paso::SystemMatrix Class Reference

this class holds a (distributed) stiffness matrix More...

#include <SystemMatrix.h>

Inheritance diagram for paso::SystemMatrix:

Public Member Functions
	SystemMatrix ()
	default constructor - throws exception. More...
	SystemMatrix (SystemMatrixType type, SystemMatrixPattern_ptr pattern, dim_t rowBlockSize, dim_t columnBlockSize, bool patternIsUnrolled, const escript::FunctionSpace &rowFS, const escript::FunctionSpace &colFS)
	~SystemMatrix ()
virtual void	nullifyRowsAndCols (escript::Data &mask_row, escript::Data &mask_col, double main_diagonal_value)
virtual void	saveMM (const std::string &filename) const
	writes the matrix to a file using the Matrix Market file format More...
virtual void	saveHB (const std::string &filename) const
	writes the matrix to a file using the Harwell-Boeing file format More...
virtual void	resetValues (bool preserveSolverData=false)
	resets the matrix entries More...
void	nullifyRows (double *mask_row, double main_diagonal_value)
void	add (dim_t, index_t *, dim_t, dim_t, index_t *, dim_t, double *)
void	makeZeroRowSums (double *left_over)
void	copyColCoupleBlock ()
void	copyRemoteCoupleBlock (bool recreatePattern)
void	fillWithGlobalCoordinates (double f1)
void	print () const
SparseMatrix_ptr	mergeSystemMatrix () const
void	mergeMainAndCouple (index_t **p_ptr, index_t **p_idx, double **p_val) const
void	mergeMainAndCouple_CSR_OFFSET0 (index_t **p_ptr, index_t **p_idx, double **p_val) const
void	mergeMainAndCouple_CSR_OFFSET0_Block (index_t **p_ptr, index_t **p_idx, double **p_val) const
void	mergeMainAndCouple_CSC_OFFSET1 (index_t **p_ptr, index_t **p_idx, double **p_val) const
void	copyMain_CSC_OFFSET1 (index_t **p_ptr, index_t **p_idx, double **p_val)
void	extendedRowsForST (dim_t *degree_ST, index_t *offset_ST, index_t *ST)
void	applyBalanceInPlace (double *x, bool RHS) const
void	applyBalance (double *x_out, const double *x, bool RHS) const
void	balance ()
double	getGlobalSize () const
void	setPreconditioner (Options *options)
void	solvePreconditioner (double *x, double *b)
void	freePreconditioner ()
index_t *	borrowMainDiagonalPointer () const
void	startCollect (const double *in) const
double *	finishCollect () const
void	startColCollect (const double *in) const
double *	finishColCollect () const
void	startRowCollect (const double *in)
double *	finishRowCollect ()
dim_t	getNumRows () const
dim_t	getNumCols () const
dim_t	getTotalNumRows () const
dim_t	getTotalNumCols () const
dim_t	getRowOverlap () const
dim_t	getColOverlap () const
dim_t	getGlobalNumRows () const
dim_t	getGlobalNumCols () const
dim_t	getGlobalTotalNumRows () const
dim_t	getGlobalTotalNumCols () const
double	getSparsity () const
dim_t	getNumOutput () const
void	copyBlockFromMainDiagonal (double *out) const
void	copyBlockToMainDiagonal (const double *in)
void	copyFromMainDiagonal (double *out) const
void	copyToMainDiagonal (const double *in)
void	setValues (double value)
void	rowSum (double *row_sum) const
void	MatrixVector (double alpha, const double *in, double beta, double *out) const
void	MatrixVector_CSR_OFFSET0 (double alpha, const double *in, double beta, double *out) const
Public Member Functions inherited from escript::AbstractSystemMatrix
	AbstractSystemMatrix ()
	Default constructor for AbstractSystemMatrix. More...
	AbstractSystemMatrix (int row_blocksize, const FunctionSpace &row_functionspace, int column_blocksize, const FunctionSpace &column_functionspace)
virtual	~AbstractSystemMatrix ()
	Destructor. More...
ASM_ptr	getPtr ()
	Returns smart pointer which is managing this object. If one does not exist yet it creates one. More...
const_ASM_ptr	getPtr () const
	Returns smart pointer which is managing this object. If one does not exist yet it creates one. More...
Data	vectorMultiply (const Data &right) const
	returns the matrix-vector product this*right More...
bool	isEmpty () const
	returns true if the matrix is empty More...
FunctionSpace	getColumnFunctionSpace () const
	returns the column function space More...
FunctionSpace	getRowFunctionSpace () const
	returns the row function space More...
int	getRowBlockSize () const
	returns the row block size More...
int	getColumnBlockSize () const
	returns the column block size More...
Data	solve (const Data &in, boost::python::object &options) const
	returns the solution u of the linear system this*u=in More...

