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                             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 {
 154     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 155     wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
 156
 157     nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, fillLocal,
 158                                    gpu_nbv,
 159                                    d_x);
 160
 161     wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
 162     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 163 }
 164
 165 gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
 166 {
 167     return pairSearch_->gridSet().cells();
 168 }
 169
 170 void
 171 nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const Nbnxm::AtomLocality           locality,
 172                                              gmx::ArrayRef<gmx::RVec>            force)
 173 {
 174
 175     /* Skip the reduction if there was no short-range GPU work to do
 176      * (either NB or both NB and bonded work). */
 177     if (!pairlistIsSimple() && !haveGpuShortRangeWork(locality))
 178     {
 179         return;
 180     }
 181
 182     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 183     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 184
 185     reduceForces(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()));
 186
 187     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 188     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 189 }
 190
 191 void
 192 nonbonded_verlet_t::atomdata_add_nbat_f_to_f_gpu(const Nbnxm::AtomLocality                   locality,
 193                                                  DeviceBuffer<float>                         totalForcesDevice,
 194                                                  void                                       *forcesPmeDevice,
 195                                                  gmx::ArrayRef<GpuEventSynchronizer* const>  dependencyList,
 196                                                  bool                                        useGpuFPmeReduction,
 197                                                  bool                                        accumulateForce)
 198 {
 199
 200     GMX_ASSERT((useGpuFPmeReduction == (forcesPmeDevice != nullptr)),
 201                "GPU PME force reduction is only valid when a non-null GPU PME force pointer is available");
 202
 203     /* Skip the reduction if there was no short-range GPU work to do
 204      * (either NB or both NB and bonded work). */
 205     if (!pairlistIsSimple() && !haveGpuShortRangeWork(locality))
 206     {
 207         return;
 208     }
 209
 210     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 211     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 212
 213     reduceForcesGpu(locality, totalForcesDevice, pairSearch_->gridSet(), forcesPmeDevice, dependencyList, gpu_nbv, useGpuFPmeReduction, accumulateForce);
 214
 215     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 216     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 217 }
 218
 219 void
 220 nonbonded_verlet_t::atomdata_init_add_nbat_f_to_f_gpu()
 221 {
 222
 223     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 224     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 225
 226     const Nbnxm::GridSet      &gridSet = pairSearch_->gridSet();
 227
 228     Nbnxm::nbnxn_gpu_init_add_nbat_f_to_f(gridSet.cells().data(),
 229                                           gpu_nbv,
 230                                           gridSet.numRealAtomsTotal());
 231
 232     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 233     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 234 }
 235
 236 real nonbonded_verlet_t::pairlistInnerRadius() const
 237 {
 238     return pairlistSets_->params().rlistInner;
 239 }
 240
 241 real nonbonded_verlet_t::pairlistOuterRadius() const
 242 {
 243     return pairlistSets_->params().rlistOuter;
 244 }
 245
 246 void nonbonded_verlet_t::changePairlistRadii(real rlistOuter,
 247                                              real rlistInner)
 248 {
 249     pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
 250 }
 251
 252 void
 253 nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu()
 254 {
 255     Nbnxm::nbnxn_gpu_init_x_to_nbat_x(pairSearch_->gridSet(), gpu_nbv);
 256 }
 257
 258 void nonbonded_verlet_t::insertNonlocalGpuDependency(const Nbnxm::InteractionLocality interactionLocality)
 259 {
 260     Nbnxm::nbnxnInsertNonlocalGpuDependency(gpu_nbv, interactionLocality);
 261 }
 262
 263 void* nonbonded_verlet_t::get_x_on_device_event()
 264 {
 265     return Nbnxm::nbnxn_get_x_on_device_event(gpu_nbv);
 266 }
 267
 268 void nonbonded_verlet_t::wait_nonlocal_x_copy_D2H_done()
 269 {
 270     Nbnxm::nbnxn_wait_nonlocal_x_copy_D2H_done(gpu_nbv);
 271 }
 272
 273 void nonbonded_verlet_t::stream_local_wait_for_nonlocal()
 274 {
 275     Nbnxm::nbnxn_stream_local_wait_for_nonlocal(gpu_nbv);
 276 }
 277
 278 /*! \endcond */