* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * 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/mdtypes/group.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/nblist.h"
#include "gromacs/nbnxm/atomdata.h"
#include "gromacs/nbnxm/gpu_data_mgmt.h"
#include "gromacs/pbcutil/ishift.h"
using Grid = Nbnxm::Grid; // TODO: Remove when refactoring this file
-// Convience alias for partial Nbnxn namespace usage
+// Convenience alias for partial Nbnxn namespace usage
using InteractionLocality = gmx::InteractionLocality;
/* We shift the i-particles backward for PBC.
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>
static constexpr int jClusterSize()
*
* \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) \param[in] ci The i-cluster index
+ * size(i-cluster)
+ * \param[in] ci The i-cluster index
*/
template<int jClusterSize, int jSubClusterIndex>
static inline int cjFromCi(int ci)
*
* \tparam layout The pair-list layout
* \tparam jSubClusterIndex The j-sub-cluster index (0/1), used when size(j-cluster) <
- * size(i-cluster) \param[in] ci The i-cluster index
+ * size(i-cluster)
+ * \param[in] ci The i-cluster index
*/
template<NbnxnLayout layout, int jSubClusterIndex>
static inline int cjFromCi(int ci)
return cj * STRIDE_P8;
}
}
-#endif // GMX_SIMD
-
+#endif // defined(GMX_NBNXN_SIMD_4XN) || defined(GMX_NBNXN_SIMD_2XNN)
-void nbnxn_init_pairlist_fep(t_nblist* nl)
+static constexpr int sizeNeededForBufferFlags(const int numAtoms)
{
- 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;
+ return (numAtoms + NBNXN_BUFFERFLAG_SIZE - 1) / NBNXN_BUFFERFLAG_SIZE;
}
-static void init_buffer_flags(nbnxn_buffer_flags_t* flags, int natoms)
+// Resets current flags to 0 and adds more flags if needed.
+static void resizeAndZeroBufferFlags(std::vector<gmx_bitmask_t>* flags, const int numAtoms)
{
- 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]));
- }
+ flags->clear();
+ flags->resize(sizeNeededForBufferFlags(numAtoms), gmx_bitmask_t{ 0 });
}
+
/* Returns the pair-list cutoff between a bounding box and a grid cell given an atom-to-atom pair-list cutoff
*
* Given a cutoff distance between atoms, this functions returns the cutoff
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();
}
// TODO: Move to pairlistset.cpp
-PairlistSet::PairlistSet(const InteractionLocality locality, const PairlistParams& pairlistParams) :
- locality_(locality),
- params_(pairlistParams)
+PairlistSet::PairlistSet(const PairlistParams& pairlistParams) :
+ params_(pairlistParams),
+ combineLists_(sc_isGpuPairListType[pairlistParams.pairlistType]), // Currently GPU lists are always combined
+ isCpuType_(!sc_isGpuPairListType[pairlistParams.pairlistType])
{
- isCpuType_ = (params_.pairlistType == PairlistType::Simple4x2
- || params_.pairlistType == PairlistType::Simple4x4
- || params_.pairlistType == PairlistType::Simple4x8);
- // Currently GPU lists are always combined
- combineLists_ = !isCpuType_;
- const int numLists = gmx_omp_nthreads_get(emntNonbonded);
+ const int numLists = gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded);
if (!combineLists_ && numLists > NBNXN_BUFFERFLAG_MAX_THREADS)
{
"%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);
+ numLists,
+ NBNXN_BUFFERFLAG_MAX_THREADS,
+ NBNXN_BUFFERFLAG_MAX_THREADS);
}
if (isCpuType_)
* impacts performance.
