/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020,2021, 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/domdec/domdec_struct.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/ns.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/nblist.h"
#include "gromacs/nbnxm/atomdata.h"
-#include "gromacs/nbnxm/nbnxm.h"
-#include "gromacs/nbnxm/nbnxm_geometry.h"
-#include "gromacs/nbnxm/nbnxm_simd.h"
-#include "gromacs/nbnxm/pairlistset.h"
+#include "gromacs/nbnxm/gpu_data_mgmt.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/vector_operations.h"
-#include "gromacs/topology/block.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/smalloc.h"
-#include "grid.h"
-#include "internal.h"
+#include "boundingboxes.h"
+#include "clusterdistancekerneltype.h"
+#include "gridset.h"
+#include "nbnxm_geometry.h"
+#include "nbnxm_simd.h"
+#include "pairlistset.h"
+#include "pairlistsets.h"
#include "pairlistwork.h"
+#include "pairsearch.h"
using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
-// Convience alias for partial Nbnxn namespace usage
-using InteractionLocality = Nbnxm::InteractionLocality;
+using BoundingBox = Nbnxm::BoundingBox; // TODO: Remove when refactoring this file
+using BoundingBox1D = Nbnxm::BoundingBox1D; // TODO: Remove when refactoring this file
+
+using Grid = Nbnxm::Grid; // TODO: Remove when refactoring this file
+
+// Convenience alias for partial Nbnxn namespace usage
+using InteractionLocality = gmx::InteractionLocality;
/* We shift the i-particles backward for PBC.
* This leads to more conditionals than shifting forward.
*/
constexpr bool c_pbcShiftBackward = true;
-
-static void nbs_cycle_clear(nbnxn_cycle_t *cc)
-{
- for (int i = 0; i < enbsCCnr; i++)
- {
- cc[i].count = 0;
- cc[i].c = 0;
- }
-}
-
-static double Mcyc_av(const nbnxn_cycle_t *cc)
-{
- return static_cast<double>(cc->c)*1e-6/cc->count;
-}
-
-static void nbs_cycle_print(FILE *fp, const nbnxn_search *nbs)
-{
- fprintf(fp, "\n");
- fprintf(fp, "ns %4d grid %4.1f search %4.1f red.f %5.3f",
- nbs->cc[enbsCCgrid].count,
- Mcyc_av(&nbs->cc[enbsCCgrid]),
- Mcyc_av(&nbs->cc[enbsCCsearch]),
- Mcyc_av(&nbs->cc[enbsCCreducef]));
-
- if (nbs->work.size() > 1)
- {
- if (nbs->cc[enbsCCcombine].count > 0)
- {
- fprintf(fp, " comb %5.2f",
- Mcyc_av(&nbs->cc[enbsCCcombine]));
- }
- fprintf(fp, " s. th");
- for (const nbnxn_search_work_t &work : nbs->work)
- {
- fprintf(fp, " %4.1f",
- Mcyc_av(&work.cc[enbsCCsearch]));
- }
- }
- fprintf(fp, "\n");
-}
-
/* Layout for the nonbonded NxN pair lists */
enum class NbnxnLayout
{
Gpu8x8x8 // i-cluster size 8, j-cluster size 8 + super-clustering
};
-#if GMX_SIMD
+#if defined(GMX_NBNXN_SIMD_4XN) || defined(GMX_NBNXN_SIMD_2XNN)
/* Returns the j-cluster size */
-template <NbnxnLayout layout>
+template<NbnxnLayout layout>
static constexpr int jClusterSize()
{
- static_assert(layout == NbnxnLayout::NoSimd4x4 || layout == NbnxnLayout::Simd4xN || layout == NbnxnLayout::Simd2xNN, "Currently jClusterSize only supports CPU layouts");
+ static_assert(layout == NbnxnLayout::NoSimd4x4 || layout == NbnxnLayout::Simd4xN
+ || layout == NbnxnLayout::Simd2xNN,
+ "Currently jClusterSize only supports CPU layouts");
- return layout == NbnxnLayout::Simd4xN ? GMX_SIMD_REAL_WIDTH : (layout == NbnxnLayout::Simd2xNN ? GMX_SIMD_REAL_WIDTH/2 : c_nbnxnCpuIClusterSize);
+ return layout == NbnxnLayout::Simd4xN
+ ? GMX_SIMD_REAL_WIDTH
+ : (layout == NbnxnLayout::Simd2xNN ? GMX_SIMD_REAL_WIDTH / 2 : c_nbnxnCpuIClusterSize);
}
/*! \brief Returns the j-cluster index given the i-cluster index.
*
* \tparam jClusterSize The number of atoms in a j-cluster
- * \tparam jSubClusterIndex The j-sub-cluster index (0/1), used when size(j-cluster) < size(i-cluster)
+ * \tparam jSubClusterIndex The j-sub-cluster index (0/1), used when size(j-cluster) <
+ * size(i-cluster)
* \param[in] ci The i-cluster index
*/
-template <int jClusterSize, int jSubClusterIndex>
+template<int jClusterSize, int jSubClusterIndex>
static inline int cjFromCi(int ci)
{
- static_assert(jClusterSize == c_nbnxnCpuIClusterSize/2 || jClusterSize == c_nbnxnCpuIClusterSize || jClusterSize == c_nbnxnCpuIClusterSize*2, "Only j-cluster sizes 2, 4 and 8 are currently implemented");
+ static_assert(jClusterSize == c_nbnxnCpuIClusterSize / 2 || jClusterSize == c_nbnxnCpuIClusterSize
+ || jClusterSize == c_nbnxnCpuIClusterSize * 2,
+ "Only j-cluster sizes 2, 4 and 8 are currently implemented");
static_assert(jSubClusterIndex == 0 || jSubClusterIndex == 1,
"Only sub-cluster indices 0 and 1 are supported");
- if (jClusterSize == c_nbnxnCpuIClusterSize/2)
+ if (jClusterSize == c_nbnxnCpuIClusterSize / 2)
{
if (jSubClusterIndex == 0)
{
/*! \brief Returns the j-cluster index given the i-cluster index.
*
* \tparam layout The pair-list layout
- * \tparam jSubClusterIndex The j-sub-cluster index (0/1), used when size(j-cluster) < size(i-cluster)
+ * \tparam jSubClusterIndex The j-sub-cluster index (0/1), used when size(j-cluster) <
+ * size(i-cluster)
* \param[in] ci The i-cluster index
*/
-template <NbnxnLayout layout, int jSubClusterIndex>
+template<NbnxnLayout layout, int jSubClusterIndex>
static inline int cjFromCi(int ci)
{
constexpr int clusterSize = jClusterSize<layout>();
}
/* Returns the nbnxn coordinate data index given the i-cluster index */
-template <NbnxnLayout layout>
+template<NbnxnLayout layout>
static inline int xIndexFromCi(int ci)
{
constexpr int clusterSize = jClusterSize<layout>();
- static_assert(clusterSize == c_nbnxnCpuIClusterSize/2 || clusterSize == c_nbnxnCpuIClusterSize || clusterSize == c_nbnxnCpuIClusterSize*2, "Only j-cluster sizes 2, 4 and 8 are currently implemented");
+ static_assert(clusterSize == c_nbnxnCpuIClusterSize / 2 || clusterSize == c_nbnxnCpuIClusterSize
+ || clusterSize == c_nbnxnCpuIClusterSize * 2,
+ "Only j-cluster sizes 2, 4 and 8 are currently implemented");
if (clusterSize <= c_nbnxnCpuIClusterSize)
{
/* Coordinates are stored packed in groups of 4 */
- return ci*STRIDE_P4;
+ return ci * STRIDE_P4;
}
else
{
/* Coordinates packed in 8, i-cluster size is half the packing width */
- return (ci >> 1)*STRIDE_P8 + (ci & 1)*(c_packX8 >> 1);
+ return (ci >> 1) * STRIDE_P8 + (ci & 1) * (c_packX8 >> 1);
}
}
/* Returns the nbnxn coordinate data index given the j-cluster index */
-template <NbnxnLayout layout>
+template<NbnxnLayout layout>
static inline int xIndexFromCj(int cj)
{
constexpr int clusterSize = jClusterSize<layout>();
- static_assert(clusterSize == c_nbnxnCpuIClusterSize/2 || clusterSize == c_nbnxnCpuIClusterSize || clusterSize == c_nbnxnCpuIClusterSize*2, "Only j-cluster sizes 2, 4 and 8 are currently implemented");
+ static_assert(clusterSize == c_nbnxnCpuIClusterSize / 2 || clusterSize == c_nbnxnCpuIClusterSize
+ || clusterSize == c_nbnxnCpuIClusterSize * 2,
+ "Only j-cluster sizes 2, 4 and 8 are currently implemented");
- if (clusterSize == c_nbnxnCpuIClusterSize/2)
+ if (clusterSize == c_nbnxnCpuIClusterSize / 2)
{
/* Coordinates are stored packed in groups of 4 */
- return (cj >> 1)*STRIDE_P4 + (cj & 1)*(c_packX4 >> 1);
+ return (cj >> 1) * STRIDE_P4 + (cj & 1) * (c_packX4 >> 1);
}
else if (clusterSize == c_nbnxnCpuIClusterSize)
{
/* Coordinates are stored packed in groups of 4 */
- return cj*STRIDE_P4;
+ return cj * STRIDE_P4;
}
else
{
/* Coordinates are stored packed in groups of 8 */
- return cj*STRIDE_P8;
- }
-}
-#endif //GMX_SIMD
-
-gmx_bool nbnxn_kernel_pairlist_simple(int nb_kernel_type)
-{
- if (nb_kernel_type == nbnxnkNotSet)
- {
- gmx_fatal(FARGS, "Non-bonded kernel type not set for Verlet-style pair-list.");
+ return cj * STRIDE_P8;
}
-
- switch (nb_kernel_type)
- {
- case nbnxnk8x8x8_GPU:
- case nbnxnk8x8x8_PlainC:
- return FALSE;
-
- case nbnxnk4x4_PlainC:
- case nbnxnk4xN_SIMD_4xN:
- case nbnxnk4xN_SIMD_2xNN:
- return TRUE;
-
- default:
- gmx_incons("Invalid nonbonded kernel type passed!");
- return FALSE;
- }
-}
-
-/* Initializes a single nbnxn_pairlist_t data structure */
-static void nbnxn_init_pairlist_fep(t_nblist *nl)
-{
- nl->type = GMX_NBLIST_INTERACTION_FREE_ENERGY;
- nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
- /* The interaction functions are set in the free energy kernel fuction */
- nl->ivdw = -1;
- nl->ivdwmod = -1;
- nl->ielec = -1;
- nl->ielecmod = -1;
-
- nl->maxnri = 0;
- nl->maxnrj = 0;
- nl->nri = 0;
- nl->nrj = 0;
- nl->iinr = nullptr;
- nl->gid = nullptr;
- nl->shift = nullptr;
- nl->jindex = nullptr;
- nl->jjnr = nullptr;
- nl->excl_fep = nullptr;
-
-}
-
-static void free_nblist(t_nblist *nl)
-{
- sfree(nl->iinr);
- sfree(nl->gid);
- sfree(nl->shift);
- sfree(nl->jindex);
- sfree(nl->jjnr);
- sfree(nl->excl_fep);
-}
-
-nbnxn_search_work_t::nbnxn_search_work_t() :
- cp0({{0}}
- ),
- buffer_flags({0, nullptr, 0}),
- ndistc(0),
- nbl_fep(new t_nblist),
- cp1({{0}})
-{
- nbnxn_init_pairlist_fep(nbl_fep.get());
-
- nbs_cycle_clear(cc);
}
+#endif // defined(GMX_NBNXN_SIMD_4XN) || defined(GMX_NBNXN_SIMD_2XNN)
-nbnxn_search_work_t::~nbnxn_search_work_t()
+static constexpr int sizeNeededForBufferFlags(const int numAtoms)
{
- sfree(buffer_flags.flag);
-
- free_nblist(nbl_fep.get());
+ return (numAtoms + NBNXN_BUFFERFLAG_SIZE - 1) / NBNXN_BUFFERFLAG_SIZE;
}
-nbnxn_search::nbnxn_search(const ivec *n_dd_cells,
- const gmx_domdec_zones_t *zones,
- gmx_bool bFEP,
- int nthread_max) :
- bFEP(bFEP),
- ePBC(epbcNONE), // The correct value will be set during the gridding
- zones(zones),
- natoms_local(0),
- natoms_nonlocal(0),
- search_count(0),
- work(nthread_max)
+// Resets current flags to 0 and adds more flags if needed.
+static void resizeAndZeroBufferFlags(std::vector<gmx_bitmask_t>* flags, const int numAtoms)
{
- // The correct value will be set during the gridding
- clear_mat(box);
- clear_ivec(dd_dim);
- int numGrids = 1;
- DomDec = n_dd_cells != nullptr;
- if (DomDec)
- {
- for (int d = 0; d < DIM; d++)
- {
- if ((*n_dd_cells)[d] > 1)
- {
- dd_dim[d] = 1;
- /* Each grid matches a DD zone */
- numGrids *= 2;
- }
- }
- }
-
- grid.resize(numGrids);
-
- /* Initialize detailed nbsearch cycle counting */
- print_cycles = (getenv("GMX_NBNXN_CYCLE") != nullptr);
- nbs_cycle_clear(cc);
+ flags->clear();
+ flags->resize(sizeNeededForBufferFlags(numAtoms), gmx_bitmask_t{ 0 });
}
-nbnxn_search *nbnxn_init_search(const ivec *n_dd_cells,
- const gmx_domdec_zones_t *zones,
- gmx_bool bFEP,
- int nthread_max)
-{
- return new nbnxn_search(n_dd_cells, zones, bFEP, nthread_max);
-}
-
-static void init_buffer_flags(nbnxn_buffer_flags_t *flags,
- int natoms)
-{
- flags->nflag = (natoms + NBNXN_BUFFERFLAG_SIZE - 1)/NBNXN_BUFFERFLAG_SIZE;
- if (flags->nflag > flags->flag_nalloc)
- {
- flags->flag_nalloc = over_alloc_large(flags->nflag);
- srenew(flags->flag, flags->flag_nalloc);
- }
- for (int b = 0; b < flags->nflag; b++)
- {
- bitmask_clear(&(flags->flag[b]));
- }
-}
/* Returns the pair-list cutoff between a bounding box and a grid cell given an atom-to-atom pair-list cutoff
*
* assigned to (when atom groups instead of individual atoms are assigned
* to cells), this distance returned can be larger than the input.
*/
-static real listRangeForBoundingBoxToGridCell(real rlist,
- const nbnxn_grid_t &grid)
+static real listRangeForBoundingBoxToGridCell(real rlist, const Grid::Dimensions& gridDims)
{
- return rlist + grid.maxAtomGroupRadius;
-
+ return rlist + gridDims.maxAtomGroupRadius;
}
/* Returns the pair-list cutoff between a grid cells given an atom-to-atom pair-list cutoff
*
* assigned to (when atom groups instead of individual atoms are assigned
* to cells), this distance returned can be larger than the input.
*/
-static real listRangeForGridCellToGridCell(real rlist,
- const nbnxn_grid_t &iGrid,
- const nbnxn_grid_t &jGrid)
+static real listRangeForGridCellToGridCell(real rlist,
+ const Grid::Dimensions& iGridDims,
+ const Grid::Dimensions& jGridDims)
{
- return rlist + iGrid.maxAtomGroupRadius + jGrid.maxAtomGroupRadius;
+ return rlist + iGridDims.maxAtomGroupRadius + jGridDims.maxAtomGroupRadius;
}
/* Determines the cell range along one dimension that
* the bounding box b0 - b1 sees.
*/
template<int dim>
-static void get_cell_range(real b0, real b1,
- const nbnxn_grid_t &jGrid,
- real d2, real rlist, int *cf, int *cl)
+static void
+get_cell_range(real b0, real b1, const Grid::Dimensions& jGridDims, real d2, real rlist, int* cf, int* cl)
{
- real listRangeBBToCell2 = gmx::square(listRangeForBoundingBoxToGridCell(rlist, jGrid));
- real distanceInCells = (b0 - jGrid.c0[dim])*jGrid.invCellSize[dim];
+ real listRangeBBToCell2 = gmx::square(listRangeForBoundingBoxToGridCell(rlist, jGridDims));
+ real distanceInCells = (b0 - jGridDims.lowerCorner[dim]) * jGridDims.invCellSize[dim];
*cf = std::max(static_cast<int>(distanceInCells), 0);
- while (*cf > 0 &&
- d2 + gmx::square((b0 - jGrid.c0[dim]) - (*cf - 1 + 1)*jGrid.cellSize[dim]) < listRangeBBToCell2)
+ while (*cf > 0
+ && d2 + gmx::square((b0 - jGridDims.lowerCorner[dim]) - (*cf - 1 + 1) * jGridDims.cellSize[dim])
+ < listRangeBBToCell2)
{
(*cf)--;
}
- *cl = std::min(static_cast<int>((b1 - jGrid.c0[dim])*jGrid.invCellSize[dim]), jGrid.numCells[dim] - 1);
- while (*cl < jGrid.numCells[dim] - 1 &&
- d2 + gmx::square((*cl + 1)*jGrid.cellSize[dim] - (b1 - jGrid.c0[dim])) < listRangeBBToCell2)
+ *cl = std::min(static_cast<int>((b1 - jGridDims.lowerCorner[dim]) * jGridDims.invCellSize[dim]),
+ jGridDims.numCells[dim] - 1);
+ while (*cl < jGridDims.numCells[dim] - 1
+ && d2 + gmx::square((*cl + 1) * jGridDims.cellSize[dim] - (b1 - jGridDims.lowerCorner[dim]))
+ < listRangeBBToCell2)
{
(*cl)++;
}
/*
static float box_dist2(float bx0, float bx1, float by0,
float by1, float bz0, float bz1,
- const nbnxn_bb_t *bb)
+ const BoundingBox *bb)
{
float d2;
float dl, dh, dm, dm0;
d2 = 0;
- dl = bx0 - bb->upper[BB_X];
- dh = bb->lower[BB_X] - bx1;
+ dl = bx0 - bb->upper.x;
+ dh = bb->lower.x - bx1;
dm = std::max(dl, dh);
dm0 = std::max(dm, 0.0f);
d2 += dm0*dm0;
- dl = by0 - bb->upper[BB_Y];
- dh = bb->lower[BB_Y] - by1;
+ dl = by0 - bb->upper.y;
+ dh = bb->lower.y - by1;
dm = std::max(dl, dh);
dm0 = std::max(dm, 0.0f);
d2 += dm0*dm0;
- dl = bz0 - bb->upper[BB_Z];
- dh = bb->lower[BB_Z] - bz1;
+ dl = bz0 - bb->upper.z;
+ dh = bb->lower.z - bz1;
dm = std::max(dl, dh);
dm0 = std::max(dm, 0.0f);
d2 += dm0*dm0;
}
*/
-/* Plain C code calculating the distance^2 between two bounding boxes */
-static float subc_bb_dist2(int si,
- const nbnxn_bb_t *bb_i_ci,
- int csj,
- gmx::ArrayRef<const nbnxn_bb_t> bb_j_all)
-{
- const nbnxn_bb_t *bb_i = bb_i_ci + si;
- const nbnxn_bb_t *bb_j = bb_j_all.data() + csj;
-
- float d2 = 0;
- float dl, dh, dm, dm0;
+#if !NBNXN_SEARCH_BB_SIMD4
- dl = bb_i->lower[BB_X] - bb_j->upper[BB_X];
- dh = bb_j->lower[BB_X] - bb_i->upper[BB_X];
+/*! \brief Plain C code calculating the distance^2 between two bounding boxes in xyz0 format
+ *
+ * \param[in] bb_i First bounding box
+ * \param[in] bb_j Second bounding box
+ */
+static float clusterBoundingBoxDistance2(const BoundingBox& bb_i, const BoundingBox& bb_j)
+{
+ float dl = bb_i.lower.x - bb_j.upper.x;
+ float dh = bb_j.lower.x - bb_i.upper.x;
+ float dm = std::max(dl, dh);
+ float dm0 = std::max(dm, 0.0F);
+ float d2 = dm0 * dm0;
+
+ dl = bb_i.lower.y - bb_j.upper.y;
+ dh = bb_j.lower.y - bb_i.upper.y;
dm = std::max(dl, dh);
- dm0 = std::max(dm, 0.0f);
- d2 += dm0*dm0;
+ dm0 = std::max(dm, 0.0F);
+ d2 += dm0 * dm0;
- dl = bb_i->lower[BB_Y] - bb_j->upper[BB_Y];
- dh = bb_j->lower[BB_Y] - bb_i->upper[BB_Y];
+ dl = bb_i.lower.z - bb_j.upper.z;
+ dh = bb_j.lower.z - bb_i.upper.z;
dm = std::max(dl, dh);
- dm0 = std::max(dm, 0.0f);
- d2 += dm0*dm0;
-
- dl = bb_i->lower[BB_Z] - bb_j->upper[BB_Z];
- dh = bb_j->lower[BB_Z] - bb_i->upper[BB_Z];
- dm = std::max(dl, dh);
- dm0 = std::max(dm, 0.0f);
- d2 += dm0*dm0;
+ dm0 = std::max(dm, 0.0F);
+ d2 += dm0 * dm0;
return d2;
}
-#if NBNXN_SEARCH_BB_SIMD4
+#else /* NBNXN_SEARCH_BB_SIMD4 */
-/* 4-wide SIMD code for bb distance for bb format xyz0 */
-static float subc_bb_dist2_simd4(int si,
- const nbnxn_bb_t *bb_i_ci,
- int csj,
- gmx::ArrayRef<const nbnxn_bb_t> bb_j_all)
+/*! \brief 4-wide SIMD code calculating the distance^2 between two bounding boxes in xyz0 format
+ *
+ * \param[in] bb_i First bounding box, should be aligned for 4-wide SIMD
+ * \param[in] bb_j Second bounding box, should be aligned for 4-wide SIMD
+ */
+static float clusterBoundingBoxDistance2(const BoundingBox& bb_i, const BoundingBox& bb_j)
{
// TODO: During SIMDv2 transition only some archs use namespace (remove when done)
using namespace gmx;
- Simd4Float bb_i_S0, bb_i_S1;
- Simd4Float bb_j_S0, bb_j_S1;
- Simd4Float dl_S;
- Simd4Float dh_S;
- Simd4Float dm_S;
- Simd4Float dm0_S;
-
- bb_i_S0 = load4(&bb_i_ci[si].lower[0]);
- bb_i_S1 = load4(&bb_i_ci[si].upper[0]);
- bb_j_S0 = load4(&bb_j_all[csj].lower[0]);
- bb_j_S1 = load4(&bb_j_all[csj].upper[0]);
+ const Simd4Float bb_i_S0 = load4(bb_i.lower.ptr());
+ const Simd4Float bb_i_S1 = load4(bb_i.upper.ptr());
+ const Simd4Float bb_j_S0 = load4(bb_j.lower.ptr());
+ const Simd4Float bb_j_S1 = load4(bb_j.upper.ptr());
- dl_S = bb_i_S0 - bb_j_S1;
- dh_S = bb_j_S0 - bb_i_S1;
+ const Simd4Float dl_S = bb_i_S0 - bb_j_S1;
+ const Simd4Float dh_S = bb_j_S0 - bb_i_S1;
- dm_S = max(dl_S, dh_S);
- dm0_S = max(dm_S, simd4SetZeroF());
+ const Simd4Float dm_S = max(dl_S, dh_S);
+ const Simd4Float dm0_S = max(dm_S, simd4SetZeroF());
return dotProduct(dm0_S, dm0_S);
}
/* Calculate bb bounding distances of bb_i[si,...,si+3] and store them in d2 */
-#define SUBC_BB_DIST2_SIMD4_XXXX_INNER(si, bb_i, d2) \
- { \
- int shi; \
- \
- Simd4Float dx_0, dy_0, dz_0; \
- Simd4Float dx_1, dy_1, dz_1; \
- \
- Simd4Float mx, my, mz; \
- Simd4Float m0x, m0y, m0z; \
- \
- Simd4Float d2x, d2y, d2z; \
- Simd4Float d2s, d2t; \
- \
- shi = (si)*NNBSBB_D*DIM; \
- \
- xi_l = load4((bb_i)+shi+0*STRIDE_PBB); \
- yi_l = load4((bb_i)+shi+1*STRIDE_PBB); \
- zi_l = load4((bb_i)+shi+2*STRIDE_PBB); \
- xi_h = load4((bb_i)+shi+3*STRIDE_PBB); \
- yi_h = load4((bb_i)+shi+4*STRIDE_PBB); \
- zi_h = load4((bb_i)+shi+5*STRIDE_PBB); \
- \
- dx_0 = xi_l - xj_h; \
- dy_0 = yi_l - yj_h; \
- dz_0 = zi_l - zj_h; \
- \
- dx_1 = xj_l - xi_h; \
- dy_1 = yj_l - yi_h; \
- dz_1 = zj_l - zi_h; \
- \
- mx = max(dx_0, dx_1); \
- my = max(dy_0, dy_1); \
- mz = max(dz_0, dz_1); \
- \
- m0x = max(mx, zero); \
- m0y = max(my, zero); \
- m0z = max(mz, zero); \
- \
- d2x = m0x * m0x; \
- d2y = m0y * m0y; \
- d2z = m0z * m0z; \
- \
- d2s = d2x + d2y; \
- d2t = d2s + d2z; \
- \
- store4((d2)+(si), d2t); \
- }
+template<int boundingBoxStart>
+static inline void gmx_simdcall clusterBoundingBoxDistance2_xxxx_simd4_inner(const float* bb_i,
+ float* d2,
+ const Simd4Float xj_l,
+ const Simd4Float yj_l,
+ const Simd4Float zj_l,
+ const Simd4Float xj_h,
+ const Simd4Float yj_h,
+ const Simd4Float zj_h)
+{
+ constexpr int stride = c_packedBoundingBoxesDimSize;
+
+ const int shi = boundingBoxStart * Nbnxm::c_numBoundingBoxBounds1D * DIM;
+
+ const Simd4Float zero = setZero();
+
+ const Simd4Float xi_l = load4(bb_i + shi + 0 * stride);
+ const Simd4Float yi_l = load4(bb_i + shi + 1 * stride);
+ const Simd4Float zi_l = load4(bb_i + shi + 2 * stride);
+ const Simd4Float xi_h = load4(bb_i + shi + 3 * stride);
+ const Simd4Float yi_h = load4(bb_i + shi + 4 * stride);
+ const Simd4Float zi_h = load4(bb_i + shi + 5 * stride);
+
+ const Simd4Float dx_0 = xi_l - xj_h;
+ const Simd4Float dy_0 = yi_l - yj_h;
+ const Simd4Float dz_0 = zi_l - zj_h;
+
+ const Simd4Float dx_1 = xj_l - xi_h;
+ const Simd4Float dy_1 = yj_l - yi_h;
+ const Simd4Float dz_1 = zj_l - zi_h;
+
+ const Simd4Float mx = max(dx_0, dx_1);
+ const Simd4Float my = max(dy_0, dy_1);
+ const Simd4Float mz = max(dz_0, dz_1);
+
+ const Simd4Float m0x = max(mx, zero);
+ const Simd4Float m0y = max(my, zero);
+ const Simd4Float m0z = max(mz, zero);
+
+ const Simd4Float d2x = m0x * m0x;
+ const Simd4Float d2y = m0y * m0y;
+ const Simd4Float d2z = m0z * m0z;
+
+ const Simd4Float d2s = d2x + d2y;
+ const Simd4Float d2t = d2s + d2z;
+
+ store4(d2 + boundingBoxStart, d2t);
+}
/* 4-wide SIMD code for nsi bb distances for bb format xxxxyyyyzzzz */
-static void subc_bb_dist2_simd4_xxxx(const float *bb_j,
- int nsi, const float *bb_i,
- float *d2)
+static void clusterBoundingBoxDistance2_xxxx_simd4(const float* bb_j, const int nsi, const float* bb_i, float* d2)
{
+ constexpr int stride = c_packedBoundingBoxesDimSize;
+
// TODO: During SIMDv2 transition only some archs use namespace (remove when done)
using namespace gmx;
- Simd4Float xj_l, yj_l, zj_l;
- Simd4Float xj_h, yj_h, zj_h;
- Simd4Float xi_l, yi_l, zi_l;
- Simd4Float xi_h, yi_h, zi_h;
-
- Simd4Float zero;
-
- zero = setZero();
+ const Simd4Float xj_l = Simd4Float(bb_j[0 * stride]);
+ const Simd4Float yj_l = Simd4Float(bb_j[1 * stride]);
+ const Simd4Float zj_l = Simd4Float(bb_j[2 * stride]);
+ const Simd4Float xj_h = Simd4Float(bb_j[3 * stride]);
+ const Simd4Float yj_h = Simd4Float(bb_j[4 * stride]);
+ const Simd4Float zj_h = Simd4Float(bb_j[5 * stride]);
- xj_l = Simd4Float(bb_j[0*STRIDE_PBB]);
- yj_l = Simd4Float(bb_j[1*STRIDE_PBB]);
- zj_l = Simd4Float(bb_j[2*STRIDE_PBB]);
- xj_h = Simd4Float(bb_j[3*STRIDE_PBB]);
- yj_h = Simd4Float(bb_j[4*STRIDE_PBB]);
- zj_h = Simd4Float(bb_j[5*STRIDE_PBB]);
-
- /* Here we "loop" over si (0,STRIDE_PBB) from 0 to nsi with step STRIDE_PBB.
