src/gromacs/nbnxm/nbnxm.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019, 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/timing/wallcycle.h"
  50
  51 #include "atomdata.h"
  52 #include "pairlistsets.h"
  53 #include "pairsearch.h"
  54
  55 /*! \cond INTERNAL */
  56
  57 void nbnxn_put_on_grid(nonbonded_verlet_t*            nb_verlet,
  58                        const matrix                   box,
  59                        int                            gridIndex,
  60                        const rvec                     lowerCorner,
  61                        const rvec                     upperCorner,
  62                        const gmx::UpdateGroupsCog*    updateGroupsCog,
  63                        gmx::Range<int>                atomRange,
  64                        real                           atomDensity,
  65                        gmx::ArrayRef<const int>       atomInfo,
  66                        gmx::ArrayRef<const gmx::RVec> x,
  67                        int                            numAtomsMoved,
  68                        const int*                     move)
  69 {
  70     nb_verlet->pairSearch_->putOnGrid(box, gridIndex, lowerCorner, upperCorner, updateGroupsCog,
  71                                       atomRange, atomDensity, atomInfo, x, numAtomsMoved, move,
  72                                       nb_verlet->nbat.get());
  73 }
  74
  75 /* Calls nbnxn_put_on_grid for all non-local domains */
  76 void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*              nbv,
  77                                 const struct gmx_domdec_zones_t* zones,
  78                                 gmx::ArrayRef<const int>         atomInfo,
  79                                 gmx::ArrayRef<const gmx::RVec>   x)
  80 {
  81     for (int zone = 1; zone < zones->n; zone++)
  82     {
  83         rvec c0, c1;
  84         for (int d = 0; d < DIM; d++)
  85         {
  86             c0[d] = zones->size[zone].bb_x0[d];
  87             c1[d] = zones->size[zone].bb_x1[d];
  88         }
  89
  90         nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
  91                           { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
  92                           nullptr);
  93     }
  94 }
  95
  96 bool nonbonded_verlet_t::isDynamicPruningStepCpu(int64_t step) const
  97 {
  98     return pairlistSets_->isDynamicPruningStepCpu(step);
  99 }
 100
 101 bool nonbonded_verlet_t::isDynamicPruningStepGpu(int64_t step) const
 102 {
 103     return pairlistSets_->isDynamicPruningStepGpu(step);
 104 }
 105
 106 gmx::ArrayRef<const int> nonbonded_verlet_t::getLocalAtomOrder() const
 107 {
 108     /* Return the atom order for the home cell (index 0) */
 109     const Nbnxm::Grid& grid = pairSearch_->gridSet().grids()[0];
 110
 111     const int numIndices = grid.atomIndexEnd() - grid.firstAtomInColumn(0);
 112
 113     return gmx::constArrayRefFromArray(pairSearch_->gridSet().atomIndices().data(), numIndices);
 114 }
 115
 116 void nonbonded_verlet_t::setLocalAtomOrder()
 117 {
 118     pairSearch_->setLocalAtomOrder();
 119 }
 120
 121 void nonbonded_verlet_t::setAtomProperties(const t_mdatoms& mdatoms, gmx::ArrayRef<const int> atomInfo)
 122 {
 123     nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), &mdatoms, atomInfo.data());
 124 }
 125
 126 void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality        locality,
 127                                             const bool                     fillLocal,
 128                                             gmx::ArrayRef<const gmx::RVec> coordinates)
 129 {
 130     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 131     wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
 132
 133     nbnxn_atomdata_copy_x_to_nbat_x(pairSearch_->gridSet(), locality, fillLocal,
 134                                     as_rvec_array(coordinates.data()), nbat.get());
 135
 136     wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
 137     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 138 }
 139
 140 void nonbonded_verlet_t::convertCoordinatesGpu(const gmx::AtomLocality locality,
 141                                                const bool              fillLocal,
 142                                                DeviceBuffer<float>     d_x,
 143                                                GpuEventSynchronizer*   xReadyOnDevice)
 144 {