*/
fepLists_[i] = std::make_unique<t_nblist>();
- nbnxn_init_pairlist_fep(fepLists_[i].get());
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
fprintf(fp, "nbl nci %zu ncj %d\n", nbl.ci.size(), nbl.ncjInUse);
const int numAtomsJCluster = grid.geometry().numAtomsJCluster;
+
+ if (grid.numCells() == 0)
+ {
+ return;
+ }
+
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,
+ 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",
+ 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[SHIFTS] = { 0 };
- int npexcl = 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;
j++;
}
}
- fprintf(fp, "nbl cell pairs, total: %zu excl: %d %.1f%%\n", nbl.cj.size(), npexcl,
+ 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++)
+ for (int s = 0; s < gmx::c_numShiftVectors; s++)
{
if (cs[s] > 0)
{
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());
+ 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,
+ 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])));
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())
{
for (int b = 0; b <= c_gpuNumClusterPerCell; b++)
{
- fprintf(fp, "nbl j-list #i-subcell %d %7d %4.1f\n", b, c[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 });
}
}
* \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 Grid& jGrid,
- NbnxnPairlistCpu* nbl,
- int icluster,
- int jclusterFirst,
- int jclusterLast,
- bool excludeSubDiagonal,
+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)
+ int* gmx_restrict numDistanceChecks)
{
const BoundingBox* gmx_restrict bb_ci = nbl->work->iClusterData.bb.data();
- const real* gmx_restrict x_ci = nbl->work->iClusterData.x.data();
-
- gmx_bool InRange;
+ const real* gmx_restrict x_ci = nbl->work->iClusterData.x.data();
- InRange = FALSE;
+ bool InRange = false;
while (!InRange && jclusterFirst <= jclusterLast)
{
real d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterFirst]);
*/
if (d2 < rbb2)
{
- InRange = TRUE;
+ InRange = true;
}
else if (d2 < rlist2)
{
return;
}
- InRange = FALSE;
+ InRange = false;
while (!InRange && jclusterLast > jclusterFirst)
{
real d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterLast]);
*/
if (d2 < rbb2)
{
- InRange = TRUE;
+ InRange = true;
}
else if (d2 < rlist2)
{
const int cj_gl = jGrid.cellOffset() * c_gpuNumClusterPerCell + cj;
- int ci1;
- if (excludeSubDiagonal && sci == scj)
- {
- ci1 = subc + 1;
- }
- else
- {
- ci1 = iGrid.numClustersPerCell()[sci];
- }
+ int ci1 = (excludeSubDiagonal && sci == scj) ? subc + 1 : iGrid.numClustersPerCell()[sci];
+
#if NBNXN_BBXXXX
/* Determine all ci1 bb distances in one call with SIMD4 */
const int offset = packedBoundingBoxesIndex(cj) + (cj & (c_packedBoundingBoxesDimSize - 1));
- clusterBoundingBoxDistance2_xxxx_simd4(jGrid.packedBoundingBoxes().data() + offset, ci1,
- pbb_ci, d2l);
+ clusterBoundingBoxDistance2_xxxx_simd4(
+ jGrid.packedBoundingBoxes().data() + offset, ci1, pbb_ci, d2l);
*numDistanceChecks += c_nbnxnGpuClusterSize * 2;
#endif
#ifndef DOXYGEN
template<typename CjListType>
JListRanges::JListRanges(int cjIndexStart, int cjIndexEnd, gmx::ArrayRef<const CjListType> cjList) :
- cjIndexStart(cjIndexStart),
- cjIndexEnd(cjIndexEnd)
+ cjIndexStart(cjIndexStart), cjIndexEnd(cjIndexEnd)
{
GMX_ASSERT(cjIndexEnd > cjIndexStart, "JListRanges should only be called with non-empty lists");
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 index = -1;
int rangeStart = ranges.cjIndexStart + ranges.numDirect;
int rangeEnd = ranges.cjIndexEnd;
- int rangeMiddle;
while (index == -1 && rangeStart < rangeEnd)
{
- rangeMiddle = (rangeStart + rangeEnd) >> 1;
+ int rangeMiddle = (rangeStart + rangeEnd) >> 1;
const int clusterMiddle = nblCj(cjList, rangeMiddle);
rangeStart = rangeMiddle + 1;
}
}
+ return index;
}
-
- return index;
}
// TODO: Get rid of the two functions below by renaming sci to ci (or something better)
/* Rellocate FEP list for size nl->maxnri, TODO: replace by C++ */
static void reallocate_nblist(t_nblist* nl)
{
