EpetraExt::HDF5 Class Reference

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

#include <EpetraExt_HDF5.h>

List of all members.

Constructor and destructor.
	HDF5 (const Epetra_Comm &Comm)
	ctor
	~HDF5 ()
	dtor
Basic operations
void	Create (const string FileName)
	Creates a new file.
void	Open (const string FileName, int AccessType=H5F_ACC_RDWR)
	Opens specified file with given access type.
void	Close ()
	Closes the file.
bool	IsOpen () const
	Returns true is a file has already been open using Open()/Create().
void	CreateGroup (const string &GroupName)
	Creates group GroupName.
bool	IsContained (const string Name)
	Returns true is Name is contained in the database.
basic non-distributed data types
void	Write (const string &GroupName, const string &DataSetName, int data)
	Writes an integer in group GroupName using intentified DataSetName.
void	Read (const string &GroupName, const string &DataSetName, int &data)
	Reads an integer from group /GroupName/DataSetName.
void	Write (const string &GroupName, const string &DataSetName, double data)
	Writes a double in group GroupName using intentified DataSetName.
void	Read (const string &GroupName, const string &DataSetName, double &data)
	Reads a double from group /GroupName/DataSetName.
void	Write (const string &GroupName, const string &DataSetName, const string &data)
	Writes a string in group GroupName using intentified DataSetName.
void	Read (const string &GroupName, const string &DataSetName, string &data)
	Reads a string from group /GroupName/DataSetName.
void	Read (const string &GroupName, const string &DataSetName, const int type, const int Length, void *data)
	Reads serial array data, of type type, from group GroupNameusing dataset name DataSetName.
void	Write (const string &GroupName, const string &DataSetName, const int type, const int Length, void *data)
	Writes serial array data, of type type, to group GroupNameusing dataset name DataSetName.
void	WriteComment (const string &GroupName, string Comment)
	Associates string Comment with group GroupName.
void	ReadComment (const string &GroupName, string &Comment)
	Reads the string associated with group GroupName.
Distributed arrays
void	Write (const string &GroupName, const string &DataSetName, int MySize, int GlobalSize, int type, const void *data)
	Writes distributed array data, of type type, to group GroupNameusing dataset name DataSetName.
void	Read (const string &GroupName, const string &DataSetName, int MySize, int GlobalSize, const int type, void *data)
	Reads distributed array data, of type type, from group GroupNameusing dataset name DataSetName.
Epetra_Map/Epetra_BlockMap
void	Write (const string &GroupName, const Epetra_Map &Map)
	Writes a Map to group GroupName.
void	Read (const string &GroupName, Epetra_Map *&Map)
	Reads a map from GroupName.
void	ReadMapProperties (const string &GroupName, int &NumGlobalElements, int &IndexBase, int &NumProc)
	Reads basic properties of specified Epetra_Map.
void	Read (const string &GroupName, Epetra_BlockMap *&Map)
	Reads a block map from GroupName.
void	Write (const string &GroupName, const Epetra_BlockMap &Map)
	Writes a block map to group GroupName.
void	ReadBlockMapProperties (const string &GroupName, int &NumGlobalElements, int &NumGlobalPoints, int &IndexBase, int &NumProc)
	Reads basic properties of specified Epetra_BlockMap.
Epetra_CrsGraph
void	Read (const string &GroupName, Epetra_CrsGraph *&Graph)
	Reads a vector from group GroupName, assumes linear distribution.
void	Read (const string &GroupName, const Epetra_Map &DomainMap, const Epetra_Map &RangeMap, Epetra_CrsGraph *&Graph)
	Reads a vector from group GroupName using given map.
void	Write (const string &GroupName, const Epetra_CrsGraph &Graph)
	Writes a distributed vector to group GroupName.
void	ReadCrsGraphProperties (const string &GroupName, int &NumGlobalRows, int &NumGlobalCols, int &NumGlobalNonzeros, int &NumGlobalDiagonals, int &MaxNumIndices)
