Chaste  Release::2017.1
Static Public Member Functions | Static Public Attributes | Static Private Member Functions | Static Private Attributes | List of all members
PetscTools Class Reference

#include <PetscTools.hpp>

+ Collaboration diagram for PetscTools:

Static Public Member Functions

static void ResetCache ()
 
static bool IsInitialised ()
 
static bool IsSequential ()
 
static bool IsParallel ()
 
static bool IsIsolated ()
 
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 MPI_Comm GetWorld ()
 
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, bool newAllocationError=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=nullptr)
 
static void ReadPetscObject (Vec &rVec, const std::string &rOutputFileFullPath, Vec rParallelLayout=nullptr)
 
static bool HasParMetis ()
 
static void Destroy (Vec &rVec)
 
static void Destroy (Mat &rMat)
 
static void SetOption (const char *pOptionName, const char *pOptionValue)
 

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.

Any PETSc operation that can be performed using the methods in this class, should be.

This ensures a consistent interface in Chaste even when PETSc arguments change between PETSc versions. For example VecDestroy takes different arguments in 3.2, and using PetscTools::Destroy(vec); takes care of this.

Definition at line 111 of file PetscTools.hpp.

Member Function Documentation

bool PetscTools::AmMaster ( )
static
Returns
whether it is the master process or not.

If not running in parallel, or if IsolateProcesses has been called, always returns true.

Definition at line 120 of file PetscTools.cpp.

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

Referenced by NodeBasedCellPopulation< DIM >::AddReceivedCells(), NodeBasedCellPopulation< DIM >::AddReceivedHaloCells(), ParallelColumnDataWriter::AdvanceAlongUnlimitedDimension(), ArchiveOpener< Archive, Stream >::ArchiveOpener(), ParallelColumnDataWriter::Close(), OutputFileHandler::CommonConstructor(), NumericFileComparison::CompareFiles(), FileComparison::CompareFiles(), 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(), OutputFileHandler::CopyFileTo(), OutputDirectoryFifoQueue::CreateNextDir(), CellMLToSharedLibraryConverter::CreateOptionsFile(), CardiacSimulation::CreateResumeXmlFile(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::DisplayRun(), ParallelColumnDataWriter::EndDefineMode(), NodesOnlyMesh< SPACE_DIM >::EnlargeBoxCollection(), ActivationOutputModifier::FinaliseAtEnd(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextBoundaryElement(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextCableElement(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), NodeBasedCellPopulation< DIM >::GetReceivedCells(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), GenericEventHandler< 11, MeshEventHandler >::HeadingsImpl(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), DistributedBoxCollection< DIM >::LoadBalance(), OutputFileHandler::MakeFoldersAndReturnFullPath(), NodeBasedCellPopulation< DIM >::NonBlockingSendCellsToNeighbourProcesses(), AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationSetup(), PCBlockDiagonal::PCBlockDiagonal(), PCLDUFactorisation::PCLDUFactorisation(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), StreeterFibreGenerator< SPACE_DIM >::PreWriteCalculations(), Citations::Print(), ExecutableSupport::Print(), ExecutableSupport::PrintError(), ProgressReporter::PrintFinalising(), ProgressReporter::PrintInitialising(), ProgressReporter::ProgressReporter(), Hdf5DataWriter::PutUnlimitedVariable(), ParallelColumnDataWriter::PutVariable(), ParallelColumnDataWriter::PutVector(), GenericEventHandler< 11, MeshEventHandler >::ReportImpl(), AbstractFileComparison::ResetFiles(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), HeartConfig::save(), AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save(), NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses(), DistributedBoxCollection< SPACE_DIM >::serialize(), AbstractFileComparison::Setup(), DistributedBoxCollection< DIM >::SetupHaloBoxes(), AbstractPdeModifier< DIM >::SetupSolve(), ExecutableSupport::ShowCopyright(), AbstractFileComparison::SkipHeaderLines(), LinearSystem::Solve(), AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve(), ProgressReporter::Update(), AbstractPdeModifier< DIM >::UpdateAtEndOfOutputTimeStep(), AbstractPdeModifier< DIM >::UpdateAtEndOfSolve(), CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write(), HeartConfig::Write(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::WriteCmguiScript(), AbstractContinuumMechanicsSolver< DIM >::WriteCurrentPressureSolution(), AbstractContinuumMechanicsSolver< DIM >::WriteCurrentSpatialSolution(), AbstractPerElementWriter< SPACE_DIM, SPACE_DIM, SPACE_DIM *SPACE_DIM >::WriteData(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMeshReader(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFileToMeshalyzer(), CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::WriteHeader(), MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::WriteInfo(), MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::WriteInfo(), BidomainProblem< DIM >::WriteInfo(), ExtendedBidomainProblem< DIM >::WriteInfo(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::WriteInfoFile(), HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles(), OdeSolution::WriteToFile(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::WriteVisualizerSetupFile(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteXdmfMasterFile(), LinearSystem::~LinearSystem(), and ProgressReporter::~ProgressReporter().

