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authorFrank Baker <fbaker@hdfgroup.org>2005-07-19 17:28:56 (GMT)
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Description: All HDF5 user documentation has been moved to a separate hdf5doc/ repository, managed under Subversion. With this 'cvs commit', all files are stripped from hdf5/doc/. THIS CHANGE IS APPLIED ONLY TO THE HDF5 DEVELOPMENT BRANCH, post Release 1.6.x; it is not applied to the release branches.
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-<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
-<html>
-<head>
-<title>Reference (H5R) and Identifier Interfaces (H5I)</title>
-
-<!-- #BeginLibraryItem "/ed_libs/styles_UG.lbi" -->
-<!--
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Copyright by the Board of Trustees of the University of Illinois. *
- * All rights reserved. *
- * *
- * This file is part of HDF5. The full HDF5 copyright notice, including *
- * terms governing use, modification, and redistribution, is contained in *
- * the files COPYING and Copyright.html. COPYING can be found at the root *
- * of the source code distribution tree; Copyright.html can be found at the *
- * root level of an installed copy of the electronic HDF5 document set and *
- * is linked from the top-level documents page. It can also be found at *
- * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
- * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- -->
-
-<link href="ed_styles/UGelect.css" rel="stylesheet" type="text/css">
-<!-- #EndLibraryItem --></head>
-
-<body bgcolor="#FFFFFF">
-
-
-<!-- #BeginLibraryItem "/ed_libs/NavBar_UG.lbi" --><hr>
-<center>
-<table border=0 width=98%>
-<tr><td valign=top align=left>
- <a href="index.html">HDF5 documents and links</a>&nbsp;<br>
- <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
- <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
- <a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide for Release 1.6</a>&nbsp;<br>
- <!--
- <a href="Glossary.html">Glossary</a><br>
- -->
-</td>
-<td valign=top align=right>
- And in this document, the
- <a href="H5.user.html"><strong>HDF5 User's Guide from Release 1.4.5:</strong></a>&nbsp;&nbsp;&nbsp;&nbsp;
- <br>
- <a href="Files.html">Files</a>&nbsp;&nbsp;
- <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
- <a href="Datatypes.html">Datatypes</a>&nbsp;&nbsp;
- <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
- <a href="Groups.html">Groups</a>&nbsp;&nbsp;
- <br>
- <a href="References.html">References</a>&nbsp;&nbsp;
- <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
- <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
- <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
- <br>
- <a href="Filters.html">Filters</a>&nbsp;&nbsp;
- <a href="Caching.html">Caching</a>&nbsp;&nbsp;
- <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
- <a href="MountingFiles.html">Mounting Files</a>&nbsp;&nbsp;
- <br>
- <a href="Performance.html">Performance</a>&nbsp;&nbsp;
- <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
- <a href="Environment.html">Environment</a>&nbsp;&nbsp;
- <a href="ddl.html">DDL</a>&nbsp;&nbsp;
-</td></tr>
-</table>
-</center>
-<hr>
-<!-- #EndLibraryItem --><h1>The Reference Interface (H5R) and <br> the Identifier Interface (H5I)</h1>
-
-<h2>1. Introduction</h2>
-
-This document discusses the kinds of references implemented
-(and planned) in HDF5 and the functions implemented (and planned)
-to support them.
-
-
-<h2>2. References</h2>
-
-This section contains an overview of the kinds of references
-implemented, or planned for implementation, in HDF5.
-
-<p>
-
-<dl>
- <dt>Object reference
- <dd>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>
- <dt>Dataset region reference
- <dd>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.
-</dl>
-
-
-<b>Note:</b> All references are treated as soft links for the
-purposes of reference counting. The library does not keep track of
-reference links and they may dangle if the object they refer to
-is deleted, moved, or not yet available.
-
-
-<h2>3. Reference Types</h2>
-
-Valid HDF5 reference types for use in the H5R functions
-are as follows:
-
-<center>
-<table>
-<tr><th align=left>Reference Type</th><th align=left>Value&nbsp;&nbsp;</th><th align=left>Description</th></tr>
-<!-- NOT USER-LEVEL INFORMATION; DELETED FROM HDF5 USER'S GUIDE
-<tr><td><code>H5R_BADTYPE</code></td>
- <td align=right><code>-1&nbsp;&nbsp;</code></td>
- <td>Invalid reference type</td></tr>
--->
-<tr><td><code>H5R_OBJECT</code></td>
- <td align=right><code>0&nbsp;&nbsp;</code></td>
- <td>Object reference</td></tr>
-<tr><td><code>H5R_DATASET_REGION</code></td>
- <td align=right><code>1&nbsp;&nbsp;</code></td>
- <td>Dataset region reference</td></tr>
-</table>
-</center>
-
-
-<h2>4. Functions</h2>
-
-Five functions, four in the H5R interface and one in the
-H5I interface, have been implemented to support references.
