src/gromacs/ewald/pme-gpu-internal.cpp

   1 /*
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   3  *
   4  * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
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  35
  36 /*! \internal \file
  37  *
  38  * \brief This file contains internal function implementations
  39  * for performing the PME calculations on GPU.
  40  *
  41  * Note that this file is compiled as regular C++ source in OpenCL builds, but
  42  * it is treated as CUDA source in CUDA-enabled GPU builds.
  43  *
  44  * \author Aleksei Iupinov <a.yupinov@gmail.com>
  45  * \ingroup module_ewald
  46  */
  47
  48 #include "gmxpre.h"
  49
  50 #include "pme-gpu-internal.h"
  51
  52 #include "config.h"
  53
  54 #include <list>
  55 #include <string>
  56
  57 #include "gromacs/compat/make_unique.h"
  58 #include "gromacs/ewald/ewald-utils.h"
  59 #include "gromacs/gpu_utils/gpu_utils.h"
  60 #include "gromacs/math/invertmatrix.h"
  61 #include "gromacs/math/units.h"
  62 #include "gromacs/timing/gpu_timing.h"
  63 #include "gromacs/utility/exceptions.h"
  64 #include "gromacs/utility/fatalerror.h"
  65 #include "gromacs/utility/gmxassert.h"
  66 #include "gromacs/utility/logger.h"
  67 #include "gromacs/utility/stringutil.h"
  68
  69 #if GMX_GPU == GMX_GPU_CUDA
  70 #include "gromacs/gpu_utils/pmalloc_cuda.h"
  71
  72 #include "pme.cuh"
  73 #elif GMX_GPU == GMX_GPU_OPENCL
  74 #include "gromacs/gpu_utils/gmxopencl.h"
  75 #endif
  76
  77 #include "gromacs/ewald/pme.h"
  78
  79 #include "pme-gpu-3dfft.h"
  80 #include "pme-gpu-constants.h"
  81 #include "pme-gpu-program-impl.h"
  82 #include "pme-gpu-timings.h"
  83 #include "pme-gpu-types.h"
  84 #include "pme-gpu-types-host.h"
  85 #include "pme-gpu-types-host-impl.h"
  86 #include "pme-gpu-utils.h"
  87 #include "pme-grid.h"
  88 #include "pme-internal.h"
  89
  90 /*! \internal \brief
  91  * Wrapper for getting a pointer to the plain C++ part of the GPU kernel parameters structure.
  92  *
  93  * \param[in] pmeGpu  The PME GPU structure.
  94  * \returns The pointer to the kernel parameters.
  95  */
  96 static PmeGpuKernelParamsBase *pme_gpu_get_kernel_params_base_ptr(const PmeGpu *pmeGpu)
  97 {
  98     // reinterpret_cast is needed because the derived CUDA structure is not known in this file
  99     auto *kernelParamsPtr = reinterpret_cast<PmeGpuKernelParamsBase *>(pmeGpu->kernelParams.get());
 100     return kernelParamsPtr;
 101 }
 102
 103 int pme_gpu_get_atom_data_alignment(const PmeGpu * /*unused*/)
 104 {
 105     //TODO: this can be simplified, as PME_ATOM_DATA_ALIGNMENT is now constant
 106     return PME_ATOM_DATA_ALIGNMENT;
 107 }
 108
 109 int pme_gpu_get_atoms_per_warp(const PmeGpu *pmeGpu)
 110 {
 111     const int order = pmeGpu->common->pme_order;
 112     GMX_ASSERT(order > 0, "Invalid PME order");
 113     return pmeGpu->programHandle_->impl_->warpSize / PME_SPREADGATHER_THREADS_PER_ATOM;
 114 }
 115
 116 void pme_gpu_synchronize(const PmeGpu *pmeGpu)
 117 {
 118     gpuStreamSynchronize(pmeGpu->archSpecific->pmeStream);
 119 }
 120
 121 void pme_gpu_alloc_energy_virial(PmeGpu *pmeGpu)
 122 {
 123     const size_t energyAndVirialSize = c_virialAndEnergyCount * sizeof(float);
 124     allocateDeviceBuffer(&pmeGpu->kernelParams->constants.d_virialAndEnergy, c_virialAndEnergyCount, pmeGpu->archSpecific->context);
 125     pmalloc(reinterpret_cast<void **>(&pmeGpu->staging.h_virialAndEnergy), energyAndVirialSize);
 126 }
 127
 128 void pme_gpu_free_energy_virial(PmeGpu *pmeGpu)
 129 {
 130     freeDeviceBuffer(&pmeGpu->kernelParams->constants.d_virialAndEnergy);
 131     pfree(pmeGpu->staging.h_virialAndEnergy);
 132     pmeGpu->staging.h_virialAndEnergy = nullptr;
 133 }
 134
 135 void pme_gpu_clear_energy_virial(const PmeGpu *pmeGpu)
 136 {
 137     clearDeviceBufferAsync(&pmeGpu->kernelParams->constants.d_virialAndEnergy, 0,
 138                            c_virialAndEnergyCount, pmeGpu->archSpecific->pmeStream);
 139 }
 140
 141 void pme_gpu_realloc_and_copy_bspline_values(PmeGpu *pmeGpu)
 142 {
 143     const int splineValuesOffset[DIM] = {
 144         0,
 145         pmeGpu->kernelParams->grid.realGridSize[XX],
 146         pmeGpu->kernelParams->grid.realGridSize[XX] + pmeGpu->kernelParams->grid.realGridSize[YY]
 147     };
 148     memcpy(&pmeGpu->kernelParams->grid.splineValuesOffset, &splineValuesOffset, sizeof(splineValuesOffset));
 149
 150     const int newSplineValuesSize = pmeGpu->kernelParams->grid.realGridSize[XX] +
 151         pmeGpu->kernelParams->grid.realGridSize[YY] +
 152         pmeGpu->kernelParams->grid.realGridSize[ZZ];
 153     const bool shouldRealloc = (newSplineValuesSize > pmeGpu->archSpecific->splineValuesSize);
 154     reallocateDeviceBuffer(&pmeGpu->kernelParams->grid.d_splineModuli, newSplineValuesSize,
 155                            &pmeGpu->archSpecific->splineValuesSize, &pmeGpu->archSpecific->splineValuesSizeAlloc, pmeGpu->archSpecific->context);
 156     if (shouldRealloc)
 157     {
 158         /* Reallocate the host buffer */
 159         pfree(pmeGpu->staging.h_splineModuli);
 160         pmalloc(reinterpret_cast<void **>(&pmeGpu->staging.h_splineModuli), newSplineValuesSize * sizeof(float));
 161     }
 162     for (int i = 0; i < DIM; i++)
 163     {
 164         memcpy(pmeGpu->staging.h_splineModuli + splineValuesOffset[i], pmeGpu->common->bsp_mod[i].data(), pmeGpu->common->bsp_mod[i].size() * sizeof(float));
 165     }
 166     /* TODO: pin original buffer instead! */
 167     copyToDeviceBuffer(&pmeGpu->kernelParams->grid.d_splineModuli, pmeGpu->staging.h_splineModuli,
 168                        0, newSplineValuesSize,
 169                        pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 170 }
 171
 172 void pme_gpu_free_bspline_values(const PmeGpu *pmeGpu)
 173 {
 174     pfree(pmeGpu->staging.h_splineModuli);
 175     freeDeviceBuffer(&pmeGpu->kernelParams->grid.d_splineModuli);
 176 }
 177
 178 void pme_gpu_realloc_forces(PmeGpu *pmeGpu)
 179 {
 180     const size_t newForcesSize = pmeGpu->nAtomsAlloc * DIM;
 181     GMX_ASSERT(newForcesSize > 0, "Bad number of atoms in PME GPU");
 182     reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_forces, newForcesSize,
 183                            &pmeGpu->archSpecific->forcesSize, &pmeGpu->archSpecific->forcesSizeAlloc, pmeGpu->archSpecific->context);
 184     pmeGpu->staging.h_forces.reserveWithPadding(pmeGpu->nAtomsAlloc);
 185     pmeGpu->staging.h_forces.resizeWithPadding(pmeGpu->kernelParams->atoms.nAtoms);
 186 }
 187
 188 void pme_gpu_free_forces(const PmeGpu *pmeGpu)
 189 {
 190     freeDeviceBuffer(&pmeGpu->kernelParams->atoms.d_forces);
 191 }
 192
 193 void pme_gpu_copy_input_forces(PmeGpu *pmeGpu)
 194 {
 195     GMX_ASSERT(pmeGpu->kernelParams->atoms.nAtoms > 0, "Bad number of atoms in PME GPU");
 196     float *h_forcesFloat = reinterpret_cast<float *>(pmeGpu->staging.h_forces.data());
 197     copyToDeviceBuffer(&pmeGpu->kernelParams->atoms.d_forces, h_forcesFloat,
 198                        0, DIM * pmeGpu->kernelParams->atoms.nAtoms,
 199                        pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 200 }
 201
 202 void pme_gpu_copy_output_forces(PmeGpu *pmeGpu)
 203 {
 204     GMX_ASSERT(pmeGpu->kernelParams->atoms.nAtoms > 0, "Bad number of atoms in PME GPU");
 205     float *h_forcesFloat = reinterpret_cast<float *>(pmeGpu->staging.h_forces.data());
 206     copyFromDeviceBuffer(h_forcesFloat, &pmeGpu->kernelParams->atoms.d_forces,
 207                          0, DIM * pmeGpu->kernelParams->atoms.nAtoms,
 208                          pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 209 }
 210
 211 void pme_gpu_realloc_coordinates(const PmeGpu *pmeGpu)
 212 {
 213     const size_t newCoordinatesSize = pmeGpu->nAtomsAlloc * DIM;
