pairlist_tuning.cpp File Reference

#include "gmxpre.h"
#include "pairlist_tuning.h"
#include <cassert>
#include <cmath>
#include <cstdlib>
#include <algorithm>
#include <filesystem>
#include <string>
#include "gromacs/domdec/domdec.h"
#include "gromacs/hardware/cpuinfo.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/calc_verletbuf.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/multipletimestepping.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/nbnxm/pairlistparams.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringutil.h"
#include "nbnxm_geometry.h"
#include "pairlistsets.h"

Include dependency graph for pairlist_tuning.cpp:

Description

Implements functions for tuning adjustable parameters for the nbnxn non-bonded search and interaction kernels.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Classes
struct	gmx::CalcVerletBufferParameters
	Struct with references for most parameters for calling calcVerletBufferSize() More...

Macros
#define	NNSTL   (sizeof(nstlist_try) / sizeof(nstlist_try[0]))
	Number of elements in the neighborsearch list trials.

Functions
static bool	gmx::supportsDynamicPairlistGenerationInterval (const t_inputrec &ir)
	Returns if we can (heuristically) change nstlist and rlist. More...
static real	gmx::getPressureTolerance (const real inputrecVerletBufferPressureTolerance)
	Returns the Verlet buffer pressure tolerance set by an env.var. or from input.
void	gmx::increaseNstlist (FILE *fplog, t_commrec *cr, t_inputrec *ir, int nstlistOnCmdline, const gmx_mtop_t *mtop, const matrix box, real effectiveAtomDensity, bool useOrEmulateGpuForNonbondeds, const CpuInfo &cpuinfo)
	Try to increase nstlist when using the Verlet cut-off scheme. More...
static real	gmx::calcPruneVerletBufferSize (const CalcVerletBufferParameters &params, const int nstlist)
	Wrapper for calcVerletBufferSize() for determining the pruning cut-off. More...
static void	gmx::setDynamicPairlistPruningParameters (const t_inputrec &inputrec, const gmx_mtop_t &mtop, const real effectiveAtomDensity, const bool useGpuList, const VerletbufListSetup &listSetup, const bool userSetNstlistPrune, const interaction_const_t &interactionConst, PairlistParams *listParams)
	Set the dynamic pairlist pruning parameters in ic. More...
static std::string	gmx::formatListSetup (const std::string &listName, int nstList, int nstListForSpacing, real rList, real interactionCutoff)
	Returns a string describing the setup of a single pair-list. More...
void	gmx::setupDynamicPairlistPruning (const MDLogger &mdlog, const t_inputrec &inputrec, const gmx_mtop_t &mtop, real effectiveAtomDensity, const interaction_const_t &interactionConst, PairlistParams *listParams)
	Set up the dynamic pairlist pruning. More...
void	gmx::printNbnxmPressureError (const MDLogger &mdlog, const t_inputrec &inputrec, const gmx_mtop_t &mtop, real effectiveAtomDensity, const PairlistParams &listParams)
	Prints an estimate of the error in the pressure due to missing interactions. More...

Variables
static const int	gmx::nbnxnReferenceNstlist = 10
	Cost of non-bonded kernels. More...
const int	gmx::nstlist_try [] = { 20, 25, 40, 50, 80, 100 }
	The values to try when switching.
static const float	gmx::c_nbnxnListSizeFactorCpu = 1.25
	Target pair-list size increase ratio for CPU.
static const float	gmx::c_nbnxnListSizeFactorIntelXeonPhi = 1.4
	Target pair-list size increase ratio for Intel KNL.
static const float	gmx::c_nbnxnListSizeFactorGPU = 1.4
	Target pair-list size increase ratio for GPU.
static const float	gmx::c_nbnxnListSizeFactorMargin = 0.1
	Never increase the size of the pair-list more than the factor above plus this margin.
static constexpr int	gmx::c_nbnxnGpuRollingListPruningInterval = 2
	The interval in steps at which we perform dynamic, rolling pruning on a GPU. More...
static const int	gmx::c_nbnxnCpuDynamicListPruningMinLifetime = 5
	The minimum nstlist for dynamic pair list pruning on CPUs. More...
static constexpr int	gmx::c_nbnxnGpuDynamicListPruningMinLifetime = 4
	The minimum nstlist for dynamic pair list pruning om GPUs. More...