src/gromacs/ewald/pme.cu

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2016,2017, by the GROMACS development team, led by
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  35
  36 /*! \internal \file
  37  * \brief This file contains internal CUDA function implementations
  38  * for performing the PME calculations on GPU.
  39  *
  40  * \author Aleksei Iupinov <a.yupinov@gmail.com>
  41  */
  42
  43 #include "gmxpre.h"
  44
  45 #include <cmath>
  46
  47 /* The rest */
  48 #include "pme.h"
  49
  50 #include "gromacs/gpu_utils/cudautils.cuh"
  51 #include "gromacs/gpu_utils/pmalloc_cuda.h"
  52 #include "gromacs/utility/gmxassert.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 #include "pme.cuh"
  56 #include "pme-3dfft.cuh"
  57 #include "pme-grid.h"
  58
  59 int pme_gpu_get_atom_data_alignment(const PmeGpu *pmeGpu)
  60 {
  61     const int order = pmeGpu->common->pme_order;
  62     GMX_ASSERT(order > 0, "Invalid PME order");
  63     return PME_ATOM_DATA_ALIGNMENT;
  64 }
  65
  66 int pme_gpu_get_atoms_per_warp(const PmeGpu *pmeGpu)
  67 {
  68     const int order = pmeGpu->common->pme_order;
  69     GMX_ASSERT(order > 0, "Invalid PME order");
  70     return PME_SPREADGATHER_ATOMS_PER_WARP;
  71 }
  72
  73 void pme_gpu_synchronize(const PmeGpu *pmeGpu)
  74 {
  75     cudaError_t stat = cudaStreamSynchronize(pmeGpu->archSpecific->pmeStream);
  76     CU_RET_ERR(stat, "Failed to synchronize the PME GPU stream!");
  77 }
  78
  79 void pme_gpu_alloc_energy_virial(const PmeGpu *pmeGpu)
  80 {
  81     const size_t energyAndVirialSize = c_virialAndEnergyCount * sizeof(float);
  82     cudaError_t  stat                = cudaMalloc((void **)&pmeGpu->kernelParams->constants.d_virialAndEnergy, energyAndVirialSize);
  83     CU_RET_ERR(stat, "cudaMalloc failed on PME energy and virial");
  84     pmalloc((void **)&pmeGpu->staging.h_virialAndEnergy, energyAndVirialSize);
  85 }
  86
  87 void pme_gpu_free_energy_virial(PmeGpu *pmeGpu)
  88 {
  89     cudaError_t stat = cudaFree(pmeGpu->kernelParams->constants.d_virialAndEnergy);
  90     CU_RET_ERR(stat, "cudaFree failed on PME energy and virial");
  91     pmeGpu->kernelParams->constants.d_virialAndEnergy = nullptr;
  92     pfree(pmeGpu->staging.h_virialAndEnergy);
  93     pmeGpu->staging.h_virialAndEnergy = nullptr;
  94 }
  95
  96 void pme_gpu_clear_energy_virial(const PmeGpu *pmeGpu)
  97 {
  98     cudaError_t stat = cudaMemsetAsync(pmeGpu->kernelParams->constants.d_virialAndEnergy, 0,
  99                                        c_virialAndEnergyCount * sizeof(float), pmeGpu->archSpecific->pmeStream);
 100     CU_RET_ERR(stat, "PME energy/virial cudaMemsetAsync error");
 101 }
 102
 103 void pme_gpu_realloc_and_copy_bspline_values(const PmeGpu *pmeGpu)
 104 {
 105     const int splineValuesOffset[DIM] = {
 106         0,
 107         pmeGpu->kernelParams->grid.realGridSize[XX],
 108         pmeGpu->kernelParams->grid.realGridSize[XX] + pmeGpu->kernelParams->grid.realGridSize[YY]
 109     };
 110     memcpy((void *)&pmeGpu->kernelParams->grid.splineValuesOffset, &splineValuesOffset, sizeof(splineValuesOffset));
 111
 112     const int newSplineValuesSize = pmeGpu->kernelParams->grid.realGridSize[XX] +
 113         pmeGpu->kernelParams->grid.realGridSize[YY] +
 114         pmeGpu->kernelParams->grid.realGridSize[ZZ];
 115     const bool shouldRealloc = (newSplineValuesSize > pmeGpu->archSpecific->splineValuesSize);
 116     cu_realloc_buffered((void **)&pmeGpu->kernelParams->grid.d_splineModuli, nullptr, sizeof(float),
