Inheritance diagram for DomainDecompMPIBase:

Public Member Functions
void	barrier () const override
	synchronizes all processes More...

unsigned	Ndistribution (unsigned localN, float minrnd, float maxrnd)
	returns total number of molecules More...

void	assertIntIdentity (int IX)
	checks identity of random number generators More...

void	assertDisjunctivity (ParticleContainer *moleculeContainer) const override

void	collCommInit (int numValues, int key=0) override
	has to call init method of a CollComm class More...

void	collCommFinalize () override
	has to call finalize method of a CollComm class More...

void	collCommAppendInt (int intValue) override
	has to call appendInt method of a CollComm class More...

void	collCommAppendUnsLong (unsigned long unsLongValue) override
	has to call appendUnsLong method of a CollComm class More...

void	collCommAppendFloat (float floatValue) override
	has to call appendFloat method of a CollComm class More...

void	collCommAppendDouble (double doubleValue) override
	has to call appendDouble method of a CollComm class More...

void	collCommAppendLongDouble (long double longDoubleValue) override
	has to call appendLongDouble method of a CollComm class More...

int	collCommGetInt () override
	has to call getInt method of a CollComm class More...

unsigned long	collCommGetUnsLong () override
	has to call getUnsLong method of a CollComm class More...

float	collCommGetFloat () override
	has to call getFloat method of a CollComm class More...

double	collCommGetDouble () override
	has to call getDouble method of a CollComm class More...

long double	collCommGetLongDouble () override
	has to call getLongDouble method of a CollComm class More...

void	collCommAllreduceSum () override
	has to call allreduceSum method of a CollComm class (none in sequential version) More...

void	collCommAllreduceSumAllowPrevious () override
	has to call allreduceSum method of a CollComm class (none in sequential version), allows for values of previous iteration. More...

void	collCommAllreduceCustom (ReduceType type) override
	has to call allreduceCustom method of a CollComm class (none in sequential version) More...

void	collCommScanSum () override
	has to call scanSum method of a CollComm class (none in sequential version) More...

void	collCommBroadcast (int root=0) override
	has to call broadcast method of a CollComm class (none in sequential version) More...

virtual void	balanceAndExchangeInitNonBlocking (bool forceRebalancing, ParticleContainer moleculeContainer, Domain domain)

virtual void	prepareNonBlockingStage (bool forceRebalancing, ParticleContainer moleculeContainer, Domain domain, unsigned int stageNumber)=0

virtual void	finishNonBlockingStage (bool forceRebalancing, ParticleContainer moleculeContainer, Domain domain, unsigned int stageNumber)=0

void	exchangeMoleculesMPI (ParticleContainer moleculeContainer, Domain domain, MessageType msgType, bool doHaloPositionCheck=true, bool removeRecvDuplicates=false)
	exchange molecules between processes More...

void	exchangeForces (ParticleContainer moleculeContainer, Domain domain) override
	Exchanges forces at the domain boundaries if it's required by the cell container. More...

std::vector< int >	getNeighbourRanks () override=0

std::vector< int >	getNeighbourRanksFullShell () override=0

virtual std::vector< CommunicationPartner >	getNeighboursFromHaloRegion (Domain *domain, const HaloRegion &haloRegion, double cutoff)=0

MPI_Datatype	getMPIParticleType ()

MPI_Datatype	getMPIParticleForceType ()

MPI_Comm	getCommunicator () override

virtual void	readXML (XMLfileUnits &xmlconfig)
	Read in XML configuration for DomainDecompMPIBase. More...

virtual void	setCommunicationScheme (const std::string &scheme, const std::string &comScheme)

virtual int	getNonBlockingStageCount () override

virtual size_t	getTotalSize () override

virtual void	printSubInfo (int offset) override

virtual void	printDecomp (const std::string &filename, Domain domain, ParticleContainer particleContainer) override
	writes information about the current decomposition into the given file More...

virtual std::string	getName () override

void	printCommunicationPartners (std::string filename) const override

Public Member Functions inherited from DomainDecompBase
	DomainDecompBase ()
	The Constructor determines the own rank and the number of the neighbours *‍/.

