HDF5 Glossary and Terms

atomic datatype
attribute
chunked layout
chunking
committed datatype
compound datatype
contiguous layout
dataset
dataspace
datatype: atomic; committed; compound; enumeration; named; opaque; variable-length
enumeration datatype
file: group; path; root group; super block

file access mode
group: member; root group
hard link
hyperslab
identifier
link: hard; soft
member
name
named datatype
opaque datatype
path
property list: data transfer; dataset access; dataset creation; file access; file creation

root group
selection: hyperslab
serialization
soft link
storage layout: chunked; chunking; contiguous
super block
variable-length datatype

atomic datatype: A datatype which cannot be decomposed into smaller units at the API level.
attribute: A small dataset that can be used to describe the nature and/or the intended usage of the object it is attached to.
chunked layout: The storage layout of a chunked dataset.
chunking: A storage layout where a dataset is partitioned into fixed-size multi-dimensional chunks. Chunking tends to improve performance and facilitates dataset extensibility.
committed datatype: A datatype that is named and stored in a file so that it can be shared. Committed datatypes can be shared. Committing is permanent; a datatype cannot be changed after being committed. Committed datatypes used to be called named datatypes.
compound datatype: A collection of one or more atomic types or small arrays of such types. Similar to a struct in C or a common block in Fortran.
contiguous layout: The storage layout of a dataset that is not chunked, so that the entire data portion of the dataset is stored in a single contiguous block.
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.
dataset: A multi-dimensional array of data elements, together with supporting metadata.
dataset access property list: A property list containing information on how a dataset is to be accessed.
dataset creation property list: A property list containing information on how raw data is organized on disk and how the raw data is compressed.
dataspace: 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 object that describes the storage format of the individual data points of a data set. There are two categories of datatypes: atomic and compound datatypes. An atomic type is a type which cannot be decomposed into smaller units at the API level. A compound datatype is a collection of one or more atomic types or small arrays of such types.
enumeration datatype: A one-to-one mapping between a set of symbols and a set of integer values, and an order is imposed on the symbols by their integer values. The symbols are passed between the application and library as character strings and all the values for a particular enumeration datatype are of the same integer type, which is not necessarily a native type.
file: A container for storing grouped collections of multi-dimensional arrays containing scientific data.
file access mode: Determines whether an existing file will be overwritten, opened for read-only access, or opened for read/write access. All newly created files are opened for both reading and writing.
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 property list used to control file metadata.
group: A structure containing zero or more HDF5 objects, together with supporting metadata. The two primary HDF5 objects are datasets and groups.
hard link: A direct association between a name and the object where both exist in a single HDF5 address space.
hyperslab: A portion of a dataset. A hyperslab selection can be a logically contiguous collection of points in a dataspace or a regular pattern of points or blocks in a dataspace.
identifier: A unique entity provided by the HDF5 library and used to access an HDF5 object such as a file, group, or dataset. In the past, an identifier might have been called a handle.
link: An association between a name and the object in an HDF5 file group.
member: A group or dataset that is in another dataset, dataset A, is a member of dataset A.
name: A slash-separated list of components that uniquely identifies an element of an HDF5 file. A name begins that begins with a slash is an absolute name which is accessed beginning with the root group of the file; all other names are relative names and the associated objects are accessed beginning with the current or specified group.
opaque datatype: A mechanism for describing data which cannot be otherwise described by HDF5. The only properties associated with opaque types are a size in bytes and an ASCII tag.
path: The slash-separated list of components that forms the name uniquely identifying an element of an HDF5 file.
property list: A collection of name/value pairs that can be passed to other HDF5 functions to control features that are typically unimportant or whose default values are usually used.
root group: The group that is the entry point to the group graph in an HDF5 file. Every HDF5 file has exactly one root group.
selection: (1) A subset of a dataset or a dataspace, up to the entire dataset or dataspace. (2) The elements of an array or dataset that are marked for I/O.
serialization: The flattening of an N-dimensional data object into a 1-dimensional object so that, for example, the data object can be transmitted over the network as a 1-dimensional bitstream.
soft link: An indirect association between a name and an object in an HDF5 file group.
storage layout: The manner in which a dataset is stored, either contiguous or chunked, in the HDF5 file.
super block: A block of data containing the information required to portably access HDF5 files on multiple platforms, followed by information about the groups and datasets in the file. The super block contains information about the size of offsets, lengths of objects, the number of entries in group tables, and additional version information for the file.
variable-length datatype: A sequence of an existing datatype (atomic, variable-length (VL), or compound) which are not fixed in length from one dataset location to another.

HDF5 documents and links
Introduction to HDF5

HDF5 User's Guide
HDF5 Reference Manual
HDF5 Application Developer's Guide

The HDF Group Help Desk:

Describes HDF5 Release 1.8.7, targeted for May 2011.