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37 * Implements common routines for PME tests.
39 * \author Aleksei Iupinov <a.yupinov@gmail.com>
40 * \ingroup module_ewald
44 #include "pmetestcommon.h"
50 #include "gromacs/domdec/domdec.h"
51 #include "gromacs/ewald/pme_gather.h"
52 #include "gromacs/ewald/pme_gpu_internal.h"
53 #include "gromacs/ewald/pme_grid.h"
54 #include "gromacs/ewald/pme_internal.h"
55 #include "gromacs/ewald/pme_redistribute.h"
56 #include "gromacs/ewald/pme_solve.h"
57 #include "gromacs/ewald/pme_spread.h"
58 #include "gromacs/fft/parallel_3dfft.h"
59 #include "gromacs/gpu_utils/gpu_utils.h"
60 #include "gromacs/math/invertmatrix.h"
61 #include "gromacs/mdtypes/commrec.h"
62 #include "gromacs/pbcutil/pbc.h"
63 #include "gromacs/topology/topology.h"
64 #include "gromacs/utility/exceptions.h"
65 #include "gromacs/utility/gmxassert.h"
66 #include "gromacs/utility/logger.h"
67 #include "gromacs/utility/stringutil.h"
69 #include "testutils/testasserts.h"
76 bool pmeSupportsInputForMode(const gmx_hw_info_t &hwinfo,
77 const t_inputrec *inputRec,
89 implemented = (pme_gpu_supports_build(nullptr) &&
90 pme_gpu_supports_hardware(hwinfo, nullptr) &&
91 pme_gpu_supports_input(*inputRec, mtop, nullptr));
95 GMX_THROW(InternalError("Test not implemented for this mode"));
100 uint64_t getSplineModuliDoublePrecisionUlps(int splineOrder)
102 /* Arbitrary ulp tolerance for sine/cosine implementation. It's
103 * hard to know what to pick without testing lots of
104 * implementations. */
105 const uint64_t sineUlps = 10;
106 return 4 * (splineOrder - 2) + 2 * sineUlps * splineOrder;
109 //! PME initialization - internal
110 static PmeSafePointer pmeInitInternal(const t_inputrec *inputRec,
112 const gmx_device_info_t *gpuInfo,
113 PmeGpuProgramHandle pmeGpuProgram,
114 const Matrix3x3 &box,
115 real ewaldCoeff_q = 1.0F,
116 real ewaldCoeff_lj = 1.0F
119 const MDLogger dummyLogger;
120 const auto runMode = (mode == CodePath::CPU) ? PmeRunMode::CPU : PmeRunMode::Mixed;
121 t_commrec dummyCommrec = {0};
122 NumPmeDomains numPmeDomains = { 1, 1 };
123 gmx_pme_t *pmeDataRaw = gmx_pme_init(&dummyCommrec, numPmeDomains, inputRec, false, false, true,
124 ewaldCoeff_q, ewaldCoeff_lj, 1, runMode, nullptr, gpuInfo, pmeGpuProgram, dummyLogger);
125 PmeSafePointer pme(pmeDataRaw); // taking ownership
127 // TODO get rid of this with proper matrix type
129 for (int i = 0; i < DIM; i++)
131 for (int j = 0; j < DIM; j++)
133 boxTemp[i][j] = box[i * DIM + j];
136 const char *boxError = check_box(-1, boxTemp);
137 GMX_RELEASE_ASSERT(boxError == nullptr, boxError);
142 invertBoxMatrix(boxTemp, pme->recipbox);
146 pme_gpu_set_testing(pme->gpu, true);
147 pme_gpu_update_input_box(pme->gpu, boxTemp);
151 GMX_THROW(InternalError("Test not implemented for this mode"));
157 //! Simple PME initialization based on input, no atom data
158 PmeSafePointer pmeInitEmpty(const t_inputrec *inputRec,
160 const gmx_device_info_t *gpuInfo,
161 PmeGpuProgramHandle pmeGpuProgram,
162 const Matrix3x3 &box,
167 return pmeInitInternal(inputRec, mode, gpuInfo, pmeGpuProgram, box, ewaldCoeff_q, ewaldCoeff_lj);
