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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/gmxcomplex.h"
#include "gromacs/math/invertmatrix.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/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/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.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"
+ Include dependency graph for pme.cpp:

Description

This file contains function definitions necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).

Author
Erik Lindahl erik@.nosp@m.kth..nosp@m.se
Berk Hess hess@.nosp@m.kth..nosp@m.se

Functions

static bool addMessageIfNotSupported (const std::list< std::string > &errorReasons, std::string *error)
 Help build a descriptive message in error if there are errorReasons why PME on GPU is not supported. More...
 
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_hardware (const gmx_hw_info_t &hwinfo, std::string *error)
 Checks whether the detected (GPU) hardware allows to run PME on GPU. More...
 
bool pme_gpu_supports_input (const t_inputrec &ir, const gmx_mtop_t &mtop, 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...
 
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.
 
bool gmx_pme_check_restrictions (int pme_order, int nkx, int nky, int nkz, int numPmeDomainsAlongX, 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, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, gmx_bool bReproducible, real ewaldcoeff_q, real ewaldcoeff_lj, int nthread, PmeRunMode runMode, PmeGpu *pmeGpu, const gmx_device_info_t *gpuInfo, PmeGpuProgramHandle 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.
 
void gmx_pme_calc_energy (gmx_pme_t *pme, gmx::ArrayRef< const gmx::RVec > x, gmx::ArrayRef< const real > q, real *V)
 Calculate the PME grid energy V for n charges. More...
 
static void calc_initial_lb_coeffs (gmx::ArrayRef< real > coefficient, const real *local_c6, const real *local_sigma)
 Calculate initial Lorentz-Berthelot coefficients for LJ-PME.
 
static void calc_next_lb_coeffs (gmx::ArrayRef< real > coefficient, 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, real chargeA[], real chargeB[], real c6A[], real c6B[], real sigmaA[], 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, int flags)
 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.
 
void gmx_pme_reinit_atoms (gmx_pme_t *pme, const int numAtoms, const real *charges)
 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...
 

Variables

const int gmxCacheLineSize = 64
 Number of bytes in a cache line. More...
 

Function Documentation

static bool addMessageIfNotSupported ( const std::list< std::string > &  errorReasons,
std::string *  error 
)
static

Help build a descriptive message in error if there are errorReasons why PME on GPU is not supported.

Returns
Whether the lack of errorReasons indicate there is support.
void gmx_pme_calc_energy ( gmx_pme_t *  pme,
gmx::ArrayRef< const gmx::RVec x,
gmx::ArrayRef< const real q,
real V 
)

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() with at least GMX_PME_SPREAD and GMX_PME_SOLVE specified. 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,
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().

int gmx_pme_do ( struct gmx_pme_t *  pme,
gmx::ArrayRef< const gmx::RVec coordinates,
gmx::ArrayRef< gmx::RVec forces,
real  chargeA[],
real  chargeB[],
real  c6A[],
real  c6B[],
real  sigmaA[],
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,
int  flags 
)

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.

Returns
0 indicates all well, non zero is an error code.
gmx_pme_t* gmx_pme_init ( const t_commrec *  cr,
const NumPmeDomains numPmeDomains,
const t_inputrec *  ir,
gmx_bool  bFreeEnergy_q,
gmx_bool  bFreeEnergy_lj,
gmx_bool  bReproducible,
real  ewaldcoeff_q,
real  ewaldcoeff_lj,
int  nthread,
PmeRunMode  runMode,
PmeGpu pmeGpu,
const gmx_device_info_t gpuInfo,
PmeGpuProgramHandle  pmeGpuProgram,
const gmx::MDLogger mdlog 
)

Construct PME data.

Exceptions
gmx::InconsistentInputErrorif input grid sizes/PME order are inconsistent.
Returns
Pointer to newly allocated and initialized PME data.
Todo:
We should evolve something like a GpuManager that holds gmx_device_info_t * and PmeGpuProgramHandle and perhaps other related things whose lifetime can/should exceed that of a task (or perhaps task manager). See Redmine #2522.
void gmx_pme_reinit_atoms ( gmx_pme_t *  pme,
int  numAtoms,
const real charges 
)

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).

Parameters
[in,out]pmeThe PME structure.
[in]numAtomsThe number of particles.
[in]chargesThe pointer to the array of particle charges.
static bool pme_gpu_check_restrictions ( const gmx_pme_t *  pme,
std::string *  error 
)
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.

Parameters
[in]pmeThe PME structure.
[out]errorThe error message if the input is not supported on GPU.
Returns
True if this PME input is possible to run on GPU, false otherwise.
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?

Parameters
[out]errorIf non-null, the error message when PME is not supported on GPU.
Returns
true if PME can run on GPU on this build, false otherwise.
bool pme_gpu_supports_hardware ( const gmx_hw_info_t &  hwinfo,
std::string *  error 
)

Checks whether the detected (GPU) hardware allows to run PME on GPU.

Parameters
[in]hwinfoInformation about the detected hardware
[out]errorIf non-null, the error message when PME is not supported on GPU.
Returns
true if PME can run on GPU on this build, false otherwise.
bool pme_gpu_supports_input ( const t_inputrec &  ir,
const gmx_mtop_t &  mtop,
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?

Parameters
[in]irInput system.
[in]mtopComplete system topology to check if an FE simulation perturbs charges.
[out]errorIf non-null, the error message if the input is not supported on GPU.
Returns
true if PME can run on GPU with this input, false otherwise.
PmeRunMode pme_run_mode ( const gmx_pme_t *  pme)

Returns the active PME codepath (CPU, GPU, mixed).

Todo:
This is a rather static data that should be managed by the higher level task scheduler.
Parameters
[in]pmeThe PME data structure.
Returns
active PME codepath.

Variable Documentation

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.