- if (gmx_debug_at)
- {
- fprintf(debug,
- "reallocating neigborlist (ielec=%d, ivdw=%d, igeometry=%d, type=%d), maxnri=%d\n",
- nl->ielec, nl->ivdw, nl->igeometry, nl->type, nl->maxnri);
- }
- srenew(nl->iinr, nl->maxnri);
- srenew(nl->gid, nl->maxnri);
- srenew(nl->shift, nl->maxnri);
- srenew(nl->jindex, nl->maxnri + 1);
+ 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
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)
+ 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 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);
gmx_fatal(FARGS,
"The Verlet scheme with %dx%d kernels and free-energy only supports up to %zu "
"energy groups",
- iGrid.geometry().numAtomsICluster, numAtomsJCluster,
+ 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 = atomIndices[ind_i];
+ const int ind_i = ci * nbl->na_ci + i;
+ const int ai = atomIndices[ind_i];
if (ai >= 0)
{
- nri = nlist->nri;
+ 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;
- bFEP_i = iGrid.atomIsPerturbed(ci - iGrid.cellOffset(), i);
+ 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)
{
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->jjnr.resize(nlist->maxnrj);
+ nlist->excl_fep.resize(nlist->maxnrj);
}
if (ngid > 1)
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 (numAtomsJCluster == jGrid.geometry().numAtomsICluster)
{
- cjr = cja - jGrid.cellOffset();
- fep_cj = jGrid.fepBits(cjr);
+ const int cjr = cja - jGrid.cellOffset();
+ fep_cj = jGrid.fepBits(cjr);
if (ngid > 1)
{
gid_cj = nbatParams.energrp[cja];
}
else if (2 * numAtomsJCluster == jGrid.geometry().numAtomsICluster)
{
- cjr = cja - jGrid.cellOffset() * 2;
+ const int cjr = cja - jGrid.cellOffset() * 2;
/* Extract half of the ci fep/energrp mask */
fep_cj = (jGrid.fepBits(cjr >> 1) >> ((cjr & 1) * numAtomsJCluster))
& ((1 << numAtomsJCluster) - 1);
}
else
{
- cjr = cja - (jGrid.cellOffset() >> 1);
+ const int cjr = cja - (jGrid.cellOffset() >> 1);
/* Combine two ci fep masks/energrp */
fep_cj = jGrid.fepBits(cjr * 2)
+ (jGrid.fepBits(cjr * 2 + 1) << jGrid.geometry().numAtomsICluster);
for (int j = 0; j < nbl->na_cj; j++)
{
/* Is this interaction perturbed and not excluded? */
- ind_j = cja * nbl->na_cj + j;
- aj = atomIndices[ind_j];
+ 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)
{
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();
if (numJClusterGroups == 0)
{
* 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 = atomIndices[ind_i];
+ const int ind_i = c_abs * nbl->na_ci + i;
+ const int ai = atomIndices[ind_i];
if (ai >= 0)
{
- nri = nlist->nri;
+ 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;
- bFEP_i = iGrid.atomIsPerturbed(c_abs - iGrid.cellOffset() * c_gpuNumClusterPerCell, i);
+ 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;
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++)
{
for (int j = 0; j < nbl->na_cj; j++)
{
/* Is this interaction perturbed and not excluded? */
- ind_j = (jGrid.cellOffset() * c_gpuNumClusterPerCell + cjr) * nbl->na_cj + j;
- aj = atomIndices[ind_j];
+ 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);
- excl_pair = a_mod_wj(j) * nbl->na_ci + i;
- excl_bit = (1U << (gcj * c_gpuNumClusterPerCell + c));
+ int excl_pair = a_mod_wj(j) * nbl->na_ci + i;
+ unsigned int 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
* 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 Nbnxm::GridSet& gridSet,
- NbnxnPairlistGpu* nbl,
- gmx_bool diagRemoved,
+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)
* 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, nbl->work->cj_ind,
+ 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");
}
/* Close this simple list i entry */
-static void closeIEntry(NbnxnPairlistCpu* nbl,
- int gmx_unused sp_max_av,
+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)
+ float gmx_unused nsp_tot_est,
+ int gmx_unused thread,
+ int gmx_unused nthread)
{
nbnxn_ci_t& ciEntry = nbl->ci.back();
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.