bool PetscTools::AmTopMost ( )
static
Returns
whether it is the right-most process or not.

If not running in parallel, or if IsolateProcesses has been called, always returns true.

Definition at line 126 of file PetscTools.cpp.

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

Referenced by NodeBasedCellPopulation< DIM >::AddReceivedCells(), NodeBasedCellPopulation< DIM >::AddReceivedHaloCells(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), NodesOnlyMesh< SPACE_DIM >::EnlargeBoxCollection(), NodeBasedCellPopulation< DIM >::GetReceivedCells(), DistributedBoxCollection< DIM >::LoadBalance(), NodeBasedCellPopulation< DIM >::NonBlockingSendCellsToNeighbourProcesses(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses(), DistributedBoxCollection< DIM >::SetupHaloBoxes(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFileToMeshalyzer(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().

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

If MPI is set up, perform a barrier synchronisation. If not, or if IsolateProcesses has been called, it's a noop.

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

Definition at line 134 of file PetscTools.cpp.

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

Referenced by ParallelColumnDataWriter::AdvanceAlongUnlimitedDimension(), ArchiveOpener< Archive, Stream >::ArchiveOpener(), GenericEventHandler< 11, MeshEventHandler >::BeginEventImpl(), BeginRoundRobin(), ElectrodesStimulusFactory< DIM >::CheckForElectrodesIntersection(), ParallelColumnDataWriter::Close(), OutputFileHandler::CommonConstructor(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), OutputFileHandler::CopyFileTo(), OutputDirectoryFifoQueue::CreateNextDir(), CellMLToSharedLibraryConverter::CreateOptionsFile(), GenericEventHandler< 11, MeshEventHandler >::EndEventImpl(), EndRoundRobin(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::GeometricPartitioning(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter(), GenericEventHandler< 11, MeshEventHandler >::HeadingsImpl(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), OutputFileHandler::MakeFoldersAndReturnFullPath(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), ExtendedBidomainProblem< DIM >::ProcessExtracellularStimulus(), GenericEventHandler< 11, MeshEventHandler >::ReportImpl(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), HeartConfig::save(), AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save(), AbstractFileComparison::Setup(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), NodeBasedCellPopulation< DIM >::Update(), AbstractContinuumMechanicsSolver< DIM >::WriteCurrentPressureSolution(), AbstractContinuumMechanicsSolver< DIM >::WriteCurrentSpatialSolution(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

void PetscTools::BeginRoundRobin ( )
static

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

Note that this is not reliable for printing output to stdout in an ordered fashion, since on some systems each process may have a separate stdout buffer, and there's no way to force a flush to the underlying output stream. See e.g. http://stackoverflow.com/questions/5182045/openmpi-mpi-barrier-problems for more info.