168 // hiding the fact that PME actually needs to know the number of atoms in advance
171 //! PME initialization with atom data
172 PmeSafePointer pmeInitAtoms(const t_inputrec *inputRec,
174 const gmx_device_info_t *gpuInfo,
175 PmeGpuProgramHandle pmeGpuProgram,
176 const CoordinatesVector &coordinates,
177 const ChargesVector &charges,
178 const Matrix3x3 &box,
179 std::shared_ptr<StatePropagatorDataGpu> stateGpu
182 const index atomCount = coordinates.size();
183 GMX_RELEASE_ASSERT(atomCount == charges.ssize(), "Mismatch in atom data");
184 PmeSafePointer pmeSafe = pmeInitInternal(inputRec, mode, gpuInfo, pmeGpuProgram, box);
185 PmeAtomComm *atc = nullptr;
190 atc = &(pmeSafe->atc[0]);
191 atc->x = coordinates;
192 atc->coefficient = charges;
193 gmx_pme_reinit_atoms(pmeSafe.get(), atomCount, charges.data());
194 /* With decomposition there would be more boilerplate atc code here, e.g. do_redist_pos_coeffs */
198 // TODO: Avoid use of atc in the GPU code path
199 atc = &(pmeSafe->atc[0]);
200 // We need to set atc->n for passing the size in the tests
201 atc->setNumAtoms(atomCount);
202 gmx_pme_reinit_atoms(pmeSafe.get(), atomCount, charges.data());
204 // TODO: Pin the host buffer and use async memory copies
205 stateGpu = std::make_unique<StatePropagatorDataGpu>(pme_gpu_get_device_stream(pmeSafe.get()),
206 pme_gpu_get_device_context(pmeSafe.get()),
207 GpuApiCallBehavior::Sync,
208 pme_gpu_get_padding_size(pmeSafe.get()));
209 stateGpu->reinit(atomCount, atomCount);
210 stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()), gmx::StatePropagatorDataGpu::AtomLocality::All);
211 pme_gpu_set_kernelparam_coordinates(pmeSafe->gpu, stateGpu->getCoordinates());
216 GMX_THROW(InternalError("Test not implemented for this mode"));
222 //! Getting local PME real grid pointer for test I/O
223 static real *pmeGetRealGridInternal(const gmx_pme_t *pme)
225 const size_t gridIndex = 0;
226 return pme->fftgrid[gridIndex];
229 //! Getting local PME real grid dimensions
230 static void pmeGetRealGridSizesInternal(const gmx_pme_t *pme,
232 IVec &gridSize, //NOLINT(google-runtime-references)
233 IVec &paddedGridSize) //NOLINT(google-runtime-references)
235 const size_t gridIndex = 0;
236 IVec gridOffsetUnused;
240 gmx_parallel_3dfft_real_limits(pme->pfft_setup[gridIndex], gridSize, gridOffsetUnused, paddedGridSize);
244 pme_gpu_get_real_grid_sizes(pme->gpu, &gridSize, &paddedGridSize);
248 GMX_THROW(InternalError("Test not implemented for this mode"));
252 //! Getting local PME complex grid pointer for test I/O
253 static t_complex *pmeGetComplexGridInternal(const gmx_pme_t *pme)
255 const size_t gridIndex = 0;
256 return pme->cfftgrid[gridIndex];
259 //! Getting local PME complex grid dimensions
260 static void pmeGetComplexGridSizesInternal(const gmx_pme_t *pme,
261 IVec &gridSize, //NOLINT(google-runtime-references)
262 IVec &paddedGridSize) //NOLINT(google-runtime-references)
264 const size_t gridIndex = 0;
265 IVec gridOffsetUnused, complexOrderUnused;
266 gmx_parallel_3dfft_complex_limits(pme->pfft_setup[gridIndex], complexOrderUnused, gridSize, gridOffsetUnused, paddedGridSize); //TODO: what about YZX ordering?