*/
nsp_max = static_cast<int>(nsp_target_av * (nsp_tot_est * 1.5 / (nsp_est + nsp_tot_est)));
}
- else
- {
- nsp_max = nsp_target_av;
- }
const int cj4_start = nbl->sci.back().cj4_ind_start;
const int cj4_end = nbl->sci.back().cj4_ind_end;
{
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;
}
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.packedBoundingBoxes(), 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.iBoundingBoxes(), ci, shx, shy, shz, work->iSuperClusterData.bb.data());
#endif
}
/* 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,
+static void icell_set_x(int ci,
+ real shx,
+ real shy,
+ real shz,
+ int stride,
+ const real* x,
ClusterDistanceKernelType gmx_unused kernelType,
NbnxnPairlistGpuWork* work)
{
/* 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)
{
- 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)
}
/* 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;
/* One rectangular volume on a face */
* Maxwell is less sensitive to the exact value.
*/
const int nsubpair_target_min = 36;
- real r_eff_sup, vol_est, nsp_est, nsp_est_nl;
const Grid& grid = gridSet.grids()[0];
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_get_rlist_effective_inc(numAtomsCluster, ls);
+ const real r_eff_sup = rlist + nbnxn_get_rlist_effective_inc(numAtomsCluster, ls);
- if (!gridSet.domainSetup().haveMultipleDomains || gridSet.domainSetup().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(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;
/* 12/2 quarter pie slices on the edges */
/* 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.
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
{
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, "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);
}
}
int nsci = nblc->sci.size();
int ncj4 = nblc->cj4.size();
int nexcl = nblc->excl.size();
- for (auto& nbl : nbls)
+ for (const auto& nbl : nbls)
{
nsci += nbl.sci.size();
ncj4 += nbl.cj4.size();
/* Each thread should copy its own data to the combined arrays,
* as otherwise data will go back and forth between different caches.
*/
- const int gmx_unused nthreads = gmx_omp_nthreads_get(emntPairsearch);
+ const int gmx_unused nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Pairsearch);
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (gmx::index n = 0; n < nbls.ssize(); n++)
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- for (auto& nbl : nbls)
+ for (const auto& nbl : nbls)
{
nblc->nci_tot += nbl.nci_tot;
}
const int nrj_target = (nrj_tot + numLists - 1) / numLists;
- GMX_ASSERT(gmx_omp_nthreads_get(emntNonbonded) == numLists,
+ 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(numLists)
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);
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.
* 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 * (iGridDims.cellSize[XX] + jGridDims.cellSize[XX]);
- bby = 0.5 * (iGridDims.cellSize[YY] + jGridDims.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
}
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
*/
GMX_ASSERT(iGrid.dimensions().numCells[XX] > 0, "Grid can't be empty");
GMX_ASSERT(numLists > 0, "We need at least one list");
- ci_block = (iGrid.numCells() * ci_block_enum)
- / (ci_block_denom * iGrid.dimensions().numCells[XX] * numLists);
+ int ci_block = (iGrid.numCells() * ci_block_enum)