 117                         &pmeGpu->archSpecific->splineValuesSize, &pmeGpu->archSpecific->splineValuesSizeAlloc, newSplineValuesSize, pmeGpu->archSpecific->pmeStream, true);
 118     if (shouldRealloc)
 119     {
 120         /* Reallocate the host buffer */
 121         pfree(pmeGpu->staging.h_splineModuli);
 122         pmalloc((void **)&pmeGpu->staging.h_splineModuli, newSplineValuesSize * sizeof(float));
 123     }
 124     for (int i = 0; i < DIM; i++)
 125     {
 126         memcpy(pmeGpu->staging.h_splineModuli + splineValuesOffset[i], pmeGpu->common->bsp_mod[i].data(), pmeGpu->common->bsp_mod[i].size() * sizeof(float));
 127     }
 128     /* TODO: pin original buffer instead! */
 129     cu_copy_H2D(pmeGpu->kernelParams->grid.d_splineModuli, pmeGpu->staging.h_splineModuli,
 130                 newSplineValuesSize * sizeof(float), pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 131 }
 132
 133 void pme_gpu_free_bspline_values(const PmeGpu *pmeGpu)
 134 {
 135     pfree(pmeGpu->staging.h_splineModuli);
 136     cu_free_buffered(pmeGpu->kernelParams->grid.d_splineModuli, &pmeGpu->archSpecific->splineValuesSize,
 137                      &pmeGpu->archSpecific->splineValuesSizeAlloc);
 138 }
 139
 140 void pme_gpu_realloc_forces(PmeGpu *pmeGpu)
 141 {
 142     const size_t newForcesSize = pmeGpu->nAtomsAlloc * DIM;
 143     GMX_ASSERT(newForcesSize > 0, "Bad number of atoms in PME GPU");
 144     cu_realloc_buffered((void **)&pmeGpu->kernelParams->atoms.d_forces, nullptr, sizeof(float),
 145                         &pmeGpu->archSpecific->forcesSize, &pmeGpu->archSpecific->forcesSizeAlloc, newForcesSize, pmeGpu->archSpecific->pmeStream, true);
 146     pmeGpu->staging.h_forces.reserve(pmeGpu->nAtomsAlloc);
 147     pmeGpu->staging.h_forces.resize(pmeGpu->kernelParams->atoms.nAtoms);
 148 }
 149
 150 void pme_gpu_free_forces(const PmeGpu *pmeGpu)
 151 {
 152     cu_free_buffered(pmeGpu->kernelParams->atoms.d_forces, &pmeGpu->archSpecific->forcesSize, &pmeGpu->archSpecific->forcesSizeAlloc);
 153 }
 154
 155 void pme_gpu_copy_input_forces(PmeGpu *pmeGpu)
 156 {
 157     const size_t forcesSize = DIM * pmeGpu->kernelParams->atoms.nAtoms * sizeof(float);
 158     GMX_ASSERT(forcesSize > 0, "Bad number of atoms in PME GPU");
 159     cu_copy_H2D(pmeGpu->kernelParams->atoms.d_forces, pmeGpu->staging.h_forces.data(), forcesSize, pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 160 }
 161
 162 void pme_gpu_copy_output_forces(PmeGpu *pmeGpu)
 163 {
 164     const size_t forcesSize   = DIM * pmeGpu->kernelParams->atoms.nAtoms * sizeof(float);
 165     GMX_ASSERT(forcesSize > 0, "Bad number of atoms in PME GPU");
 166     cu_copy_D2H(pmeGpu->staging.h_forces.data(), pmeGpu->kernelParams->atoms.d_forces, forcesSize, pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 167 }
 168
 169 void pme_gpu_realloc_coordinates(const PmeGpu *pmeGpu)
 170 {
 171     const size_t newCoordinatesSize = pmeGpu->nAtomsAlloc * DIM;
 172     GMX_ASSERT(newCoordinatesSize > 0, "Bad number of atoms in PME GPU");
 173     cu_realloc_buffered((void **)&pmeGpu->kernelParams->atoms.d_coordinates, nullptr, sizeof(float),
 174                         &pmeGpu->archSpecific->coordinatesSize, &pmeGpu->archSpecific->coordinatesSizeAlloc, newCoordinatesSize, pmeGpu->archSpecific->pmeStream, true);
 175     if (c_usePadding)
 176     {
 177         const size_t paddingIndex = DIM * pmeGpu->kernelParams->atoms.nAtoms;
 178         const size_t paddingCount = DIM * pmeGpu->nAtomsAlloc - paddingIndex;
 179         if (paddingCount > 0)
 180         {
