PetscTools Class Reference

#include <PetscTools.hpp>

Collaboration diagram for PetscTools:

Static Public Member Functions
static void	ResetCache ()
static bool	IsSequential ()
static unsigned	GetNumProcs ()
static unsigned	GetMyRank ()
static bool	AmMaster ()
static bool	AmTopMost ()
static void	Barrier (const std::string callerId="")
static Vec	CreateVec (int size)
static Vec	CreateVec (int size, double value)
static Vec	CreateVec (std::vector< double > data)
static void	SetupMat (Mat &rMat, int numRows, int numColumns, MatType matType=(MatType) MATMPIAIJ, int numLocalRows=PETSC_DECIDE, int numLocalColumns=PETSC_DECIDE)
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)
static void	ReadPetscObject (Vec &rVec, const std::string &rOutputFileFullPath)
static void	SetMaxNumNonzerosIfMatMpiAij (unsigned maxColsPerRowIfMatMpiAij)
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	mMaxNumNonzerosIfMatMpiAij = 54
static unsigned	mRank = 0

Detailed Description

A helper class of static methods.

Definition at line 54 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, 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().

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 114 of file PetscTools.cpp.

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

Referenced by ParallelColumnDataWriter::AdvanceAlongUnlimitedDimension(), ParallelColumnDataWriter::Close(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), OutputDirectoryFifoQueue::CreateNextDir(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter(), GenericEventHandler< 13, HeartEventHandler >::Headings(), HoneycombMeshGenerator::Make2dPeriodicCryptMesh(), OutputFileHandler::MakeFoldersAndReturnFullPath(), OutputFileHandler::OutputFileHandler(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodesWithMetisBinaries(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), GenericEventHandler< 13, HeartEventHandler >::Report(), QuadraticMesh< DIM >::RunMesherAndReadMesh(), AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save(), HeartConfig::save(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), CardiacElectroMechanicsProblem< DIM >::Solve(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile(), and HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode().

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 75 of file PetscTools.hpp.

References mNumProcessors, and ResetCache().

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

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

Create a Vec from the given data.

Parameters:

data

some data

Definition at line 183 of file PetscTools.cpp.

References CreateVec().

Vec PetscTools::CreateVec	(	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 167 of file PetscTools.cpp.

References CreateVec().

Vec PetscTools::CreateVec ( int size ) [static]

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

Parameters:

size

the size of the vector

Definition at line 157 of file PetscTools.cpp.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), AbstractNonlinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CONCRETE >::CreateConstantInitialGuess(), CreateVec(), PCBlockDiagonal::PCBlockDiagonalCreate(), and PCLDUFactorisation::PCLDUFactorisationCreate().

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 245 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 230 of file PetscTools.cpp.

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.

Referenced by ArchiveOpener< Archive, Stream >::ArchiveOpener(), NonlinearElasticityAssembler< DIM >::AssembleSystem(), Barrier(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetAnyNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodePartitioning(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), GenericEventHandler< 13, HeartEventHandler >::Report(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping(), AbstractNonlinearElasticityAssembler< DIM >::TakeNewtonStep(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::UpdateQueueFromRemote(), and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile().

unsigned PetscTools::GetNumProcs ( ) [static]

Returns total number of processors

Definition at line 86 of file PetscTools.cpp.

References CheckCache(), and mNumProcessors.

bool PetscTools::IsSequential ( ) [static]

Just returns whether there is one process or not.

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(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::DistanceMapCalculator(), GenericEventHandler< 13, HeartEventHandler >::Headings(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodePartitioning(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), and GenericEventHandler< 13, HeartEventHandler >::Report().

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

Read a previously dumped Petsc object from disk.

Parameters:

	rVec	a vector
	rOutputFileFullPath	where to read the matrix from

Definition at line 275 of file PetscTools.cpp.

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

Read a previously dumped Petsc object from disk.

Parameters:

	rMat	a matrix
	rOutputFileFullPath	where to read the matrix from

Definition at line 260 of file PetscTools.cpp.

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 131 of file PetscTools.cpp.

Referenced by 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 139 of file PetscTools.cpp.

References ReplicateBool().

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), CellMLToSharedLibraryConverter::ConvertCellmlToSo(), BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), ReplicatableVector::Resize(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), and AbstractCardiacPde< 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 45 of file PetscTools.cpp.

References mNumProcessors, mPetscIsInitialised, and mRank.

Referenced by CheckCache().

void PetscTools::SetMaxNumNonzerosIfMatMpiAij ( unsigned maxColsPerRowIfMatMpiAij ) [static]

Set the number of nonzeros per row that PETSc will preallocate memory for.

Parameters:

maxColsPerRowIfMatMpiAij

The maximum number of non zeros per row. This value is problem dependent. Since the call to set this depends on the matrix-type (eg MatMPIAIJSetPreallocation/MatSeqAIJSetPreallocation), preallocation using this value is done only if the matrix-type is MATMPIAIJ (the default). WITH OTHER TYPES OF MATRIX NO PREALLOCATION IS DONE AND YOU MUST PREALLOCATE MANUALLY (by calling the appropriate method)!

Definition at line 290 of file PetscTools.cpp.

References mMaxNumNonzerosIfMatMpiAij.

void PetscTools::SetupMat	(	Mat &	rMat,
		int	numRows,
		int	numColumns,
		MatType	matType = `(MatType) MATMPIAIJ`,
		int	numLocalRows = `PETSC_DECIDE`,
		int	numLocalColumns = `PETSC_DECIDE`
	)			`[static]`

Set up a matrix - set the size using the given parameters, the type (default MATMPIAIJ). 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
	matType	the matrix type (defaults to MATMPIAIJ)
	numLocalRows	the number of local rows (detaults to PETSC_DECIDE)
	numLocalColumns	the number of local columns (detaults to PETSC_DECIDE)