-The H5I function is also useful outside the context of references.
-<p>
-<dl>
- <dt><em>herr_t</em> <code>H5Rcreate(</code><em>void *</em><code>reference,</code>
- <em>hid_t</em> <code>loc_id,</code>
- <em>const char *</em><code>name,</code>
- <em>H5R_type_t</em> <code>type,</code>
- <em>hid_t</em> <code>space_id)</code>
- <dd><code>H5Rcreate</code> creates an object which is a
- particular type of reference (specified with the
- <code>type</code> parameter) to some file object and/or
- location specified with the <code>space_id</code> parameter.
- For dataset region references, the selection specified
- in the dataspace is the portion of the dataset which
- will be referred to.
- <p>
-
- <dt><em>hid_t</em> <code>H5Rdereference(</code><em>hid_t</em> <code>dset,</code>
- <em>H5R_type_t</em> <code>rtype,</code>
- <em>void *</em><code>reference)</code>
- <dd><code>H5Rdereference</code> opens the object referenced
- and returns an identifier for that object.
- The parameter <code>reference</code> specifies a reference of
- type <code>rtype</code> that is stored in the dataset
- <code>dset</code>.
- <p>
-
- <dt><em>int</em> <code>H5Rget_object_type(</code><em>hid_t</em> <code>obj_id,</code>
- <em>void *</em><code>reference)</code>
- <dd><code>H5Rget_object_type</code> retrieves the type of object
- that an object reference points to.
- The parameter <code>obj_id</code> specifies the dataset
- containing the reference object or the location identifier
- of the object that the dataset is located within.
- The parameter <code>reference</code> specifies the
- reference being queried.
- <p>
-
- <dt><em>H5S_t</em> <code>H5Rget_region(</code><em>H5D_t</em> <code>dataset,</code>
- <em>H5R_type_t</em> <code>type,</code>
- <em>void *</em><code>reference)</code>
- <dd><code>H5Rget_region</code> creates a copy of dataspace of
- the dataset that is pointed to and defines a selection in
- the copy which is the location (or region) pointed to.
- The parameter <code>ref</code> specifies a reference of
- type <code>rtype</code> that is stored in the dataset
- <code>dset</code>.
- <p>
-
- <dt><em>H5I_type_t</em> <code>H5Iget_type(</code><em>hid_t</em> <code>id)</code>
- <dd>Returns the type of object referred to by the
- identifier <code>id</code>. Valid return values appear
- in the following list:
- <center>
- <table>
- <tr valign=bottom><td><code>H5I_FILE</code></td>
- <td>File objects</td></tr>
- <tr valign=bottom><td><code>H5I_GROUP</code></td>
- <td>Group objects</td></tr>
- <tr valign=bottom><td><code>H5I_DATATYPE</code></td>
- <td>Datatype objects</td></tr>
- <tr valign=bottom><td><code>H5I_DATASPACE</code></td>
- <td>Dataspace objects</td></tr>
- <tr valign=bottom><td><code>H5I_DATASET</code></td>
- <td>Dataset objects</td></tr>
- <tr valign=bottom><td><code>H5I_ATTR</code></td>
- <td>Attribute objects</td></tr>
- </table>
- </center>
- <p>
- This function was inspired by the need of users to figure
- out which type of object closing function
- (<code>H5Dclose</code>, <code>H5Gclose</code>, etc.)
- to call after a call to <code>H5Rdereference</code>,
- but it is also of general use.
- <p>
-</dl>
-
-
-
-<h2>5. Examples</h2>
-
-<b>Object Reference Writing Example</b>
-<br>
-Create a dataset which has links to other datasets as part
-of its raw data and write the dataset to the file.