 181             cudaError_t stat = cudaMemsetAsync(pmeGpu->kernelParams->atoms.d_coordinates + paddingIndex, 0, paddingCount * sizeof(float), pmeGpu->archSpecific->pmeStream);
 182             CU_RET_ERR(stat, "PME failed to clear the padded coordinates");
 183         }
 184     }
 185 }
 186
 187 void pme_gpu_copy_input_coordinates(const PmeGpu *pmeGpu, const rvec *h_coordinates)
 188 {
 189     GMX_ASSERT(h_coordinates, "Bad host-side coordinate buffer in PME GPU");
 190 #if GMX_DOUBLE
 191     GMX_RELEASE_ASSERT(false, "Only single precision is supported");
 192     GMX_UNUSED_VALUE(h_coordinates);
 193 #else
 194     cu_copy_H2D(pmeGpu->kernelParams->atoms.d_coordinates, const_cast<rvec *>(h_coordinates),
 195                 pmeGpu->kernelParams->atoms.nAtoms * sizeof(rvec), pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 196 #endif
 197 }
 198
 199 void pme_gpu_free_coordinates(const PmeGpu *pmeGpu)
 200 {
 201     cu_free_buffered(pmeGpu->kernelParams->atoms.d_coordinates, &pmeGpu->archSpecific->coordinatesSize, &pmeGpu->archSpecific->coordinatesSizeAlloc);
 202 }
 203
 204 void pme_gpu_realloc_and_copy_input_coefficients(const PmeGpu *pmeGpu, const float *h_coefficients)
 205 {
 206     GMX_ASSERT(h_coefficients, "Bad host-side charge buffer in PME GPU");
 207     const size_t newCoefficientsSize = pmeGpu->nAtomsAlloc;
 208     GMX_ASSERT(newCoefficientsSize > 0, "Bad number of atoms in PME GPU");
 209     cu_realloc_buffered((void **)&pmeGpu->kernelParams->atoms.d_coefficients, nullptr, sizeof(float),
 210                         &pmeGpu->archSpecific->coefficientsSize, &pmeGpu->archSpecific->coefficientsSizeAlloc,
 211                         newCoefficientsSize, pmeGpu->archSpecific->pmeStream, true);
 212     cu_copy_H2D(pmeGpu->kernelParams->atoms.d_coefficients, const_cast<float *>(h_coefficients),
 213                 pmeGpu->kernelParams->atoms.nAtoms * sizeof(float), pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 214     if (c_usePadding)
 215     {
 216         const size_t paddingIndex = pmeGpu->kernelParams->atoms.nAtoms;
 217         const size_t paddingCount = pmeGpu->nAtomsAlloc - paddingIndex;
 218         if (paddingCount > 0)
 219         {
 220             cudaError_t stat = cudaMemsetAsync(pmeGpu->kernelParams->atoms.d_coefficients + paddingIndex, 0, paddingCount * sizeof(float), pmeGpu->archSpecific->pmeStream);
 221             CU_RET_ERR(stat, "PME failed to clear the padded charges");
 222         }
 223     }
 224 }
 225
 226 void pme_gpu_free_coefficients(const PmeGpu *pmeGpu)
 227 {
 228     cu_free_buffered(pmeGpu->kernelParams->atoms.d_coefficients, &pmeGpu->archSpecific->coefficientsSize, &pmeGpu->archSpecific->coefficientsSizeAlloc);
 229 }
 230
 231 void pme_gpu_realloc_spline_data(const PmeGpu *pmeGpu)
 232 {
 233     const int    order             = pmeGpu->common->pme_order;
 234     const int    alignment         = pme_gpu_get_atoms_per_warp(pmeGpu);
 235     const size_t nAtomsPadded      = ((pmeGpu->nAtomsAlloc + alignment - 1) / alignment) * alignment;
 236     const int    newSplineDataSize = DIM * order * nAtomsPadded;
 237     GMX_ASSERT(newSplineDataSize > 0, "Bad number of atoms in PME GPU");
 238     /* Two arrays of the same size */
 239     const bool shouldRealloc        = (newSplineDataSize > pmeGpu->archSpecific->splineDataSize);
 240     int        currentSizeTemp      = pmeGpu->archSpecific->splineDataSize;
 241     int        currentSizeTempAlloc = pmeGpu->archSpecific->splineDataSizeAlloc;
 242     cu_realloc_buffered((void **)&pmeGpu->kernelParams->atoms.d_theta, nullptr, sizeof(float),