	~DomainDecompBase () override
	The Destructor finalizes MPI.

void	exchangeMolecules (ParticleContainer moleculeContainer, Domain domain)
	exchange molecules between processes More...

virtual bool	queryBalanceAndExchangeNonBlocking (bool forceRebalancing, ParticleContainer moleculeContainer, Domain domain, double etime)
	Checks whether the balance and exchange step can be performed non-blocking. More...

virtual void	balanceAndExchange (double lastTraversalTime, bool forceRebalancing, ParticleContainer moleculeContainer, Domain domain)
	balance the load (and optimize communication) and exchange boundary particles More...

virtual bool	procOwnsPos (double x, double y, double z, Domain *domain) final
	find out whether the given position belongs to the domain of this process More...

void	getBoundingBoxMinMax (Domain domain, double min, double *max)
	get the minimum and maximum coordinate of the bounding box of this process' domain More...

virtual double	getBoundingBoxMin (int dimension, Domain *domain)
	get the minimum of the bounding box of this process' domain in the given dimension (0,1,2) More...

virtual double	getBoundingBoxMax (int dimension, Domain *domain)
	get the maximum of the bounding box of this process' domain in the given dimension (0,1,2) More...

virtual int	getRank () const
	returns the own rank More...

virtual int	getNumProcs () const
	returns the number of processes More...

virtual double	getTime () const
	returns the time in seconds since some time in the past

double	getIOCutoffRadius (int dim, Domain domain, ParticleContainer moleculeContainer)
	returns an cutoff radius for a dimension for a global linked cells datastructure More...

void	writeMoleculesToMPIFileBinary (const std::string &filename, ParticleContainer *moleculeContainer) const
	appends molecule data to the file. The format is the same as that of the input file This version uses, MPI IO. More...

void	writeMoleculesToFile (const std::string &filename, ParticleContainer *moleculeContainer, bool binary=false) const
	appends molecule data to the file. The format is the same as that of the input file If MPI is enabled and binary files are supposed to be written this function will call writeMoleculesToMPIFileBinary(). Otherwise, to ensure that not more than one process writes to the file at any time, there is a loop over all processes with a barrier in between. More...

void	updateSendLeavingWithCopies (bool sendTogether)

bool	sendLeavingWithCopies () const

virtual std::vector< std::vector< std::vector< int > > >	getAllRanks ()

Protected Member Functions
virtual void	prepareNonBlockingStageImpl (ParticleContainer moleculeContainer, Domain domain, unsigned int stageNumber, MessageType msgType, bool removeRecvDuplicates=false)

virtual void	finishNonBlockingStageImpl (ParticleContainer moleculeContainer, Domain domain, unsigned int stageNumber, MessageType msgType, bool removeRecvDuplicates=false)

Protected Member Functions inherited from DomainDecompBase
void	addLeavingMolecules (std::vector< Molecule > &&invalidMolecules, ParticleContainer *moleculeContainer)

void	handleDomainLeavingParticles (unsigned dim, ParticleContainer *moleculeContainer) const

void	handleDomainLeavingParticlesDirect (const HaloRegion &haloRegion, ParticleContainer *moleculeContainer, std::vector< Molecule > &invalidParticles) const

void	handleForceExchange (unsigned dim, ParticleContainer *moleculeContainer) const
	Does the force exchange for each dimension. Will be called for dim=0, 1 and 2. More...

virtual void	handleForceExchangeDirect (const HaloRegion &haloRegion, ParticleContainer *moleculeContainer) const

void	populateHaloLayerWithCopies (unsigned dim, ParticleContainer *moleculeContainer) const

void	populateHaloLayerWithCopiesDirect (const HaloRegion &haloRegion, ParticleContainer *moleculeContainer, bool positionCheck=true) const

Protected Attributes
MPI_Datatype	_mpiParticleType

MPI_Datatype	_mpiParticleForceType

MPI_Comm	_comm

std::unique_ptr< NeighbourCommunicationScheme >	_neighbourCommunicationScheme

bool	_forceDirectPP {false}

Protected Attributes inherited from DomainDecompBase
int	_rank
	the id of the current process

int	_numProcs
	total number of processes in the simulation

Member Function Documentation

◆ assertDisjunctivity()

void DomainDecompMPIBase::assertDisjunctivity ( ParticleContainer * moleculeContainer ) const

overridevirtual

Todo:: FIXME: This implementation does not scale.

Reimplemented from DomainDecompBase.

◆ assertIntIdentity()

void DomainDecompMPIBase::assertIntIdentity ( int IX )

virtual

checks identity of random number generators

Reimplemented from DomainDecompBase.