269 //! Getting the PME grid memory buffer and its sizes - template definition
270 template<typename ValueType> static void pmeGetGridAndSizesInternal(const gmx_pme_t * /*unused*/, CodePath /*unused*/, ValueType * & /*unused*/, IVec & /*unused*/, IVec & /*unused*/) //NOLINT(google-runtime-references)
272 GMX_THROW(InternalError("Deleted function call"));
273 // explicitly deleting general template does not compile in clang/icc, see https://llvm.org/bugs/show_bug.cgi?id=17537
276 //! Getting the PME real grid memory buffer and its sizes
277 template<> void pmeGetGridAndSizesInternal<real>(const gmx_pme_t *pme, CodePath mode, real * &grid, IVec &gridSize, IVec &paddedGridSize)
279 grid = pmeGetRealGridInternal(pme);
280 pmeGetRealGridSizesInternal(pme, mode, gridSize, paddedGridSize);
283 //! Getting the PME complex grid memory buffer and its sizes
284 template<> void pmeGetGridAndSizesInternal<t_complex>(const gmx_pme_t *pme, CodePath /*unused*/, t_complex * &grid, IVec &gridSize, IVec &paddedGridSize)
286 grid = pmeGetComplexGridInternal(pme);
287 pmeGetComplexGridSizesInternal(pme, gridSize, paddedGridSize);
290 //! PME spline calculation and charge spreading
291 void pmePerformSplineAndSpread(gmx_pme_t *pme, CodePath mode, // TODO const qualifiers elsewhere
292 bool computeSplines, bool spreadCharges)
294 GMX_RELEASE_ASSERT(pme != nullptr, "PME data is not initialized");
295 PmeAtomComm *atc = &(pme->atc[0]);
296 const size_t gridIndex = 0;
297 const bool computeSplinesForZeroCharges = true;
298 real *fftgrid = spreadCharges ? pme->fftgrid[gridIndex] : nullptr;
299 real *pmegrid = pme->pmegrid[gridIndex].grid.grid;
304 spread_on_grid(pme, atc, &pme->pmegrid[gridIndex], computeSplines, spreadCharges,
305 fftgrid, computeSplinesForZeroCharges, gridIndex);
306 if (spreadCharges && !pme->bUseThreads)
308 wrap_periodic_pmegrid(pme, pmegrid);
309 copy_pmegrid_to_fftgrid(pme, pmegrid, fftgrid, gridIndex);
314 pme_gpu_spread(pme->gpu, gridIndex, fftgrid, computeSplines, spreadCharges);
318 GMX_THROW(InternalError("Test not implemented for this mode"));
322 //! Getting the internal spline data buffer pointer
323 static real *pmeGetSplineDataInternal(const gmx_pme_t *pme, PmeSplineDataType type, int dimIndex)
325 GMX_ASSERT((0 <= dimIndex) && (dimIndex < DIM), "Invalid dimension index");
326 const PmeAtomComm *atc = &(pme->atc[0]);
327 const size_t threadIndex = 0;
328 real *splineBuffer = nullptr;
331 case PmeSplineDataType::Values:
332 splineBuffer = atc->spline[threadIndex].theta.coefficients[dimIndex];
335 case PmeSplineDataType::Derivatives:
336 splineBuffer = atc->spline[threadIndex].dtheta.coefficients[dimIndex];
340 GMX_THROW(InternalError("Unknown spline data type"));
346 void pmePerformSolve(const gmx_pme_t *pme, CodePath mode,
347 PmeSolveAlgorithm method, real cellVolume,
348 GridOrdering gridOrdering, bool computeEnergyAndVirial)
350 t_complex *h_grid = pmeGetComplexGridInternal(pme);
351 const bool useLorentzBerthelot = false;
352 const size_t threadIndex = 0;
356 if (gridOrdering != GridOrdering::YZX)
358 GMX_THROW(InternalError("Test not implemented for this mode"));
362 case PmeSolveAlgorithm::Coulomb:
363 solve_pme_yzx(pme, h_grid, cellVolume,
