src/gromacs/nbnxm/nbnxm.cpp

   1 /*
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   4  * Copyright (c) 2019,2020,2021, 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 #include "gromacs/utility/message_string_collector.h"
  52
  53 #include "nbnxm_gpu.h"
  54 #include "pairlistsets.h"
  55 #include "pairsearch.h"
  56
  57 /*! \cond INTERNAL */
  58
  59 void nbnxn_put_on_grid(nonbonded_verlet_t*            nb_verlet,
  60                        const matrix                   box,
  61                        int                            gridIndex,
  62                        const rvec                     lowerCorner,
  63                        const rvec                     upperCorner,
  64                        const gmx::UpdateGroupsCog*    updateGroupsCog,
  65                        gmx::Range<int>                atomRange,
  66                        real                           atomDensity,
  67                        gmx::ArrayRef<const int64_t>   atomInfo,
  68                        gmx::ArrayRef<const gmx::RVec> x,
  69                        int                            numAtomsMoved,
  70                        const int*                     move)
  71 {
  72     nb_verlet->pairSearch_->putOnGrid(box,
  73                                       gridIndex,
  74                                       lowerCorner,
  75                                       upperCorner,
  76                                       updateGroupsCog,
  77                                       atomRange,
  78                                       atomDensity,
  79                                       atomInfo,
  80                                       x,
  81                                       numAtomsMoved,
  82                                       move,
  83                                       nb_verlet->nbat.get());
  84 }
  85
  86 /* Calls nbnxn_put_on_grid for all non-local domains */
  87 void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*              nbv,
  88                                 const struct gmx_domdec_zones_t* zones,
  89                                 gmx::ArrayRef<const int64_t>     atomInfo,
  90                                 gmx::ArrayRef<const gmx::RVec>   x)
  91 {
  92     for (int zone = 1; zone < zones->n; zone++)
  93     {
  94         rvec c0, c1;
  95         for (int d = 0; d < DIM; d++)
  96         {
  97             c0[d] = zones->size[zone].bb_x0[d];
  98             c1[d] = zones->size[zone].bb_x1[d];
  99         }
 100
 101         nbnxn_put_on_grid(nbv,
 102                           nullptr,
 103                           zone,
 104                           c0,
 105                           c1,
 106                           nullptr,
 107                           { zones->cg_range[zone], zones->cg_range[zone + 1] },
 108                           -1,
 109                           atomInfo,
 110                           x,
 111                           0,
 112                           nullptr);
 113     }
 114 }
 115
 116 bool nonbonded_verlet_t::isDynamicPruningStepCpu(int64_t step) const
 117 {
 118     return pairlistSets_->isDynamicPruningStepCpu(step);
 119 }
 120
 121 bool nonbonded_verlet_t::isDynamicPruningStepGpu(int64_t step) const
 122 {
 123     return pairlistSets_->isDynamicPruningStepGpu(step);
 124 }
 125
 126 gmx::ArrayRef<const int> nonbonded_verlet_t::getLocalAtomOrder() const
 127 {
 128     /* Return the atom order for the home cell (index 0) */
 129     const Nbnxm::Grid& grid = pairSearch_->gridSet().grids()[0];
 130
 131     const int numIndices = grid.atomIndexEnd() - grid.firstAtomInColumn(0);
 132
 133     return gmx::constArrayRefFromArray(pairSearch_->gridSet().atomIndices().data(), numIndices);
 134 }
 135
 136 void nonbonded_verlet_t::setLocalAtomOrder() const
 137 {
 138     pairSearch_->setLocalAtomOrder();
 139 }
 140
 141 void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef<const int>     atomTypes,
 142                                            gmx::ArrayRef<const real>    atomCharges,
 143                                            gmx::ArrayRef<const int64_t> atomInfo) const
 144 {
 145     nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), atomTypes, atomCharges, atomInfo);
 146 }
 147
 148 void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality        locality,
 149                                             gmx::ArrayRef<const gmx::RVec> coordinates)
 150 {
