PetscTools Class Reference

#include <PetscTools.hpp>

Collaboration diagram for PetscTools:

Static Public Member Functions
static void	ResetCache ()
static bool	IsSequential ()
static bool	IsParallel ()
static unsigned	GetNumProcs ()
static unsigned	GetMyRank ()
static bool	AmMaster ()
static bool	AmTopMost ()
static void	Barrier (const std::string callerId="")
static void	BeginRoundRobin ()
static void	EndRoundRobin ()
static void	IsolateProcesses (bool isolate=true)
static Vec	CreateVec (int size, int localSize=PETSC_DECIDE, bool ignoreOffProcEntries=true)
static Vec	CreateVec (std::vector< double > data)
static Vec	CreateAndSetVec (int size, double value)
static void	SetupMat (Mat &rMat, int numRows, int numColumns, unsigned rowPreallocation, int numLocalRows=PETSC_DECIDE, int numLocalColumns=PETSC_DECIDE, bool ignoreOffProcEntries=true)
static bool	ReplicateBool (bool flag)
static void	ReplicateException (bool flag)
static void	DumpPetscObject (const Mat &rMat, const std::string &rOutputFileFullPath)
static void	DumpPetscObject (const Vec &rVec, const std::string &rOutputFileFullPath)
static void	ReadPetscObject (Mat &rMat, const std::string &rOutputFileFullPath, Vec rParallelLayout=NULL)
static void	ReadPetscObject (Vec &rVec, const std::string &rOutputFileFullPath, Vec rParallelLayout=NULL)
Static Public Attributes
static const unsigned	MASTER_RANK = 0
Static Private Member Functions
static void	CheckCache ()
Static Private Attributes
static bool	mPetscIsInitialised = false
static unsigned	mNumProcessors = 0
static unsigned	mRank = 0
static bool	mIsolateProcesses = false

Detailed Description

A helper class of static methods.

Definition at line 58 of file PetscTools.hpp.

Member Function Documentation

bool PetscTools::AmMaster ( ) [static]

Just returns whether it is the master process or not.

If not running in parallel, always returns true.

Definition at line 98 of file PetscTools.cpp.

References CheckCache(), MASTER_RANK, mIsolateProcesses, and mRank.

bool PetscTools::AmTopMost ( ) [static]

Just returns whether it is the right-most process or not.

If not running in parallel, always returns true.

Definition at line 104 of file PetscTools.cpp.

References CheckCache(), mNumProcessors, and mRank.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

void PetscTools::Barrier ( const std::string callerId = "" ) [static]

If MPI is set up, perform a barrier synchronisation. If not, it's a noop.

Parameters:

callerId

only used in debug mode; printed before & after the barrier call

Definition at line 112 of file PetscTools.cpp.

References CheckCache(), GetMyRank(), mIsolateProcesses, and mPetscIsInitialised.

void PetscTools::BeginRoundRobin ( ) [static]

Call at the start of a block of code that should be executed by each process in turn.

Definition at line 127 of file PetscTools.cpp.

References Barrier(), and GetMyRank().

Referenced by GenericEventHandler< 1, EventHandler >::ReportImpl(), ExecutableSupport::ShowParallelLaunching(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

static void PetscTools::CheckCache ( ) [inline, static, private]

Private method makes sure that (if this is the first use within a test) then PETSc has been probed.

Definition at line 80 of file PetscTools.hpp.

References mNumProcessors, and ResetCache().

Referenced by AmMaster(), AmTopMost(), Barrier(), GetMyRank(), GetNumProcs(), IsParallel(), IsSequential(), and ReplicateBool().

Vec PetscTools::CreateAndSetVec	(	int	size,
		double	value
	)			`[static]`

Create a vector of the specified size with all values set to be the given constant. SetFromOptions is called.

Parameters:

	size	the size of the vector
	value	the value to set each entry

Definition at line 219 of file PetscTools.cpp.

References CreateVec().

Referenced by OdeLinearSystemSolver::OdeLinearSystemSolver(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), and AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::VerifyJacobian().