 214     GMX_ASSERT(newCoordinatesSize > 0, "Bad number of atoms in PME GPU");
 215     reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_coordinates, newCoordinatesSize,
 216                            &pmeGpu->archSpecific->coordinatesSize, &pmeGpu->archSpecific->coordinatesSizeAlloc, pmeGpu->archSpecific->context);
 217     if (c_usePadding)
 218     {
 219         const size_t paddingIndex = DIM * pmeGpu->kernelParams->atoms.nAtoms;
 220         const size_t paddingCount = DIM * pmeGpu->nAtomsAlloc - paddingIndex;
 221         if (paddingCount > 0)
 222         {
 223             clearDeviceBufferAsync(&pmeGpu->kernelParams->atoms.d_coordinates, paddingIndex,
 224                                    paddingCount, pmeGpu->archSpecific->pmeStream);
 225         }
 226     }
 227 }
 228
 229 void pme_gpu_copy_input_coordinates(const PmeGpu *pmeGpu, const rvec *h_coordinates)
 230 {
 231     GMX_ASSERT(h_coordinates, "Bad host-side coordinate buffer in PME GPU");
 232 #if GMX_DOUBLE
 233     GMX_RELEASE_ASSERT(false, "Only single precision is supported");
 234     GMX_UNUSED_VALUE(h_coordinates);
 235 #else
 236     const float *h_coordinatesFloat = reinterpret_cast<const float *>(h_coordinates);
 237     copyToDeviceBuffer(&pmeGpu->kernelParams->atoms.d_coordinates, h_coordinatesFloat,
 238                        0, pmeGpu->kernelParams->atoms.nAtoms * DIM,
 239                        pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 240 #endif
 241 }
 242
 243 void pme_gpu_free_coordinates(const PmeGpu *pmeGpu)
 244 {
 245     freeDeviceBuffer(&pmeGpu->kernelParams->atoms.d_coordinates);
 246 }
 247
 248 void pme_gpu_realloc_and_copy_input_coefficients(const PmeGpu *pmeGpu, const float *h_coefficients)
 249 {
 250     GMX_ASSERT(h_coefficients, "Bad host-side charge buffer in PME GPU");
 251     const size_t newCoefficientsSize = pmeGpu->nAtomsAlloc;
 252     GMX_ASSERT(newCoefficientsSize > 0, "Bad number of atoms in PME GPU");
 253     reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_coefficients, newCoefficientsSize,
 254                            &pmeGpu->archSpecific->coefficientsSize, &pmeGpu->archSpecific->coefficientsSizeAlloc, pmeGpu->archSpecific->context);
 255     copyToDeviceBuffer(&pmeGpu->kernelParams->atoms.d_coefficients, const_cast<float *>(h_coefficients),
 256                        0, pmeGpu->kernelParams->atoms.nAtoms,
 257                        pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 258     if (c_usePadding)
 259     {
 260         const size_t paddingIndex = pmeGpu->kernelParams->atoms.nAtoms;
 261         const size_t paddingCount = pmeGpu->nAtomsAlloc - paddingIndex;
 262         if (paddingCount > 0)
 263         {
 264             clearDeviceBufferAsync(&pmeGpu->kernelParams->atoms.d_coefficients, paddingIndex,
 265                                    paddingCount, pmeGpu->archSpecific->pmeStream);
 266         }
 267     }
 268 }
 269
 270 void pme_gpu_free_coefficients(const PmeGpu *pmeGpu)
 271 {
 272     freeDeviceBuffer(&pmeGpu->kernelParams->atoms.d_coefficients);
 273 }
 274
 275 void pme_gpu_realloc_spline_data(PmeGpu *pmeGpu)
 276 {
 277     const int    order             = pmeGpu->common->pme_order;
 278     const int    alignment         = pme_gpu_get_atoms_per_warp(pmeGpu);
 279     const size_t nAtomsPadded      = ((pmeGpu->nAtomsAlloc + alignment - 1) / alignment) * alignment;
 280     const int    newSplineDataSize = DIM * order * nAtomsPadded;
 281     GMX_ASSERT(newSplineDataSize > 0, "Bad number of atoms in PME GPU");
 282     /* Two arrays of the same size */
 283     const bool shouldRealloc        = (newSplineDataSize > pmeGpu->archSpecific->splineDataSize);
 284     int        currentSizeTemp      = pmeGpu->archSpecific->splineDataSize;
 285     int        currentSizeTempAlloc = pmeGpu->archSpecific->splineDataSizeAlloc;
 286     reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_theta, newSplineDataSize,
 287                            &currentSizeTemp, &currentSizeTempAlloc, pmeGpu->archSpecific->context);
 288     reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_dtheta, newSplineDataSize,
 289                            &pmeGpu->archSpecific->splineDataSize, &pmeGpu->archSpecific->splineDataSizeAlloc, pmeGpu->archSpecific->context);
 290     // the host side reallocation
 291     if (shouldRealloc)
 292     {
 293         pfree(pmeGpu->staging.h_theta);
 294         pmalloc(reinterpret_cast<void **>(&pmeGpu->staging.h_theta), newSplineDataSize * sizeof(float));
 295         pfree(pmeGpu->staging.h_dtheta);
 296         pmalloc(reinterpret_cast<void **>(&pmeGpu->staging.h_dtheta), newSplineDataSize * sizeof(float));
 297     }
 298 }
 299
 300 void pme_gpu_free_spline_data(const PmeGpu *pmeGpu)
 301 {
 302     /* Two arrays of the same size */
 303     freeDeviceBuffer(&pmeGpu->kernelParams->atoms.d_theta);
 304     freeDeviceBuffer(&pmeGpu->kernelParams->atoms.d_dtheta);
 305     pfree(pmeGpu->staging.h_theta);
 306     pfree(pmeGpu->staging.h_dtheta);
 307 }
 308
 309 void pme_gpu_realloc_grid_indices(PmeGpu *pmeGpu)
 310 {
 311     const size_t newIndicesSize = DIM * pmeGpu->nAtomsAlloc;
 312     GMX_ASSERT(newIndicesSize > 0, "Bad number of atoms in PME GPU");
 313     reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_gridlineIndices, newIndicesSize,
 314                            &pmeGpu->archSpecific->gridlineIndicesSize, &pmeGpu->archSpecific->gridlineIndicesSizeAlloc, pmeGpu->archSpecific->context);
 315     pfree(pmeGpu->staging.h_gridlineIndices);
 316     pmalloc(reinterpret_cast<void **>(&pmeGpu->staging.h_gridlineIndices), newIndicesSize * sizeof(int));
 317 }
 318
 319 void pme_gpu_free_grid_indices(const PmeGpu *pmeGpu)
 320 {
 321     freeDeviceBuffer(&pmeGpu->kernelParams->atoms.d_gridlineIndices);
 322     pfree(pmeGpu->staging.h_gridlineIndices);
 323 }
 324
 325 void pme_gpu_realloc_grids(PmeGpu *pmeGpu)
 326 {
 327     auto     *kernelParamsPtr = pmeGpu->kernelParams.get();
 328     const int newRealGridSize = kernelParamsPtr->grid.realGridSizePadded[XX] *
 329         kernelParamsPtr->grid.realGridSizePadded[YY] *
 330         kernelParamsPtr->grid.realGridSizePadded[ZZ];
 331     const int newComplexGridSize = kernelParamsPtr->grid.complexGridSizePadded[XX] *
 332         kernelParamsPtr->grid.complexGridSizePadded[YY] *
 333         kernelParamsPtr->grid.complexGridSizePadded[ZZ] * 2;
 334     // Multiplied by 2 because we count complex grid size for complex numbers, but all allocations/pointers are float
 335     if (pmeGpu->archSpecific->performOutOfPlaceFFT)
 336     {
 337         /* 2 separate grids */
 338         reallocateDeviceBuffer(&kernelParamsPtr->grid.d_fourierGrid, newComplexGridSize,
 339                                &pmeGpu->archSpecific->complexGridSize, &pmeGpu->archSpecific->complexGridSizeAlloc, pmeGpu->archSpecific->context);
 340         reallocateDeviceBuffer(&kernelParamsPtr->grid.d_realGrid, newRealGridSize,
 341                                &pmeGpu->archSpecific->realGridSize, &pmeGpu->archSpecific->realGridSizeAlloc, pmeGpu->archSpecific->context);
 342     }
 343     else
 344     {
 345         /* A single buffer so that any grid will fit */
 346         const int newGridsSize = std::max(newRealGridSize, newComplexGridSize);
 347         reallocateDeviceBuffer(&kernelParamsPtr->grid.d_realGrid, newGridsSize,
 348                                &pmeGpu->archSpecific->realGridSize, &pmeGpu->archSpecific->realGridSizeAlloc, pmeGpu->archSpecific->context);
 349         kernelParamsPtr->grid.d_fourierGrid   = kernelParamsPtr->grid.d_realGrid;
 350         pmeGpu->archSpecific->complexGridSize = pmeGpu->archSpecific->realGridSize;
 351         // the size might get used later for copying the grid
