EpetraExt::HDF5 Class Reference

class HDF5: A class for storing Epetra objects in parallel binary files More...

#include <EpetraExt_HDF5.h>

	HDF5 (const Epetra_Comm &Comm)
	Constructor. More...
	~HDF5 ()
	Destructor. More...
void	Create (const std::string FileName)
	Create a new file. More...
void	Open (const std::string FileName, int AccessType=H5F_ACC_RDWR)
	Open specified file with given access type. More...
void	Close ()
	Close the file. More...
void	Flush ()
	Flush the content to the file. More...
bool	IsOpen () const
	Return true if a file has already been opened using Open()/Create() More...
void	CreateGroup (const std::string &GroupName)
	Create group GroupName. More...
bool	IsContained (std::string Name, std::string GroupName="")
	Return true if Name is contained in the database. More...
void	Write (const std::string &GroupName, const std::string &DataSetName, int data)
	Write an integer in group GroupName using the given DataSetName. More...
void	Read (const std::string &GroupName, const std::string &DataSetName, int &data)
	Read an integer from group /GroupName/DataSetName. More...
void	Write (const std::string &GroupName, const std::string &DataSetName, double data)
	Write a double in group GroupName using the given DataSetName. More...
void	Read (const std::string &GroupName, const std::string &DataSetName, double &data)
	Read a double from group /GroupName/DataSetName. More...
void	Write (const std::string &GroupName, const std::string &DataSetName, const std::string &data)
	Write a string in group GroupName using the given DataSetName. More...
void	Read (const std::string &GroupName, const std::string &DataSetName, std::string &data)
	Read a string from group /GroupName/DataSetName. More...
void	Read (const std::string &GroupName, const std::string &DataSetName, const hid_t type, const int Length, void *data)
	Read the serial array data, of type type, from group GroupName, using the dataset name DataSetName. More...
void	Write (const std::string &GroupName, const std::string &DataSetName, const hid_t type, const int Length, const void *data)
	Write the serial array data, of type type, to group GroupName, using the dataset name DataSetName. More...
void	WriteComment (const std::string &GroupName, std::string Comment)
	Associate string Comment with group GroupName. More...
void	ReadComment (const std::string &GroupName, std::string &Comment)
	Read the string associated with group GroupName. More...
void	Write (const std::string &GroupName, const std::string &DataSetName, int MySize, int GlobalSize, hid_t type, const void *data)
	Write the distributed array data, of type type, to group GroupName, using dataset name DataSetName. More...
void	Read (const std::string &GroupName, const std::string &DataSetName, int MySize, int GlobalSize, const hid_t type, void *data)
	Read the distributed array data, of type type, from group GroupName, using dataset name DataSetName. More...
void	Write (const std::string &GroupName, const Epetra_Map &Map)
	Write a Map to group GroupName. More...
void	Read (const std::string &GroupName, Epetra_Map *&Map)
	Read a map from GroupName. More...
void	ReadMapProperties (const std::string &GroupName, int &NumGlobalElements, int &IndexBase, int &NumProc)
	Read basic properties of specified Epetra_Map. More...
void	Read (const std::string &GroupName, Epetra_BlockMap *&Map)
	Read a block map from GroupName. More...
void	Write (const std::string &GroupName, const Epetra_BlockMap &Map)
	Write a block map to group GroupName. More...
void	ReadBlockMapProperties (const std::string &GroupName, int &NumGlobalElements, int &NumGlobalPoints, int &IndexBase, int &NumProc)
	Read basic properties of specified Epetra_BlockMap. More...
void	Read (const std::string &GroupName, Epetra_CrsGraph *&Graph)
	Read a vector from group GroupName, assuming linear distribution. More...
void	Read (const std::string &GroupName, const Epetra_Map &DomainMap, const Epetra_Map &RangeMap, Epetra_CrsGraph *&Graph)
	Read a vector from group GroupName using the given map. More...
void	Write (const std::string &GroupName, const Epetra_CrsGraph &Graph)
	Write a distributed vector to group GroupName. More...
void	ReadCrsGraphProperties (const std::string &GroupName, int &NumGlobalRows, int &NumGlobalCols, int &NumGlobalNonzeros, int &NumGlobalDiagonals, int &MaxNumIndices)