-<p>
-
-<pre>
-{
- hid_t file1;
- hid_t dataset1;
- hid_t datatype, dataspace;
- char buf[128];
- hobj_ref_t link;
- hobj_ref_t data[10][10];
- int rank;
- size_t dimsf[2];
- int i, j;
-
- /* Open the file */
- file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
-
- /* Describe the size of the array and create the data space */
- rank=2;
- dimsf[0] = 10;
- dimsf[1] = 10;
- dataspace = H5Screate_simple(rank, dimsf, NULL);
-
- /* Define datatype */
- datatype = H5Tcopy(H5T_STD_REF_OBJ);
-
- /* Create a dataset */
- dataset1=H5Dcreate(file1,"Dataset One",datatype,dataspace,H5P_DEFAULT);
-
- /* Construct array of OIDs for other datasets in the file */
- /* somewhat hokey and artificial, but demonstrates the point */
- for(i=0; i<10; i++)
- for(j=0; j<10; j++)
- {
- sprintf(buf,"/Group/Linked Set %d-%d",i,j);
- if(H5Rcreate(&link,file1,buf,H5R_OBJECT,-1)>0)
- data[i][j]=link;
- } /* end for */
-
- /* Write the data to the dataset using default transfer properties. */
- H5Dwrite(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
-
- /* Close everything */
- H5Sclose(dataspace);
- H5Tclose(datatype);
- H5Dclose(dataset1);
- H5Fclose(file1);
-}
-</pre>
-
-
-<b>Object Reference Reading Example</b>
-<br>
-Open a dataset which has links to other datasets as part of
-its raw data and read in those links.
-<p>
-
-<pre>
-{
- hid_t file1;
- hid_t dataset1, tmp_dset;
- href_t data[10][10];
- int i, j;
-
- /* Open the file */
- file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
-
- /* Open the dataset */
- dataset1=H5Dopen(file1,"Dataset One",H5P_DEFAULT);
-
- /*
- * Read the data to the dataset using default transfer properties.
- * (we are assuming the dataset is the same and not querying the
- * dimensions, etc.)
- */
- H5Dread(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
-
- /* Analyze array of OIDs of linked datasets in the file */
- /* somewhat hokey and artificial, but demonstrates the point */
- for(i=0; i<10; i++)
- for(j=0; j<10; i++)
- {
- if((tmp_dset=H5Rdereference(dataset, H5T_STD_REF_OBJ, data[i][j]))>0)
- {
- <perform operations on linked dataset>
- } /* end if */
- H5Dclose(tmp_dset);
- } /* end for */
-
-
- /* Close everything */
- H5Dclose(dataset1);
- H5Fclose(file1);
-}
-</pre>
-
-
-<b>Dataset Region Reference Writing Example</b>
-<br>
-Create a dataset which has links to other dataset regions
-(single elements in this case) as part of its raw data and
-write the dataset to the file.
-<p>
-
-<pre>
-{
- hid_t file1;
- hid_t dataset1, dataset2;
- hid_t datatype, dataspace1, dataspace2;
- char buf[128];
- href_t link;
- href_t data[10][10]; /* HDF5 reference type */
- int rank;
- size_t dimsf[2];
- hsize_t start[3],count[3];
- int i, j;
-
- /* Open the file */
- file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
-
- /* Describe the size of the array and create the data space */
- rank=2;
- dimsf[0] = 10;
- dimsf[1] = 10;
- dataspace1 = H5Screate_simple(rank, dimsf, NULL);
-
- /* Define Dataset Region Reference datatype */
- datatype = H5Tcopy(H5T_STD_REF_DATAREG);
-
- /* Create a dataset */
- dataset1=H5Dcreate(file1,"Dataset One",datatype,dataspace1,H5P_DEFAULT);
-
- /* Construct array of OIDs for other datasets in the file */
- /* (somewhat artificial, but demonstrates the point) */
- for(i=0; i<10; i++)
- for(j=0; j<10; i++)
- {
- sprintf(buf,"/Group/Linked Set %d-%d",i,j);
-
- /* Get the dataspace for the object to point to */
- dataset2=H5Dopen(file1,buf,H5P_DEFAULT);
- dataspace2=H5Dget_space(dataspace2);
-
- /* Select the region to point to */
- /* (could be different region for each pointer) */
- start[0]=5; start[1]=4; start[2]=3;
- count[0]=2; count[1]=4; count[2]=1;
- H5Sselect_hyperslab(dataspace2,H5S_SELECT_SET,start,NULL,count,NULL);
-
- if(H5Rcreate(&link,file1,buf,H5R_REF_DATAREG,dataspace2)>0)
- /* Store the reference */
- data[i][j]=link;
-
- H5Sclose(dataspace2);
- H5Dclose(dataspace2);
- } /* end for */
-
- /* Write the data to the dataset using default transfer properties. */
- H5Dwrite(dataset, H5T_STD_REF_DATAREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
-
- /* Close everything */
- H5Sclose(dataspace);
- H5Tclose(datatype);
- H5Dclose(dataset1);
- H5Fclose(file1);
-}
-</pre>
-
-
-<b>Dataset Region Reference Reading Example</b>
-<br>
-Open a dataset which has links to other datasets regions
-(single elements in this case) as part of its raw data and
-read in those links.