 352     }
 353 }
 354
 355 void pme_gpu_free_grids(const PmeGpu *pmeGpu)
 356 {
 357     if (pmeGpu->archSpecific->performOutOfPlaceFFT)
 358     {
 359         freeDeviceBuffer(&pmeGpu->kernelParams->grid.d_fourierGrid);
 360     }
 361     freeDeviceBuffer(&pmeGpu->kernelParams->grid.d_realGrid);
 362 }
 363
 364 void pme_gpu_clear_grids(const PmeGpu *pmeGpu)
 365 {
 366     clearDeviceBufferAsync(&pmeGpu->kernelParams->grid.d_realGrid, 0,
 367                            pmeGpu->archSpecific->realGridSize, pmeGpu->archSpecific->pmeStream);
 368 }
 369
 370 void pme_gpu_realloc_and_copy_fract_shifts(PmeGpu *pmeGpu)
 371 {
 372     pme_gpu_free_fract_shifts(pmeGpu);
 373
 374     auto        *kernelParamsPtr = pmeGpu->kernelParams.get();
 375
 376     const int    nx                  = kernelParamsPtr->grid.realGridSize[XX];
 377     const int    ny                  = kernelParamsPtr->grid.realGridSize[YY];
 378     const int    nz                  = kernelParamsPtr->grid.realGridSize[ZZ];
 379     const int    cellCount           = c_pmeNeighborUnitcellCount;
 380     const int    gridDataOffset[DIM] = {0, cellCount * nx, cellCount * (nx + ny)};
 381
 382     memcpy(kernelParamsPtr->grid.tablesOffsets, &gridDataOffset, sizeof(gridDataOffset));
 383
 384     const int    newFractShiftsSize  = cellCount * (nx + ny + nz);
 385
 386 #if GMX_GPU == GMX_GPU_CUDA
 387     initParamLookupTable(kernelParamsPtr->grid.d_fractShiftsTable,
 388                          kernelParamsPtr->fractShiftsTableTexture,
 389                          pmeGpu->common->fsh.data(),
 390                          newFractShiftsSize,
 391                          pmeGpu->deviceInfo);
 392
 393     initParamLookupTable(kernelParamsPtr->grid.d_gridlineIndicesTable,
 394                          kernelParamsPtr->gridlineIndicesTableTexture,
 395                          pmeGpu->common->nn.data(),
 396                          newFractShiftsSize,
 397                          pmeGpu->deviceInfo);
 398 #elif GMX_GPU == GMX_GPU_OPENCL
 399     // No dedicated texture routines....
 400     allocateDeviceBuffer(&kernelParamsPtr->grid.d_fractShiftsTable, newFractShiftsSize, pmeGpu->archSpecific->context);
 401     allocateDeviceBuffer(&kernelParamsPtr->grid.d_gridlineIndicesTable, newFractShiftsSize, pmeGpu->archSpecific->context);
 402     copyToDeviceBuffer(&kernelParamsPtr->grid.d_fractShiftsTable, pmeGpu->common->fsh.data(),
 403                        0, newFractShiftsSize,
 404                        pmeGpu->archSpecific->pmeStream, GpuApiCallBehavior::Async, nullptr);
 405     copyToDeviceBuffer(&kernelParamsPtr->grid.d_gridlineIndicesTable, pmeGpu->common->nn.data(),
 406                        0, newFractShiftsSize,
 407                        pmeGpu->archSpecific->pmeStream, GpuApiCallBehavior::Async, nullptr);
 408 #endif
 409 }
 410
 411 void pme_gpu_free_fract_shifts(const PmeGpu *pmeGpu)
 412 {
 413     auto *kernelParamsPtr = pmeGpu->kernelParams.get();
 414 #if GMX_GPU == GMX_GPU_CUDA
 415     destroyParamLookupTable(kernelParamsPtr->grid.d_fractShiftsTable,
 416                             kernelParamsPtr->fractShiftsTableTexture,
 417                             pmeGpu->deviceInfo);
 418     destroyParamLookupTable(kernelParamsPtr->grid.d_gridlineIndicesTable,
 419                             kernelParamsPtr->gridlineIndicesTableTexture,
 420                             pmeGpu->deviceInfo);
 421 #elif GMX_GPU == GMX_GPU_OPENCL
 422     freeDeviceBuffer(&kernelParamsPtr->grid.d_fractShiftsTable);
 423     freeDeviceBuffer(&kernelParamsPtr->grid.d_gridlineIndicesTable);
 424 #endif
 425 }
 426
 427 bool pme_gpu_stream_query(const PmeGpu *pmeGpu)
 428 {
 429     return haveStreamTasksCompleted(pmeGpu->archSpecific->pmeStream);
 430 }
 431
 432 void pme_gpu_copy_input_gather_grid(const PmeGpu *pmeGpu, float *h_grid)
 433 {
 434     copyToDeviceBuffer(&pmeGpu->kernelParams->grid.d_realGrid, h_grid,
 435                        0, pmeGpu->archSpecific->realGridSize,
 436                        pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 437 }
 438
 439 void pme_gpu_copy_output_spread_grid(const PmeGpu *pmeGpu, float *h_grid)
 440 {
 441     copyFromDeviceBuffer(h_grid, &pmeGpu->kernelParams->grid.d_realGrid,
 442                          0, pmeGpu->archSpecific->realGridSize,
 443                          pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 444     pmeGpu->archSpecific->syncSpreadGridD2H.markEvent(pmeGpu->archSpecific->pmeStream);
 445 }
 446
 447 void pme_gpu_copy_output_spread_atom_data(const PmeGpu *pmeGpu)
 448 {
 449     const int    alignment        = pme_gpu_get_atoms_per_warp(pmeGpu);
 450     const size_t nAtomsPadded     = ((pmeGpu->nAtomsAlloc + alignment - 1) / alignment) * alignment;
 451     const size_t splinesCount     = DIM * nAtomsPadded * pmeGpu->common->pme_order;
 452     auto        *kernelParamsPtr  = pmeGpu->kernelParams.get();
 453     copyFromDeviceBuffer(pmeGpu->staging.h_dtheta, &kernelParamsPtr->atoms.d_dtheta,
 454                          0, splinesCount,
 455                          pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 456     copyFromDeviceBuffer(pmeGpu->staging.h_theta, &kernelParamsPtr->atoms.d_theta,
 457                          0, splinesCount,
 458                          pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 459     copyFromDeviceBuffer(pmeGpu->staging.h_gridlineIndices, &kernelParamsPtr->atoms.d_gridlineIndices,
 460                          0, kernelParamsPtr->atoms.nAtoms * DIM,
 461                          pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 462 }
 463
 464 void pme_gpu_copy_input_gather_atom_data(const PmeGpu *pmeGpu)
 465 {
 466     const int    alignment       = pme_gpu_get_atoms_per_warp(pmeGpu);
 467     const size_t nAtomsPadded    = ((pmeGpu->nAtomsAlloc + alignment - 1) / alignment) * alignment;
 468     const size_t splinesCount    = DIM * nAtomsPadded * pmeGpu->common->pme_order;
 469     auto        *kernelParamsPtr = pmeGpu->kernelParams.get();
 470     if (c_usePadding)
 471     {
 472         // TODO: could clear only the padding and not the whole thing, but this is a test-exclusive code anyway
 473         clearDeviceBufferAsync(&kernelParamsPtr->atoms.d_gridlineIndices, 0,
 474                                pmeGpu->nAtomsAlloc * DIM, pmeGpu->archSpecific->pmeStream);
 475         clearDeviceBufferAsync(&kernelParamsPtr->atoms.d_dtheta, 0,
 476                                pmeGpu->nAtomsAlloc * pmeGpu->common->pme_order * DIM, pmeGpu->archSpecific->pmeStream);
 477         clearDeviceBufferAsync(&kernelParamsPtr->atoms.d_theta, 0,
 478                                pmeGpu->nAtomsAlloc * pmeGpu->common->pme_order * DIM, pmeGpu->archSpecific->pmeStream);
 479     }
 480     copyToDeviceBuffer(&kernelParamsPtr->atoms.d_dtheta, pmeGpu->staging.h_dtheta,
 481                        0, splinesCount,
 482                        pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 483     copyToDeviceBuffer(&kernelParamsPtr->atoms.d_theta, pmeGpu->staging.h_theta,
 484                        0, splinesCount,
 485                        pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 486     copyToDeviceBuffer(&kernelParamsPtr->atoms.d_gridlineIndices, pmeGpu->staging.h_gridlineIndices,
 487                        0, kernelParamsPtr->atoms.nAtoms * DIM,
 488                        pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
 489 }
 490
 491 void pme_gpu_sync_spread_grid(const PmeGpu *pmeGpu)
 492 {
 493     pmeGpu->archSpecific->syncSpreadGridD2H.waitForEvent();
 494 }
 495
 496 void pme_gpu_init_internal(PmeGpu *pmeGpu)
 497 {
 498 #if GMX_GPU == GMX_GPU_CUDA
 499     // Prepare to use the device that this PME task was assigned earlier.
