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If you do not have * - * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - --> - -<link href="ed_styles/GenElect.css" rel="stylesheet" type="text/css"> -<!-- #EndLibraryItem --></head> - -<body> - - -<!-- #BeginLibraryItem "/ed_libs/NavBar_ADevG.lbi" --><hr> -<center> -<table border=0 width=98%> -<tr><td valign=top align=left> - <a href="index.html">HDF5 documents and links</a> <br> - <a href="H5.intro.html">Introduction to HDF5</a> <br> - <!-- - <a href="Glossary.html">Glossary</a><br> - --> -</td> -<td valign=top align=right> - <a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide</a> <br> - <a href="RM_H5Front.html">HDF5 Reference Manual</a> <br> - <a href="ADGuide.html">HDF5 Application Developer's Guide</a> <br> -</td></tr> -</table> -</center> -<hr> -<!-- #EndLibraryItem --><center> -<h1>HDF5 Glossary</h1> -</center> - -<center> -<table width=90% border=0> -<tr><td valign=top align=left width=33%> -<dl> - <dt><a href="#Glossary-AtomicDType">atomic datatype</a> - <dt><a href="#Glossary-Attribute">attribute</a> -<!--<dt><a href="#Glossary-BasicDType">basic datatype</a>--> - <dt><a href="#Glossary-LayoutChunked">chunked layout</a> - <dt><a href="#Glossary-Chunking">chunking</a> -<!--<dt><a href="#Glossary-ComplexDType">complex datatype</a>--> - <dt><a href="#Glossary-CompoundDType">compound datatype</a> -<!--<dt>compound element--> - <dt><a href="#Glossary-LayoutContig">contiguous layout</a> -<!--<dt>conversion function--> - <dt><a href="#Glossary-Dataset">dataset</a> - <dt><a href="#Glossary-Dataspace">dataspace</a> -<!--<dl>--> -<!-- <dt>dimensions--> -<!-- <dt>selection--> -<!--</dl>--> - <dt><a href="#Glossary-Datatype">datatype</a> - <dl> - <dt><a href="#Glossary-AtomicDType">atomic</a> -<!-- <dt><a href="#Glossary-BasicDType">basic</a>--> -<!-- <dt><a href="#Glossary-ComplexDType">complex</a>--> - <dt><a href="#Glossary-CompoundDType">compound</a> -<!-- <dt>conversion function--> -<!-- <dt><a href="#Glossary-DiskIO">disk I/O</a>--> - <dt><a href="#Glossary-DTypeEnum">enumeration</a> - <dt><a href="#Glossary-DTypeNamed">named</a> - <dt><a href="#Glossary-DTypeOpaque">opaque</a> -<!-- <dt>transient--> - <dt><a href="#Glossary-DTypeVLen">variable-length</a> - </dl> -<!--<dt>DDL--> -<!--<dt>dimensions--> -<!--<dt><a href="#Glossary-DiskIO">disk I/O datatype</a>--> -<!--<dt>element--> - <dt><a href="#Glossary-DTypeEnum">enumeration datatype</a> - <dt><a href="#Glossary-File">file</a> - <dl> -<!-- <dt>compound element--> -<!-- <dt>element--> - <dt><a href="#Glossary-Group">group</a> - <dt><a href="#Glossary-Path">path</a> - <dt><a href="#Glossary-RootGroup">root group</a> - <dt><a href="#Glossary-SuperBlock">super block</a> - </dl> -</dl> -</td> -<td valign=top align=left width=34%> -<dl> - <dt><a href="#Glossary-FileAccessMode">file access mode</a> - <dt><a href="#Glossary-Group">group</a> - <dl> -<!-- <dt>element--> - <dt><a href="#Glossary-GroupMember">member</a> - <dt><a href="#Glossary-RootGroup">root group</a> - </dl> - <dt><a href="#Glossary-LinkHard">hard link</a> -<!--<dt>HDF5--> - <dt><a href="#Glossary-Hyperslab">hyperslab</a> - <dt><a href="#Glossary-Identifier">identifier</a> - <dt><a href="#Glossary-Link">link</a> - <dl> - <dt><a href="#Glossary-LinkHard">hard</a> - <dt><a href="#Glossary-LinkSoft">soft</a> -<!-- <dt><a href="#Glossary-LinkSoftName">soft link name</a>--> -<!-- <dt>target--> - </dl> - <dt><a href="#Glossary-GroupMember">member</a> - <dt><a href="#Glossary-Name">name</a> - <dt><a href="#Glossary-DTypeNamed">named datatype</a> - <dt><a href="#Glossary-DTypeOpaque">opaque datatype</a> - <dt><a href="#Glossary-Path">path</a> -<!--<dt>parallel I/O--> - <dt><a href="#Glossary-PList">property list</a> - <dl> - <dt><a href="#Glossary-PListDataTransfer">data transfer</a> - <dt><a href="#Glossary-PListDSetAccess">dataset access</a> - <dt><a href="#Glossary-PListDSetCreate">dataset creation</a> - <dt><a href="#Glossary-PListFileAccess">file access</a> - <dt><a href="#Glossary-PListFileCreate">file creation</a> - </dl> -</dl> -</td> -<td valign=top align=left width=33%> -<dl> - <dt><a href="#Glossary-RootGroup">root group</a> - <dt><a href="#Glossary-Selection">selection</a> - <dl> - <dt><a href="#Glossary-Hyperslab">hyperslab</a> -<!