PetscTools Class Reference

#include <PetscTools.hpp>

Collaboration diagram for PetscTools:

List of all members.

Static Public Member Functions

static void ResetCache ()

static bool IsSequential ()

static unsigned GetNumProcs ()

static unsigned GetMyRank ()

static bool AmMaster ()

static void Barrier ()

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, int maxColsPerRowIfMatMpiAij=54)

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 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

Detailed Description

A helper class of static methods.

Definition at line 48 of file PetscTools.hpp.

Member Function Documentation

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 61 of file PetscTools.hpp.

References mNumProcessors, and ResetCache().

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

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 40 of file PetscTools.cpp.

References mNumProcessors, mPetscIsInitialised, and mRank.

Referenced by CheckCache().

bool PetscTools::IsSequential ( ) [static]

Just returns whether there is one process or not.

Definition at line 75 of file PetscTools.cpp.

References CheckCache(), and mNumProcessors.

Referenced by GenericEventHandler< 9, CancerEventHandler >::Headings(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), and GenericEventHandler< 9, CancerEventHandler >::Report().

unsigned PetscTools::GetNumProcs ( ) [static]

Returns total number of processors

Definition at line 81 of file PetscTools.cpp.

References CheckCache(), and mNumProcessors.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::CheckCompatibilityCondition(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisBinaryNodePartitioning(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), and GenericEventHandler< 9, CancerEventHandler >::Report().

unsigned PetscTools::GetMyRank ( ) [static]

Return our rank.

If PETSc has not been initialized, returns 0.

Definition at line 87 of file PetscTools.cpp.

References CheckCache(), and mRank.

Referenced by ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), ArchiveLocationInfo::GetProcessUniqueFilePath(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisBinaryNodePartitioning(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), GenericEventHandler< 9, CancerEventHandler >::Report(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping(), and ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping().

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 93 of file PetscTools.cpp.

References CheckCache(), MASTER_RANK, and mRank.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), Hdf5ToMeshalyzerConverter::Hdf5ToMeshalyzerConverter(), GenericEventHandler< 9, CancerEventHandler >::Headings(), OutputFileHandler::OutputFileHandler(), Hdf5DataWriter::PutUnlimitedVariable(), GenericEventHandler< 9, CancerEventHandler >::Report(), CardiacElectroMechanicsProblem< DIM >::Solve(), Hdf5ToMeshalyzerConverter::Write(), PostProcessingWriter::WriteApdMapFile(), PostProcessingWriter::WriteConductionVelocityMap(), HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode(), PostProcessingWriter::WriteMaxUpstrokeVelocityMap(), and PostProcessingWriter::WriteUpstrokeTimeMap().

void PetscTools::Barrier ( ) [static]

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

Definition at line 103 of file PetscTools.cpp.

References CheckCache(), and mPetscIsInitialised.

Referenced by CuboidMeshConstructor< DIM >::Construct(), GenericEventHandler< 9, CancerEventHandler >::Headings(), HoneycombMeshGenerator::Make2dPeriodicCryptMesh(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisBinaryNodePartitioning(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodesWithMetisBinaries(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), GenericEventHandler< 9, CancerEventHandler >::Report(), and HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode().

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 134 of file PetscTools.cpp.

Referenced by AbstractNonlinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CONCRETE >::CreateConstantInitialGuess(), and 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 144 of file PetscTools.cpp.

References CreateVec().

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

Create a Vec from the given data.

Parameters:

data

some data

Definition at line 160 of file PetscTools.cpp.

References CreateVec().

void PetscTools::SetupMat	(	Mat &	rMat,
		int	numRows,
		int	numColumns,
		MatType	matType = `(MatType) MATMPIAIJ`,
		int	numLocalRows = `PETSC_DECIDE`,
		int	numLocalColumns = `PETSC_DECIDE`,
		int	maxColsPerRowIfMatMpiAij = `54`
	)			`[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)
	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 182 of file PetscTools.cpp.

Referenced by LinearSystem::LinearSystem(), LinearSystem::SetupVectorAndMatrix(), SimplePetscNonlinearSolver::Solve(), and AbstractNonlinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CONCRETE >::VerifyJacobian().

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 114 of file PetscTools.cpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::SolveCellSystems().

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

Another helper method to get a single value from a vector in 1 line than Petsc's usual 4 or 5. DOES NOT check that the requested component is local, DOES do bound-checking.

Todo:: Think if there is an efficient compromise between this method and the full weight of ReplicatableVector (broadcast single values to all processors). How do you know who has the value?

Dumps a given Petsc object to disk.

Parameters:

	rMat	a matrix
	rOutputFileFullPath	where to dump the matrix to disk

Definition at line 208 of file PetscTools.cpp.

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 223 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 238 of file PetscTools.cpp.

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 253 of file PetscTools.cpp.

Member Data Documentation

bool PetscTools::mPetscIsInitialised = false [static, private]

Whether PETSc has been initialised.

Definition at line 52 of file PetscTools.hpp.

Referenced by Barrier(), and ResetCache().

unsigned PetscTools::mNumProcessors = 0 [static, private]

The total number of processors.

Definition at line 55 of file PetscTools.hpp.

Referenced by CheckCache(), GetNumProcs(), IsSequential(), and ResetCache().

unsigned PetscTools::mRank = 0 [static, private]

Which processors we are.

Definition at line 58 of file PetscTools.hpp.

Referenced by AmMaster(), GetMyRank(), and ResetCache().

const unsigned PetscTools::MASTER_RANK = 0 [static]

As a convention, we consider processor 0 the master process

Definition at line 74 of file PetscTools.hpp.

Referenced by AmMaster().

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

/tmp/release_1.1/global/src/PetscTools.hpp
/tmp/release_1.1/global/src/PetscTools.cpp


Static Public Member Functions
static void	ResetCache ()
static bool	IsSequential ()
static unsigned	GetNumProcs ()
static unsigned	GetMyRank ()
static bool	AmMaster ()
static void	Barrier ()
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, int maxColsPerRowIfMatMpiAij=54)
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 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