DistributedVectorFactory Class Reference

#include <DistributedVectorFactory.hpp>

Collaboration diagram for DistributedVectorFactory:

List of all members.

Public Member Functions

DistributedVectorFactory (Vec vec)

DistributedVectorFactory (unsigned size, PetscInt local=PETSC_DECIDE)

DistributedVectorFactory (DistributedVectorFactory *pOriginalFactory)

DistributedVectorFactory (unsigned lo, unsigned hi, unsigned size, unsigned numProcs=PetscTools::GetNumProcs())

~DistributedVectorFactory ()

Vec CreateVec ()

Vec CreateVec (unsigned stride)

DistributedVector CreateDistributedVector (Vec vec)

bool IsGlobalIndexLocal (unsigned globalIndex)

unsigned GetLocalOwnership () const

unsigned GetHigh () const

unsigned GetLow () const

unsigned GetProblemSize () const

unsigned GetNumProcs () const

DistributedVectorFactory * GetOriginalFactory ()

void SetFromFactory (DistributedVectorFactory *pFactory)

Static Public Member Functions

static void SetCheckNumberOfProcessesOnLoad (bool checkNumberOfProcessesOnLoad=true)

static bool CheckNumberOfProcessesOnLoad ()

Private Member Functions

void CheckForPetsc ()

void CalculateOwnership (Vec vec)

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

Private Attributes

unsigned mLo

unsigned mHi

unsigned mProblemSize

unsigned mNumProcs

bool mPetscStatusKnown

DistributedVectorFactory * mpOriginalFactory

Static Private Attributes

static bool msCheckNumberOfProcessesOnLoad = true

Friends

class boost::serialization::access

Detailed Description

Factory for creating PETSc vectors distributed across processes.

Replacement for the vector creation portions of DistributedVector (which was implemented using static methods and data), the factory class allows several patterns of PETSc vector length (and distributions among processes) to co-exist.

All vectors created by a factory instance will have the same base size and parallelisation pattern.

Definition at line 50 of file DistributedVectorFactory.hpp.

Constructor & Destructor Documentation

DistributedVectorFactory::DistributedVectorFactory ( Vec vec )

Set the problem with an existing PETSc vector -- must have stride=1.

Parameters:

vec

is a PETSc vector which we want to use as the pattern for future vectors produced by this factory

Definition at line 73 of file DistributedVectorFactory.cpp.

References CalculateOwnership().

DistributedVectorFactory::DistributedVectorFactory	(	unsigned	size,
		PetscInt	local = `PETSC_DECIDE`
	)

Set the problem size specifying distribution over local processor.

Parameters:

	size	the problem size
	local	defaults to PETSc's default

Definition at line 80 of file DistributedVectorFactory.cpp.

References CalculateOwnership(), CheckForPetsc(), and PetscTools::CreateVec().

DistributedVectorFactory::DistributedVectorFactory ( DistributedVectorFactory * pOriginalFactory )

Constructor for use in archiving. Note that this constructor is only called when the number of processes is different from the original. Therefore, the orignal local node ownership cannot be used, and a new even partition will be applied.

Parameters:

pOriginalFactory

see mpOriginalFactory

Definition at line 92 of file DistributedVectorFactory.cpp.

References CalculateOwnership(), PetscTools::CreateVec(), GetProblemSize(), and mpOriginalFactory.

DistributedVectorFactory::DistributedVectorFactory	(	unsigned	lo,
		unsigned	hi,
		unsigned	size,
		unsigned	numProcs = `PetscTools::GetNumProcs()`
	)

Constructor intended for use in archiving. Allows complete manual specification of the factory.

Parameters:

	lo	first index owned by this process
	hi	one beyond last index owned by this process
	size	total size of vectors
	numProcs	the number of processes expected (defaults to the current number)

Definition at line 105 of file DistributedVectorFactory.cpp.

References CheckForPetsc().

DistributedVectorFactory::~DistributedVectorFactory ( )

Destructor deletes mpOriginalFactory if it exists

Definition at line 118 of file DistributedVectorFactory.cpp.

References mpOriginalFactory.

Member Function Documentation

void DistributedVectorFactory::CheckForPetsc ( ) [private]

Double check (in debug code) that PETSc has been initialised properly

Definition at line 124 of file DistributedVectorFactory.cpp.

References mPetscStatusKnown.

Referenced by CalculateOwnership(), and DistributedVectorFactory().

void DistributedVectorFactory::CalculateOwnership ( Vec vec ) [private]

Helper method for the constructors

Parameters:

vec

the sample PETSc vector from which to calculate ownerships

Definition at line 38 of file DistributedVectorFactory.cpp.

References CheckForPetsc(), PetscTools::GetNumProcs(), mHi, mLo, mNumProcs, mPetscStatusKnown, and mProblemSize.

Referenced by DistributedVectorFactory().

template<class Archive>

void DistributedVectorFactory::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Archive the member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Definition at line 99 of file DistributedVectorFactory.hpp.

