Gromacs
2024.4
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#include "gmxpre.h"
#include "pme.h"
#include "config.h"
#include <cassert>
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <algorithm>
#include <list>
#include "gromacs/domdec/domdec.h"
#include "gromacs/ewald/ewald_utils.h"
#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/math/boxmatrix.h"
#include "gromacs/math/gmxcomplex.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/message_string_collector.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/unique_cptr.h"
#include "calculate_spline_moduli.h"
#include "pme_gather.h"
#include "pme_gpu_internal.h"
#include "pme_grid.h"
#include "pme_internal.h"
#include "pme_redistribute.h"
#include "pme_solve.h"
#include "pme_spline_work.h"
#include "pme_spread.h"
This file contains function definitions necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).
Functions | |
bool | pme_gpu_supports_build (std::string *error) |
Checks whether the GROMACS build allows to run PME on GPU. TODO: this partly duplicates an internal PME assert function pme_gpu_check_restrictions(), except that works with a formed gmx_pme_t structure. Should that one go away/work with inputrec? More... | |
bool | pme_gpu_supports_input (const t_inputrec &ir, std::string *error) |
Checks whether the input system allows to run PME on GPU. TODO: this partly duplicates an internal PME assert function pme_gpu_check_restrictions(), except that works with a formed gmx_pme_t structure. Should that one go away/work with inputrec? More... | |
bool | pme_gpu_mixed_mode_supports_input (const t_inputrec &ir, std::string *error) |
Checks whether the input system allows to run PME on GPU in Mixed mode. Assumes that the input system is compatible with GPU PME otherwise, that is, before calling this function one should check that pme_gpu_supports_input returns true . More... | |
static bool | pme_gpu_check_restrictions (const gmx_pme_t *pme, std::string *error) |
Finds out if PME with given inputs is possible to run on GPU. This function is an internal final check, validating the whole PME structure on creation, but it still duplicates the preliminary checks from the above (externally exposed) pme_gpu_supports_input() - just in case. More... | |
PmeRunMode | pme_run_mode (const gmx_pme_t *pme) |
Returns the active PME codepath (CPU, GPU, mixed). More... | |
gmx::PinningPolicy | pme_get_pinning_policy () |
Return the pinning policy appropriate for this build configuration for relevant buffers used for PME task on this rank (e.g. running on a GPU). | |
static void | setup_coordinate_communication (PmeAtomComm *atc) |
Set up coordinate communication. | |
static int | mult_up (int n, int f) |
Round n up to the next multiple of f . | |
static double | estimate_pme_load_imbalance (struct gmx_pme_t *pme) |
Return estimate of the load imbalance from the PME grid not being a good match for the number of PME ranks. | |
static void | init_overlap_comm (pme_overlap_t *ol, int norder, MPI_Comm comm, int nnodes, int nodeid, int ndata, int commplainsize) |
Initialize data structure for communication. | |
int | minimalPmeGridSize (int pmeOrder) |
Return the smallest allowed PME grid size for pmeOrder . | |
int | numGridLinesForExtendedHaloRegion (int pmeOrder, real haloExtentForAtomDisplacement, real gridSpacing) |
Calculates the number of grid lines used as halo region for PME decomposition. More... | |
real | getGridSpacingFromBox (const matrix box, const ivec gridDim) |
Gets grid spacing from simulation box and grid dimension. More... | |
bool | gmx_pme_check_restrictions (int pme_order, int nkx, int nky, int nkz, int numPmeDomainsAlongX, int numPmeDomainsAlongY, int extendedHaloRegion, bool useGpuPme, bool useThreads, bool errorsAreFatal) |
Check restrictions on pme_order and the PME grid nkx,nky,nkz. More... | |
static int | div_round_up (int enumerator, int denominator) |
Round enumerator . | |
gmx_pme_t * | gmx_pme_init (const t_commrec *cr, const NumPmeDomains &numPmeDomains, const t_inputrec *ir, const matrix box, real haloExtentForAtomDisplacement, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, gmx_bool bReproducible, real ewaldcoeff_q, real ewaldcoeff_lj, int nthread, PmeRunMode runMode, PmeGpu *pmeGpu, const DeviceContext *deviceContext, const DeviceStream *deviceStream, const PmeGpuProgram *pmeGpuProgram, const gmx::MDLogger &mdlog) |
Construct PME data. More... | |
void | gmx_pme_reinit (struct gmx_pme_t **pmedata, const t_commrec *cr, struct gmx_pme_t *pme_src, const t_inputrec *ir, const ivec grid_size, real ewaldcoeff_q, real ewaldcoeff_lj) |
As gmx_pme_init, but takes most settings, except the grid/Ewald coefficients, from pme_src. This is only called when the PME cut-off/grid size changes. | |