+ /* Here we "loop" over si (0,stride) from 0 to nsi with step stride.
* But as we know the number of iterations is 1 or 2, we unroll manually.
*/
- SUBC_BB_DIST2_SIMD4_XXXX_INNER(0, bb_i, d2);
- if (STRIDE_PBB < nsi)
+ clusterBoundingBoxDistance2_xxxx_simd4_inner<0>(bb_i, d2, xj_l, yj_l, zj_l, xj_h, yj_h, zj_h);
+ if (stride < nsi)
{
- SUBC_BB_DIST2_SIMD4_XXXX_INNER(STRIDE_PBB, bb_i, d2);
+ clusterBoundingBoxDistance2_xxxx_simd4_inner<stride>(bb_i, d2, xj_l, yj_l, zj_l, xj_h, yj_h, zj_h);
}
}
/* Returns if any atom pair from two clusters is within distance sqrt(rlist2) */
static inline gmx_bool
-clusterpair_in_range(const NbnxnPairlistGpuWork &work,
- int si,
- int csj, int stride, const real *x_j,
- real rlist2)
+clusterpair_in_range(const NbnxnPairlistGpuWork& work, int si, int csj, int stride, const real* x_j, real rlist2)
{
#if !GMX_SIMD4_HAVE_REAL
* All coordinates are stored as xyzxyz...
*/
- const real *x_i = work.iSuperClusterData.x.data();
+ const real* x_i = work.iSuperClusterData.x.data();
for (int i = 0; i < c_nbnxnGpuClusterSize; i++)
{
- int i0 = (si*c_nbnxnGpuClusterSize + i)*DIM;
+ int i0 = (si * c_nbnxnGpuClusterSize + i) * DIM;
for (int j = 0; j < c_nbnxnGpuClusterSize; j++)
{
- int j0 = (csj*c_nbnxnGpuClusterSize + j)*stride;
+ int j0 = (csj * c_nbnxnGpuClusterSize + j) * stride;
- real d2 = gmx::square(x_i[i0 ] - x_j[j0 ]) + gmx::square(x_i[i0+1] - x_j[j0+1]) + gmx::square(x_i[i0+2] - x_j[j0+2]);
+ real d2 = gmx::square(x_i[i0] - x_j[j0]) + gmx::square(x_i[i0 + 1] - x_j[j0 + 1])
+ + gmx::square(x_i[i0 + 2] - x_j[j0 + 2]);
if (d2 < rlist2)
{
static_assert(c_nbnxnGpuClusterSize == 8 || c_nbnxnGpuClusterSize == 4,
"A cluster is hard-coded to 4/8 atoms.");
- Simd4Real rc2_S = Simd4Real(rlist2);
+ Simd4Real rc2_S{ rlist2 };
- const real *x_i = work.iSuperClusterData.xSimd.data();
+ const real* x_i = work.iSuperClusterData.xSimd.data();
- int dim_stride = c_nbnxnGpuClusterSize*DIM;
- Simd4Real ix_S0 = load4(x_i + si*dim_stride + 0*GMX_SIMD4_WIDTH);
- Simd4Real iy_S0 = load4(x_i + si*dim_stride + 1*GMX_SIMD4_WIDTH);
- Simd4Real iz_S0 = load4(x_i + si*dim_stride + 2*GMX_SIMD4_WIDTH);
+ int dim_stride = c_nbnxnGpuClusterSize * DIM;
+ Simd4Real ix_S0 = load4(x_i + si * dim_stride + 0 * GMX_SIMD4_WIDTH);
+ Simd4Real iy_S0 = load4(x_i + si * dim_stride + 1 * GMX_SIMD4_WIDTH);
+ Simd4Real iz_S0 = load4(x_i + si * dim_stride + 2 * GMX_SIMD4_WIDTH);
- Simd4Real ix_S1, iy_S1, iz_S1;
+ Simd4Real ix_S1, iy_S1, iz_S1;
if (c_nbnxnGpuClusterSize == 8)
{
- ix_S1 = load4(x_i + si*dim_stride + 3*GMX_SIMD4_WIDTH);
- iy_S1 = load4(x_i + si*dim_stride + 4*GMX_SIMD4_WIDTH);
- iz_S1 = load4(x_i + si*dim_stride + 5*GMX_SIMD4_WIDTH);
+ ix_S1 = load4(x_i + si * dim_stride + 3 * GMX_SIMD4_WIDTH);
+ iy_S1 = load4(x_i + si * dim_stride + 4 * GMX_SIMD4_WIDTH);
+ iz_S1 = load4(x_i + si * dim_stride + 5 * GMX_SIMD4_WIDTH);
}
/* We loop from the outer to the inner particles to maximize
* the chance that we find a pair in range quickly and return.
*/
- int j0 = csj*c_nbnxnGpuClusterSize;
+ int j0 = csj * c_nbnxnGpuClusterSize;
int j1 = j0 + c_nbnxnGpuClusterSize - 1;
while (j0 < j1)
{
Simd4Bool wco_S3;
Simd4Bool wco_any_S01, wco_any_S23, wco_any_S;
- jx0_S = Simd4Real(x_j[j0*stride+0]);
- jy0_S = Simd4Real(x_j[j0*stride+1]);
- jz0_S = Simd4Real(x_j[j0*stride+2]);
+ jx0_S = Simd4Real(x_j[j0 * stride + 0]);
+ jy0_S = Simd4Real(x_j[j0 * stride + 1]);
+ jz0_S = Simd4Real(x_j[j0 * stride + 2]);
- jx1_S = Simd4Real(x_j[j1*stride+0]);
- jy1_S = Simd4Real(x_j[j1*stride+1]);
- jz1_S = Simd4Real(x_j[j1*stride+2]);
+ jx1_S = Simd4Real(x_j[j1 * stride + 0]);
+ jy1_S = Simd4Real(x_j[j1 * stride + 1]);
+ jz1_S = Simd4Real(x_j[j1 * stride + 2]);
/* Calculate distance */
- dx_S0 = ix_S0 - jx0_S;
- dy_S0 = iy_S0 - jy0_S;
- dz_S0 = iz_S0 - jz0_S;
- dx_S2 = ix_S0 - jx1_S;
- dy_S2 = iy_S0 - jy1_S;
- dz_S2 = iz_S0 - jz1_S;
+ dx_S0 = ix_S0 - jx0_S;
+ dy_S0 = iy_S0 - jy0_S;
+ dz_S0 = iz_S0 - jz0_S;
+ dx_S2 = ix_S0 - jx1_S;
+ dy_S2 = iy_S0 - jy1_S;
+ dz_S2 = iz_S0 - jz1_S;
if (c_nbnxnGpuClusterSize == 8)
{
- dx_S1 = ix_S1 - jx0_S;
- dy_S1 = iy_S1 - jy0_S;
- dz_S1 = iz_S1 - jz0_S;
- dx_S3 = ix_S1 - jx1_S;
- dy_S3 = iy_S1 - jy1_S;
- dz_S3 = iz_S1 - jz1_S;
+ dx_S1 = ix_S1 - jx0_S;
+ dy_S1 = iy_S1 - jy0_S;
+ dz_S1 = iz_S1 - jz0_S;
+ dx_S3 = ix_S1 - jx1_S;
+ dy_S3 = iy_S1 - jy1_S;
+ dz_S3 = iz_S1 - jz1_S;
}
/* rsq = dx*dx+dy*dy+dz*dz */
- rsq_S0 = norm2(dx_S0, dy_S0, dz_S0);
- rsq_S2 = norm2(dx_S2, dy_S2, dz_S2);
+ rsq_S0 = norm2(dx_S0, dy_S0, dz_S0);
+ rsq_S2 = norm2(dx_S2, dy_S2, dz_S2);
if (c_nbnxnGpuClusterSize == 8)
{
- rsq_S1 = norm2(dx_S1, dy_S1, dz_S1);
- rsq_S3 = norm2(dx_S3, dy_S3, dz_S3);
+ rsq_S1 = norm2(dx_S1, dy_S1, dz_S1);
+ rsq_S3 = norm2(dx_S3, dy_S3, dz_S3);
}
- wco_S0 = (rsq_S0 < rc2_S);
- wco_S2 = (rsq_S2 < rc2_S);
+ wco_S0 = (rsq_S0 < rc2_S);
+ wco_S2 = (rsq_S2 < rc2_S);
if (c_nbnxnGpuClusterSize == 8)
{
- wco_S1 = (rsq_S1 < rc2_S);
- wco_S3 = (rsq_S3 < rc2_S);
+ wco_S1 = (rsq_S1 < rc2_S);
+ wco_S3 = (rsq_S3 < rc2_S);
}
if (c_nbnxnGpuClusterSize == 8)
{
- wco_any_S01 = wco_S0 || wco_S1;
- wco_any_S23 = wco_S2 || wco_S3;
- wco_any_S = wco_any_S01 || wco_any_S23;
+ wco_any_S01 = wco_S0 || wco_S1;
+ wco_any_S23 = wco_S2 || wco_S3;
+ wco_any_S = wco_any_S01 || wco_any_S23;
}
else
{
}
/* Returns the j-cluster index for index cjIndex in a cj list */
-static inline int nblCj(gmx::ArrayRef<const nbnxn_cj_t> cjList,
- int cjIndex)
+static inline int nblCj(gmx::ArrayRef<const nbnxn_cj_t> cjList, int cjIndex)
{
return cjList[cjIndex].cj;
}
/* Returns the j-cluster index for index cjIndex in a cj4 list */
-static inline int nblCj(gmx::ArrayRef<const nbnxn_cj4_t> cj4List,
- int cjIndex)
+static inline int nblCj(gmx::ArrayRef<const nbnxn_cj4_t> cj4List, int cjIndex)
{
- return cj4List[cjIndex/c_nbnxnGpuJgroupSize].cj[cjIndex & (c_nbnxnGpuJgroupSize - 1)];
+ return cj4List[cjIndex / c_nbnxnGpuJgroupSize].cj[cjIndex & (c_nbnxnGpuJgroupSize - 1)];
}
/* Returns the i-interaction mask of the j sub-cell for index cj_ind */
-static unsigned int nbl_imask0(const NbnxnPairlistGpu *nbl, int cj_ind)
+static unsigned int nbl_imask0(const NbnxnPairlistGpu* nbl, int cj_ind)
{
- return nbl->cj4[cj_ind/c_nbnxnGpuJgroupSize].imei[0].imask;
+ return nbl->cj4[cj_ind / c_nbnxnGpuJgroupSize].imei[0].imask;
}
-/* Initializes a single NbnxnPairlistCpu data structure */
-static void nbnxn_init_pairlist(NbnxnPairlistCpu *nbl)
+NbnxnPairlistCpu::NbnxnPairlistCpu() :
+ na_ci(c_nbnxnCpuIClusterSize),
+ na_cj(0),
+ rlist(0),
+ ncjInUse(0),
+ nci_tot(0),
+ work(std::make_unique<NbnxnPairlistCpuWork>())
{
- nbl->na_ci = c_nbnxnCpuIClusterSize;
- nbl->na_cj = 0;
- nbl->ci.clear();
- nbl->ciOuter.clear();
- nbl->ncjInUse = 0;
- nbl->cj.clear();
- nbl->cjOuter.clear();
- nbl->nci_tot = 0;
-
- nbl->work = new NbnxnPairlistCpuWork();
}
NbnxnPairlistGpu::NbnxnPairlistGpu(gmx::PinningPolicy pinningPolicy) :
na_ci(c_nbnxnGpuClusterSize),
na_cj(c_nbnxnGpuClusterSize),
- na_sc(c_gpuNumClusterPerCell*c_nbnxnGpuClusterSize),
+ na_sc(c_gpuNumClusterPerCell * c_nbnxnGpuClusterSize),
rlist(0),
- sci({}, {pinningPolicy}),
- cj4({}, {pinningPolicy}),
- excl({}, {pinningPolicy}),
- nci_tot(0)
+ sci({}, { pinningPolicy }),
+ cj4({}, { pinningPolicy }),
+ excl({}, { pinningPolicy }),
+ nci_tot(0),
+ work(std::make_unique<NbnxnPairlistGpuWork>())
{
static_assert(c_nbnxnGpuNumClusterPerSupercluster == c_gpuNumClusterPerCell,
"The search code assumes that the a super-cluster matches a search grid cell");
- static_assert(sizeof(cj4[0].imei[0].imask)*8 >= c_nbnxnGpuJgroupSize*c_gpuNumClusterPerCell,
- "The i super-cluster cluster interaction mask does not contain a sufficient number of bits");
+ static_assert(sizeof(cj4[0].imei[0].imask) * 8 >= c_nbnxnGpuJgroupSize * c_gpuNumClusterPerCell,
+ "The i super-cluster cluster interaction mask does not contain a sufficient "
+ "number of bits");
- static_assert(sizeof(excl[0])*8 >= c_nbnxnGpuJgroupSize*c_gpuNumClusterPerCell, "The GPU exclusion mask does not contain a sufficient number of bits");
+ static_assert(sizeof(excl[0]) * 8 >= c_nbnxnGpuJgroupSize * c_gpuNumClusterPerCell,
+ "The GPU exclusion mask does not contain a sufficient number of bits");
// We always want a first entry without any exclusions
excl.resize(1);
-
- work = new NbnxnPairlistGpuWork();
}
-void nbnxn_init_pairlist_set(nbnxn_pairlist_set_t *nbl_list,
- gmx_bool bSimple, gmx_bool bCombined)
+// TODO: Move to pairlistset.cpp
+PairlistSet::PairlistSet(const PairlistParams& pairlistParams) :
+ params_(pairlistParams),
+ combineLists_(sc_isGpuPairListType[pairlistParams.pairlistType]), // Currently GPU lists are always combined
+ isCpuType_(!sc_isGpuPairListType[pairlistParams.pairlistType])
{
- GMX_RELEASE_ASSERT(!bSimple || !bCombined, "Can only combine non-simple lists");
- nbl_list->bSimple = bSimple;
- nbl_list->bCombined = bCombined;
+ const int numLists = gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded);
- nbl_list->nnbl = gmx_omp_nthreads_get(emntNonbonded);
-
- if (!nbl_list->bCombined &&
- nbl_list->nnbl > NBNXN_BUFFERFLAG_MAX_THREADS)
+ if (!combineLists_ && numLists > NBNXN_BUFFERFLAG_MAX_THREADS)
{
- gmx_fatal(FARGS, "%d OpenMP threads were requested. Since the non-bonded force buffer reduction is prohibitively slow with more than %d threads, we do not allow this. Use %d or less OpenMP threads.",
- nbl_list->nnbl, NBNXN_BUFFERFLAG_MAX_THREADS, NBNXN_BUFFERFLAG_MAX_THREADS);
+ gmx_fatal(FARGS,
+ "%d OpenMP threads were requested. Since the non-bonded force buffer reduction "
+ "is prohibitively slow with more than %d threads, we do not allow this. Use %d "
+ "or less OpenMP threads.",
+ numLists,
+ NBNXN_BUFFERFLAG_MAX_THREADS,
+ NBNXN_BUFFERFLAG_MAX_THREADS);
}
- if (bSimple)
+ if (isCpuType_)
{
- snew(nbl_list->nbl, nbl_list->nnbl);
- if (nbl_list->nnbl > 1)
+ cpuLists_.resize(numLists);
+ if (numLists > 1)
{
- snew(nbl_list->nbl_work, nbl_list->nnbl);
+ cpuListsWork_.resize(numLists);
}
}
else
{
- snew(nbl_list->nblGpu, nbl_list->nnbl);
+ /* Only list 0 is used on the GPU, use normal allocation for i>0 */
+ gpuLists_.emplace_back(gmx::PinningPolicy::PinnedIfSupported);
+ /* Lists 0 to numLists are use for constructing lists in parallel
+ * on the CPU using numLists threads (and then merged into list 0).
+ */
+ for (int i = 1; i < numLists; i++)
+ {
+ gpuLists_.emplace_back(gmx::PinningPolicy::CannotBePinned);
+ }
}
- snew(nbl_list->nbl_fep, nbl_list->nnbl);
- /* Execute in order to avoid memory interleaving between threads */
-#pragma omp parallel for num_threads(nbl_list->nnbl) schedule(static)
- for (int i = 0; i < nbl_list->nnbl; i++)
+ if (params_.haveFep)
{
- try
- {
- /* Allocate the nblist data structure locally on each thread
- * to optimize memory access for NUMA architectures.
- */
- if (bSimple)
- {
- nbl_list->nbl[i] = new NbnxnPairlistCpu();
+ fepLists_.resize(numLists);
- nbnxn_init_pairlist(nbl_list->nbl[i]);
- if (nbl_list->nnbl > 1)
- {
- nbl_list->nbl_work[i] = new NbnxnPairlistCpu();
- nbnxn_init_pairlist(nbl_list->nbl_work[i]);
- }
- }
- else
+ /* Execute in order to avoid memory interleaving between threads */
+#pragma omp parallel for num_threads(numLists) schedule(static)
+ for (int i = 0; i < numLists; i++)
+ {
+ try
{
- /* Only list 0 is used on the GPU, use normal allocation for i>0 */
- auto pinningPolicy = (i == 0 ? gmx::PinningPolicy::PinnedIfSupported : gmx::PinningPolicy::CannotBePinned);
-
- nbl_list->nblGpu[i] = new NbnxnPairlistGpu(pinningPolicy);
+ /* We used to allocate all normal lists locally on each thread
+ * as well. The question is if allocating the object on the
+ * master thread (but all contained list memory thread local)
+ * impacts performance.
+ */
+ fepLists_[i] = std::make_unique<t_nblist>();
}
-
- snew(nbl_list->nbl_fep[i], 1);
- nbnxn_init_pairlist_fep(nbl_list->nbl_fep[i]);
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
}
/* Print statistics of a pair list, used for debug output */
-static void print_nblist_statistics(FILE *fp, const NbnxnPairlistCpu *nbl,
- const nbnxn_search *nbs, real rl)
+static void print_nblist_statistics(FILE* fp,
+ const NbnxnPairlistCpu& nbl,
+ const Nbnxm::GridSet& gridSet,
+ const real rl)
{
- const nbnxn_grid_t *grid;
- int cs[SHIFTS];
- int npexcl;
-
- grid = &nbs->grid[0];
+ const Grid& grid = gridSet.grids()[0];
+ const Grid::Dimensions& dims = grid.dimensions();
- fprintf(fp, "nbl nci %zu ncj %d\n",
- nbl->ci.size(), nbl->ncjInUse);
- fprintf(fp, "nbl na_cj %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
- nbl->na_cj, rl, nbl->ncjInUse, nbl->ncjInUse/static_cast<double>(grid->nc),
- nbl->ncjInUse/static_cast<double>(grid->nc)*grid->na_cj,
- nbl->ncjInUse/static_cast<double>(grid->nc)*grid->na_cj/(0.5*4.0/3.0*M_PI*rl*rl*rl*grid->nc*grid->na_cj/(grid->size[XX]*grid->size[YY]*grid->size[ZZ])));
+ fprintf(fp, "nbl nci %zu ncj %d\n", nbl.ci.size(), nbl.ncjInUse);
+ const int numAtomsJCluster = grid.geometry().numAtomsJCluster;
- fprintf(fp, "nbl average j cell list length %.1f\n",
- 0.25*nbl->ncjInUse/std::max(static_cast<double>(nbl->ci.size()), 1.0));
-
- for (int s = 0; s < SHIFTS; s++)
+ if (grid.numCells() == 0)
{
- cs[s] = 0;
+ return;
}
- npexcl = 0;
- for (const nbnxn_ci_t &ciEntry : nbl->ci)
+
+ const double numAtomsPerCell = nbl.ncjInUse / static_cast<double>(grid.numCells()) * numAtomsJCluster;
+ fprintf(fp,
+ "nbl na_cj %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
+ nbl.na_cj,
+ rl,
+ nbl.ncjInUse,
+ nbl.ncjInUse / static_cast<double>(grid.numCells()),
+ numAtomsPerCell,
+ numAtomsPerCell
+ / (0.5 * 4.0 / 3.0 * M_PI * rl * rl * rl * grid.numCells() * numAtomsJCluster
+ / (dims.gridSize[XX] * dims.gridSize[YY] * dims.gridSize[ZZ])));
+
+ fprintf(fp,
+ "nbl average j cell list length %.1f\n",
+ 0.25 * nbl.ncjInUse / std::max(static_cast<double>(nbl.ci.size()), 1.0));
+
+ int cs[gmx::c_numShiftVectors] = { 0 };
+ int npexcl = 0;
+ for (const nbnxn_ci_t& ciEntry : nbl.ci)
{
- cs[ciEntry.shift & NBNXN_CI_SHIFT] +=
- ciEntry.cj_ind_end - ciEntry.cj_ind_start;
+ cs[ciEntry.shift & NBNXN_CI_SHIFT] += ciEntry.cj_ind_end - ciEntry.cj_ind_start;
int j = ciEntry.cj_ind_start;
- while (j < ciEntry.cj_ind_end &&
- nbl->cj[j].excl != NBNXN_INTERACTION_MASK_ALL)
+ while (j < ciEntry.cj_ind_end && nbl.cj[j].excl != NBNXN_INTERACTION_MASK_ALL)
{
npexcl++;
j++;
}
}
- fprintf(fp, "nbl cell pairs, total: %zu excl: %d %.1f%%\n",
- nbl->cj.size(), npexcl, 100*npexcl/std::max(static_cast<double>(nbl->cj.size()), 1.0));
- for (int s = 0; s < SHIFTS; s++)
+ fprintf(fp,
+ "nbl cell pairs, total: %zu excl: %d %.1f%%\n",
+ nbl.cj.size(),
+ npexcl,
+ 100 * npexcl / std::max(static_cast<double>(nbl.cj.size()), 1.0));
+ for (int s = 0; s < gmx::c_numShiftVectors; s++)
{
if (cs[s] > 0)
{
}
/* Print statistics of a pair lists, used for debug output */
-static void print_nblist_statistics(FILE *fp, const NbnxnPairlistGpu *nbl,
- const nbnxn_search *nbs, real rl)
+static void print_nblist_statistics(FILE* fp,
+ const NbnxnPairlistGpu& nbl,
+ const Nbnxm::GridSet& gridSet,
+ const real rl)
{
- const nbnxn_grid_t *grid;
- int b;
- int c[c_gpuNumClusterPerCell + 1];
- double sum_nsp, sum_nsp2;
- int nsp_max;
-
- /* This code only produces correct statistics with domain decomposition */
- grid = &nbs->grid[0];
-
- fprintf(fp, "nbl nsci %zu ncj4 %zu nsi %d excl4 %zu\n",
- nbl->sci.size(), nbl->cj4.size(), nbl->nci_tot, nbl->excl.size());
- fprintf(fp, "nbl na_c %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
- nbl->na_ci, rl, nbl->nci_tot, nbl->nci_tot/static_cast<double>(grid->nsubc_tot),
- nbl->nci_tot/static_cast<double>(grid->nsubc_tot)*grid->na_c,
- nbl->nci_tot/static_cast<double>(grid->nsubc_tot)*grid->na_c/(0.5*4.0/3.0*M_PI*rl*rl*rl*grid->nsubc_tot*grid->na_c/(grid->size[XX]*grid->size[YY]*grid->size[ZZ])));
-
- sum_nsp = 0;
- sum_nsp2 = 0;
- nsp_max = 0;
- for (int si = 0; si <= c_gpuNumClusterPerCell; si++)
- {
- c[si] = 0;
- }
- for (const nbnxn_sci_t &sci : nbl->sci)
+ const Grid& grid = gridSet.grids()[0];
+ const Grid::Dimensions& dims = grid.dimensions();
+
+ fprintf(fp,
+ "nbl nsci %zu ncj4 %zu nsi %d excl4 %zu\n",
+ nbl.sci.size(),
+ nbl.cj4.size(),
+ nbl.nci_tot,
+ nbl.excl.size());
+ const int numAtomsCluster = grid.geometry().numAtomsICluster;
+ const double numAtomsPerCell = nbl.nci_tot / static_cast<double>(grid.numClusters()) * numAtomsCluster;
+ fprintf(fp,
+ "nbl na_c %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
+ nbl.na_ci,
+ rl,
+ nbl.nci_tot,
+ nbl.nci_tot / static_cast<double>(grid.numClusters()),
+ numAtomsPerCell,
+ numAtomsPerCell
+ / (0.5 * 4.0 / 3.0 * M_PI * rl * rl * rl * grid.numClusters() * numAtomsCluster
+ / (dims.gridSize[XX] * dims.gridSize[YY] * dims.gridSize[ZZ])));
+
+ double sum_nsp = 0;
+ double sum_nsp2 = 0;
+ int nsp_max = 0;
+ int c[c_gpuNumClusterPerCell + 1] = { 0 };
+ for (const nbnxn_sci_t& sci : nbl.sci)
{
int nsp = 0;
for (int j4 = sci.cj4_ind_start; j4 < sci.cj4_ind_end; j4++)
{
for (int j = 0; j < c_nbnxnGpuJgroupSize; j++)
{
- b = 0;
+ int b = 0;
for (int si = 0; si < c_gpuNumClusterPerCell; si++)
{
- if (nbl->cj4[j4].imei[0].imask & (1U << (j*c_gpuNumClusterPerCell + si)))
+ if (nbl.cj4[j4].imei[0].imask & (1U << (j * c_gpuNumClusterPerCell + si)))
{
b++;
}
c[b]++;
}
}
- sum_nsp += nsp;
- sum_nsp2 += nsp*nsp;
- nsp_max = std::max(nsp_max, nsp);
+ sum_nsp += nsp;
+ sum_nsp2 += nsp * nsp;
+ nsp_max = std::max(nsp_max, nsp);
}
- if (!nbl->sci.empty())
+ if (!nbl.sci.empty())
{
- sum_nsp /= nbl->sci.size();
- sum_nsp2 /= nbl->sci.size();
+ sum_nsp /= nbl.sci.size();
+ sum_nsp2 /= nbl.sci.size();
}
- fprintf(fp, "nbl #cluster-pairs: av %.1f stddev %.1f max %d\n",
- sum_nsp, std::sqrt(sum_nsp2 - sum_nsp*sum_nsp), nsp_max);
+ fprintf(fp,
+ "nbl #cluster-pairs: av %.1f stddev %.1f max %d\n",
+ sum_nsp,
+ std::sqrt(sum_nsp2 - sum_nsp * sum_nsp),
+ nsp_max);
- if (!nbl->cj4.empty())
+ if (!nbl.cj4.empty())
{
- for (b = 0; b <= c_gpuNumClusterPerCell; b++)
+ for (int b = 0; b <= c_gpuNumClusterPerCell; b++)
{
- fprintf(fp, "nbl j-list #i-subcell %d %7d %4.1f\n",
- b, c[b], 100.0*c[b]/size_t {nbl->cj4.size()*c_nbnxnGpuJgroupSize});
+ fprintf(fp,
+ "nbl j-list #i-subcell %d %7d %4.1f\n",
+ b,
+ c[b],
+ 100.0 * c[b] / size_t{ nbl.cj4.size() * c_nbnxnGpuJgroupSize });
}
}
}
-/* Returns a pointer to the exclusion mask for j-cluster-group \p cj4 and warp \p warp
+/* Returns a reference to the exclusion mask for j-cluster-group \p cj4 and warp \p warp
* Generates a new exclusion entry when the j-cluster-group uses
* the default all-interaction mask at call time, so the returned mask
* can be modified when needed.