 243                         &currentSizeTemp, &currentSizeTempAlloc, newSplineDataSize, pmeGpu->archSpecific->pmeStream, true);
 244     cu_realloc_buffered((void **)&pmeGpu->kernelParams->atoms.d_dtheta, nullptr, sizeof(float),
 245                         &pmeGpu->archSpecific->splineDataSize, &pmeGpu->archSpecific->splineDataSizeAlloc, newSplineDataSize, pmeGpu->archSpecific->pmeStream, true);
 246     // the host side reallocation
 247     if (shouldRealloc)
 248     {
 249         pfree(pmeGpu->staging.h_theta);
 250         pmalloc((void **)&pmeGpu->staging.h_theta, newSplineDataSize * sizeof(float));
 251         pfree(pmeGpu->staging.h_dtheta);
 252         pmalloc((void **)&pmeGpu->staging.h_dtheta, newSplineDataSize * sizeof(float));
 253     }
 254 }
 255
 256 void pme_gpu_free_spline_data(const PmeGpu *pmeGpu)
 257 {
 258     /* Two arrays of the same size */
 259     cu_free_buffered(pmeGpu->kernelParams->atoms.d_theta);
 260     cu_free_buffered(pmeGpu->kernelParams->atoms.d_dtheta, &pmeGpu->archSpecific->splineDataSize, &pmeGpu->archSpecific->splineDataSizeAlloc);
 261     pfree(pmeGpu->staging.h_theta);
 262     pfree(pmeGpu->staging.h_dtheta);
 263 }
 264
 265 void pme_gpu_realloc_grid_indices(const PmeGpu *pmeGpu)
 266 {
 267     const size_t newIndicesSize = DIM * pmeGpu->nAtomsAlloc;
 268     GMX_ASSERT(newIndicesSize > 0, "Bad number of atoms in PME GPU");
 269     cu_realloc_buffered((void **)&pmeGpu->kernelParams->atoms.d_gridlineIndices, nullptr, sizeof(int),
 270                         &pmeGpu->archSpecific->gridlineIndicesSize, &pmeGpu->archSpecific->gridlineIndicesSizeAlloc, newIndicesSize, pmeGpu->archSpecific->pmeStream, true);
 271     pfree(pmeGpu->staging.h_gridlineIndices);
 272     pmalloc((void **)&pmeGpu->staging.h_gridlineIndices, newIndicesSize * sizeof(int));
 273 }
 274
 275 void pme_gpu_free_grid_indices(const PmeGpu *pmeGpu)
 276 {
 277     cu_free_buffered(pmeGpu->kernelParams->atoms.d_gridlineIndices, &pmeGpu->archSpecific->gridlineIndicesSize, &pmeGpu->archSpecific->gridlineIndicesSizeAlloc);
 278     pfree(pmeGpu->staging.h_gridlineIndices);
 279 }
 280
 281 void pme_gpu_realloc_grids(PmeGpu *pmeGpu)
 282 {
 283     auto     *kernelParamsPtr = pmeGpu->kernelParams.get();
 284     const int newRealGridSize = kernelParamsPtr->grid.realGridSizePadded[XX] *
 285         kernelParamsPtr->grid.realGridSizePadded[YY] *
 286         kernelParamsPtr->grid.realGridSizePadded[ZZ];
 287     const int newComplexGridSize = kernelParamsPtr->grid.complexGridSizePadded[XX] *
 288         kernelParamsPtr->grid.complexGridSizePadded[YY] *
 289         kernelParamsPtr->grid.complexGridSizePadded[ZZ] * 2;
 290     // Multiplied by 2 because we count complex grid size for complex numbers, but all allocations/pointers are float
 291     if (pmeGpu->archSpecific->performOutOfPlaceFFT)
 292     {
 293         /* 2 separate grids */
 294         cu_realloc_buffered((void **)&kernelParamsPtr->grid.d_fourierGrid, nullptr, sizeof(float),
 295                             &pmeGpu->archSpecific->complexGridSize, &pmeGpu->archSpecific->complexGridSizeAlloc,
 296                             newComplexGridSize, pmeGpu->archSpecific->pmeStream, true);
 297         cu_realloc_buffered((void **)&kernelParamsPtr->grid.d_realGrid, nullptr, sizeof(float),
 298                             &pmeGpu->archSpecific->realGridSize, &pmeGpu->archSpecific->realGridSizeAlloc,
 299                             newRealGridSize, pmeGpu->archSpecific->pmeStream, true);
 300     }
 301     else