Definition at line 150 of file PetscTools.cpp.

References Barrier(), and GetMyRank().

Referenced by ActivationOutputModifier::FinaliseAtEnd(), GenericEventHandler< 11, MeshEventHandler >::ReportImpl(), ExecutableSupport::ShowParallelLaunching(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFileToMeshalyzer(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().

static void PetscTools::CheckCache ( )
inlinestaticprivate

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

Definition at line 128 of file PetscTools.hpp.

References ResetCache().

Referenced by AmMaster(), AmTopMost(), Barrier(), GetMyRank(), GetNumProcs(), IsInitialised(), 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
sizethe size of the vector
valuethe value to set each entry
Returns
new PETSc vector

Definition at line 254 of file PetscTools.cpp.

References CreateVec().

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

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

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

Parameters
sizethe size of the vector
localSizethe local number of items owned by this process
ignoreOffProcEntrieswhether to ignore entries destined to be stored on a separate processor when assembling (eliminates global reductions).
Returns
new PETSc vector

Definition at line 214 of file PetscTools.cpp.

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

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

Create a Vec from the given data.

Parameters
datasome data
Returns
new PETSc vector

Definition at line 234 of file PetscTools.cpp.

References CreateVec().

static void PetscTools::Destroy ( Vec &  rVec)
inlinestatic

Destroy method Note that PETSc 3.1 and previous destroy based on a PETSc object but PETSc 3.2 and later destroy based on a pointer to a PETSc object

Parameters
rVeca reference to the PETSc object

Definition at line 352 of file PetscTools.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AllocateMatrixMemory(), AbstractContinuumMechanicsSolver< DIM >::ApplyDirichletBoundaryConditions(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem(), BidomainSolver< ELEMENT_DIM, SPACE_DIM >::BidomainSolver(), PetscMatTools::CheckEquality(), PetscMatTools::CheckSymmetry(), AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeJacobianNumerically(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), DistributedVectorFactory::DistributedVectorFactory(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), HasParMetis(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseForSolve(), ExtendedBidomainProblem< DIM >::load(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 2 >::load(), PCBlockDiagonal::PCBlockDiagonal(), PCBlockDiagonal::PCBlockDiagonalCreate(), PCLDUFactorisation::PCLDUFactorisation(), PCLDUFactorisation::PCLDUFactorisationCreate(), PCTwoLevelsBlockDiagonal::PCTwoLevelsBlockDiagonalCreate(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), Hdf5DataWriter::PutStripedVector(), Hdf5DataWriter::PutVector(), ParallelColumnDataWriter::PutVectorStripe(), ReadPetscObject(), ReplicatableVector::RemovePetscContext(), ReplicatableVector::Replicate(), MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::SetIdentityBlockToLhsMatrix(), PetscVecTools::SetupInterleavedVectorScatterGather(), SimplePetscNonlinearSolver::Solve(), StokesFlowSolver< DIM >::Solve(), SimpleNewtonNonlinearSolver::Solve(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), LinearSystem::Solve(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SolveAndWriteResultsToFile(), OdeLinearSystemSolver::SolveOneTimeStep(), AbstractNonlinearElasticitySolver< DIM >::SolveSnes(), AbstractNonlinearElasticitySolver< DIM >::TakeNewtonStep(), ParabolicGrowingDomainPdeModifier< DIM >::UpdateAtEndOfTimeStep(), EllipticGrowingDomainPdeModifier< DIM >::UpdateAtEndOfTimeStep(), ParabolicBoxDomainPdeModifier< DIM >::UpdateAtEndOfTimeStep(), EllipticBoxDomainPdeModifier< DIM >::UpdateAtEndOfTimeStep(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), ParabolicGrowingDomainPdeModifier< DIM >::UpdateSolutionVector(), AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::VerifyJacobian(), VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep(), ExtendedBidomainProblem< DIM >::WriteOneStep(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteOutputDataToHdf5(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem(), AbstractContinuumMechanicsSolver< DIM >::~AbstractContinuumMechanicsSolver(), AbstractPdeModifier< DIM >::~AbstractPdeModifier(), CellVecData::~CellVecData(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::~ExtendedBidomainSolver(), Hdf5DataWriter::~Hdf5DataWriter(), LinearSystem::~LinearSystem(), MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::~MonodomainPurkinjeSolver(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::~MonodomainSolver(), OdeLinearSystemSolver::~OdeLinearSystemSolver(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::~OperatorSplittingMonodomainSolver(), ParallelColumnDataWriter::~ParallelColumnDataWriter(), and PCTwoLevelsBlockDiagonal::~PCTwoLevelsBlockDiagonal().