Vec DistributedVectorFactory::CreateVec ( )

Create a PETSc vector of the problem size

Returns:: the created vector

Definition at line 142 of file DistributedVectorFactory.cpp.

References PetscTools::CreateVec(), mHi, mLo, and mProblemSize.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GenerateNullBasis(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), ParallelColumnDataWriter::PutVectorStripe(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), and Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write().

Vec DistributedVectorFactory::CreateVec ( unsigned stride )

Create a striped PETSc vector of size: stride * problem size

Parameters:

stride

Definition at line 148 of file DistributedVectorFactory.cpp.

References mHi, mLo, and mProblemSize.

DistributedVector DistributedVectorFactory::CreateDistributedVector ( Vec vec )

Create a distributed vector which wraps a given petsc vector

Parameters:

vec

is the vector

Returns:: the distributed vector

Definition at line 155 of file DistributedVectorFactory.cpp.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToNonlinearResidual(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GenerateNullBasis(), ParallelColumnDataWriter::PutVectorStripe(), MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SolveCellSystems().

bool DistributedVectorFactory::IsGlobalIndexLocal ( unsigned globalIndex )

Test if the given global index is owned by the current process, i.e. is local to it.

Parameters:

globalIndex

a global index

Definition at line 137 of file DistributedVectorFactory.cpp.

References mHi, and mLo.

Referenced by HeartGeometryInformation< SPACE_DIM >::CalculateBoundingBoxOfSurface(), and HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

unsigned DistributedVectorFactory::GetLocalOwnership ( ) const [inline]

Returns:: The number of elements in the vector owned by the local process

Definition at line 175 of file DistributedVectorFactory.hpp.

References mHi, and mLo.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), Hdf5DataWriter::DefineFixedDimension(), Hdf5DataWriter::Hdf5DataWriter(), AbstractCardiacTissue< SPACE_DIM >::load(), and AbstractCardiacTissue< SPACE_DIM >::save().

unsigned DistributedVectorFactory::GetHigh ( ) const [inline]

Returns:: mHi - The next index above the top one owned by the process.

Definition at line 183 of file DistributedVectorFactory.hpp.

References mHi.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), CardiacSimulation::CreateAndRun(), Hdf5DataWriter::DefineFixedDimension(), DistributedVector::DistributedVector(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DumbNodePartitioning(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetCardiacCell(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::ReplicateCaches(), SetFromFactory(), and CardiacElectroMechanicsProblem< DIM >::Solve().

unsigned DistributedVectorFactory::GetLow ( ) const [inline]

Returns:: mLo - The lowest index owned by the process.

Definition at line 191 of file DistributedVectorFactory.hpp.

References mLo.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), CardiacSimulation::CreateAndRun(), Hdf5DataWriter::DefineFixedDimension(), DistributedVector::DistributedVector(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DumbNodePartitioning(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetCardiacCell(), AbstractCardiacTissue< SPACE_DIM >::load(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::ReplicateCaches(), AbstractCardiacTissue< SPACE_DIM >::save(), SetFromFactory(), and CardiacElectroMechanicsProblem< DIM >::Solve().

unsigned DistributedVectorFactory::GetProblemSize ( ) const [inline]

Returns:: The number of elements in (normal) vectors created by CreateVec()

Definition at line 199 of file DistributedVectorFactory.hpp.

References mProblemSize.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), DistributedVector::DistributedVector(), DistributedVectorFactory(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DumbNodePartitioning(), and SetFromFactory().

unsigned DistributedVectorFactory::GetNumProcs ( ) const [inline]

Returns:: mNumProcs - how many processes this factory is expecting.

Definition at line 207 of file DistributedVectorFactory.hpp.

References mNumProcs.

Referenced by AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::load(), CardiacSimulationArchiver< PROBLEM_CLASS >::Migrate(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetDistributedVectorFactory(), and SetFromFactory().

static void DistributedVectorFactory::SetCheckNumberOfProcessesOnLoad ( bool checkNumberOfProcessesOnLoad = true ) [inline, static]

Set whether, when loading an instance from an archive, to check that the current number of processes matches that used in creating the archive.

Parameters:

checkNumberOfProcessesOnLoad

Definition at line 218 of file DistributedVectorFactory.hpp.

References msCheckNumberOfProcessesOnLoad.

Referenced by CardiacSimulationArchiver< PROBLEM_CLASS >::Migrate().

static bool DistributedVectorFactory::CheckNumberOfProcessesOnLoad ( ) [inline, static]

Determine whether, when loading an instance from an archive, to check that the current number of processes matches that used in creating the archive.

Definition at line 227 of file DistributedVectorFactory.hpp.

References msCheckNumberOfProcessesOnLoad.