real | gmx_pme_calc_energy (gmx_pme_t *pme, gmx::ArrayRef< const gmx::RVec > x, gmx::ArrayRef< const real > q) |
Calculate the PME grid energy V for n charges. More... | |
static void | calc_initial_lb_coeffs (gmx::ArrayRef< real > coefficient, gmx::ArrayRef< const real > local_c6, gmx::ArrayRef< const real > local_sigma) |
Calculate initial Lorentz-Berthelot coefficients for LJ-PME. | |
static void | calc_next_lb_coeffs (gmx::ArrayRef< real > coefficient, gmx::ArrayRef< const real > local_sigma) |
Calculate next Lorentz-Berthelot coefficients for LJ-PME. | |
int | gmx_pme_do (struct gmx_pme_t *pme, gmx::ArrayRef< const gmx::RVec > coordinates, gmx::ArrayRef< gmx::RVec > forces, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const real > c6A, gmx::ArrayRef< const real > c6B, gmx::ArrayRef< const real > sigmaA, gmx::ArrayRef< const real > sigmaB, const matrix box, const t_commrec *cr, int maxshift_x, int maxshift_y, t_nrnb *nrnb, gmx_wallcycle *wcycle, matrix vir_q, matrix vir_lj, real *energy_q, real *energy_lj, real lambda_q, real lambda_lj, real *dvdlambda_q, real *dvdlambda_lj, const gmx::StepWorkload &stepWork) |
Do a PME calculation on a CPU for the long range electrostatics and/or LJ. More... | |
void | gmx_pme_destroy (gmx_pme_t *pme) |
Destroys the PME data structure (including shared data). | |
void | gmx_pme_destroy (gmx_pme_t *pme, bool destroySharedData) |
Destroys the PME data structure. More... | |
void | gmx_pme_reinit_atoms (gmx_pme_t *pme, const int numAtoms, gmx::ArrayRef< const real > chargesA, gmx::ArrayRef< const real > chargesB) |
This function updates the local atom data on GPU after DD (charges, coordinates, etc.). TODO: it should update the PME CPU atom data as well. (currently PME CPU call gmx_pme_do() gets passed the input pointers for each computation). More... | |
bool | gmx_pme_grid_matches (const gmx_pme_t &pme, const ivec grid_size) |
Return whether the grid of pme is identical to grid_size . | |
Variables | |
const int | gmxCacheLineSize = 64 |
Number of bytes in a cache line. More... | |
real getGridSpacingFromBox | ( | const matrix | box, |
const ivec | gridDim | ||
) |
Gets grid spacing from simulation box and grid dimension.
[in] | box | Simulation box |
[in] | gridDim | Fourier grid dimension |
real gmx_pme_calc_energy | ( | gmx_pme_t * | pme, |
gmx::ArrayRef< const gmx::RVec > | x, | ||
gmx::ArrayRef< const real > | q | ||
) |
Calculate the PME grid energy V for n charges.
The potential (found in pme
) must have been found already with a call to gmx_pme_do(). Note that the charges are not spread on the grid in the pme struct. Currently does not work in parallel or with free energy.
bool gmx_pme_check_restrictions | ( | int | pme_order, |
int | nkx, | ||
int | nky, | ||
int | nkz, | ||
int | numPmeDomainsAlongX, | ||
int | numPmeDomainsAlongY, | ||
int | extendedHaloRegion, | ||
bool | useGpuPme, | ||
bool | useThreads, | ||
bool | errorsAreFatal | ||
) |
Check restrictions on pme_order and the PME grid nkx,nky,nkz.
With errorsAreFatal=true, an exception or fatal error is generated on violation of restrictions. With errorsAreFatal=false, false is returned on violation of restrictions. When all restrictions are obeyed, true is returned. Argument useThreads tells if any MPI rank doing PME uses more than 1 threads. If at calling useThreads is unknown, pass true for conservative checking.
The PME GPU restrictions are checked separately during pme_gpu_init().
void gmx_pme_destroy | ( | gmx_pme_t * | pme, |
bool | destroySharedData | ||
) |
Destroys the PME data structure.
pme | The data structure to destroy. |
destroySharedData | Set to false if pme is a copy created by gmx_pme_reinit, and only it should be destroyed, while shared data should be preserved. If true , the shared data will be destroyed, like in gmx_pme_destroy(gmx_pme_t* pme) . |
int gmx_pme_do | ( | struct gmx_pme_t * | pme, |
gmx::ArrayRef< const gmx::RVec > | coordinates, | ||
gmx::ArrayRef< gmx::RVec > | forces, | ||
gmx::ArrayRef< const real > | chargeA, | ||
gmx::ArrayRef< const real > | chargeB, | ||
gmx::ArrayRef< const real > | c6A, | ||
gmx::ArrayRef< const real > | c6B, | ||
gmx::ArrayRef< const real > | sigmaA, | ||
gmx::ArrayRef< const real > | sigmaB, | ||
const matrix | box, | ||
const t_commrec * | cr, | ||
int | maxshift_x, | ||
int | maxshift_y, | ||
t_nrnb * | nrnb, | ||
gmx_wallcycle * | wcycle, | ||
matrix | vir_q, | ||
matrix | vir_lj, | ||
real * | energy_q, | ||
real * | energy_lj, | ||
real | lambda_q, | ||
real | lambda_lj, | ||
real * | dvdlambda_q, | ||
real * | dvdlambda_lj, | ||
const gmx::StepWorkload & | stepWork | ||
) |
Do a PME calculation on a CPU for the long range electrostatics and/or LJ.