+ / (ci_block_denom * iGrid.dimensions().numCells[XX] * numLists);
const int numAtomsPerCell = iGrid.geometry().numAtomsPerCell;
switch (kernelType)
{
case ClusterDistanceKernelType::CpuPlainC:
- makeClusterListSimple(jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ makeClusterListSimple(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#ifdef GMX_NBNXN_SIMD_4XN
case ClusterDistanceKernelType::CpuSimd_4xM:
- makeClusterListSimd4xn(jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ makeClusterListSimd4xn(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#endif
#ifdef GMX_NBNXN_SIMD_2XNN
case ClusterDistanceKernelType::CpuSimd_2xMM:
- makeClusterListSimd2xnn(jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ 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 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,
+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 void setBufferFlags(const NbnxnPairlistGpu gmx_unused& nbl,
- int gmx_unused ncj_old_j,
- int gmx_unused gridj_flag_shift,
+ int gmx_unused ncj_old_j,
+ int gmx_unused gridj_flag_shift,
gmx_bitmask_t gmx_unused* gridj_flag,
- int gmx_unused th)
+ int gmx_unused th)
{
GMX_ASSERT(false, "This function should never be called");
}
T* nbl,
t_nblist* nbl_fep)
{
- int na_cj_2log;
matrix box;
real 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;
if (jGrid.geometry().isSimple != pairlistIsSimple(*nbl)
|| iGrid.geometry().isSimple != pairlistIsSimple(*nbl))
sync_work(nbl);
GMX_ASSERT(nbl->na_ci == jGrid.geometry().numAtomsICluster,
"The cluster sizes in the list and grid should match");
- nbl->na_cj = JClusterSizePerListType[pairlistType];
- na_cj_2log = get_2log(nbl->na_cj);
+ nbl->na_cj = JClusterSizePerListType[pairlistType];
+ const int na_cj_2log = get_2log(nbl->na_cj);
nbl->rlist = rlist;
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();
}
gridSet.getBox(box);
* 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);
const Grid::Dimensions& iGridDims = iGrid.dimensions();
const Grid::Dimensions& jGridDims = jGrid.dimensions();
- rbb2 = boundingbox_only_distance2(iGridDims, jGridDims, nbl->rlist, pairlistIsSimple(*nbl));
+ const float rbb2 =
+ boundingbox_only_distance2(iGridDims, jGridDims, nbl->rlist, pairlistIsSimple(*nbl));
if (debug)
{
if (debug)
{
- fprintf(debug, "nbl nc_i %d col.av. %.1f ci_block %d\n", iGrid.numCells(),
- iGrid.numCells() / static_cast<double>(iGrid.numColumns()), 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.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;
}
- ncj_old_i = getNumSimpleJClustersInList(*nbl);
+ const int ncj_old_i = getNumSimpleJClustersInList(*nbl);
- d2cx = 0;
+ real d2cx = 0;
if (!isIntraGridList && shp[XX] == 0)
{
- if (bSimple)
- {
- bx1 = bb_i[ci].upper.x;
- }
- else
- {
- bx1 = iGridDims.lowerCorner[XX] + (real(ci_x) + 1) * iGridDims.cellSize[XX];
- }
+ const real bx1 =
+ bSimple ? bb_i[ci].upper.x
+ : iGridDims.lowerCorner[XX] + (real(ci_x) + 1) * iGridDims.cellSize[XX];
if (bx1 < jGridDims.lowerCorner[XX])
{
d2cx = gmx::square(jGridDims.lowerCorner[XX] - bx1);
}
}
- ci_xy = ci_x * iGridDims.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 = real(tz) * box[ZZ][ZZ];
- bz0 = bbcz_i[ci].lower + shz;
- bz1 = bbcz_i[ci].upper + 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 / real(iGrid.numCellsInColumn(ci_xy));
+ real bz1_frac = bz1 / real(iGrid.numCellsInColumn(ci_xy));
if (bz1_frac < 0)
{
bz1_frac = 0;
{