	Read basic properties of specified Epetra_CrsGraph. More...
void	Write (const std::string &GroupName, const Epetra_IntVector &x)
	Write a distributed vector to group GroupName. More...
void	Read (const std::string &GroupName, Epetra_IntVector *&X)
	Read a vector from group GroupName, assuming linear distribution. More...
void	Read (const std::string &GroupName, const Epetra_Map &Map, Epetra_IntVector *&X)
	Read a vector from group GroupName using the given map. More...
void	ReadIntVectorProperties (const std::string &GroupName, int &GlobalLength)
	Read basic properties of specified Epetra_IntVector. More...
void	Write (const std::string &GroupName, const Epetra_MultiVector &x, bool writeTranspose=false)
	Write a distributed vector (or its transpose) to group GroupName. More...
void	Read (const std::string &GroupName, Epetra_MultiVector *&X, bool writeTranspose=false, const int &indexBase=0)
	Read a vector (or its transpose) from group GroupName. More...
void	Read (const std::string &GroupName, const Epetra_Map &Map, Epetra_MultiVector *&X, bool writeTranspose=false)
	Read a vector from group GroupName using the given map. More...
void	ReadMultiVectorProperties (const std::string &GroupName, int &GlobalLength, int &NumVectors)
	Read basic properties of specified Epetra_MultiVector. More...
void	Write (const std::string &GroupName, const Epetra_RowMatrix &Matrix)
	Write a distributed RowMatrix to group GroupName. More...
void	Read (const std::string &GroupName, Epetra_CrsMatrix *&A)
	Read a square matrix from group GroupName, assuming linear distribution. More...
void	Read (const std::string &GroupName, const Epetra_Map &DomainMap, const Epetra_Map &RangeMap, Epetra_CrsMatrix *&A)
	Read a matrix from group GroupName with given range and domain maps. More...
void	ReadCrsMatrixProperties (const std::string &GroupName, int &NumGlobalRows, int &NumGlobalCols, int &NumNonzeros, int &NumGlobalDiagonals, int &MaxNumEntries, double &NormOne, double &NormInf)
	Read basic properties of specified Epetra_CrsMatrix. More...
void	Write (const std::string &GroupName, const Teuchos::ParameterList &List)
	Write a parameter list to group GroupName. More...
void	Read (const std::string &GroupName, Teuchos::ParameterList &List)
	Read a parameter list from group GroupName. More...
void	Write (const std::string &GroupName, const DistArray< int > &array)
	Write an EpetraExt::DistArray<int> to group GroupName. More...
void	Read (const std::string &GroupName, DistArray< int > *&array)
	Read an EpetraExt::DistArray<int> from group GroupName. More...
void	Read (const std::string &GroupName, const Epetra_Map &Map, DistArray< int > *&array)
	Read an EpetraExt::DistArray<int> from group GroupName. More...
void	ReadIntDistArrayProperties (const std::string &GroupName, int &GlobalLength, int &RowSize)
	Read the global number of elements and type for a generic handle object. More...
void	Write (const std::string &GroupName, const DistArray< double > &array)
	Write an EpetraExt::DistArray<int> to group GroupName. More...
void	Read (const std::string &GroupName, DistArray< double > *&array)
	Read an EpetraExt::DistArray<int> from group GroupName. More...
void	Read (const std::string &GroupName, const Epetra_Map &Map, DistArray< double > *&array)
	Read an EpetraExt::DistArray<int> from group GroupName. More...
void	ReadDoubleDistArrayProperties (const std::string &GroupName, int &GlobalLength, int &RowSize)
	Read the global number of elements and type for a generic handle object. More...
void	Write (const std::string &GroupName, const Handle &List)
	Write an Epetra_DistObject to group GroupName. More...
void	Read (const std::string &GroupName, Handle &List)
	Read an Epetra_DistObject from group GroupName. More...
void	ReadHandleProperties (const std::string &GroupName, std::string &Type, int &NumGlobalElements)
	Read the global number of elements and type for a generic handle object. More...
const Epetra_Comm &	Comm_
	This object's communicator. More...
std::string	FileName_
	FileName currently open. More...
bool	IsOpen_
	If true, a file is currently open. More...
hid_t	file_id_
	file ID for HDF5. More...
hid_t	plist_id_
herr_t	status
const Epetra_Comm &	Comm () const
	Returns a reference to this object's communicator. More...