Computes the PME forces and the energy and viral, when requested, for all atoms in coordinates
. Forces, when requested, are added to the buffer forces
, which is allowed to contain more elements than the number of elements in coordinates
. The meaning of flags
is defined above, and determines which parts of the calculation are performed.
gmx_pme_t* gmx_pme_init | ( | const t_commrec * | cr, |
const NumPmeDomains & | numPmeDomains, | ||
const t_inputrec * | ir, | ||
const matrix | box, | ||
real | haloExtentForAtomDisplacement, | ||
gmx_bool | bFreeEnergy_q, | ||
gmx_bool | bFreeEnergy_lj, | ||
gmx_bool | bReproducible, | ||
real | ewaldcoeff_q, | ||
real | ewaldcoeff_lj, | ||
int | nthread, | ||
PmeRunMode | runMode, | ||
PmeGpu * | pmeGpu, | ||
const DeviceContext * | deviceContext, | ||
const DeviceStream * | deviceStream, | ||
const PmeGpuProgram * | pmeGpuProgram, | ||
const gmx::MDLogger & | mdlog | ||
) |
Construct PME data.
gmx::InconsistentInputError | if input grid sizes/PME order are inconsistent. |
GpuManager
that holds DeviceInformation*
and PmeGpuProgram*
and perhaps other related things whose lifetime can/should exceed that of a task (or perhaps task manager). See Issue #2522. void gmx_pme_reinit_atoms | ( | gmx_pme_t * | pme, |
int | numAtoms, | ||
gmx::ArrayRef< const real > | chargesA, | ||
gmx::ArrayRef< const real > | chargesB | ||
) |
This function updates the local atom data on GPU after DD (charges, coordinates, etc.). TODO: it should update the PME CPU atom data as well. (currently PME CPU call gmx_pme_do() gets passed the input pointers for each computation).
[in,out] | pme | The PME structure. |
[in] | numAtoms | The number of particles. |
[in] | chargesA | The pointer to the array of particle charges in the normal state or FEP state A. Can be nullptr if PME is not performed on the GPU. |
[in] | chargesB | The pointer to the array of particle charges in state B. Only used if charges are perturbed and can otherwise be nullptr. |
int numGridLinesForExtendedHaloRegion | ( | int | pmeOrder, |
real | haloExtentForAtomDisplacement, | ||
real | gridSpacing | ||
) |
Calculates the number of grid lines used as halo region for PME decomposition.
This function is only used for PME GPU decomposition case
[in] | pmeOrder | PME interpolation order |
[in] | haloExtentForAtomDisplacement | extent of halo region in nm to account for atom displacement |
[in] | gridSpacing | spacing between grid lines |
|
static |
Finds out if PME with given inputs is possible to run on GPU. This function is an internal final check, validating the whole PME structure on creation, but it still duplicates the preliminary checks from the above (externally exposed) pme_gpu_supports_input() - just in case.
[in] | pme | The PME structure. |
[out] | error | The error message if the input is not supported on GPU. |
bool pme_gpu_mixed_mode_supports_input | ( | const t_inputrec & | ir, |
std::string * | error | ||
) |
Checks whether the input system allows to run PME on GPU in Mixed mode. Assumes that the input system is compatible with GPU PME otherwise, that is, before calling this function one should check that pme_gpu_supports_input returns true
.
[in] | ir | Input system. |
[out] | error | If non-null, the error message if the input is not supported. |
bool pme_gpu_supports_build | ( | std::string * | error | ) |
Checks whether the GROMACS build allows to run PME on GPU. TODO: this partly duplicates an internal PME assert function pme_gpu_check_restrictions(), except that works with a formed gmx_pme_t structure. Should that one go away/work with inputrec?
[out] | error | If non-null, the error message when PME is not supported on GPU. |
bool pme_gpu_supports_input | ( | const t_inputrec & | ir, |
std::string * | error | ||
) |
Checks whether the input system allows to run PME on GPU. TODO: this partly duplicates an internal PME assert function pme_gpu_check_restrictions(), except that works with a formed gmx_pme_t structure. Should that one go away/work with inputrec?
[in] | ir | Input system. |
[out] | error | If non-null, the error message if the input is not supported on GPU. |
PmeRunMode pme_run_mode | ( | const gmx_pme_t * | pme | ) |
Returns the active PME codepath (CPU, GPU, mixed).
[in] | pme | The PME data structure. |
const int gmxCacheLineSize = 64 |
Number of bytes in a cache line.
Must also be a multiple of the SIMD and SIMD4 register size, to preserve alignment.