 500     // Other entities, such as CUDA timing events, are known to implicitly use the device context.
 501     CU_RET_ERR(cudaSetDevice(pmeGpu->deviceInfo->id), "Switching to PME CUDA device");
 502 #endif
 503
 504     /* Allocate the target-specific structures */
 505     pmeGpu->archSpecific.reset(new PmeGpuSpecific());
 506     pmeGpu->kernelParams.reset(new PmeGpuKernelParams());
 507
 508     pmeGpu->archSpecific->performOutOfPlaceFFT = true;
 509     /* This should give better performance, according to the cuFFT documentation.
 510      * The performance seems to be the same though.
 511      * TODO: PME could also try to pick up nice grid sizes (with factors of 2, 3, 5, 7).
 512      */
 513
 514     // TODO: this is just a convenient reuse because programHandle_ currently is in charge of creating context
 515     pmeGpu->archSpecific->context = pmeGpu->programHandle_->impl_->context;
 516
 517     // timing enabling - TODO put this in gpu_utils (even though generally this is just option handling?) and reuse in NB
 518     if (GMX_GPU == GMX_GPU_CUDA)
 519     {
 520         /* WARNING: CUDA timings are incorrect with multiple streams.
 521          *          This is the main reason why they are disabled by default.
 522          */
 523         // TODO: Consider turning on by default when we can detect nr of streams.
 524         pmeGpu->archSpecific->useTiming = (getenv("GMX_ENABLE_GPU_TIMING") != nullptr);
 525     }
 526     else if (GMX_GPU == GMX_GPU_OPENCL)
 527     {
 528         pmeGpu->archSpecific->useTiming = (getenv("GMX_DISABLE_GPU_TIMING") == nullptr);
 529     }
 530
 531 #if GMX_GPU == GMX_GPU_CUDA
 532     pmeGpu->maxGridWidthX = pmeGpu->deviceInfo->prop.maxGridSize[0];
 533 #elif GMX_GPU == GMX_GPU_OPENCL
 534     pmeGpu->maxGridWidthX = INT32_MAX / 2;
 535     // TODO: is there no really global work size limit in OpenCL?
 536 #endif
 537
 538     /* Creating a PME GPU stream:
 539      * - default high priority with CUDA
 540      * - no priorities implemented yet with OpenCL; see #2532
 541      */
 542 #if GMX_GPU == GMX_GPU_CUDA
 543     cudaError_t stat;
 544     int         highest_priority, lowest_priority;
 545     stat = cudaDeviceGetStreamPriorityRange(&lowest_priority, &highest_priority);
 546     CU_RET_ERR(stat, "PME cudaDeviceGetStreamPriorityRange failed");
 547     stat = cudaStreamCreateWithPriority(&pmeGpu->archSpecific->pmeStream,
 548                                         cudaStreamDefault, //cudaStreamNonBlocking,
 549                                         highest_priority);
 550     CU_RET_ERR(stat, "cudaStreamCreateWithPriority on the PME stream failed");
 551 #elif GMX_GPU == GMX_GPU_OPENCL
 552     cl_command_queue_properties queueProperties = pmeGpu->archSpecific->useTiming ? CL_QUEUE_PROFILING_ENABLE : 0;
 553     cl_device_id                device_id       = pmeGpu->deviceInfo->ocl_gpu_id.ocl_device_id;
 554     cl_int                      clError;
 555     pmeGpu->archSpecific->pmeStream = clCreateCommandQueue(pmeGpu->archSpecific->context,
 556                                                            device_id, queueProperties, &clError);
 557     if (clError != CL_SUCCESS)
 558     {
 559         GMX_THROW(gmx::InternalError("Failed to create PME command queue"));
 560     }
 561 #endif
 562 }
 563
 564 void pme_gpu_destroy_specific(const PmeGpu *pmeGpu)
 565 {
 566 #if GMX_GPU == GMX_GPU_CUDA
 567     /* Destroy the CUDA stream */
 568     cudaError_t stat = cudaStreamDestroy(pmeGpu->archSpecific->pmeStream);
 569     CU_RET_ERR(stat, "PME cudaStreamDestroy error");
 570 #elif GMX_GPU == GMX_GPU_OPENCL
 571     cl_int clError = clReleaseCommandQueue(pmeGpu->archSpecific->pmeStream);
 572     if (clError != CL_SUCCESS)
 573     {
 574         gmx_warning("Failed to destroy PME command queue");
 575     }
 576 #endif
 577 }
 578
 579 void pme_gpu_reinit_3dfft(const PmeGpu *pmeGpu)
 580 {
 581     if (pme_gpu_performs_FFT(pmeGpu))
 582     {
 583         pmeGpu->archSpecific->fftSetup.resize(0);
 584         for (int i = 0; i < pmeGpu->common->ngrids; i++)
 585         {
 586             pmeGpu->archSpecific->fftSetup.push_back(gmx::compat::make_unique<GpuParallel3dFft>(pmeGpu));
 587         }
 588     }
 589 }
 590
 591 void pme_gpu_destroy_3dfft(const PmeGpu *pmeGpu)
 592 {
 593     pmeGpu->archSpecific->fftSetup.resize(0);
 594 }
 595
 596 int getSplineParamFullIndex(int order, int splineIndex, int dimIndex, int atomIndex, int atomsPerWarp)
 597 {
 598     if (order != 4)
 599     {
 600         throw order;
 601     }
 602     constexpr int fixedOrder = 4;
 603     GMX_UNUSED_VALUE(fixedOrder);
 604
 605     const int atomWarpIndex = atomIndex % atomsPerWarp;
 606     const int warpIndex     = atomIndex / atomsPerWarp;
 607     int       indexBase, result;
 608     switch (atomsPerWarp)
 609     {
 610         case 1:
 611             indexBase = getSplineParamIndexBase<fixedOrder, 1>(warpIndex, atomWarpIndex);
 612             result    = getSplineParamIndex<fixedOrder, 1>(indexBase, dimIndex, splineIndex);
 613             break;
 614
 615         case 2:
 616             indexBase = getSplineParamIndexBase<fixedOrder, 2>(warpIndex, atomWarpIndex);
 617             result    = getSplineParamIndex<fixedOrder, 2>(indexBase, dimIndex, splineIndex);
 618             break;
 619
 620         case 4:
 621             indexBase = getSplineParamIndexBase<fixedOrder, 4>(warpIndex, atomWarpIndex);
 622             result    = getSplineParamIndex<fixedOrder, 4>(indexBase, dimIndex, splineIndex);
 623             break;
 624
 625         case 8:
 626             indexBase = getSplineParamIndexBase<fixedOrder, 8>(warpIndex, atomWarpIndex);
 627             result    = getSplineParamIndex<fixedOrder, 8>(indexBase, dimIndex, splineIndex);
 628             break;
 629
 630         default:
 631             GMX_THROW(gmx::NotImplementedError(gmx::formatString("Test function call not unrolled for atomsPerWarp = %d in getSplineParamFullIndex", atomsPerWarp)));
 632     }
 633     return result;
 634 }
 635
 636 gmx::ArrayRef<gmx::RVec> pme_gpu_get_forces(PmeGpu *pmeGpu)
 637 {
 638     return pmeGpu->staging.h_forces;
 639 }
 640
 641 void pme_gpu_get_energy_virial(const PmeGpu *pmeGpu, real *energy, matrix virial)
 642 {
 643     for (int j = 0; j < c_virialAndEnergyCount; j++)
 644     {
 645         GMX_ASSERT(std::isfinite(pmeGpu->staging.h_virialAndEnergy[j]), "PME GPU produces incorrect energy/virial.");
 646     }
 647