 302     {
 303         /* A single buffer so that any grid will fit */
 304         const int newGridsSize = std::max(newRealGridSize, newComplexGridSize);
 305         cu_realloc_buffered((void **)&kernelParamsPtr->grid.d_realGrid, nullptr, sizeof(float),
 306                             &pmeGpu->archSpecific->realGridSize, &pmeGpu->archSpecific->realGridSizeAlloc,
 307                             newGridsSize, pmeGpu->archSpecific->pmeStream, true);
 308         kernelParamsPtr->grid.d_fourierGrid   = kernelParamsPtr->grid.d_realGrid;
 309         pmeGpu->archSpecific->complexGridSize = pmeGpu->archSpecific->realGridSize;
 310         // the size might get used later for copying the grid
 311     }
 312 }
 313
 314 void pme_gpu_free_grids(const PmeGpu *pmeGpu)
 315 {
 316     if (pmeGpu->archSpecific->performOutOfPlaceFFT)
 317     {
 318         cu_free_buffered(pmeGpu->kernelParams->grid.d_fourierGrid);
 319     }
 320     cu_free_buffered(pmeGpu->kernelParams->grid.d_realGrid,
 321                      &pmeGpu->archSpecific->realGridSize, &pmeGpu->archSpecific->realGridSizeAlloc);
 322 }
 323
 324 void pme_gpu_clear_grids(const PmeGpu *pmeGpu)
 325 {
 326     cudaError_t stat = cudaMemsetAsync(pmeGpu->kernelParams->grid.d_realGrid, 0,
 327                                        pmeGpu->archSpecific->realGridSize * sizeof(float), pmeGpu->archSpecific->pmeStream);
 328     /* Should the complex grid be cleared in some weird case? */
 329     CU_RET_ERR(stat, "cudaMemsetAsync on the PME grid error");
 330 }
 331
 332 void pme_gpu_realloc_and_copy_fract_shifts(PmeGpu *pmeGpu)
 333 {
 334     pme_gpu_free_fract_shifts(pmeGpu);
 335
 336     auto        *kernelParamsPtr = pmeGpu->kernelParams.get();
 337
 338     const int    nx                  = kernelParamsPtr->grid.realGridSize[XX];
 339     const int    ny                  = kernelParamsPtr->grid.realGridSize[YY];
 340     const int    nz                  = kernelParamsPtr->grid.realGridSize[ZZ];
 341     const int    cellCount           = c_pmeNeighborUnitcellCount;
 342     const int    gridDataOffset[DIM] = {0, cellCount * nx, cellCount * (nx + ny)};
 343
 344     memcpy(kernelParamsPtr->grid.tablesOffsets, &gridDataOffset, sizeof(gridDataOffset));
 345
 346     const int    newFractShiftsSize  = cellCount * (nx + ny + nz);
 347
 348     initParamLookupTable(kernelParamsPtr->grid.d_fractShiftsTable,
 349                          kernelParamsPtr->fractShiftsTableTexture,
 350                          &pme_gpu_get_fract_shifts_texref(),
 351                          pmeGpu->common->fsh.data(),
 352                          newFractShiftsSize,
 353                          pmeGpu->deviceInfo);
 354
 355     initParamLookupTable(kernelParamsPtr->grid.d_gridlineIndicesTable,
 356                          kernelParamsPtr->gridlineIndicesTableTexture,
 357                          &pme_gpu_get_gridline_texref(),
 358                          pmeGpu->common->nn.data(),
 359                          newFractShiftsSize,
 360                          pmeGpu->deviceInfo);
 361 }
 362
 363 void pme_gpu_free_fract_shifts(const PmeGpu *pmeGpu)
 364 {
 365     auto *kernelParamsPtr = pmeGpu->kernelParams.get();
 366     destroyParamLookupTable(kernelParamsPtr->grid.d_fractShiftsTable,
 367                             kernelParamsPtr->fractShiftsTableTexture,
 368                             &pme_gpu_get_fract_shifts_texref(),
 369                             pmeGpu->deviceInfo);
 370     destroyParamLookupTable(kernelParamsPtr->grid.d_gridlineIndicesTable,