*/
-static nbnxn_excl_t *get_exclusion_mask(NbnxnPairlistGpu *nbl,
- int cj4,
- int warp)
+static nbnxn_excl_t& get_exclusion_mask(NbnxnPairlistGpu* nbl, int cj4, int warp)
{
if (nbl->cj4[cj4].imei[warp].excl_ind == 0)
{
nbl->cj4[cj4].imei[warp].excl_ind = oldSize;
}
- return &nbl->excl[nbl->cj4[cj4].imei[warp].excl_ind];
+ return nbl->excl[nbl->cj4[cj4].imei[warp].excl_ind];
}
-static void set_self_and_newton_excls_supersub(NbnxnPairlistGpu *nbl,
- int cj4_ind, int sj_offset,
- int i_cluster_in_cell)
+/* Sets self exclusions and excludes half of the double pairs in the self cluster-pair \p nbl->cj4[cj4Index].cj[jOffsetInGroup]
+ *
+ * \param[in,out] nbl The cluster pair list
+ * \param[in] cj4Index The j-cluster group index into \p nbl->cj4
+ * \param[in] jOffsetInGroup The j-entry offset in \p nbl->cj4[cj4Index]
+ * \param[in] iClusterInCell The i-cluster index in the cell
+ */
+static void setSelfAndNewtonExclusionsGpu(NbnxnPairlistGpu* nbl,
+ const int cj4Index,
+ const int jOffsetInGroup,
+ const int iClusterInCell)
{
- nbnxn_excl_t *excl[c_nbnxnGpuClusterpairSplit];
-
- /* Here we only set the set self and double pair exclusions */
+ constexpr int numJatomsPerPart = c_nbnxnGpuClusterSize / c_nbnxnGpuClusterpairSplit;
- /* Reserve extra elements, so the resize() in get_exclusion_mask()
- * will not invalidate excl entries in the loop below
- */
- nbl->excl.reserve(nbl->excl.size() + c_nbnxnGpuClusterpairSplit);
- for (int w = 0; w < c_nbnxnGpuClusterpairSplit; w++)
+ /* The exclusions are stored separately for each part of the split */
+ for (int part = 0; part < c_nbnxnGpuClusterpairSplit; part++)
{
- excl[w] = get_exclusion_mask(nbl, cj4_ind, w);
- }
+ const int jOffset = part * numJatomsPerPart;
+ /* Make a new exclusion mask entry for each part, if we don't already have one yet */
+ nbnxn_excl_t& excl = get_exclusion_mask(nbl, cj4Index, part);
- /* Only minor < major bits set */
- for (int ej = 0; ej < nbl->na_ci; ej++)
- {
- int w = (ej>>2);
- for (int ei = ej; ei < nbl->na_ci; ei++)
+ /* Set all bits with j-index <= i-index */
+ for (int jIndexInPart = 0; jIndexInPart < numJatomsPerPart; jIndexInPart++)
{
- excl[w]->pair[(ej & (c_nbnxnGpuJgroupSize-1))*nbl->na_ci + ei] &=
- ~(1U << (sj_offset*c_gpuNumClusterPerCell + i_cluster_in_cell));
+ for (int i = jOffset + jIndexInPart; i < c_nbnxnGpuClusterSize; i++)
+ {
+ excl.pair[jIndexInPart * c_nbnxnGpuClusterSize + i] &=
+ ~(1U << (jOffsetInGroup * c_gpuNumClusterPerCell + iClusterInCell));
+ }
}
}
}
/* Returns a diagonal or off-diagonal interaction mask for cj-size=2 */
gmx_unused static unsigned int get_imask_simd_j2(gmx_bool rdiag, int ci, int cj)
{
- return (rdiag && ci*2 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_0 :
- (rdiag && ci*2+1 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_1 :
- NBNXN_INTERACTION_MASK_ALL));
+ return (rdiag && ci * 2 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_0
+ : (rdiag && ci * 2 + 1 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_1
+ : NBNXN_INTERACTION_MASK_ALL));
}
/* Returns a diagonal or off-diagonal interaction mask for cj-size=4 */
/* Returns a diagonal or off-diagonal interaction mask for cj-size=8 */
gmx_unused static unsigned int get_imask_simd_j8(gmx_bool rdiag, int ci, int cj)
{
- return (rdiag && ci == cj*2 ? NBNXN_INTERACTION_MASK_DIAG_J8_0 :
- (rdiag && ci == cj*2+1 ? NBNXN_INTERACTION_MASK_DIAG_J8_1 :
- NBNXN_INTERACTION_MASK_ALL));
+ return (rdiag && ci == cj * 2 ? NBNXN_INTERACTION_MASK_DIAG_J8_0
+ : (rdiag && ci == cj * 2 + 1 ? NBNXN_INTERACTION_MASK_DIAG_J8_1
+ : NBNXN_INTERACTION_MASK_ALL));
}
#if GMX_SIMD
-#if GMX_SIMD_REAL_WIDTH == 2
-#define get_imask_simd_4xn get_imask_simd_j2
-#endif
-#if GMX_SIMD_REAL_WIDTH == 4
-#define get_imask_simd_4xn get_imask_simd_j4
-#endif
-#if GMX_SIMD_REAL_WIDTH == 8
-#define get_imask_simd_4xn get_imask_simd_j8
-#define get_imask_simd_2xnn get_imask_simd_j4
-#endif
-#if GMX_SIMD_REAL_WIDTH == 16
-#define get_imask_simd_2xnn get_imask_simd_j8
-#endif
+# if GMX_SIMD_REAL_WIDTH == 2
+# define get_imask_simd_4xn get_imask_simd_j2
+# endif
+# if GMX_SIMD_REAL_WIDTH == 4
+# define get_imask_simd_4xn get_imask_simd_j4
+# endif
+# if GMX_SIMD_REAL_WIDTH == 8
+# define get_imask_simd_4xn get_imask_simd_j8
+# define get_imask_simd_2xnn get_imask_simd_j4
+# endif
+# if GMX_SIMD_REAL_WIDTH == 16
+# define get_imask_simd_2xnn get_imask_simd_j8
+# endif
#endif
/* Plain C code for checking and adding cluster-pairs to the list.
* \param[in] rbb2 The squared cut-off for putting cluster-pairs in the list based on bounding box distance only
* \param[in,out] numDistanceChecks The number of distance checks performed
*/
-static void
-makeClusterListSimple(const nbnxn_grid_t &jGrid,
- NbnxnPairlistCpu * nbl,
- int icluster,
- int jclusterFirst,
- int jclusterLast,
- bool excludeSubDiagonal,
- const real * gmx_restrict x_j,
- real rlist2,
- float rbb2,
- int * gmx_restrict numDistanceChecks)
+static void makeClusterListSimple(const Grid& jGrid,
+ NbnxnPairlistCpu* nbl,
+ int icluster,
+ int jclusterFirst,
+ int jclusterLast,
+ bool excludeSubDiagonal,
+ const real* gmx_restrict x_j,
+ real rlist2,
+ float rbb2,
+ int* gmx_restrict numDistanceChecks)
{
- const nbnxn_bb_t * gmx_restrict bb_ci = nbl->work->iClusterData.bb.data();
- const real * gmx_restrict x_ci = nbl->work->iClusterData.x.data();
-
- gmx_bool InRange;
+ const BoundingBox* gmx_restrict bb_ci = nbl->work->iClusterData.bb.data();
+ const real* gmx_restrict x_ci = nbl->work->iClusterData.x.data();
- InRange = FALSE;
+ bool InRange = false;
while (!InRange && jclusterFirst <= jclusterLast)
{
- real d2 = subc_bb_dist2(0, bb_ci, jclusterFirst, jGrid.bb);
+ real d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterFirst]);
*numDistanceChecks += 2;
/* Check if the distance is within the distance where
*/
if (d2 < rbb2)
{
- InRange = TRUE;
+ InRange = true;
}
else if (d2 < rlist2)
{
- int cjf_gl = jGrid.cell0 + jclusterFirst;
+ int cjf_gl = jGrid.cellOffset() + jclusterFirst;
for (int i = 0; i < c_nbnxnCpuIClusterSize && !InRange; i++)
{
for (int j = 0; j < c_nbnxnCpuIClusterSize; j++)
{
- InRange = InRange ||
- (gmx::square(x_ci[i*STRIDE_XYZ+XX] - x_j[(cjf_gl*c_nbnxnCpuIClusterSize+j)*STRIDE_XYZ+XX]) +
- gmx::square(x_ci[i*STRIDE_XYZ+YY] - x_j[(cjf_gl*c_nbnxnCpuIClusterSize+j)*STRIDE_XYZ+YY]) +
- gmx::square(x_ci[i*STRIDE_XYZ+ZZ] - x_j[(cjf_gl*c_nbnxnCpuIClusterSize+j)*STRIDE_XYZ+ZZ]) < rlist2);
+ InRange =
+ InRange
+ || (gmx::square(x_ci[i * STRIDE_XYZ + XX]
+ - x_j[(cjf_gl * c_nbnxnCpuIClusterSize + j) * STRIDE_XYZ + XX])
+ + gmx::square(x_ci[i * STRIDE_XYZ + YY]
+ - x_j[(cjf_gl * c_nbnxnCpuIClusterSize + j) * STRIDE_XYZ + YY])
+ + gmx::square(x_ci[i * STRIDE_XYZ + ZZ]
+ - x_j[(cjf_gl * c_nbnxnCpuIClusterSize + j) * STRIDE_XYZ + ZZ])
+ < rlist2);
}
}
- *numDistanceChecks += c_nbnxnCpuIClusterSize*c_nbnxnCpuIClusterSize;
+ *numDistanceChecks += c_nbnxnCpuIClusterSize * c_nbnxnCpuIClusterSize;
}
if (!InRange)
{
return;
}
- InRange = FALSE;
+ InRange = false;
while (!InRange && jclusterLast > jclusterFirst)
{
- real d2 = subc_bb_dist2(0, bb_ci, jclusterLast, jGrid.bb);
+ real d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterLast]);
*numDistanceChecks += 2;
/* Check if the distance is within the distance where
*/
if (d2 < rbb2)
{
- InRange = TRUE;
+ InRange = true;
}
else if (d2 < rlist2)
{
- int cjl_gl = jGrid.cell0 + jclusterLast;
+ int cjl_gl = jGrid.cellOffset() + jclusterLast;
for (int i = 0; i < c_nbnxnCpuIClusterSize && !InRange; i++)
{
for (int j = 0; j < c_nbnxnCpuIClusterSize; j++)
{
- InRange = InRange ||
- (gmx::square(x_ci[i*STRIDE_XYZ+XX] - x_j[(cjl_gl*c_nbnxnCpuIClusterSize+j)*STRIDE_XYZ+XX]) +
- gmx::square(x_ci[i*STRIDE_XYZ+YY] - x_j[(cjl_gl*c_nbnxnCpuIClusterSize+j)*STRIDE_XYZ+YY]) +
- gmx::square(x_ci[i*STRIDE_XYZ+ZZ] - x_j[(cjl_gl*c_nbnxnCpuIClusterSize+j)*STRIDE_XYZ+ZZ]) < rlist2);
+ InRange =
+ InRange
+ || (gmx::square(x_ci[i * STRIDE_XYZ + XX]
+ - x_j[(cjl_gl * c_nbnxnCpuIClusterSize + j) * STRIDE_XYZ + XX])
+ + gmx::square(x_ci[i * STRIDE_XYZ + YY]
+ - x_j[(cjl_gl * c_nbnxnCpuIClusterSize + j) * STRIDE_XYZ + YY])
+ + gmx::square(x_ci[i * STRIDE_XYZ + ZZ]
+ - x_j[(cjl_gl * c_nbnxnCpuIClusterSize + j) * STRIDE_XYZ + ZZ])
+ < rlist2);
}
}
- *numDistanceChecks += c_nbnxnCpuIClusterSize*c_nbnxnCpuIClusterSize;
+ *numDistanceChecks += c_nbnxnCpuIClusterSize * c_nbnxnCpuIClusterSize;
}
if (!InRange)
{
{
/* Store cj and the interaction mask */
nbnxn_cj_t cjEntry;
- cjEntry.cj = jGrid.cell0 + jcluster;
+ cjEntry.cj = jGrid.cellOffset() + jcluster;
cjEntry.excl = get_imask(excludeSubDiagonal, icluster, jcluster);
nbl->cj.push_back(cjEntry);
}
}
#ifdef GMX_NBNXN_SIMD_4XN
-#include "gromacs/nbnxm/pairlist_simd_4xm.h"
+# include "pairlist_simd_4xm.h"
#endif
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "gromacs/nbnxm/pairlist_simd_2xmm.h"
+# include "pairlist_simd_2xmm.h"
#endif
/* Plain C or SIMD4 code for making a pair list of super-cell sci vs scj.
* Checks bounding box distances and possibly atom pair distances.
*/
-static void make_cluster_list_supersub(const nbnxn_grid_t &iGrid,
- const nbnxn_grid_t &jGrid,
- NbnxnPairlistGpu *nbl,
- const int sci,
- const int scj,
- const bool excludeSubDiagonal,
- const int stride,
- const real *x,
- const real rlist2,
- const float rbb2,
- int *numDistanceChecks)
+static void make_cluster_list_supersub(const Grid& iGrid,
+ const Grid& jGrid,
+ NbnxnPairlistGpu* nbl,
+ const int sci,
+ const int scj,
+ const bool excludeSubDiagonal,
+ const int stride,
+ const real* x,
+ const real rlist2,
+ const float rbb2,
+ int* numDistanceChecks)
{
- NbnxnPairlistGpuWork &work = *nbl->work;
+ NbnxnPairlistGpuWork& work = *nbl->work;
#if NBNXN_BBXXXX
- const float *pbb_ci = work.iSuperClusterData.bbPacked.data();
+ const float* pbb_ci = work.iSuperClusterData.bbPacked.data();
#else
- const nbnxn_bb_t *bb_ci = work.iSuperClusterData.bb.data();
+ const BoundingBox* bb_ci = work.iSuperClusterData.bb.data();
#endif
- assert(c_nbnxnGpuClusterSize == iGrid.na_c);
- assert(c_nbnxnGpuClusterSize == jGrid.na_c);
+ assert(c_nbnxnGpuClusterSize == iGrid.geometry().numAtomsICluster);
+ assert(c_nbnxnGpuClusterSize == jGrid.geometry().numAtomsICluster);
/* We generate the pairlist mainly based on bounding-box distances
* and do atom pair distance based pruning on the GPU.
#define PRUNE_LIST_CPU_ALL 0
#if PRUNE_LIST_CPU_ONE
- int ci_last = -1;
+ int ci_last = -1;
#endif
- float *d2l = work.distanceBuffer.data();
+ float* d2l = work.distanceBuffer.data();
- for (int subc = 0; subc < jGrid.nsubc[scj]; subc++)
+ for (int subc = 0; subc < jGrid.numClustersPerCell()[scj]; subc++)
{
- const int cj4_ind = work.cj_ind/c_nbnxnGpuJgroupSize;
- const int cj_offset = work.cj_ind - cj4_ind*c_nbnxnGpuJgroupSize;
- const int cj = scj*c_gpuNumClusterPerCell + subc;
+ const int cj4_ind = work.cj_ind / c_nbnxnGpuJgroupSize;
+ const int cj_offset = work.cj_ind - cj4_ind * c_nbnxnGpuJgroupSize;
+ const int cj = scj * c_gpuNumClusterPerCell + subc;
- const int cj_gl = jGrid.cell0*c_gpuNumClusterPerCell + cj;
+ const int cj_gl = jGrid.cellOffset() * c_gpuNumClusterPerCell + cj;
+
+ int ci1 = (excludeSubDiagonal && sci == scj) ? subc + 1 : iGrid.numClustersPerCell()[sci];
- int ci1;
- if (excludeSubDiagonal && sci == scj)
- {
- ci1 = subc + 1;
- }
- else
- {
- ci1 = iGrid.nsubc[sci];
- }
#if NBNXN_BBXXXX
/* Determine all ci1 bb distances in one call with SIMD4 */
- subc_bb_dist2_simd4_xxxx(jGrid.pbb.data() + (cj >> STRIDE_PBB_2LOG)*NNBSBB_XXXX + (cj & (STRIDE_PBB-1)),
- ci1, pbb_ci, d2l);
- *numDistanceChecks += c_nbnxnGpuClusterSize*2;
+ const int offset = packedBoundingBoxesIndex(cj) + (cj & (c_packedBoundingBoxesDimSize - 1));
+ clusterBoundingBoxDistance2_xxxx_simd4(
+ jGrid.packedBoundingBoxes().data() + offset, ci1, pbb_ci, d2l);
+ *numDistanceChecks += c_nbnxnGpuClusterSize * 2;
#endif
int npair = 0;
#if !NBNXN_BBXXXX
/* Determine the bb distance between ci and cj */
- d2l[ci] = subc_bb_dist2(ci, bb_ci, cj, jGrid.bb);
+ d2l[ci] = clusterBoundingBoxDistance2(bb_ci[ci], jGrid.jBoundingBoxes()[cj]);
*numDistanceChecks += 2;
#endif
float d2 = d2l[ci];
* or within the cut-off and there is at least one atom pair
* within the cut-off. This check is very costly.
*/
- *numDistanceChecks += c_nbnxnGpuClusterSize*c_nbnxnGpuClusterSize;
- if (d2 < rbb2 ||
- (d2 < rlist2 &&
- clusterpair_in_range(work, ci, cj_gl, stride, x, rlist2)))
+ *numDistanceChecks += c_nbnxnGpuClusterSize * c_nbnxnGpuClusterSize;
+ if (d2 < rbb2 || (d2 < rlist2 && clusterpair_in_range(work, ci, cj_gl, stride, x, rlist2)))
#else
/* Check if the distance between the two bounding boxes
* in within the pair-list cut-off.
#endif
{
/* Flag this i-subcell to be taken into account */
- imask |= (1U << (cj_offset*c_gpuNumClusterPerCell + ci));
+ imask |= (1U << (cj_offset * c_gpuNumClusterPerCell + ci));
#if PRUNE_LIST_CPU_ONE
ci_last = ci;
/* If we only found 1 pair, check if any atoms are actually
* within the cut-off, so we could get rid of it.
*/
- if (npair == 1 && d2l[ci_last] >= rbb2 &&
- !clusterpair_in_range(work, ci_last, cj_gl, stride, x, rlist2))
+ if (npair == 1 && d2l[ci_last] >= rbb2
+ && !clusterpair_in_range(work, ci_last, cj_gl, stride, x, rlist2))
{
- imask &= ~(1U << (cj_offset*c_gpuNumClusterPerCell + ci_last));
+ imask &= ~(1U << (cj_offset * c_gpuNumClusterPerCell + ci_last));
npair--;
}
#endif
{
nbl->cj4.resize(nbl->cj4.size() + 1);
}
- nbnxn_cj4_t *cj4 = &nbl->cj4[cj4_ind];
+ nbnxn_cj4_t* cj4 = &nbl->cj4[cj4_ind];
cj4->cj[cj_offset] = cj_gl;
*/
if (excludeSubDiagonal && sci == scj)
{
- set_self_and_newton_excls_supersub(nbl, cj4_ind, cj_offset, subc);
+ setSelfAndNewtonExclusionsGpu(nbl, cj4_ind, cj_offset, subc);
}
/* Copy the cluster interaction mask to the list */
/* Increase the closing index in i super-cell list */
nbl->sci.back().cj4_ind_end =
- (nbl->work->cj_ind + c_nbnxnGpuJgroupSize - 1)/c_nbnxnGpuJgroupSize;
+ (nbl->work->cj_ind + c_nbnxnGpuJgroupSize - 1) / c_nbnxnGpuJgroupSize;
}
}
}
/* Returns how many contiguous j-clusters we have starting in the i-list */
-template <typename CjListType>
+template<typename CjListType>
static int numContiguousJClusters(const int cjIndexStart,
const int cjIndexEnd,
gmx::ArrayRef<const CjListType> cjList)
{
const int firstJCluster = nblCj(cjList, cjIndexStart);
- int numContiguous = 0;
+ int numContiguous = 0;
- while (cjIndexStart + numContiguous < cjIndexEnd &&
- nblCj(cjList, cjIndexStart + numContiguous) == firstJCluster + numContiguous)
+ while (cjIndexStart + numContiguous < cjIndexEnd
+ && nblCj(cjList, cjIndexStart + numContiguous) == firstJCluster + numContiguous)
{
numContiguous++;
}
struct JListRanges
{
/*! \brief Constructs a j-list range from \p cjList with the given index range */
- template <typename CjListType>
- JListRanges(int cjIndexStart,
- int cjIndexEnd,
- gmx::ArrayRef<const CjListType> cjList);
+ template<typename CjListType>
+ JListRanges(int cjIndexStart, int cjIndexEnd, gmx::ArrayRef<const CjListType> cjList);
int cjIndexStart; //!< The start index in the j-list
int cjIndexEnd; //!< The end index in the j-list
int cjFirst; //!< The j-cluster with index cjIndexStart
int cjLast; //!< The j-cluster with index cjIndexEnd-1
- int numDirect; //!< Up to cjIndexStart+numDirect the j-clusters are cjFirst + the index offset
+ int numDirect; //!< Up to cjIndexStart+numDirect the j-clusters are cjFirst + the index offset
};
#ifndef DOXYGEN
-template <typename CjListType>
-JListRanges::JListRanges(int cjIndexStart,
- int cjIndexEnd,
- gmx::ArrayRef<const CjListType> cjList) :
- cjIndexStart(cjIndexStart),
- cjIndexEnd(cjIndexEnd)
+template<typename CjListType>
+JListRanges::JListRanges(int cjIndexStart, int cjIndexEnd, gmx::ArrayRef<const CjListType> cjList) :
+ cjIndexStart(cjIndexStart), cjIndexEnd(cjIndexEnd)
{
GMX_ASSERT(cjIndexEnd > cjIndexStart, "JListRanges should only be called with non-empty lists");
- cjFirst = nblCj(cjList, cjIndexStart);
- cjLast = nblCj(cjList, cjIndexEnd - 1);
+ cjFirst = nblCj(cjList, cjIndexStart);
+ cjLast = nblCj(cjList, cjIndexEnd - 1);
/* Determine how many contiguous j-cells we have starting
* from the first i-cell. This number can be used to directly
* Note: This code is executed very often and therefore performance is
* important. It should be inlined and fully optimized.
*/
-template <typename CjListType>
-static inline int
-findJClusterInJList(int jCluster,
- const JListRanges &ranges,
- gmx::ArrayRef<const CjListType> cjList)
+template<typename CjListType>
+static inline int findJClusterInJList(int jCluster,
+ const JListRanges& ranges,
+ gmx::ArrayRef<const CjListType> cjList)
{
- int index;
-
if (jCluster < ranges.cjFirst + ranges.numDirect)
{
/* We can calculate the index directly using the offset */
- index = ranges.cjIndexStart + jCluster - ranges.cjFirst;
+ return ranges.cjIndexStart + jCluster - ranges.cjFirst;
}
else
{
/* Search for jCluster using bisection */
- index = -1;
- int rangeStart = ranges.cjIndexStart + ranges.numDirect;
- int rangeEnd = ranges.cjIndexEnd;
- int rangeMiddle;
+ int index = -1;
+ int rangeStart = ranges.cjIndexStart + ranges.numDirect;
+ int rangeEnd = ranges.cjIndexEnd;
while (index == -1 && rangeStart < rangeEnd)
{
- rangeMiddle = (rangeStart + rangeEnd) >> 1;
+ int rangeMiddle = (rangeStart + rangeEnd) >> 1;
const int clusterMiddle = nblCj(cjList, rangeMiddle);
if (jCluster == clusterMiddle)
{
- index = rangeMiddle;
+ index = rangeMiddle;
}
else if (jCluster < clusterMiddle)
{
- rangeEnd = rangeMiddle;
+ rangeEnd = rangeMiddle;
}
else
{
rangeStart = rangeMiddle + 1;
}
}
+ return index;
}
-
- return index;
}
// TODO: Get rid of the two functions below by renaming sci to ci (or something better)
/* Return the i-entry in the list we are currently operating on */
-static nbnxn_ci_t *getOpenIEntry(NbnxnPairlistCpu *nbl)
+static nbnxn_ci_t* getOpenIEntry(NbnxnPairlistCpu* nbl)
{
return &nbl->ci.back();
}
/* Return the i-entry in the list we are currently operating on */
-static nbnxn_sci_t *getOpenIEntry(NbnxnPairlistGpu *nbl)
+static nbnxn_sci_t* getOpenIEntry(NbnxnPairlistGpu* nbl)
{
return &nbl->sci.back();
}
* Set all atom-pair exclusions from the topology stored in exclusions
* as masks in the pair-list for simple list entry iEntry.
*/
-static void
-setExclusionsForIEntry(const nbnxn_search *nbs,
- NbnxnPairlistCpu *nbl,
- gmx_bool diagRemoved,
- int na_cj_2log,
- const nbnxn_ci_t &iEntry,
- const t_blocka &exclusions)
+static void setExclusionsForIEntry(const Nbnxm::GridSet& gridSet,
+ NbnxnPairlistCpu* nbl,
+ gmx_bool diagRemoved,
+ int na_cj_2log,
+ const nbnxn_ci_t& iEntry,
+ const ListOfLists<int>& exclusions)
{
if (iEntry.cj_ind_end == iEntry.cj_ind_start)
{
return;
}
- const JListRanges ranges(iEntry.cj_ind_start, iEntry.cj_ind_end, gmx::makeConstArrayRef(nbl->cj));
+ const JListRanges ranges(iEntry.cj_ind_start, iEntry.cj_ind_end, gmx::makeConstArrayRef(nbl->cj));
- const int iCluster = iEntry.ci;
+ const int iCluster = iEntry.ci;
- gmx::ArrayRef<const int> cell = nbs->cell;
+ gmx::ArrayRef<const int> cell = gridSet.cells();
+ gmx::ArrayRef<const int> atomIndices = gridSet.atomIndices();
/* Loop over the atoms in the i-cluster */
for (int i = 0; i < nbl->na_ci; i++)
{
- const int iIndex = iCluster*nbl->na_ci + i;
- const int iAtom = nbs->a[iIndex];
+ const int iIndex = iCluster * nbl->na_ci + i;
+ const int iAtom = atomIndices[iIndex];
if (iAtom >= 0)
{
/* Loop over the topology-based exclusions for this i-atom */
- for (int exclIndex = exclusions.index[iAtom]; exclIndex < exclusions.index[iAtom + 1]; exclIndex++)
+ for (const int jAtom : exclusions[iAtom])
{
- const int jAtom = exclusions.a[exclIndex];
-
if (jAtom == iAtom)
{
/* The self exclusion are already set, save some time */
if (jCluster >= ranges.cjFirst && jCluster <= ranges.cjLast)
{
const int index =
- findJClusterInJList(jCluster, ranges,
- gmx::makeConstArrayRef(nbl->cj));
+ findJClusterInJList(jCluster, ranges, gmx::makeConstArrayRef(nbl->cj));
if (index >= 0)
{
/* We found an exclusion, clear the corresponding
* interaction bit.
*/
- const int innerJ = jIndex - (jCluster << na_cj_2log);
+ const int innerJ = jIndex - (jCluster << na_cj_2log);
nbl->cj[index].excl &= ~(1U << ((i << na_cj_2log) + innerJ));
}
}
/* Add a new i-entry to the FEP list and copy the i-properties */
-static inline void fep_list_new_nri_copy(t_nblist *nlist)
+static inline void fep_list_new_nri_copy(t_nblist* nlist)
{
/* Add a new i-entry */
nlist->nri++;
assert(nlist->nri < nlist->maxnri);
/* Duplicate the last i-entry, except for jindex, which continues */
- nlist->iinr[nlist->nri] = nlist->iinr[nlist->nri-1];
- nlist->shift[nlist->nri] = nlist->shift[nlist->nri-1];
- nlist->gid[nlist->nri] = nlist->gid[nlist->nri-1];
+ nlist->iinr[nlist->nri] = nlist->iinr[nlist->nri - 1];
+ nlist->shift[nlist->nri] = nlist->shift[nlist->nri - 1];
+ nlist->gid[nlist->nri] = nlist->gid[nlist->nri - 1];
nlist->jindex[nlist->nri] = nlist->nrj;
}
+/* Rellocate FEP list for size nl->maxnri, TODO: replace by C++ */
+static void reallocate_nblist(t_nblist* nl)
+{
+ nl->iinr.resize(nl->maxnri);
+ nl->gid.resize(nl->maxnri);
+ nl->shift.resize(nl->maxnri);
+ nl->jindex.resize(nl->maxnri + 1);
+}
+
/* For load balancing of the free-energy lists over threads, we set
* the maximum nrj size of an i-entry to 40. This leads to good
* load balancing in the worst case scenario of a single perturbed
* LJ parameters have been zeroed in the nbnxn data structure.
