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<HTML><HEAD>
<TITLE>HDF5 Tutorial - Glossary
</TITLE> 
</HEAD>

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 [ <A HREF="title.html"><I>HDF5 Tutorial Top</I></A> ]
<H1>
<BIG><BIG><BIG><FONT COLOR="#c101cd">Glossary</FONT>
</BIG></BIG></BIG></H1>

<hr noshade size=1>

<BODY>
<DL>
<DT><B>ATTRIBUTE</B>   
<DD>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.

<P>
<DT><B>BOOT BLOCK</B>
<DD>HDF5 files are composed of a "boot 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 boot 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. 
<P>
<DT><B>DATASET</B>     
<DD>An HDF5 dataset is a multi-dimensional array of data elements, 
            together with supporting metadata. 

<P>
<DT><B>DATASPACE</B>   
<DD>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.

<P>
<DT><B>DATATYPE</B>    
<DD>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.

<P>
<DT><B>DATASET CREATION PROPERTY LIST</B>
<DD>        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:
<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>DATA TRANSFER PROPERTY LIST</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>DDL</B>         
<DD>DDL is a Data Description Language that describes HDF5 objects 
            in Backus-Naur Form.
 
<P>

<DT><B>FILE ACCESS MODES</B>
<DD>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:
<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>FILE ACCESS PROPERTY LIST</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>FILE CREATION PROPERTY LIST</B>
<DD>     The file creation property list is used to control the 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. 
 Symbol Table Parameters: 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>GROUP</B> 
<DD>A Group is a structure containing zero or more HDF5 objects, 
            together with supporting metadata. The two primary HDF5 objects 
            are datasets and groups.
<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>HDF5 FILE</B>
<DD>An HDF5 file is a container for storing grouped collections 
            of multi-dimensional arrays containing scientific data. 
<P>

<DT><B>H5DUMP</B> 
<DD>h5dump is an HDF5 tool that describes the HDF5 file contents in DDL.
<P>

<DT><B>HYPERSLAB</B>
<DD>
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. 
<P>
<DT><B>MOUNTING FILES</B>
<DD>
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. 
<P>

<DT><B>NAMES</B> 
<DD>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.
<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><B>REFERENCE</B>
<DD>
<B>OBJECT REFERENCE:</B><BR>
    A reference to an entire object in the current HDF5 file.  
    <P>
    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.
<P>
<B>DATASET REGION REFERENCE:</B><BR>
    Reference to a specific dataset region.
    <P>  
    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.
<P>
<DT><B>THREADSAFE (HDF5)</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. 

</DL>

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<BR> <H6>Last Modified: March 16, 2001</H6><BR>
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