const real shy = real(ty) * box[YY][YY] + real(tz) * box[ZZ][YY];
- if (bSimple)
- {
- by0 = bb_i[ci].lower.y + shy;
- by1 = bb_i[ci].upper.y + shy;
- }
- else
- {
- by0 = iGridDims.lowerCorner[YY] + (real(ci_y)) * iGridDims.cellSize[YY] + shy;
- by1 = iGridDims.lowerCorner[YY] + (real(ci_y) + 1) * iGridDims.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;
+ 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;
+ real d2z_cy = d2z;
if (by1 < jGridDims.lowerCorner[YY])
{
d2z_cy += gmx::square(jGridDims.lowerCorner[YY] - by1);
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 =
real(tx) * box[XX][XX] + real(ty) * box[YY][XX] + real(tz) * box[ZZ][XX];
- if (bSimple)
- {
- bx0 = bb_i[ci].lower.x + shx;
- bx1 = bb_i[ci].upper.x + shx;
- }
- else
- {
- bx0 = iGridDims.lowerCorner[XX] + (real(ci_x)) * iGridDims.cellSize[XX] + shx;
- bx1 = iGridDims.lowerCorner[XX] + (real(ci_x) + 1) * iGridDims.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;
+ int cxf, cxl; //NOLINT(cppcoreguidelines-init-variables)
get_cell_range<XX>(bx0, bx1, jGridDims, d2z_cy, rlist, &cxf, &cxl);
if (cxf > cxl)
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(),
- kernelType, nbl->work.get());
+ 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++)
{
const real cx_real = cx;
- d2zx = d2z;
+ real d2zx = d2z;
if (jGridDims.lowerCorner[XX] + cx_real * jGridDims.cellSize[XX] > bx1)
{
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++)
{
jGrid.firstCellInColumn(cx * jGridDims.numCells[YY] + cy + 1);
const real cy_real = cy;
- d2zxy = d2zx;
+ real d2zxy = d2zx;
if (jGridDims.lowerCorner[YY] + cy_real * jGridDims.cellSize[YY] > by1)
{
d2zxy += gmx::square(jGridDims.lowerCorner[YY]
*/
int midCell =
columnStart
- + static_cast<int>(bz1_frac
- * static_cast<real>(columnEnd - 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.
/* 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);
}
"column");
/* For f buffer flags with simple lists */
- ncj_old_j = getNumSimpleJClustersInList(*nbl);
-
- makeClusterListWrapper(nbl, iGrid, ci, jGrid, firstCell, lastCell,
- excludeSubDiagonal, nbat, rlist2, rbb2,
- kernelType, &numDistanceChecks);
+ const int ncj_old_j = getNumSimpleJClustersInList(*nbl);
+
+ makeClusterListWrapper(nbl,
+ iGrid,
+ ci,
+ jGrid,
+ firstCell,
+ lastCell,
+ excludeSubDiagonal,
+ nbat,
+ rlist2,
+ rbb2,
+ kernelType,
+ &numDistanceChecks);
if (bFBufferFlag)
{
if (!exclusions.empty())
{
/* Set the exclusions for this ci list */
- setExclusionsForIEntry(gridSet, nbl, excludeSubDiagonal, na_cj_2log,
- *getOpenIEntry(nbl), exclusions);
+ setExclusionsForIEntry(
+ gridSet, nbl, excludeSubDiagonal, na_cj_2log, *getOpenIEntry(nbl), exclusions);
}
if (haveFep)
{
- make_fep_list(gridSet.atomIndices(), nbat, nbl, excludeSubDiagonal,
- getOpenIEntry(nbl), shx, shy, shz, rl_fep2, iGrid, jGrid, nbl_fep);
+ make_fep_list(gridSet.atomIndices(),
+ nbat,
+ nbl,
+ excludeSubDiagonal,
+ getOpenIEntry(nbl),
+ shx,
+ shy,
+ shz,
+ rl_fep2,
+ iGrid,
+ jGrid,
+ nbl_fep);
}
/* Close this ci list */
if (bFBufferFlag && getNumSimpleJClustersInList(*nbl) > ncj_old_i)
{
- bitmask_init_bit(&(work->buffer_flags.flag[(iGrid.cellOffset() + ci) >> gridi_flag_shift]), th);
+ bitmask_init_bit(&(work->buffer_flags[(iGrid.cellOffset() + ci) >> gridi_flag_shift]), th);
}
}
static void reduce_buffer_flags(gmx::ArrayRef<PairsearchWork> searchWork,
int nsrc,
- const nbnxn_buffer_flags_t* dest)