Detailed Description

class HDF5: A class for storing Epetra objects in parallel binary files

Introduction

The HDF5 class reads and writes data using the HDF5 parallel binary data format. HDF5 has the following advantages:

• the file format is binary and portable. Being binary, its size is very compact;
• the file format can be read and written in parallel;
• MATLAB contains a built-in HDF5 data reader, making it easy to interface Trilinos applications with MATLAB and vice-versa;
• the HDF5 library may already be installed on your system; otherwise, it is easy to build from the source tarball on the official NCSA HDF5 web page;
• HDF5 objects are like a file system, and they can contain directories and files. This means that more data can be stored in the same file. One can also append new data to an existing file, or read only one data set;
• It is very easy to add metadata to your data; for example a string describing the machine where the code was executed, the parameter list used for the preconditioner or the nonlinear solver, the convergence history, and so on;
• The number of processors reading a given object does not have to be the same as the number used to write the object.

In order to use HDF5, make sure to set the CMake Boolean option EpetraExt_USING_HDF5 when building Trilinos. You may have to tell CMake where to find the HDF5 library and header files, if they are not installed in their default locations.

The class supports input (I), output (O), or both (I/O) for the following distributed Epetra objects:

• Epetra_Map (I/O);
• Epetra_BlockMap (I/O);
• Epetra_CrsGraph (I/O);
• Epetra_RowMatrix (O);
• Epetra_CrsMatrix (I/O);
• Epetra_IntVector (I/O);
• Epetra_MultiVector (I/O).

The class also supports some non-distributed types:

• Teuchos::ParameterList (I/O);
• basic data types like scalar int and double variables (I/O);
• and arrays of arbitrary data type are supported (I/O).

The HDF5 class assumes that non-distributed data types have the same value on all processors.

This class also provides utility methods:

• CreateGroup() creates the specified group in the file;
• IsContained() returns true is the specified group is already contained in the file;
• WriteComment() allows to write any string as comment for a group;
• a method to write and read a distributed array of arbitrary type.

By using these methods, as well as the other methods to write non-distributed types, one can read and write any serial or distributed object.

Data Model

The HDF5 library itself can be used to define very general data formats. Our HDF5 class, instead, is structured around the concept of groups. A group is an entity, for example a scalar value, an Epetra_Map, or a Teuchos::ParameterList. Within each group, different datasets describe the content of the group. For example, an Epetra_MultiVector is specified by datasets NumVectors and Values, which contain the number of vectors and the numerical values, respectively. The comment of each group is a character string that must match the class name.

Our HDF5 class has the following limitations:

• Objects stored in a file cannot be deleted. If you want to do that, you should read the content of the file, then create a new file and store in it the information to keep;
• it is not possible to overwrite distributed objects.

Errors

When an error occurs, a EpetraExt::Exception is thrown. The Print() method of the Exception class returns a description of what went wrong.

Example of usage

First, one must create an HDF5 class, then either Open() or Create() the file:

// Comm is an Epetra_Comm communicator wrapper object.
EpetraExt::HDF5 HDF5(Comm);
HDF5.Create("myfile.h5");

Writing commands might be as follows:

Epetra_Map* Map = <create map here>
Epetra_Map* BlockMap = <create block map here>
Epetra_RowMatrix* Matrix = <create matrix here>
Epetra_MultiVector* LHS = <...>
Epetra_MultiVector* RHS = <...>

// write a map, whose group name contains the number of processors
HDF5.Write("map-" + toString(Comm.NumProc()), *Map);
HDF5.Write("matrix", *Matrix);
HDF5.Write("LHS", LHS);
HDF5.Write("RHS", RHS);

To write a Teuchos::ParameterList, simply do

HDF5.Write("EpetraExtList", EpetraExtList);

The file can contain metadata as well. Each metadatum is defined by a group and a dataset name. A group may contain more than one dataset, and may be a new group or an already existing group. For example, to specify the numerical quadrature formula used to assemble the matrix, do as follows:

HDF5.Write("matrix", "quadrature order", 3);

Alternatively, datasets may be assigned to a new group, let's say "my parameters":

HDF5.Write("my parameters", "latitude", 12);
HDF5.Write("my parameters", "longitude", 67);
HDF5.Write("my parameters", "angle", 12.3);

vector<int> iarray(3); 
iarray[0] = 0, iarray[1] = 1; iarray[2] = 2;
HDF5.Write("my parameters", "int array", H5T_NATIVE_INT, 3, &iarray[0]);

vector<double> darray(3); 
darray[0] = 0.1, darray[1] = 1.1; darray[2] = 2.1;
HDF5.Write("my parameters", "double array", H5T_NATIVE_DOUBLE, 3, &darray[0]);

Note that all non-distributed datasets must have the same value on all processors.

