src/gromacs/nbnxm/nbnxm.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
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   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                             ddZone,
  60                        const rvec                      lowerCorner,
  61                        const rvec                      upperCorner,
  62                        const gmx::UpdateGroupsCog     *updateGroupsCog,
  63                        int                             atomStart,
  64                        int                             atomEnd,
  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, ddZone, lowerCorner, upperCorner,
  72                                       updateGroupsCog, atomStart, atomEnd, atomDensity,
  73                                       atomInfo, x, numAtomsMoved, move,
  74                                       nb_verlet->nbat.get());
  75 }
  76
  77 /* Calls nbnxn_put_on_grid for all non-local domains */
  78 void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t              *nbv,
  79                                 const struct gmx_domdec_zones_t *zones,
  80                                 gmx::ArrayRef<const int>         atomInfo,
  81                                 gmx::ArrayRef<const gmx::RVec>   x)
  82 {
  83     for (int zone = 1; zone < zones->n; zone++)
  84     {
  85         rvec c0, c1;
  86         for (int d = 0; d < DIM; d++)
  87         {
  88             c0[d] = zones->size[zone].bb_x0[d];
  89             c1[d] = zones->size[zone].bb_x1[d];
  90         }
  91
  92         nbnxn_put_on_grid(nbv, nullptr,
  93                           zone, c0, c1,
  94                           nullptr,
  95                           zones->cg_range[zone],
  96                           zones->cg_range[zone+1],
  97                           -1,
  98                           atomInfo,
  99                           x,
 100                           0, nullptr);
 101     }
 102 }
 103
 104 bool nonbonded_verlet_t::isDynamicPruningStepCpu(int64_t step) const
 105 {
 106     return pairlistSets_->isDynamicPruningStepCpu(step);
 107 }
 108
 109 bool nonbonded_verlet_t::isDynamicPruningStepGpu(int64_t step) const
 110 {
 111     return pairlistSets_->isDynamicPruningStepGpu(step);
 112 }
 113
 114 gmx::ArrayRef<const int> nonbonded_verlet_t::getLocalAtomOrder() const
 115 {
 116     /* Return the atom order for the home cell (index 0) */
 117     const Nbnxm::Grid &grid       = pairSearch_->gridSet().grids()[0];
 118
 119     const int          numIndices = grid.atomIndexEnd() - grid.firstAtomInColumn(0);
 120
 121     return gmx::constArrayRefFromArray(pairSearch_->gridSet().atomIndices().data(), numIndices);
 122 }
 123
 124 void nonbonded_verlet_t::setLocalAtomOrder()
 125 {
 126     pairSearch_->setLocalAtomOrder();
 127 }
 128
 129 void nonbonded_verlet_t::setAtomProperties(const t_mdatoms          &mdatoms,
 130                                            gmx::ArrayRef<const int>  atomInfo)
 131 {
 132     nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), &mdatoms, atomInfo.data());
 133 }
 134
 135 void nonbonded_verlet_t::convertCoordinates(const Nbnxm::AtomLocality       locality,
 136                                             const bool                      fillLocal,
 137                                             gmx::ArrayRef<const gmx::RVec>  coordinates)
 138 {
 139     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 140     wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
 141
 142     nbnxn_atomdata_copy_x_to_nbat_x(pairSearch_->gridSet(), locality, fillLocal,
 143                                     as_rvec_array(coordinates.data()),
 144                                     nbat.get());
 145
 146     wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
 147     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 148 }
 149
 150 void nonbonded_verlet_t::convertCoordinatesGpu(const Nbnxm::AtomLocality        locality,
 151                                                const bool                       fillLocal,
 152                                                DeviceBuffer<float>              d_x,
 153                                                GpuEventSynchronizer            *xReadyOnDevice)
 154 {
 155     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 156     wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
 157
 158     nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, fillLocal,
 159                                    gpu_nbv,
 160                                    d_x,