Static Public Member Functions
static SystemMatrix_ptr	loadMM_toCSR (const char *filename)
static SystemMatrix_ptr	loadMM_toCSC (const char *filename)
static int	getSystemMatrixTypeId (int solver, int preconditioner, int package, bool symmetry, const escript::JMPI &mpi_info)

Public Attributes
SystemMatrixType	type
SystemMatrixPattern_ptr	pattern
dim_t	logical_row_block_size
dim_t	logical_col_block_size
dim_t	row_block_size
dim_t	col_block_size
dim_t	block_size
escript::Distribution_ptr	row_distribution
escript::Distribution_ptr	col_distribution
escript::JMPI	mpi_info
Coupler_ptr< real_t >	col_coupler
Coupler_ptr< real_t >	row_coupler
SparseMatrix_ptr	mainBlock
	main block More...
SparseMatrix_ptr	col_coupleBlock
	coupling to neighbouring processors (row - col) More...
SparseMatrix_ptr	row_coupleBlock
	coupling to neighbouring processors (col - row) More...
SparseMatrix_ptr	remote_coupleBlock
	coupling of rows-cols on neighbouring processors (may not be valid) More...
bool	is_balanced
double *	balance_vector
index_t *	global_id
	stores the global ids for all cols in col_coupleBlock More...
index_t	solver_package
	package code controlling the solver pointer More...
void *	solver_p
	pointer to data needed by a solver More...

Private Member Functions
virtual void	setToSolution (escript::Data &out, escript::Data &in, boost::python::object &options) const
	solves the linear system this*out=in More...
virtual void	ypAx (escript::Data &y, escript::Data &x) const
	performs y+=this*x More...
void	solve (double *out, double *in, Options *options) const

Detailed Description

this class holds a (distributed) stiffness matrix

Constructor & Destructor Documentation

SystemMatrix() [1/2]

paso::SystemMatrix::SystemMatrix

(

)

default constructor - throws exception.

SystemMatrix() [2/2]

paso::SystemMatrix::SystemMatrix	(	SystemMatrixType	ntype,
		SystemMatrixPattern_ptr	npattern,
		dim_t	rowBlockSize,
		dim_t	colBlockSize,
		bool	patternIsUnrolled,
		const escript::FunctionSpace &	rowFS,
		const escript::FunctionSpace &	colFS
	)

Allocates a SystemMatrix of given type using the given matrix pattern. Values are initialized with zero. If patternIsUnrolled and type & MATRIX_FORMAT_BLK1, it is assumed that the pattern is already unrolled to match the requested block size and offsets. Otherwise unrolling and offset adjustment will be performed.

References MATRIX_FORMAT_BLK1, MATRIX_FORMAT_CSC, MATRIX_FORMAT_DEFAULT, MATRIX_FORMAT_DIAGONAL_BLOCK, and MATRIX_FORMAT_OFFSET1.

~SystemMatrix()

paso::SystemMatrix::~SystemMatrix

(

)

References escript::AbstractSystemMatrix::getPtr(), paso::Preconditioner_solve(), and solver_p.

Member Function Documentation

add()

void paso::SystemMatrix::add	(	dim_t	,
		index_t *	,
		dim_t	,
		dim_t	,
		index_t *	,
		dim_t	,
		double *
	)

applyBalance()

void paso::SystemMatrix::applyBalance	(	double *	x_out,
		const double *	x,
		bool	RHS
	)		const

applyBalanceInPlace()

void paso::SystemMatrix::applyBalanceInPlace	(	double *	x,
		bool	RHS
	)		const

balance()

void paso::SystemMatrix::balance

(

)

References balance_vector.

borrowMainDiagonalPointer()

index_t * paso::SystemMatrix::borrowMainDiagonalPointer

(

)

const

References block_size, pattern, row_block_size, and rowSum().

copyBlockFromMainDiagonal()

void paso::SystemMatrix::copyBlockFromMainDiagonal ( double *  out ) const

inline

References mainBlock.

copyBlockToMainDiagonal()

void paso::SystemMatrix::copyBlockToMainDiagonal ( const double *  in )

inline

References col_coupleBlock, and mainBlock.

copyColCoupleBlock()

void paso::SystemMatrix::copyColCoupleBlock

(

)

copies the col_coupleBlock into row_coupleBlock. WARNING: this method uses mpi_requests of the coupler attached to the matrix. No reordering on the received columns is performed. In practice this means that components in row_coupleBlock->pattern->index and row_coupler->connector->recv->shared are ordered by increasing value. Note that send and receive row_coupler->connectors are swapping roles.

