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37 #ifndef GMX_NBNXM_PAIRLIST_H
38 #define GMX_NBNXM_PAIRLIST_H
42 #include "gromacs/gpu_utils/hostallocator.h"
43 #include "gromacs/math/vectypes.h"
44 #include "gromacs/mdtypes/locality.h"
45 #include "gromacs/mdtypes/nblist.h"
46 #include "gromacs/utility/basedefinitions.h"
47 #include "gromacs/utility/defaultinitializationallocator.h"
48 #include "gromacs/utility/enumerationhelpers.h"
49 #include "gromacs/utility/real.h"
51 // This file with constants is separate from this file to be able
52 // to include it during OpenCL jitting without including config.h
53 #include "constants.h"
54 #include "pairlistparams.h"
56 struct NbnxnPairlistCpuWork;
57 struct NbnxnPairlistGpuWork;
60 /* Convenience type for vector with aligned memory */
62 using AlignedVector = std::vector<T, gmx::AlignedAllocator<T>>;
64 /* Convenience type for vector that avoids initialization at resize() */
66 using FastVector = std::vector<T, gmx::DefaultInitializationAllocator<T>>;
68 /* A buffer data structure of 64 bytes
69 * to be placed at the beginning and end of structs
70 * to avoid cache invalidation of the real contents
71 * of the struct by writes to neighboring memory.
76 } gmx_cache_protect_t;
78 /* This is the actual cluster-pair list j-entry.
79 * cj is the j-cluster.
80 * The interaction bits in excl are indexed i-major, j-minor.
81 * The cj entries are sorted such that ones with exclusions come first.
82 * This means that once a full mask (=NBNXN_INTERACTION_MASK_ALL)
83 * is found, all subsequent j-entries in the i-entry also have full masks.
87 int cj; /* The j-cluster */
88 unsigned int excl; /* The exclusion (interaction) bits */
91 /* In nbnxn_ci_t the integer shift contains the shift in the lower 7 bits.
92 * The upper bits contain information for non-bonded kernel optimization.
93 * Simply calculating LJ and Coulomb for all pairs in a cluster pair is fine.
94 * But three flags can be used to skip interactions, currently only for subc=0
95 * !(shift & NBNXN_CI_DO_LJ(subc)) => we can skip LJ for all pairs
96 * shift & NBNXN_CI_HALF_LJ(subc) => we can skip LJ for the second half of i
97 * !(shift & NBNXN_CI_DO_COUL(subc)) => we can skip Coulomb for all pairs
99 #define NBNXN_CI_SHIFT 127
100 #define NBNXN_CI_DO_LJ(subc) (1 << (7 + 3 * (subc)))
101 #define NBNXN_CI_HALF_LJ(subc) (1 << (8 + 3 * (subc)))
102 #define NBNXN_CI_DO_COUL(subc) (1 << (9 + 3 * (subc)))
104 /* Cluster-pair Interaction masks
105 * Bit i*j-cluster-size + j tells if atom i and j interact.