 648     GMX_ASSERT(energy, "Invalid energy output pointer in PME GPU");
 649     unsigned int j = 0;
 650     virial[XX][XX] = 0.25f * pmeGpu->staging.h_virialAndEnergy[j++];
 651     virial[YY][YY] = 0.25f * pmeGpu->staging.h_virialAndEnergy[j++];
 652     virial[ZZ][ZZ] = 0.25f * pmeGpu->staging.h_virialAndEnergy[j++];
 653     virial[XX][YY] = virial[YY][XX] = 0.25f * pmeGpu->staging.h_virialAndEnergy[j++];
 654     virial[XX][ZZ] = virial[ZZ][XX] = 0.25f * pmeGpu->staging.h_virialAndEnergy[j++];
 655     virial[YY][ZZ] = virial[ZZ][YY] = 0.25f * pmeGpu->staging.h_virialAndEnergy[j++];
 656     *energy        = 0.5f * pmeGpu->staging.h_virialAndEnergy[j++];
 657 }
 658
 659 void pme_gpu_update_input_box(PmeGpu gmx_unused       *pmeGpu,
 660                               const matrix gmx_unused  box)
 661 {
 662 #if GMX_DOUBLE
 663     GMX_THROW(gmx::NotImplementedError("PME is implemented for single-precision only on GPU"));
 664 #else
 665     matrix  scaledBox;
 666     pmeGpu->common->boxScaler->scaleBox(box, scaledBox);
 667     auto   *kernelParamsPtr      = pme_gpu_get_kernel_params_base_ptr(pmeGpu);
 668     kernelParamsPtr->current.boxVolume = scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ];
 669     GMX_ASSERT(kernelParamsPtr->current.boxVolume != 0.0f, "Zero volume of the unit cell");
 670     matrix recipBox;
 671     gmx::invertBoxMatrix(scaledBox, recipBox);
 672
 673     /* The GPU recipBox is transposed as compared to the CPU recipBox.
 674      * Spread uses matrix columns (while solve and gather use rows).
 675      * There is no particular reason for this; it might be further rethought/optimized for better access patterns.
 676      */
 677     const real newRecipBox[DIM][DIM] =
 678     {
 679         {recipBox[XX][XX], recipBox[YY][XX], recipBox[ZZ][XX]},
 680         {             0.0, recipBox[YY][YY], recipBox[ZZ][YY]},
 681         {             0.0,              0.0, recipBox[ZZ][ZZ]}
 682     };
 683     memcpy(kernelParamsPtr->current.recipBox, newRecipBox, sizeof(matrix));
 684 #endif
 685 }
 686
 687 /*! \brief \libinternal
 688  * (Re-)initializes all the PME GPU data related to the grid size and cut-off.
 689  *
 690  * \param[in] pmeGpu            The PME GPU structure.
 691  */
 692 static void pme_gpu_reinit_grids(PmeGpu *pmeGpu)
 693 {
 694     auto *kernelParamsPtr = pme_gpu_get_kernel_params_base_ptr(pmeGpu);
 695     kernelParamsPtr->grid.ewaldFactor = (M_PI * M_PI) / (pmeGpu->common->ewaldcoeff_q * pmeGpu->common->ewaldcoeff_q);
 696
 697     /* The grid size variants */
 698     for (int i = 0; i < DIM; i++)
 699     {
 700         kernelParamsPtr->grid.realGridSize[i]       = pmeGpu->common->nk[i];
 701         kernelParamsPtr->grid.realGridSizeFP[i]     = static_cast<float>(kernelParamsPtr->grid.realGridSize[i]);
 702         kernelParamsPtr->grid.realGridSizePadded[i] = kernelParamsPtr->grid.realGridSize[i];
 703
 704         // The complex grid currently uses no padding;
 705         // if it starts to do so, then another test should be added for that
 706         kernelParamsPtr->grid.complexGridSize[i]       = kernelParamsPtr->grid.realGridSize[i];
 707         kernelParamsPtr->grid.complexGridSizePadded[i] = kernelParamsPtr->grid.realGridSize[i];
 708     }
 709     /* FFT: n real elements correspond to (n / 2 + 1) complex elements in minor dimension */
 710     if (!pme_gpu_performs_FFT(pmeGpu))
 711     {
 712         // This allows for GPU spreading grid and CPU fftgrid to have the same layout, so that we can copy the data directly
 713         kernelParamsPtr->grid.realGridSizePadded[ZZ] = (kernelParamsPtr->grid.realGridSize[ZZ] / 2 + 1) * 2;
 714     }
 715
 716     /* GPU FFT: n real elements correspond to (n / 2 + 1) complex elements in minor dimension */
 717     kernelParamsPtr->grid.complexGridSize[ZZ] /= 2;
 718     kernelParamsPtr->grid.complexGridSize[ZZ]++;
 719     kernelParamsPtr->grid.complexGridSizePadded[ZZ] = kernelParamsPtr->grid.complexGridSize[ZZ];
 720
 721     pme_gpu_realloc_and_copy_fract_shifts(pmeGpu);
 722     pme_gpu_realloc_and_copy_bspline_values(pmeGpu);
 723     pme_gpu_realloc_grids(pmeGpu);
 724     pme_gpu_reinit_3dfft(pmeGpu);
 725 }
 726
 727 /* Several GPU functions that refer to the CPU PME data live here.
 728  * We would like to keep these away from the GPU-framework specific code for clarity,
 729  * as well as compilation issues with MPI.
 730  */
 731
 732 /*! \brief \libinternal
 733  * Copies everything useful from the PME CPU to the PME GPU structure.
 734  * The goal is to minimize interaction with the PME CPU structure in the GPU code.
 735  *
 736  * \param[in] pme         The PME structure.
 737  */
 738 static void pme_gpu_copy_common_data_from(const gmx_pme_t *pme)
 739 {
 740     /* TODO: Consider refactoring the CPU PME code to use the same structure,
 741      * so that this function becomes 2 lines */
 742     PmeGpu *pmeGpu             = pme->gpu;
 743     pmeGpu->common->ngrids        = pme->ngrids;
 744     pmeGpu->common->epsilon_r     = pme->epsilon_r;
 745     pmeGpu->common->ewaldcoeff_q  = pme->ewaldcoeff_q;
 746     pmeGpu->common->nk[XX]        = pme->nkx;
 747     pmeGpu->common->nk[YY]        = pme->nky;
 748     pmeGpu->common->nk[ZZ]        = pme->nkz;
 749     pmeGpu->common->pme_order     = pme->pme_order;
 750     for (int i = 0; i < DIM; i++)
 751     {
 752         pmeGpu->common->bsp_mod[i].assign(pme->bsp_mod[i], pme->bsp_mod[i] + pmeGpu->common->nk[i]);
 753     }
 754     const int cellCount = c_pmeNeighborUnitcellCount;
 755     pmeGpu->common->fsh.resize(0);
 756     pmeGpu->common->fsh.insert(pmeGpu->common->fsh.end(), pme->fshx, pme->fshx + cellCount * pme->nkx);
 757     pmeGpu->common->fsh.insert(pmeGpu->common->fsh.end(), pme->fshy, pme->fshy + cellCount * pme->nky);
 758     pmeGpu->common->fsh.insert(pmeGpu->common->fsh.end(), pme->fshz, pme->fshz + cellCount * pme->nkz);
 759     pmeGpu->common->nn.resize(0);
 760     pmeGpu->common->nn.insert(pmeGpu->common->nn.end(), pme->nnx, pme->nnx + cellCount * pme->nkx);
 761     pmeGpu->common->nn.insert(pmeGpu->common->nn.end(), pme->nny, pme->nny + cellCount * pme->nky);
 762     pmeGpu->common->nn.insert(pmeGpu->common->nn.end(), pme->nnz, pme->nnz + cellCount * pme->nkz);
 763     pmeGpu->common->runMode   = pme->runMode;
 764     pmeGpu->common->boxScaler = pme->boxScaler;
 765 }
 766
 767 /*! \libinternal \brief
 768  * Initializes the PME GPU data at the beginning of the run.