-- <dt>point--> - </dl> - <dt><a href="#Glossary-Serialization">serialization</a> - <dt><a href="#Glossary-LinkSoft">soft link</a> -<!--<dt><a href="#Glossary-LinkSoftName">soft link name</a>--> - <dt><a href="#Glossary-StorageLayout">storage layout</a> - <dl> - <dt><a href="#Glossary-LayoutChunked">chunked</a> - <dt><a href="#Glossary-Chunking">chunking</a> - <dt><a href="#Glossary-LayoutContig">contiguous</a> - </dl> - <dt><a href="#Glossary-SuperBlock">super block</a> -<!--<dt>target--> -<!--<dt>threadsafe--> -<!--<dt>transient datatype--> - <dt><a href="#Glossary-DTypeVLen">variable-length datatype</a> -</dl> -</td></tr> -</table> -</center> - -<hr> - - -<DL> - -<dt><strong><a name="Glossary-AtomicDType">atomic datatype</a></strong> - <dd>A datatype which cannot be decomposed into smaller units at the - API level. -<P> - -<DT><a name="Glossary-Attribute"><B>attribute</B></a> -<DD>A small dataset that can be used to describe the nature and/or - the intended usage of the object it is attached to. -<P> - -<!-- -<dt><strong><a name="Glossary-Basic">basic datatypes</a></strong> - <ul> - <li>char - 8-bit character (only for ASCII information) - <li>int8 - 8-bit signed integer - <li>uint8 - 8-bit unsigned integer - <li>int16 - 16-bit signed integer - <li>uint16 - 16-bit unsigned integer - <li>int32 - 32-bit signed integer - <li>uint32 - 32-bit unsigned integer - <li>intn - "native" signed integer - <li>uintn - "native" unsigned integer - <li>int64 - 64-bit signed integer (new) - <li>uint64 - 64-bit unsigned integer (new) - <li>float32 - 32-bit IEEE float - <li>float64 - 64-bit IEEE float - </ul> -<P> ---> - -<dt><strong><a name="Glossary-LayoutChunked">chunked layout</a></strong> -<dd>The storage layout of a chunked dataset. -<P> - -<dt><strong><a name="Glossary-Chunking">chunking</a></strong> -<dd>A storage layout where a dataset is partitioned into fixed-size - multi-dimensional chunks. Chunking tends to improve performance - and facilitates dataset extensibility. -<P> - -<dt><strong><a name="Glossary-CompoundDType">compound datatype</a></strong> -<dd>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. -<P> - -<!-- -<dt><strong><a name="Glossary-ComplexDType">complex datatype</a></strong> -<dd>A collection of one or more atomic types or small arrays of such types. - <ul> - <li>hid_t - 32-bit unsigned integer used as ID for memory objects - <li>hoid_t - 32-bit unsigned integer (currently) used as ID for - disk-based objects - <li>hbool_t - boolean to indicate true/false/error codes from functions - <li>herr_t - 32-bit integer to indicate succeed/fail codes from - functions - </ul> -<P> ---> - -<dt><strong><a name="Glossary-LayoutContig">contiguous layout</a></strong> -<dd>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. -<P> - -<DT><B><a name="Glossary-PListDataTransfer">data transfer property list</a></B> -<DD>The data transfer property list is used to control various aspects - of the I/O, such as caching hints or collective I/O information. -<P> - -<DT><B><a name="Glossary-Dataset">dataset</a></B> -<DD>A multi-dimensional array of data elements, together with - supporting metadata. -<P> - -<!-- NEW PAGE --> -<DT><B><a name="Glossary-PListDSetAccess">dataset access property list</a></B> -<DD>A property list containing information on how a dataset is to be accessed. -<P> - -<DT><B><a name="Glossary-PListDSetCreate">dataset creation property list</a></B> -<DD>A property list containing 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: - <UL> - <B> Layout:</B> - <UL> - <LI>H5D_COMPACT: Data is small and can be stored in object header (not - implemented yet). This eliminates disk seek/read requests. - <LI>H5D_CONTIGUOUS: (<B>default</B>) The data is large, non-extendible, - non-compressible, non-sparse, and can be stored externally. - <LI>H5D_CHUNKED: The data is large and can be extended in any dimension. - It is partitioned into chunks so each chunk is the same logical size. - </UL> - <B>Compression:</B> (gzip compression)<BR> - <B>External Storage Properties:</B> The data must be contiguous to be - stored externally. It allows you to store - the data in one or more non-HDF5 files. - </UL> ---> -<P> - -<DT><B><a name="Glossary-Dataspace">dataspace</a></B> -<DD>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. -<P> - -<DT><B><a name="Glossary-Datatype">datatype</a></B> -<DD>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. -<P> - -<!-- -<DT><B>DDL</B> -<DD>A detailed description of the HDF5 format and objects, written in a - Data Description Language using Backus-Naur Form. -<P> ---> - -<!-- -<dt><strong><a name="Glossary-DiskIO">disk I/O datatypes</a></strong> -<ul> - <li>hoff_t - (64-bit?) offset on disk in bytes - <li>hlen_t - (64-bit?) length on disk in bytes -</ul> -<P> ---> - -<dt><strong><a name="Glossary-DTypeEnum">enumeration datatype</a></strong> -<dd>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. -<P> - -<DT><B><a name="Glossary-File">file</a></B> -<DD>A container for storing grouped collections of - multi-dimensional arrays containing scientific data. -<P> - -<DT><B><a name="Glossary-FileAccessMode">file access mode</a></B> -<DD>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. -<!-- - Possible values are: - <PRE> - 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. - </PRE> ---> -<P> - -<DT><B><a name="Glossary-PListFileAccess">file access property list</a></B> -<DD>File access property lists are used to control different methods - of performing I/O on files: -<!-- - <UL> - <B>Unbuffered I/O:</B> Local permanent files can be accessed with the - functions described in Section 2 of the Posix manual, namely open(), - lseek(), read(), write(), and close(). <BR> - <B>Buffered I/O:</B> Local permanent files can be accessed with the - functions declared in the stdio.h header file, namely fopen(), - fseek(), fread(), fwrite(), and fclose().<BR> - <B>Memory I/O:</B> Local temporary files can be created and accessed - directly from memory without ever creating permanent storage. - The library uses malloc() and free() to create storage space for the - file<BR> - <B>Parallel Files using MPI I/O:</B> This driver allows parallel access - to a file through the MPI I/O library. The parameters which can be - modified are the MPI communicator, the info object, and the access mode. - The communicator and info object are saved and then passed to - MPI_File_open() during file creation or open. The access_mode - controls the kind of parallel access the application intends.<BR> - <B>Data Alignment:</B> Sometimes file access is faster if certain things - are aligned on file blocks. This can be controlled by setting alignment - properties of a file access property list with the H5Pset_alignment() - function. - </UL> ---> -<P> - -<DT><B><a name="Glossary-PListFileCreate">file creation property list</a></B> -<DD>The property list used to control file metadata. -<!-- - The parameters that can be modified are: - <UL> - <B>User-Block Size:</B> The "user-block" is a fixed length block - of data located at the beginning of the file which is ignored - by the HDF5 library and may be used to store any data information - found to be useful to applications. - <BR> - <B>Offset and Length Sizes:</B> The number of bytes used to store the - offset and length of objects in the HDF5 file can be controlled - with this parameter. - <BR> - <b>Symbol Table Parameters:</b> The size of symbol table B-trees can - be controlled by setting the 1/2 rank and 1/2 node size - parameters of the B-tree. - <BR> - <B>Indexed Storage Parameters:</B> The size of indexed storage - B-trees can be controlled by setting the 1/2 rank and 1/2 node - size parameters of the B-tree. - </UL> ---> -<P> - -<DT><B><a name="Glossary-Group">group</a></B> -<DD>A structure containing zero or more HDF5 objects, - together with supporting metadata. - The two primary HDF5 objects are datasets and groups. -<P> - -<dt><strong><a name="Glossary-LinkHard">hard link</a></strong> -<dd>A direct association between a name and the object where both exist - in a single HDF5 address space. -<P> - -<!-- -<DT><B>HDF5</B> -<DD>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 - <P> - <UL> - <LI>by including the information needed to understand the data - within the file - <P> - <LI>by providing a library of C, FORTRAN, and other language - programs that reduce the work required to provide efficient - writing and reading - even with parallel IO - </UL> -<P> ---> - -<DT><B><a name="Glossary-Hyperslab">hyperslab</a></B> -<DD>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. -<P> - -<dt><strong><a name="Glossary-Identifier">identifier</a></strong> -<dd>A unique entity provided by the HDF5 library and used to access - an HDF5 object, such as a file, goup, dataset, datatype, etc. -<P> - -<dt><strong><a name="Glossary-Link">link</a></strong> -<dd>An association between a name and the object in an HDF5 file group. -<P> - -<dt><strong><a name="Glossary-GroupMember">member</a></strong> -<dd>A group or dataset that is in another dataset, <i>dataset A</i>, - is a member of <i>dataset A</i>. -<P> - -<DT><B><a name="Glossary-Name">name</a></B> -<DD>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. -<P> - -<dt><strong><a name="Glossary-DTypeNamed">named datatype</a></strong> -<dd>A datatype that is named and stored in a file. Naming is permanent; - a datatype cannot be changed after being named. -<P> - -<dt><strong><a name="Glossary-DTypeOpaque">opaque datatype</a></strong> -<dd>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. -<P> - -<!-- -<DT><B>parallel I/O HDF5</B> -<DD>The parallel I/O version of HDF5 supports parallel file access using - MPI (Message Passing Interface). -<P> ---> - -<dt><strong><a name="Glossary-Path">path</a></strong> -<dd>The slash-separated list of components that forms the name - uniquely identifying an element of an HDF5 file. -<P> - -<dt><strong><a name="Glossary-PList">property list</a></strong> -<dd>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. -<P> - -<dt><strong><a name="Glossary-RootGroup">root group</a></strong> -<dd>The group that is the entry point to the group graph in an HDF5 file. - Every HDF5 file has exactly one root group. -<P> - -<dt><strong><a name="Glossary-Selection">selection</a></strong> -<dd>(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. -<P> - -<dt><strong><a name="Glossary-Serialization">serialization</a></strong> -<dd>The flattening of an <em>N</em>-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. -<P> - -<dt><strong><a name="Glossary-LinkSoft">soft link</a></strong> -<dd>An indirect association between a name and an object in an - HDF5 file group. -<P> - -<dt><strong><a name="Glossary-StorageLayout">storage layout</a></strong> -<dd>The manner in which a dataset is stored, either contiguous or - chunked, in the HDF5 file. -<P> - -<DT><B><a name="Glossary-SuperBlock">super block</a></B> -<DD>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. -<P> - -<!-- -<DT><B>threadsafe</B> -<DD>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: - <UL> - <LI>the HDF-5 library does not create or destroy threads. - <LI>the HDF-5 library uses modest amounts of per-thread - private memory. - <LI>the HDF-5 library only locks/unlocks it's own locks (no locks - are passed in or returned from HDF), and the internal locking - is guaranteed to be deadlock free. - </UL> - <P> - 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. -<P> ---> - -<dt><strong><a name="Glossary-DTypeVLen">variable-length datatype</a></strong> -<dd>A sequence of an existing datatype (atomic, variable-length (VL), - or compound) which are not fixed in length from one dataset location - to another. -<P> - -</DL> - - -<!-- #BeginLibraryItem "/ed_libs/NavBar_ADevG.lbi" --><hr> -<center> -<table border=0 width=98%> -<tr><td valign=top align=left> - <a href="index.html">HDF5 documents and links</a> <br> - <a href="H5.intro.html">Introduction to HDF5</a> <br> - <!-- - <a href="Glossary.html">Glossary</a><br> - --> -</td> -<td valign=top align=right> - <a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide</a> <br> - <a href="RM_H5Front.html">HDF5 Reference Manual</a> <br> - <a href="ADGuide.html">HDF5 Application Developer's Guide</a> <br> -</td></tr> -</table> -</center> -<hr> -<!-- #EndLibraryItem --><!-- #BeginLibraryItem "/ed_libs/Footer.lbi" --><address> -<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a> -<br> -Describes HDF5 Release 1.7, the unreleased development branch; working toward HDF5 Release 1.8.0 -</address><!-- #EndLibraryItem --><SCRIPT LANGUAGE="JAVASCRIPT"> -<!-- -document.writeln("Last modified: 24 February 2004"); ---> -</SCRIPT> - -</body> -</html> |