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Glossary


ATTRIBUTE
An HDF5 attribute is a small dataset that can be used to describe the nature and/or the intended usage of the object it is attached to.

DATASET
An HDF5 dataset is a multi-dimensional array of data elements, together with supporting metadata.

DATASPACE
An HDF5 dataspace is an object that describes the dimensionality of the data array. A dataspace is either a regular N-dimensional array of data points, called a simple dataspace, or a more general collection of data points organized in another manner, called a complex dataspace.

DATATYPE
An HDF5 Datatype is an object that describes the type of the element in an HDF5 multi-dimensional array. There are two categories of datatypes: atomic and compound data types. An atomic type is a type which cannot be decomposed into smaller units at the API level. A compound is a collection of one or more atomic types or small arrays of such types.

DATASET CREATION PROPERTY LIST
The Dataset Creation Property List contains information on how raw data is organized on disk and how the raw data is compressed. The dataset API partitions these terms by layout, compression, and external storage:

DATA TRANSFER PROPERTY LIST
The data transfer property list is used to control various aspects of the I/O, such as caching hints or collective I/O information.

DDL
DDL is a Data Description Language that describes HDF5 objects in Backus-Naur Form.

FILE ACCESS MODES
The file access modes determine whether an existing file will be overwritten. All newly created files are opened for both reading and writing. Possible values are:
  H5F_ACC_RDWR:   Allow read and write access to file. 
  H5F_ACC_RDONLY: Allow read-only access to file. 
  H5F_ACC_TRUNC:  Truncate file, if it already exists, erasing all data 
                  previously stored in the file. 
  H5F_ACC_EXCL:   Fail if file already exists. 
  H5F_ACC_DEBUG:  Print debug information. 
  H5P_DEFAULT:    Apply default file access and creation properties. 

FILE ACCESS PROPERTY LIST
File access property lists are used to control different methods of performing I/O on files:

FILE CREATION PROPERTY LIST
The file creation property list is used to control the file metadata. The parameters that can be modified are:

GROUP
A Group is a structure containing zero or more HDF5 objects, together with supporting metadata. The two primary HDF5 objects are datasets and groups.

HDF5
HDF5 is an abbreviation for Hierarchical Data Format Version 5. This file format is intended to make it easy to write and read scientific data

HDF5 FILE
An HDF5 file is a container for storing grouped collections of multi-dimensional arrays containing scientific data.

H5DUMP
h5dump is an HDF5 tool that describes the HDF5 file contents in DDL.

HYPERSLAB
A hyperslab is a portion of a dataset. A hyperslab selection can be a logically contiguous collection of points in a dataspace, or it can be a regular pattern of points or blocks in a dataspace.

MOUNTING FILES
HDF5 allows you to combine two or more HDF5 files in a manner similar to mounting files in UNIX. The group structure and metadata from one file appear as though they exist in another file.

NAMES
HDF5 object names are a slash-separated list of components. A name which begins with a slash is an absolute name which is accessed beginning with the root group of the file while all other relative names are accessed beginning with the specified group.

PARALLEL I/O (HDF5)
The parallel I/O version of HDF5 supports parallel file access using MPI (Message Passing Interface).

REFERENCE
OBJECT REFERENCE:
A reference to an entire object in the current HDF5 file.

An object reference points to an entire object in the current HDF5 file by storing the relative file address (OID) of the object header for the object pointed to. The relative file address of an object header is constant for the life of the object. An object reference is of a fixed size in the file.

DATASET REGION REFERENCE:
Reference to a specific dataset region.

A dataset region reference points to a region of a dataset in the current HDF5 file by storing the OID of the dataset and the global heap offset of the region referenced. The region referenced is located by retrieving the coordinates of the areas in the region from the global heap. A dataset region reference is of a variable size in the file.

THREADSAFE (HDF5)
A "thread-safe" version of HDF-5 (TSHDF5) is one that can be called from any thread of a multi-threaded program. Any calls to HDF can be made in any order, and each individual HDF call will perform correctly. A calling program does not have to explicitly lock the HDF library in order to do I/O. Applications programmers may assume that the TSHDF5 guarantees the following:

These properties mean that the TSHDF5 library will not interfere with an application's use of threads. A TSHDF5 library is the same library as regular HDF-5 library, with additional code to synchronize access to the HDF-5 library's internal data structures.

USER BLOCK
HDF5 files are composed of a "user block" describing information required to portably access files on multiple platforms, followed by information about the groups in a file and the datasets in the file. The user block contains information about the size of offsets and lengths of objects, the number of entries in symbol tables (used to store groups) and additional version information for the file.


NCSA
The National Center for Supercomputing Applications

University of Illinois at Urbana-Champaign

hdfhelp@ncsa.uiuc.edu

Last Modified: November 2, 2001