References block_size, MPI_DOUBLE, mpi_info, row_coupleBlock, and row_coupler.

copyFromMainDiagonal()

void paso::SystemMatrix::copyFromMainDiagonal ( double *  out ) const

inline

copyMain_CSC_OFFSET1()

void paso::SystemMatrix::copyMain_CSC_OFFSET1	(	index_t **	p_ptr,
		index_t **	p_idx,
		double **	p_val
	)

copyRemoteCoupleBlock()

void paso::SystemMatrix::copyRemoteCoupleBlock

(

bool

recreatePattern

)

References col_coupler, and mpi_info.

copyToMainDiagonal()

void paso::SystemMatrix::copyToMainDiagonal ( const double *  in )

inline

References MATRIX_FORMAT_CSC, MATRIX_FORMAT_OFFSET1, and type.

extendedRowsForST()

void paso::SystemMatrix::extendedRowsForST	(	dim_t *	degree_ST,
		index_t *	offset_ST,
		index_t *	ST
	)

References col_coupler, and mpi_info.

fillWithGlobalCoordinates()

void paso::SystemMatrix::fillWithGlobalCoordinates

(

double

f1

)

References block_size, mainBlock, and pattern.

finishColCollect()

double* paso::SystemMatrix::finishColCollect ( ) const

inline

References mainBlock.

finishCollect()

double* paso::SystemMatrix::finishCollect ( ) const

inline

References row_coupler.

finishRowCollect()

double* paso::SystemMatrix::finishRowCollect ( )

inline

References getNumRows(), and row_block_size.

freePreconditioner()

void paso::SystemMatrix::freePreconditioner

(

)

getColOverlap()

dim_t paso::SystemMatrix::getColOverlap ( ) const

inline

References MATRIX_FORMAT_CSC, pattern, and type.

getGlobalNumCols()

dim_t paso::SystemMatrix::getGlobalNumCols ( ) const

inline

References col_block_size.

getGlobalNumRows()

dim_t paso::SystemMatrix::getGlobalNumRows ( ) const

inline

getGlobalSize()

double paso::SystemMatrix::getGlobalSize

(

)

const

getGlobalTotalNumCols()

dim_t paso::SystemMatrix::getGlobalTotalNumCols ( ) const

inline

getGlobalTotalNumRows()

dim_t paso::SystemMatrix::getGlobalTotalNumRows ( ) const

inline

getNumCols()

dim_t paso::SystemMatrix::getNumCols ( ) const

inline

References row_coupler.

Referenced by getNumRows().

getNumOutput()

dim_t paso::SystemMatrix::getNumOutput ( ) const

inline

References mainBlock.

getNumRows()

dim_t paso::SystemMatrix::getNumRows ( ) const

inline

References col_block_size, and getNumCols().

Referenced by finishRowCollect().

getRowOverlap()

dim_t paso::SystemMatrix::getRowOverlap ( ) const

inline

getSparsity()

double paso::SystemMatrix::getSparsity ( ) const

inline

getSystemMatrixTypeId()

int paso::SystemMatrix::getSystemMatrixTypeId ( int  solver, int  preconditioner, int  package, bool  symmetry, const escript::JMPI &  mpi_info  )

static

Referenced by ripley::RipleyDomain::getSystemMatrixTypeId(), dudley::DudleyDomain::getSystemMatrixTypeId(), and finley::FinleyDomain::getSystemMatrixTypeId().

getTotalNumCols()

dim_t paso::SystemMatrix::getTotalNumCols ( ) const

inline

References MATRIX_FORMAT_CSC, pattern, and type.

getTotalNumRows()

dim_t paso::SystemMatrix::getTotalNumRows ( ) const

inline

References col_coupler.

loadMM_toCSC()

SystemMatrix_ptr paso::SystemMatrix::loadMM_toCSC ( const char *  filename )

static

loadMM_toCSR()

SystemMatrix_ptr paso::SystemMatrix::loadMM_toCSR ( const char *  filename )

static

makeZeroRowSums()

void paso::SystemMatrix::makeZeroRowSums

(

double *

left_over

)

MatrixVector()

void paso::SystemMatrix::MatrixVector	(	double	alpha,
		const double *	in,
		double	beta,
		double *	out
	)		const

MatrixVector_CSR_OFFSET0()

void paso::SystemMatrix::MatrixVector_CSR_OFFSET0	(	double	alpha,
		const double *	in,
		double	beta,
		double *	out
	)		const