 145     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 146     wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
 147
 148     nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, fillLocal, gpu_nbv, d_x, xReadyOnDevice);
 149
 150     wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
 151     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 152 }
 153
 154 gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
 155 {
 156     return pairSearch_->gridSet().cells();
 157 }
 158
 159 void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality  locality,
 160                                                   gmx::ArrayRef<gmx::RVec> force)
 161 {
 162
 163     /* Skip the reduction if there was no short-range GPU work to do
 164      * (either NB or both NB and bonded work). */
 165     if (!pairlistIsSimple() && !haveGpuShortRangeWork(locality))
 166     {
 167         return;
 168     }
 169
 170     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 171     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 172
 173     reduceForces(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()));
 174
 175     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 176     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 177 }
 178
 179 void nonbonded_verlet_t::atomdata_add_nbat_f_to_f_gpu(const gmx::AtomLocality locality,
 180                                                       DeviceBuffer<float>     totalForcesDevice,
 181                                                       void*                   forcesPmeDevice,
 182                                                       gmx::ArrayRef<GpuEventSynchronizer* const> dependencyList,
 183                                                       bool useGpuFPmeReduction,
 184                                                       bool accumulateForce)
 185 {
 186
 187     GMX_ASSERT((useGpuFPmeReduction == (forcesPmeDevice != nullptr)),
 188                "GPU PME force reduction is only valid when a non-null GPU PME force pointer is "
 189                "available");
 190
 191     /* Skip the reduction if there was no short-range GPU work to do
 192      * (either NB or both NB and bonded work). */
 193     if (!pairlistIsSimple() && !haveGpuShortRangeWork(locality))
 194     {
 195         return;
 196     }
 197
 198     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 199     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 200
 201     reduceForcesGpu(locality, totalForcesDevice, pairSearch_->gridSet(), forcesPmeDevice,
 202                     dependencyList, gpu_nbv, useGpuFPmeReduction, accumulateForce);
 203
 204     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 205     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 206 }
 207
 208 void nonbonded_verlet_t::atomdata_init_add_nbat_f_to_f_gpu(GpuEventSynchronizer* const localReductionDone)
 209 {
 210
 211     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 212     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 213
 214     const Nbnxm::GridSet& gridSet = pairSearch_->gridSet();
 215
 216     Nbnxm::nbnxn_gpu_init_add_nbat_f_to_f(gridSet.cells().data(), gpu_nbv,
 217                                           gridSet.numRealAtomsTotal(), localReductionDone);
 218
 219     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 220     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 221 }
 222
 223 real nonbonded_verlet_t::pairlistInnerRadius() const
 224 {
 225     return pairlistSets_->params().rlistInner;
 226 }
 227
 228 real nonbonded_verlet_t::pairlistOuterRadius() const
 229 {
 230     return pairlistSets_->params().rlistOuter;
 231 }
 232
 233 void nonbonded_verlet_t::changePairlistRadii(real rlistOuter, real rlistInner)
 234 {
 235     pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
 236 }
 237
 238 void nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu()
 239 {
 240     Nbnxm::nbnxn_gpu_init_x_to_nbat_x(pairSearch_->gridSet(), gpu_nbv);
 241 }
 242
 243 void nonbonded_verlet_t::insertNonlocalGpuDependency(const gmx::InteractionLocality interactionLocality)
 244 {
 245     Nbnxm::nbnxnInsertNonlocalGpuDependency(gpu_nbv, interactionLocality);
 246 }
 247
 248 void nonbonded_verlet_t::wait_nonlocal_x_copy_D2H_done()
 249 {
 250     Nbnxm::nbnxn_wait_nonlocal_x_copy_D2H_done(gpu_nbv);
 251 }
 252
 253 void nonbonded_verlet_t::stream_local_wait_for_nonlocal()
 254 {
 255     Nbnxm::nbnxn_stream_local_wait_for_nonlocal(gpu_nbv);
 256 }
 257
 258 /*! \endcond */