◆ balanceAndExchangeInitNonBlocking()

void DomainDecompMPIBase::balanceAndExchangeInitNonBlocking	(	bool	forceRebalancing,
		ParticleContainer *	moleculeContainer,
		Domain *	domain
	)

virtual

Initialises the non-blocking balance and exchange. Nothing really important needs to be done here. Some ideas: decide between possible communication schemes,...

Parameters

forceRebalancing	true if rebalancing should be forced
moleculeContainer	pointer to the molecule container
domain	pointer to the domain

◆ barrier()

void DomainDecompMPIBase::barrier ( ) const

inlineoverridevirtual

synchronizes all processes

Reimplemented from DomainDecompBase.

◆ collCommAllreduceCustom()

void DomainDecompMPIBase::collCommAllreduceCustom ( ReduceType type )

inlineoverridevirtual

has to call allreduceCustom method of a CollComm class (none in sequential version)

Reimplemented from DomainDecompBase.

◆ collCommAllreduceSum()

void DomainDecompMPIBase::collCommAllreduceSum ( )

inlineoverridevirtual

has to call allreduceSum method of a CollComm class (none in sequential version)

Reimplemented from DomainDecompBase.

◆ collCommAllreduceSumAllowPrevious()

void DomainDecompMPIBase::collCommAllreduceSumAllowPrevious ( )

overridevirtual

has to call allreduceSum method of a CollComm class (none in sequential version), allows for values of previous iteration.

Reimplemented from DomainDecompBase.

◆ collCommAppendDouble()

void DomainDecompMPIBase::collCommAppendDouble ( double doubleValue )

inlineoverridevirtual

has to call appendDouble method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommAppendFloat()

void DomainDecompMPIBase::collCommAppendFloat ( float floatValue )

inlineoverridevirtual

has to call appendFloat method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommAppendInt()

void DomainDecompMPIBase::collCommAppendInt ( int intValue )

inlineoverridevirtual

has to call appendInt method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommAppendLongDouble()

void DomainDecompMPIBase::collCommAppendLongDouble ( long double longDoubleValue )

inlineoverridevirtual

has to call appendLongDouble method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommAppendUnsLong()

void DomainDecompMPIBase::collCommAppendUnsLong ( unsigned long unsLongValue )

inlineoverridevirtual

has to call appendUnsLong method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommBroadcast()

void DomainDecompMPIBase::collCommBroadcast ( int root = 0 )

inlineoverridevirtual

has to call broadcast method of a CollComm class (none in sequential version)

Reimplemented from DomainDecompBase.

◆ collCommFinalize()

void DomainDecompMPIBase::collCommFinalize ( )

inlineoverridevirtual

has to call finalize method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommGetDouble()

double DomainDecompMPIBase::collCommGetDouble ( )

inlineoverridevirtual

has to call getDouble method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommGetFloat()

float DomainDecompMPIBase::collCommGetFloat ( )

inlineoverridevirtual

has to call getFloat method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommGetInt()

int DomainDecompMPIBase::collCommGetInt ( )

inlineoverridevirtual

has to call getInt method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommGetLongDouble()

long double DomainDecompMPIBase::collCommGetLongDouble ( )

inlineoverridevirtual

has to call getLongDouble method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommGetUnsLong()

unsigned long DomainDecompMPIBase::collCommGetUnsLong ( )

inlineoverridevirtual

has to call getUnsLong method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommInit()

void DomainDecompMPIBase::collCommInit	(	int	numValues,
		int	key = `0`
	)

inlineoverridevirtual

has to call init method of a CollComm class

Reimplemented from DomainDecompBase.

◆ collCommScanSum()

void DomainDecompMPIBase::collCommScanSum ( )

inlineoverridevirtual

has to call scanSum method of a CollComm class (none in sequential version)

Reimplemented from DomainDecompBase.

◆ exchangeForces()

void DomainDecompMPIBase::exchangeForces	(	ParticleContainer *	moleculeContainer,
		Domain *	domain
	)

overridevirtual

Exchanges forces at the domain boundaries if it's required by the cell container.

Parameters

moleculeContainer	The particle container
domain

Reimplemented from DomainDecompBase.

