#include <memory>
#include "gromacs/math/vectypes.h"
-#include "gromacs/nbnxm/pairlist.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
struct gmx_enerdata_t;
struct gmx_hw_info_t;
struct gmx_mtop_t;
+struct gmx_wallcycle;
struct interaction_const_t;
struct nbnxn_pairlist_set_t;
struct nbnxn_search;
struct nonbonded_verlet_t;
+enum class PairlistType;
struct t_blocka;
struct t_commrec;
struct t_lambda;
class UpdateGroupsCog;
}
+namespace Nbnxm
+{
+enum class KernelType;
+}
+
+/*! \libinternal
+ * \brief The setup for generating and pruning the nbnxn pair list.
+ *
+ * Without dynamic pruning rlistOuter=rlistInner.
+ */
+struct NbnxnListParameters
+{
+ /*! \brief Constructor producing a struct with dynamic pruning disabled
+ */
+ NbnxnListParameters(Nbnxm::KernelType kernelType,
+ real rlist);
+
+ PairlistType pairlistType; //!< The type of cluster-pair list
+ bool useDynamicPruning; //!< Are we using dynamic pair-list pruning
+ int nstlistPrune; //!< Pair-list dynamic pruning interval
+ real rlistOuter; //!< Cut-off of the larger, outer pair-list
+ real rlistInner; //!< Cut-off of the smaller, inner pair-list
+ int numRollingParts; //!< The number parts to divide the pair-list into for rolling pruning, a value of 1 gives no rolling pruning
+};
+
/*! \brief Resources that can be used to execute non-bonded kernels on */
enum class NonbondedResource : int
{
struct nonbonded_verlet_t
{
public:
+ class PairlistSets
+ {
+ public:
+ PairlistSets(const NbnxnListParameters &listParams,
+ bool haveMultipleDomains,
+ int minimumIlistCountForGpuBalancing);
+
+ //! Construct the pairlist set for the given locality
+ void construct(Nbnxm::InteractionLocality iLocality,
+ nbnxn_search *nbs,
+ nbnxn_atomdata_t *nbat,
+ const t_blocka *excl,
+ Nbnxm::KernelType kernelbType,
+ int64_t step,
+ t_nrnb *nrnb);
+
+ //! Dispatches the dynamic pruning kernel for the given locality
+ void dispatchPruneKernel(Nbnxm::InteractionLocality iLocality,
+ const nbnxn_atomdata_t *nbat,
+ const rvec *shift_vec,
+ Nbnxm::KernelType kernelbType);
+
+ //! Returns the pair list parameters
+ const NbnxnListParameters ¶ms() const
+ {
+ return params_;
+ }
+
+ //! Returns the number of steps performed with the current pair list
+ int numStepsWithPairlist(int64_t step) const
+ {
+ return step - outerListCreationStep_;
+ }
+
+ //! Returns whether step is a dynamic list pruning step, for CPU lists only
+ bool isDynamicPairlistPruningStep(int64_t step) const
+ {
+ return (params_.useDynamicPruning &&
+ numStepsWithPairlist(step) % params_.nstlistPrune == 0);
+ }
+
+ //! Changes the pair-list outer and inner radius
+ void changeRadii(real rlistOuter,
+ real rlistInner)
+ {
+ params_.rlistOuter = rlistOuter;
+ params_.rlistInner = rlistInner;
+ }
+
+ //! Returns the pair-list set for the given locality
+ const nbnxn_pairlist_set_t &pairlistSet(Nbnxm::InteractionLocality iLocality) const
+ {
+ if (iLocality == Nbnxm::InteractionLocality::Local)
+ {
+ return *localSet_;
+ }
+ else
+ {
+ GMX_ASSERT(nonlocalSet_, "Need a non-local set when requesting access");
+ return *nonlocalSet_;
+ }
+ }
+
+ private:
+ //! Returns the pair-list set for the given locality
+ nbnxn_pairlist_set_t &pairlistSet(Nbnxm::InteractionLocality iLocality)
+ {
+ if (iLocality == Nbnxm::InteractionLocality::Local)
+ {
+ return *localSet_;
+ }
+ else
+ {
+ GMX_ASSERT(nonlocalSet_, "Need a non-local set when requesting access");
+ return *nonlocalSet_;
+ }
+ }
+
+ //! Parameters for the search and list pruning setup
+ NbnxnListParameters params_;
+ //! Pair list balancing parameter for use with GPU
+ int minimumIlistCountForGpuBalancing_;
+ //! Local pairlist set
+ std::unique_ptr<nbnxn_pairlist_set_t> localSet_;
+ //! Non-local pairlist set
+ std::unique_ptr<nbnxn_pairlist_set_t> nonlocalSet_;