107 // TODO: Rename according to convention when moving into Nbnxn namespace
108 /* All interaction mask is the same for all kernels */
109 constexpr unsigned int NBNXN_INTERACTION_MASK_ALL = 0xffffffffU;
110 /* 4x4 kernel diagonal mask */
111 constexpr unsigned int NBNXN_INTERACTION_MASK_DIAG = 0x08ceU;
112 /* 4x2 kernel diagonal masks */
113 constexpr unsigned int NBNXN_INTERACTION_MASK_DIAG_J2_0 = 0x0002U;
114 constexpr unsigned int NBNXN_INTERACTION_MASK_DIAG_J2_1 = 0x002fU;
115 /* 4x8 kernel diagonal masks */
116 constexpr unsigned int NBNXN_INTERACTION_MASK_DIAG_J8_0 = 0xf0f8fcfeU;
117 constexpr unsigned int NBNXN_INTERACTION_MASK_DIAG_J8_1 = 0x0080c0e0U;
119 /* Simple pair-list i-unit */
122 int ci; /* i-cluster */
123 int shift; /* Shift vector index plus possible flags, see above */
124 int cj_ind_start; /* Start index into cj */
125 int cj_ind_end; /* End index into cj */
128 /* Grouped pair-list i-unit */
131 /* Returns the number of j-cluster groups in this entry */
132 int numJClusterGroups() const { return cj4_ind_end - cj4_ind_start; }
134 int sci; /* i-super-cluster */
135 int shift; /* Shift vector index plus possible flags */
136 int cj4_ind_start; /* Start index into cj4 */
137 int cj4_ind_end; /* End index into cj4 */
140 /* Interaction data for a j-group for one warp */
143 // The i-cluster interactions mask for 1 warp
144 unsigned int imask = 0U;
145 // Index into the exclusion array for 1 warp, default index 0 which means no exclusions
151 int cj[c_nbnxnGpuJgroupSize]; /* The 4 j-clusters */
152 nbnxn_im_ei_t imei[c_nbnxnGpuClusterpairSplit]; /* The i-cluster mask data for 2 warps */
155 /* Struct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist */
158 /* Constructor, sets no exclusions, so all atom pairs interacting */
159 MSVC_DIAGNOSTIC_IGNORE(26495) // pair is not being initialized!
162 for (unsigned int& pairEntry : pair)
164 pairEntry = NBNXN_INTERACTION_MASK_ALL;
167 MSVC_DIAGNOSTIC_RESET
169 /* Topology exclusion interaction bits per warp */
170 unsigned int pair[c_nbnxnGpuExclSize];
173 /* Cluster pairlist type for use on CPUs */
174 struct NbnxnPairlistCpu
178 gmx_cache_protect_t cp0;
180 int na_ci; /* The number of atoms per i-cluster */
181 int na_cj; /* The number of atoms per j-cluster */
182 real rlist; /* The radius for constructing the list */
183 FastVector<nbnxn_ci_t> ci; /* The i-cluster list */
184 FastVector<nbnxn_ci_t> ciOuter; /* The outer, unpruned i-cluster list */
186 FastVector<nbnxn_cj_t> cj; /* The j-cluster list, size ncj */
187 FastVector<nbnxn_cj_t> cjOuter; /* The outer, unpruned j-cluster list */
188 int ncjInUse; /* The number of j-clusters that are used by ci entries in this list, will be <= cj.size() */
190 int nci_tot; /* The total number of i clusters */
192 /* Working data storage for list construction */
193 std::unique_ptr<NbnxnPairlistCpuWork> work;
195 gmx_cache_protect_t cp1;
198 /* Cluster pairlist type, with extra hierarchies, for on the GPU
200 * NOTE: for better performance when combining lists over threads,
201 * all vectors should use default initialization. But when
202 * changing this, excl should be intialized when adding entries.
204 struct NbnxnPairlistGpu
208 * \param[in] pinningPolicy Sets the pinning policy for all buffers used on the GPU
210 NbnxnPairlistGpu(gmx::PinningPolicy pinningPolicy);
212 gmx_cache_protect_t cp0;
214 int na_ci; /* The number of atoms per i-cluster */
215 int na_cj; /* The number of atoms per j-cluster */
216 int na_sc; /* The number of atoms per super cluster */
217 real rlist; /* The radius for constructing the list */
218 // The i-super-cluster list, indexes into cj4;
219 gmx::HostVector<nbnxn_sci_t> sci;
220 // The list of 4*j-cluster groups
221 gmx::HostVector<nbnxn_cj4_t> cj4;
222 // Atom interaction bits (non-exclusions)
223 gmx::HostVector<nbnxn_excl_t> excl;
224 // The total number of i-clusters
227 /* Working data storage for list construction */
228 std::unique_ptr<NbnxnPairlistGpuWork> work;
230 gmx_cache_protect_t cp1;
233 //! Initializes a free-energy pair-list
234 void nbnxn_init_pairlist_fep(t_nblist* nl);