◆ exchangeMoleculesMPI()

void DomainDecompMPIBase::exchangeMoleculesMPI	(	ParticleContainer *	moleculeContainer,
		Domain *	domain,
		MessageType	msgType,
		bool	doHaloPositionCheck = `true`,
		bool	removeRecvDuplicates = `false`
	)

exchange molecules between processes

molecules which aren't in the domain of their process any more are transferred to their neighbours. Additionally, the molecules for the halo-region are transferred. To reduce the number of neighbours a single process has to communicate with, particles that i.e. have to be moved to the lower right neighbour are moved to the right neighbour first and then from the right neighbour to the lower neighbour.

Parameters

moleculeContainer	needed to get those molecules which have to be exchanged
domain	is e.g. needed to get the size of the local domain

◆ finishNonBlockingStage()

virtual void DomainDecompMPIBase::finishNonBlockingStage	(	bool	forceRebalancing,
		ParticleContainer *	moleculeContainer,
		Domain *	domain,
		unsigned int	stageNumber
	)

pure virtual

Finishes the stageNumber'th stage. This includes receiving the particles, that have to be received in that stage.

Parameters

forceRebalancing	true if rebalancing should be forced
moleculeContainer	pointer to the molecule container
domain	pointer to the domain
stageNumber	the number of the stage, the communication is in.

Implemented in DomainDecomposition, GeneralDomainDecomposition, and KDDecomposition.

◆ finishNonBlockingStageImpl()

void DomainDecompMPIBase::finishNonBlockingStageImpl	(	ParticleContainer *	moleculeContainer,
		Domain *	domain,
		unsigned int	stageNumber,
		MessageType	msgType,
		bool	removeRecvDuplicates = `false`
	)

protectedvirtual

Finishes the stageNumber'th stage. This includes receiving the particles, that have to be received in that stage.

Parameters

forceRebalancing	true if rebalancing should be forced
moleculeContainer	pointer to the molecule container
domain	pointer to the domain
stageNumber	the number of the stage, the communication is in.

◆ getCommunicator()

MPI_Comm DomainDecompMPIBase::getCommunicator ( )

inlineoverridevirtual

Reimplemented from DomainDecompBase.

◆ getName()

virtual std::string DomainDecompMPIBase::getName ( )

inlineoverridevirtual

Reimplemented from DomainDecompBase.

◆ getNeighbourRanks()

std::vector<int> DomainDecompMPIBase::getNeighbourRanks ( )

overridepure virtual

Reimplemented from DomainDecompBase.

◆ getNeighbourRanksFullShell()

std::vector<int> DomainDecompMPIBase::getNeighbourRanksFullShell ( )

overridepure virtual

Reimplemented from DomainDecompBase.

Implemented in DomainDecomposition.

◆ getNonBlockingStageCount()

int DomainDecompMPIBase::getNonBlockingStageCount ( )

overridevirtual

Specifies the amount of non-blocking stages, when performing overlapping balanceAndExchange and computation. For a communication scheme, where only direct neighbours communicate, 3 stages of communication are necessary, since the particles have to be transmitted in the x-direction first, then in the y-direction, then in the z-direction.

Returns: The amount of communication stages. Returns -1 if it is not possible.

Reimplemented from DomainDecompBase.

◆ getTotalSize()

size_t DomainDecompMPIBase::getTotalSize ( )

overridevirtual

Reimplemented from DomainDecompBase.

◆ Ndistribution()

unsigned DomainDecompMPIBase::Ndistribution	(	unsigned	localN,
		float *	minrnd,
		float *	maxrnd
	)

virtual

returns total number of molecules

Reimplemented from DomainDecompBase.

◆ prepareNonBlockingStage()

virtual void DomainDecompMPIBase::prepareNonBlockingStage	(	bool	forceRebalancing,
		ParticleContainer *	moleculeContainer,
		Domain *	domain,
		unsigned int	stageNumber
	)

pure virtual

Prepares the stageNumber'th stage. This includes sending particles, that have to be send in that stage.

Parameters

forceRebalancing	true if rebalancing should be forced
moleculeContainer	pointer to the molecule container
domain	pointer to the domain
stageNumber	the number of the stage, the communication is in.

Implemented in DomainDecomposition, GeneralDomainDecomposition, and KDDecomposition.