* Simultaneously make a group pair list for the perturbed pairs.
*/
-static void make_fep_list(const nbnxn_search *nbs,
- const nbnxn_atomdata_t *nbat,
- NbnxnPairlistCpu *nbl,
- gmx_bool bDiagRemoved,
- nbnxn_ci_t *nbl_ci,
- real gmx_unused shx,
- real gmx_unused shy,
- real gmx_unused shz,
- real gmx_unused rlist_fep2,
- const nbnxn_grid_t &iGrid,
- const nbnxn_grid_t &jGrid,
- t_nblist *nlist)
+static void make_fep_list(gmx::ArrayRef<const int> atomIndices,
+ const nbnxn_atomdata_t* nbat,
+ NbnxnPairlistCpu* nbl,
+ gmx_bool bDiagRemoved,
+ nbnxn_ci_t* nbl_ci,
+ real gmx_unused shx,
+ real gmx_unused shy,
+ real gmx_unused shz,
+ real gmx_unused rlist_fep2,
+ const Grid& iGrid,
+ const Grid& jGrid,
+ t_nblist* nlist)
{
- int ci, cj_ind_start, cj_ind_end, cja, cjr;
- int nri_max;
- int ngid, gid_i = 0, gid_j, gid;
- int egp_shift, egp_mask;
- int gid_cj = 0;
- int ind_i, ind_j, ai, aj;
- int nri;
- gmx_bool bFEP_i, bFEP_i_all;
+ int gid_i = 0;
+ int gid_cj = 0;
if (nbl_ci->cj_ind_end == nbl_ci->cj_ind_start)
{
return;
}
- ci = nbl_ci->ci;
+ const int ci = nbl_ci->ci;
- cj_ind_start = nbl_ci->cj_ind_start;
- cj_ind_end = nbl_ci->cj_ind_end;
+ const int cj_ind_start = nbl_ci->cj_ind_start;
+ const int cj_ind_end = nbl_ci->cj_ind_end;
/* In worst case we have alternating energy groups
* and create #atom-pair lists, which means we need the size
* of a cluster pair (na_ci*na_cj) times the number of cj's.
*/
- nri_max = nbl->na_ci*nbl->na_cj*(cj_ind_end - cj_ind_start);
+ const int nri_max = nbl->na_ci * nbl->na_cj * (cj_ind_end - cj_ind_start);
if (nlist->nri + nri_max > nlist->maxnri)
{
nlist->maxnri = over_alloc_large(nlist->nri + nri_max);
reallocate_nblist(nlist);
}
- const nbnxn_atomdata_t::Params &nbatParams = nbat->params();
+ const int numAtomsJCluster = jGrid.geometry().numAtomsJCluster;
- ngid = nbatParams.nenergrp;
+ const nbnxn_atomdata_t::Params& nbatParams = nbat->params();
- if (ngid*jGrid.na_cj > gmx::index(sizeof(gid_cj)*8))
+ const int ngid = nbatParams.nenergrp;
+
+ /* TODO: Consider adding a check in grompp and changing this to an assert */
+ const int numBitsInEnergyGroupIdsForAtomsInJCluster = sizeof(gid_cj) * 8;
+ if (ngid * numAtomsJCluster > numBitsInEnergyGroupIdsForAtomsInJCluster)
{
- gmx_fatal(FARGS, "The Verlet scheme with %dx%d kernels and free-energy only supports up to %zu energy groups",
- iGrid.na_c, jGrid.na_cj, (sizeof(gid_cj)*8)/jGrid.na_cj);
+ gmx_fatal(FARGS,
+ "The Verlet scheme with %dx%d kernels and free-energy only supports up to %zu "
+ "energy groups",
+ iGrid.geometry().numAtomsICluster,
+ numAtomsJCluster,
+ (sizeof(gid_cj) * 8) / numAtomsJCluster);
}
- egp_shift = nbatParams.neg_2log;
- egp_mask = (1 << egp_shift) - 1;
+ const int egp_shift = nbatParams.neg_2log;
+ const int egp_mask = (1 << egp_shift) - 1;
/* Loop over the atoms in the i sub-cell */
- bFEP_i_all = TRUE;
+ bool bFEP_i_all = true;
for (int i = 0; i < nbl->na_ci; i++)
{
- ind_i = ci*nbl->na_ci + i;
- ai = nbs->a[ind_i];
+ const int ind_i = ci * nbl->na_ci + i;
+ const int ai = atomIndices[ind_i];
if (ai >= 0)
{
- nri = nlist->nri;
- nlist->jindex[nri+1] = nlist->jindex[nri];
- nlist->iinr[nri] = ai;
+ int nri = nlist->nri;
+ nlist->jindex[nri + 1] = nlist->jindex[nri];
+ nlist->iinr[nri] = ai;
/* The actual energy group pair index is set later */
- nlist->gid[nri] = 0;
- nlist->shift[nri] = nbl_ci->shift & NBNXN_CI_SHIFT;
+ nlist->gid[nri] = 0;
+ nlist->shift[nri] = nbl_ci->shift & NBNXN_CI_SHIFT;
- bFEP_i = ((iGrid.fep[ci - iGrid.cell0] & (1 << i)) != 0u);
+ bool bFEP_i = iGrid.atomIsPerturbed(ci - iGrid.cellOffset(), i);
bFEP_i_all = bFEP_i_all && bFEP_i;
- if (nlist->nrj + (cj_ind_end - cj_ind_start)*nbl->na_cj > nlist->maxnrj)
+ if (nlist->nrj + (cj_ind_end - cj_ind_start) * nbl->na_cj > nlist->maxnrj)
{
- nlist->maxnrj = over_alloc_small(nlist->nrj + (cj_ind_end - cj_ind_start)*nbl->na_cj);
- srenew(nlist->jjnr, nlist->maxnrj);
- srenew(nlist->excl_fep, nlist->maxnrj);
+ nlist->maxnrj = over_alloc_small(nlist->nrj + (cj_ind_end - cj_ind_start) * nbl->na_cj);
+ nlist->jjnr.resize(nlist->maxnrj);
+ nlist->excl_fep.resize(nlist->maxnrj);
}
if (ngid > 1)
{
- gid_i = (nbatParams.energrp[ci] >> (egp_shift*i)) & egp_mask;
+ gid_i = (nbatParams.energrp[ci] >> (egp_shift * i)) & egp_mask;
}
for (int cj_ind = cj_ind_start; cj_ind < cj_ind_end; cj_ind++)
{
- unsigned int fep_cj;
+ unsigned int fep_cj = 0U;
+ gid_cj = 0;
- cja = nbl->cj[cj_ind].cj;
+ const int cja = nbl->cj[cj_ind].cj;
- if (jGrid.na_cj == jGrid.na_c)
+ if (numAtomsJCluster == jGrid.geometry().numAtomsICluster)
{
- cjr = cja - jGrid.cell0;
- fep_cj = jGrid.fep[cjr];
+ const int cjr = cja - jGrid.cellOffset();
+ fep_cj = jGrid.fepBits(cjr);
if (ngid > 1)
{
gid_cj = nbatParams.energrp[cja];
}
}
- else if (2*jGrid.na_cj == jGrid.na_c)
+ else if (2 * numAtomsJCluster == jGrid.geometry().numAtomsICluster)
{
- cjr = cja - jGrid.cell0*2;
+ const int cjr = cja - jGrid.cellOffset() * 2;
/* Extract half of the ci fep/energrp mask */
- fep_cj = (jGrid.fep[cjr>>1] >> ((cjr&1)*jGrid.na_cj)) & ((1<<jGrid.na_cj) - 1);
+ fep_cj = (jGrid.fepBits(cjr >> 1) >> ((cjr & 1) * numAtomsJCluster))
+ & ((1 << numAtomsJCluster) - 1);
if (ngid > 1)
{
- gid_cj = nbatParams.energrp[cja>>1] >> ((cja&1)*jGrid.na_cj*egp_shift) & ((1<<(jGrid.na_cj*egp_shift)) - 1);
+ gid_cj = nbatParams.energrp[cja >> 1] >> ((cja & 1) * numAtomsJCluster * egp_shift)
+ & ((1 << (numAtomsJCluster * egp_shift)) - 1);
}
}
else
{
- cjr = cja - (jGrid.cell0>>1);
+ const int cjr = cja - (jGrid.cellOffset() >> 1);
/* Combine two ci fep masks/energrp */
- fep_cj = jGrid.fep[cjr*2] + (jGrid.fep[cjr*2+1] << jGrid.na_c);
+ fep_cj = jGrid.fepBits(cjr * 2)
+ + (jGrid.fepBits(cjr * 2 + 1) << jGrid.geometry().numAtomsICluster);
if (ngid > 1)
{
- gid_cj = nbatParams.energrp[cja*2] + (nbatParams.energrp[cja*2+1] << (jGrid.na_c*egp_shift));
+ gid_cj = nbatParams.energrp[cja * 2]
+ + (nbatParams.energrp[cja * 2 + 1]
+ << (jGrid.geometry().numAtomsICluster * egp_shift));
}
}
for (int j = 0; j < nbl->na_cj; j++)
{
/* Is this interaction perturbed and not excluded? */
- ind_j = cja*nbl->na_cj + j;
- aj = nbs->a[ind_j];
- if (aj >= 0 &&
- (bFEP_i || (fep_cj & (1 << j))) &&
- (!bDiagRemoved || ind_j >= ind_i))
+ const int ind_j = cja * nbl->na_cj + j;
+ const int aj = atomIndices[ind_j];
+ if (aj >= 0 && (bFEP_i || (fep_cj & (1 << j))) && (!bDiagRemoved || ind_j >= ind_i))
{
if (ngid > 1)
{
- gid_j = (gid_cj >> (j*egp_shift)) & egp_mask;
- gid = GID(gid_i, gid_j, ngid);
+ const int gid_j = (gid_cj >> (j * egp_shift)) & egp_mask;
+ const int gid = GID(gid_i, gid_j, ngid);
- if (nlist->nrj > nlist->jindex[nri] &&
- nlist->gid[nri] != gid)
+ if (nlist->nrj > nlist->jindex[nri] && nlist->gid[nri] != gid)
{
/* Energy group pair changed: new list */
fep_list_new_nri_copy(nlist);
}
/* Add it to the FEP list */
- nlist->jjnr[nlist->nrj] = aj;
- nlist->excl_fep[nlist->nrj] = (nbl->cj[cj_ind].excl >> (i*nbl->na_cj + j)) & 1;
+ nlist->jjnr[nlist->nrj] = aj;
+ nlist->excl_fep[nlist->nrj] =
+ (nbl->cj[cj_ind].excl >> (i * nbl->na_cj + j)) & 1;
nlist->nrj++;
/* Exclude it from the normal list.
* but we need to avoid 0/0, as perturbed atoms
* can be on top of each other.
*/
- nbl->cj[cj_ind].excl &= ~(1U << (i*nbl->na_cj + j));
+ nbl->cj[cj_ind].excl &= ~(1U << (i * nbl->na_cj + j));
}
}
}
{
/* All interactions are perturbed, we can skip this entry */
nbl_ci->cj_ind_end = cj_ind_start;
- nbl->ncjInUse -= cj_ind_end - cj_ind_start;
+ nbl->ncjInUse -= cj_ind_end - cj_ind_start;
}
}
/* Convert a j-cluster to a cj4 group */
static inline int cj_to_cj4(int cj)
{
- return cj/c_nbnxnGpuJgroupSize;
+ return cj / c_nbnxnGpuJgroupSize;
}
/* Return the index of an j-atom within a warp */
static inline int a_mod_wj(int a)
{
- return a & (c_nbnxnGpuClusterSize/c_nbnxnGpuClusterpairSplit - 1);
+ return a & (c_nbnxnGpuClusterSize / c_nbnxnGpuClusterpairSplit - 1);
}
/* As make_fep_list above, but for super/sub lists. */
-static void make_fep_list(const nbnxn_search *nbs,
- const nbnxn_atomdata_t *nbat,
- NbnxnPairlistGpu *nbl,
- gmx_bool bDiagRemoved,
- const nbnxn_sci_t *nbl_sci,
- real shx,
- real shy,
- real shz,
- real rlist_fep2,
- const nbnxn_grid_t &iGrid,
- const nbnxn_grid_t &jGrid,
- t_nblist *nlist)
+static void make_fep_list(gmx::ArrayRef<const int> atomIndices,
+ const nbnxn_atomdata_t* nbat,
+ NbnxnPairlistGpu* nbl,
+ gmx_bool bDiagRemoved,
+ const nbnxn_sci_t* nbl_sci,
+ real shx,
+ real shy,
+ real shz,
+ real rlist_fep2,
+ const Grid& iGrid,
+ const Grid& jGrid,
+ t_nblist* nlist)
{
- int nri_max;
- int c_abs;
- int ind_i, ind_j, ai, aj;
- int nri;
- gmx_bool bFEP_i;
- real xi, yi, zi;
- const nbnxn_cj4_t *cj4;
-
- const int numJClusterGroups = nbl_sci->numJClusterGroups();
+ const int numJClusterGroups = nbl_sci->numJClusterGroups();
if (numJClusterGroups == 0)
{
/* Empty list */
return;
}
- const int sci = nbl_sci->sci;
+ const int sci = nbl_sci->sci;
const int cj4_ind_start = nbl_sci->cj4_ind_start;
const int cj4_ind_end = nbl_sci->cj4_ind_end;
* So for each of the na_sc i-atoms, we need max one FEP list
* for each max_nrj_fep j-atoms.
*/
- nri_max = nbl->na_sc*nbl->na_cj*(1 + (numJClusterGroups*c_nbnxnGpuJgroupSize)/max_nrj_fep);
+ const int nri_max =
+ nbl->na_sc * nbl->na_cj * (1 + (numJClusterGroups * c_nbnxnGpuJgroupSize) / max_nrj_fep);
if (nlist->nri + nri_max > nlist->maxnri)
{
nlist->maxnri = over_alloc_large(nlist->nri + nri_max);
/* Loop over the atoms in the i super-cluster */
for (int c = 0; c < c_gpuNumClusterPerCell; c++)
{
- c_abs = sci*c_gpuNumClusterPerCell + c;
+ const int c_abs = sci * c_gpuNumClusterPerCell + c;
for (int i = 0; i < nbl->na_ci; i++)
{
- ind_i = c_abs*nbl->na_ci + i;
- ai = nbs->a[ind_i];
+ const int ind_i = c_abs * nbl->na_ci + i;
+ const int ai = atomIndices[ind_i];
if (ai >= 0)
{
- nri = nlist->nri;
- nlist->jindex[nri+1] = nlist->jindex[nri];
- nlist->iinr[nri] = ai;
+ int nri = nlist->nri;
+ nlist->jindex[nri + 1] = nlist->jindex[nri];
+ nlist->iinr[nri] = ai;
/* With GPUs, energy groups are not supported */
- nlist->gid[nri] = 0;
- nlist->shift[nri] = nbl_sci->shift & NBNXN_CI_SHIFT;
+ nlist->gid[nri] = 0;
+ nlist->shift[nri] = nbl_sci->shift & NBNXN_CI_SHIFT;
- bFEP_i = ((iGrid.fep[c_abs - iGrid.cell0*c_gpuNumClusterPerCell] & (1 << i)) != 0u);
+ const bool bFEP_i =
+ iGrid.atomIsPerturbed(c_abs - iGrid.cellOffset() * c_gpuNumClusterPerCell, i);
- xi = nbat->x()[ind_i*nbat->xstride+XX] + shx;
- yi = nbat->x()[ind_i*nbat->xstride+YY] + shy;
- zi = nbat->x()[ind_i*nbat->xstride+ZZ] + shz;
+ real xi = nbat->x()[ind_i * nbat->xstride + XX] + shx;
+ real yi = nbat->x()[ind_i * nbat->xstride + YY] + shy;
+ real zi = nbat->x()[ind_i * nbat->xstride + ZZ] + shz;
- const int nrjMax = nlist->nrj + numJClusterGroups*c_nbnxnGpuJgroupSize*nbl->na_cj;
+ const int nrjMax = nlist->nrj + numJClusterGroups * c_nbnxnGpuJgroupSize * nbl->na_cj;
if (nrjMax > nlist->maxnrj)
{
nlist->maxnrj = over_alloc_small(nrjMax);
- srenew(nlist->jjnr, nlist->maxnrj);
- srenew(nlist->excl_fep, nlist->maxnrj);
+ nlist->jjnr.resize(nlist->maxnrj);
+ nlist->excl_fep.resize(nlist->maxnrj);
}
for (int cj4_ind = cj4_ind_start; cj4_ind < cj4_ind_end; cj4_ind++)
{
- cj4 = &nbl->cj4[cj4_ind];
+ const nbnxn_cj4_t* cj4 = &nbl->cj4[cj4_ind];
for (int gcj = 0; gcj < c_nbnxnGpuJgroupSize; gcj++)
{
- unsigned int fep_cj;
-
- if ((cj4->imei[0].imask & (1U << (gcj*c_gpuNumClusterPerCell + c))) == 0)
+ if ((cj4->imei[0].imask & (1U << (gcj * c_gpuNumClusterPerCell + c))) == 0)
{
/* Skip this ci for this cj */
continue;
}
- const int cjr =
- cj4->cj[gcj] - jGrid.cell0*c_gpuNumClusterPerCell;
-
- fep_cj = jGrid.fep[cjr];
+ const int cjr = cj4->cj[gcj] - jGrid.cellOffset() * c_gpuNumClusterPerCell;
- if (bFEP_i || fep_cj != 0)
+ if (bFEP_i || jGrid.clusterIsPerturbed(cjr))
{
for (int j = 0; j < nbl->na_cj; j++)
{
/* Is this interaction perturbed and not excluded? */
- ind_j = (jGrid.cell0*c_gpuNumClusterPerCell + cjr)*nbl->na_cj + j;
- aj = nbs->a[ind_j];
- if (aj >= 0 &&
- (bFEP_i || (fep_cj & (1 << j))) &&
- (!bDiagRemoved || ind_j >= ind_i))
+ const int ind_j =
+ (jGrid.cellOffset() * c_gpuNumClusterPerCell + cjr) * nbl->na_cj + j;
+ const int aj = atomIndices[ind_j];
+ if (aj >= 0 && (bFEP_i || jGrid.atomIsPerturbed(cjr, j))
+ && (!bDiagRemoved || ind_j >= ind_i))
{
- int excl_pair;
- unsigned int excl_bit;
- real dx, dy, dz;
+ const int jHalf =
+ j / (c_nbnxnGpuClusterSize / c_nbnxnGpuClusterpairSplit);
+ nbnxn_excl_t& excl = get_exclusion_mask(nbl, cj4_ind, jHalf);
- const int jHalf = j/(c_nbnxnGpuClusterSize/c_nbnxnGpuClusterpairSplit);
- nbnxn_excl_t *excl =
- get_exclusion_mask(nbl, cj4_ind, jHalf);
+ int excl_pair = a_mod_wj(j) * nbl->na_ci + i;
+ unsigned int excl_bit = (1U << (gcj * c_gpuNumClusterPerCell + c));
- excl_pair = a_mod_wj(j)*nbl->na_ci + i;
- excl_bit = (1U << (gcj*c_gpuNumClusterPerCell + c));
-
- dx = nbat->x()[ind_j*nbat->xstride+XX] - xi;
- dy = nbat->x()[ind_j*nbat->xstride+YY] - yi;
- dz = nbat->x()[ind_j*nbat->xstride+ZZ] - zi;
+ real dx = nbat->x()[ind_j * nbat->xstride + XX] - xi;
+ real dy = nbat->x()[ind_j * nbat->xstride + YY] - yi;
+ real dz = nbat->x()[ind_j * nbat->xstride + ZZ] - zi;
/* The unpruned GPU list has more than 2/3
* of the atom pairs beyond rlist. Using
* relative to the fast GPU kernels.
* So we prune the FEP list here.
*/
- if (dx*dx + dy*dy + dz*dz < rlist_fep2)
+ if (dx * dx + dy * dy + dz * dz < rlist_fep2)
{
if (nlist->nrj - nlist->jindex[nri] >= max_nrj_fep)
{
}
/* Add it to the FEP list */
- nlist->jjnr[nlist->nrj] = aj;
- nlist->excl_fep[nlist->nrj] = (excl->pair[excl_pair] & excl_bit) ? 1 : 0;
+ nlist->jjnr[nlist->nrj] = aj;
+ nlist->excl_fep[nlist->nrj] =
+ (excl.pair[excl_pair] & excl_bit) ? 1 : 0;
nlist->nrj++;
}
* been set to zero, but we need to avoid 0/0,
* as perturbed atoms can be on top of each other.
*/
- excl->pair[excl_pair] &= ~excl_bit;
+ excl.pair[excl_pair] &= ~excl_bit;
}
}
* Sets all atom-pair exclusions from the topology stored in exclusions
* as masks in the pair-list for i-super-cluster list entry iEntry.
*/
-static void
-setExclusionsForIEntry(const nbnxn_search *nbs,
- NbnxnPairlistGpu *nbl,
- gmx_bool diagRemoved,
- int gmx_unused na_cj_2log,
- const nbnxn_sci_t &iEntry,
- const t_blocka &exclusions)
+static void setExclusionsForIEntry(const Nbnxm::GridSet& gridSet,
+ NbnxnPairlistGpu* nbl,
+ gmx_bool diagRemoved,
+ int gmx_unused na_cj_2log,
+ const nbnxn_sci_t& iEntry,
+ const ListOfLists<int>& exclusions)
{
if (iEntry.numJClusterGroups() == 0)
{
* Note that here we can not use cj4_ind_end, since the last cj4
* can be only partially filled, so we use cj_ind.
*/
- const JListRanges ranges(iEntry.cj4_ind_start*c_nbnxnGpuJgroupSize,
+ const JListRanges ranges(iEntry.cj4_ind_start * c_nbnxnGpuJgroupSize,
nbl->work->cj_ind,
gmx::makeConstArrayRef(nbl->cj4));
GMX_ASSERT(nbl->na_ci == c_nbnxnGpuClusterSize, "na_ci should match the GPU cluster size");
- constexpr int c_clusterSize = c_nbnxnGpuClusterSize;
- constexpr int c_superClusterSize = c_nbnxnGpuNumClusterPerSupercluster*c_nbnxnGpuClusterSize;
+ constexpr int c_clusterSize = c_nbnxnGpuClusterSize;
+ constexpr int c_superClusterSize = c_nbnxnGpuNumClusterPerSupercluster * c_nbnxnGpuClusterSize;
- const int iSuperCluster = iEntry.sci;
+ const int iSuperCluster = iEntry.sci;
- gmx::ArrayRef<const int> cell = nbs->cell;
+ gmx::ArrayRef<const int> atomIndices = gridSet.atomIndices();
+ gmx::ArrayRef<const int> cell = gridSet.cells();
/* Loop over the atoms in the i super-cluster */
for (int i = 0; i < c_superClusterSize; i++)
{
- const int iIndex = iSuperCluster*c_superClusterSize + i;
- const int iAtom = nbs->a[iIndex];
+ const int iIndex = iSuperCluster * c_superClusterSize + i;
+ const int iAtom = atomIndices[iIndex];
if (iAtom >= 0)
{
- const int iCluster = i/c_clusterSize;
+ const int iCluster = i / c_clusterSize;
/* Loop over the topology-based exclusions for this i-atom */
- for (int exclIndex = exclusions.index[iAtom]; exclIndex < exclusions.index[iAtom + 1]; exclIndex++)
+ for (const int jAtom : exclusions[iAtom])
{
- const int jAtom = exclusions.a[exclIndex];
-
if (jAtom == iAtom)
{
/* The self exclusions are already set, save some time */
* Either of these changes triggers peeling of the exclIndex
* loop, which apparently leads to far less efficient code.
*/
- if (diagRemoved && jIndex <= iSuperCluster*nbl->na_sc + i)
+ if (diagRemoved && jIndex <= iSuperCluster * nbl->na_sc + i)
{
continue;
}
- const int jCluster = jIndex/c_clusterSize;
+ const int jCluster = jIndex / c_clusterSize;
/* Check whether the cluster is in our list? */
if (jCluster >= ranges.cjFirst && jCluster <= ranges.cjLast)
{
const int index =
- findJClusterInJList(jCluster, ranges,
- gmx::makeConstArrayRef(nbl->cj4));
+ findJClusterInJList(jCluster, ranges, gmx::makeConstArrayRef(nbl->cj4));
if (index >= 0)
{
/* We found an exclusion, clear the corresponding
* interaction bit.
*/
- const unsigned int pairMask = (1U << (cj_mod_cj4(index)*c_gpuNumClusterPerCell + iCluster));
+ const unsigned int pairMask =
+ (1U << (cj_mod_cj4(index) * c_gpuNumClusterPerCell + iCluster));
/* Check if the i-cluster interacts with the j-cluster */
if (nbl_imask0(nbl, index) & pairMask)
{
- const int innerI = (i & (c_clusterSize - 1));
+ const int innerI = (i & (c_clusterSize - 1));
const int innerJ = (jIndex & (c_clusterSize - 1));
/* Determine which j-half (CUDA warp) we are in */
- const int jHalf = innerJ/(c_clusterSize/c_nbnxnGpuClusterpairSplit);
+ const int jHalf = innerJ / (c_clusterSize / c_nbnxnGpuClusterpairSplit);
- nbnxn_excl_t *interactionMask =
- get_exclusion_mask(nbl, cj_to_cj4(index), jHalf);
+ nbnxn_excl_t& interactionMask =
+ get_exclusion_mask(nbl, cj_to_cj4(index), jHalf);
- interactionMask->pair[a_mod_wj(innerJ)*c_clusterSize + innerI] &= ~pairMask;
+ interactionMask.pair[a_mod_wj(innerJ) * c_clusterSize + innerI] &= ~pairMask;
}
}
}
}
/* Make a new ci entry at the back of nbl->ci */
-static void addNewIEntry(NbnxnPairlistCpu *nbl, int ci, int shift, int flags)
+static void addNewIEntry(NbnxnPairlistCpu* nbl, int ci, int shift, int flags)
{
nbnxn_ci_t ciEntry;
- ciEntry.ci = ci;
- ciEntry.shift = shift;
+ ciEntry.ci = ci;
+ ciEntry.shift = shift;
/* Store the interaction flags along with the shift */
- ciEntry.shift |= flags;
- ciEntry.cj_ind_start = nbl->cj.size();
- ciEntry.cj_ind_end = nbl->cj.size();
+ ciEntry.shift |= flags;
+ ciEntry.cj_ind_start = nbl->cj.size();
+ ciEntry.cj_ind_end = nbl->cj.size();
nbl->ci.push_back(ciEntry);
}
/* Make a new sci entry at index nbl->nsci */
-static void addNewIEntry(NbnxnPairlistGpu *nbl, int sci, int shift, int gmx_unused flags)
+static void addNewIEntry(NbnxnPairlistGpu* nbl, int sci, int shift, int gmx_unused flags)
{
nbnxn_sci_t sciEntry;
sciEntry.sci = sci;
/* Sort the simple j-list cj on exclusions.
* Entries with exclusions will all be sorted to the beginning of the list.
