#include "gmxpre.h"
#include "pairlist_tuning.h"
#include <cassert>
#include <cmath>
#include <cstdlib>
#include <algorithm>
#include <string>
#include "gromacs/domdec/domdec.h"
#include "gromacs/hardware/cpuinfo.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/multipletimestepping.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.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	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	supportsDynamicPairlistGenerationInterval (const t_inputrec &ir)
	Returns if we can (heuristically) change nstlist and rlist. More...

static real	getPressureTolerance (const real inputrecVerletBufferPressureTolerance)
	Returns the Verlet buffer pressure tolerance set by an env.var. or from input.

void	increaseNstlist (FILE fp, t_commrec cr, t_inputrec ir, int nstlist_cmdline, const gmx_mtop_t mtop, const matrix box, const real effectiveAtomDensity, bool useOrEmulateGpuForNonbondeds, const gmx::CpuInfo &cpuinfo)
	Try to increase nstlist when using the Verlet cut-off scheme. More...

static real	calcPruneVerletBufferSize (const CalcVerletBufferParameters &params, const int nstlist)
	Wrapper for calcVerletBufferSize() for determining the pruning cut-off. More...

static void	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	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	setupDynamicPairlistPruning (const gmx::MDLogger &mdlog, const t_inputrec &inputrec, const gmx_mtop_t &mtop, const real effectiveAtomDensity, const interaction_const_t &interactionConst, PairlistParams *listParams)
	Set up the dynamic pairlist pruning. More...

void	printNbnxmPressureError (const gmx::MDLogger &mdlog, const t_inputrec &inputrec, const gmx_mtop_t &mtop, const real effectiveAtomDensity, const PairlistParams &listParams)
	Prints an estimate of the error in the pressure due to missing interactions. More...

Variables
static const int	nbnxnReferenceNstlist = 10
	Cost of non-bonded kernels. More...

const int	nstlist_try [] = { 20, 25, 40, 50, 80, 100 }
	The values to try when switching.

static const float	c_nbnxnListSizeFactorCpu = 1.25
	Target pair-list size increase ratio for CPU.

static const float	c_nbnxnListSizeFactorIntelXeonPhi = 1.4
	Target pair-list size increase ratio for Intel KNL.

static const float	c_nbnxnListSizeFactorGPU = 1.4
	Target pair-list size increase ratio for GPU.

static const float	c_nbnxnListSizeFactorMargin = 0.1
	Never increase the size of the pair-list more than the factor above plus this margin.

static const int	c_nbnxnGpuRollingListPruningInterval = 2
	The interval in steps at which we perform dynamic, rolling pruning on a GPU. More...

static const int	c_nbnxnCpuDynamicListPruningMinLifetime = 5
	The minimum nstlist for dynamic pair list pruning on CPUs. More...

static const int	c_nbnxnGpuDynamicListPruningMinLifetime = 4
	The minimum nstlist for dynamic pair list pruning om GPUs. More...

Function Documentation

static real calcPruneVerletBufferSize	(	const CalcVerletBufferParameters &	params,
		const int	nstlist
	)

static

Wrapper for calcVerletBufferSize() for determining the pruning cut-off.

Parameters

[in]	params	References to most parameters for calcVerletBufferSize()
[in]	nstlist	The pruning interval, also used for setting the list lifetime

Returns: The cut-off for pruning the pairlist

static std::string formatListSetup	(	const std::string &	listName,
		int	nstList,
		int	nstListForSpacing,
		real	rList,
		real	interactionCutoff
	)

static

Returns a string describing the setup of a single pair-list.

Parameters

[in]	listName	Short name of the list, can be ""
[in]	nstList	The list update interval in steps
[in]	nstListForSpacing	Update interval for setting the number characters for printing `nstList`
[in]	rList	List cut-off radius
[in]	interactionCutoff	The interaction cut-off, use for printing the list buffer size

void increaseNstlist	(	FILE *	fplog,
		t_commrec *	cr,
		t_inputrec *	ir,
		int	nstlistOnCmdline,
		const gmx_mtop_t *	mtop,
		const matrix	box,
		real	effectiveAtomDensity,
		bool	useOrEmulateGpuForNonbondeds,
		const gmx::CpuInfo &	cpuinfo
	)

Try to increase nstlist when using the Verlet cut-off scheme.

Parameters

[in,out]	fplog	Log file
[in]	cr	The communication record
[in]	ir	The input parameter record
[in]	nstlistOnCmdline	The value of nstlist provided on the command line
[in]	mtop	The global topology
[in]	box	The unit cell
[in]	effectiveAtomDensity	The effective atom density
[in]	useOrEmulateGpuForNonbondeds	Tells if we are using a GPU for non-bondeds
[in]	cpuinfo	Information about the CPU(s)

void printNbnxmPressureError	(	const gmx::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.

The NBNxM algorithm tolerates a few missing pair interactions. Missing pair interactions will lead to a systematic overestimates of the pressure when dispersion forces dominate at the cut-off distance. This routine prints an overestimate of the error in the average pressure.

Parameters

[in,out]	mdlog	MD logger
[in]	inputrec	The input parameter record
[in]	mtop	The global topology
[in]	effectiveAtomDensity	The effective atom density of the system
[in]	listParams	The list setup parameters

static void 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
	)

static

Set the dynamic pairlist pruning parameters in ic.

Parameters

[in]	inputrec	The input parameter record
[in]	mtop	The global topology
[in]	effectiveAtomDensity	The effective atom density of the system
[in]	useGpuList	Tells if we are using a GPU type pairlist
[in]	listSetup	The nbnxn pair list setup
[in]	userSetNstlistPrune	The user set ic->nstlistPrune (using an env.var.)
[in]	interactionConst	The nonbonded interactions constants
[in,out]	listParams	The list setup parameters

void setupDynamicPairlistPruning	(	const gmx::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.

Parameters

[in,out]	mdlog	MD logger
[in]	inputrec	The input parameter record
[in]	mtop	The global topology
[in]	effectiveAtomDensity	The effective atom density of the system
[in]	interactionConst	The nonbonded interactions constants
[in,out]	listParams	The list setup parameters

static bool supportsDynamicPairlistGenerationInterval ( const t_inputrec & ir )

static

Returns if we can (heuristically) change nstlist and rlist.

Parameters

[in] ir The input parameter record

Variable Documentation

const int c_nbnxnCpuDynamicListPruningMinLifetime = 5

static

The minimum nstlist for dynamic pair list pruning on CPUs.

In most cases going lower than 5 will lead to a too high pruning cost.

const int c_nbnxnGpuDynamicListPruningMinLifetime = 4

static

The minimum nstlist for dynamic pair list pruning om GPUs.

In most cases going lower than 4 will lead to a too high pruning cost. This value should be a multiple of c_nbnxnGpuRollingListPruningInterval

const int c_nbnxnGpuRollingListPruningInterval = 2

static

The interval in steps at which we perform dynamic, rolling pruning on a GPU.

Ideally we should auto-tune this value. Not considering overheads, 1 would be the ideal value. But 2 seems a reasonable compromise that reduces GPU kernel launch overheads and also avoids inefficiency on large GPUs when pruning small lists. Because with domain decomposition we alternate local/non-local pruning at even/odd steps, which gives a period of 2, this value currenly needs to be 2, which is indirectly asserted when the GPU pruning is dispatched during the force evaluation.

const int nbnxnReferenceNstlist = 10

static

Cost of non-bonded kernels.

We determine the extra cost of the non-bonded kernels compared to a reference nstlist value of 10 (which is the default in grompp).

Description

Classes

Macros

Functions

Variables

Function Documentation

Variable Documentation