static void PetscTools::Destroy ( Mat &  rMat)
inlinestatic

Destroy method Note that PETSc 3.1 and previous destroy based on a PETSc object but PETSc 3.2 and later destroy based on a pointer to a PETSc object

Parameters
rMata reference to the PETSc object

Definition at line 368 of file PetscTools.hpp.

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

Dumps a given PETSc object to disk.

Parameters
rMata matrix
rOutputFileFullPathwhere to dump the matrix to disk

Definition at line 333 of file PetscTools.cpp.

References PETSC_DESTROY_PARAM.

Referenced by LinearSystem::AddRhsMultipleValues(), ParabolicGrowingDomainPdeModifier< DIM >::serialize(), EllipticGrowingDomainPdeModifier< DIM >::serialize(), ParabolicBoxDomainPdeModifier< DIM >::serialize(), and EllipticBoxDomainPdeModifier< DIM >::serialize().

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

Dumps a given PETSc object to disk.

Parameters
rVeca vector
rOutputFileFullPathwhere to dump the vector to disk

Definition at line 347 of file PetscTools.cpp.

References PETSC_DESTROY_PARAM.

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 160 of file PetscTools.cpp.

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

Referenced by ActivationOutputModifier::FinaliseAtEnd(), GenericEventHandler< 11, MeshEventHandler >::ReportImpl(), ExecutableSupport::ShowParallelLaunching(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFileToMeshalyzer(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().

unsigned PetscTools::GetMyRank ( )
static
Returns
our rank.

If PETSc has not been initialized, returns 0.

Definition at line 114 of file PetscTools.cpp.

References CheckCache(), and mRank.

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), ArchiveOpener< Archive, Stream >::ArchiveOpener(), CompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), IncompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), CellId::AssignCellId(), Barrier(), BeginRoundRobin(), NodesOnlyMesh< SPACE_DIM >::CalculateNodesOutsideLocalDomain(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::DoAssemble(), EndRoundRobin(), ActivationOutputModifier::FinaliseAtEnd(), FormDebugHead(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::GeometricPartitioning(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCableElement(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetCardiacCellOrHaloCell(), NodesOnlyMesh< SPACE_DIM >::GetMaximumNodeIndex(), NodesOnlyMesh< SPACE_DIM >::GetNextAvailableIndex(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), DistributedBoxCollection< DIM >::GetProcessOwningNode(), DistributedBoxCollection< DIM >::LoadBalance(), CardiacSimulationArchiver< PROBLEM_CLASS >::Migrate(), NodeBasedCellPopulation< DIM >::NonBlockingSendCellsToNeighbourProcesses(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodeAndElementPartitioning(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), Timer::Print(), ExecutableSupport::PrintError(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), GenericEventHandler< 11, MeshEventHandler >::ReportImpl(), NodeBasedCellPopulation< DIM >::SendCellsToNeighbourProcesses(), DistributedBoxCollection< SPACE_DIM >::serialize(), ExecutableSupport::ShowParallelLaunching(), StokesFlowSolver< DIM >::Solve(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SolveCellSystems(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping(), NodesOnlyMesh< SPACE_DIM >::SolveNodeMapping(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping(), AbstractNonlinearElasticitySolver< DIM >::TakeNewtonStep(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::UpdateQueueFromRemote(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), ExecutableSupport::WriteMachineInfoFile(), ExecutableSupport::WriteProvenanceInfoFile(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), and NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile().

unsigned PetscTools::GetNumProcs ( )
static
Returns
total number of processors.