364 computeEnergyAndVirial, pme->nthread, threadIndex);
367 case PmeSolveAlgorithm::LennardJones:
368 solve_pme_lj_yzx(pme, &h_grid, useLorentzBerthelot,
369 cellVolume, computeEnergyAndVirial, pme->nthread, threadIndex);
373 GMX_THROW(InternalError("Test not implemented for this mode"));
380 case PmeSolveAlgorithm::Coulomb:
381 pme_gpu_solve(pme->gpu, h_grid, gridOrdering, computeEnergyAndVirial);
385 GMX_THROW(InternalError("Test not implemented for this mode"));
390 GMX_THROW(InternalError("Test not implemented for this mode"));
394 //! PME force gathering
395 void pmePerformGather(gmx_pme_t *pme, CodePath mode,
396 PmeForceOutputHandling inputTreatment, ForcesVector &forces)
398 PmeAtomComm *atc = &(pme->atc[0]);
399 const index atomCount = atc->numAtoms();
400 GMX_RELEASE_ASSERT(forces.ssize() == atomCount, "Invalid force buffer size");
401 const bool forceReductionWithInput = (inputTreatment == PmeForceOutputHandling::ReduceWithInput);
402 const real scale = 1.0;
403 const size_t threadIndex = 0;
404 const size_t gridIndex = 0;
405 real *pmegrid = pme->pmegrid[gridIndex].grid.grid;
406 real *fftgrid = pme->fftgrid[gridIndex];
412 if (atc->nthread == 1)
414 // something which is normally done in serial spline computation (make_thread_local_ind())
415 atc->spline[threadIndex].n = atomCount;
417 copy_fftgrid_to_pmegrid(pme, fftgrid, pmegrid, gridIndex, pme->nthread, threadIndex);
418 unwrap_periodic_pmegrid(pme, pmegrid);
419 gather_f_bsplines(pme, pmegrid, !forceReductionWithInput, atc, &atc->spline[threadIndex], scale);
424 // Variable initialization needs a non-switch scope
425 PmeOutput output = pme_gpu_getOutput(*pme, GMX_PME_CALC_F);
426 GMX_ASSERT(forces.size() == output.forces_.size(), "Size of force buffers did not match");
427 if (forceReductionWithInput)
429 std::copy(std::begin(forces), std::end(forces), std::begin(output.forces_));
431 pme_gpu_gather(pme->gpu, inputTreatment, reinterpret_cast<float *>(fftgrid));
432 std::copy(std::begin(output.forces_), std::end(output.forces_), std::begin(forces));
437 GMX_THROW(InternalError("Test not implemented for this mode"));
441 //! PME test finalization before fetching the outputs
442 void pmeFinalizeTest(const gmx_pme_t *pme, CodePath mode)
450 pme_gpu_synchronize(pme->gpu);
454 GMX_THROW(InternalError("Test not implemented for this mode"));
458 //! Setting atom spline values/derivatives to be used in spread/gather
459 void pmeSetSplineData(const gmx_pme_t *pme, CodePath mode,
460 const SplineParamsDimVector &splineValues, PmeSplineDataType type, int dimIndex)
462 const PmeAtomComm *atc = &(pme->atc[0]);
463 const index atomCount = atc->numAtoms();
464 const index pmeOrder = pme->pme_order;
465 const index dimSize = pmeOrder * atomCount;
466 GMX_RELEASE_ASSERT(dimSize == splineValues.ssize(), "Mismatch in spline data");
467 real *splineBuffer = pmeGetSplineDataInternal(pme, type, dimIndex);
472 std::copy(splineValues.begin(), splineValues.end(), splineBuffer);
476 std::copy(splineValues.begin(), splineValues.end(), splineBuffer);
477 pme_gpu_transform_spline_atom_data(pme->gpu, atc, type, dimIndex, PmeLayoutTransform::HostToGpu);
481 GMX_THROW(InternalError("Test not implemented for this mode"));