 151     wallcycle_start(wcycle_, WallCycleCounter::NbXFBufOps);
 152     wallcycle_sub_start(wcycle_, WallCycleSubCounter::NBXBufOps);
 153
 154     nbnxn_atomdata_copy_x_to_nbat_x(
 155             pairSearch_->gridSet(), locality, as_rvec_array(coordinates.data()), nbat.get());
 156
 157     wallcycle_sub_stop(wcycle_, WallCycleSubCounter::NBXBufOps);
 158     wallcycle_stop(wcycle_, WallCycleCounter::NbXFBufOps);
 159 }
 160
 161 void nonbonded_verlet_t::convertCoordinatesGpu(const gmx::AtomLocality locality,
 162                                                DeviceBuffer<gmx::RVec> d_x,
 163                                                GpuEventSynchronizer*   xReadyOnDevice)
 164 {
 165     wallcycle_start(wcycle_, WallCycleCounter::LaunchGpu);
 166     wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuNBXBufOps);
 167
 168     nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, gpu_nbv, d_x, xReadyOnDevice);
 169
 170     wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuNBXBufOps);
 171     wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
 172 }
 173
 174 gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
 175 {
 176     return pairSearch_->gridSet().cells();
 177 }
 178
 179 void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality  locality,
 180                                                   gmx::ArrayRef<gmx::RVec> force)
 181 {
 182
 183     /* Skip the reduction if there was no short-range GPU work to do
 184      * (either NB or both NB and bonded work). */
 185     if (!pairlistIsSimple() && !Nbnxm::haveGpuShortRangeWork(gpu_nbv, atomToInteractionLocality(locality)))
 186     {
 187         return;
 188     }
 189
 190     wallcycle_start(wcycle_, WallCycleCounter::NbXFBufOps);
 191     wallcycle_sub_start(wcycle_, WallCycleSubCounter::NBFBufOps);
 192
 193     reduceForces(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()));
 194
 195     wallcycle_sub_stop(wcycle_, WallCycleSubCounter::NBFBufOps);
 196     wallcycle_stop(wcycle_, WallCycleCounter::NbXFBufOps);
 197 }
 198
 199 int nonbonded_verlet_t::getNumAtoms(const gmx::AtomLocality locality) const
 200 {
 201     int numAtoms = 0;
 202     switch (locality)
 203     {
 204         case gmx::AtomLocality::All: numAtoms = pairSearch_->gridSet().numRealAtomsTotal(); break;
 205         case gmx::AtomLocality::Local: numAtoms = pairSearch_->gridSet().numRealAtomsLocal(); break;
 206         case gmx::AtomLocality::NonLocal:
 207             numAtoms = pairSearch_->gridSet().numRealAtomsTotal()
 208                        - pairSearch_->gridSet().numRealAtomsLocal();
 209             break;
 210         case gmx::AtomLocality::Count:
 211             GMX_ASSERT(false, "Count is invalid locality specifier");
 212             break;
 213     }
 214     return numAtoms;
 215 }
 216
 217 real nonbonded_verlet_t::pairlistInnerRadius() const
 218 {
 219     return pairlistSets_->params().rlistInner;
 220 }
 221
 222 real nonbonded_verlet_t::pairlistOuterRadius() const
 223 {
 224     return pairlistSets_->params().rlistOuter;
 225 }
 226
 227 void nonbonded_verlet_t::changePairlistRadii(real rlistOuter, real rlistInner) const
 228 {
 229     pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
 230 }
 231
 232 void nonbonded_verlet_t::setupGpuShortRangeWork(const gmx::ListedForcesGpu*    listedForcesGpu,
 233                                                 const gmx::InteractionLocality iLocality) const
 234 {
 235     if (useGpu() && !emulateGpu())
 236     {
 237         Nbnxm::setupGpuShortRangeWork(gpu_nbv, listedForcesGpu, iLocality);
 238     }
 239 }
 240
 241 void nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu() const
 242 {
 243     Nbnxm::nbnxn_gpu_init_x_to_nbat_x(pairSearch_->gridSet(), gpu_nbv);
 244 }
 245
 246 bool buildSupportsNonbondedOnGpu(std::string* error)
 247 {
 248     gmx::MessageStringCollector errorReasons;
 249     // Before changing the prefix string, make sure that it is not searched for in regression tests.
 250     errorReasons.startContext("Nonbonded interactions on GPUs are not supported in:");
 251     errorReasons.appendIf(GMX_DOUBLE, "Double precision build of GROMACS");
 252     errorReasons.appendIf(!GMX_GPU, "Non-GPU build of GROMACS.");
 253     errorReasons.finishContext();
 254     if (error != nullptr)
 255     {
 256         *error = errorReasons.toString();
 257     }
 258     return errorReasons.isEmpty();
 259 }
 260
 261 /*! \endcond */