Definition at line 108 of file PetscTools.cpp.

References CheckCache(), and mNumProcessors.

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), CellId::AssignCellId(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CalculateHaloNodesFromNodeExchange(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateNodeExchange(), DistributedVectorFactory::CalculateOwnership(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::ComputeDistanceMap(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::DistanceMapCalculator(), DistributedBoxCollection< DIM >::DistributedBoxCollection(), EndRoundRobin(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::GeometricPartitioning(), NodesOnlyMesh< SPACE_DIM >::GetMaximumNodeIndex(), NodesOnlyMesh< SPACE_DIM >::GetNextAvailableIndex(), CardiacSimulationArchiver< PROBLEM_CLASS >::Migrate(), ObjectCommunicator< CLASS >::ObjectCommunicator(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodeAndElementPartitioning(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), GenericEventHandler< 11, MeshEventHandler >::ReportImpl(), DistributedVectorFactory::rGetGlobalLows(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), DistributedQuadraticMesh< DIM >::serialize(), DistributedVectorFactory::serialize(), DistributedBoxCollection< SPACE_DIM >::serialize(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetDistributedVectorFactory(), DistributedVectorFactory::SetOriginalFactory(), ExecutableSupport::ShowParallelLaunching(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SolveCellSystems(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::UpdateQueueFromRemote(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::WorkOnLocalQueue(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingParallelMesh(), and ExecutableSupport::WriteMachineInfoFile().

MPI_Comm PetscTools::GetWorld ( )
static

Get the MPI Communicator representing the whole set of running processes. This will normally be PETSC_COMM_WORLD, unless IsolateProcesses has been called, in which case it will be PETSC_COMM_SELF.

Returns
the MPI Communicator representing the whole set of running processes

Definition at line 174 of file PetscTools.cpp.

References mIsolateProcesses.

Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellCyclePhaseCount(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellMutationStateCount(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellProliferativeTypeCount(), NodeBasedCellPopulation< DIM >::GetSizeOfCellPopulation(), NodesOnlyMesh< SPACE_DIM >::GetWidth(), ObjectCommunicator< CLASS >::IRecvObject(), NodesOnlyMesh< SPACE_DIM >::IsANodeCloseToDomainBoundary(), ObjectCommunicator< CLASS >::ISendObject(), ObjectCommunicator< CLASS >::RecvObject(), GenericEventHandler< 11, MeshEventHandler >::ReportImpl(), ObjectCommunicator< CLASS >::SendObject(), and ObjectCommunicator< CLASS >::SendRecvObject().

bool PetscTools::HasParMetis ( )
static

Checks if PETSc has been configured with ParMetis partioning support.

Returns
true If ParMetis partitioning (via PETSc) is available

Definition at line 445 of file PetscTools.cpp.

References Destroy(), PETSC_DESTROY_PARAM, and SetupMat().

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning(), and NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning().

bool PetscTools::IsInitialised ( )
static
Returns
whether PETSc has been initialised yet.

Definition at line 85 of file PetscTools.cpp.

References CheckCache(), and mPetscIsInitialised.

Referenced by Citations::Register().

bool PetscTools::IsIsolated ( )
static
Returns
whether this process is isolated, i.e. IsolateProcesses has been called.

Definition at line 103 of file PetscTools.cpp.

References mIsolateProcesses.

Referenced by GenericEventHandler< 11, MeshEventHandler >::ReportImpl().

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 and AmTopMost always return true, Barrier becomes a no-op, and ReplicateBool doesn't replicate.