DistributedVectorFactory* DistributedVectorFactory::GetOriginalFactory ( ) [inline]

If msCheckNumberOfProcessesOnLoad is not set, and this factory was loaded from an archive, then return a factory with the settings from the archive, which may not be the same as ours - if running on a different number of processes from the original, we will have used PETSC_DECIDE to set the local ownership on load.

Definition at line 238 of file DistributedVectorFactory.hpp.

References mpOriginalFactory.

Referenced by AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::load(), and CardiacSimulationArchiver< PROBLEM_CLASS >::Migrate().

void DistributedVectorFactory::SetFromFactory ( DistributedVectorFactory * pFactory )

Set mLo and mHi from another vector factory. Used by archiving.

Parameters:

pFactory

the factory to set from.

Definition at line 59 of file DistributedVectorFactory.cpp.

References EXCEPTION, GetHigh(), GetLow(), GetNumProcs(), GetProblemSize(), mHi, mLo, mNumProcs, and mProblemSize.

Referenced by AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::load().

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Definition at line 90 of file DistributedVectorFactory.hpp.

Member Data Documentation

unsigned DistributedVectorFactory::mLo [private]

The first entry owned by the current processor.

Definition at line 55 of file DistributedVectorFactory.hpp.

Referenced by CalculateOwnership(), CreateVec(), GetLocalOwnership(), GetLow(), IsGlobalIndexLocal(), and SetFromFactory().

unsigned DistributedVectorFactory::mHi [private]

One above the last entry owned by the current processor.

Definition at line 57 of file DistributedVectorFactory.hpp.

Referenced by CalculateOwnership(), CreateVec(), GetHigh(), GetLocalOwnership(), IsGlobalIndexLocal(), and SetFromFactory().

unsigned DistributedVectorFactory::mProblemSize [private]

The problem size, i.e. the number of nodes in the mesh (the number of unknowns may be larger in a Stripe).

Definition at line 59 of file DistributedVectorFactory.hpp.

Referenced by CalculateOwnership(), CreateVec(), GetProblemSize(), and SetFromFactory().

unsigned DistributedVectorFactory::mNumProcs [private]

How many processes this factory is expecting.

Definition at line 61 of file DistributedVectorFactory.hpp.

Referenced by CalculateOwnership(), GetNumProcs(), and SetFromFactory().

bool DistributedVectorFactory::mPetscStatusKnown [private]

Whether we've checked that PETSc is initialised.

Definition at line 63 of file DistributedVectorFactory.hpp.

Referenced by CalculateOwnership(), and CheckForPetsc().

bool DistributedVectorFactory::msCheckNumberOfProcessesOnLoad = true [static, private]

Whether, when loading an instance from an archive, to check that the current number of processes matches that used in creating the archive.

Definition at line 69 of file DistributedVectorFactory.hpp.

Referenced by CheckNumberOfProcessesOnLoad(), and SetCheckNumberOfProcessesOnLoad().

DistributedVectorFactory* DistributedVectorFactory::mpOriginalFactory [private]

If msCheckNumberOfProcessesOnLoad is set and this instance was loaded from an archive, this points to a factory with the settings from the archive, which may not be the same as this instance.

Definition at line 75 of file DistributedVectorFactory.hpp.

Referenced by DistributedVectorFactory(), GetOriginalFactory(), and ~DistributedVectorFactory().

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

global/src/parallel/DistributedVectorFactory.hpp
global/src/parallel/DistributedVectorFactory.cpp


Public Member Functions
	DistributedVectorFactory (Vec vec)
	DistributedVectorFactory (unsigned size, PetscInt local=PETSC_DECIDE)
	DistributedVectorFactory (DistributedVectorFactory *pOriginalFactory)
	DistributedVectorFactory (unsigned lo, unsigned hi, unsigned size, unsigned numProcs=PetscTools::GetNumProcs())
	~DistributedVectorFactory ()
Vec	CreateVec ()
Vec	CreateVec (unsigned stride)
DistributedVector	CreateDistributedVector (Vec vec)
bool	IsGlobalIndexLocal (unsigned globalIndex)
unsigned	GetLocalOwnership () const
unsigned	GetHigh () const
unsigned	GetLow () const
unsigned	GetProblemSize () const
unsigned	GetNumProcs () const
DistributedVectorFactory *	GetOriginalFactory ()
void	SetFromFactory (DistributedVectorFactory *pFactory)
Static Public Member Functions
static void	SetCheckNumberOfProcessesOnLoad (bool checkNumberOfProcessesOnLoad=true)
static bool	CheckNumberOfProcessesOnLoad ()
Private Member Functions
void	CheckForPetsc ()
void	CalculateOwnership (Vec vec)
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
unsigned	mLo
unsigned	mHi
unsigned	mProblemSize
unsigned	mNumProcs
bool	mPetscStatusKnown
DistributedVectorFactory *	mpOriginalFactory
Static Private Attributes
static bool	msCheckNumberOfProcessesOnLoad = true
Friends
class	boost::serialization::access