Vec PetscTools::CreateVec ( std::vector< double > data ) [static]

Create a Vec from the given data.

Parameters:

data

some data

Definition at line 199 of file PetscTools.cpp.

References CreateVec().

Vec PetscTools::CreateVec	(	int	size,
		int	localSize = `PETSC_DECIDE`,
		bool	ignoreOffProcEntries = `true`
	)			`[static]`

Create a vector of the specified size. SetFromOptions is called.

Parameters:

	size	the size of the vector
	localSize	the local number of items owned by this process
	ignoreOffProcEntries	whether to ignore entries destined to be stored on a separate processor when assembling (eliminates global reductions).

Definition at line 179 of file PetscTools.cpp.

Referenced by AbstractNonlinearElasticitySolver< DIM >::AllocateMatrixMemory(), AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobianNumerically(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), CreateAndSetVec(), CreateVec(), PetscMatTools::GetMatrixRowDistributed(), LinearSystem::LinearSystem(), PCBlockDiagonal::PCBlockDiagonalCreate(), PCLDUFactorisation::PCLDUFactorisationCreate(), PCTwoLevelsBlockDiagonal::PCTwoLevelsBlockDiagonalCreate(), Hdf5DataWriter::PutStripedVector(), Hdf5DataWriter::PutVector(), PetscVecTools::SetupInterleavedVectorScatterGather(), AbstractNonlinearElasticitySolver< DIM >::TakeNewtonStep(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

void PetscTools::DumpPetscObject	(	const Vec &	rVec,
		const std::string &	rOutputFileFullPath
	)			`[static]`

Dumps a given PETSc object to disk.

Parameters:

	rVec	a vector
	rOutputFileFullPath	where to dump the vector to disk

Definition at line 306 of file PetscTools.cpp.

void PetscTools::DumpPetscObject	(	const Mat &	rMat,
		const std::string &	rOutputFileFullPath
	)			`[static]`

Dumps a given PETSc object to disk.

Parameters:

	rMat	a matrix
	rOutputFileFullPath	where to dump the matrix to disk

Definition at line 292 of file PetscTools.cpp.

void PetscTools::EndRoundRobin ( ) [static]

Call at the end of a block of code that should be executed by each process in turn.

Definition at line 137 of file PetscTools.cpp.

References Barrier(), GetMyRank(), and GetNumProcs().

Referenced by GenericEventHandler< 1, EventHandler >::ReportImpl(), ExecutableSupport::ShowParallelLaunching(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

unsigned PetscTools::GetMyRank ( ) [static]

Return our rank.

If PETSc has not been initialized, returns 0.

Definition at line 92 of file PetscTools.cpp.

References CheckCache(), and mRank.

unsigned PetscTools::GetNumProcs ( ) [static]

Returns total number of processors.

Definition at line 86 of file PetscTools.cpp.

References CheckCache(), and mNumProcessors.

void PetscTools::IsolateProcesses ( bool isolate = true ) [static]

Where work can be split between isolated processes, it would be nice to be able to do so easily without worrying about collective calls made inside classes such as OutputFileHandler leading to deadlock. This method attempts to enable this behaviour. If the flag is set then AmMaster always returns true, Barrier becomes a no-op, and ReplicateBool doesn't replicate.

Parameters:

isolate

whether to consider processes as isolated

Definition at line 146 of file PetscTools.cpp.

References mIsolateProcesses.

bool PetscTools::IsParallel ( ) [static]

Just returns whether there is more than one process.

Definition at line 80 of file PetscTools.cpp.

References CheckCache(), and mNumProcessors.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), GenericEventHandler< 1, EventHandler >::HeadingsImpl(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), GenericEventHandler< 1, EventHandler >::ReportImpl(), and ExecutableSupport::ShowParallelLaunching().

bool PetscTools::IsSequential ( ) [static]

Just returns whether there is one process or not.

Definition at line 74 of file PetscTools.cpp.