485 //! Setting gridline indices to be used in spread/gather
486 void pmeSetGridLineIndices(gmx_pme_t *pme, CodePath mode,
487 const GridLineIndicesVector &gridLineIndices)
489 PmeAtomComm *atc = &(pme->atc[0]);
490 const index atomCount = atc->numAtoms();
491 GMX_RELEASE_ASSERT(atomCount == gridLineIndices.ssize(), "Mismatch in gridline indices size");
493 IVec paddedGridSizeUnused, gridSize(0, 0, 0);
494 pmeGetRealGridSizesInternal(pme, mode, gridSize, paddedGridSizeUnused);
496 for (const auto &index : gridLineIndices)
498 for (int i = 0; i < DIM; i++)
500 GMX_RELEASE_ASSERT((0 <= index[i]) && (index[i] < gridSize[i]), "Invalid gridline index");
507 memcpy(pme->gpu->staging.h_gridlineIndices, gridLineIndices.data(), atomCount * sizeof(gridLineIndices[0]));
511 atc->idx.resize(gridLineIndices.size());
512 std::copy(gridLineIndices.begin(), gridLineIndices.end(), atc->idx.begin());
515 GMX_THROW(InternalError("Test not implemented for this mode"));
519 //! Getting plain index into the complex 3d grid
520 inline size_t pmeGetGridPlainIndexInternal(const IVec &index, const IVec &paddedGridSize, GridOrdering gridOrdering)
523 switch (gridOrdering)
525 case GridOrdering::YZX:
526 result = (index[YY] * paddedGridSize[ZZ] + index[ZZ]) * paddedGridSize[XX] + index[XX];
529 case GridOrdering::XYZ:
530 result = (index[XX] * paddedGridSize[YY] + index[YY]) * paddedGridSize[ZZ] + index[ZZ];
534 GMX_THROW(InternalError("Test not implemented for this mode"));
539 //! Setting real or complex grid
540 template<typename ValueType>
541 static void pmeSetGridInternal(const gmx_pme_t *pme, CodePath mode,
542 GridOrdering gridOrdering,
543 const SparseGridValuesInput<ValueType> &gridValues)
545 IVec gridSize(0, 0, 0), paddedGridSize(0, 0, 0);
547 pmeGetGridAndSizesInternal<ValueType>(pme, mode, grid, gridSize, paddedGridSize);
551 case CodePath::GPU: // intentional absence of break, the grid will be copied from the host buffer in testing mode
553 std::memset(grid, 0, paddedGridSize[XX] * paddedGridSize[YY] * paddedGridSize[ZZ] * sizeof(ValueType));
554 for (const auto &gridValue : gridValues)
556 for (int i = 0; i < DIM; i++)
558 GMX_RELEASE_ASSERT((0 <= gridValue.first[i]) && (gridValue.first[i] < gridSize[i]), "Invalid grid value index");
560 const size_t gridValueIndex = pmeGetGridPlainIndexInternal(gridValue.first, paddedGridSize, gridOrdering);
561 grid[gridValueIndex] = gridValue.second;
566 GMX_THROW(InternalError("Test not implemented for this mode"));
570 //! Setting real grid to be used in gather
571 void pmeSetRealGrid(const gmx_pme_t *pme, CodePath mode,
572 const SparseRealGridValuesInput &gridValues)
574 pmeSetGridInternal<real>(pme, mode, GridOrdering::XYZ, gridValues);
577 //! Setting complex grid to be used in solve
578 void pmeSetComplexGrid(const gmx_pme_t *pme, CodePath mode,
579 GridOrdering gridOrdering,
580 const SparseComplexGridValuesInput &gridValues)
582 pmeSetGridInternal<t_complex>(pme, mode, gridOrdering, gridValues);
585 //! Getting the single dimension's spline values or derivatives
586 SplineParamsDimVector pmeGetSplineData(const gmx_pme_t *pme, CodePath mode,
587 PmeSplineDataType type, int dimIndex)
589 GMX_RELEASE_ASSERT(pme != nullptr, "PME data is not initialized");
590 const PmeAtomComm *atc = &(pme->atc[0]);
591 const size_t atomCount = atc->numAtoms();
592 const size_t pmeOrder = pme->pme_order;
593 const size_t dimSize = pmeOrder * atomCount;
595 real *sourceBuffer = pmeGetSplineDataInternal(pme, type, dimIndex);
596 SplineParamsDimVector result;
600 pme_gpu_transform_spline_atom_data(pme->gpu, atc, type, dimIndex, PmeLayoutTransform::GpuToHost);
601 result = arrayRefFromArray(sourceBuffer, dimSize);
605 result = arrayRefFromArray(sourceBuffer, dimSize);
609 GMX_THROW(InternalError("Test not implemented for this mode"));
614 //! Getting the gridline indices
615 GridLineIndicesVector pmeGetGridlineIndices(const gmx_pme_t *pme, CodePath mode)
617 GMX_RELEASE_ASSERT(pme != nullptr, "PME data is not initialized");
618 const PmeAtomComm *atc = &(pme->atc[0]);
619 const size_t atomCount = atc->numAtoms();
621 GridLineIndicesVector gridLineIndices;
625 gridLineIndices = arrayRefFromArray(reinterpret_cast<IVec *>(pme->gpu->staging.h_gridlineIndices), atomCount);
629 gridLineIndices = atc->idx;
633 GMX_THROW(InternalError("Test not implemented for this mode"));
635 return gridLineIndices;
638 //! Getting real or complex grid - only non zero values
639 template<typename ValueType>
640 static SparseGridValuesOutput<ValueType> pmeGetGridInternal(const gmx_pme_t *pme, CodePath mode, GridOrdering gridOrdering)
642 IVec gridSize(0, 0, 0), paddedGridSize(0, 0, 0);
644 pmeGetGridAndSizesInternal<ValueType>(pme, mode, grid, gridSize, paddedGridSize);
645 SparseGridValuesOutput<ValueType> gridValues;
648 case CodePath::GPU: // intentional absence of break
651 for (int ix = 0; ix < gridSize[XX]; ix++)
653 for (int iy = 0; iy < gridSize[YY]; iy++)
655 for (int iz = 0; iz < gridSize[ZZ]; iz++)
657 IVec temp(ix, iy, iz);
658 const size_t gridValueIndex = pmeGetGridPlainIndexInternal(temp, paddedGridSize, gridOrdering);
659 const ValueType value = grid[gridValueIndex];
660 if (value != ValueType {})
662 auto key = formatString("Cell %d %d %d", ix, iy, iz);
663 gridValues[key] = value;
671 GMX_THROW(InternalError("Test not implemented for this mode"));
676 //! Getting the real grid (spreading output of pmePerformSplineAndSpread())
677 SparseRealGridValuesOutput pmeGetRealGrid(const gmx_pme_t *pme, CodePath mode)
679 return pmeGetGridInternal<real>(pme, mode, GridOrdering::XYZ);
682 //! Getting the complex grid output of pmePerformSolve()
683 SparseComplexGridValuesOutput pmeGetComplexGrid(const gmx_pme_t *pme, CodePath mode,
684 GridOrdering gridOrdering)
686 return pmeGetGridInternal<t_complex>(pme, mode, gridOrdering);
689 //! Getting the reciprocal energy and virial
690 PmeOutput pmeGetReciprocalEnergyAndVirial(const gmx_pme_t *pme, CodePath mode,
691 PmeSolveAlgorithm method)
699 case PmeSolveAlgorithm::Coulomb:
700 get_pme_ener_vir_q(pme->solve_work, pme->nthread, &output);
703 case PmeSolveAlgorithm::LennardJones:
704 get_pme_ener_vir_lj(pme->solve_work, pme->nthread, &output);
708 GMX_THROW(InternalError("Test not implemented for this mode"));
714 case PmeSolveAlgorithm::Coulomb:
715 pme_gpu_getEnergyAndVirial(*pme, &output);
719 GMX_THROW(InternalError("Test not implemented for this mode"));
724 GMX_THROW(InternalError("Test not implemented for this mode"));