 161                                    xReadyOnDevice);
 162
 163     wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
 164     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 165 }
 166
 167 gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
 168 {
 169     return pairSearch_->gridSet().cells();
 170 }
 171
 172 void
 173 nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const Nbnxm::AtomLocality           locality,
 174                                              gmx::ArrayRef<gmx::RVec>            force)
 175 {
 176
 177     /* Skip the reduction if there was no short-range GPU work to do
 178      * (either NB or both NB and bonded work). */
 179     if (!pairlistIsSimple() && !haveGpuShortRangeWork(locality))
 180     {
 181         return;
 182     }
 183
 184     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 185     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 186
 187     reduceForces(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()));
 188
 189     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 190     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 191 }
 192
 193 void
 194 nonbonded_verlet_t::atomdata_add_nbat_f_to_f_gpu(const Nbnxm::AtomLocality                   locality,
 195                                                  DeviceBuffer<float>                         totalForcesDevice,
 196                                                  void                                       *forcesPmeDevice,
 197                                                  gmx::ArrayRef<GpuEventSynchronizer* const>  dependencyList,
 198                                                  bool                                        useGpuFPmeReduction,
 199                                                  bool                                        accumulateForce)
 200 {
 201
 202     GMX_ASSERT((useGpuFPmeReduction == (forcesPmeDevice != nullptr)),
 203                "GPU PME force reduction is only valid when a non-null GPU PME force pointer is available");
 204
 205     /* Skip the reduction if there was no short-range GPU work to do
 206      * (either NB or both NB and bonded work). */
 207     if (!pairlistIsSimple() && !haveGpuShortRangeWork(locality))
 208     {
 209         return;
 210     }
 211
 212     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 213     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 214
 215     reduceForcesGpu(locality, totalForcesDevice, pairSearch_->gridSet(), forcesPmeDevice, dependencyList, gpu_nbv, useGpuFPmeReduction, accumulateForce);
 216
 217     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 218     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 219 }
 220
 221 void
 222 nonbonded_verlet_t::atomdata_init_add_nbat_f_to_f_gpu()
 223 {
 224
 225     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 226     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 227
 228     const Nbnxm::GridSet      &gridSet = pairSearch_->gridSet();
 229
 230     Nbnxm::nbnxn_gpu_init_add_nbat_f_to_f(gridSet.cells().data(),
 231                                           gpu_nbv,
 232                                           gridSet.numRealAtomsTotal());
 233
 234     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 235     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 236 }
 237
 238 real nonbonded_verlet_t::pairlistInnerRadius() const
 239 {
 240     return pairlistSets_->params().rlistInner;
 241 }
 242
 243 real nonbonded_verlet_t::pairlistOuterRadius() const
 244 {
 245     return pairlistSets_->params().rlistOuter;
 246 }
 247
 248 void nonbonded_verlet_t::changePairlistRadii(real rlistOuter,
 249                                              real rlistInner)
 250 {
 251     pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
 252 }
 253
 254 void
 255 nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu()
 256 {
 257     Nbnxm::nbnxn_gpu_init_x_to_nbat_x(pairSearch_->gridSet(), gpu_nbv);
 258 }
 259
 260 void nonbonded_verlet_t::insertNonlocalGpuDependency(const Nbnxm::InteractionLocality interactionLocality)
 261 {
 262     Nbnxm::nbnxnInsertNonlocalGpuDependency(gpu_nbv, interactionLocality);
 263 }
 264
 265 void* nonbonded_verlet_t::get_x_on_device_event()
 266 {
 267     return Nbnxm::nbnxn_get_x_on_device_event(gpu_nbv);
 268 }
 269
 270 void nonbonded_verlet_t::wait_nonlocal_x_copy_D2H_done()
 271 {
 272     Nbnxm::nbnxn_wait_nonlocal_x_copy_D2H_done(gpu_nbv);
 273 }
 274
 275 void nonbonded_verlet_t::stream_local_wait_for_nonlocal()
 276 {
 277     Nbnxm::nbnxn_stream_local_wait_for_nonlocal(gpu_nbv);
 278 }
 279
 280 /*! \endcond */