 371                             kernelParamsPtr->gridlineIndicesTableTexture,
 372                             &pme_gpu_get_gridline_texref(),
 373                             pmeGpu->deviceInfo);
 374 }
 375
 376 bool pme_gpu_stream_query(const PmeGpu *pmeGpu)
 377 {
 378     return haveStreamTasksCompleted(pmeGpu->archSpecific->pmeStream);
 379 }
 380
 381 void pme_gpu_copy_input_gather_grid(const PmeGpu *pmeGpu, float *h_grid)
 382 {
 383     const size_t gridSize = pmeGpu->archSpecific->realGridSize * sizeof(float);
 384     cu_copy_H2D(pmeGpu->kernelParams->grid.d_realGrid, h_grid, gridSize, pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 385 }
 386
 387 void pme_gpu_copy_output_spread_grid(const PmeGpu *pmeGpu, float *h_grid)
 388 {
 389     const size_t gridSize = pmeGpu->archSpecific->realGridSize * sizeof(float);
 390     cu_copy_D2H(h_grid, pmeGpu->kernelParams->grid.d_realGrid, gridSize, pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 391     cudaError_t  stat = cudaEventRecord(pmeGpu->archSpecific->syncSpreadGridD2H, pmeGpu->archSpecific->pmeStream);
 392     CU_RET_ERR(stat, "PME spread grid sync event record failure");
 393 }
 394
 395 void pme_gpu_copy_output_spread_atom_data(const PmeGpu *pmeGpu)
 396 {
 397     const int    alignment       = pme_gpu_get_atoms_per_warp(pmeGpu);
 398     const size_t nAtomsPadded    = ((pmeGpu->nAtomsAlloc + alignment - 1) / alignment) * alignment;
 399     const size_t splinesSize     = DIM * nAtomsPadded * pmeGpu->common->pme_order * sizeof(float);
 400     auto        *kernelParamsPtr = pmeGpu->kernelParams.get();
 401     cu_copy_D2H(pmeGpu->staging.h_dtheta, kernelParamsPtr->atoms.d_dtheta, splinesSize, pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 402     cu_copy_D2H(pmeGpu->staging.h_theta, kernelParamsPtr->atoms.d_theta, splinesSize, pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 403     cu_copy_D2H(pmeGpu->staging.h_gridlineIndices, kernelParamsPtr->atoms.d_gridlineIndices,
 404                 kernelParamsPtr->atoms.nAtoms * DIM * sizeof(int), pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 405 }
 406
 407 void pme_gpu_copy_input_gather_atom_data(const PmeGpu *pmeGpu)
 408 {
 409     const int    alignment       = pme_gpu_get_atoms_per_warp(pmeGpu);
 410     const size_t nAtomsPadded    = ((pmeGpu->nAtomsAlloc + alignment - 1) / alignment) * alignment;
 411     const size_t splinesSize     = DIM * nAtomsPadded * pmeGpu->common->pme_order * sizeof(float);
 412     auto        *kernelParamsPtr = pmeGpu->kernelParams.get();
 413     if (c_usePadding)
 414     {
 415         const size_t gridlineIndicesSizePerAtom = DIM * sizeof(int);
 416         const size_t splineDataSizePerAtom      = pmeGpu->common->pme_order * DIM * sizeof(float);
 417         // TODO: could clear only the padding and not the whole thing, but this is a test-exclusive code anyway
 418         CU_RET_ERR(cudaMemsetAsync(kernelParamsPtr->atoms.d_gridlineIndices, 0, pmeGpu->nAtomsAlloc * gridlineIndicesSizePerAtom, pmeGpu->archSpecific->pmeStream),
 419                    "PME failed to clear the gridline indices");
 420         CU_RET_ERR(cudaMemsetAsync(kernelParamsPtr->atoms.d_dtheta, 0, pmeGpu->nAtomsAlloc * splineDataSizePerAtom, pmeGpu->archSpecific->pmeStream),
 421                    "PME failed to clear the spline derivatives");
 422         CU_RET_ERR(cudaMemsetAsync(kernelParamsPtr->atoms.d_theta, 0, pmeGpu->nAtomsAlloc * splineDataSizePerAtom, pmeGpu->archSpecific->pmeStream),
 423                    "PME failed to clear the spline values");
 424     }