*/
-static void sort_cj_excl(nbnxn_cj_t *cj, int ncj,
- NbnxnPairlistCpuWork *work)
+static void sort_cj_excl(nbnxn_cj_t* cj, int ncj, NbnxnPairlistCpuWork* work)
{
work->cj.resize(ncj);
}
}
/* Check if there are exclusions at all or not just the first entry */
- if (!((jnew == 0) ||
- (jnew == 1 && cj[0].excl != NBNXN_INTERACTION_MASK_ALL)))
+ if (!((jnew == 0) || (jnew == 1 && cj[0].excl != NBNXN_INTERACTION_MASK_ALL)))
{
for (int j = 0; j < ncj; j++)
{
}
/* Close this simple list i entry */
-static void closeIEntry(NbnxnPairlistCpu *nbl,
- int gmx_unused sp_max_av,
- gmx_bool gmx_unused progBal,
- float gmx_unused nsp_tot_est,
- int gmx_unused thread,
- int gmx_unused nthread)
+static void closeIEntry(NbnxnPairlistCpu* nbl,
+ int gmx_unused sp_max_av,
+ gmx_bool gmx_unused progBal,
+ float gmx_unused nsp_tot_est,
+ int gmx_unused thread,
+ int gmx_unused nthread)
{
- nbnxn_ci_t &ciEntry = nbl->ci.back();
+ nbnxn_ci_t& ciEntry = nbl->ci.back();
/* All content of the new ci entry have already been filled correctly,
* we only need to sort and increase counts or remove the entry when empty.
const int jlen = ciEntry.cj_ind_end - ciEntry.cj_ind_start;
if (jlen > 0)
{
- sort_cj_excl(nbl->cj.data() + ciEntry.cj_ind_start, jlen, nbl->work);
+ sort_cj_excl(nbl->cj.data() + ciEntry.cj_ind_start, jlen, nbl->work.get());
/* The counts below are used for non-bonded pair/flop counts
* and should therefore match the available kernel setups.
{
nbl->work->ncj_noq += jlen;
}
- else if ((ciEntry.shift & NBNXN_CI_HALF_LJ(0)) ||
- !(ciEntry.shift & NBNXN_CI_DO_LJ(0)))
+ else if ((ciEntry.shift & NBNXN_CI_HALF_LJ(0)) || !(ciEntry.shift & NBNXN_CI_DO_LJ(0)))
{
nbl->work->ncj_hlj += jlen;
}
* As the lists get concatenated later, this estimate depends
* both on nthread and our own thread index.
*/
-static void split_sci_entry(NbnxnPairlistGpu *nbl,
- int nsp_target_av,
- gmx_bool progBal, float nsp_tot_est,
- int thread, int nthread)
+static void split_sci_entry(NbnxnPairlistGpu* nbl,
+ int nsp_target_av,
+ gmx_bool progBal,
+ float nsp_tot_est,
+ int thread,
+ int nthread)
{
- int nsp_max;
+
+ int nsp_max = nsp_target_av;
if (progBal)
{
- float nsp_est;
-
/* Estimate the total numbers of ci's of the nblist combined
* over all threads using the target number of ci's.
*/
- nsp_est = (nsp_tot_est*thread)/nthread + nbl->nci_tot;
+ float nsp_est = (nsp_tot_est * thread) / nthread + nbl->nci_tot;
/* The first ci blocks should be larger, to avoid overhead.
* The last ci blocks should be smaller, to improve load balancing.
* and ensures that the total number of blocks end up equal to
* that of equally sized blocks of size nsp_target_av.
*/
- nsp_max = static_cast<int>(nsp_target_av*(nsp_tot_est*1.5/(nsp_est + nsp_tot_est)));
- }
- else
- {
- nsp_max = nsp_target_av;
+ nsp_max = static_cast<int>(nsp_target_av * (nsp_tot_est * 1.5 / (nsp_est + nsp_tot_est)));
}
const int cj4_start = nbl->sci.back().cj4_ind_start;
const int cj4_end = nbl->sci.back().cj4_ind_end;
const int j4len = cj4_end - cj4_start;
- if (j4len > 1 && j4len*c_gpuNumClusterPerCell*c_nbnxnGpuJgroupSize > nsp_max)
+ if (j4len > 1 && j4len * c_gpuNumClusterPerCell * c_nbnxnGpuJgroupSize > nsp_max)
{
/* Modify the last ci entry and process the cj4's again */
- int nsp = 0;
- int nsp_sci = 0;
- int nsp_cj4_e = 0;
- int nsp_cj4 = 0;
+ int nsp = 0;
+ int nsp_sci = 0;
+ int nsp_cj4_e = 0;
+ int nsp_cj4 = 0;
for (int cj4 = cj4_start; cj4 < cj4_end; cj4++)
{
int nsp_cj4_p = nsp_cj4;
/* Count the number of cluster pairs in this cj4 group */
- nsp_cj4 = 0;
- for (int p = 0; p < c_gpuNumClusterPerCell*c_nbnxnGpuJgroupSize; p++)
+ nsp_cj4 = 0;
+ for (int p = 0; p < c_gpuNumClusterPerCell * c_nbnxnGpuJgroupSize; p++)
{
nsp_cj4 += (nbl->cj4[cj4].imei[0].imask >> p) & 1;
}
sciNew.cj4_ind_start = cj4;
nbl->sci.push_back(sciNew);
- nsp_sci = nsp;
- nsp_cj4_e = nsp_cj4_p;
- nsp = 0;
+ nsp_sci = nsp;
+ nsp_cj4_e = nsp_cj4_p;
+ nsp = 0;
}
nsp += nsp_cj4;
}
}
/* Clost this super/sub list i entry */
-static void closeIEntry(NbnxnPairlistGpu *nbl,
- int nsp_max_av,
- gmx_bool progBal, float nsp_tot_est,
- int thread, int nthread)
+static void closeIEntry(NbnxnPairlistGpu* nbl, int nsp_max_av, gmx_bool progBal, float nsp_tot_est, int thread, int nthread)
{
- nbnxn_sci_t &sciEntry = *getOpenIEntry(nbl);
+ nbnxn_sci_t& sciEntry = *getOpenIEntry(nbl);
/* All content of the new ci entry have already been filled correctly,
* we only need to, potentially, split or remove the entry when empty.
/* We can only have complete blocks of 4 j-entries in a list,
* so round the count up before closing.
*/
- int ncj4 = (nbl->work->cj_ind + c_nbnxnGpuJgroupSize - 1)/c_nbnxnGpuJgroupSize;
- nbl->work->cj_ind = ncj4*c_nbnxnGpuJgroupSize;
+ int ncj4 = (nbl->work->cj_ind + c_nbnxnGpuJgroupSize - 1) / c_nbnxnGpuJgroupSize;
+ nbl->work->cj_ind = ncj4 * c_nbnxnGpuJgroupSize;
if (nsp_max_av > 0)
{
/* Measure the size of the new entry and potentially split it */
- split_sci_entry(nbl, nsp_max_av, progBal, nsp_tot_est,
- thread, nthread);
+ split_sci_entry(nbl, nsp_max_av, progBal, nsp_tot_est, thread, nthread);
}
}
else
}
/* Syncs the working array before adding another grid pair to the GPU list */
-static void sync_work(NbnxnPairlistCpu gmx_unused *nbl)
-{
-}
+static void sync_work(NbnxnPairlistCpu gmx_unused* nbl) {}
/* Syncs the working array before adding another grid pair to the GPU list */
-static void sync_work(NbnxnPairlistGpu *nbl)
+static void sync_work(NbnxnPairlistGpu* nbl)
{
- nbl->work->cj_ind = nbl->cj4.size()*c_nbnxnGpuJgroupSize;
+ nbl->work->cj_ind = nbl->cj4.size() * c_nbnxnGpuJgroupSize;
}
/* Clears an NbnxnPairlistCpu data structure */
-static void clear_pairlist(NbnxnPairlistCpu *nbl)
+static void clear_pairlist(NbnxnPairlistCpu* nbl)
{
nbl->ci.clear();
nbl->cj.clear();
- nbl->ncjInUse = 0;
- nbl->nci_tot = 0;
+ nbl->ncjInUse = 0;
+ nbl->nci_tot = 0;
nbl->ciOuter.clear();
nbl->cjOuter.clear();
}
/* Clears an NbnxnPairlistGpu data structure */
-static void clear_pairlist(NbnxnPairlistGpu *nbl)
+static void clear_pairlist(NbnxnPairlistGpu* nbl)
{
nbl->sci.clear();
nbl->cj4.clear();
nbl->nci_tot = 0;
}
-/* Clears a group scheme pair list */
-static void clear_pairlist_fep(t_nblist *nl)
+/* Clears an atom-atom-style pair list */
+static void clear_pairlist_fep(t_nblist* nl)
{
nl->nri = 0;
nl->nrj = 0;
- if (nl->jindex == nullptr)
+ if (nl->jindex.empty())
{
- snew(nl->jindex, 1);
+ nl->jindex.resize(1);
}
nl->jindex[0] = 0;
}
/* Sets a simple list i-cell bounding box, including PBC shift */
-static inline void set_icell_bb_simple(gmx::ArrayRef<const nbnxn_bb_t> bb,
- int ci,
- real shx, real shy, real shz,
- nbnxn_bb_t *bb_ci)
+static inline void
+set_icell_bb_simple(gmx::ArrayRef<const BoundingBox> bb, int ci, real shx, real shy, real shz, BoundingBox* bb_ci)
{
- bb_ci->lower[BB_X] = bb[ci].lower[BB_X] + shx;
- bb_ci->lower[BB_Y] = bb[ci].lower[BB_Y] + shy;
- bb_ci->lower[BB_Z] = bb[ci].lower[BB_Z] + shz;
- bb_ci->upper[BB_X] = bb[ci].upper[BB_X] + shx;
- bb_ci->upper[BB_Y] = bb[ci].upper[BB_Y] + shy;
- bb_ci->upper[BB_Z] = bb[ci].upper[BB_Z] + shz;
+ bb_ci->lower.x = bb[ci].lower.x + shx;
+ bb_ci->lower.y = bb[ci].lower.y + shy;
+ bb_ci->lower.z = bb[ci].lower.z + shz;
+ bb_ci->upper.x = bb[ci].upper.x + shx;
+ bb_ci->upper.y = bb[ci].upper.y + shy;
+ bb_ci->upper.z = bb[ci].upper.z + shz;
}
/* Sets a simple list i-cell bounding box, including PBC shift */
-static inline void set_icell_bb(const nbnxn_grid_t &iGrid,
- int ci,
- real shx, real shy, real shz,
- NbnxnPairlistCpuWork *work)
+static inline void set_icell_bb(const Grid& iGrid, int ci, real shx, real shy, real shz, NbnxnPairlistCpuWork* work)
{
- set_icell_bb_simple(iGrid.bb, ci, shx, shy, shz, &work->iClusterData.bb[0]);
+ set_icell_bb_simple(iGrid.iBoundingBoxes(), ci, shx, shy, shz, &work->iClusterData.bb[0]);
}
#if NBNXN_BBXXXX
/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
-static void set_icell_bbxxxx_supersub(gmx::ArrayRef<const float> bb,
- int ci,
- real shx, real shy, real shz,
- float *bb_ci)
+static void set_icell_bbxxxx_supersub(gmx::ArrayRef<const float> bb, int ci, real shx, real shy, real shz, float* bb_ci)
{
- int ia = ci*(c_gpuNumClusterPerCell >> STRIDE_PBB_2LOG)*NNBSBB_XXXX;
- for (int m = 0; m < (c_gpuNumClusterPerCell >> STRIDE_PBB_2LOG)*NNBSBB_XXXX; m += NNBSBB_XXXX)
+ constexpr int cellBBStride = packedBoundingBoxesIndex(c_gpuNumClusterPerCell);
+ constexpr int pbbStride = c_packedBoundingBoxesDimSize;
+ const int ia = ci * cellBBStride;
+ for (int m = 0; m < cellBBStride; m += c_packedBoundingBoxesSize)
{
- for (int i = 0; i < STRIDE_PBB; i++)
+ for (int i = 0; i < pbbStride; i++)
{
- bb_ci[m+0*STRIDE_PBB+i] = bb[ia+m+0*STRIDE_PBB+i] + shx;
- bb_ci[m+1*STRIDE_PBB+i] = bb[ia+m+1*STRIDE_PBB+i] + shy;
- bb_ci[m+2*STRIDE_PBB+i] = bb[ia+m+2*STRIDE_PBB+i] + shz;
- bb_ci[m+3*STRIDE_PBB+i] = bb[ia+m+3*STRIDE_PBB+i] + shx;
- bb_ci[m+4*STRIDE_PBB+i] = bb[ia+m+4*STRIDE_PBB+i] + shy;
- bb_ci[m+5*STRIDE_PBB+i] = bb[ia+m+5*STRIDE_PBB+i] + shz;
+ bb_ci[m + 0 * pbbStride + i] = bb[ia + m + 0 * pbbStride + i] + shx;
+ bb_ci[m + 1 * pbbStride + i] = bb[ia + m + 1 * pbbStride + i] + shy;
+ bb_ci[m + 2 * pbbStride + i] = bb[ia + m + 2 * pbbStride + i] + shz;
+ bb_ci[m + 3 * pbbStride + i] = bb[ia + m + 3 * pbbStride + i] + shx;
+ bb_ci[m + 4 * pbbStride + i] = bb[ia + m + 4 * pbbStride + i] + shy;
+ bb_ci[m + 5 * pbbStride + i] = bb[ia + m + 5 * pbbStride + i] + shz;
}
}
}
#endif
/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
-gmx_unused static void set_icell_bb_supersub(gmx::ArrayRef<const nbnxn_bb_t> bb,
- int ci,
- real shx, real shy, real shz,
- nbnxn_bb_t *bb_ci)
+gmx_unused static void set_icell_bb_supersub(gmx::ArrayRef<const BoundingBox> bb,
+ int ci,
+ real shx,
+ real shy,
+ real shz,
+ BoundingBox* bb_ci)
{
for (int i = 0; i < c_gpuNumClusterPerCell; i++)
{
- set_icell_bb_simple(bb, ci*c_gpuNumClusterPerCell+i,
- shx, shy, shz,
- &bb_ci[i]);
+ set_icell_bb_simple(bb, ci * c_gpuNumClusterPerCell + i, shx, shy, shz, &bb_ci[i]);
}
}
/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
-gmx_unused static void set_icell_bb(const nbnxn_grid_t &iGrid,
- int ci,
- real shx, real shy, real shz,
- NbnxnPairlistGpuWork *work)
+gmx_unused static void set_icell_bb(const Grid& iGrid, int ci, real shx, real shy, real shz, NbnxnPairlistGpuWork* work)
{
#if NBNXN_BBXXXX
- set_icell_bbxxxx_supersub(iGrid.pbb, ci, shx, shy, shz,
- work->iSuperClusterData.bbPacked.data());
+ set_icell_bbxxxx_supersub(
+ iGrid.packedBoundingBoxes(), ci, shx, shy, shz, work->iSuperClusterData.bbPacked.data());
#else
- set_icell_bb_supersub(iGrid.bb, ci, shx, shy, shz,
- work->iSuperClusterData.bb.data());
+ set_icell_bb_supersub(iGrid.iBoundingBoxes(), ci, shx, shy, shz, work->iSuperClusterData.bb.data());
#endif
}
/* Copies PBC shifted i-cell atom coordinates x,y,z to working array */
-static void icell_set_x_simple(int ci,
- real shx, real shy, real shz,
- int stride, const real *x,
- NbnxnPairlistCpuWork::IClusterData *iClusterData)
+static void icell_set_x_simple(int ci,
+ real shx,
+ real shy,
+ real shz,
+ int stride,
+ const real* x,
+ NbnxnPairlistCpuWork::IClusterData* iClusterData)
{
- const int ia = ci*c_nbnxnCpuIClusterSize;
+ const int ia = ci * c_nbnxnCpuIClusterSize;
for (int i = 0; i < c_nbnxnCpuIClusterSize; i++)
{
- iClusterData->x[i*STRIDE_XYZ+XX] = x[(ia+i)*stride+XX] + shx;
- iClusterData->x[i*STRIDE_XYZ+YY] = x[(ia+i)*stride+YY] + shy;
- iClusterData->x[i*STRIDE_XYZ+ZZ] = x[(ia+i)*stride+ZZ] + shz;
+ iClusterData->x[i * STRIDE_XYZ + XX] = x[(ia + i) * stride + XX] + shx;
+ iClusterData->x[i * STRIDE_XYZ + YY] = x[(ia + i) * stride + YY] + shy;
+ iClusterData->x[i * STRIDE_XYZ + ZZ] = x[(ia + i) * stride + ZZ] + shz;
}
}
-static void icell_set_x(int ci,
- real shx, real shy, real shz,
- int stride, const real *x,
- int nb_kernel_type,
- NbnxnPairlistCpuWork *work)
+static void icell_set_x(int ci,
+ real shx,
+ real shy,
+ real shz,
+ int stride,
+ const real* x,
+ const ClusterDistanceKernelType kernelType,
+ NbnxnPairlistCpuWork* work)
{
- switch (nb_kernel_type)
+ switch (kernelType)
{
#if GMX_SIMD
-#ifdef GMX_NBNXN_SIMD_4XN
- case nbnxnk4xN_SIMD_4xN:
+# ifdef GMX_NBNXN_SIMD_4XN
+ case ClusterDistanceKernelType::CpuSimd_4xM:
icell_set_x_simd_4xn(ci, shx, shy, shz, stride, x, work);
break;
-#endif
-#ifdef GMX_NBNXN_SIMD_2XNN
- case nbnxnk4xN_SIMD_2xNN:
+# endif
+# ifdef GMX_NBNXN_SIMD_2XNN
+ case ClusterDistanceKernelType::CpuSimd_2xMM:
icell_set_x_simd_2xnn(ci, shx, shy, shz, stride, x, work);
break;
+# endif
#endif
-#endif
- case nbnxnk4x4_PlainC:
+ case ClusterDistanceKernelType::CpuPlainC:
icell_set_x_simple(ci, shx, shy, shz, stride, x, &work->iClusterData);
break;
- default:
- GMX_ASSERT(false, "Unhandled case");
- break;
+ default: GMX_ASSERT(false, "Unhandled case"); break;
}
}
/* Copies PBC shifted super-cell atom coordinates x,y,z to working array */
-static void icell_set_x(int ci,
- real shx, real shy, real shz,
- int stride, const real *x,
- int gmx_unused nb_kernel_type,
- NbnxnPairlistGpuWork *work)
+static void icell_set_x(int ci,
+ real shx,
+ real shy,
+ real shz,
+ int stride,
+ const real* x,
+ ClusterDistanceKernelType gmx_unused kernelType,
+ NbnxnPairlistGpuWork* work)
{
#if !GMX_SIMD4_HAVE_REAL
- real * x_ci = work->iSuperClusterData.x.data();
+ real* x_ci = work->iSuperClusterData.x.data();
- int ia = ci*c_gpuNumClusterPerCell*c_nbnxnGpuClusterSize;
- for (int i = 0; i < c_gpuNumClusterPerCell*c_nbnxnGpuClusterSize; i++)
+ int ia = ci * c_gpuNumClusterPerCell * c_nbnxnGpuClusterSize;
+ for (int i = 0; i < c_gpuNumClusterPerCell * c_nbnxnGpuClusterSize; i++)
{
- x_ci[i*DIM + XX] = x[(ia+i)*stride + XX] + shx;
- x_ci[i*DIM + YY] = x[(ia+i)*stride + YY] + shy;
- x_ci[i*DIM + ZZ] = x[(ia+i)*stride + ZZ] + shz;
+ x_ci[i * DIM + XX] = x[(ia + i) * stride + XX] + shx;
+ x_ci[i * DIM + YY] = x[(ia + i) * stride + YY] + shy;
+ x_ci[i * DIM + ZZ] = x[(ia + i) * stride + ZZ] + shz;
}
#else /* !GMX_SIMD4_HAVE_REAL */
- real * x_ci = work->iSuperClusterData.xSimd.data();
+ real* x_ci = work->iSuperClusterData.xSimd.data();
for (int si = 0; si < c_gpuNumClusterPerCell; si++)
{
for (int i = 0; i < c_nbnxnGpuClusterSize; i += GMX_SIMD4_WIDTH)
{
- int io = si*c_nbnxnGpuClusterSize + i;
- int ia = ci*c_gpuNumClusterPerCell*c_nbnxnGpuClusterSize + io;
+ int io = si * c_nbnxnGpuClusterSize + i;
+ int ia = ci * c_gpuNumClusterPerCell * c_nbnxnGpuClusterSize + io;
for (int j = 0; j < GMX_SIMD4_WIDTH; j++)
{
- x_ci[io*DIM + j + XX*GMX_SIMD4_WIDTH] = x[(ia + j)*stride + XX] + shx;
- x_ci[io*DIM + j + YY*GMX_SIMD4_WIDTH] = x[(ia + j)*stride + YY] + shy;
- x_ci[io*DIM + j + ZZ*GMX_SIMD4_WIDTH] = x[(ia + j)*stride + ZZ] + shz;
+ x_ci[io * DIM + j + XX * GMX_SIMD4_WIDTH] = x[(ia + j) * stride + XX] + shx;
+ x_ci[io * DIM + j + YY * GMX_SIMD4_WIDTH] = x[(ia + j) * stride + YY] + shy;
+ x_ci[io * DIM + j + ZZ * GMX_SIMD4_WIDTH] = x[(ia + j) * stride + ZZ] + shz;
}
}
}
#endif /* !GMX_SIMD4_HAVE_REAL */
}
-static real minimum_subgrid_size_xy(const nbnxn_grid_t &grid)
+static real minimum_subgrid_size_xy(const Grid& grid)
{
- if (grid.bSimple)
+ const Grid::Dimensions& dims = grid.dimensions();
+
+ if (grid.geometry().isSimple)
{
- return std::min(grid.cellSize[XX], grid.cellSize[YY]);
+ return std::min(dims.cellSize[XX], dims.cellSize[YY]);
}
else
{
- return std::min(grid.cellSize[XX]/c_gpuNumClusterPerCellX,
- grid.cellSize[YY]/c_gpuNumClusterPerCellY);
+ return std::min(dims.cellSize[XX] / c_gpuNumClusterPerCellX,
+ dims.cellSize[YY] / c_gpuNumClusterPerCellY);
}
}
-static real effective_buffer_1x1_vs_MxN(const nbnxn_grid_t &iGrid,
- const nbnxn_grid_t &jGrid)
+static real effective_buffer_1x1_vs_MxN(const Grid& iGrid, const Grid& jGrid)
{
const real eff_1x1_buffer_fac_overest = 0.1;
* Smaller tolerances or using RF lead to a smaller effective buffer,
* so 10% gives a safe overestimate.
*/
- return eff_1x1_buffer_fac_overest*(minimum_subgrid_size_xy(iGrid) +
- minimum_subgrid_size_xy(jGrid));
-}
-
-/* Clusters at the cut-off only increase rlist by 60% of their size */
-static real nbnxn_rlist_inc_outside_fac = 0.6;
-
-/* Due to the cluster size the effective pair-list is longer than
- * that of a simple atom pair-list. This function gives the extra distance.
- */
-real nbnxn_get_rlist_effective_inc(int cluster_size_j, real atom_density)
-{
- int cluster_size_i;
- real vol_inc_i, vol_inc_j;
-
- /* We should get this from the setup, but currently it's the same for
- * all setups, including GPUs.
- */
- cluster_size_i = c_nbnxnCpuIClusterSize;
-
- vol_inc_i = (cluster_size_i - 1)/atom_density;
- vol_inc_j = (cluster_size_j - 1)/atom_density;
-
- return nbnxn_rlist_inc_outside_fac*std::cbrt(vol_inc_i + vol_inc_j);
+ return eff_1x1_buffer_fac_overest * (minimum_subgrid_size_xy(iGrid) + minimum_subgrid_size_xy(jGrid));
}
/* Estimates the interaction volume^2 for non-local interactions */
-static real nonlocal_vol2(const struct gmx_domdec_zones_t *zones, const rvec ls, real r)
+static real nonlocal_vol2(const struct gmx_domdec_zones_t* zones, const rvec ls, real r)
{
- real cl, ca, za;
- real vold_est;
- real vol2_est_tot;
-
- vol2_est_tot = 0;
+ real vol2_est_tot = 0;
/* Here we simply add up the volumes of 1, 2 or 3 1D decomposition
* not home interaction volume^2. As these volumes are not additive,
{
if (zones->shift[z][XX] + zones->shift[z][YY] + zones->shift[z][ZZ] == 1)
{
- cl = 0;
- ca = 1;
- za = 1;
+ real cl = 0;
+ real ca = 1;
+ real za = 1;
for (int d = 0; d < DIM; d++)
{
if (zones->shift[z][d] == 0)
{
- cl += 0.5*ls[d];
+ cl += 0.5 * ls[d];
ca *= ls[d];
za *= zones->size[z].x1[d] - zones->size[z].x0[d];
}
}
/* 4 octants of a sphere */
- vold_est = 0.25*M_PI*r*r*r*r;
+ real vold_est = 0.25 * M_PI * r * r * r * r;
/* 4 quarter pie slices on the edges */
- vold_est += 4*cl*M_PI/6.0*r*r*r;
+ vold_est += 4 * cl * M_PI / 6.0 * r * r * r;
/* One rectangular volume on a face */
- vold_est += ca*0.5*r*r;
+ vold_est += ca * 0.5 * r * r;
- vol2_est_tot += vold_est*za;
+ vol2_est_tot += vold_est * za;
}
}
}
/* Estimates the average size of a full j-list for super/sub setup */
-static void get_nsubpair_target(const nbnxn_search *nbs,
- const InteractionLocality iloc,
- const real rlist,
- const int min_ci_balanced,
- int *nsubpair_target,
- float *nsubpair_tot_est)
+static void get_nsubpair_target(const Nbnxm::GridSet& gridSet,
+ const InteractionLocality iloc,
+ const real rlist,
+ const int min_ci_balanced,
+ int* nsubpair_target,
+ float* nsubpair_tot_est)
{
/* The target value of 36 seems to be the optimum for Kepler.
* Maxwell is less sensitive to the exact value.
*/
- const int nsubpair_target_min = 36;
- rvec ls;
- real r_eff_sup, vol_est, nsp_est, nsp_est_nl;
+ const int nsubpair_target_min = 36;
- const nbnxn_grid_t &grid = nbs->grid[0];
+ const Grid& grid = gridSet.grids()[0];
/* We don't need to balance list sizes if:
* - We didn't request balancing.
* since we will always generate at least #cells lists.
* - We don't have any cells, since then there won't be any lists.
*/
- if (min_ci_balanced <= 0 || grid.nc >= min_ci_balanced || grid.nc == 0)
+ if (min_ci_balanced <= 0 || grid.numCells() >= min_ci_balanced || grid.numCells() == 0)
{
/* nsubpair_target==0 signals no balancing */
*nsubpair_target = 0;
return;
}
- ls[XX] = (grid.c1[XX] - grid.c0[XX])/(grid.numCells[XX]*c_gpuNumClusterPerCellX);
- ls[YY] = (grid.c1[YY] - grid.c0[YY])/(grid.numCells[YY]*c_gpuNumClusterPerCellY);
- ls[ZZ] = grid.na_c/(grid.atom_density*ls[XX]*ls[YY]);
+ gmx::RVec ls;
+ const int numAtomsCluster = grid.geometry().numAtomsICluster;
+ const Grid::Dimensions& dims = grid.dimensions();
- /* The average length of the diagonal of a sub cell */
- real diagonal = std::sqrt(ls[XX]*ls[XX] + ls[YY]*ls[YY] + ls[ZZ]*ls[ZZ]);
+ ls[XX] = dims.cellSize[XX] / c_gpuNumClusterPerCellX;
+ ls[YY] = dims.cellSize[YY] / c_gpuNumClusterPerCellY;
+ ls[ZZ] = numAtomsCluster / (dims.atomDensity * ls[XX] * ls[YY]);
/* The formulas below are a heuristic estimate of the average nsj per si*/
- r_eff_sup = rlist + nbnxn_rlist_inc_outside_fac*gmx::square((grid.na_c - 1.0)/grid.na_c)*0.5*diagonal;
+ const real r_eff_sup = rlist + nbnxn_get_rlist_effective_inc(numAtomsCluster, ls);
- if (!nbs->DomDec || nbs->zones->n == 1)
- {
- nsp_est_nl = 0;
- }
- else
+ real nsp_est_nl = 0;
+ if (gridSet.domainSetup().haveMultipleDomains && gridSet.domainSetup().zones->n != 1)
{
- nsp_est_nl =
- gmx::square(grid.atom_density/grid.na_c)*
- nonlocal_vol2(nbs->zones, ls, r_eff_sup);
+ nsp_est_nl = gmx::square(dims.atomDensity / numAtomsCluster)
+ * nonlocal_vol2(gridSet.domainSetup().zones, ls, r_eff_sup);
}
+ real nsp_est = nsp_est_nl;
if (iloc == InteractionLocality::Local)
{
/* Sub-cell interacts with itself */
- vol_est = ls[XX]*ls[YY]*ls[ZZ];
+ real vol_est = ls[XX] * ls[YY] * ls[ZZ];
/* 6/2 rectangular volume on the faces */
- vol_est += (ls[XX]*ls[YY] + ls[XX]*ls[ZZ] + ls[YY]*ls[ZZ])*r_eff_sup;
+ vol_est += (ls[XX] * ls[YY] + ls[XX] * ls[ZZ] + ls[YY] * ls[ZZ]) * r_eff_sup;
/* 12/2 quarter pie slices on the edges */
- vol_est += 2*(ls[XX] + ls[YY] + ls[ZZ])*0.25*M_PI*gmx::square(r_eff_sup);
+ vol_est += 2 * (ls[XX] + ls[YY] + ls[ZZ]) * 0.25 * M_PI * gmx::square(r_eff_sup);
/* 4 octants of a sphere */
- vol_est += 0.5*4.0/3.0*M_PI*gmx::power3(r_eff_sup);
+ vol_est += 0.5 * 4.0 / 3.0 * M_PI * gmx::power3(r_eff_sup);
/* Estimate the number of cluster pairs as the local number of
* clusters times the volume they interact with times the density.