-<p>
-
-<pre>
-{
- hid_t file1;
- hid_t dataset1, tmp_dset;
- hid_t dataspace;
- href_t data[10][10]; /* HDF5 reference type */
- int i, j;
-
- /* Open the file */
- file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
-
- /* Open the dataset */
- dataset1=H5Dopen(file1,"Dataset One",H5P_DEFAULT);
-
- /*
- * Read the data to the dataset using default transfer properties.
- * (we are assuming the dataset is the same and not querying the
- * dimensions, etc.)
- */
- H5Dread(dataset, H5T_STD_REF_DATAREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
-
- /* Analyze array of OIDs of linked datasets in the file */
- /* (somewhat artificial, but demonstrates the point) */
- for(i=0; i<10; i++)
- for(j=0; j<10; i++)
- {
- if((tmp_dset=H5Rdereference(dataset, H5D_STD_REF_DATAREG,data[i][j]))>0)
- {
- /* Get the dataspace with the pointed to region selected */
- dataspace=H5Rget_space(data[i][j]);
-
- <perform operation on linked dataset region>
-
- H5Sclose(dataspace);
- } /* end if */
- H5Dclose(tmp_dset);
- } /* end for */
-
-
- /* Close everything */
- H5Dclose(dataset1);
- H5Fclose(file1);
-}
-</pre>
-<!--
-
-<h1>Material to Be Omitted!!!</h1>
-
-Additional material above will also need to be deleted or
-commented out.
-<p>
-
-<h2>"Kinds of Reference" Information</h2>
-
-<dl>
- <dt>Dataset Offset Reference
- <dd>Reference to a specific byte sequence in a dataset (3)
- <dt>Disk Offset Reference
- <dd>Reference to a specific byte sequence in a file (3)
- <dt>External Object Reference
- <dd>Reference to an entire object in another HDF5 file (3)
- <dt>External Dataset Region Reference
- <dd>Reference an a specific dataset region in another HDF5 file (3)
- <dt>External Dataset Offset Reference
- <dd>Reference to a specific byte sequence in a dataset in
- another HDF5 file (3)
- <dt>External Disk Offset Reference
- <dd>Reference to a specific byte sequence in another HDF5 file (3)
- <dt>Generic Reference
- <dd>A reference which may be any of the types defined above. (3)
-</dl>
-
-Notes:
-<ul>
- <li>1 - Planned for in final release.
- <li>2 - Most useful reference types to tackle next
- <li>3 - Optional reference types.
-</ul>
-
-<h2>Comments</h2>
-<pre>
- Reference types are atomic types and may be included as fields in compound
- datatypes.
-
- There are (at least) three levels of reference strength:
- Weak - We allow the user to store any type of reference in an array
- of references. (u.e., the array of references in the example above
- could be a mix of Object, Dataset Region and Internal references)
- Medium - We force the user to stick with a particular type of
- reference within a dataset, but the datasets pointed to (with
- Object and Dataset Region references) may be of any datatype
- or dataspace.
- Strong - We force the user to stick with a particular type of
- reference and Object and Dataset Region references must point to
- datasets with the same datatype.
- Extra Strong - We force the user to stick with a particular type of
- reference and Object and Dataset Region references must point to
- datasets with the same datatype <i>and</i> dataspace.
-
- The library is currently implemented with "medium" strength references.
-</pre>
-
-
-<h2>Reference Type</h2>
-
-<center>
-<table>
-<tr><td><code>H5R_MAXTYPE</code></td>
- <td align=right><code>3&nbsp;&nbsp;</code></td>
- <td>Highest type in group (invalid as true type)</td></tr>
-</table>
-</center>
-
-
-<h2>Information Regarding Specific Kinds of References</h2>
-
-<dl>
-<dt>Dataset Offset Reference
- <dd>Points to a sequence of bytes within a dataset in
- the current HDF5 file by storing the OID of the dataset and the byte
- length and offset of the sequence within the dataset. The offset is
- the logical byte offset within the dataset, meaning that the data is
- de-compressed before returning the sequence of bytes requested. No
- interpretation of the data at that location is provided. However,
- if the dataset is extendible and the size of the dimensions are changed,
- the element(s) that the sequence is located within may vary. Fixed size
- in file.