Parameters
isolatewhether to consider processes as isolated

Definition at line 169 of file PetscTools.cpp.

References mIsolateProcesses.

bool PetscTools::IsParallel ( )
static
Returns
whether there is more than one process.

Definition at line 97 of file PetscTools.cpp.

References CheckCache(), and mNumProcessors.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), FormDebugHead(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellCyclePhaseCount(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellMutationStateCount(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellProliferativeTypeCount(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), GenericEventHandler< 11, MeshEventHandler >::HeadingsImpl(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), DistributedBoxCollection< DIM >::IsHaloBox(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodeAndElementPartitioning(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), Timer::Print(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), GenericEventHandler< 11, MeshEventHandler >::ReportImpl(), CellId::serialize(), ExecutableSupport::ShowParallelLaunching(), and XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

bool PetscTools::IsSequential ( )
static
Returns
whether there is one process or not.

Definition at line 91 of file PetscTools.cpp.

References CheckCache(), mIsolateProcesses, and mNumProcessors.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), AbstractContinuumMechanicsSolver< DIM >::AllocateMatrixMemory(), CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::DistanceMapCalculator(), NodeBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), HoneycombMeshGenerator::HoneycombMeshGenerator(), DistributedBoxCollection< DIM >::IsInteriorBox(), NodeBasedCellPopulationWithParticles< DIM >::NodeBasedCellPopulationWithParticles(), PCTwoLevelsBlockDiagonal::PCTwoLevelsBlockDiagonalCreate(), AbstractNonlinearElasticitySolver< DIM >::SetKspSolverAndPcType(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles(), SetupMat(), FineCoarseMeshPair< DIM >::ShareCoarseElementData(), FineCoarseMeshPair< DIM >::ShareFineElementData(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), and NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile().

void PetscTools::ReadPetscObject ( Mat &  rMat,
const std::string &  rOutputFileFullPath,
Vec  rParallelLayout = nullptr 
)
static

Read a previously dumped PETSc object from disk.

Parameters
rMata matrix
rOutputFileFullPathwhere to read the matrix from
rParallelLayoutIf provided, rMat will have the same parallel layout. Its content is irrelevant.
Todo:
: #1082 work out appropriate nz allocation.

Definition at line 361 of file PetscTools.cpp.

References Destroy(), PETSC_DESTROY_PARAM, and SetupMat().

Referenced by LinearSystem::AddRhsMultipleValues(), ParabolicGrowingDomainPdeModifier< DIM >::serialize(), EllipticGrowingDomainPdeModifier< DIM >::serialize(), ParabolicBoxDomainPdeModifier< DIM >::serialize(), and EllipticBoxDomainPdeModifier< DIM >::serialize().

void PetscTools::ReadPetscObject ( Vec &  rVec,
const std::string &  rOutputFileFullPath,
Vec  rParallelLayout = nullptr 
)
static

Read a previously dumped PETSc object from disk.

Parameters
rVeca vector
rOutputFileFullPathwhere to read the matrix from
rParallelLayoutIf provided, rMat will have the same parallel layout. Its content is irrelevant.

Definition at line 412 of file PetscTools.cpp.

References PETSC_DESTROY_PARAM.

bool PetscTools::ReplicateBool ( bool  flag)
static

Boolean OR of flags between processes.

Parameters
flagis set to true on this process.
Returns
true if any process' flag is set to true.

Definition at line 186 of file PetscTools.cpp.

References CheckCache(), mIsolateProcesses, and mPetscIsInitialised.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), BidomainProblem< DIM >::AnalyseMeshForBath(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::ComputeDistanceMap(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary(), AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::HasDirichletBoundaryConditions(), ReplicateException(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::UpdateQueueFromRemote(), and Hdf5DataWriter::WriteCache().

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
flagis set to true if this process has thrown.

