PetscTools Class Reference

#include <PetscTools.hpp>

Collaboration diagram for PetscTools:

Collaboration graph
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List of all members.

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, int localSize=PETSC_DECIDE)
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)
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 void Terminate (const std::string &rMessage, const std::string &rFilename, unsigned lineNumber)

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 65 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 83 of file PetscTools.hpp.

References mNumProcessors, and ResetCache().

Referenced by AmMaster(), AmTopMost(), 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 47 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 82 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(), FormDebugHead(), GenericEventHandler< 13, HeartEventHandler >::Headings(), HoneycombMeshGenerator::HoneycombMeshGenerator(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodePartitioning(), PCTwoLevelsBlockDiagonal::PCTwoLevelsBlockDiagonalCreate(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), GenericEventHandler< 13, HeartEventHandler >::Report(), SetupMat(), and ExecutableSupport::ShowParallelLaunching().

unsigned PetscTools::GetNumProcs (  )  [static]

Returns total number of processors

Definition at line 88 of file PetscTools.cpp.

References CheckCache(), and mNumProcessors.

Referenced by NonlinearElasticitySolver< DIM >::AllocateMatrixMemory(), DistributedVectorFactory::CalculateOwnership(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::ComputeDistanceMap(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::DistanceMapCalculator(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), CardiacSimulationArchiver< PROBLEM_CLASS >::Migrate(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), GenericEventHandler< 13, HeartEventHandler >::Report(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetDistributedVectorFactory(), ExecutableSupport::ShowParallelLaunching(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::UpdateQueueFromRemote(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::WorkOnLocalQueue(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile(), and ExecutableSupport::WriteMachineInfoFile().

unsigned PetscTools::GetMyRank (  )  [static]

Return our rank.

If PETSc has not been initialized, returns 0.

Definition at line 94 of file PetscTools.cpp.

References CheckCache(), and mRank.

Referenced by ArchiveOpener< Archive, Stream >::ArchiveOpener(), NonlinearElasticitySolver< DIM >::AssembleSystem(), Barrier(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), FormDebugHead(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), ExecutableSupport::PrintError(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), GenericEventHandler< 13, HeartEventHandler >::Report(), ExecutableSupport::ShowParallelLaunching(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping(), AbstractNonlinearElasticitySolver< DIM >::TakeNewtonStep(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::UpdateQueueFromRemote(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile(), ExecutableSupport::WriteMachineInfoFile(), and ExecutableSupport::WriteProvenanceInfoFile().

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 100 of file PetscTools.cpp.

References CheckCache(), MASTER_RANK, and mRank.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), ParallelColumnDataWriter::AdvanceAlongUnlimitedDimension(), CellBasedSimulationWithPdes< DIM >::AfterSolve(), ArchiveOpener< Archive, Stream >::ArchiveOpener(), ParallelColumnDataWriter::Close(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), CellMLToSharedLibraryConverter::ConvertCellmlToSo(), CardiacSimulation::CreateAndRun(), OutputDirectoryFifoQueue::CreateNextDir(), ParallelColumnDataWriter::EndDefineMode(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), GenericEventHandler< 13, HeartEventHandler >::Headings(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), HoneycombMeshGenerator::Make2dPeriodicMesh(), OutputFileHandler::MakeFoldersAndReturnFullPath(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), OutputFileHandler::OutputFileHandler(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), ExecutableSupport::PrintError(), ProgressReporter::PrintFinalising(), ProgressReporter::PrintInitialising(), ProgressReporter::ProgressReporter(), Hdf5DataWriter::PutUnlimitedVariable(), ParallelColumnDataWriter::PutVariable(), ParallelColumnDataWriter::PutVector(), GenericEventHandler< 13, HeartEventHandler >::Report(), AbstractCardiacTissue< SPACE_DIM >::save(), HeartConfig::save(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), CellBasedSimulationWithPdes< DIM >::SetupWritePdeSolution(), ExecutableSupport::ShowCopyright(), LinearSystem::Solve(), ProgressReporter::Update(), HeartConfig::Write(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMeshReader(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile(), MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::WriteInfo(), BidomainProblem< DIM >::WriteInfo(), HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode(), CellBasedSimulationWithPdes< DIM >::WritePdeSolution(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg(), OdeSolution::WriteToFile(), LinearSystem::~LinearSystem(), and ProgressReporter::~ProgressReporter().