 769  * TODO: this should become PmeGpu::PmeGpu()
 770  *
 771  * \param[in,out] pme            The PME structure.
 772  * \param[in,out] gpuInfo        The GPU information structure.
 773  * \param[in]     pmeGpuProgram  The handle to the program/kernel data created outside (e.g. in unit tests/runner)
 774  */
 775 static void pme_gpu_init(gmx_pme_t               *pme,
 776                          const gmx_device_info_t *gpuInfo,
 777                          PmeGpuProgramHandle      pmeGpuProgram)
 778 {
 779     pme->gpu          = new PmeGpu();
 780     PmeGpu *pmeGpu = pme->gpu;
 781     changePinningPolicy(&pmeGpu->staging.h_forces, pme_get_pinning_policy());
 782     pmeGpu->common = std::make_shared<PmeShared>();
 783
 784     /* These settings are set here for the whole run; dynamic ones are set in pme_gpu_reinit() */
 785     /* A convenience variable. */
 786     pmeGpu->settings.useDecomposition = (pme->nnodes == 1);
 787     /* TODO: CPU gather with GPU spread is broken due to different theta/dtheta layout. */
 788     pmeGpu->settings.performGPUGather = true;
 789
 790     pme_gpu_set_testing(pmeGpu, false);
 791
 792     pmeGpu->deviceInfo = gpuInfo;
 793     GMX_ASSERT(pmeGpuProgram != nullptr, "GPU kernels must be already compiled");
 794     pmeGpu->programHandle_ = pmeGpuProgram;
 795
 796     pme_gpu_init_internal(pmeGpu);
 797     pme_gpu_alloc_energy_virial(pmeGpu);
 798
 799     pme_gpu_copy_common_data_from(pme);
 800
 801     GMX_ASSERT(pmeGpu->common->epsilon_r != 0.0f, "PME GPU: bad electrostatic coefficient");
 802
 803     auto *kernelParamsPtr = pme_gpu_get_kernel_params_base_ptr(pmeGpu);
 804     kernelParamsPtr->constants.elFactor = ONE_4PI_EPS0 / pmeGpu->common->epsilon_r;
 805 }
 806
 807 void pme_gpu_transform_spline_atom_data(const PmeGpu *pmeGpu, const pme_atomcomm_t *atc,
 808                                         PmeSplineDataType type, int dimIndex, PmeLayoutTransform transform)
 809 {
 810     // The GPU atom spline data is laid out in a different way currently than the CPU one.
 811     // This function converts the data from GPU to CPU layout (in the host memory).
 812     // It is only intended for testing purposes so far.
 813     // Ideally we should use similar layouts on CPU and GPU if we care about mixed modes and their performance
 814     // (e.g. spreading on GPU, gathering on CPU).
 815     GMX_RELEASE_ASSERT(atc->nthread == 1, "Only the serial PME data layout is supported");
 816     const uintmax_t threadIndex  = 0;
 817     const auto      atomCount    = pme_gpu_get_kernel_params_base_ptr(pmeGpu)->atoms.nAtoms;
 818     const auto      atomsPerWarp = pme_gpu_get_atoms_per_warp(pmeGpu);
 819     const auto      pmeOrder     = pmeGpu->common->pme_order;
 820
 821     real           *cpuSplineBuffer;
 822     float          *h_splineBuffer;
 823     switch (type)
 824     {
 825         case PmeSplineDataType::Values:
 826             cpuSplineBuffer = atc->spline[threadIndex].theta[dimIndex];
 827             h_splineBuffer  = pmeGpu->staging.h_theta;
 828             break;
 829
 830         case PmeSplineDataType::Derivatives:
 831             cpuSplineBuffer = atc->spline[threadIndex].dtheta[dimIndex];
 832             h_splineBuffer  = pmeGpu->staging.h_dtheta;
 833             break;
 834
 835         default:
 836             GMX_THROW(gmx::InternalError("Unknown spline data type"));
 837     }
 838
 839     for (auto atomIndex = 0; atomIndex < atomCount; atomIndex++)
 840     {
 841         for (auto orderIndex = 0; orderIndex < pmeOrder; orderIndex++)
 842         {
 843             const auto gpuValueIndex = getSplineParamFullIndex(pmeOrder, orderIndex, dimIndex, atomIndex, atomsPerWarp);
 844             const auto cpuValueIndex = atomIndex * pmeOrder + orderIndex;
 845             GMX_ASSERT(cpuValueIndex < atomCount * pmeOrder, "Atom spline data index out of bounds (while transforming GPU data layout for host)");
 846             switch (transform)
 847             {
 848                 case PmeLayoutTransform::GpuToHost:
 849                     cpuSplineBuffer[cpuValueIndex] = h_splineBuffer[gpuValueIndex];
 850                     break;
 851
 852                 case PmeLayoutTransform::HostToGpu:
 853                     h_splineBuffer[gpuValueIndex] = cpuSplineBuffer[cpuValueIndex];
 854                     break;
 855
 856                 default:
 857                     GMX_THROW(gmx::InternalError("Unknown layout transform"));
 858             }
 859         }
 860     }
 861 }
 862
 863 void pme_gpu_get_real_grid_sizes(const PmeGpu *pmeGpu, gmx::IVec *gridSize, gmx::IVec *paddedGridSize)
 864 {
 865     GMX_ASSERT(gridSize != nullptr, "");
 866     GMX_ASSERT(paddedGridSize != nullptr, "");
 867     GMX_ASSERT(pmeGpu != nullptr, "");
 868     auto *kernelParamsPtr = pme_gpu_get_kernel_params_base_ptr(pmeGpu);
 869     for (int i = 0; i < DIM; i++)
 870     {
 871         (*gridSize)[i]       = kernelParamsPtr->grid.realGridSize[i];
 872         (*paddedGridSize)[i] = kernelParamsPtr->grid.realGridSizePadded[i];
 873     }
 874 }
 875
 876 void pme_gpu_reinit(gmx_pme_t               *pme,
 877                     const gmx_device_info_t *gpuInfo,
 878                     PmeGpuProgramHandle      pmeGpuProgram)
 879 {
 880     if (!pme_gpu_active(pme))
 881     {
 882         return;
 883     }
 884
 885     if (!pme->gpu)
 886     {
 887         /* First-time initialization */
 888         pme_gpu_init(pme, gpuInfo, pmeGpuProgram);
 889     }
 890     else
 891     {
 892         /* After this call nothing in the GPU code should refer to the gmx_pme_t *pme itself - until the next pme_gpu_reinit */
 893         pme_gpu_copy_common_data_from(pme);
 894     }
 895     /* GPU FFT will only get used for a single rank.*/
 896     pme->gpu->settings.performGPUFFT   = (pme->gpu->common->runMode == PmeRunMode::GPU) && !pme_gpu_uses_dd(pme->gpu);
 897     pme->gpu->settings.performGPUSolve = (pme->gpu->common->runMode == PmeRunMode::GPU);
 898
 899     /* Reinit active timers */
 900     pme_gpu_reinit_timings(pme->gpu);
 901
 902     pme_gpu_reinit_grids(pme->gpu);
 903     // Note: if timing the reinit launch overhead becomes more relevant
 904     // (e.g. with regulat PP-PME re-balancing), we should pass wcycle here.
 905     pme_gpu_reinit_computation(pme, nullptr);
 906     /* Clear the previous box - doesn't hurt, and forces the PME CPU recipbox
 907      * update for mixed mode on grid switch. TODO: use shared recipbox field.