*/
- nsp_est = grid.nsubc_tot*vol_est*grid.atom_density/grid.na_c;
+ nsp_est = grid.numClusters() * vol_est * dims.atomDensity / numAtomsCluster;
/* Subtract the non-local pair count */
nsp_est -= nsp_est_nl;
- /* For small cut-offs nsp_est will be an underesimate.
+ /* For small cut-offs nsp_est will be an underestimate.
* With DD nsp_est_nl is an overestimate so nsp_est can get negative.
* So to avoid too small or negative nsp_est we set a minimum of
* all cells interacting with all 3^3 direct neighbors (3^3-1)/2+1=14.
* groups of atoms we'll anyhow be limited by nsubpair_target_min,
* so this overestimation will not matter.
*/
- nsp_est = std::max(nsp_est, grid.nsubc_tot*14._real);
+ nsp_est = std::max(nsp_est, grid.numClusters() * 14._real);
if (debug)
{
- fprintf(debug, "nsp_est local %5.1f non-local %5.1f\n",
- nsp_est, nsp_est_nl);
+ fprintf(debug, "nsp_est local %5.1f non-local %5.1f\n", nsp_est, nsp_est_nl);
}
}
- else
- {
- nsp_est = nsp_est_nl;
- }
/* Thus the (average) maximum j-list size should be as follows.
* Since there is overhead, we shouldn't make the lists too small
* (and we can't chop up j-groups) so we use a minimum target size of 36.
*/
- *nsubpair_target = std::max(nsubpair_target_min,
- roundToInt(nsp_est/min_ci_balanced));
- *nsubpair_tot_est = static_cast<int>(nsp_est);
+ *nsubpair_target = std::max(nsubpair_target_min, roundToInt(nsp_est / min_ci_balanced));
+ *nsubpair_tot_est = nsp_est;
if (debug)
{
- fprintf(debug, "nbl nsp estimate %.1f, nsubpair_target %d\n",
- nsp_est, *nsubpair_target);
+ fprintf(debug, "nbl nsp estimate %.1f, nsubpair_target %d\n", nsp_est, *nsubpair_target);
}
}
/* Debug list print function */
-static void print_nblist_ci_cj(FILE *fp, const NbnxnPairlistCpu *nbl)
+static void print_nblist_ci_cj(FILE* fp, const NbnxnPairlistCpu& nbl)
{
- for (const nbnxn_ci_t &ciEntry : nbl->ci)
+ for (const nbnxn_ci_t& ciEntry : nbl.ci)
{
- fprintf(fp, "ci %4d shift %2d ncj %3d\n",
- ciEntry.ci, ciEntry.shift,
- ciEntry.cj_ind_end - ciEntry.cj_ind_start);
+ fprintf(fp, "ci %4d shift %2d ncj %3d\n", ciEntry.ci, ciEntry.shift, ciEntry.cj_ind_end - ciEntry.cj_ind_start);
for (int j = ciEntry.cj_ind_start; j < ciEntry.cj_ind_end; j++)
{
- fprintf(fp, " cj %5d imask %x\n",
- nbl->cj[j].cj,
- nbl->cj[j].excl);
+ fprintf(fp, " cj %5d imask %x\n", nbl.cj[j].cj, nbl.cj[j].excl);
}
}
}
/* Debug list print function */
-static void print_nblist_sci_cj(FILE *fp, const NbnxnPairlistGpu *nbl)
+static void print_nblist_sci_cj(FILE* fp, const NbnxnPairlistGpu& nbl)
{
- for (const nbnxn_sci_t &sci : nbl->sci)
+ for (const nbnxn_sci_t& sci : nbl.sci)
{
- fprintf(fp, "ci %4d shift %2d ncj4 %2d\n",
- sci.sci, sci.shift,
- sci.numJClusterGroups());
+ fprintf(fp, "ci %4d shift %2d ncj4 %2d\n", sci.sci, sci.shift, sci.numJClusterGroups());
int ncp = 0;
for (int j4 = sci.cj4_ind_start; j4 < sci.cj4_ind_end; j4++)
{
for (int j = 0; j < c_nbnxnGpuJgroupSize; j++)
{
- fprintf(fp, " sj %5d imask %x\n",
- nbl->cj4[j4].cj[j],
- nbl->cj4[j4].imei[0].imask);
+ fprintf(fp, " sj %5d imask %x\n", nbl.cj4[j4].cj[j], nbl.cj4[j4].imei[0].imask);
for (int si = 0; si < c_gpuNumClusterPerCell; si++)
{
- if (nbl->cj4[j4].imei[0].imask & (1U << (j*c_gpuNumClusterPerCell + si)))
+ if (nbl.cj4[j4].imei[0].imask & (1U << (j * c_gpuNumClusterPerCell + si)))
{
ncp++;
}
}
}
}
- fprintf(fp, "ci %4d shift %2d ncj4 %2d ncp %3d\n",
- sci.sci, sci.shift,
- sci.numJClusterGroups(),
- ncp);
+ fprintf(fp, "ci %4d shift %2d ncj4 %2d ncp %3d\n", sci.sci, sci.shift, sci.numJClusterGroups(), ncp);
}
}
/* Combine pair lists *nbl generated on multiple threads nblc */
-static void combine_nblists(int nnbl, NbnxnPairlistGpu **nbl,
- NbnxnPairlistGpu *nblc)
+static void combine_nblists(gmx::ArrayRef<const NbnxnPairlistGpu> nbls, NbnxnPairlistGpu* nblc)
{
int nsci = nblc->sci.size();
int ncj4 = nblc->cj4.size();
int nexcl = nblc->excl.size();
- for (int i = 0; i < nnbl; i++)
+ for (const auto& nbl : nbls)
{
- nsci += nbl[i]->sci.size();
- ncj4 += nbl[i]->cj4.size();
- nexcl += nbl[i]->excl.size();
+ nsci += nbl.sci.size();
+ ncj4 += nbl.cj4.size();
+ nexcl += nbl.excl.size();
}
/* Resize with the final, combined size, so we can fill in parallel */
/* Each thread should copy its own data to the combined arrays,
* as otherwise data will go back and forth between different caches.
*/
-#if GMX_OPENMP && !(defined __clang_analyzer__)
- int nthreads = gmx_omp_nthreads_get(emntPairsearch);
-#endif
+ const int gmx_unused nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Pairsearch);
#pragma omp parallel for num_threads(nthreads) schedule(static)
- for (int n = 0; n < nnbl; n++)
+ for (gmx::index n = 0; n < nbls.ssize(); n++)
{
try
{
int cj4_offset = ncj4;
int excl_offset = nexcl;
- for (int i = n; i < nnbl; i++)
+ for (gmx::index i = n; i < nbls.ssize(); i++)
{
- sci_offset -= nbl[i]->sci.size();
- cj4_offset -= nbl[i]->cj4.size();
- excl_offset -= nbl[i]->excl.size();
+ sci_offset -= nbls[i].sci.size();
+ cj4_offset -= nbls[i].cj4.size();
+ excl_offset -= nbls[i].excl.size();
}
- const NbnxnPairlistGpu &nbli = *nbl[n];
+ const NbnxnPairlistGpu& nbli = nbls[n];
for (size_t i = 0; i < nbli.sci.size(); i++)
{
- nblc->sci[sci_offset + i] = nbli.sci[i];
+ nblc->sci[sci_offset + i] = nbli.sci[i];
nblc->sci[sci_offset + i].cj4_ind_start += cj4_offset;
- nblc->sci[sci_offset + i].cj4_ind_end += cj4_offset;
+ nblc->sci[sci_offset + i].cj4_ind_end += cj4_offset;
}
for (size_t j4 = 0; j4 < nbli.cj4.size(); j4++)
{
- nblc->cj4[cj4_offset + j4] = nbli.cj4[j4];
+ nblc->cj4[cj4_offset + j4] = nbli.cj4[j4];
nblc->cj4[cj4_offset + j4].imei[0].excl_ind += excl_offset;
nblc->cj4[cj4_offset + j4].imei[1].excl_ind += excl_offset;
}
nblc->excl[excl_offset + j4] = nbli.excl[j4];
}
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- for (int n = 0; n < nnbl; n++)
+ for (const auto& nbl : nbls)
{
- nblc->nci_tot += nbl[n]->nci_tot;
+ nblc->nci_tot += nbl.nci_tot;
}
}
-static void balance_fep_lists(const nbnxn_search *nbs,
- nbnxn_pairlist_set_t *nbl_lists)
+static void balance_fep_lists(gmx::ArrayRef<std::unique_ptr<t_nblist>> fepLists,
+ gmx::ArrayRef<PairsearchWork> work)
{
- int nnbl;
- int nri_tot, nrj_tot, nrj_target;
- int th_dest;
- t_nblist *nbld;
-
- nnbl = nbl_lists->nnbl;
+ const int numLists = fepLists.ssize();
- if (nnbl == 1)
+ if (numLists == 1)
{
/* Nothing to balance */
return;
}
/* Count the total i-lists and pairs */
- nri_tot = 0;
- nrj_tot = 0;
- for (int th = 0; th < nnbl; th++)
+ int nri_tot = 0;
+ int nrj_tot = 0;
+ for (const auto& list : fepLists)
{
- nri_tot += nbl_lists->nbl_fep[th]->nri;
- nrj_tot += nbl_lists->nbl_fep[th]->nrj;
+ nri_tot += list->nri;
+ nrj_tot += list->nrj;
}
- nrj_target = (nrj_tot + nnbl - 1)/nnbl;
+ const int nrj_target = (nrj_tot + numLists - 1) / numLists;
- assert(gmx_omp_nthreads_get(emntNonbonded) == nnbl);
+ GMX_ASSERT(gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded) == numLists,
+ "We should have as many work objects as FEP lists");
-#pragma omp parallel for schedule(static) num_threads(nnbl)
- for (int th = 0; th < nnbl; th++)
+#pragma omp parallel for schedule(static) num_threads(numLists)
+ for (int th = 0; th < numLists; th++)
{
try
{
- t_nblist *nbl = nbs->work[th].nbl_fep.get();
+ t_nblist* nbl = work[th].nbl_fep.get();
/* Note that here we allocate for the total size, instead of
* a per-thread esimate (which is hard to obtain).
if (nri_tot > nbl->maxnri || nrj_tot > nbl->maxnrj)
{
nbl->maxnrj = over_alloc_small(nrj_tot);
- srenew(nbl->jjnr, nbl->maxnrj);
- srenew(nbl->excl_fep, nbl->maxnrj);
+ nbl->jjnr.resize(nbl->maxnrj);
+ nbl->excl_fep.resize(nbl->maxnrj);
}
clear_pairlist_fep(nbl);
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
/* Loop over the source lists and assign and copy i-entries */
- th_dest = 0;
- nbld = nbs->work[th_dest].nbl_fep.get();
- for (int th = 0; th < nnbl; th++)
+ int th_dest = 0;
+ t_nblist* nbld = work[th_dest].nbl_fep.get();
+ for (int th = 0; th < numLists; th++)
{
- t_nblist *nbls;
-
- nbls = nbl_lists->nbl_fep[th];
+ const t_nblist* nbls = fepLists[th].get();
for (int i = 0; i < nbls->nri; i++)
{
- int nrj;
-
/* The number of pairs in this i-entry */
- nrj = nbls->jindex[i+1] - nbls->jindex[i];
+ const int nrj = nbls->jindex[i + 1] - nbls->jindex[i];
/* Decide if list th_dest is too large and we should procede
* to the next destination list.
*/
- if (th_dest+1 < nnbl && nbld->nrj > 0 &&
- nbld->nrj + nrj - nrj_target > nrj_target - nbld->nrj)
+ if (th_dest + 1 < numLists && nbld->nrj > 0
+ && nbld->nrj + nrj - nrj_target > nrj_target - nbld->nrj)
{
th_dest++;
- nbld = nbs->work[th_dest].nbl_fep.get();
+ nbld = work[th_dest].nbl_fep.get();
}
nbld->iinr[nbld->nri] = nbls->iinr[i];
nbld->gid[nbld->nri] = nbls->gid[i];
nbld->shift[nbld->nri] = nbls->shift[i];
- for (int j = nbls->jindex[i]; j < nbls->jindex[i+1]; j++)
+ for (int j = nbls->jindex[i]; j < nbls->jindex[i + 1]; j++)
{
nbld->jjnr[nbld->nrj] = nbls->jjnr[j];
nbld->excl_fep[nbld->nrj] = nbls->excl_fep[j];
}
/* Swap the list pointers */
- for (int th = 0; th < nnbl; th++)
+ for (int th = 0; th < numLists; th++)
{
- t_nblist *nbl_tmp = nbs->work[th].nbl_fep.release();
- nbs->work[th].nbl_fep.reset(nbl_lists->nbl_fep[th]);
- nbl_lists->nbl_fep[th] = nbl_tmp;
+ fepLists[th].swap(work[th].nbl_fep);
if (debug)
{
- fprintf(debug, "nbl_fep[%d] nri %4d nrj %4d\n",
- th,
- nbl_lists->nbl_fep[th]->nri,
- nbl_lists->nbl_fep[th]->nrj);
+ fprintf(debug, "nbl_fep[%d] nri %4d nrj %4d\n", th, fepLists[th]->nri, fepLists[th]->nrj);
}
}
}
/* Returns the next ci to be processes by our thread */
-static gmx_bool next_ci(const nbnxn_grid_t &grid,
- int nth, int ci_block,
- int *ci_x, int *ci_y,
- int *ci_b, int *ci)
+static gmx_bool next_ci(const Grid& grid, int nth, int ci_block, int* ci_x, int* ci_y, int* ci_b, int* ci)
{
(*ci_b)++;
(*ci)++;
if (*ci_b == ci_block)
{
/* Jump to the next block assigned to this task */
- *ci += (nth - 1)*ci_block;
- *ci_b = 0;
+ *ci += (nth - 1) * ci_block;
+ *ci_b = 0;
}
- if (*ci >= grid.nc)
+ if (*ci >= grid.numCells())
{
return FALSE;
}
- while (*ci >= grid.cxy_ind[*ci_x*grid.numCells[YY] + *ci_y + 1])
+ while (*ci >= grid.firstCellInColumn(*ci_x * grid.dimensions().numCells[YY] + *ci_y + 1))
{
*ci_y += 1;
- if (*ci_y == grid.numCells[YY])
+ if (*ci_y == grid.dimensions().numCells[YY])
{
*ci_x += 1;
- *ci_y = 0;
+ *ci_y = 0;
}
}
/* Returns the distance^2 for which we put cell pairs in the list
* without checking atom pair distances. This is usually < rlist^2.
*/
-static float boundingbox_only_distance2(const nbnxn_grid_t &iGrid,
- const nbnxn_grid_t &jGrid,
- real rlist,
- gmx_bool simple)
+static float boundingbox_only_distance2(const Grid::Dimensions& iGridDims,
+ const Grid::Dimensions& jGridDims,
+ real rlist,
+ gmx_bool simple)
{
/* If the distance between two sub-cell bounding boxes is less
* than this distance, do not check the distance between
* is only performed when only 1 out of 8 sub-cells in within range,
* this is because the GPU is much faster than the cpu.
*/
- real bbx, bby;
- real rbb2;
- bbx = 0.5*(iGrid.cellSize[XX] + jGrid.cellSize[XX]);
- bby = 0.5*(iGrid.cellSize[YY] + jGrid.cellSize[YY]);
+ real bbx = 0.5 * (iGridDims.cellSize[XX] + jGridDims.cellSize[XX]);
+ real bby = 0.5 * (iGridDims.cellSize[YY] + jGridDims.cellSize[YY]);
if (!simple)
{
bbx /= c_gpuNumClusterPerCellX;
bby /= c_gpuNumClusterPerCellY;
}
- rbb2 = std::max(0.0, rlist - 0.5*std::sqrt(bbx*bbx + bby*bby));
- rbb2 = rbb2 * rbb2;
+ real rbb2 = std::max(0.0, rlist - 0.5 * std::sqrt(bbx * bbx + bby * bby));
+ rbb2 = rbb2 * rbb2;
#if !GMX_DOUBLE
return rbb2;
#else
- return (float)((1+GMX_FLOAT_EPS)*rbb2);
+ return static_cast<float>((1 + GMX_FLOAT_EPS) * rbb2);
#endif
}
-static int get_ci_block_size(const nbnxn_grid_t &iGrid,
- gmx_bool bDomDec, int nth)
+static int get_ci_block_size(const Grid& iGrid, const bool haveMultipleDomains, const int numLists)
{
const int ci_block_enum = 5;
const int ci_block_denom = 11;
const int ci_block_min_atoms = 16;
- int ci_block;
/* Here we decide how to distribute the blocks over the threads.
* We use prime numbers to try to avoid that the grid size becomes
* zone boundaries with 3D domain decomposition. At the same time
* the blocks will not become too small.
*/
- ci_block = (iGrid.nc*ci_block_enum)/(ci_block_denom*iGrid.numCells[XX]*nth);
+ GMX_ASSERT(iGrid.dimensions().numCells[XX] > 0, "Grid can't be empty");
+ GMX_ASSERT(numLists > 0, "We need at least one list");
+ int ci_block = (iGrid.numCells() * ci_block_enum)
+ / (ci_block_denom * iGrid.dimensions().numCells[XX] * numLists);
+
+ const int numAtomsPerCell = iGrid.geometry().numAtomsPerCell;
/* Ensure the blocks are not too small: avoids cache invalidation */
- if (ci_block*iGrid.na_sc < ci_block_min_atoms)
+ if (ci_block * numAtomsPerCell < ci_block_min_atoms)
{
- ci_block = (ci_block_min_atoms + iGrid.na_sc - 1)/iGrid.na_sc;
+ ci_block = (ci_block_min_atoms + numAtomsPerCell - 1) / numAtomsPerCell;
}
/* Without domain decomposition
* or with less than 3 blocks per task, divide in nth blocks.
*/
- if (!bDomDec || nth*3*ci_block > iGrid.nc)
+ if (!haveMultipleDomains || numLists * 3 * ci_block > iGrid.numCells())
{
- ci_block = (iGrid.nc + nth - 1)/nth;
+ ci_block = (iGrid.numCells() + numLists - 1) / numLists;
}
- if (ci_block > 1 && (nth - 1)*ci_block >= iGrid.nc)
+ if (ci_block > 1 && (numLists - 1) * ci_block >= iGrid.numCells())
{
/* Some threads have no work. Although reducing the block size
* does not decrease the block count on the first few threads,
return bufferFlagShift;
}
-static bool pairlistIsSimple(const NbnxnPairlistCpu gmx_unused &pairlist)
+static bool pairlistIsSimple(const NbnxnPairlistCpu gmx_unused& pairlist)
{
return true;
}
-static bool pairlistIsSimple(const NbnxnPairlistGpu gmx_unused &pairlist)
+static bool pairlistIsSimple(const NbnxnPairlistGpu gmx_unused& pairlist)
{
return false;
}
-static void makeClusterListWrapper(NbnxnPairlistCpu *nbl,
- const nbnxn_grid_t gmx_unused &iGrid,
- const int ci,
- const nbnxn_grid_t &jGrid,
- const int firstCell,
- const int lastCell,
- const bool excludeSubDiagonal,
- const nbnxn_atomdata_t *nbat,
- const real rlist2,
- const real rbb2,
- const int nb_kernel_type,
- int *numDistanceChecks)
+static void makeClusterListWrapper(NbnxnPairlistCpu* nbl,
+ const Grid gmx_unused& iGrid,
+ const int ci,
+ const Grid& jGrid,
+ const int firstCell,
+ const int lastCell,
+ const bool excludeSubDiagonal,
+ const nbnxn_atomdata_t* nbat,
+ const real rlist2,
+ const real rbb2,
+ const ClusterDistanceKernelType kernelType,
+ int* numDistanceChecks)
{
- switch (nb_kernel_type)
- {
- case nbnxnk4x4_PlainC:
- makeClusterListSimple(jGrid,
- nbl, ci, firstCell, lastCell,
- excludeSubDiagonal,
- nbat->x().data(),
- rlist2, rbb2,
- numDistanceChecks);
+ switch (kernelType)
+ {
+ case ClusterDistanceKernelType::CpuPlainC:
+ makeClusterListSimple(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#ifdef GMX_NBNXN_SIMD_4XN
- case nbnxnk4xN_SIMD_4xN:
- makeClusterListSimd4xn(jGrid,
- nbl, ci, firstCell, lastCell,
- excludeSubDiagonal,
- nbat->x().data(),
- rlist2, rbb2,
- numDistanceChecks);
+ case ClusterDistanceKernelType::CpuSimd_4xM:
+ makeClusterListSimd4xn(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#endif
#ifdef GMX_NBNXN_SIMD_2XNN
- case nbnxnk4xN_SIMD_2xNN:
- makeClusterListSimd2xnn(jGrid,
- nbl, ci, firstCell, lastCell,
- excludeSubDiagonal,
- nbat->x().data(),
- rlist2, rbb2,
- numDistanceChecks);
+ case ClusterDistanceKernelType::CpuSimd_2xMM:
+ makeClusterListSimd2xnn(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#endif
+ default: GMX_ASSERT(false, "Unhandled kernel type");
}
}
-static void makeClusterListWrapper(NbnxnPairlistGpu *nbl,
- const nbnxn_grid_t &gmx_unused iGrid,
- const int ci,
- const nbnxn_grid_t &jGrid,
- const int firstCell,
- const int lastCell,
- const bool excludeSubDiagonal,
- const nbnxn_atomdata_t *nbat,
- const real rlist2,
- const real rbb2,
- const int gmx_unused nb_kernel_type,
- int *numDistanceChecks)
+static void makeClusterListWrapper(NbnxnPairlistGpu* nbl,
+ const Grid& gmx_unused iGrid,
+ const int ci,
+ const Grid& jGrid,
+ const int firstCell,
+ const int lastCell,
+ const bool excludeSubDiagonal,
+ const nbnxn_atomdata_t* nbat,
+ const real rlist2,
+ const real rbb2,
+ ClusterDistanceKernelType gmx_unused kernelType,
+ int* numDistanceChecks)
{
for (int cj = firstCell; cj <= lastCell; cj++)
{
- make_cluster_list_supersub(iGrid, jGrid,
- nbl, ci, cj,
- excludeSubDiagonal,
- nbat->xstride, nbat->x().data(),
- rlist2, rbb2,
- numDistanceChecks);
+ make_cluster_list_supersub(
+ iGrid, jGrid, nbl, ci, cj, excludeSubDiagonal, nbat->xstride, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
}
}
-static int getNumSimpleJClustersInList(const NbnxnPairlistCpu &nbl)
+static int getNumSimpleJClustersInList(const NbnxnPairlistCpu& nbl)
{
return nbl.cj.size();
}
-static int getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu &nbl)
+static int getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu& nbl)
{
return 0;
}
-static void incrementNumSimpleJClustersInList(NbnxnPairlistCpu *nbl,
- int ncj_old_j)
+static void incrementNumSimpleJClustersInList(NbnxnPairlistCpu* nbl, int ncj_old_j)
{
- nbl->ncjInUse += nbl->cj.size() - ncj_old_j;
+ nbl->ncjInUse += nbl->cj.size();
+ nbl->ncjInUse -= ncj_old_j;
}
-static void incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused *nbl,
- int gmx_unused ncj_old_j)
+static void incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused* nbl, int gmx_unused ncj_old_j)
{
}
-static void checkListSizeConsistency(const NbnxnPairlistCpu &nbl,
- const bool haveFreeEnergy)
+static void checkListSizeConsistency(const NbnxnPairlistCpu& nbl, const bool haveFreeEnergy)
{
GMX_RELEASE_ASSERT(static_cast<size_t>(nbl.ncjInUse) == nbl.cj.size() || haveFreeEnergy,
"Without free-energy all cj pair-list entries should be in use. "
"this check is only here to catch bugs");
}
-static void checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused &nbl,
- bool gmx_unused haveFreeEnergy)
+static void checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused& nbl, bool gmx_unused haveFreeEnergy)
{
/* We currently can not check consistency here */
}
/* Set the buffer flags for newly added entries in the list */
-static void setBufferFlags(const NbnxnPairlistCpu &nbl,
+static void setBufferFlags(const NbnxnPairlistCpu& nbl,
const int ncj_old_j,
const int gridj_flag_shift,
- gmx_bitmask_t *gridj_flag,
+ gmx_bitmask_t* gridj_flag,
const int th)
{
if (gmx::ssize(nbl.cj) > ncj_old_j)
}
}
-static void setBufferFlags(const NbnxnPairlistGpu gmx_unused &nbl,
+static void setBufferFlags(const NbnxnPairlistGpu gmx_unused& nbl,
int gmx_unused ncj_old_j,
int gmx_unused gridj_flag_shift,
- gmx_bitmask_t gmx_unused *gridj_flag,
- int gmx_unused th)
+ gmx_bitmask_t gmx_unused* gridj_flag,
+ int gmx_unused th)
{
GMX_ASSERT(false, "This function should never be called");
}
/* Generates the part of pair-list nbl assigned to our thread */
-template <typename T>
-static void nbnxn_make_pairlist_part(const nbnxn_search *nbs,
- const nbnxn_grid_t &iGrid,
- const nbnxn_grid_t &jGrid,
- nbnxn_search_work_t *work,
- const nbnxn_atomdata_t *nbat,
- const t_blocka &exclusions,
- real rlist,
- int nb_kernel_type,
- int ci_block,
- gmx_bool bFBufferFlag,
- int nsubpair_max,
- gmx_bool progBal,
- float nsubpair_tot_est,
- int th, int nth,
- T *nbl,
- t_nblist *nbl_fep)
+template<typename T>
+static void nbnxn_make_pairlist_part(const Nbnxm::GridSet& gridSet,
+ const Grid& iGrid,
+ const Grid& jGrid,
+ PairsearchWork* work,
+ const nbnxn_atomdata_t* nbat,
+ const ListOfLists<int>& exclusions,
+ real rlist,
+ const PairlistType pairlistType,
+ int ci_block,
+ gmx_bool bFBufferFlag,
+ int nsubpair_max,
+ gmx_bool progBal,
+ float nsubpair_tot_est,
+ int th,
+ int nth,
+ T* nbl,
+ t_nblist* nbl_fep)
{
- int na_cj_2log;
- matrix box;
- real rlist2, rl_fep2 = 0;
- float rbb2;
- int ci_b, ci, ci_x, ci_y, ci_xy;
- ivec shp;
- real bx0, bx1, by0, by1, bz0, bz1;
- real bz1_frac;
- real d2cx, d2z, d2z_cx, d2z_cy, d2zx, d2zxy, d2xy;
- int cxf, cxl, cyf, cyf_x, cyl;
- int numDistanceChecks;
- int gridi_flag_shift = 0, gridj_flag_shift = 0;
- gmx_bitmask_t *gridj_flag = nullptr;
- int ncj_old_i, ncj_old_j;
-
- nbs_cycle_start(&work->cc[enbsCCsearch]);
-
- if (jGrid.bSimple != pairlistIsSimple(*nbl) ||
- iGrid.bSimple != pairlistIsSimple(*nbl))
+ matrix box;
+ real rl_fep2 = 0;
+ ivec shp;
+ int gridi_flag_shift = 0, gridj_flag_shift = 0;
+ gmx_bitmask_t* gridj_flag = nullptr;
+
+ if (jGrid.geometry().isSimple != pairlistIsSimple(*nbl)
+ || iGrid.geometry().isSimple != pairlistIsSimple(*nbl))
{
gmx_incons("Grid incompatible with pair-list");
}
sync_work(nbl);
- GMX_ASSERT(nbl->na_ci == jGrid.na_c, "The cluster sizes in the list and grid should match");
- nbl->na_cj = nbnxn_kernel_to_cluster_j_size(nb_kernel_type);
- na_cj_2log = get_2log(nbl->na_cj);
+ GMX_ASSERT(nbl->na_ci == jGrid.geometry().numAtomsICluster,
+ "The cluster sizes in the list and grid should match");
+ nbl->na_cj = JClusterSizePerListType[pairlistType];
+ const int na_cj_2log = get_2log(nbl->na_cj);
- nbl->rlist = rlist;
+ nbl->rlist = rlist;
if (bFBufferFlag)
{
gridi_flag_shift = getBufferFlagShift(nbl->na_ci);
gridj_flag_shift = getBufferFlagShift(nbl->na_cj);
- gridj_flag = work->buffer_flags.flag;
+ gridj_flag = work->buffer_flags.data();
}
- copy_mat(nbs->box, box);
+ gridSet.getBox(box);
- rlist2 = nbl->rlist*nbl->rlist;
+ const bool haveFep = gridSet.haveFep();
- if (nbs->bFEP && !pairlistIsSimple(*nbl))
+ const real rlist2 = nbl->rlist * nbl->rlist;
+
+ // Select the cluster pair distance kernel type
+ const ClusterDistanceKernelType kernelType = getClusterDistanceKernelType(pairlistType, *nbat);
+
+ if (haveFep && !pairlistIsSimple(*nbl))
{
/* Determine an atom-pair list cut-off distance for FEP atom pairs.