+ gmx::ArrayRef<gmx_bitmask_t> dest)
{
for (int s = 0; s < nsrc; s++)
{
- gmx_bitmask_t* flag = searchWork[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++;
}
}
}
}
-
+ const auto numFlags = static_cast<double>(flags.size());
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));
+ "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,
+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)
+ 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;
}
}
-#if defined(__GNUC__) && !defined(__clang__) && !defined(__ICC) && __GNUC__ == 7
+#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")
return ncjTotal;
}
-#if defined(__GNUC__) && !defined(__clang__) && !defined(__ICC) && __GNUC__ == 7
+#if defined(__GNUC__) && !defined(__clang__) && __GNUC__ == 7
# pragma GCC pop_options
#endif
/* 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);
}
else
{
- copySelectedListRange<false>(srcCi, src, &dest, flag, iFlagShift,
- jFlagShift, t);
+ copySelectedListRange<false>(
+ srcCi, src, &dest, flag, iFlagShift, jFlagShift, t);
}
}
cjGlobal += ncj;
}
/* 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,
+static Range<int> getJZoneRange(const gmx_domdec_zones_t* ddZones,
const InteractionLocality locality,
const int iZone)
{
else if (iZone == 0)
{
/* Non-local: we need to avoid the local (zone 0 vs 0) interactions */
- return { 1, *ddZones.iZones[iZone].jZoneRange.end() };
+ return { 1, *ddZones->iZones[iZone].jZoneRange.end() };
}
else
{
/* Non-local with non-local i-zone: use all j-zones */
- return ddZones.iZones[iZone].jZoneRange;
+ return ddZones->iZones[iZone].jZoneRange;
}
}
//! Prepares CPU lists produced by the search for dynamic pruning
static void prepareListsForDynamicPruning(gmx::ArrayRef<NbnxnPairlistCpu> lists);
-void PairlistSet::constructPairlists(const Nbnxm::GridSet& gridSet,
+void PairlistSet::constructPairlists(gmx::InteractionLocality locality,
+ const Nbnxm::GridSet& gridSet,
gmx::ArrayRef<PairsearchWork> searchWork,
nbnxn_atomdata_t* nbat,
const ListOfLists<int>& exclusions,
{
const real rlist = params_.rlistOuter;
- int nsubpair_target;
- float nsubpair_tot_est;
- int ci_block;
- gmx_bool progBal;
- int np_tot, np_noq, np_hlj, nap;
-
const int numLists = (isCpuType_ ? cpuLists_.size() : gpuLists_.size());
if (debug)
nbat->bUseBufferFlags = (nbat->out.size() > 1);
/* We should re-init the flags before making the first list */
- if (nbat->bUseBufferFlags && locality_ == InteractionLocality::Local)
+ if (nbat->bUseBufferFlags && locality == InteractionLocality::Local)
{
- init_buffer_flags(&nbat->buffer_flags, nbat->numAtoms());
+ resizeAndZeroBufferFlags(&nbat->buffer_flags, nbat->numAtoms());
}
+ int nsubpair_target = 0;
+ float nsubpair_tot_est = 0.0F;
if (!isCpuType_ && minimumIlistCountForGpuBalancing > 0)
{
- get_nsubpair_target(gridSet, locality_, rlist, minimumIlistCountForGpuBalancing,
- &nsubpair_target, &nsubpair_tot_est);
- }
- else
- {
- nsubpair_target = 0;
- nsubpair_tot_est = 0;
+ get_nsubpair_target(
+ gridSet, locality, rlist, minimumIlistCountForGpuBalancing, &nsubpair_target, &nsubpair_tot_est);
}
/* Clear all pair-lists */
}
}
- const gmx_domdec_zones_t& ddZones = *gridSet.domainSetup().zones;
+ 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_);
+ const auto iZoneRange = getIZoneRange(gridSet.domainSetup(), locality);
for (const int iZone : iZoneRange)
{
const Grid& iGrid = gridSet.grids()[iZone];