-
-<dt>Disk Offset Reference
- <dd>Points to a sequence of bytes in the current
- HDF5 file by storing the byte length and offset of the sequence within
- the file, relative to the super block (as are all the other high-level
- addresses used in the file). The offset is the absolute byte offset
- within the file, no interpretation of the data at that location is
- provided. Fixed size in file.
-
-<dt>External Object Reference
- <dd>Points to an entire object in another HDF5 file by
- storing a global heap offset which points to the URL of the external
- file and the OID of the object pointed to. Variable size in file.
-
-<dt>External Dataset Region Reference
- <dd>Points to a region of a dataset in
- another HDF5 file by storing a global heap offset which points to the
- URL of the external file, OID of the dataset and the coordinates of the
- region. Variable size in file.
-
-<dt>External Dataset Offset Reference
- <dd>Points to a sequence of bytes within a
- dataset in another HDF5 file by storing a global heap offset which
- points to the URL of the external file, the OID of the dataset and the
- byte length and offset of the sequence within the dataset. The offset
- is the logical byte offset within the dataset, meaning that the data is
- de-compressed before returning the sequence of bytes requested.
- However, if the dataset is not stored contiguously and the size of the
- dimensions are changed, the element(s) that the sequence is located
- within may vary. Variable size in file.
-
-<dt>External Disk Offset Reference
- <dd>Points to a sequence of bytes in another
- HDF5 file by storing a global heap reference which points to the URL
- of the external file and the byte length and offset of the sequence
- within the file. The offset is the absolute byte offset within the
- file, no interpretation of the data at that location is provided.
- Variable size in file.
-
-<dt>Generic Reference
- <dd>A reference which may contain any of the other
- references defined above. (Mostly useful for implementing "weak"
- strength pointers within the medium strength model we are using)
- Variable size in file.
-
-</dl>
-
-<h2>Implementation Details</h2>
-
-<dl>
-<dt>File Storage
- <dd>In order to efficiently index an array, each element must be the
- same size when stored in the dataset on disk. Fixed-sized references
- will be stored directly in the dataset array on disk; variable-sized
- references will have a fixed-size head offset stored in the array on
- disk with a file heap used to store the actual variable-sized
- information stored in the heap.
-
-<dt>Memory Storage
- <dd>Each <code>href_t</code> object in memory is a struct containing
- a pointer type and union of information required for each
- pointer type.
- Information in this structure is not designed for users to view.
- Non-C APIs may have to mangle this structure in some way, in order
- to provide users with access to references in a language-appropriate
- way.
-</dl>
-
--->
-
-
-<!-- #BeginLibraryItem "/ed_libs/NavBar_UG.lbi" --><hr>
-<center>
-<table border=0 width=98%>
-<tr><td valign=top align=left>
- <a href="index.html">HDF5 documents and links</a>&nbsp;<br>
- <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
- <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
- <a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide for Release 1.6</a>&nbsp;<br>
- <!--
- <a href="Glossary.html">Glossary</a><br>
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- And in this document, the
- <a href="H5.user.html"><strong>HDF5 User's Guide from Release 1.4.5:</strong></a>&nbsp;&nbsp;&nbsp;&nbsp;
- <br>
- <a href="Files.html">Files</a>&nbsp;&nbsp;
- <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
- <a href="Datatypes.html">Datatypes</a>&nbsp;&nbsp;
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- <a href="References.html">References</a>&nbsp;&nbsp;
- <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
- <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
- <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
- <br>
- <a href="Filters.html">Filters</a>&nbsp;&nbsp;
- <a href="Caching.html">Caching</a>&nbsp;&nbsp;
- <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
- <a href="MountingFiles.html">Mounting Files</a>&nbsp;&nbsp;
- <br>
- <a href="Performance.html">Performance</a>&nbsp;&nbsp;
- <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
- <a href="Environment.html">Environment</a>&nbsp;&nbsp;
- <a href="ddl.html">DDL</a>&nbsp;&nbsp;
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-<hr>
-<!-- #EndLibraryItem --><!-- #BeginLibraryItem "/ed_libs/Footer.lbi" --><address>
-<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
-<br>
-Describes HDF5 Release 1.4.5, February 2003
-</address><!-- #EndLibraryItem -->
-
-Last modified: 2 August 2004
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