 908      */
 909     std::memset(pme->gpu->common->previousBox, 0, sizeof(pme->gpu->common->previousBox));
 910 }
 911
 912 void pme_gpu_destroy(PmeGpu *pmeGpu)
 913 {
 914     /* Free lots of data */
 915     pme_gpu_free_energy_virial(pmeGpu);
 916     pme_gpu_free_bspline_values(pmeGpu);
 917     pme_gpu_free_forces(pmeGpu);
 918     pme_gpu_free_coordinates(pmeGpu);
 919     pme_gpu_free_coefficients(pmeGpu);
 920     pme_gpu_free_spline_data(pmeGpu);
 921     pme_gpu_free_grid_indices(pmeGpu);
 922     pme_gpu_free_fract_shifts(pmeGpu);
 923     pme_gpu_free_grids(pmeGpu);
 924
 925     pme_gpu_destroy_3dfft(pmeGpu);
 926
 927     /* Free the GPU-framework specific data last */
 928     pme_gpu_destroy_specific(pmeGpu);
 929
 930     delete pmeGpu;
 931 }
 932
 933 void pme_gpu_reinit_atoms(PmeGpu *pmeGpu, const int nAtoms, const real *charges)
 934 {
 935     auto      *kernelParamsPtr = pme_gpu_get_kernel_params_base_ptr(pmeGpu);
 936     kernelParamsPtr->atoms.nAtoms = nAtoms;
 937     const int  alignment = pme_gpu_get_atom_data_alignment(pmeGpu);
 938     pmeGpu->nAtomsPadded = ((nAtoms + alignment - 1) / alignment) * alignment;
 939     const int  nAtomsAlloc   = c_usePadding ? pmeGpu->nAtomsPadded : nAtoms;
 940     const bool haveToRealloc = (pmeGpu->nAtomsAlloc < nAtomsAlloc); /* This check might be redundant, but is logical */
 941     pmeGpu->nAtomsAlloc = nAtomsAlloc;
 942
 943 #if GMX_DOUBLE
 944     GMX_RELEASE_ASSERT(false, "Only single precision supported");
 945     GMX_UNUSED_VALUE(charges);
 946 #else
 947     pme_gpu_realloc_and_copy_input_coefficients(pmeGpu, reinterpret_cast<const float *>(charges));
 948     /* Could also be checked for haveToRealloc, but the copy always needs to be performed */
 949 #endif
 950
 951     if (haveToRealloc)
 952     {
 953         pme_gpu_realloc_coordinates(pmeGpu);
 954         pme_gpu_realloc_forces(pmeGpu);
 955         pme_gpu_realloc_spline_data(pmeGpu);
 956         pme_gpu_realloc_grid_indices(pmeGpu);
 957     }
 958 }
 959
 960 void pme_gpu_3dfft(const PmeGpu *pmeGpu, gmx_fft_direction dir, int grid_index)
 961 {
 962     int   timerId = (dir == GMX_FFT_REAL_TO_COMPLEX) ? gtPME_FFT_R2C : gtPME_FFT_C2R;
 963
 964     pme_gpu_start_timing(pmeGpu, timerId);
 965     pmeGpu->archSpecific->fftSetup[grid_index]->perform3dFft(dir, pme_gpu_fetch_timing_event(pmeGpu, timerId));
 966     pme_gpu_stop_timing(pmeGpu, timerId);
 967 }
 968
 969 /*! \brief
 970  * Given possibly large \p blockCount, returns a compact 1D or 2D grid for kernel scheduling,
 971  * to minimize number of unused blocks.
 972  */
 973 std::pair<int, int> inline pmeGpuCreateGrid(const PmeGpu *pmeGpu, int blockCount)
 974 {
 975     // How many maximum widths in X do we need (hopefully just one)
 976     const int minRowCount = (blockCount + pmeGpu->maxGridWidthX - 1) / pmeGpu->maxGridWidthX;
 977     // Trying to make things even
 978     const int colCount = (blockCount + minRowCount - 1) / minRowCount;
 979     GMX_ASSERT((colCount * minRowCount - blockCount) >= 0, "pmeGpuCreateGrid: totally wrong");
 980     GMX_ASSERT((colCount * minRowCount - blockCount) < minRowCount, "pmeGpuCreateGrid: excessive blocks");
 981     return std::pair<int, int>(colCount, minRowCount);
 982 }
 983
 984 void pme_gpu_spread(const PmeGpu    *pmeGpu,
 985                     int gmx_unused   gridIndex,
 986                     real            *h_grid,
 987                     bool             computeSplines,
 988                     bool             spreadCharges)
 989 {
 990     GMX_ASSERT(computeSplines || spreadCharges, "PME spline/spread kernel has invalid input (nothing to do)");
 991     const auto   *kernelParamsPtr = pmeGpu->kernelParams.get();
 992     GMX_ASSERT(kernelParamsPtr->atoms.nAtoms > 0, "No atom data in PME GPU spread");
 993
 994     const size_t blockSize  = pmeGpu->programHandle_->impl_->spreadWorkGroupSize;
 995
 996     const int    order         = pmeGpu->common->pme_order;
 997     const int    atomsPerBlock = blockSize / PME_SPREADGATHER_THREADS_PER_ATOM;
 998     // TODO: pick smaller block size in runtime if needed
 999     // (e.g. on 660 Ti where 50% occupancy is ~25% faster than 100% occupancy with RNAse (~17.8k atoms))
1000     // If doing so, change atomsPerBlock in the kernels as well.
1001     // TODO: test varying block sizes on modern arch-s as well
1002     // TODO: also consider using cudaFuncSetCacheConfig() for preferring shared memory on older architectures
1003     //(for spline data mostly, together with varying PME_GPU_PARALLEL_SPLINE define)
1004     GMX_ASSERT(!c_usePadding || !(PME_ATOM_DATA_ALIGNMENT % atomsPerBlock), "inconsistent atom data padding vs. spreading block size");
1005
1006     const int          blockCount = pmeGpu->nAtomsPadded / atomsPerBlock;
1007     auto               dimGrid    = pmeGpuCreateGrid(pmeGpu, blockCount);
1008
1009     KernelLaunchConfig config;
1010     config.blockSize[0] = config.blockSize[1] = order;
1011     config.blockSize[2] = atomsPerBlock;
1012     config.gridSize[0]  = dimGrid.first;
1013     config.gridSize[1]  = dimGrid.second;
1014     config.stream       = pmeGpu->archSpecific->pmeStream;
1015
1016     if (order != 4)
1017     {
1018         GMX_THROW(gmx::NotImplementedError("The code for pme_order != 4 was not implemented!"));
1019     }
1020
1021     int  timingId;
1022     PmeGpuProgramImpl::PmeKernelHandle kernelPtr = nullptr;
1023     if (computeSplines)
1024     {
1025         if (spreadCharges)
1026         {
1027             timingId  = gtPME_SPLINEANDSPREAD;
1028             kernelPtr = pmeGpu->programHandle_->impl_->splineAndSpreadKernel;
1029         }
1030         else
1031         {
1032             timingId  = gtPME_SPLINE;
1033             kernelPtr = pmeGpu->programHandle_->impl_->splineKernel;
1034         }
1035     }
1036     else
1037     {
1038         timingId  = gtPME_SPREAD;
1039         kernelPtr = pmeGpu->programHandle_->impl_->spreadKernel;
1040     }
1041
1042     pme_gpu_start_timing(pmeGpu, timingId);
1043     auto      *timingEvent = pme_gpu_fetch_timing_event(pmeGpu, timingId);
1044 #if c_canEmbedBuffers
1045     const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, config, kernelParamsPtr);
1046 #else
1047     const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, config, kernelParamsPtr,
1048                                                       &kernelParamsPtr->atoms.d_theta,
1049                                                       &kernelParamsPtr->atoms.d_dtheta,
1050                                                       &kernelParamsPtr->atoms.d_gridlineIndices,
1051                                                       &kernelParamsPtr->grid.d_realGrid,
1052                                                       &kernelParamsPtr->grid.d_fractShiftsTable,
1053                                                       &kernelParamsPtr->grid.d_gridlineIndicesTable,
1054                                                       &kernelParamsPtr->atoms.d_coefficients,
1055                                                       &kernelParamsPtr->atoms.d_coordinates
1056                                                       );
1057 #endif
1058
1059     launchGpuKernel(kernelPtr, config, timingEvent, "PME spline/spread", kernelArgs);
1060     pme_gpu_stop_timing(pmeGpu, timingId);
1061
1062     const bool copyBackGrid = spreadCharges && (pme_gpu_is_testing(pmeGpu) || !pme_gpu_performs_FFT(pmeGpu));
1063     if (copyBackGrid)
1064     {
1065         pme_gpu_copy_output_spread_grid(pmeGpu, h_grid);
1066     }
1067     const bool copyBackAtomData = computeSplines && (pme_gpu_is_testing(pmeGpu) || !pme_gpu_performs_gather(pmeGpu));
1068     if (copyBackAtomData)
1069     {
1070         pme_gpu_copy_output_spread_atom_data(pmeGpu);
1071     }
1072 }
1073