Reading data is as easy as writing. Let us consider how to read an Epetra_CrsMatrix. Other Epetra objects having a similar behavior. The ReadCrsMatrixProperties() method can be used to query for some matrix properties without reading the whole matrix:

int NumGlobalRows, NumGlobalCols, NumGlobalNonzeros;
int NumGlobalDiagonals, MaxNumEntries;
double NormOne, NormInf;

ReadCrsMatrixProperties(GroupName, NumGlobalRows, NumGlobalCols,
                        NumGlobalNonzeros, NumGlobalDiagonals, MaxNumEntries,
                        NormOne, NormInf);

The above call is not required, and can be skipped. In order to read the Epetra_CrsMatrix, do as follows:

Epetra_CrsMatrix* NewMatrix = NULL;
HDF5.Read("matrix", NewMatrix);

In this case, NewMatrix is based on a linear map. If the matrix's DomainMap() and RangeMap() are known and non-trivial, one can use

HDF5.Read("matrix", DomainMap, RangeMap, NewMatrix);

Reading metadata looks like:

HDF5.Read("my parameters", "latitude", new_latitude);
HDF5.Read("my parameters", "longitude", new_longitude);
HDF5.Read("my parameters", "int array", H5T_NATIVE_INT, 3, &new_iarray[0]);
HDF5.Read("my parameters", "double array", H5T_NATIVE_DOUBLE, 3, &new_darray[0]);

To analyze the content of the file, one can use "h5dump filename.h5" or "h5dump filename.h5 -H".

MATLAB Interface

MATLAB provides built-in functions to read, write, and query HDF5 files: hdf5read, hdf5write, and hdf5info, respectively. For example, to read the above Epetra_CrsMatrix into MATLAB as a sparse matrix, do as follows:

NumGlobalRows = double(hdf5read('myfile.h5', '/matrix/NumGlobalRows/'));
NumGlobalCols = double(hdf5read('myfile.h5', '/matrix/NumGlobalCols/'));
ROW = double(hdf5read('myfile.h5', '/matrix/ROW/'));
COL = double(hdf5read('myfile.h5', '/matrix/COL/'));
VAL = hdf5read('myfile.h5', '/matrix/VAL/');
A = sparse(ROW + 1, COL + 1, VAL, NumGlobalRows, NumGlobalCols);

The use of double() is required by Matlab's sparse function, since it does not accept int32 data.

To dump a MATLAB matrix (in this case, A) to the file matlab.h5, do as follows:

n = 10;
A = speye(n, n);
[ROW,COL,VAL] = find(A);
hdf5write('matlab.h5', '/speye/__type__',           'Epetra_RowMatrix');
hdf5write('matlab.h5', '/speye/NumGlobalRows',      int32(n), 'WriteMode', 'append');
hdf5write('matlab.h5', '/speye/NumGlobalCols',      int32(n), 'WriteMode', 'append');
hdf5write('matlab.h5', '/speye/NumGlobalNonzeros',  int32(n), 'WriteMode', 'append');
hdf5write('matlab.h5', '/speye/NumGlobalDiagonals', int32(n), 'WriteMode', 'append');
hdf5write('matlab.h5', '/speye/MaxNumEntries',      int32(1), 'WriteMode', 'append');
hdf5write('matlab.h5', '/speye/NormOne',            1.0,      'WriteMode', 'append');
hdf5write('matlab.h5', '/speye/NormInf',            1.0,      'WriteMode', 'append');
hdf5write('matlab.h5', '/speye/ROW', int32(ROW - 1), 'WriteMode', 'append');
hdf5write('matlab.h5', '/speye/COL', int32(COL - 1), 'WriteMode', 'append');
hdf5write('matlab.h5', '/speye/VAL', VAL,            'WriteMode', 'append');

Note that the type specification must reflect the Epetra class name.