Definition at line 198 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(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), ExtendedBidomainTissue< 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(), 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 58 of file PetscTools.cpp.

References mNumProcessors, mPetscIsInitialised, and mRank.

Referenced by CheckCache(), PetscSetupUtils::InitialisePetsc(), and PetscSetupUtils::ResetStatusCache().

static void PetscTools::SetOption ( const char *  pOptionName,
const char *  pOptionValue 
)
inlinestatic

Set a PETSc option. This is a wrapper for PetscOptionsSetValue, which changed signature in PETSc 3.7.

Parameters
pOptionNamethe option name
pOptionValuethe option value

Definition at line 384 of file PetscTools.hpp.

Referenced by PCBlockDiagonal::PCBlockDiagonalSetUp(), PCLDUFactorisation::PCLDUFactorisationSetUp(), PCTwoLevelsBlockDiagonal::PCTwoLevelsBlockDiagonalSetUp(), LinearSystem::ResetKspSolver(), AbstractNonlinearElasticitySolver< DIM >::SetKspSolverAndPcType(), LinearSystem::Solve(), and AbstractNonlinearElasticitySolver< DIM >::SolveSnes().

void PetscTools::SetupMat ( Mat &  rMat,
int  numRows,
int  numColumns,
unsigned  rowPreallocation,
int  numLocalRows = PETSC_DECIDE,
int  numLocalColumns = PETSC_DECIDE,
bool  ignoreOffProcEntries = true,
bool  newAllocationError = 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
rMatthe matrix
numRowsthe number of rows in the matrix
numColumnsthe number of columns in the matrix
rowPreallocationthe 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.
numLocalRowsthe number of local rows (defaults to PETSC_DECIDE)
numLocalColumnsthe number of local columns (defaults to PETSC_DECIDE)
ignoreOffProcEntriestells PETSc to drop off-processor entries
newAllocationErrortells PETSc whether to set the MAT_NEW_NONZERO_ALLOCATION_ERR. ** currently only used in PETSc 3.3 and later ** in PETSc 3.2 and earlier MAT_NEW_NONZERO_ALLOCATION_ERR defaults to false in PETSc 3.3 MAT_NEW_NONZERO_ALLOCATION_ERR defaults to true

Definition at line 268 of file PetscTools.cpp.

References IsSequential().

Referenced by AbstractContinuumMechanicsSolver< DIM >::AllocateMatrixMemory(), Hdf5DataWriter::ApplyPermutation(), Hdf5DataWriter::DefineFixedDimensionUsingMatrix(), HasParMetis(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::InitialiseForSolve(), BidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), LinearSystem::LinearSystem(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), ReadPetscObject(), LinearSystem::SetPrecondMatrixIsDifferentFromLhs(), SimplePetscNonlinearSolver::Solve(), and AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::VerifyJacobian().

Member Data Documentation

const unsigned PetscTools::MASTER_RANK =0
static

As a convention, we consider processor 0 the master process.

Definition at line 141 of file PetscTools.hpp.

Referenced by AmMaster().

bool PetscTools::mIsolateProcesses = false
staticprivate

Whether to pretend that we're just running many master processes independently.

Definition at line 125 of file PetscTools.hpp.

Referenced by AmMaster(), AmTopMost(), Barrier(), GetWorld(), IsIsolated(), IsolateProcesses(), IsSequential(), and ReplicateBool().

unsigned PetscTools::mNumProcessors = 0
staticprivate

The total number of processors.

Definition at line 119 of file PetscTools.hpp.

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

bool PetscTools::mPetscIsInitialised = false
staticprivate

Whether PETSc has been initialised.

Definition at line 116 of file PetscTools.hpp.

Referenced by Barrier(), IsInitialised(), ReplicateBool(), and ResetCache().

unsigned PetscTools::mRank = 0
staticprivate

Which processors we are.

Definition at line 122 of file PetscTools.hpp.

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

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