	Reads basic properties of specified Epetra_CrsGraph.
Epetra_IntVector
void	Write (const string &GroupName, const Epetra_IntVector &x)
	Writes a distributed vector to group GroupName.
void	Read (const string &GroupName, Epetra_IntVector *&X)
	Reads a vector from group GroupName, assumes linear distribution.
void	Read (const string &GroupName, const Epetra_Map &Map, Epetra_IntVector *&X)
	Reads a vector from group GroupName using given map.
void	ReadIntVectorProperties (const string &GroupName, int &GlobalLength)
	Reads basic properties of specified Epetra_IntVector.
Epetra_MultiVector
void	Write (const string &GroupName, const Epetra_MultiVector &x)
	Writes a distributed vector to group GroupName.
void	Read (const string &GroupName, Epetra_MultiVector *&X)
	Reads a vector from group GroupName, assumes linear distribution.
void	Read (const string &GroupName, const Epetra_Map &Map, Epetra_MultiVector *&X)
	Reads a vector from group GroupName using given map.
void	ReadMultiVectorProperties (const string &GroupName, int &GlobalLength, int &NumVectors)
	Reads basic properties of specified Epetra_MultiVector.
Epetra_RowMatrix/Epetra_CrsMatrix
void	Write (const string &GroupName, const Epetra_RowMatrix &Matrix)
	Writes a distributed RowMatrix to group GroupName.
void	Read (const string &GroupName, Epetra_CrsMatrix *&A)
	Reads a square matrix from group GroupName, assumes linear distribution.
void	Read (const string &GroupName, const Epetra_Map &DomainMap, const Epetra_Map &RangeMap, Epetra_CrsMatrix *&A)
	Reads a matrix from group GroupName with given range and domain maps.
void	ReadCrsMatrixProperties (const string &GroupName, int &NumGlobalRows, int &NumGlobalCols, int &NumNonzeros, int &NumGlobalDiagonals, int &MaxNumEntries, double &NormOne, double &NormInf)
	Reads basic properties of specified Epetra_CrsMatrix.
Teuchos::ParameterList
void	Write (const string &GroupName, const Teuchos::ParameterList &List)
	Writes a parameter list to group GroupName.
void	Read (const string &GroupName, Teuchos::ParameterList &List)
	Reads a parameter list from group GroupName.
EpetraExt::DistArray<int>
void	Write (const string &GroupName, const DistArray< int > &array)
	Writes an EpetraExt::DistArray<int> to group GroupName.
void	Read (const string &GroupName, DistArray< int > *&array)
	Reads an EpetraExt::DistArray<int> from group GroupName.
void	Read (const string &GroupName, const Epetra_Map &Map, DistArray< int > *&array)
	Reads an EpetraExt::DistArray<int> from group GroupName.
void	ReadIntDistArrayProperties (const string &GroupName, int &GlobalLength, int &RowSize)
	Reads the global number of elements and type for a generic handle object.
EpetraExt::DistArray<double>
void	Write (const string &GroupName, const DistArray< double > &array)
	Writes an EpetraExt::DistArray<int> to group GroupName.
void	Read (const string &GroupName, DistArray< double > *&array)
	Reads an EpetraExt::DistArray<int> from group GroupName.
void	Read (const string &GroupName, const Epetra_Map &Map, DistArray< double > *&array)
	Reads an EpetraExt::DistArray<int> from group GroupName.
void	ReadDoubleDistArrayProperties (const string &GroupName, int &GlobalLength, int &RowSize)
	Reads the global number of elements and type for a generic handle object.
Generic distributed object
void	Write (const string &GroupName, const Handle &List)
	Writes an Epetra_DistObject to group GroupName.
void	Read (const string &GroupName, Handle &List)
	Reads an Epetra_DistObject from group GroupName.
void	ReadHandleProperties (const string &GroupName, string &Type, int &NumGlobalElements)
	Reads the global number of elements and type for a generic handle object.
Private Data
const Epetra_Comm &	Comm () const
	Returns a reference to the communicator of this object.
const Epetra_Comm &	Comm_
	Communicator of this object.
string	FileName_
	FileName currently open.
bool	IsOpen_
	If true, a file is currently open.
hid_t	file_id_
	file ID for HDF5.
hid_t	plist_id_
herr_t	status

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Detailed Description

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

Introduction

Class HDF5 allows to read and write 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 application with MATLAB, and vice-versa;
• the library is easy to build: just download the tarball from the official NCSA HDF5 web page, configure/make/make install, and everything should work. While building Trilinos, then you just have to specify the location of the header files using --with-incdirs, the location of the library using --with-ldflags, and the HDF5 library using --with-libs. Note that you might need to add "-lz" to the list of libraries; this library is typically already installed on your system;
• HDF5 are like a file system, and they can contain directories and files. This means that more data can be stored in the same file. Besides, one can append new data to an existing file, or read only one data set;
• It is very easy to add "meta-data" to your data; for example a string containing information about 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 data does not have to coincide with that used to write the data.

The class supports 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). It is meant that the non-distributed data types have the same value on all processors.

Some utility methods are provided:

• 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 is provided.

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; this class, instead, is only structured around the concept of groups. A group is an entity, like 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.

The 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 on it the information to keep;
• it is not possible to overwrite distributed objects.

Errors

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

Example of usage

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

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

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

Alternatively, datasets can 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 are supposed to have the same value on all processors.

Reading data is a easy as writing. Let us consider how to read an Epetra_CrsMatrix, other Epetra objects having a similar bejavior. Method ReadCrsMatrixProperties() 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. The actual reading is:

Epetra_CrsMatrix* NewMatrix = 0;
HDF5.Read("matrix", NewMatrix);

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

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

Reading meta-data 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

Reading HDF5 files from MATLAB is very, since the built-in functions hdf5read, hdf5write, hdf5info. For example, to read the above Matrix from MATLAB, one can do:

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 sparse, which does not accept int32 data.

To dump on file matlab.h5 a MATLAB matrix (in this case, A), one can proceed 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 __type__ specification, that must reflect the Epetra class name.

To dump on file matlab.h5 a MATLAB dense array (in this case, x), one can proceed 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.

To write a Map from MATLAB follows a very similar pattern. The following example shows how to define a map that can be used with 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.

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 288 of file EpetraExt_HDF5.h.

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Constructor & Destructor Documentation

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

ctor Definition at line 220 of file EpetraExt_HDF5.cpp.

EpetraExt::HDF5::~HDF5 (   )  [inline]

dtor Definition at line 296 of file EpetraExt_HDF5.h.

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Member Function Documentation

void EpetraExt::HDF5::Create (  const string  FileName  )

Creates a new file. Definition at line 226 of file EpetraExt_HDF5.cpp.

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

Opens specified file with given access type. Definition at line 256 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::Close (   )  [inline]

Closes the file. Definition at line 312 of file EpetraExt_HDF5.h.

bool EpetraExt::HDF5::IsOpen (   )  const [inline]

Returns true is a file has already been open using Open()/Create(). Definition at line 319 of file EpetraExt_HDF5.h.

void EpetraExt::HDF5::CreateGroup (  const string &  GroupName  )  [inline]

Creates group GroupName. Definition at line 325 of file EpetraExt_HDF5.h.

bool EpetraExt::HDF5::IsContained (  const string  Name  )

Returns true is Name is contained in the database. Definition at line 278 of file EpetraExt_HDF5.cpp.

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

Writes an integer in group GroupName using intentified DataSetName. Definition at line 1260 of file EpetraExt_HDF5.cpp.

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

Reads an integer from group /GroupName/DataSetName. Definition at line 1304 of file EpetraExt_HDF5.cpp.

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

Writes a double in group GroupName using intentified DataSetName. Definition at line 1282 of file EpetraExt_HDF5.cpp.

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

Reads a double from group /GroupName/DataSetName. Definition at line 1326 of file EpetraExt_HDF5.cpp.

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

Writes a string in group GroupName using intentified DataSetName. Definition at line 1348 of file EpetraExt_HDF5.cpp.

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

Reads a string from group /GroupName/DataSetName. Definition at line 1379 of file EpetraExt_HDF5.cpp.

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

Reads serial array data, of type type, from group GroupNameusing dataset name DataSetName. Definition at line 1439 of file EpetraExt_HDF5.cpp.

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

Writes serial array data, of type type, to group GroupNameusing dataset name DataSetName. Definition at line 1412 of file EpetraExt_HDF5.cpp.

void EpetraExt::HDF5::WriteComment (  const string &  GroupName, string  Comment )  [inline]

Associates string Comment with group GroupName. Definition at line 365 of file EpetraExt_HDF5.h.

void EpetraExt::HDF5::ReadComment (  const string &  GroupName, string &  Comment )  [inline]

Reads the string associated with group GroupName. Definition at line 371 of file EpetraExt_HDF5.h.

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

Writes distributed array data, of type type, to group GroupNameusing dataset name DataSetName. Definition at line 1470 of file EpetraExt_HDF5.cpp.

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

Reads distributed array data, of type type, from group GroupNameusing dataset name DataSetName. Definition at line 1520 of file EpetraExt_HDF5.cpp.

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

Writes a Map to group GroupName. Definition at line 389 of file EpetraExt_HDF5.cpp.

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

Reads a map from GroupName. Definition at line 408 of file EpetraExt_HDF5.cpp.

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

Reads basic properties of specified Epetra_Map. Definition at line 434 of file EpetraExt_HDF5.cpp.

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

Reads a block map from GroupName. Definition at line 328 of file EpetraExt_HDF5.cpp.

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

Writes a block map to group GroupName. Definition at line 297 of file EpetraExt_HDF5.cpp.

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

Reads basic properties of specified Epetra_BlockMap. Definition at line 364 of file EpetraExt_HDF5.cpp.

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

Reads a vector from group GroupName, assumes linear distribution. Definition at line 597 of file EpetraExt_HDF5.cpp.

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

Reads a vector from group GroupName using given map. Definition at line 640 of file EpetraExt_HDF5.cpp.

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

Writes a distributed vector to group GroupName. Definition at line 559 of file EpetraExt_HDF5.cpp.

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

Reads basic properties of specified Epetra_CrsGraph. Definition at line 613 of file EpetraExt_HDF5.cpp.

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

Writes a distributed vector to group GroupName. Definition at line 461 of file EpetraExt_HDF5.cpp.

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

Reads a vector from group GroupName, assumes linear distribution. Definition at line 488 of file EpetraExt_HDF5.cpp.

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

Reads a vector from group GroupName using given map. Definition at line 503 of file EpetraExt_HDF5.cpp.

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

Reads basic properties of specified Epetra_IntVector. Definition at line 536 of file EpetraExt_HDF5.cpp.

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

Writes a distributed vector to group GroupName. Definition at line 886 of file EpetraExt_HDF5.cpp.

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

Reads a vector from group GroupName, assumes linear distribution. Definition at line 975 of file EpetraExt_HDF5.cpp.

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

Reads a vector from group GroupName using given map. Definition at line 958 of file EpetraExt_HDF5.cpp.

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

Reads basic properties of specified Epetra_MultiVector. Definition at line 1031 of file EpetraExt_HDF5.cpp.

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

Writes a distributed RowMatrix to group GroupName. Definition at line 693 of file EpetraExt_HDF5.cpp.

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

Reads a square matrix from group GroupName, assumes linear distribution. Definition at line 737 of file EpetraExt_HDF5.cpp.

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

Reads a matrix from group GroupName with given range and domain maps. Definition at line 755 of file EpetraExt_HDF5.cpp.

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

Reads basic properties of specified Epetra_CrsMatrix. Definition at line 797 of file EpetraExt_HDF5.cpp.

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

Writes a parameter list to group GroupName. Definition at line 832 of file EpetraExt_HDF5.cpp.

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

Reads a parameter list from group GroupName. Definition at line 850 of file EpetraExt_HDF5.cpp.

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

Writes an EpetraExt::DistArray<int> to group GroupName. Definition at line 1056 of file EpetraExt_HDF5.cpp.

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

Reads an EpetraExt::DistArray<int> from group GroupName. Definition at line 1118 of file EpetraExt_HDF5.cpp.

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

Reads an EpetraExt::DistArray<int> from group GroupName. Definition at line 1086 of file EpetraExt_HDF5.cpp.

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

Reads the global number of elements and type for a generic handle object. Definition at line 1133 of file EpetraExt_HDF5.cpp.

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

Writes an EpetraExt::DistArray<int> to group GroupName. Definition at line 1158 of file EpetraExt_HDF5.cpp.

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

Reads an EpetraExt::DistArray<int> from group GroupName. Definition at line 1220 of file EpetraExt_HDF5.cpp.

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

Reads an EpetraExt::DistArray<int> from group GroupName. Definition at line 1188 of file EpetraExt_HDF5.cpp.

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

Reads the global number of elements and type for a generic handle object. Definition at line 1235 of file EpetraExt_HDF5.cpp.

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

Writes an Epetra_DistObject to group GroupName. Definition at line 28 of file EpetraExt_HDF5_DistObject.cpp.

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

Reads an Epetra_DistObject from group GroupName. Definition at line 115 of file EpetraExt_HDF5_DistObject.cpp.

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

Reads the global number of elements and type for a generic handle object. Definition at line 188 of file EpetraExt_HDF5_DistObject.cpp.

const Epetra_Comm& EpetraExt::HDF5::Comm (   )  const [inline, private]

Returns a reference to the communicator of this object. Definition at line 557 of file EpetraExt_HDF5.h.

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Member Data Documentation

const Epetra_Comm& EpetraExt::HDF5::Comm_ [private]

Communicator of this object. Definition at line 563 of file EpetraExt_HDF5.h.

string EpetraExt::HDF5::FileName_ [private]

FileName currently open. Definition at line 565 of file EpetraExt_HDF5.h.

bool EpetraExt::HDF5::IsOpen_ [private]

If true, a file is currently open. Definition at line 567 of file EpetraExt_HDF5.h.

hid_t EpetraExt::HDF5::file_id_ [private]

file ID for HDF5. Definition at line 570 of file EpetraExt_HDF5.h.

hid_t EpetraExt::HDF5::plist_id_ [private]

Definition at line 571 of file EpetraExt_HDF5.h.

herr_t EpetraExt::HDF5::status [private]

Definition at line 572 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

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