 425     cu_copy_H2D(kernelParamsPtr->atoms.d_dtheta, pmeGpu->staging.h_dtheta, splinesSize, pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 426     cu_copy_H2D(kernelParamsPtr->atoms.d_theta, pmeGpu->staging.h_theta, splinesSize, pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 427     cu_copy_H2D(kernelParamsPtr->atoms.d_gridlineIndices, pmeGpu->staging.h_gridlineIndices,
 428                 kernelParamsPtr->atoms.nAtoms * DIM * sizeof(int), pmeGpu->settings.transferKind, pmeGpu->archSpecific->pmeStream);
 429 }
 430
 431 void pme_gpu_sync_spread_grid(const PmeGpu *pmeGpu)
 432 {
 433     cudaError_t stat = cudaEventSynchronize(pmeGpu->archSpecific->syncSpreadGridD2H);
 434     CU_RET_ERR(stat, "Error while waiting for the PME GPU spread grid to be copied to the host");
 435 }
 436
 437 void pme_gpu_init_internal(PmeGpu *pmeGpu)
 438 {
 439     /* Allocate the target-specific structures */
 440     pmeGpu->archSpecific.reset(new PmeGpuSpecific());
 441     pmeGpu->kernelParams.reset(new PmeGpuKernelParams());
 442
 443     pmeGpu->archSpecific->performOutOfPlaceFFT = true;
 444     /* This should give better performance, according to the cuFFT documentation.
 445      * The performance seems to be the same though.
 446      * TODO: PME could also try to pick up nice grid sizes (with factors of 2, 3, 5, 7).
 447      */
 448
 449     /* WARNING: CUDA timings are incorrect with multiple streams.
 450      *          This is the main reason why they are disabled by default.
 451      */
 452     // TODO: Consider turning on by default when we can detect nr of streams.
 453     pmeGpu->archSpecific->useTiming = (getenv("GMX_ENABLE_GPU_TIMING") != nullptr);
 454
 455     /* Creating a PME CUDA stream */
 456     cudaError_t stat;
 457     int         highest_priority, lowest_priority;
 458     stat = cudaDeviceGetStreamPriorityRange(&lowest_priority, &highest_priority);
 459     CU_RET_ERR(stat, "PME cudaDeviceGetStreamPriorityRange failed");
 460     stat = cudaStreamCreateWithPriority(&pmeGpu->archSpecific->pmeStream,
 461                                         cudaStreamDefault, //cudaStreamNonBlocking,
 462                                         highest_priority);
 463     CU_RET_ERR(stat, "cudaStreamCreateWithPriority on the PME stream failed");
 464 }
 465
 466 void pme_gpu_destroy_specific(const PmeGpu *pmeGpu)
 467 {
 468     /* Destroy the CUDA stream */
 469     cudaError_t stat = cudaStreamDestroy(pmeGpu->archSpecific->pmeStream);
 470     CU_RET_ERR(stat, "PME cudaStreamDestroy error");
 471 }
 472
 473 void pme_gpu_init_sync_events(const PmeGpu *pmeGpu)
 474 {
 475     const auto  eventFlags = cudaEventDisableTiming;
 476     CU_RET_ERR(cudaEventCreateWithFlags(&pmeGpu->archSpecific->syncSpreadGridD2H, eventFlags), "cudaEventCreate on syncSpreadGridD2H failed");
 477 }
 478
 479 void pme_gpu_destroy_sync_events(const PmeGpu *pmeGpu)
 480 {
 481     CU_RET_ERR(cudaEventDestroy(pmeGpu->archSpecific->syncSpreadGridD2H), "cudaEventDestroy failed on syncSpreadGridD2H");
 482 }
 483
 484 void pme_gpu_reinit_3dfft(const PmeGpu *pmeGpu)
 485 {
 486     if (pme_gpu_performs_FFT(pmeGpu))
 487     {
 488         pmeGpu->archSpecific->fftSetup.resize(0);
 489         for (int i = 0; i < pmeGpu->common->ngrids; i++)
 490         {
 491             pmeGpu->archSpecific->fftSetup.push_back(std::unique_ptr<GpuParallel3dFft>(new GpuParallel3dFft(pmeGpu)));
 492         }
 493     }
 494 }
 495
 496 void pme_gpu_destroy_3dfft(const PmeGpu *pmeGpu)
 497 {
 498     pmeGpu->archSpecific->fftSetup.resize(0);
 499 }