< Reaction field
+ EwaldTab, //!< Tabulated Ewald with single cut-off
+ EwaldTabTwin, //!< Tabulated Ewald with twin cut-off
+ EwaldAna, //!< Analytical Ewald with single cut-off
+ EwaldAnaTwin, //!< Analytical Ewald with twin cut-off
+ Count //!< Number of valid values
+};
+
+//! Number of possible \ref ElecType values.
+constexpr int c_numElecTypes = static_cast<int>(ElecType::Count);
+
+/*! \brief Nbnxm VdW GPU kernel flavors.
+ *
+ * The enumerates values correspond to the LJ implementations in the GPU non-bonded
+ * kernels.
+ *
+ * The column-order of pointers to different electrostatic kernels defined in
+ * nbnxn_cuda_ocl.cpp/.cu by the nb_*_kfunc_ptr function pointer table
+ * should match the order of enumerated types below.
+ */
+enum class VdwType : int
+{
+ Cut, //!< Plain cut-off
+ CutCombGeom, //!< Cut-off with geometric combination rules
+ CutCombLB, //!< Cut-off with Lorentz-Berthelot combination rules
+ FSwitch, //!< Smooth force switch
+ PSwitch, //!< Smooth potential switch
+ EwaldGeom, //!< Ewald with geometric combination rules
+ EwaldLB, //!< Ewald with Lorentz-Berthelot combination rules
+ Count //!< Number of valid values
+};
+
+//! Number of possible \ref VdwType values.
+constexpr int c_numVdwTypes = static_cast<int>(VdwType::Count);
/*! \brief Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation */
enum class KernelType : int
//! 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();
+ void setLocalAtomOrder() const;
//! Returns the index position of the atoms on the search grid
gmx::ArrayRef<const int> getGridIndices() const;
void constructPairlist(gmx::InteractionLocality iLocality,
const gmx::ListOfLists<int>& exclusions,
int64_t step,
- t_nrnb* nrnb);
+ t_nrnb* nrnb) const;
//! Updates all the atom properties in Nbnxm
- void setAtomProperties(gmx::ArrayRef<const int> atomTypes,
- gmx::ArrayRef<const real> atomCharges,
- gmx::ArrayRef<const int> atomInfo);
+ void setAtomProperties(gmx::ArrayRef<const int> atomTypes,
+ gmx::ArrayRef<const real> atomCharges,
+ gmx::ArrayRef<const int64_t> atomInfo) const;
/*!\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.
+ * transformed.
+ * \param[in] coordinates Coordinates in plain rvec format to be transformed.
*/
- void convertCoordinates(gmx::AtomLocality locality, bool fillLocal, gmx::ArrayRef<const gmx::RVec> coordinates);
+ void convertCoordinates(gmx::AtomLocality locality, 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<gmx::RVec> 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);
+ void atomdata_init_copy_x_to_nbat_x_gpu() const;
//! Returns a reference to the pairlist sets
const PairlistSets& pairlistSets() const { return *pairlistSets_; }
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);
+ void dispatchPruneKernelCpu(gmx::InteractionLocality iLocality,
+ gmx::ArrayRef<const gmx::RVec> shift_vec) const;
//! 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);
+ void dispatchNonbondedKernel(gmx::InteractionLocality iLocality,
+ const interaction_const_t& ic,
+ const gmx::StepWorkload& stepWork,
+ int clearF,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ gmx::ArrayRef<real> repulsionDispersionSR,
+ gmx::ArrayRef<real> CoulombSR,
+ t_nrnb* nrnb) const;
+
+ //! Executes the non-bonded free-energy kernels, local + non-local, always runs on the CPU
+ void dispatchFreeEnergyKernels(const gmx::ArrayRefWithPadding<const gmx::RVec>& coords,
+ gmx::ForceWithShiftForces* forceWithShiftForces,
+ bool useSimd,
+ int ntype,
+ real rlist,
+ const interaction_const_t& ic,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ gmx::ArrayRef<const real> nbfp,
+ gmx::ArrayRef<const real> nbfp_grid,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ gmx::ArrayRef<const int> typeA,
+ gmx::ArrayRef<const int> typeB,
+ t_lambda* fepvals,
+ gmx::ArrayRef<const 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
*/
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<gmx::RVec> 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.
+ /*! \brief Get the number of atoms for a given locality
*
- * \param localReductionDone Pointer to an event synchronizer that marks the completion of the local f buffer ops kernel.
+ * \param [in] locality Local or non-local
+ * \returns The number of atoms for given locality
*/
- void atomdata_init_add_nbat_f_to_f_gpu(GpuEventSynchronizer* localReductionDone);
-
- /*! \brief return GPU pointer to f in rvec format */
- void* get_gpu_frvec();
+ int getNumAtoms(gmx::AtomLocality locality) const;
//! Return the kernel setup
const Nbnxm::KernelSetup& kernelSetup() const { return kernelSetup_; }
real pairlistOuterRadius() const;
//! Changes the pair-list outer and inner radius
- void changePairlistRadii(real rlistOuter, real rlistInner);
+ void changePairlistRadii(real rlistOuter, real rlistInner) const;
//! Set up internal flags that indicate what type of short-range work there is.
- void setupGpuShortRangeWork(const gmx::GpuBonded* gpuBonded, gmx::InteractionLocality iLocality);
+ void setupGpuShortRangeWork(const gmx::ListedForcesGpu* listedForcesGpu,
+ gmx::InteractionLocality iLocality) const;
+
+ void setupFepThreadedForceBuffer(int numAtomsForce);
// 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
private:
//! The non-bonded setup, also affects the pairlist construction kernel
Nbnxm::KernelSetup kernelSetup_;
+
//! \brief Pointer to wallcycle structure.
gmx_wallcycle* wcycle_;
+ //! \brief The non-bonded free-energy kernel dispatcher
+ std::unique_ptr<FreeEnergyDispatch> freeEnergyDispatch_;
+
public:
//! GPU Nbnxm data, only used with a physical GPU (TODO: use unique_ptr)
NbnxmGpu* gpu_nbv;
/*! \brief Creates an Nbnxm object */
std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger& mdlog,
- const t_inputrec* ir,
- const t_forcerec* fr,
- const t_commrec* cr,
+ const t_inputrec& inputrec,
+ const t_forcerec& forcerec,
+ const t_commrec* commrec,
const gmx_hw_info_t& hardwareInfo,
bool useGpuForNonbonded,
const gmx::DeviceStreamManager* deviceStreamManager,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
matrix box,
gmx_wallcycle* wcycle);
const gmx::UpdateGroupsCog* updateGroupsCog,
gmx::Range<int> atomRange,
real atomDensity,
- gmx::ArrayRef<const int> atomInfo,
+ gmx::ArrayRef<const int64_t> atomInfo,
gmx::ArrayRef<const gmx::RVec> x,
int numAtomsMoved,
const int* move);
*/
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 int64_t> atomInfo,
gmx::ArrayRef<const gmx::RVec> x);
+/*! \brief Check if GROMACS has been built with GPU support.
+ *
+ * \param[in] error Pointer to error string or nullptr.
+ * \todo Move this to NB module once it exists.
+ */
+bool buildSupportsNonbondedOnGpu(std::string* error);
+
#endif // GMX_NBNXN_NBNXM_H
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff