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pme_gpu_internal.cpp File Reference
#include "gmxpre.h"
#include "pme_gpu_internal.h"
#include "config.h"
#include <list>
#include <memory>
#include <string>
#include "gromacs/ewald/ewald_utils.h"
#include "gromacs/fft/gpu_3dfft.h"
#include "gromacs/gpu_utils/device_context.h"
#include "gromacs/gpu_utils/device_stream.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/gpu_utils/pmalloc.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/ewald/pme_coordinate_receiver_gpu.h"
#include "gromacs/hardware/device_information.h"
#include "gromacs/math/boxmatrix.h"
#include "gromacs/math/units.h"
#include "gromacs/timing/gpu_timing.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/stringutil.h"
#include "pme_gpu_calculate_splines.h"
#include "pme_gpu_constants.h"
#include "pme_gpu_grid.h"
#include "pme_gpu_program_impl.h"
#include "pme_gpu_timings.h"
#include "pme_gpu_types.h"
#include "pme_gpu_types_host.h"
#include "pme_gpu_types_host_impl.h"
#include "pme_grid.h"
#include "pme_internal.h"
#include "pme_solve.h"
+ Include dependency graph for pme_gpu_internal.cpp:

Description

This file contains internal function implementations for performing the PME calculations on GPU.

Note that this file is compiled as regular C++ source in OpenCL builds, but it is treated as CUDA source in CUDA-enabled GPU builds.

Author
Aleksei Iupinov a.yup.nosp@m.inov.nosp@m.@gmai.nosp@m.l.co.nosp@m.m

Functions

static PmeGpuKernelParamsBasepme_gpu_get_kernel_params_base_ptr (const PmeGpu *pmeGpu)
 Wrapper for getting a pointer to the plain C++ part of the GPU kernel parameters structure. More...
 
int pme_gpu_get_atom_data_block_size ()
 Returns the size of the block size requirement. More...
 
int pme_gpu_get_atoms_per_warp (const PmeGpu *pmeGpu)
 Return the number of atoms per warp.
 
void pme_gpu_synchronize (const PmeGpu *pmeGpu)
 Synchronizes the current computation, waiting for the GPU kernels/transfers to finish. More...
 
void pme_gpu_alloc_energy_virial (PmeGpu *pmeGpu)
 Allocates the fixed size energy and virial buffer both on GPU and CPU. More...
 
void pme_gpu_free_energy_virial (PmeGpu *pmeGpu)
 Frees the energy and virial memory both on GPU and CPU. More...
 
void pme_gpu_clear_energy_virial (const PmeGpu *pmeGpu, const bool gpuGraphWithSeparatePmeRank)
 Clears the energy and virial memory on GPU with 0. Should be called at the end of PME computation which returned energy/virial. More...
 
void pme_gpu_realloc_and_copy_bspline_values (PmeGpu *pmeGpu, const int gridIndex)
 Reallocates and copies the pre-computed B-spline values to the GPU. More...
 
void pme_gpu_free_bspline_values (const PmeGpu *pmeGpu)
 Frees the pre-computed B-spline values on the GPU (and the transfer CPU buffers). More...
 
void pme_gpu_realloc_forces (PmeGpu *pmeGpu)
 Reallocates the GPU buffer for the PME forces. More...
 
void pme_gpu_free_forces (const PmeGpu *pmeGpu)
 Frees the GPU buffer for the PME forces. More...
 
void pme_gpu_copy_input_forces (PmeGpu *pmeGpu)
 Copies the forces from the CPU buffer to the GPU (to reduce them with the PME GPU gathered forces). To be called e.g. after the bonded calculations. More...
 
void pme_gpu_copy_output_forces (PmeGpu *pmeGpu)
 Copies the forces from the GPU to the CPU buffer. To be called after the gathering stage. More...
 
void pme_gpu_realloc_and_copy_input_coefficients (const PmeGpu *pmeGpu, const float *h_coefficients, const int gridIndex)
 Reallocates the buffer on the GPU and copies the charges/coefficients from the CPU buffer. Clears the padded part if needed. More...
 
void pme_gpu_free_coefficients (const PmeGpu *pmeGpu)
 Frees the charges/coefficients on the GPU. More...
 
void pme_gpu_realloc_spline_data (PmeGpu *pmeGpu)
 Reallocates the buffers on the GPU and the host for the atoms spline data. More...
 
void pme_gpu_free_spline_data (const PmeGpu *pmeGpu)
 Frees the buffers on the GPU for the atoms spline data. More...
 
void pme_gpu_realloc_grid_indices (PmeGpu *pmeGpu)
 Reallocates the buffers on the GPU and the host for the particle gridline indices. More...
 
void pme_gpu_free_grid_indices (const PmeGpu *pmeGpu)
 Frees the buffer on the GPU for the particle gridline indices. More...
 
void pme_gpu_realloc_grids (PmeGpu *pmeGpu)
 Reallocates the real space grid and the complex reciprocal grid (if needed) on the GPU. More...
 
void pme_gpu_free_grids (const PmeGpu *pmeGpu)
 Frees the real space grid and the complex reciprocal grid (if needed) on the GPU. More...
 
void pme_gpu_reinit_haloexchange (PmeGpu *pmeGpu)
 Reinitialize PME halo exchange parameters and staging device buffers for MPI communication. More...
 
void pme_gpu_free_haloexchange (const PmeGpu *pmeGpu)
 Frees device staging buffers used for PME halo exchange. More...
 
void pme_gpu_clear_grids (const PmeGpu *pmeGpu)
 Clears the real space grid on the GPU. Should be called at the end of each computation. More...
 
void pme_gpu_realloc_and_copy_fract_shifts (PmeGpu *pmeGpu)
 Reallocates and copies the pre-computed fractional coordinates' shifts to the GPU. More...
 
void pme_gpu_free_fract_shifts (const PmeGpu *pmeGpu)
 Frees the pre-computed fractional coordinates' shifts on the GPU. More...
 
bool pme_gpu_stream_query (const PmeGpu *pmeGpu)
 Checks whether work in the PME GPU stream has completed. More...
 
void pme_gpu_copy_input_gather_grid (const PmeGpu *pmeGpu, const float *h_grid, const int gridIndex)
 Copies the input real-space grid from the host to the GPU. More...
 
void pme_gpu_copy_output_spread_grid (const PmeGpu *pmeGpu, float *h_grid, const int gridIndex)
 Copies the output real-space grid from the GPU to the host. More...
 
void pme_gpu_copy_output_spread_atom_data (const PmeGpu *pmeGpu)
 Copies the spread output spline data and gridline indices from the GPU to the host. More...
 
void pme_gpu_copy_input_gather_atom_data (const PmeGpu *pmeGpu)
 Copies the gather input spline data and gridline indices from the host to the GPU. More...
 
void pme_gpu_sync_spread_grid (const PmeGpu *pmeGpu)
 Waits for the grid copying to the host-side buffer after spreading to finish. More...
 
static void pme_gpu_init_internal (PmeGpu *pmeGpu, const DeviceContext &deviceContext, const DeviceStream &deviceStream)
 Internal GPU initialization for PME. More...
 
static gmx::FftBackend getFftBackend (const PmeGpu *pmeGpu)
 Wrapper for getting FFT backend depending on Gromacs GPU backend compilation flags. More...
 
void pme_gpu_reinit_3dfft (const PmeGpu *pmeGpu)
 Initializes the CUDA FFT structures. More...
 
void pme_gpu_destroy_3dfft (const PmeGpu *pmeGpu)
 Destroys the CUDA FFT structures. More...
 
void pme_gpu_getEnergyAndVirial (const gmx_pme_t &pme, const float lambda, PmeOutput *output)
 Returns the energy and virial GPU outputs, useful for testing. More...
 
static void pme_gpu_getForceOutput (PmeGpu *pmeGpu, PmeOutput *output)
 Sets the force-related members in output. More...
 
PmeOutput pme_gpu_getOutput (const gmx_pme_t &pme, const bool computeEnergyAndVirial, const real lambdaQ)
 Returns the GPU outputs (forces, energy and virial) More...
 
void pme_gpu_update_input_box (PmeGpu gmx_unused *pmeGpu, const matrix gmx_unused box)
 
static void pme_gpu_reinit_grids (PmeGpu *pmeGpu)
 (Re-)initializes all the PME GPU data related to the grid size and cut-off. More...
 
static void pme_gpu_copy_common_data_from (const gmx_pme_t *pme)
 Copies everything useful from the PME CPU to the PME GPU structure. The goal is to minimize interaction with the PME CPU structure in the GPU code. More...
 
static void pme_gpu_select_best_performing_pme_spreadgather_kernels (PmeGpu *pmeGpu)
 uses heuristics to select the best performing PME gather and scatter kernels More...
 
static void pme_gpu_init (gmx_pme_t *pme, const DeviceContext &deviceContext, const DeviceStream &deviceStream, const PmeGpuProgram *pmeGpuProgram)
 Initializes the PME GPU data at the beginning of the run. TODO: this should become PmeGpu::PmeGpu() More...
 
void pme_gpu_get_real_grid_sizes (const PmeGpu *pmeGpu, gmx::IVec *gridSize, gmx::IVec *paddedGridSize)
 Get the normal/padded grid dimensions of the real-space PME grid on GPU. Only used in tests. More...
 
void pme_gpu_reinit (gmx_pme_t *pme, const DeviceContext *deviceContext, const DeviceStream *deviceStream, const PmeGpuProgram *pmeGpuProgram, const bool useMdGpuGraph)
 (Re-)initializes the PME GPU data at the beginning of the run or on DLB. More...
 
void pme_gpu_destroy (PmeGpu *pmeGpu)
 Destroys the PME GPU data at the end of the run. More...
 
void pme_gpu_reinit_atoms (PmeGpu *pmeGpu, const int nAtoms, const real *chargesA, const real *chargesB)
 Reallocates the local atoms data (charges, coordinates, etc.). Copies the charges to the GPU. More...
 
static CommandEventpme_gpu_fetch_timing_event (const PmeGpu *pmeGpu, PmeStage pmeStageId)
 Returns raw timing event from the corresponding GpuRegionTimer (if timings are enabled). In CUDA result can be nullptr stub, per GpuRegionTimer implementation. More...
 
void pme_gpu_3dfft (const PmeGpu *pmeGpu, gmx_fft_direction dir, const int grid_index)
 3D FFT R2C/C2R routine. More...
 
std::pair< int, int > pmeGpuCreateGrid (const PmeGpu *pmeGpu, int blockCount)
 Given possibly large blockCount, returns a compact 1D or 2D grid for kernel scheduling, to minimize number of unused blocks.
 
static auto selectSplineAndSpreadKernelPtr (const PmeGpu *pmeGpu, ThreadsPerAtom threadsPerAtom, bool writeSplinesToGlobal, const int numGrids)
 Returns a pointer to appropriate spline and spread kernel based on the input bool values. More...
 
static auto selectSplineKernelPtr (const PmeGpu *pmeGpu, ThreadsPerAtom threadsPerAtom, bool gmx_unused writeSplinesToGlobal, const int numGrids)
 Returns a pointer to appropriate spline kernel based on the input bool values. More...
 
static auto selectSpreadKernelPtr (const PmeGpu *pmeGpu, ThreadsPerAtom threadsPerAtom, bool writeSplinesToGlobal, const int numGrids)
 Returns a pointer to appropriate spread kernel based on the input bool values. More...
 
static int manageSyncWithPpCoordinateSenderGpu (const PmeGpu *pmeGpu, gmx::PmeCoordinateReceiverGpu *pmeCoordinateReceiverGpu, bool usePipeline=false, int pipelineStage=0)
 Manages synchronization with remote GPU's PP coordinate sender, for a stage of the communication operation. For thread-MPI, an event associated with a stage of the operation is enqueued to the GPU stream that will be used by the consumer. For lib-MPI, the CPU task executing this function will wait for a stage to be completed. In each case, the rank of the sender associated with the corresponding stage is returned. More...
 
void pme_gpu_spread (const PmeGpu *pmeGpu, GpuEventSynchronizer *xReadyOnDevice, real **h_grids, gmx_parallel_3dfft_t *fftSetup, bool computeSplines, bool spreadCharges, const real lambda, const bool useGpuDirectComm, gmx::PmeCoordinateReceiverGpu *pmeCoordinateReceiverGpu, const bool useMdGpuGraph, gmx_wallcycle *wcycle)
 A GPU spline computation and charge spreading function. More...
 
void pme_gpu_solve (const PmeGpu *pmeGpu, const int gridIndex, t_complex *h_grid, GridOrdering gridOrdering, bool computeEnergyAndVirial)
 A GPU Fourier space solving function. More...
 
auto selectGatherKernelPtr (const PmeGpu *pmeGpu, ThreadsPerAtom threadsPerAtom, bool readSplinesFromGlobal, const int numGrids)
 Returns a pointer to appropriate gather kernel based on the inputvalues. More...
 
void pme_gpu_gather (PmeGpu *pmeGpu, real **h_grids, gmx_parallel_3dfft_t *fftSetup, const float lambda, gmx_wallcycle *wcycle, bool computeVirial)
 A GPU force gathering function. More...
 
DeviceBuffer< gmx::RVecpme_gpu_get_kernelparam_forces (const PmeGpu *pmeGpu)
 Return pointer to device copy of force data. More...
 
void pme_gpu_set_kernelparam_useNvshmem (const PmeGpu *pmeGpu, bool useNvshmem)
 
void pme_gpu_set_kernelparam_coordinates (const PmeGpu *pmeGpu, DeviceBuffer< gmx::RVec > d_x)
 Sets the device pointer to coordinate data. More...
 
GpuEventSynchronizer * pme_gpu_get_forces_ready_synchronizer (const PmeGpu *pmeGpu)
 Return pointer to the sync object triggered after the PME force calculation completion. More...
 

Variables

constexpr int c_pmeAtomDataBlockSize = 64
 Atom data block size (in terms of number of atoms). This is the least common multiple of number of atoms processed by a single block/workgroup of the spread and gather kernels. The GPU atom data buffers must be padded, which means that the numbers of atoms used for determining the size of the memory allocation must be divisible by this.
 

Function Documentation

static gmx::FftBackend getFftBackend ( const PmeGpu pmeGpu)
static

Wrapper for getting FFT backend depending on Gromacs GPU backend compilation flags.

Parameters
[in]pmeGpuThe PME GPU structure.
Returns
FftBackend enum value.
static int manageSyncWithPpCoordinateSenderGpu ( const PmeGpu pmeGpu,
gmx::PmeCoordinateReceiverGpu *  pmeCoordinateReceiverGpu,
bool  usePipeline = false,
int  pipelineStage = 0 
)
static

Manages synchronization with remote GPU's PP coordinate sender, for a stage of the communication operation. For thread-MPI, an event associated with a stage of the operation is enqueued to the GPU stream that will be used by the consumer. For lib-MPI, the CPU task executing this function will wait for a stage to be completed. In each case, the rank of the sender associated with the corresponding stage is returned.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]pmeCoordinateReceiverGpuThe PME coordinate reciever GPU object
[in]usePipelineWhether pipelining is in use for PME-PP communication
[in]pipelineStageStage of the PME-PP communication pipeline
Returns
Rank of remote sender associated with this stage
void pme_gpu_3dfft ( const PmeGpu pmeGpu,
enum gmx_fft_direction  direction,
int  gridIndex = 0 
)

3D FFT R2C/C2R routine.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]directionTransform direction (real-to-complex or complex-to-real)
[in]gridIndexThe index of the grid to use. 0 is Coulomb in the normal state or FEP state A and 1 is Coulomb in FEP state B.
void pme_gpu_alloc_energy_virial ( PmeGpu pmeGpu)

Allocates the fixed size energy and virial buffer both on GPU and CPU.

Parameters
[in,out]pmeGpuThe PME GPU structure.
void pme_gpu_clear_energy_virial ( const PmeGpu pmeGpu,
bool  gpuGraphWithSeparatePmeRank 
)

Clears the energy and virial memory on GPU with 0. Should be called at the end of PME computation which returned energy/virial.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]gpuGraphWithSeparatePmeRankWhether MD GPU Graph with separate PME rank is in use.
void pme_gpu_clear_grids ( const PmeGpu pmeGpu)

Clears the real space grid on the GPU. Should be called at the end of each computation.

Parameters
[in]pmeGpuThe PME GPU structure.
static void pme_gpu_copy_common_data_from ( const gmx_pme_t *  pme)
static

Copies everything useful from the PME CPU to the PME GPU structure. The goal is to minimize interaction with the PME CPU structure in the GPU code.

Parameters
[in]pmeThe PME structure.
void pme_gpu_copy_input_forces ( PmeGpu pmeGpu)

Copies the forces from the CPU buffer to the GPU (to reduce them with the PME GPU gathered forces). To be called e.g. after the bonded calculations.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_copy_input_gather_atom_data ( const PmeGpu pmeGpu)

Copies the gather input spline data and gridline indices from the host to the GPU.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_copy_input_gather_grid ( const PmeGpu pmeGpu,
const float *  h_grid,
int  gridIndex = 0 
)

Copies the input real-space grid from the host to the GPU.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]h_gridThe host-side grid buffer.
[in]gridIndexThe index of the grid to use. 0 is Coulomb in the normal state or FEP state A and 1 is Coulomb in FEP state B.
void pme_gpu_copy_output_forces ( PmeGpu pmeGpu)

Copies the forces from the GPU to the CPU buffer. To be called after the gathering stage.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_copy_output_spread_atom_data ( const PmeGpu pmeGpu)

Copies the spread output spline data and gridline indices from the GPU to the host.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_copy_output_spread_grid ( const PmeGpu pmeGpu,
float *  h_grid,
int  gridIndex = 0 
)

Copies the output real-space grid from the GPU to the host.

Parameters
[in]pmeGpuThe PME GPU structure.
[out]h_gridThe host-side grid buffer.
[in]gridIndexThe index of the grid to use. 0 is Coulomb in the normal state or FEP state A and 1 is Coulomb in FEP state B.
void pme_gpu_destroy ( PmeGpu pmeGpu)

Destroys the PME GPU data at the end of the run.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_destroy_3dfft ( const PmeGpu pmeGpu)

Destroys the CUDA FFT structures.

Parameters
[in]pmeGpuThe PME GPU structure.
static CommandEvent* pme_gpu_fetch_timing_event ( const PmeGpu pmeGpu,
PmeStage  pmeStageId 
)
static

Returns raw timing event from the corresponding GpuRegionTimer (if timings are enabled). In CUDA result can be nullptr stub, per GpuRegionTimer implementation.

Parameters
[in]pmeGpuThe PME GPU data structure.
[in]pmeStageIdThe PME GPU stage gtPME_ index from the enum in src/gromacs/timing/gpu_timing.h
void pme_gpu_free_bspline_values ( const PmeGpu pmeGpu)

Frees the pre-computed B-spline values on the GPU (and the transfer CPU buffers).

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_free_coefficients ( const PmeGpu pmeGpu)

Frees the charges/coefficients on the GPU.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_free_energy_virial ( PmeGpu pmeGpu)

Frees the energy and virial memory both on GPU and CPU.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_free_forces ( const PmeGpu pmeGpu)

Frees the GPU buffer for the PME forces.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_free_fract_shifts ( const PmeGpu pmeGpu)

Frees the pre-computed fractional coordinates' shifts on the GPU.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_free_grid_indices ( const PmeGpu pmeGpu)

Frees the buffer on the GPU for the particle gridline indices.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_free_grids ( const PmeGpu pmeGpu)

Frees the real space grid and the complex reciprocal grid (if needed) on the GPU.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_free_haloexchange ( const PmeGpu pmeGpu)

Frees device staging buffers used for PME halo exchange.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_free_spline_data ( const PmeGpu pmeGpu)

Frees the buffers on the GPU for the atoms spline data.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_gather ( PmeGpu pmeGpu,
float **  h_grids,
gmx_parallel_3dfft_t fftSetup,
float  lambda,
gmx_wallcycle *  wcycle,
bool  computeVirial 
)

A GPU force gathering function.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]h_gridsThe host-side grid buffer (used only in testing mode).
[in]fftSetupHost-side FFT setup structure used in Mixed mode
[in]lambdaThe lambda value to use.
[in]wcycleThe wallclock counter.
[in]computeVirialWhether this is a virial step.
int pme_gpu_get_atom_data_block_size ( )

Returns the size of the block size requirement.

The GPU version of PME requires that the coordinates array have a size divisible by the returned number.

Returns
Number of atoms in a single GPU atom data chunk, which determines a minimum divisor of the size of the memory allocated.
GpuEventSynchronizer* pme_gpu_get_forces_ready_synchronizer ( const PmeGpu pmeGpu)

Return pointer to the sync object triggered after the PME force calculation completion.

Parameters
[in]pmeGpuThe PME GPU structure.
Returns
Pointer to sync object
static PmeGpuKernelParamsBase* pme_gpu_get_kernel_params_base_ptr ( const PmeGpu pmeGpu)
static

Wrapper for getting a pointer to the plain C++ part of the GPU kernel parameters structure.

Parameters
[in]pmeGpuThe PME GPU structure.
Returns
The pointer to the kernel parameters.
DeviceBuffer<gmx::RVec> pme_gpu_get_kernelparam_forces ( const PmeGpu pmeGpu)

Return pointer to device copy of force data.

Parameters
[in]pmeGpuThe PME GPU structure.
Returns
Pointer to force data
void pme_gpu_get_real_grid_sizes ( const PmeGpu pmeGpu,
gmx::IVec gridSize,
gmx::IVec paddedGridSize 
)

Get the normal/padded grid dimensions of the real-space PME grid on GPU. Only used in tests.

Parameters
[in]pmeGpuThe PME GPU structure.
[out]gridSizePointer to the grid dimensions to fill in.
[out]paddedGridSizePointer to the padded grid dimensions to fill in.
void pme_gpu_getEnergyAndVirial ( const gmx_pme_t &  pme,
float  lambda,
PmeOutput *  output 
)

Returns the energy and virial GPU outputs, useful for testing.

It is the caller's responsibility to be aware of whether the GPU handled the solve stage.

Parameters
[in]pmeThe PME structure.
[in]lambdaThe lambda value to use when calculating the results.
[out]outputPointer to output where energy and virial should be stored.
static void pme_gpu_getForceOutput ( PmeGpu pmeGpu,
PmeOutput *  output 
)
static

Sets the force-related members in output.

Parameters
[in]pmeGpuPME GPU data structure
[out]outputPointer to PME output data structure
PmeOutput pme_gpu_getOutput ( const gmx_pme_t &  pme,
bool  computeEnergyAndVirial,
real  lambdaQ 
)

Returns the GPU outputs (forces, energy and virial)

Parameters
[in]pmeThe PME structure.
[in]computeEnergyAndVirialWhether the energy and virial are being computed
[in]lambdaQThe Coulomb lambda to use when finalizing the output.
Returns
The output object.
static void pme_gpu_init ( gmx_pme_t *  pme,
const DeviceContext &  deviceContext,
const DeviceStream deviceStream,
const PmeGpuProgram pmeGpuProgram 
)
static

Initializes the PME GPU data at the beginning of the run. TODO: this should become PmeGpu::PmeGpu()

Parameters
[in,out]pmeThe PME structure.
[in]deviceContextThe GPU context.
[in]deviceStreamThe GPU stream.
[in,out]pmeGpuProgramThe handle to the program/kernel data created outside (e.g. in unit tests/runner)
static void pme_gpu_init_internal ( PmeGpu pmeGpu,
const DeviceContext &  deviceContext,
const DeviceStream deviceStream 
)
static

Internal GPU initialization for PME.

Parameters
[in]pmeGpuGPU PME data.
[in]deviceContextGPU context.
[in]deviceStreamGPU stream.
void pme_gpu_realloc_and_copy_bspline_values ( PmeGpu pmeGpu,
int  gridIndex = 0 
)

Reallocates and copies the pre-computed B-spline values to the GPU.

Parameters
[in,out]pmeGpuThe PME GPU structure.
[in]gridIndexThe index of the grid to use. 0 is Coulomb in the normal state or FEP state A and 1 is Coulomb in FEP state B.
void pme_gpu_realloc_and_copy_fract_shifts ( PmeGpu pmeGpu)

Reallocates and copies the pre-computed fractional coordinates' shifts to the GPU.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_realloc_and_copy_input_coefficients ( const PmeGpu pmeGpu,
const float *  h_coefficients,
int  gridIndex = 0 
)

Reallocates the buffer on the GPU and copies the charges/coefficients from the CPU buffer. Clears the padded part if needed.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]h_coefficientsThe input atom charges/coefficients.
[in]gridIndexThe index of the grid to use. 0 is Coulomb in the normal state or FEP state A and 1 is Coulomb in FEP state B.

Does not need to be done for every PME computation, only whenever the local charges change. (So, in the beginning of the run, or on DD step).

void pme_gpu_realloc_forces ( PmeGpu pmeGpu)

Reallocates the GPU buffer for the PME forces.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_realloc_grid_indices ( PmeGpu pmeGpu)

Reallocates the buffers on the GPU and the host for the particle gridline indices.

Parameters
[in,out]pmeGpuThe PME GPU structure.
void pme_gpu_realloc_grids ( PmeGpu pmeGpu)

Reallocates the real space grid and the complex reciprocal grid (if needed) on the GPU.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_realloc_spline_data ( PmeGpu pmeGpu)

Reallocates the buffers on the GPU and the host for the atoms spline data.

Parameters
[in,out]pmeGpuThe PME GPU structure.
void pme_gpu_reinit ( gmx_pme_t *  pme,
const DeviceContext *  deviceContext,
const DeviceStream deviceStream,
const PmeGpuProgram pmeGpuProgram,
bool  useMdGpuGraph 
)

(Re-)initializes the PME GPU data at the beginning of the run or on DLB.

Parameters
[in,out]pmeThe PME structure.
[in]deviceContextThe GPU context.
[in]deviceStreamThe GPU stream.
[in,out]pmeGpuProgramThe handle to the program/kernel data created outside (e.g. in unit tests/runner)
[in]useMdGpuGraphWhether MD GPU Graph is in use
Exceptions
gmx::NotImplementedErrorif this generally valid PME structure is not valid for GPU runs.
void pme_gpu_reinit_3dfft ( const PmeGpu pmeGpu)

Initializes the CUDA FFT structures.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_reinit_atoms ( PmeGpu pmeGpu,
int  nAtoms,
const real chargesA,
const real chargesB = nullptr 
)

Reallocates the local atoms data (charges, coordinates, etc.). Copies the charges to the GPU.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]nAtomsThe number of particles.
[in]chargesAThe pointer to the host-side array of particle charges in the unperturbed state or FEP state A.
[in]chargesBThe pointer to the host-side array of particle charges in FEP state B.

This is a function that should only be called in the beginning of the run and on domain decomposition. Should be called before the pme_gpu_set_io_ranges.

static void pme_gpu_reinit_grids ( PmeGpu pmeGpu)
static

(Re-)initializes all the PME GPU data related to the grid size and cut-off.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_reinit_haloexchange ( PmeGpu pmeGpu)

Reinitialize PME halo exchange parameters and staging device buffers for MPI communication.

Parameters
[in]pmeGpuThe PME GPU structure.
static void pme_gpu_select_best_performing_pme_spreadgather_kernels ( PmeGpu pmeGpu)
static

uses heuristics to select the best performing PME gather and scatter kernels

Parameters
[in,out]pmeGpuThe PME GPU structure.
void pme_gpu_set_kernelparam_coordinates ( const PmeGpu pmeGpu,
DeviceBuffer< gmx::RVec d_x 
)

Sets the device pointer to coordinate data.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]d_xPointer to coordinate data
void pme_gpu_solve ( const PmeGpu pmeGpu,
int  gridIndex,
t_complex *  h_grid,
GridOrdering  gridOrdering,
bool  computeEnergyAndVirial 
)

A GPU Fourier space solving function.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]gridIndexThe index of the grid to use. 0 is Coulomb in the normal state or FEP state A and 1 is Coulomb in FEP state B.
[in,out]h_gridThe host-side input and output Fourier grid buffer (used only with testing or host-side FFT)
[in]gridOrderingSpecifies the dimenion ordering of the complex grid. TODO: store this information?
[in]computeEnergyAndVirialTells if the energy and virial computation should be performed.
void pme_gpu_spread ( const PmeGpu pmeGpu,
GpuEventSynchronizer *  xReadyOnDevice,
float **  h_grids,
gmx_parallel_3dfft_t fftSetup,
bool  computeSplines,
bool  spreadCharges,
real  lambda,
bool  useGpuDirectComm,
gmx::PmeCoordinateReceiverGpu *  pmeCoordinateReceiverGpu,
bool  useMdGpuGraph,
gmx_wallcycle *  wcycle 
)

A GPU spline computation and charge spreading function.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]xReadyOnDeviceEvent synchronizer indicating that the coordinates are ready in the device memory; can be nullptr when invoked on a separate PME rank or from PME tests.
[out]h_gridsThe host-side grid buffers (used only if the result of the spread is expected on the host, e.g. testing or host-side FFT)
[in]fftSetupHost-side FFT setup structure used in Mixed mode
[in]computeSplinesShould the computation of spline parameters and gridline indices be performed.
[in]spreadChargesShould the charges/coefficients be spread on the grid.
[in]lambdaThe lambda value of the current system state.
[in]useGpuDirectCommWhether direct GPU PME-PP communication is active
[in]pmeCoordinateReceiverGpuCoordinate receiver object, which must be valid when direct GPU PME-PP communication is active
[in]useMdGpuGraphWhether MD GPU Graph is in use.
[in]wcycleThe wallclock counter.
bool pme_gpu_stream_query ( const PmeGpu pmeGpu)

Checks whether work in the PME GPU stream has completed.

Parameters
[in]pmeGpuThe PME GPU structure.
Returns
True if work in the PME stream has completed.
void pme_gpu_sync_spread_grid ( const PmeGpu pmeGpu)

Waits for the grid copying to the host-side buffer after spreading to finish.

Parameters
[in]pmeGpuThe PME GPU structure.
void pme_gpu_synchronize ( const PmeGpu pmeGpu)

Synchronizes the current computation, waiting for the GPU kernels/transfers to finish.

Parameters
[in]pmeGpuThe PME GPU structure.
auto selectGatherKernelPtr ( const PmeGpu pmeGpu,
ThreadsPerAtom  threadsPerAtom,
bool  readSplinesFromGlobal,
const int  numGrids 
)
inline

Returns a pointer to appropriate gather kernel based on the inputvalues.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]threadsPerAtomControls whether we should use order or order*order threads per atom
[in]readSplinesFromGlobalbool controlling if we should write spline data to global memory
[in]numGridsNumber of grids to use. numGrids == 2 if Coulomb is perturbed.
Returns
Pointer to CUDA kernel
static auto selectSplineAndSpreadKernelPtr ( const PmeGpu pmeGpu,
ThreadsPerAtom  threadsPerAtom,
bool  writeSplinesToGlobal,
const int  numGrids 
)
static

Returns a pointer to appropriate spline and spread kernel based on the input bool values.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]threadsPerAtomControls whether we should use order or order*order threads per atom
[in]writeSplinesToGlobalbool controlling if we should write spline data to global memory
[in]numGridsNumber of grids to use. numGrids == 2 if Coulomb is perturbed.
Returns
Pointer to CUDA kernel
static auto selectSplineKernelPtr ( const PmeGpu pmeGpu,
ThreadsPerAtom  threadsPerAtom,
bool gmx_unused  writeSplinesToGlobal,
const int  numGrids 
)
static

Returns a pointer to appropriate spline kernel based on the input bool values.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]threadsPerAtomControls whether we should use order or order*order threads per atom
[in]writeSplinesToGlobalbool controlling if we should write spline data to global memory
[in]numGridsNumber of grids to use. numGrids == 2 if Coulomb is perturbed.
Returns
Pointer to CUDA kernel
static auto selectSpreadKernelPtr ( const PmeGpu pmeGpu,
ThreadsPerAtom  threadsPerAtom,
bool  writeSplinesToGlobal,
const int  numGrids 
)
static

Returns a pointer to appropriate spread kernel based on the input bool values.

Parameters
[in]pmeGpuThe PME GPU structure.
[in]threadsPerAtomControls whether we should use order or order*order threads per atom
[in]writeSplinesToGlobalbool controlling if we should write spline data to global memory
[in]numGridsNumber of grids to use. numGrids == 2 if Coulomb is perturbed.
Returns
Pointer to CUDA kernel