To dump a MATLAB dense array (in this case, x) to the file matlab.h5, do as follows:

n = 10;
x = [zeros(n,1), rand(n, 1)]';
hdf5write('matlab.h5', '/x/__type__',    'Epetra_MultiVector');
hdf5write('matlab.h5', '/x/GlobalLength',int32(n), 'WriteMode', 'append');
hdf5write('matlab.h5', '/x/NumVectors',  int32(2), 'WriteMode', 'append');
hdf5write('matlab.h5', '/x/Values',      x,        'WriteMode', 'append');

Note that MATLAB vectors must be stored as row vectors.

You can also write a Map from MATLAB for use by Epetra. The following example shows how to define an Epetra_Map that distributes data over two processors:

IndexBase = 0;
NumMyElements = [5 5];
n = 10;
MyGlobalElements = [5 6 7 8 9 0 1 2 3 4];
hdf5write('matlab.h5', '/map-2/__type__',          'Epetra_Map');
hdf5write('matlab.h5', '/map-2/NumGlobalElements', int32(n),                'WriteMode', 'append');
hdf5write('matlab.h5', '/map-2/IndexBase',         int32(IndexBase),        'WriteMode', 'append');
hdf5write('matlab.h5', '/map-2/NumProc',           int32(2),                'WriteMode', 'append');
hdf5write('matlab.h5', '/map-2/NumMyElements',     int32(NumMyElements),    'WriteMode', 'append');
hdf5write('matlab.h5', '/map-2/MyGlobalElements',  int32(MyGlobalElements), 'WriteMode', 'append');

Author

Marzio Sala, D-INFK/ETHZ

Date

Last updated on 16-Mar-06. Documentation revised by Mark Hoemmen (05 Oct 2011) for spelling, grammar, and clarity.

Todo:

• all distributed objects are assumed in local state, this is not necessary (just easier)
• Epetra_VbrMatrix input has to be done, now it is considered as an Epetra_RowMatrix

Definition at line 332 of file EpetraExt_HDF5.h.

Constructor & Destructor Documentation

EpetraExt::HDF5::HDF5

(

const Epetra_Comm &

Comm

)

Constructor.

Definition at line 272 of file EpetraExt_HDF5.cpp.

EpetraExt::HDF5::~HDF5 ( )

inline

Destructor.

Definition at line 341 of file EpetraExt_HDF5.h.

Member Function Documentation

void EpetraExt::HDF5::Create

(

const std::string

FileName

)

Create a new file.

Definition at line 278 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Open	(	const std::string	FileName,
		int	AccessType = H5F_ACC_RDWR
	)

Open specified file with given access type.

Definition at line 365 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Close ( )

inline

Close the file.

Definition at line 357 of file EpetraExt_HDF5.h.

void EpetraExt::HDF5::Flush ( )

inline

Flush the content to the file.

Definition at line 364 of file EpetraExt_HDF5.h.

bool EpetraExt::HDF5::IsOpen ( ) const

inline

Return true if a file has already been opened using Open()/Create()

Definition at line 370 of file EpetraExt_HDF5.h.

void EpetraExt::HDF5::CreateGroup ( const std::string &  GroupName )

inline

Create group GroupName.

Definition at line 376 of file EpetraExt_HDF5.h.

bool EpetraExt::HDF5::IsContained	(	std::string	Name,
		std::string	GroupName = ""
	)

Return true if Name is contained in the database.

Definition at line 395 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const std::string &	DataSetName,
		int	data
	)

Write an integer in group GroupName using the given DataSetName.

Definition at line 1460 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const std::string &	DataSetName,
		int &	data
	)

Read an integer from group /GroupName/DataSetName.

Definition at line 1504 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const std::string &	DataSetName,
		double	data
	)

Write a double in group GroupName using the given DataSetName.

Definition at line 1482 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const std::string &	DataSetName,
		double &	data
	)

Read a double from group /GroupName/DataSetName.

Definition at line 1526 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const std::string &	DataSetName,
		const std::string &	data
	)

Write a string in group GroupName using the given DataSetName.

Definition at line 1548 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const std::string &	DataSetName,
		std::string &	data
	)

Read a string from group /GroupName/DataSetName.

Definition at line 1579 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const std::string &	DataSetName,
		const hid_t	type,
		const int	Length,
		void *	data
	)

Read the serial array data, of type type, from group GroupName, using the dataset name DataSetName.

Definition at line 1639 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const std::string &	DataSetName,
		const hid_t	type,
		const int	Length,
		const void *	data
	)

Write the serial array data, of type type, to group GroupName, using the dataset name DataSetName.

Definition at line 1612 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::WriteComment ( const std::string &  GroupName, std::string  Comment  )

inline

Associate string Comment with group GroupName.

Definition at line 416 of file EpetraExt_HDF5.h.

void EpetraExt::HDF5::ReadComment ( const std::string &  GroupName, std::string &  Comment  )

inline

Read the string associated with group GroupName.

Definition at line 422 of file EpetraExt_HDF5.h.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const std::string &	DataSetName,
		int	MySize,
		int	GlobalSize,
		hid_t	type,
		const void *	data
	)

Write the distributed array data, of type type, to group GroupName, using dataset name DataSetName.

Definition at line 1670 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const std::string &	DataSetName,
		int	MySize,
		int	GlobalSize,
		const hid_t	type,
		void *	data
	)

Read the distributed array data, of type type, from group GroupName, using dataset name DataSetName.

Definition at line 1720 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const Epetra_Map &	Map
	)

Write a Map to group GroupName.

Definition at line 520 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		Epetra_Map *&	Map
	)

Read a map from GroupName.

Definition at line 539 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::ReadMapProperties	(	const std::string &	GroupName,
		int &	NumGlobalElements,
		int &	IndexBase,
		int &	NumProc
	)

Read basic properties of specified Epetra_Map.

Definition at line 565 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		Epetra_BlockMap *&	Map
	)

Read a block map from GroupName.

Definition at line 459 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const Epetra_BlockMap &	Map
	)

Write a block map to group GroupName.

Definition at line 428 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::ReadBlockMapProperties	(	const std::string &	GroupName,
		int &	NumGlobalElements,
		int &	NumGlobalPoints,
		int &	IndexBase,
		int &	NumProc
	)

Read basic properties of specified Epetra_BlockMap.

Definition at line 495 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		Epetra_CrsGraph *&	Graph
	)

Read a vector from group GroupName, assuming linear distribution.

Definition at line 728 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const Epetra_Map &	DomainMap,
		const Epetra_Map &	RangeMap,
		Epetra_CrsGraph *&	Graph
	)

Read a vector from group GroupName using the given map.

Definition at line 771 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const Epetra_CrsGraph &	Graph
	)

Write a distributed vector to group GroupName.

Definition at line 690 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::ReadCrsGraphProperties	(	const std::string &	GroupName,
		int &	NumGlobalRows,
		int &	NumGlobalCols,
		int &	NumGlobalNonzeros,
		int &	NumGlobalDiagonals,
		int &	MaxNumIndices
	)

Read basic properties of specified Epetra_CrsGraph.

Definition at line 744 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const Epetra_IntVector &	x
	)

Write a distributed vector to group GroupName.

Definition at line 592 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		Epetra_IntVector *&	X
	)

Read a vector from group GroupName, assuming linear distribution.

Definition at line 619 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const Epetra_Map &	Map,
		Epetra_IntVector *&	X
	)

Read a vector from group GroupName using the given map.

Definition at line 634 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::ReadIntVectorProperties	(	const std::string &	GroupName,
		int &	GlobalLength
	)

Read basic properties of specified Epetra_IntVector.

Definition at line 667 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const Epetra_MultiVector &	x,
		bool	writeTranspose = false
	)

Write a distributed vector (or its transpose) to group GroupName.

Write the transpose if writeTranspose is true.

Definition at line 1017 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		Epetra_MultiVector *&	X,
		bool	writeTranspose = false,
		const int &	indexBase = 0
	)

Read a vector (or its transpose) from group GroupName.

This method assumes a linear distribution. Read the transpose if writeTranspose is true.

Definition at line 1126 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const Epetra_Map &	Map,
		Epetra_MultiVector *&	X,
		bool	writeTranspose = false
	)

Read a vector from group GroupName using the given map.

Read the transpose if writeTranspose is true.

Definition at line 1109 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::ReadMultiVectorProperties	(	const std::string &	GroupName,
		int &	GlobalLength,
		int &	NumVectors
	)

Read basic properties of specified Epetra_MultiVector.

Definition at line 1231 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const Epetra_RowMatrix &	Matrix
	)

Write a distributed RowMatrix to group GroupName.

Definition at line 824 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		Epetra_CrsMatrix *&	A
	)

Read a square matrix from group GroupName, assuming linear distribution.

Definition at line 868 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const Epetra_Map &	DomainMap,
		const Epetra_Map &	RangeMap,
		Epetra_CrsMatrix *&	A
	)

Read a matrix from group GroupName with given range and domain maps.

Definition at line 886 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::ReadCrsMatrixProperties	(	const std::string &	GroupName,
		int &	NumGlobalRows,
		int &	NumGlobalCols,
		int &	NumNonzeros,
		int &	NumGlobalDiagonals,
		int &	MaxNumEntries,
		double &	NormOne,
		double &	NormInf
	)

Read basic properties of specified Epetra_CrsMatrix.

Definition at line 928 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const Teuchos::ParameterList &	List
	)

Write a parameter list to group GroupName.

Definition at line 963 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		Teuchos::ParameterList &	List
	)

Read a parameter list from group GroupName.

Definition at line 981 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const DistArray< int > &	array
	)

Write an EpetraExt::DistArray<int> to group GroupName.

Definition at line 1256 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		DistArray< int > *&	array
	)

Read an EpetraExt::DistArray<int> from group GroupName.

Definition at line 1318 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const Epetra_Map &	Map,
		DistArray< int > *&	array
	)

Read an EpetraExt::DistArray<int> from group GroupName.

Definition at line 1286 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::ReadIntDistArrayProperties	(	const std::string &	GroupName,
		int &	GlobalLength,
		int &	RowSize
	)

Read the global number of elements and type for a generic handle object.

Definition at line 1333 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const DistArray< double > &	array
	)

Write an EpetraExt::DistArray<int> to group GroupName.

Definition at line 1358 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		DistArray< double > *&	array
	)

Read an EpetraExt::DistArray<int> from group GroupName.

Definition at line 1420 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		const Epetra_Map &	Map,
		DistArray< double > *&	array
	)

Read an EpetraExt::DistArray<int> from group GroupName.

Definition at line 1388 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::ReadDoubleDistArrayProperties	(	const std::string &	GroupName,
		int &	GlobalLength,
		int &	RowSize
	)

Read the global number of elements and type for a generic handle object.

Definition at line 1435 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Write	(	const std::string &	GroupName,
		const Handle &	List
	)

Write an Epetra_DistObject to group GroupName.

Definition at line 71 of file EpetraExt_HDF5_DistObject.cpp.

void EpetraExt::HDF5::Read	(	const std::string &	GroupName,
		Handle &	List
	)

Read an Epetra_DistObject from group GroupName.

Definition at line 158 of file EpetraExt_HDF5_DistObject.cpp.

void EpetraExt::HDF5::ReadHandleProperties	(	const std::string &	GroupName,
		std::string &	Type,
		int &	NumGlobalElements
	)

Read the global number of elements and type for a generic handle object.

Definition at line 231 of file EpetraExt_HDF5_DistObject.cpp.

const Epetra_Comm& EpetraExt::HDF5::Comm ( ) const

inlineprivate

Returns a reference to this object's communicator.

Definition at line 617 of file EpetraExt_HDF5.h.

Member Data Documentation

const Epetra_Comm& EpetraExt::HDF5::Comm_

private

This object's communicator.

Definition at line 623 of file EpetraExt_HDF5.h.

std::string EpetraExt::HDF5::FileName_

private

FileName currently open.

Definition at line 625 of file EpetraExt_HDF5.h.

bool EpetraExt::HDF5::IsOpen_

private

If true, a file is currently open.

Definition at line 627 of file EpetraExt_HDF5.h.

hid_t EpetraExt::HDF5::file_id_

private

file ID for HDF5.

Definition at line 630 of file EpetraExt_HDF5.h.

hid_t EpetraExt::HDF5::plist_id_

private

Definition at line 631 of file EpetraExt_HDF5.h.

herr_t EpetraExt::HDF5::status

private

Definition at line 632 of file EpetraExt_HDF5.h.

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

• EpetraExt_HDF5.h
• EpetraExt_HDF5.cpp
• EpetraExt_HDF5_DistObject.cpp