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 106 of file PetscTools.cpp.

References CheckCache(), mNumProcessors, and mRank.

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

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 116 of file PetscTools.cpp.

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

Referenced by ParallelColumnDataWriter::AdvanceAlongUnlimitedDimension(), GenericEventHandler< 13, HeartEventHandler >::BeginEvent(), ParallelColumnDataWriter::Close(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), OutputDirectoryFifoQueue::CreateNextDir(), GenericEventHandler< 13, HeartEventHandler >::EndEvent(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter(), GenericEventHandler< 13, HeartEventHandler >::Headings(), HoneycombMeshGenerator::Make2dPeriodicMesh(), OutputFileHandler::MakeFoldersAndReturnFullPath(), OutputFileHandler::OutputFileHandler(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), GenericEventHandler< 13, HeartEventHandler >::Report(), AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save(), AbstractCardiacTissue< SPACE_DIM >::save(), HeartConfig::save(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), ExecutableSupport::ShowParallelLaunching(), 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().

Vec PetscTools::CreateVec ( int  size,
int  localSize = PETSC_DECIDE 
) [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

Definition at line 159 of file PetscTools.cpp.

Referenced by AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobianNumerically(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), CreateAndSetVec(), CreateVec(), DistributedVectorFactory::CreateVec(), DistributedVectorFactory::DistributedVectorFactory(), LinearSystem::LinearSystem(), PCBlockDiagonal::PCBlockDiagonalCreate(), PCLDUFactorisation::PCLDUFactorisationCreate(), PCTwoLevelsBlockDiagonal::PCTwoLevelsBlockDiagonalCreate(), Hdf5DataWriter::PutStripedVector(), Hdf5DataWriter::PutVector(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

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

Create a Vec from the given data.

Parameters:
data some data

Definition at line 169 of file PetscTools.cpp.

References CreateVec().

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 191 of file PetscTools.cpp.

References CreateVec().

Referenced by AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::VerifyJacobian().

void PetscTools::SetupMat ( Mat &  rMat,
int  numRows,
int  numColumns,
unsigned  rowPreallocation,
int  numLocalRows = PETSC_DECIDE,
int  numLocalColumns = PETSC_DECIDE 
) [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)

Todo:
#1216 Fix the 1, 0.7 hack

Definition at line 207 of file PetscTools.cpp.

References IsSequential().

Referenced by Hdf5DataWriter::ApplyPermutation(), Hdf5DataWriter::DefineFixedDimensionUsingMatrix(), MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), LinearSystem::LinearSystem(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), ReadPetscObject(), SimplePetscNonlinearSolver::Solve(), and AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::VerifyJacobian().

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 133 of file PetscTools.cpp.

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 141 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 >::ConstructFromMeshReader(), CellMLToSharedLibraryConverter::ConvertCellmlToSo(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), ReplicatableVector::Resize(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SolveCellSystems().

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 250 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 265 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 280 of file PetscTools.cpp.

References SetupMat().

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 324 of file PetscTools.cpp.

void PetscTools::Terminate ( const std::string &  rMessage,
const std::string &  rFilename,
unsigned  lineNumber 
) [static]

Level 4 error (Termination). Execution cannot continue from this point and hence should be terminated (even when running with NDEBUG).

Parameters:
rMessage An error message to appear on the screen
rFilename which source file produced the termination error
lineNumber which line number of the source file produced the termination error

Definition at line 349 of file PetscTools.cpp.

Member Data Documentation

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

Whether PETSc has been initialised.

Definition at line 69 of file PetscTools.hpp.

Referenced by Barrier(), and ResetCache().

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

The total number of processors.

Definition at line 72 of file PetscTools.hpp.

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

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

Which processors we are.

Definition at line 80 of file PetscTools.hpp.

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

const unsigned PetscTools::MASTER_RANK = 0 [static]

As a convention, we consider processor 0 the master process

Definition at line 96 of file PetscTools.hpp.

Referenced by AmMaster().

The documentation for this class was generated from the following files:
Generated on Mon Nov 1 12:37:13 2010 for Chaste by  doxygen 1.5.5