References CheckCache(), and mNumProcessors.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), AbstractNonlinearElasticitySolver< DIM >::AllocateMatrixMemory(), CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::DistanceMapCalculator(), FormDebugHead(), HoneycombMeshGenerator::HoneycombMeshGenerator(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), PCTwoLevelsBlockDiagonal::PCTwoLevelsBlockDiagonalCreate(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles(), SetupMat(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

void PetscTools::ReadPetscObject	(	Vec &	rVec,
		const std::string &	rOutputFileFullPath,
		Vec	rParallelLayout = `NULL`
	)			`[static]`

Read a previously dumped PETSc object from disk.

Parameters:

	rVec	a vector
	rOutputFileFullPath	where to read the matrix from
	rParallelLayout	If provided, rMat will have the same parallel layout. Its content is irrelevant.

Definition at line 363 of file PetscTools.cpp.

void PetscTools::ReadPetscObject	(	Mat &	rMat,
		const std::string &	rOutputFileFullPath,
		Vec	rParallelLayout = `NULL`
	)			`[static]`

Read a previously dumped PETSc object from disk.

Parameters:

	rMat	a matrix
	rOutputFileFullPath	where to read the matrix from
	rParallelLayout	If provided, rMat will have the same parallel layout. Its content is irrelevant.

Todo:: : #1082 work out appropriate nz allocation.

Definition at line 320 of file PetscTools.cpp.

References SetupMat().

bool PetscTools::ReplicateBool ( bool flag ) [static]

Boolean AND of a flags between processes

Parameters:

flag

is set to true on this process.

Returns:: true if any process' flag is set to true.

Definition at line 151 of file PetscTools.cpp.

References CheckCache(), mIsolateProcesses, and mPetscIsInitialised.

Referenced by BidomainProblem< DIM >::AnalyseMeshForBath(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::ComputeDistanceMap(), AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::HasDirichletBoundaryConditions(), ReplicateException(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), and DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::UpdateQueueFromRemote().

void PetscTools::ReplicateException ( bool flag ) [static]

Ensure exceptions are handled cleanly in parallel code, by causing all processes to throw if any one does.

Parameters:

flag

is set to true if this process has thrown.

Definition at line 163 of file PetscTools.cpp.

References EXCEPTION, and ReplicateBool().

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), CellMLToSharedLibraryConverter::ConvertCellmlToSo(), ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), ExtendedBidomainTissue< SPACE_DIM >::CreateGGapConductivities(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue(), ReplicatableVector::Resize(), ElectrodesStimulusFactory< DIM >::SetCompatibleExtracellularStimulus(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetUpHaloCells(), AdaptiveBidomainProblem::Solve(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), ExtendedBidomainTissue< SPACE_DIM >::SolveCellSystems(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SolveCellSystems().

void PetscTools::ResetCache ( ) [static]

Reset our cached values: whether PETSc is initialised, how many processors there are, and which one we are.

Definition at line 47 of file PetscTools.cpp.

References mNumProcessors, mPetscIsInitialised, and mRank.

Referenced by CheckCache().

void PetscTools::SetupMat	(	Mat &	rMat,
		int	numRows,
		int	numColumns,
		unsigned	rowPreallocation,
		int	numLocalRows = `PETSC_DECIDE`,
		int	numLocalColumns = `PETSC_DECIDE`,
		bool	ignoreOffProcEntries = `true`
	)			`[static]`

Set up a matrix - set the size using the given parameters. The number of local rows and columns is by default PETSC_DECIDE. SetFromOptions is called.

Parameters:

	rMat	the matrix
	numRows	the number of rows in the matrix
	numColumns	the number of columns in the matrix
	rowPreallocation	the max number of nonzero entries expected on a row A value of 0 is allowed: no preallocation is then done and the user must preallocate the memory for the matrix themselves.
	numLocalRows	the number of local rows (defaults to PETSC_DECIDE)
	numLocalColumns	the number of local columns (defaults to PETSC_DECIDE)
	ignoreOffProcEntries	tells PETSc to drop off-processor entries