References col_coupleBlock, MATRIX_FORMAT_DIAGONAL_BLOCK, paso::SparseMatrix_MatrixVector_CSR_OFFSET0(), paso::SparseMatrix_MatrixVector_CSR_OFFSET0_DIAG(), and type.

mergeMainAndCouple()

void paso::SystemMatrix::mergeMainAndCouple	(	index_t **	p_ptr,
		index_t **	p_idx,
		double **	p_val
	)		const

mergeMainAndCouple_CSC_OFFSET1()

void paso::SystemMatrix::mergeMainAndCouple_CSC_OFFSET1	(	index_t **	p_ptr,
		index_t **	p_idx,
		double **	p_val
	)		const

mergeMainAndCouple_CSR_OFFSET0()

void paso::SystemMatrix::mergeMainAndCouple_CSR_OFFSET0	(	index_t **	p_ptr,
		index_t **	p_idx,
		double **	p_val
	)		const

mergeMainAndCouple_CSR_OFFSET0_Block()

void paso::SystemMatrix::mergeMainAndCouple_CSR_OFFSET0_Block	(	index_t **	p_ptr,
		index_t **	p_idx,
		double **	p_val
	)		const

mergeSystemMatrix()

SparseMatrix_ptr paso::SystemMatrix::mergeSystemMatrix

(

)

const

Merges the system matrix which is distributed on several MPI ranks into a complete sparse matrix on rank 0. Used by the Merged Solver.

nullifyRows()

void paso::SystemMatrix::nullifyRows	(	double *	mask_row,
		double	main_diagonal_value
	)

Nullifies rows in the matrix. The rows are marked by positive values in mask_row. Values on the main diagonal which are marked to set to zero by mask_row are set to main_diagonal_value.

nullifyRowsAndCols()

void paso::SystemMatrix::nullifyRowsAndCols ( escript::Data &  mask_row, escript::Data &  mask_col, double  main_diagonal_value  )

virtual

Nullifies rows and columns in the matrix. The rows and columns are marked by positive values in mask_row and mask_col. Values on the main diagonal which are marked to set to zero by both mask_row and mask_col are set to main_diagonal_value.

Reimplemented from escript::AbstractSystemMatrix.

print()

void paso::SystemMatrix::print

(

)

const

References block_size, col_coupleBlock, and global_id.

resetValues()

void paso::SystemMatrix::resetValues ( bool  preserveSolverData = false )

virtual

resets the matrix entries

Reimplemented from escript::AbstractSystemMatrix.

rowSum()

void paso::SystemMatrix::rowSum ( double *  row_sum ) const

inline

Referenced by borrowMainDiagonalPointer().

saveHB()

virtual void paso::SystemMatrix::saveHB ( const std::string &  filename ) const

inlinevirtual

writes the matrix to a file using the Harwell-Boeing file format

Reimplemented from escript::AbstractSystemMatrix.

saveMM()

virtual void paso::SystemMatrix::saveMM ( const std::string &  filename ) const

inlinevirtual

writes the matrix to a file using the Matrix Market file format

Reimplemented from escript::AbstractSystemMatrix.

setPreconditioner()

void paso::SystemMatrix::setPreconditioner

(

Options *

options

)

References paso::Preconditioner_free(), and solver_p.

setToSolution()

void paso::SystemMatrix::setToSolution ( escript::Data &  out, escript::Data &  in, boost::python::object &  options  ) const

privatevirtual

solves the linear system this*out=in

Reimplemented from escript::AbstractSystemMatrix.

setValues()

void paso::SystemMatrix::setValues ( double  value )

inline

solve()

void paso::SystemMatrix::solve ( double *  out, double *  in, Options *  options  ) const

private

solvePreconditioner()

void paso::SystemMatrix::solvePreconditioner	(	double *	x,
		double *	b
	)

Applies the preconditioner. This method needs to be called within a parallel region. Barrier synchronization is performed before the evaluation to make sure that the input vector is available

References col_coupleBlock, mainBlock, MPI_DOUBLE, mpi_info, and MPI_SUM.

startColCollect()

void paso::SystemMatrix::startColCollect ( const double *  in ) const

inline

References row_coupler.

startCollect()

void paso::SystemMatrix::startCollect ( const double *  in ) const

inline

References col_coupler.

startRowCollect()

void paso::SystemMatrix::startRowCollect ( const double *  in )

inline

References mainBlock.

ypAx()

void paso::SystemMatrix::ypAx ( escript::Data &  y, escript::Data &  x  ) const

privatevirtual

performs y+=this*x

Reimplemented from escript::AbstractSystemMatrix.