* We should not simply use rlist, since then we would not have
* the small, effective buffering of the NxN lists.
* The buffer is on overestimate, but the resulting cost for pairs
- * beyond rlist is neglible compared to the FEP pairs within rlist.
+ * beyond rlist is negligible compared to the FEP pairs within rlist.
*/
rl_fep2 = nbl->rlist + effective_buffer_1x1_vs_MxN(iGrid, jGrid);
{
fprintf(debug, "nbl_fep atom-pair rlist %f\n", rl_fep2);
}
- rl_fep2 = rl_fep2*rl_fep2;
+ rl_fep2 = rl_fep2 * rl_fep2;
}
- rbb2 = boundingbox_only_distance2(iGrid, jGrid, nbl->rlist, pairlistIsSimple(*nbl));
+ const Grid::Dimensions& iGridDims = iGrid.dimensions();
+ const Grid::Dimensions& jGridDims = jGrid.dimensions();
+
+ const float rbb2 =
+ boundingbox_only_distance2(iGridDims, jGridDims, nbl->rlist, pairlistIsSimple(*nbl));
if (debug)
{
/* Check if we need periodicity shifts.
* Without PBC or with domain decomposition we don't need them.
*/
- if (d >= ePBC2npbcdim(nbs->ePBC) || nbs->dd_dim[d])
+ if (d >= numPbcDimensions(gridSet.domainSetup().pbcType)
+ || gridSet.domainSetup().haveMultipleDomainsPerDim[d])
{
shp[d] = 0;
}
else
{
- const real listRangeCellToCell = listRangeForGridCellToGridCell(rlist, iGrid, jGrid);
- if (d == XX &&
- box[XX][XX] - fabs(box[YY][XX]) - fabs(box[ZZ][XX]) < listRangeCellToCell)
+ const real listRangeCellToCell =
+ listRangeForGridCellToGridCell(rlist, iGrid.dimensions(), jGrid.dimensions());
+ if (d == XX && box[XX][XX] - fabs(box[YY][XX]) - fabs(box[ZZ][XX]) < listRangeCellToCell)
{
shp[d] = 2;
}
}
}
}
- const bool bSimple = pairlistIsSimple(*nbl);
- gmx::ArrayRef<const nbnxn_bb_t> bb_i;
+ const bool bSimple = pairlistIsSimple(*nbl);
+ gmx::ArrayRef<const BoundingBox> bb_i;
#if NBNXN_BBXXXX
- gmx::ArrayRef<const float> pbb_i;
+ gmx::ArrayRef<const float> pbb_i;
if (bSimple)
{
- bb_i = iGrid.bb;
+ bb_i = iGrid.iBoundingBoxes();
}
else
{
- pbb_i = iGrid.pbb;
+ pbb_i = iGrid.packedBoundingBoxes();
}
#else
/* We use the normal bounding box format for both grid types */
- bb_i = iGrid.bb;
+ bb_i = iGrid.iBoundingBoxes();
#endif
- gmx::ArrayRef<const float> bbcz_i = iGrid.bbcz;
- gmx::ArrayRef<const int> flags_i = iGrid.flags;
- gmx::ArrayRef<const float> bbcz_j = jGrid.bbcz;
- int cell0_i = iGrid.cell0;
+ gmx::ArrayRef<const BoundingBox1D> bbcz_i = iGrid.zBoundingBoxes();
+ gmx::ArrayRef<const int> flags_i = iGrid.clusterFlags();
+ gmx::ArrayRef<const BoundingBox1D> bbcz_j = jGrid.zBoundingBoxes();
+ int cell0_i = iGrid.cellOffset();
if (debug)
{
- fprintf(debug, "nbl nc_i %d col.av. %.1f ci_block %d\n",
- iGrid.nc, iGrid.nc/static_cast<double>(iGrid.numCells[XX]*iGrid.numCells[YY]), ci_block);
+ fprintf(debug,
+ "nbl nc_i %d col.av. %.1f ci_block %d\n",
+ iGrid.numCells(),
+ iGrid.numCells() / static_cast<double>(iGrid.numColumns()),
+ ci_block);
}
- numDistanceChecks = 0;
+ int numDistanceChecks = 0;
- const real listRangeBBToJCell2 = gmx::square(listRangeForBoundingBoxToGridCell(rlist, jGrid));
+ const real listRangeBBToJCell2 =
+ gmx::square(listRangeForBoundingBoxToGridCell(rlist, jGrid.dimensions()));
/* Initially ci_b and ci to 1 before where we want them to start,
* as they will both be incremented in next_ci.
*/
- ci_b = -1;
- ci = th*ci_block - 1;
- ci_x = 0;
- ci_y = 0;
+ int ci_b = -1;
+ int ci = th * ci_block - 1;
+ int ci_x = 0;
+ int ci_y = 0;
while (next_ci(iGrid, nth, ci_block, &ci_x, &ci_y, &ci_b, &ci))
{
if (bSimple && flags_i[ci] == 0)
{
continue;
}
+ const int ncj_old_i = getNumSimpleJClustersInList(*nbl);
- ncj_old_i = getNumSimpleJClustersInList(*nbl);
-
- d2cx = 0;
+ real d2cx = 0;
if (!isIntraGridList && shp[XX] == 0)
{
- if (bSimple)
- {
- bx1 = bb_i[ci].upper[BB_X];
- }
- else
+ const real bx1 =
+ bSimple ? bb_i[ci].upper.x
+ : iGridDims.lowerCorner[XX] + (real(ci_x) + 1) * iGridDims.cellSize[XX];
+ if (bx1 < jGridDims.lowerCorner[XX])
{
- bx1 = iGrid.c0[XX] + (ci_x+1)*iGrid.cellSize[XX];
- }
- if (bx1 < jGrid.c0[XX])
- {
- d2cx = gmx::square(jGrid.c0[XX] - bx1);
+ d2cx = gmx::square(jGridDims.lowerCorner[XX] - bx1);
if (d2cx >= listRangeBBToJCell2)
{
}
}
- ci_xy = ci_x*iGrid.numCells[YY] + ci_y;
+ int ci_xy = ci_x * iGridDims.numCells[YY] + ci_y;
/* Loop over shift vectors in three dimensions */
for (int tz = -shp[ZZ]; tz <= shp[ZZ]; tz++)
{
- const real shz = tz*box[ZZ][ZZ];
+ const real shz = real(tz) * box[ZZ][ZZ];
- bz0 = bbcz_i[ci*NNBSBB_D ] + shz;
- bz1 = bbcz_i[ci*NNBSBB_D+1] + shz;
+ real bz0 = bbcz_i[ci].lower + shz;
+ real bz1 = bbcz_i[ci].upper + shz;
- if (tz == 0)
- {
- d2z = 0;
- }
- else if (tz < 0)
+ real d2z = 0;
+ if (tz < 0)
{
d2z = gmx::square(bz1);
}
- else
+ else if (tz > 0)
{
d2z = gmx::square(bz0 - box[ZZ][ZZ]);
}
- d2z_cx = d2z + d2cx;
+ const real d2z_cx = d2z + d2cx;
if (d2z_cx >= rlist2)
{
continue;
}
- bz1_frac = bz1/(iGrid.cxy_ind[ci_xy+1] - iGrid.cxy_ind[ci_xy]);
+ real bz1_frac = bz1 / real(iGrid.numCellsInColumn(ci_xy));
if (bz1_frac < 0)
{
bz1_frac = 0;
for (int ty = -shp[YY]; ty <= shp[YY]; ty++)
{
- const real shy = ty*box[YY][YY] + tz*box[ZZ][YY];
+ const real shy = real(ty) * box[YY][YY] + real(tz) * box[ZZ][YY];
- if (bSimple)
- {
- by0 = bb_i[ci].lower[BB_Y] + shy;
- by1 = bb_i[ci].upper[BB_Y] + shy;
- }
- else
- {
- by0 = iGrid.c0[YY] + (ci_y )*iGrid.cellSize[YY] + shy;
- by1 = iGrid.c0[YY] + (ci_y+1)*iGrid.cellSize[YY] + shy;
- }
+ const real by0 = bSimple ? bb_i[ci].lower.y + shy
+ : iGridDims.lowerCorner[YY]
+ + (real(ci_y)) * iGridDims.cellSize[YY] + shy;
+ const real by1 = bSimple ? bb_i[ci].upper.y + shy
+ : iGridDims.lowerCorner[YY]
+ + (real(ci_y) + 1) * iGridDims.cellSize[YY] + shy;
- get_cell_range<YY>(by0, by1,
- jGrid,
- d2z_cx, rlist,
- &cyf, &cyl);
+ int cyf, cyl; //NOLINT(cppcoreguidelines-init-variables)
+ get_cell_range<YY>(by0, by1, jGridDims, d2z_cx, rlist, &cyf, &cyl);
if (cyf > cyl)
{
continue;
}
- d2z_cy = d2z;
- if (by1 < jGrid.c0[YY])
+ real d2z_cy = d2z;
+ if (by1 < jGridDims.lowerCorner[YY])
{
- d2z_cy += gmx::square(jGrid.c0[YY] - by1);
+ d2z_cy += gmx::square(jGridDims.lowerCorner[YY] - by1);
}
- else if (by0 > jGrid.c1[YY])
+ else if (by0 > jGridDims.upperCorner[YY])
{
- d2z_cy += gmx::square(by0 - jGrid.c1[YY]);
+ d2z_cy += gmx::square(by0 - jGridDims.upperCorner[YY]);
}
for (int tx = -shp[XX]; tx <= shp[XX]; tx++)
{
- const int shift = XYZ2IS(tx, ty, tz);
+ const int shift = xyzToShiftIndex(tx, ty, tz);
- const bool excludeSubDiagonal = (isIntraGridList && shift == CENTRAL);
+ const bool excludeSubDiagonal = (isIntraGridList && shift == gmx::c_centralShiftIndex);
- if (c_pbcShiftBackward && isIntraGridList && shift > CENTRAL)
+ if (c_pbcShiftBackward && isIntraGridList && shift > gmx::c_centralShiftIndex)
{
continue;
}
- const real shx = tx*box[XX][XX] + ty*box[YY][XX] + tz*box[ZZ][XX];
+ const real shx =
+ real(tx) * box[XX][XX] + real(ty) * box[YY][XX] + real(tz) * box[ZZ][XX];
- if (bSimple)
- {
- bx0 = bb_i[ci].lower[BB_X] + shx;
- bx1 = bb_i[ci].upper[BB_X] + shx;
- }
- else
- {
- bx0 = iGrid.c0[XX] + (ci_x )*iGrid.cellSize[XX] + shx;
- bx1 = iGrid.c0[XX] + (ci_x+1)*iGrid.cellSize[XX] + shx;
- }
+ const real bx0 = bSimple ? bb_i[ci].lower.x + shx
+ : iGridDims.lowerCorner[XX]
+ + (real(ci_x)) * iGridDims.cellSize[XX] + shx;
+ const real bx1 = bSimple ? bb_i[ci].upper.x + shx
+ : iGridDims.lowerCorner[XX]
+ + (real(ci_x) + 1) * iGridDims.cellSize[XX] + shx;
- get_cell_range<XX>(bx0, bx1,
- jGrid,
- d2z_cy, rlist,
- &cxf, &cxl);
+ int cxf, cxl; //NOLINT(cppcoreguidelines-init-variables)
+ get_cell_range<XX>(bx0, bx1, jGridDims, d2z_cy, rlist, &cxf, &cxl);
if (cxf > cxl)
{
continue;
}
- addNewIEntry(nbl, cell0_i+ci, shift, flags_i[ci]);
+ addNewIEntry(nbl, cell0_i + ci, shift, flags_i[ci]);
- if ((!c_pbcShiftBackward || excludeSubDiagonal) &&
- cxf < ci_x)
+ if ((!c_pbcShiftBackward || excludeSubDiagonal) && cxf < ci_x)
{
/* Leave the pairs with i > j.
* x is the major index, so skip half of it.
cxf = ci_x;
}
- set_icell_bb(iGrid, ci, shx, shy, shz,
- nbl->work);
+ set_icell_bb(iGrid, ci, shx, shy, shz, nbl->work.get());
- icell_set_x(cell0_i+ci, shx, shy, shz,
- nbat->xstride, nbat->x().data(),
- nb_kernel_type,
- nbl->work);
+ icell_set_x(cell0_i + ci,
+ shx,
+ shy,
+ shz,
+ nbat->xstride,
+ nbat->x().data(),
+ kernelType,
+ nbl->work.get());
for (int cx = cxf; cx <= cxl; cx++)
{
- d2zx = d2z;
- if (jGrid.c0[XX] + cx*jGrid.cellSize[XX] > bx1)
+ const real cx_real = cx;
+ real d2zx = d2z;
+ if (jGridDims.lowerCorner[XX] + cx_real * jGridDims.cellSize[XX] > bx1)
{
- d2zx += gmx::square(jGrid.c0[XX] + cx*jGrid.cellSize[XX] - bx1);
+ d2zx += gmx::square(jGridDims.lowerCorner[XX]
+ + cx_real * jGridDims.cellSize[XX] - bx1);
}
- else if (jGrid.c0[XX] + (cx+1)*jGrid.cellSize[XX] < bx0)
+ else if (jGridDims.lowerCorner[XX] + (cx_real + 1) * jGridDims.cellSize[XX] < bx0)
{
- d2zx += gmx::square(jGrid.c0[XX] + (cx+1)*jGrid.cellSize[XX] - bx0);
+ d2zx += gmx::square(jGridDims.lowerCorner[XX]
+ + (cx_real + 1) * jGridDims.cellSize[XX] - bx0);
}
- if (isIntraGridList &&
- cx == 0 &&
- (!c_pbcShiftBackward || shift == CENTRAL) &&
- cyf < ci_y)
- {
- /* Leave the pairs with i > j.
- * Skip half of y when i and j have the same x.
- */
- cyf_x = ci_y;
- }
- else
- {
- cyf_x = cyf;
- }
+ /* When true, leave the pairs with i > j.
+ * Skip half of y when i and j have the same x.
+ */
+ const bool skipHalfY = (isIntraGridList && cx == 0
+ && (!c_pbcShiftBackward || shift == gmx::c_centralShiftIndex)
+ && cyf < ci_y);
+ const int cyf_x = skipHalfY ? ci_y : cyf;
for (int cy = cyf_x; cy <= cyl; cy++)
{
- const int columnStart = jGrid.cxy_ind[cx*jGrid.numCells[YY] + cy];
- const int columnEnd = jGrid.cxy_ind[cx*jGrid.numCells[YY] + cy + 1];
-
- d2zxy = d2zx;
- if (jGrid.c0[YY] + cy*jGrid.cellSize[YY] > by1)
+ const int columnStart =
+ jGrid.firstCellInColumn(cx * jGridDims.numCells[YY] + cy);
+ const int columnEnd =
+ jGrid.firstCellInColumn(cx * jGridDims.numCells[YY] + cy + 1);
+
+ const real cy_real = cy;
+ real d2zxy = d2zx;
+ if (jGridDims.lowerCorner[YY] + cy_real * jGridDims.cellSize[YY] > by1)
{
- d2zxy += gmx::square(jGrid.c0[YY] + cy*jGrid.cellSize[YY] - by1);
+ d2zxy += gmx::square(jGridDims.lowerCorner[YY]
+ + cy_real * jGridDims.cellSize[YY] - by1);
}
- else if (jGrid.c0[YY] + (cy+1)*jGrid.cellSize[YY] < by0)
+ else if (jGridDims.lowerCorner[YY] + (cy_real + 1) * jGridDims.cellSize[YY] < by0)
{
- d2zxy += gmx::square(jGrid.c0[YY] + (cy+1)*jGrid.cellSize[YY] - by0);
+ d2zxy += gmx::square(jGridDims.lowerCorner[YY]
+ + (cy_real + 1) * jGridDims.cellSize[YY] - by0);
}
if (columnStart < columnEnd && d2zxy < listRangeBBToJCell2)
{
* but we do not do this because it would
* complicate this code even more.
*/
- int midCell = columnStart + static_cast<int>(bz1_frac*(columnEnd - columnStart));
+ int midCell =
+ columnStart
+ + static_cast<int>(
+ bz1_frac * static_cast<real>(columnEnd - columnStart));
if (midCell >= columnEnd)
{
midCell = columnEnd - 1;
}
- d2xy = d2zxy - d2z;
+ const real d2xy = d2zxy - d2z;
/* Find the lowest cell that can possibly
* be within range.
* if it is within range.
*/
int downTestCell = midCell;
- while (downTestCell >= columnStart &&
- (bbcz_j[downTestCell*NNBSBB_D + 1] >= bz0 ||
- d2xy + gmx::square(bbcz_j[downTestCell*NNBSBB_D + 1] - bz0) < rlist2))
+ while (downTestCell >= columnStart
+ && (bbcz_j[downTestCell].upper >= bz0
+ || d2xy + gmx::square(bbcz_j[downTestCell].upper - bz0) < rlist2))
{
downTestCell--;
}
* if it is within range.
*/
int upTestCell = midCell + 1;
- while (upTestCell < columnEnd &&
- (bbcz_j[upTestCell*NNBSBB_D] <= bz1 ||
- d2xy + gmx::square(bbcz_j[upTestCell*NNBSBB_D] - bz1) < rlist2))
+ while (upTestCell < columnEnd
+ && (bbcz_j[upTestCell].lower <= bz1
+ || d2xy + gmx::square(bbcz_j[upTestCell].lower - bz1) < rlist2))
{
upTestCell++;
}
lastCell = -1;
for (int k = columnStart; k < columnEnd; k++)
{
- if (d2xy + gmx::square(bbcz_j[k*NNBSBB_D + 1] - bz0) < rlist2 &&
- k < firstCell)
+ if (d2xy + gmx::square(bbcz_j[k * NNBSBB_D + 1] - bz0) < rlist2
+ && k < firstCell)
{
firstCell = k;
}
- if (d2xy + gmx::square(bbcz_j[k*NNBSBB_D] - bz1) < rlist2 &&
- k > lastCell)
+ if (d2xy + gmx::square(bbcz_j[k * NNBSBB_D] - bz1) < rlist2
+ && k > lastCell)
{
lastCell = k;
}
/* We want each atom/cell pair only once,
* only use cj >= ci.
*/
- if (!c_pbcShiftBackward || shift == CENTRAL)
+ if (!c_pbcShiftBackward || shift == gmx::c_centralShiftIndex)
{
firstCell = std::max(firstCell, ci);
}
if (firstCell <= lastCell)
{
- GMX_ASSERT(firstCell >= columnStart && lastCell < columnEnd, "The range should reside within the current grid column");
+ GMX_ASSERT(firstCell >= columnStart && lastCell < columnEnd,
+ "The range should reside within the current grid "
+ "column");
/* For f buffer flags with simple lists */
- ncj_old_j = getNumSimpleJClustersInList(*nbl);
+ const int ncj_old_j = getNumSimpleJClustersInList(*nbl);
makeClusterListWrapper(nbl,
- iGrid, ci,
- jGrid, firstCell, lastCell,
+ iGrid,
+ ci,
+ jGrid,
+ firstCell,
+ lastCell,
excludeSubDiagonal,
nbat,
- rlist2, rbb2,
- nb_kernel_type,
+ rlist2,
+ rbb2,
+ kernelType,
&numDistanceChecks);
if (bFBufferFlag)
{
- setBufferFlags(*nbl, ncj_old_j, gridj_flag_shift,
- gridj_flag, th);
+ setBufferFlags(*nbl, ncj_old_j, gridj_flag_shift, gridj_flag, th);
}
incrementNumSimpleJClustersInList(nbl, ncj_old_j);
}
}
- /* Set the exclusions for this ci list */
- setExclusionsForIEntry(nbs,
- nbl,
- excludeSubDiagonal,
- na_cj_2log,
- *getOpenIEntry(nbl),
- exclusions);
+ if (!exclusions.empty())
+ {
+ /* Set the exclusions for this ci list */
+ setExclusionsForIEntry(
+ gridSet, nbl, excludeSubDiagonal, na_cj_2log, *getOpenIEntry(nbl), exclusions);
+ }
- if (nbs->bFEP)
+ if (haveFep)
{
- make_fep_list(nbs, nbat, nbl,
+ make_fep_list(gridSet.atomIndices(),
+ nbat,
+ nbl,
excludeSubDiagonal,
getOpenIEntry(nbl),
- shx, shy, shz,
+ shx,
+ shy,
+ shz,
rl_fep2,
- iGrid, jGrid, nbl_fep);
+ iGrid,
+ jGrid,
+ nbl_fep);
}
/* Close this ci list */
- closeIEntry(nbl,
- nsubpair_max,
- progBal, nsubpair_tot_est,
- th, nth);
+ closeIEntry(nbl, nsubpair_max, progBal, nsubpair_tot_est, th, nth);
}
}
}
if (bFBufferFlag && getNumSimpleJClustersInList(*nbl) > ncj_old_i)
{
- bitmask_init_bit(&(work->buffer_flags.flag[(iGrid.cell0+ci) >> gridi_flag_shift]), th);
+ bitmask_init_bit(&(work->buffer_flags[(iGrid.cellOffset() + ci) >> gridi_flag_shift]), th);
}
}
work->ndistc = numDistanceChecks;
- nbs_cycle_stop(&work->cc[enbsCCsearch]);
-
- checkListSizeConsistency(*nbl, nbs->bFEP);
+ checkListSizeConsistency(*nbl, haveFep);
if (debug)
{
fprintf(debug, "number of distance checks %d\n", numDistanceChecks);
- print_nblist_statistics(debug, nbl, nbs, rlist);
+ print_nblist_statistics(debug, *nbl, gridSet, rlist);
- if (nbs->bFEP)
+ if (haveFep)
{
fprintf(debug, "nbl FEP list pairs: %d\n", nbl_fep->nrj);
}
}
}
-static void reduce_buffer_flags(const nbnxn_search *nbs,
- int nsrc,
- const nbnxn_buffer_flags_t *dest)
+static void reduce_buffer_flags(gmx::ArrayRef<PairsearchWork> searchWork,
+ int nsrc,
+ gmx::ArrayRef<gmx_bitmask_t> dest)
{
for (int s = 0; s < nsrc; s++)
{
- gmx_bitmask_t * flag = nbs->work[s].buffer_flags.flag;
+ gmx::ArrayRef<gmx_bitmask_t> flags(searchWork[s].buffer_flags);
- for (int b = 0; b < dest->nflag; b++)
+ for (size_t b = 0; b < dest.size(); b++)
{
- bitmask_union(&(dest->flag[b]), flag[b]);
+ gmx_bitmask_t& flag = dest[b];
+ bitmask_union(&flag, flags[b]);
}
}
}
-static void print_reduction_cost(const nbnxn_buffer_flags_t *flags, int nout)
+static void print_reduction_cost(gmx::ArrayRef<const gmx_bitmask_t> flags, int nout)
{
- int nelem, nkeep, ncopy, nred, out;
- gmx_bitmask_t mask_0;
+ int nelem = 0;
+ int nkeep = 0;
+ int ncopy = 0;
+ int nred = 0;
- nelem = 0;
- nkeep = 0;
- ncopy = 0;
- nred = 0;
+ gmx_bitmask_t mask_0; // NOLINT(cppcoreguidelines-init-variables)
bitmask_init_bit(&mask_0, 0);
- for (int b = 0; b < flags->nflag; b++)
+ for (const gmx_bitmask_t& flag_mask : flags)
{
- if (bitmask_is_equal(flags->flag[b], mask_0))
+ if (bitmask_is_equal(flag_mask, mask_0))
{
/* Only flag 0 is set, no copy of reduction required */
nelem++;
nkeep++;
}
- else if (!bitmask_is_zero(flags->flag[b]))
+ else if (!bitmask_is_zero(flag_mask))
{
int c = 0;
- for (out = 0; out < nout; out++)
+ for (int out = 0; out < nout; out++)
{
- if (bitmask_is_set(flags->flag[b], out))
+ if (bitmask_is_set(flag_mask, out))
{
c++;
}
}
}
}
-
- fprintf(debug, "nbnxn reduction: #flag %d #list %d elem %4.2f, keep %4.2f copy %4.2f red %4.2f\n",
- flags->nflag, nout,
- nelem/static_cast<double>(flags->nflag),
- nkeep/static_cast<double>(flags->nflag),
- ncopy/static_cast<double>(flags->nflag),
- nred/static_cast<double>(flags->nflag));
+ const auto numFlags = static_cast<double>(flags.size());
+ fprintf(debug,
+ "nbnxn reduction: #flag %zu #list %d elem %4.2f, keep %4.2f copy %4.2f red %4.2f\n",
+ flags.size(),
+ nout,
+ nelem / numFlags,
+ nkeep / numFlags,
+ ncopy / numFlags,
+ nred / numFlags);
}
/* Copies the list entries from src to dest when cjStart <= *cjGlobal < cjEnd.
* When setFlags==true, flag bit t is set in flag for all i and j clusters.
*/
template<bool setFlags>
-static void copySelectedListRange(const nbnxn_ci_t * gmx_restrict srcCi,
- const NbnxnPairlistCpu * gmx_restrict src,
- NbnxnPairlistCpu * gmx_restrict dest,
- gmx_bitmask_t *flag,
- int iFlagShift, int jFlagShift, int t)
+static void copySelectedListRange(const nbnxn_ci_t* gmx_restrict srcCi,
+ const NbnxnPairlistCpu* gmx_restrict src,
+ NbnxnPairlistCpu* gmx_restrict dest,
+ gmx_bitmask_t* flag,
+ int iFlagShift,
+ int jFlagShift,
+ int t)
{
const int ncj = srcCi->cj_ind_end - srcCi->cj_ind_start;
dest->ci.push_back(*srcCi);
dest->ci.back().cj_ind_start = dest->cj.size();
- dest->ci.back().cj_ind_end = dest->cj.size() + ncj;
+ dest->ci.back().cj_ind_end = dest->ci.back().cj_ind_start + ncj;
if (setFlags)
{
}
}
+#if defined(__GNUC__) && !defined(__clang__) && __GNUC__ == 7
+/* Avoid gcc 7 avx512 loop vectorization bug (actually only needed with -mavx512f) */
+# pragma GCC push_options
+# pragma GCC optimize("no-tree-vectorize")
+#endif
+
+/* Returns the number of cluster pairs that are in use summed over all lists */
+static int countClusterpairs(gmx::ArrayRef<const NbnxnPairlistCpu> pairlists)
+{
+ /* gcc 7 with -mavx512f can miss the contributions of 16 consecutive
+ * elements to the sum calculated in this loop. Above we have disabled
+ * loop vectorization to avoid this bug.