- const auto jZoneRange = getJZoneRange(ddZones, locality_, iZone);
+ const auto jZoneRange = getJZoneRange(ddZones, locality, iZone);
for (int jZone : jZoneRange)
{
searchCycleCounting->start(enbsCCsearch);
- ci_block = get_ci_block_size(iGrid, gridSet.domainSetup().haveMultipleDomains, numLists);
+ 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 = (locality_ == InteractionLocality::Local || ddZones.n <= 2);
+ const bool progBal = (locality == InteractionLocality::Local || ddZones->n <= 2);
#pragma omp parallel for num_threads(numLists) schedule(static)
for (int th = 0; th < numLists; th++)
*/
if (nbat->bUseBufferFlags && (iZone == 0 && jZone == 0))
{
- init_buffer_flags(&searchWork[th].buffer_flags, nbat->numAtoms());
+ resizeAndZeroBufferFlags(&searchWork[th].buffer_flags, nbat->numAtoms());
}
if (combineLists_ && th > 0)
/* Divide the i cells equally over the pairlists */
if (isCpuType_)
{
- nbnxn_make_pairlist_part(gridSet, iGrid, jGrid, &work, nbat, exclusions, rlist,
- params_.pairlistType, ci_block, nbat->bUseBufferFlags,
- nsubpair_target, progBal, nsubpair_tot_est, th,
- numLists, &cpuLists_[th], fepListPtr);
+ nbnxn_make_pairlist_part(gridSet,
+ iGrid,
+ jGrid,
+ &work,
+ nbat,
+ exclusions,
+ rlist,
+ params_.pairlistType,
+ ci_block,
+ nbat->bUseBufferFlags,
+ nsubpair_target,
+ progBal,
+ nsubpair_tot_est,
+ th,
+ numLists,
+ &cpuLists_[th],
+ fepListPtr);
}
else
{
- nbnxn_make_pairlist_part(gridSet, iGrid, jGrid, &work, nbat, exclusions, rlist,
- params_.pairlistType, ci_block, nbat->bUseBufferFlags,
- nsubpair_target, progBal, nsubpair_tot_est, th,
- numLists, &gpuLists_[th], fepListPtr);
+ nbnxn_make_pairlist_part(gridSet,
+ iGrid,
+ jGrid,
+ &work,
+ nbat,
+ exclusions,
+ rlist,
+ params_.pairlistType,
+ ci_block,
+ nbat->bUseBufferFlags,
+ nsubpair_target,
+ progBal,
+ nsubpair_tot_est,
+ th,
+ numLists,
+ &gpuLists_[th],
+ fepListPtr);
}
work.cycleCounter.stop();
}
searchCycleCounting->stop(enbsCCsearch);
- np_tot = 0;
- np_noq = 0;
- np_hlj = 0;
+ 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, searchWork[th].ndistc);
np_tot += nbl.nci_tot;
}
}
- if (isCpuType_)
- {
- nap = cpuLists_[0].na_ci * cpuLists_[0].na_cj;
- }
- else
- {
- nap = gmx::square(gpuLists_[0].na_ci);
- }
+ 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 (nbat->bUseBufferFlags)
{
- reduce_buffer_flags(searchWork, numLists, &nbat->buffer_flags);
+ reduce_buffer_flags(searchWork, numLists, nbat->buffer_flags);
}
if (gridSet.haveFep())
if (nbat->bUseBufferFlags)
{
- print_reduction_cost(&nbat->buffer_flags, numLists);
+ print_reduction_cost(nbat->buffer_flags, numLists);
}
}
"exclusions should either be empty or the number of lists should match the number of "
"local i-atoms");
- pairlistSet(iLocality).constructPairlists(gridSet, pairSearch->work(), nbat, exclusions,
- minimumIlistCountForGpuBalancing_, nrnb,
+ pairlistSet(iLocality).constructPairlists(iLocality,
+ gridSet,
+ pairSearch->work(),
+ nbat,
+ exclusions,
+ minimumIlistCountForGpuBalancing_,
+ nrnb,
&pairSearch->cycleCounting_);
if (iLocality == InteractionLocality::Local)
void nonbonded_verlet_t::constructPairlist(const InteractionLocality iLocality,
const ListOfLists<int>& exclusions,
int64_t step,
- t_nrnb* nrnb)
+ t_nrnb* nrnb) const
{
pairlistSets_->construct(iLocality, pairSearch_.get(), nbat.get(), exclusions, step, nrnb);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff