src/gromacs/nbnxm/nbnxm.cpp

   1 /*
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   3  *
   4  * Copyright (c) 2019,2020, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
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  35
  36 /*! \internal \file
  37  * \brief
  38  * Implements the Nbnxm class
  39  *
  40  * \author Berk Hess <hess@kth.se>
  41  * \ingroup module_nbnxm
  42  */
  43
  44 #include "gmxpre.h"
  45
  46 #include "nbnxm.h"
  47
  48 #include "gromacs/domdec/domdec_struct.h"
  49 #include "gromacs/nbnxm/atomdata.h"
  50 #include "gromacs/timing/wallcycle.h"
  51
  52 #include "nbnxm_gpu.h"
  53 #include "pairlistsets.h"
  54 #include "pairsearch.h"
  55
  56 /*! \cond INTERNAL */
  57
  58 void nbnxn_put_on_grid(nonbonded_verlet_t*            nb_verlet,
  59                        const matrix                   box,
  60                        int                            gridIndex,
  61                        const rvec                     lowerCorner,
  62                        const rvec                     upperCorner,
  63                        const gmx::UpdateGroupsCog*    updateGroupsCog,
  64                        gmx::Range<int>                atomRange,
  65                        real                           atomDensity,
  66                        gmx::ArrayRef<const int>       atomInfo,
  67                        gmx::ArrayRef<const gmx::RVec> x,
  68                        int                            numAtomsMoved,
  69                        const int*                     move)
  70 {
  71     nb_verlet->pairSearch_->putOnGrid(box, gridIndex, lowerCorner, upperCorner, updateGroupsCog,
  72                                       atomRange, atomDensity, atomInfo, x, numAtomsMoved, move,
  73                                       nb_verlet->nbat.get());
  74 }
  75
  76 /* Calls nbnxn_put_on_grid for all non-local domains */
  77 void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*              nbv,
  78                                 const struct gmx_domdec_zones_t* zones,
  79                                 gmx::ArrayRef<const int>         atomInfo,
  80                                 gmx::ArrayRef<const gmx::RVec>   x)
  81 {
  82     for (int zone = 1; zone < zones->n; zone++)
  83     {
  84         rvec c0, c1;
  85         for (int d = 0; d < DIM; d++)
  86         {
  87             c0[d] = zones->size[zone].bb_x0[d];
  88             c1[d] = zones->size[zone].bb_x1[d];
  89         }
  90
  91         nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
  92                           { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
  93                           nullptr);
  94     }
  95 }
  96
  97 bool nonbonded_verlet_t::isDynamicPruningStepCpu(int64_t step) const
  98 {
  99     return pairlistSets_->isDynamicPruningStepCpu(step);
 100 }
 101
 102 bool nonbonded_verlet_t::isDynamicPruningStepGpu(int64_t step) const
 103 {
 104     return pairlistSets_->isDynamicPruningStepGpu(step);
 105 }
 106
 107 gmx::ArrayRef<const int> nonbonded_verlet_t::getLocalAtomOrder() const
 108 {
 109     /* Return the atom order for the home cell (index 0) */
 110     const Nbnxm::Grid& grid = pairSearch_->gridSet().grids()[0];
 111
 112     const int numIndices = grid.atomIndexEnd() - grid.firstAtomInColumn(0);
 113
 114     return gmx::constArrayRefFromArray(pairSearch_->gridSet().atomIndices().data(), numIndices);
 115 }
 116
 117 void nonbonded_verlet_t::setLocalAtomOrder()
 118 {
 119     pairSearch_->setLocalAtomOrder();
 120 }
 121
 122 void nonbonded_verlet_t::setAtomProperties(const t_mdatoms& mdatoms, gmx::ArrayRef<const int> atomInfo)
 123 {
 124     nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), &mdatoms, atomInfo.data());
 125 }
 126
 127 void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality        locality,
 128                                             const bool                     fillLocal,
 129                                             gmx::ArrayRef<const gmx::RVec> coordinates)
 130 {
 131     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 132     wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
 133
 134     nbnxn_atomdata_copy_x_to_nbat_x(pairSearch_->gridSet(), locality, fillLocal,
 135                                     as_rvec_array(coordinates.data()), nbat.get());
 136
 137     wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
 138     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 139 }
 140
 141 void nonbonded_verlet_t::convertCoordinatesGpu(const gmx::AtomLocality locality,
 142                                                const bool              fillLocal,
 143                                                DeviceBuffer<float>     d_x,
 144                                                GpuEventSynchronizer*   xReadyOnDevice)
 145 {
 146     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 147     wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
 148
 149     nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, fillLocal, gpu_nbv, d_x, xReadyOnDevice);
 150
 151     wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
 152     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 153 }
 154
 155 gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
 156 {
 157     return pairSearch_->gridSet().cells();
 158 }
 159
 160 void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality  locality,
 161                                                   gmx::ArrayRef<gmx::RVec> force)
 162 {
 163
 164     /* Skip the reduction if there was no short-range GPU work to do
 165      * (either NB or both NB and bonded work). */
 166     if (!pairlistIsSimple() && !Nbnxm::haveGpuShortRangeWork(gpu_nbv, locality))
 167     {
 168         return;
 169     }
 170
 171     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 172     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 173
 174     reduceForces(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()));
 175
 176     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 177     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 178 }
 179
 180 void nonbonded_verlet_t::atomdata_add_nbat_f_to_f_gpu(const gmx::AtomLocality locality,
 181                                                       DeviceBuffer<float>     totalForcesDevice,
 182                                                       void*                   forcesPmeDevice,
 183                                                       gmx::ArrayRef<GpuEventSynchronizer* const> dependencyList,
 184                                                       bool useGpuFPmeReduction,
 185                                                       bool accumulateForce)
 186 {
 187
 188     GMX_ASSERT((useGpuFPmeReduction == (forcesPmeDevice != nullptr)),
 189                "GPU PME force reduction is only valid when a non-null GPU PME force pointer is "
 190                "available");
 191
 192     /* Skip the reduction if there was no short-range GPU work to do
 193      * (either NB or both NB and bonded work). */
 194     if (!pairlistIsSimple() && !Nbnxm::haveGpuShortRangeWork(gpu_nbv, locality))
 195     {
 196         return;
 197     }
 198
 199     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 200     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 201
 202     reduceForcesGpu(locality, totalForcesDevice, pairSearch_->gridSet(), forcesPmeDevice,
 203                     dependencyList, gpu_nbv, useGpuFPmeReduction, accumulateForce);
 204
 205     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 206     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 207 }
 208
 209 void nonbonded_verlet_t::atomdata_init_add_nbat_f_to_f_gpu(GpuEventSynchronizer* const localReductionDone)
 210 {
 211
 212     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 213     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 214
 215     const Nbnxm::GridSet& gridSet = pairSearch_->gridSet();
 216
 217     Nbnxm::nbnxn_gpu_init_add_nbat_f_to_f(gridSet.cells().data(), gpu_nbv,
 218                                           gridSet.numRealAtomsTotal(), localReductionDone);
 219
 220     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 221     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 222 }
 223
 224 real nonbonded_verlet_t::pairlistInnerRadius() const
 225 {
 226     return pairlistSets_->params().rlistInner;
 227 }
 228
 229 real nonbonded_verlet_t::pairlistOuterRadius() const
 230 {
 231     return pairlistSets_->params().rlistOuter;
 232 }
 233
 234 void nonbonded_verlet_t::changePairlistRadii(real rlistOuter, real rlistInner)
 235 {
 236     pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
 237 }
 238
 239 void nonbonded_verlet_t::setupGpuShortRangeWork(const gmx::GpuBonded*          gpuBonded,
 240                                                 const gmx::InteractionLocality iLocality)
 241 {
 242     if (useGpu() && !emulateGpu())
 243     {
 244         Nbnxm::setupGpuShortRangeWork(gpu_nbv, gpuBonded, iLocality);
 245     }
 246 }
 247
 248 void nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu()
 249 {
 250     Nbnxm::nbnxn_gpu_init_x_to_nbat_x(pairSearch_->gridSet(), gpu_nbv);
 251 }
 252
 253 void nonbonded_verlet_t::insertNonlocalGpuDependency(const gmx::InteractionLocality interactionLocality)
 254 {
 255     Nbnxm::nbnxnInsertNonlocalGpuDependency(gpu_nbv, interactionLocality);
 256 }
 257
 258 /*! \endcond */