+ */
+ int ncjTotal = 0;
+ for (const auto& pairlist : pairlists)
+ {
+ ncjTotal += pairlist.ncjInUse;
+ }
+ return ncjTotal;
+}
+
+#if defined(__GNUC__) && !defined(__clang__) && __GNUC__ == 7
+# pragma GCC pop_options
+#endif
+
/* This routine re-balances the pairlists such that all are nearly equally
* sized. Only whole i-entries are moved between lists. These are moved
* between the ends of the lists, such that the buffer reduction cost should
* to reduction of parts of the force buffer that could be avoided. But since
* the original lists are quite balanced, this will only give minor overhead.
*/
-static void rebalanceSimpleLists(int numLists,
- NbnxnPairlistCpu * const * const srcSet,
- NbnxnPairlistCpu **destSet,
- gmx::ArrayRef<nbnxn_search_work_t> searchWork)
+static void rebalanceSimpleLists(gmx::ArrayRef<const NbnxnPairlistCpu> srcSet,
+ gmx::ArrayRef<NbnxnPairlistCpu> destSet,
+ gmx::ArrayRef<PairsearchWork> searchWork)
{
- int ncjTotal = 0;
- for (int s = 0; s < numLists; s++)
- {
- ncjTotal += srcSet[s]->ncjInUse;
- }
- int ncjTarget = (ncjTotal + numLists - 1)/numLists;
+ const int ncjTotal = countClusterpairs(srcSet);
+ const int numLists = srcSet.ssize();
+ const int ncjTarget = (ncjTotal + numLists - 1) / numLists;
#pragma omp parallel num_threads(numLists)
{
- int t = gmx_omp_get_thread_num();
+ int t = gmx_omp_get_thread_num();
- int cjStart = ncjTarget* t;
- int cjEnd = ncjTarget*(t + 1);
+ int cjStart = ncjTarget * t;
+ int cjEnd = ncjTarget * (t + 1);
/* The destination pair-list for task/thread t */
- NbnxnPairlistCpu *dest = destSet[t];
+ NbnxnPairlistCpu& dest = destSet[t];
- clear_pairlist(dest);
- dest->na_cj = srcSet[0]->na_cj;
+ clear_pairlist(&dest);
+ dest.na_cj = srcSet[0].na_cj;
/* Note that the flags in the work struct (still) contain flags
* for all entries that are present in srcSet->nbl[t].
*/
- gmx_bitmask_t *flag = searchWork[t].buffer_flags.flag;
+ gmx_bitmask_t* flag = &searchWork[t].buffer_flags[0];
- int iFlagShift = getBufferFlagShift(dest->na_ci);
- int jFlagShift = getBufferFlagShift(dest->na_cj);
+ int iFlagShift = getBufferFlagShift(dest.na_ci);
+ int jFlagShift = getBufferFlagShift(dest.na_cj);
- int cjGlobal = 0;
+ int cjGlobal = 0;
for (int s = 0; s < numLists && cjGlobal < cjEnd; s++)
{
- const NbnxnPairlistCpu *src = srcSet[s];
+ const NbnxnPairlistCpu* src = &srcSet[s];
if (cjGlobal + src->ncjInUse > cjStart)
{
for (gmx::index i = 0; i < gmx::ssize(src->ci) && cjGlobal < cjEnd; i++)
{
- const nbnxn_ci_t *srcCi = &src->ci[i];
+ const nbnxn_ci_t* srcCi = &src->ci[i];
int ncj = srcCi->cj_ind_end - srcCi->cj_ind_start;
if (cjGlobal >= cjStart)
{
*/
if (s != t)
{
- copySelectedListRange
- <true>
- (srcCi, src, dest,
- flag, iFlagShift, jFlagShift, t);
+ copySelectedListRange<true>(srcCi, src, &dest, flag, iFlagShift, jFlagShift, t);
}
else
{
- copySelectedListRange
- <false>
- (srcCi, src,
- dest, flag, iFlagShift, jFlagShift, t);
+ copySelectedListRange<false>(
+ srcCi, src, &dest, flag, iFlagShift, jFlagShift, t);
}
}
cjGlobal += ncj;
}
}
- dest->ncjInUse = dest->cj.size();
+ dest.ncjInUse = dest.cj.size();
}
#ifndef NDEBUG
- int ncjTotalNew = 0;
- for (int s = 0; s < numLists; s++)
- {
- ncjTotalNew += destSet[s]->ncjInUse;
- }
- GMX_RELEASE_ASSERT(ncjTotalNew == ncjTotal, "The total size of the lists before and after rebalancing should match");
+ const int ncjTotalNew = countClusterpairs(destSet);
+ GMX_RELEASE_ASSERT(ncjTotalNew == ncjTotal,
+ "The total size of the lists before and after rebalancing should match");
#endif
}
/* Returns if the pairlists are so imbalanced that it is worth rebalancing. */
-static bool checkRebalanceSimpleLists(const nbnxn_pairlist_set_t *listSet)
+static bool checkRebalanceSimpleLists(gmx::ArrayRef<const NbnxnPairlistCpu> lists)
{
- int numLists = listSet->nnbl;
+ int numLists = lists.ssize();
int ncjMax = 0;
int ncjTotal = 0;
for (int s = 0; s < numLists; s++)
{
- ncjMax = std::max(ncjMax, listSet->nbl[s]->ncjInUse);
- ncjTotal += listSet->nbl[s]->ncjInUse;
+ ncjMax = std::max(ncjMax, lists[s].ncjInUse);
+ ncjTotal += lists[s].ncjInUse;
}
if (debug)
{
*/
const real rebalanceTolerance = 1.03;
- return numLists*ncjMax > ncjTotal*rebalanceTolerance;
+ return real(numLists * ncjMax) > real(ncjTotal) * rebalanceTolerance;
}
/* Perform a count (linear) sort to sort the smaller lists to the end.
* better load balancing than using a list sorted on exact load.
* This function swaps the pointer in the pair list to avoid a copy operation.
*/
-static void sort_sci(NbnxnPairlistGpu *nbl)
+static void sort_sci(NbnxnPairlistGpu* nbl)
{
if (nbl->cj4.size() <= nbl->sci.size())
{
return;
}
- NbnxnPairlistGpuWork &work = *nbl->work;
+ NbnxnPairlistGpuWork& work = *nbl->work;
/* We will distinguish differences up to double the average */
- const int m = (2*nbl->cj4.size())/nbl->sci.size();
+ const int m = static_cast<int>((2 * ssize(nbl->cj4)) / ssize(nbl->sci));
/* Resize work.sci_sort so we can sort into it */
work.sci_sort.resize(nbl->sci.size());
- std::vector<int> &sort = work.sortBuffer;
+ std::vector<int>& sort = work.sortBuffer;
/* Set up m + 1 entries in sort, initialized at 0 */
sort.clear();
sort.resize(m + 1, 0);
/* Count the entries of each size */
- for (const nbnxn_sci_t &sci : nbl->sci)
+ for (const nbnxn_sci_t& sci : nbl->sci)
{
int i = std::min(m, sci.numJClusterGroups());
sort[i]++;
/* Calculate the offset for each count */
int s0 = sort[m];
sort[m] = 0;
- for (int i = m - 1; i >= 0; i--)
+ for (gmx::index i = m - 1; i >= 0; i--)
{
int s1 = sort[i];
sort[i] = sort[i + 1] + s0;
/* Sort entries directly into place */
gmx::ArrayRef<nbnxn_sci_t> sci_sort = work.sci_sort;
- for (const nbnxn_sci_t &sci : nbl->sci)
+ for (const nbnxn_sci_t& sci : nbl->sci)
{
- int i = std::min(m, sci.numJClusterGroups());
+ int i = std::min(m, sci.numJClusterGroups());
sci_sort[sort[i]++] = sci;
}
std::swap(nbl->sci, work.sci_sort);
}
-/* Make a local or non-local pair-list, depending on iloc */
-void nbnxn_make_pairlist(nbnxn_search *nbs,
- nbnxn_atomdata_t *nbat,
- const t_blocka *excl,
- const real rlist,
- const int min_ci_balanced,
- nbnxn_pairlist_set_t *nbl_list,
- const InteractionLocality iloc,
- const int nb_kernel_type,
- t_nrnb *nrnb)
+/* Returns the i-zone range for pairlist construction for the give locality */
+static Range<int> getIZoneRange(const Nbnxm::GridSet::DomainSetup& domainSetup,
+ const InteractionLocality locality)
{
- int nsubpair_target;
- float nsubpair_tot_est;
- int nnbl;
- int ci_block;
- gmx_bool CombineNBLists;
- gmx_bool progBal;
- int np_tot, np_noq, np_hlj, nap;
-
- nnbl = nbl_list->nnbl;
- CombineNBLists = nbl_list->bCombined;
-
- if (debug)
+ if (domainSetup.doTestParticleInsertion)
{
- fprintf(debug, "ns making %d nblists\n", nnbl);
+ /* With TPI we do grid 1, the inserted molecule, versus grid 0, the rest */
+ return { 1, 2 };
}
-
- nbat->bUseBufferFlags = (nbat->out.size() > 1);
- /* We should re-init the flags before making the first list */
- if (nbat->bUseBufferFlags && iloc == InteractionLocality::Local)
+ else if (locality == InteractionLocality::Local)
{
- init_buffer_flags(&nbat->buffer_flags, nbat->numAtoms());
+ /* Local: only zone (grid) 0 vs 0 */
+ return { 0, 1 };
}
+ else
+ {
+ /* Non-local: we need all i-zones */
+ return { 0, int(domainSetup.zones->iZones.size()) };
+ }
+}
- int nzi;
- if (iloc == InteractionLocality::Local)
+/* Returns the j-zone range for pairlist construction for the give locality and i-zone */
+static Range<int> getJZoneRange(const gmx_domdec_zones_t* ddZones,
+ const InteractionLocality locality,
+ const int iZone)
+{
+ if (locality == InteractionLocality::Local)
{
- /* Only zone (grid) 0 vs 0 */
- nzi = 1;
+ /* Local: zone 0 vs 0 or with TPI 1 vs 0 */
+ return { 0, 1 };
+ }
+ else if (iZone == 0)
+ {
+ /* Non-local: we need to avoid the local (zone 0 vs 0) interactions */
+ return { 1, *ddZones->iZones[iZone].jZoneRange.end() };
}
else
{
- nzi = nbs->zones->nizone;
+ /* Non-local with non-local i-zone: use all j-zones */
+ return ddZones->iZones[iZone].jZoneRange;
}
+}
- if (!nbl_list->bSimple && min_ci_balanced > 0)
+//! Prepares CPU lists produced by the search for dynamic pruning
+static void prepareListsForDynamicPruning(gmx::ArrayRef<NbnxnPairlistCpu> lists);
+
+void PairlistSet::constructPairlists(gmx::InteractionLocality locality,
+ const Nbnxm::GridSet& gridSet,
+ gmx::ArrayRef<PairsearchWork> searchWork,
+ nbnxn_atomdata_t* nbat,
+ const ListOfLists<int>& exclusions,
+ const int minimumIlistCountForGpuBalancing,
+ t_nrnb* nrnb,
+ SearchCycleCounting* searchCycleCounting)
+{
+ const real rlist = params_.rlistOuter;
+
+ const int numLists = (isCpuType_ ? cpuLists_.size() : gpuLists_.size());
+
+ if (debug)
{
- get_nsubpair_target(nbs, iloc, rlist, min_ci_balanced,
- &nsubpair_target, &nsubpair_tot_est);
+ fprintf(debug, "ns making %d nblists\n", numLists);
}
- else
+
+ nbat->bUseBufferFlags = (nbat->out.size() > 1);
+ /* We should re-init the flags before making the first list */
+ if (nbat->bUseBufferFlags && locality == InteractionLocality::Local)
+ {
+ resizeAndZeroBufferFlags(&nbat->buffer_flags, nbat->numAtoms());
+ }
+
+ int nsubpair_target = 0;
+ float nsubpair_tot_est = 0.0F;
+ if (!isCpuType_ && minimumIlistCountForGpuBalancing > 0)
{
- nsubpair_target = 0;
- nsubpair_tot_est = 0;
+ get_nsubpair_target(
+ gridSet, locality, rlist, minimumIlistCountForGpuBalancing, &nsubpair_target, &nsubpair_tot_est);
}
/* Clear all pair-lists */
- for (int th = 0; th < nnbl; th++)
+ for (int th = 0; th < numLists; th++)
{
- if (nbl_list->bSimple)
+ if (isCpuType_)
{
- clear_pairlist(nbl_list->nbl[th]);
+ clear_pairlist(&cpuLists_[th]);
}
else
{
- clear_pairlist(nbl_list->nblGpu[th]);
+ clear_pairlist(&gpuLists_[th]);
}
- if (nbs->bFEP)
+ if (params_.haveFep)
{
- clear_pairlist_fep(nbl_list->nbl_fep[th]);
+ clear_pairlist_fep(fepLists_[th].get());
}
}
- for (int zi = 0; zi < nzi; zi++)
+ const gmx_domdec_zones_t* ddZones = gridSet.domainSetup().zones;
+ GMX_ASSERT(locality == InteractionLocality::Local || ddZones != nullptr,
+ "Nonlocal interaction locality with null ddZones.");
+
+ const auto iZoneRange = getIZoneRange(gridSet.domainSetup(), locality);
+
+ for (const int iZone : iZoneRange)
{
- const nbnxn_grid_t &iGrid = nbs->grid[zi];
+ const Grid& iGrid = gridSet.grids()[iZone];
- int zj0;
- int zj1;
- if (iloc == InteractionLocality::Local)
- {
- zj0 = 0;
- zj1 = 1;
- }
- else
- {
- zj0 = nbs->zones->izone[zi].j0;
- zj1 = nbs->zones->izone[zi].j1;
- if (zi == 0)
- {
- zj0++;
- }
- }
- for (int zj = zj0; zj < zj1; zj++)
+ const auto jZoneRange = getJZoneRange(ddZones, locality, iZone);
+
+ for (int jZone : jZoneRange)
{
- const nbnxn_grid_t &jGrid = nbs->grid[zj];
+ const Grid& jGrid = gridSet.grids()[jZone];
if (debug)
{
- fprintf(debug, "ns search grid %d vs %d\n", zi, zj);
+ fprintf(debug, "ns search grid %d vs %d\n", iZone, jZone);
}
- nbs_cycle_start(&nbs->cc[enbsCCsearch]);
+ searchCycleCounting->start(enbsCCsearch);
- ci_block = get_ci_block_size(iGrid, nbs->DomDec, nnbl);
+ const int ci_block =
+ get_ci_block_size(iGrid, gridSet.domainSetup().haveMultipleDomains, numLists);
/* With GPU: generate progressively smaller lists for
* load balancing for local only or non-local with 2 zones.
*/
- progBal = (iloc == InteractionLocality::Local || nbs->zones->n <= 2);
+ const bool progBal = (locality == InteractionLocality::Local || ddZones->n <= 2);
-#pragma omp parallel for num_threads(nnbl) schedule(static)
- for (int th = 0; th < nnbl; th++)
+#pragma omp parallel for num_threads(numLists) schedule(static)
+ for (int th = 0; th < numLists; th++)
{
try
{
/* Re-init the thread-local work flag data before making
* the first list (not an elegant conditional).
*/
- if (nbat->bUseBufferFlags && ((zi == 0 && zj == 0)))
+ if (nbat->bUseBufferFlags && (iZone == 0 && jZone == 0))
{
- init_buffer_flags(&nbs->work[th].buffer_flags, nbat->numAtoms());
+ resizeAndZeroBufferFlags(&searchWork[th].buffer_flags, nbat->numAtoms());
}
- if (CombineNBLists && th > 0)
+ if (combineLists_ && th > 0)
{
- GMX_ASSERT(!nbl_list->bSimple, "Can only combine GPU lists");
+ GMX_ASSERT(!isCpuType_, "Can only combine GPU lists");
- clear_pairlist(nbl_list->nblGpu[th]);
+ clear_pairlist(&gpuLists_[th]);
}
- /* Divide the i super cell equally over the nblists */
- if (nbl_list->bSimple)
+ PairsearchWork& work = searchWork[th];
+
+ work.cycleCounter.start();
+
+ t_nblist* fepListPtr = (fepLists_.empty() ? nullptr : fepLists_[th].get());
+
+ /* Divide the i cells equally over the pairlists */
+ if (isCpuType_)
{
- nbnxn_make_pairlist_part(nbs, iGrid, jGrid,
- &nbs->work[th], nbat, *excl,
+ nbnxn_make_pairlist_part(gridSet,
+ iGrid,
+ jGrid,
+ &work,
+ nbat,
+ exclusions,
rlist,
- nb_kernel_type,
+ params_.pairlistType,
ci_block,
nbat->bUseBufferFlags,
nsubpair_target,
- progBal, nsubpair_tot_est,
- th, nnbl,
- nbl_list->nbl[th],
- nbl_list->nbl_fep[th]);
+ progBal,
+ nsubpair_tot_est,
+ th,
+ numLists,
+ &cpuLists_[th],
+ fepListPtr);
}
else
{
- nbnxn_make_pairlist_part(nbs, iGrid, jGrid,
- &nbs->work[th], nbat, *excl,
+ nbnxn_make_pairlist_part(gridSet,
+ iGrid,
+ jGrid,
+ &work,
+ nbat,
+ exclusions,
rlist,
- nb_kernel_type,
+ params_.pairlistType,
ci_block,
nbat->bUseBufferFlags,
nsubpair_target,
- progBal, nsubpair_tot_est,
- th, nnbl,
- nbl_list->nblGpu[th],
- nbl_list->nbl_fep[th]);
+ progBal,
+ nsubpair_tot_est,
+ th,
+ numLists,
+ &gpuLists_[th],
+ fepListPtr);
}
+
+ work.cycleCounter.stop();
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- nbs_cycle_stop(&nbs->cc[enbsCCsearch]);
+ searchCycleCounting->stop(enbsCCsearch);
- np_tot = 0;
- np_noq = 0;
- np_hlj = 0;
- for (int th = 0; th < nnbl; th++)
+ int np_tot = 0;
+ int np_noq = 0;
+ int np_hlj = 0;
+ for (int th = 0; th < numLists; th++)
{
- inc_nrnb(nrnb, eNR_NBNXN_DIST2, nbs->work[th].ndistc);
+ inc_nrnb(nrnb, eNR_NBNXN_DIST2, searchWork[th].ndistc);
- if (nbl_list->bSimple)
+ if (isCpuType_)
{
- NbnxnPairlistCpu *nbl = nbl_list->nbl[th];
- np_tot += nbl->cj.size();
- np_noq += nbl->work->ncj_noq;
- np_hlj += nbl->work->ncj_hlj;
+ const NbnxnPairlistCpu& nbl = cpuLists_[th];
+ np_tot += nbl.cj.size();
+ np_noq += nbl.work->ncj_noq;
+ np_hlj += nbl.work->ncj_hlj;
}
else
{
- NbnxnPairlistGpu *nbl = nbl_list->nblGpu[th];
+ const NbnxnPairlistGpu& nbl = gpuLists_[th];
/* This count ignores potential subsequent pair pruning */
- np_tot += nbl->nci_tot;
+ np_tot += nbl.nci_tot;
}
}
- if (nbl_list->bSimple)
- {
- nap = nbl_list->nbl[0]->na_ci*nbl_list->nbl[0]->na_cj;
- }
- else
- {
- nap = gmx::square(nbl_list->nblGpu[0]->na_ci);
- }
- nbl_list->natpair_ljq = (np_tot - np_noq)*nap - np_hlj*nap/2;
- nbl_list->natpair_lj = np_noq*nap;
- nbl_list->natpair_q = np_hlj*nap/2;
+ const int nap = isCpuType_ ? cpuLists_[0].na_ci * cpuLists_[0].na_cj
+ : gmx::square(gpuLists_[0].na_ci);
+
+ natpair_ljq_ = (np_tot - np_noq) * nap - np_hlj * nap / 2;
+ natpair_lj_ = np_noq * nap;
+ natpair_q_ = np_hlj * nap / 2;
- if (CombineNBLists && nnbl > 1)
+ if (combineLists_ && numLists > 1)
{
- GMX_ASSERT(!nbl_list->bSimple, "Can only combine GPU lists");
- NbnxnPairlistGpu **nbl = nbl_list->nblGpu;
+ GMX_ASSERT(!isCpuType_, "Can only combine GPU lists");
- nbs_cycle_start(&nbs->cc[enbsCCcombine]);
+ searchCycleCounting->start(enbsCCcombine);
- combine_nblists(nnbl-1, nbl+1, nbl[0]);
+ combine_nblists(gmx::constArrayRefFromArray(&gpuLists_[1], numLists - 1), &gpuLists_[0]);
- nbs_cycle_stop(&nbs->cc[enbsCCcombine]);
+ searchCycleCounting->stop(enbsCCcombine);
}
}
}
- if (nbl_list->bSimple)
+ if (isCpuType_)
{
- if (nnbl > 1 && checkRebalanceSimpleLists(nbl_list))
+ if (numLists > 1 && checkRebalanceSimpleLists(cpuLists_))
{
- rebalanceSimpleLists(nbl_list->nnbl, nbl_list->nbl, nbl_list->nbl_work, nbs->work);
+ rebalanceSimpleLists(cpuLists_, cpuListsWork_, searchWork);
- /* Swap the pointer of the sets of pair lists */
- NbnxnPairlistCpu **tmp = nbl_list->nbl;
- nbl_list->nbl = nbl_list->nbl_work;
- nbl_list->nbl_work = tmp;
+ /* Swap the sets of pair lists */
+ cpuLists_.swap(cpuListsWork_);
}
}
else
{
/* Sort the entries on size, large ones first */
- if (CombineNBLists || nnbl == 1)
+ if (combineLists_ || gpuLists_.size() == 1)
{
- sort_sci(nbl_list->nblGpu[0]);
+ sort_sci(&gpuLists_[0]);
}
else
{
-#pragma omp parallel for num_threads(nnbl) schedule(static)
- for (int th = 0; th < nnbl; th++)
+#pragma omp parallel for num_threads(numLists) schedule(static)
+ for (int th = 0; th < numLists; th++)
{
try
{
- sort_sci(nbl_list->nblGpu[th]);
+ sort_sci(&gpuLists_[th]);
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
}
}
if (nbat->bUseBufferFlags)
{
- reduce_buffer_flags(nbs, nbl_list->nnbl, &nbat->buffer_flags);
+ reduce_buffer_flags(searchWork, numLists, nbat->buffer_flags);
}
- if (nbs->bFEP)
+ if (gridSet.haveFep())
{
/* Balance the free-energy lists over all the threads */
- balance_fep_lists(nbs, nbl_list);
+ balance_fep_lists(fepLists_, searchWork);
}
- if (nbl_list->bSimple)
+ if (isCpuType_)
{
/* This is a fresh list, so not pruned, stored using ci.
* ciOuter is invalid at this point.
*/
- GMX_ASSERT(nbl_list->nbl[0]->ciOuter.empty(), "ciOuter is invalid so it should be empty");
- }
-
- /* Special performance logging stuff (env.var. GMX_NBNXN_CYCLE) */
- if (iloc == InteractionLocality::Local)
- {
- nbs->search_count++;
- }
- if (nbs->print_cycles &&
- (!nbs->DomDec || iloc == InteractionLocality::NonLocal) &&
- nbs->search_count % 100 == 0)
- {
- nbs_cycle_print(stderr, nbs);
+ GMX_ASSERT(cpuLists_[0].ciOuter.empty(), "ciOuter is invalid so it should be empty");
}
/* If we have more than one list, they either got rebalancing (CPU)
* or combined (GPU), so we should dump the final result to debug.
*/
- if (debug && nbl_list->nnbl > 1)
+ if (debug)
{
- if (nbl_list->bSimple)
+ if (isCpuType_ && cpuLists_.size() > 1)
{
- for (int t = 0; t < nbl_list->nnbl; t++)
+ for (auto& cpuList : cpuLists_)
{
- print_nblist_statistics(debug, nbl_list->nbl[t], nbs, rlist);
+ print_nblist_statistics(debug, cpuList, gridSet, rlist);
}
}
- else
+ else if (!isCpuType_ && gpuLists_.size() > 1)
{
- print_nblist_statistics(debug, nbl_list->nblGpu[0], nbs, rlist);
+ print_nblist_statistics(debug, gpuLists_[0], gridSet, rlist);
}
}
{
if (gmx_debug_at)
{
- if (nbl_list->bSimple)
+ if (isCpuType_)
{
- for (int t = 0; t < nbl_list->nnbl; t++)
+ for (auto& cpuList : cpuLists_)
{
- print_nblist_ci_cj(debug, nbl_list->nbl[t]);
+ print_nblist_ci_cj(debug, cpuList);
}
}
else
{
- print_nblist_sci_cj(debug, nbl_list->nblGpu[0]);
+ print_nblist_sci_cj(debug, gpuLists_[0]);
}
}
if (nbat->bUseBufferFlags)
{
- print_reduction_cost(&nbat->buffer_flags, nbl_list->nnbl);
+ print_reduction_cost(nbat->buffer_flags, numLists);
}
}
+
+ if (params_.useDynamicPruning && isCpuType_)
+ {
+ prepareListsForDynamicPruning(cpuLists_);
+ }
+}
+
+void PairlistSets::construct(const InteractionLocality iLocality,
+ PairSearch* pairSearch,
+ nbnxn_atomdata_t* nbat,
+ const ListOfLists<int>& exclusions,
+ const int64_t step,
+ t_nrnb* nrnb)
+{
+ const auto& gridSet = pairSearch->gridSet();
+ const auto* ddZones = gridSet.domainSetup().zones;
+
+ /* The Nbnxm code can also work with more exclusions than those in i-zones only
+ * when using DD, but the equality check can catch more issues.
+ */
+ GMX_RELEASE_ASSERT(
+ exclusions.empty() || (!ddZones && exclusions.ssize() == gridSet.numRealAtomsTotal())
+ || (ddZones && exclusions.ssize() == ddZones->cg_range[ddZones->iZones.size()]),
+ "exclusions should either be empty or the number of lists should match the number of "
+ "local i-atoms");
+
+ pairlistSet(iLocality).constructPairlists(iLocality,
+ gridSet,
+ pairSearch->work(),
+ nbat,
+ exclusions,
+ minimumIlistCountForGpuBalancing_,
+ nrnb,
+ &pairSearch->cycleCounting_);
+
+ if (iLocality == InteractionLocality::Local)
+ {
+ outerListCreationStep_ = step;
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(outerListCreationStep_ == step,
+ "Outer list should be created at the same step as the inner list");
+ }
+
+ /* Special performance logging stuff (env.var. GMX_NBNXN_CYCLE) */
+ if (iLocality == InteractionLocality::Local)
+ {
+ pairSearch->cycleCounting_.searchCount_++;
+ }
+ if (pairSearch->cycleCounting_.recordCycles_
+ && (!pairSearch->gridSet().domainSetup().haveMultipleDomains || iLocality == InteractionLocality::NonLocal)
+ && pairSearch->cycleCounting_.searchCount_ % 100 == 0)
+ {
+ pairSearch->cycleCounting_.printCycles(stderr, pairSearch->work());
+ }
}
-void nbnxnPrepareListForDynamicPruning(nbnxn_pairlist_set_t *listSet)
+void nonbonded_verlet_t::constructPairlist(const InteractionLocality iLocality,
+ const ListOfLists<int>& exclusions,
+ int64_t step,
+ t_nrnb* nrnb) const
{
- GMX_RELEASE_ASSERT(listSet->bSimple, "Should only be called for simple lists");
+ pairlistSets_->construct(iLocality, pairSearch_.get(), nbat.get(), exclusions, step, nrnb);
+
+ if (useGpu())
+ {
+ /* Launch the transfer of the pairlist to the GPU.
+ *
+ * NOTE: The launch overhead is currently not timed separately
+ */
+ Nbnxm::gpu_init_pairlist(gpu_nbv, pairlistSets().pairlistSet(iLocality).gpuList(), iLocality);
+ }
+}
+static void prepareListsForDynamicPruning(gmx::ArrayRef<NbnxnPairlistCpu> lists)
+{
/* TODO: Restructure the lists so we have actual outer and inner
* list objects so we can set a single pointer instead of
* swapping several pointers.
*/
- for (int i = 0; i < listSet->nnbl; i++)
+ for (auto& list : lists)
{
- NbnxnPairlistCpu &list = *listSet->nbl[i];
-
/* The search produced a list in ci/cj.
* Swap the list pointers so we get the outer list is ciOuter,cjOuter
* and we can prune that to get an inner list in ci/cj.
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff