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diff --git a/doc/html/Tutor/glossary.html b/doc/html/Tutor/glossary.html new file mode 100644 index 0000000..84a938d --- /dev/null +++ b/doc/html/Tutor/glossary.html @@ -0,0 +1,234 @@ +<HTML><HEAD> +<TITLE>HDF5 Tutorial - Glossary +</TITLE> +</HEAD> + +<body bgcolor="#ffffff"> + +<!-- BEGIN MAIN BODY --> + +<A HREF="http://www.ncsa.uiuc.edu/"><img border=0 +src="http://www.ncsa.uiuc.edu/Images/NCSAhome/footerlogo.gif" +width=78 height=27 alt="NCSA"><P></A> + + [ <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>DATA TYPE</B> +<DD>An HDF5 Data Type 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>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>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> + +<!-- BEGIN FOOTER INFO --> + +<P><hr noshade size=1> +<font face="arial,helvetica" size="-1"> + <a href="http://www.ncsa.uiuc.edu/"><img border=0 + src="http://www.ncsa.uiuc.edu/Images/NCSAhome/footerlogo.gif" + width=78 height=27 alt="NCSA"><br> + The National Center for Supercomputing Applications</A><br> + <a href="http://www.uiuc.edu/">University of Illinois + at Urbana-Champaign</a><br> + <br> +<!-- <A HREF="helpdesk.mail.html"> --> +<A HREF="mailto:hdfhelp@ncsa.uiuc.edu"> +hdfhelp@ncsa.uiuc.edu</A> +<BR> <H6>Last Modified: September 1, 1999</H6><BR> +<!-- modified by Barbara Jones - bljones@ncsa.uiuc.edu --> +</FONT> +<BR> +<!-- <A HREF="mailto:hdfhelp@ncsa.uiuc.edu"> --> + +</BODY> +</HTML> + + + |