Member Data Documentation

balance_vector

double* paso::SystemMatrix::balance_vector

matrix may be balanced by a diagonal matrix D=diagonal(balance_vector) if is_balanced is true, the matrix stored is D*A*D where A is the original matrix. When the system of linear equations is solved we solve D*A*D*y=c. So to solve A*x=b one needs to set c=D*b and x=D*y.

Referenced by balance().

block_size

dim_t paso::SystemMatrix::block_size

Referenced by borrowMainDiagonalPointer(), copyColCoupleBlock(), fillWithGlobalCoordinates(), and print().

col_block_size

dim_t paso::SystemMatrix::col_block_size

Referenced by dudley::AssembleParameters::AssembleParameters(), finley::AssembleParameters::AssembleParameters(), getGlobalNumCols(), and getNumRows().

col_coupleBlock

SparseMatrix_ptr paso::SystemMatrix::col_coupleBlock

coupling to neighbouring processors (row - col)

Referenced by copyBlockToMainDiagonal(), MatrixVector_CSR_OFFSET0(), print(), and solvePreconditioner().

col_coupler

Coupler_ptr<real_t> paso::SystemMatrix::col_coupler

Referenced by copyRemoteCoupleBlock(), extendedRowsForST(), getTotalNumRows(), and startCollect().

col_distribution

escript::Distribution_ptr paso::SystemMatrix::col_distribution

Referenced by dudley::AssembleParameters::AssembleParameters(), and finley::AssembleParameters::AssembleParameters().

global_id

index_t* paso::SystemMatrix::global_id

mutable

stores the global ids for all cols in col_coupleBlock

Referenced by print().

is_balanced

bool paso::SystemMatrix::is_balanced

logical_col_block_size

dim_t paso::SystemMatrix::logical_col_block_size

logical_row_block_size

dim_t paso::SystemMatrix::logical_row_block_size

Referenced by dudley::AssembleParameters::AssembleParameters(), and finley::AssembleParameters::AssembleParameters().

mainBlock

SparseMatrix_ptr paso::SystemMatrix::mainBlock

main block

Referenced by copyBlockFromMainDiagonal(), copyBlockToMainDiagonal(), fillWithGlobalCoordinates(), finishColCollect(), getNumOutput(), solvePreconditioner(), and startRowCollect().

mpi_info

escript::JMPI paso::SystemMatrix::mpi_info

Referenced by copyColCoupleBlock(), copyRemoteCoupleBlock(), extendedRowsForST(), and solvePreconditioner().

pattern

SystemMatrixPattern_ptr paso::SystemMatrix::pattern

Referenced by borrowMainDiagonalPointer(), fillWithGlobalCoordinates(), getColOverlap(), and getTotalNumCols().

remote_coupleBlock

SparseMatrix_ptr paso::SystemMatrix::remote_coupleBlock

coupling of rows-cols on neighbouring processors (may not be valid)

row_block_size

dim_t paso::SystemMatrix::row_block_size

Referenced by dudley::AssembleParameters::AssembleParameters(), finley::AssembleParameters::AssembleParameters(), borrowMainDiagonalPointer(), and finishRowCollect().

row_coupleBlock

SparseMatrix_ptr paso::SystemMatrix::row_coupleBlock

coupling to neighbouring processors (col - row)

Referenced by copyColCoupleBlock().

row_coupler

Coupler_ptr<real_t> paso::SystemMatrix::row_coupler

Referenced by copyColCoupleBlock(), finishCollect(), getNumCols(), and startColCollect().

row_distribution

escript::Distribution_ptr paso::SystemMatrix::row_distribution

Referenced by dudley::AssembleParameters::AssembleParameters(), and finley::AssembleParameters::AssembleParameters().

solver_p

void* paso::SystemMatrix::solver_p

pointer to data needed by a solver

Referenced by setPreconditioner(), and ~SystemMatrix().

solver_package

index_t paso::SystemMatrix::solver_package

mutable

package code controlling the solver pointer

type

SystemMatrixType paso::SystemMatrix::type

Referenced by copyToMainDiagonal(), getColOverlap(), getTotalNumCols(), and MatrixVector_CSR_OFFSET0().

---

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

• SystemMatrix.h
• solve.cpp
• SystemMatrix.cpp
• SystemMatrix_copyRemoteCoupleBlock.cpp
• SystemMatrix_debug.cpp
• SystemMatrix_extendedRows.cpp
• SystemMatrix_loadMM.cpp
• SystemMatrix_MatrixVector.cpp
• SystemMatrix_mergeMainAndCouple.cpp