1074 void pme_gpu_solve(const PmeGpu *pmeGpu, t_complex *h_grid,
1075                    GridOrdering gridOrdering, bool computeEnergyAndVirial)
1076 {
1077     const bool   copyInputAndOutputGrid = pme_gpu_is_testing(pmeGpu) || !pme_gpu_performs_FFT(pmeGpu);
1078
1079     auto        *kernelParamsPtr = pmeGpu->kernelParams.get();
1080
1081     float       *h_gridFloat = reinterpret_cast<float *>(h_grid);
1082     if (copyInputAndOutputGrid)
1083     {
1084         copyToDeviceBuffer(&kernelParamsPtr->grid.d_fourierGrid, h_gridFloat,
1085                            0, pmeGpu->archSpecific->complexGridSize,
1086                            pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
1087     }
1088
1089     int majorDim = -1, middleDim = -1, minorDim = -1;
1090     switch (gridOrdering)
1091     {
1092         case GridOrdering::YZX:
1093             majorDim  = YY;
1094             middleDim = ZZ;
1095             minorDim  = XX;
1096             break;
1097
1098         case GridOrdering::XYZ:
1099             majorDim  = XX;
1100             middleDim = YY;
1101             minorDim  = ZZ;
1102             break;
1103
1104         default:
1105             GMX_ASSERT(false, "Implement grid ordering here and below for the kernel launch");
1106     }
1107
1108     const size_t maxBlockSize      = pmeGpu->programHandle_->impl_->solveMaxWorkGroupSize;
1109
1110     const int    gridLineSize       = pmeGpu->kernelParams->grid.complexGridSize[minorDim];
1111     const int    gridLinesPerBlock  = std::max(maxBlockSize / gridLineSize, 1UL);
1112     const int    blocksPerGridLine  = (gridLineSize + maxBlockSize - 1) / maxBlockSize;
1113     const int    cellsPerBlock      = gridLineSize * gridLinesPerBlock;
1114     const size_t warpSize           = pmeGpu->programHandle_->impl_->warpSize;
1115     const int    blockSize          = (cellsPerBlock + warpSize - 1) / warpSize * warpSize;
1116
1117
1118     KernelLaunchConfig config;
1119     config.blockSize[0] = blockSize;
1120     config.gridSize[0]  = blocksPerGridLine;
1121     // rounding up to full warps so that shuffle operations produce defined results
1122     config.gridSize[1]  = (pmeGpu->kernelParams->grid.complexGridSize[middleDim] + gridLinesPerBlock - 1) / gridLinesPerBlock;
1123     config.gridSize[2]  = pmeGpu->kernelParams->grid.complexGridSize[majorDim];
1124     config.stream       = pmeGpu->archSpecific->pmeStream;
1125
1126     int  timingId = gtPME_SOLVE;
1127     PmeGpuProgramImpl::PmeKernelHandle kernelPtr = nullptr;
1128     if (gridOrdering == GridOrdering::YZX)
1129     {
1130         kernelPtr = computeEnergyAndVirial ?
1131             pmeGpu->programHandle_->impl_->solveYZXEnergyKernel :
1132             pmeGpu->programHandle_->impl_->solveYZXKernel;
1133     }
1134     else if (gridOrdering == GridOrdering::XYZ)
1135     {
1136         kernelPtr = computeEnergyAndVirial ?
1137             pmeGpu->programHandle_->impl_->solveXYZEnergyKernel :
1138             pmeGpu->programHandle_->impl_->solveXYZKernel;
1139     }
1140
1141     pme_gpu_start_timing(pmeGpu, timingId);
1142     auto      *timingEvent = pme_gpu_fetch_timing_event(pmeGpu, timingId);
1143 #if c_canEmbedBuffers
1144     const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, config, kernelParamsPtr);
1145 #else
1146     const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, config, kernelParamsPtr,
1147                                                       &kernelParamsPtr->grid.d_splineModuli,
1148                                                       &kernelParamsPtr->constants.d_virialAndEnergy,
1149                                                       &kernelParamsPtr->grid.d_fourierGrid);
1150 #endif
1151     launchGpuKernel(kernelPtr, config, timingEvent, "PME solve", kernelArgs);
1152     pme_gpu_stop_timing(pmeGpu, timingId);
1153
1154     if (computeEnergyAndVirial)
1155     {
1156         copyFromDeviceBuffer(pmeGpu->staging.h_virialAndEnergy, &kernelParamsPtr->constants.d_virialAndEnergy,
1157                              0, c_virialAndEnergyCount,
1158                              pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
1159     }
1160
1161     if (copyInputAndOutputGrid)
1162     {
1163         copyFromDeviceBuffer(h_gridFloat, &kernelParamsPtr->grid.d_fourierGrid,
1164                              0, pmeGpu->archSpecific->complexGridSize,
1165                              pmeGpu->archSpecific->pmeStream, pmeGpu->settings.transferKind, nullptr);
1166     }
1167 }
1168
1169 void pme_gpu_gather(PmeGpu                *pmeGpu,
1170                     PmeForceOutputHandling forceTreatment,
1171                     const float           *h_grid
1172                     )
1173 {
1174     /* Copying the input CPU forces for reduction */
1175     if (forceTreatment != PmeForceOutputHandling::Set)
1176     {
1177         pme_gpu_copy_input_forces(pmeGpu);
1178     }
1179
1180     const int    order           = pmeGpu->common->pme_order;
1181     const auto  *kernelParamsPtr = pmeGpu->kernelParams.get();
1182
1183     if (!pme_gpu_performs_FFT(pmeGpu) || pme_gpu_is_testing(pmeGpu))
1184     {
1185         pme_gpu_copy_input_gather_grid(pmeGpu, const_cast<float *>(h_grid));
1186     }
1187
1188     if (pme_gpu_is_testing(pmeGpu))
1189     {
1190         pme_gpu_copy_input_gather_atom_data(pmeGpu);
1191     }
1192
1193     const size_t blockSize     = pmeGpu->programHandle_->impl_->gatherWorkGroupSize;
1194     const int    atomsPerBlock = blockSize / PME_SPREADGATHER_THREADS_PER_ATOM;
1195     GMX_ASSERT(!c_usePadding || !(PME_ATOM_DATA_ALIGNMENT % atomsPerBlock), "inconsistent atom data padding vs. gathering block size");
1196
1197     const int          blockCount = pmeGpu->nAtomsPadded / atomsPerBlock;
1198     auto               dimGrid    = pmeGpuCreateGrid(pmeGpu, blockCount);
1199
1200     KernelLaunchConfig config;
1201     config.blockSize[0] = config.blockSize[1] = order;
1202     config.blockSize[2] = atomsPerBlock;
1203     config.gridSize[0]  = dimGrid.first;
1204     config.gridSize[1]  = dimGrid.second;
1205     config.stream       = pmeGpu->archSpecific->pmeStream;
1206
1207     if (order != 4)
1208     {
1209         GMX_THROW(gmx::NotImplementedError("The code for pme_order != 4 was not implemented!"));
1210     }
1211
1212     // TODO test different cache configs
1213
1214     int  timingId = gtPME_GATHER;
1215     // TODO design kernel selection getters and make PmeGpu a friend of PmeGpuProgramImpl
1216     PmeGpuProgramImpl::PmeKernelHandle kernelPtr = (forceTreatment == PmeForceOutputHandling::Set) ?
1217         pmeGpu->programHandle_->impl_->gatherKernel :
1218         pmeGpu->programHandle_->impl_->gatherReduceWithInputKernel;
1219
1220     pme_gpu_start_timing(pmeGpu, timingId);
1221     auto      *timingEvent = pme_gpu_fetch_timing_event(pmeGpu, timingId);
1222 #if c_canEmbedBuffers
1223     const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, config, kernelParamsPtr);
1224 #else
1225     const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, config, kernelParamsPtr,
1226                                                       &kernelParamsPtr->atoms.d_coefficients,
1227                                                       &kernelParamsPtr->grid.d_realGrid,
1228                                                       &kernelParamsPtr->atoms.d_theta,
1229                                                       &kernelParamsPtr->atoms.d_dtheta,
1230                                                       &kernelParamsPtr->atoms.d_gridlineIndices,
1231                                                       &kernelParamsPtr->atoms.d_forces);
1232 #endif
1233     launchGpuKernel(kernelPtr, config, timingEvent, "PME gather", kernelArgs);
1234     pme_gpu_stop_timing(pmeGpu, timingId);
1235
1236     pme_gpu_copy_output_forces(pmeGpu);
1237 }