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/nbnxm/atomdata.h"
  50 #include "gromacs/timing/wallcycle.h"
  51
  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
 151 void nonbonded_verlet_t::copyCoordinatesToGpu(const Nbnxm::AtomLocality       locality,
 152                                               const bool                      fillLocal,
 153                                               gmx::ArrayRef<const gmx::RVec>  coordinatesHost)
 154 {
 155     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 156     wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
 157
 158     nbnxn_atomdata_copy_x_to_gpu(pairSearch_->gridSet(), locality, fillLocal,
 159                                  nbat.get(), gpu_nbv,
 160                                  as_rvec_array(coordinatesHost.data()));
 161
 162     wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
 163     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 164 }
 165
 166 DeviceBuffer<float> nonbonded_verlet_t::getDeviceCoordinates()
 167 {
 168     return nbnxn_atomdata_get_x_gpu(gpu_nbv);
 169 }
 170
 171 void nonbonded_verlet_t::convertCoordinatesGpu(const Nbnxm::AtomLocality       locality,
 172                                                const bool                      fillLocal,
 173                                                DeviceBuffer<float>             coordinatesDevice)
 174 {
 175     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 176     wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
 177
 178     nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, fillLocal,
 179                                    gpu_nbv,
 180                                    coordinatesDevice);
 181
 182     wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
 183     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 184 }
 185
 186 gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
 187 {
 188     return pairSearch_->gridSet().cells();
 189 }
 190
 191 void
 192 nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const Nbnxm::AtomLocality           locality,
 193                                              gmx::ArrayRef<gmx::RVec>            force)
 194 {
 195
 196     /* Skip the reduction if there was no short-range GPU work to do
 197      * (either NB or both NB and bonded work). */
 198     if (!pairlistIsSimple() && !haveGpuShortRangeWork(locality))
 199     {
 200         return;
 201     }
 202
 203     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 204     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 205
 206     reduceForces<false>(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()), nullptr, nullptr, gpu_nbv, false, false);
 207
 208     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 209     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 210 }
 211
 212 void
 213 nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const Nbnxm::AtomLocality           locality,
 214                                              gmx::ArrayRef<gmx::RVec>            force,
 215                                              void                               *fPmeDeviceBuffer,
 216                                              GpuEventSynchronizer               *pmeForcesReady,
 217                                              BufferOpsUseGpu                     useGpu,
 218                                              bool                                useGpuFPmeReduction,
 219                                              bool                                accumulateForce)
 220 {
 221
 222     GMX_ASSERT(!((useGpu == BufferOpsUseGpu::False) && accumulateForce),
 223                "Accumulatation of force is only valid when GPU buffer ops are active");
 224
 225     GMX_ASSERT((useGpuFPmeReduction == (fPmeDeviceBuffer != nullptr)),
 226                "GPU PME force reduction is only valid when a non-null GPU PME force pointer is available");
 227
 228     /* Skip the reduction if there was no short-range GPU work to do
 229      * (either NB or both NB and bonded work). */
 230     if (!pairlistIsSimple() && !haveGpuShortRangeWork(locality))
 231     {
 232         return;
 233     }
 234
 235     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 236     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 237
 238     auto fn = useGpu == BufferOpsUseGpu::True ? reduceForces<true> : reduceForces<false>;
 239     fn(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()), fPmeDeviceBuffer, pmeForcesReady, gpu_nbv, useGpuFPmeReduction, accumulateForce);
 240
 241     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 242     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 243 }
 244
 245 void
 246 nonbonded_verlet_t::atomdata_init_add_nbat_f_to_f_gpu()
 247 {
 248
 249     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 250     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 251
 252     const Nbnxm::GridSet      &gridSet = pairSearch_->gridSet();
 253
 254     Nbnxm::nbnxn_gpu_init_add_nbat_f_to_f(gridSet.cells().data(),
 255                                           gpu_nbv,
 256                                           gridSet.numRealAtomsTotal());
 257
 258     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 259     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 260 }
 261
 262 real nonbonded_verlet_t::pairlistInnerRadius() const
 263 {
 264     return pairlistSets_->params().rlistInner;
 265 }
 266
 267 real nonbonded_verlet_t::pairlistOuterRadius() const
 268 {
 269     return pairlistSets_->params().rlistOuter;
 270 }
 271
 272 void nonbonded_verlet_t::changePairlistRadii(real rlistOuter,
 273                                              real rlistInner)
 274 {
 275     pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
 276 }
 277
 278 void
 279 nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu()
 280 {
 281     Nbnxm::nbnxn_gpu_init_x_to_nbat_x(pairSearch_->gridSet(), gpu_nbv);
 282 }
 283
 284 void nonbonded_verlet_t::insertNonlocalGpuDependency(const Nbnxm::InteractionLocality interactionLocality)
 285 {
 286     Nbnxm::nbnxnInsertNonlocalGpuDependency(gpu_nbv, interactionLocality);
 287 }
 288
 289 void nonbonded_verlet_t::launch_copy_f_to_gpu(rvec *f, const Nbnxm::AtomLocality locality)
 290 {
 291     nbnxn_launch_copy_f_to_gpu(locality,
 292                                pairSearch_->gridSet(),
 293                                gpu_nbv,
 294                                f);
 295 }
 296
 297 void nonbonded_verlet_t::launch_copy_f_from_gpu(rvec *f, const Nbnxm::AtomLocality locality)
 298 {
 299     nbnxn_launch_copy_f_from_gpu(locality,
 300                                  pairSearch_->gridSet(),
 301                                  gpu_nbv,
 302                                  f);
 303 }
 304
 305 void nonbonded_verlet_t::wait_for_gpu_force_reduction(const Nbnxm::AtomLocality locality)
 306 {
 307     nbnxn_wait_for_gpu_force_reduction(locality, gpu_nbv);
 308 }
 309
 310 /*! \endcond */