◆ prepareNonBlockingStageImpl()

void DomainDecompMPIBase::prepareNonBlockingStageImpl	(	ParticleContainer *	moleculeContainer,
		Domain *	domain,
		unsigned int	stageNumber,
		MessageType	msgType,
		bool	removeRecvDuplicates = `false`
	)

protectedvirtual

Prepares the stageNumber'th stage. This includes sending particles, that have to be send in that stage.

Parameters

moleculeContainer	pointer to the molecule container
domain	pointer to the domain
stageNumber	the number of the stage, the communication is in.

◆ printCommunicationPartners()

void DomainDecompMPIBase::printCommunicationPartners ( std::string filename ) const

overridevirtual

Reimplemented from DomainDecompBase.

◆ printDecomp()

void DomainDecompMPIBase::printDecomp	(	const std::string &	filename,
		Domain *	domain,
		ParticleContainer *	particleContainer
	)

overridevirtual

writes information about the current decomposition into the given file

Parameters

filename	name of the file into which the data will be written
domain	e.g. needed to get the bounding boxes
particleContainer	needed to print information about the parts of the decomposition

Reimplemented from DomainDecompBase.

◆ printSubInfo()

void DomainDecompMPIBase::printSubInfo ( int offset )

overridevirtual

Reimplemented from DomainDecompBase.

◆ readXML()

void DomainDecompMPIBase::readXML ( XMLfileUnits & xmlconfig )

virtual

Read in XML configuration for DomainDecompMPIBase.

The following xml object structure is handled by this method:

<parallelisation type="DomainDecomposition" OR "KDDecomposition">
  <!--default: indirect, unless in autopas mode-->
     <CommunicationScheme>indirect OR direct OR direct-pp</CommunicationScheme>
     <!--default: no-->
     <overlappingCollectives>yes OR no</overlappingCollectives>
     <!--default: 5-->
     <overlappingStartAtStep></overlappingStartAtStep>
     <!--default: yes-->
     <useSequentialFallback>yes OR no</useSequentialFallback>
  <!-- structure handled by DomainDecomposition or KDDecomposition -->
</parallelisation>

Reimplemented from DomainDecompBase.

Reimplemented in DomainDecomposition, GeneralDomainDecomposition, and KDDecomposition.

◆ setCommunicationScheme()

void DomainDecompMPIBase::setCommunicationScheme	(	const std::string &	scheme,
		const std::string &	comScheme
	)

virtual

Sets the communicationScheme.

Note: If this function is called dynamically, make sure to reinitialise the CommunicationPartners before exchanging molecules!

Parameters

scheme
comScheme

Member Data Documentation

◆ _forceDirectPP

bool DomainDecompMPIBase::_forceDirectPP {false}

protected

Indicates whether the direct-pp communication scheme should be forced. Flag to indicate necessity to use the direct-pp neighbour communication scheme. Can be overwritten by any child class.

Note: Intended to be used in readXML().

The documentation for this class was generated from the following files:

src/parallel/DomainDecompMPIBase.h
src/parallel/DomainDecompMPIBase.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Member Function Documentation

◆ assertDisjunctivity()

◆ assertIntIdentity()

◆ balanceAndExchangeInitNonBlocking()

◆ barrier()

◆ collCommAllreduceCustom()

◆ collCommAllreduceSum()

◆ collCommAllreduceSumAllowPrevious()

◆ collCommAppendDouble()

◆ collCommAppendFloat()

◆ collCommAppendInt()

◆ collCommAppendLongDouble()

◆ collCommAppendUnsLong()

◆ collCommBroadcast()

◆ collCommFinalize()

◆ collCommGetDouble()

◆ collCommGetFloat()

◆ collCommGetInt()

◆ collCommGetLongDouble()

◆ collCommGetUnsLong()

◆ collCommInit()

◆ collCommScanSum()

◆ exchangeForces()

◆ exchangeMoleculesMPI()

◆ finishNonBlockingStage()

◆ finishNonBlockingStageImpl()

◆ getCommunicator()

◆ getName()

◆ getNeighbourRanks()

◆ getNeighbourRanksFullShell()

◆ getNonBlockingStageCount()

◆ getTotalSize()

◆ Ndistribution()

◆ prepareNonBlockingStage()

◆ prepareNonBlockingStageImpl()

◆ printCommunicationPartners()

◆ printDecomp()

◆ printSubInfo()

◆ readXML()

◆ setCommunicationScheme()

Member Data Documentation

◆ _forceDirectPP