+ //! MD step at with the outer lists in pairlistSets_ were created
+ int64_t outerListCreationStep_;
+ };
+
//! Returns whether a GPU is use for the non-bonded calculations
bool useGpu() const
{
//! Initialize the pair list sets, TODO this should be private
void initPairlistSets(bool haveMultipleDomains);
- //! Returns a reference to the pairlist set for the requested locality
- const nbnxn_pairlist_set_t &pairlistSet(Nbnxm::InteractionLocality iLocality) const
- {
- GMX_ASSERT(static_cast<size_t>(iLocality) < pairlistSets_.size(),
- "The requested locality should be in the list");
- return pairlistSets_[static_cast<int>(iLocality)];
- }
-
//! Constructs the pairlist for the given locality
void constructPairlist(Nbnxm::InteractionLocality iLocality,
const t_blocka *excl,
int64_t step,
- t_nrnb *nrnb)
+ t_nrnb *nrnb);
+
+ //! Returns a reference to the pairlist sets
+ const PairlistSets &pairlistSets() const
{
- nbnxn_make_pairlist(this, iLocality, &pairlistSets_[static_cast<int>(iLocality)], excl, step, nrnb);
+ return *pairlistSets_;
}
//! Dispatches the dynamic pruning kernel for the given locality
void dispatchPruneKernel(Nbnxm::InteractionLocality iLocality,
- const rvec *shift_vec)
- {
- GMX_ASSERT(static_cast<size_t>(iLocality) < pairlistSets_.size(),
- "The requested locality should be in the list");
- NbnxnDispatchPruneKernel(&pairlistSets_[static_cast<int>(iLocality)],
- kernelSetup_.kernelType, nbat, shift_vec);
- }
-
- //! Dispatches the non-bonded free-energy kernel, always runs on the CPU
+ const rvec *shift_vec);
+
+ //! \brief Executes the non-bonded kernel of the GPU or launches it on the GPU
+ void dispatchNonbondedKernel(Nbnxm::InteractionLocality iLocality,
+ const interaction_const_t &ic,
+ int forceFlags,
+ int clearF,
+ t_forcerec *fr,
+ gmx_enerdata_t *enerd,
+ t_nrnb *nrnb);
+
+ //! Executes the non-bonded free-energy kernel, always runs on the CPU
void dispatchFreeEnergyKernel(Nbnxm::InteractionLocality iLocality,
t_forcerec *fr,
rvec x[],
int forceFlags,
t_nrnb *nrnb);
+ //! Add the forces stored in nbat to f, zeros the forces in nbat */
+ void atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality locality,
+ rvec *f,
+ gmx_wallcycle *wcycle);
+
//! Return the kernel setup
const Nbnxm::KernelSetup &kernelSetup() const
{
kernelSetup_ = kernelSetup;
}
- //! Parameters for the search and list pruning setup
- std::unique_ptr<NbnxnListParameters> listParams;
+ // 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<nbnxn_search> nbs;
- private:
- //! Local and, optionally, non-local pairlist sets
- std::vector<nbnxn_pairlist_set_t> pairlistSets_;
- public:
//! Atom data
nbnxn_atomdata_t *nbat;
public:
gmx_nbnxn_gpu_t *gpu_nbv; /**< pointer to GPU nb verlet data */
- int min_ci_balanced; /**< pair list balancing parameter used for the 8x8x8 GPU kernels */
};
namespace Nbnxm
/*! \brief Returns the index position of the atoms on the pairlist search grid */
gmx::ArrayRef<const int> nbnxn_get_gridindices(const nbnxn_search* nbs);
-/*! \brief Returns the number of steps performed with the current pair list */
-int nbnxnNumStepsWithPairlist(const nonbonded_verlet_t &nbv,
- Nbnxm::InteractionLocality ilocality,
- int64_t step);
-
-/*! \brief Returns whether step is a dynamic list pruning step */
-bool nbnxnIsDynamicPairlistPruningStep(const nonbonded_verlet_t &nbv,
- Nbnxm::InteractionLocality ilocality,
- int64_t step);
-
-/*! \brief Executes the non-bonded kernel of the GPU or launches it on the GPU */
-void NbnxnDispatchKernel(nonbonded_verlet_t *nbv,
- Nbnxm::InteractionLocality iLocality,
- const interaction_const_t &ic,
- int forceFlags,
- int clearF,
- t_forcerec *fr,
- gmx_enerdata_t *enerd,
- t_nrnb *nrnb);
-
#endif // GMX_NBNXN_NBNXN_H
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