hdf5/doxygen/dox/LearnBasics3.dox

/** @page LBPropsList Property Lists Basics
Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
<hr>

\section secLBPList What is a Property (or Property List)?
In HDF5, a property or property list is a characteristic or feature associated with an HDF5 object.
There are default properties which handle the most common needs. These default properties are
specified by passing in #H5P_DEFAULT for the Property List parameter of a function. Default properties
can be modified by use of the \ref H5P interface and function parameters.

The \ref H5P API allows a user to take advantage of the more powerful features in HDF5. It typically
supports unusual cases when creating or accessing HDF5 objects. There is a programming model for
working with Property Lists in HDF5 (see below).

For examples of modifying a property list, see these tutorial topics:
\li \see \ref LBDsetLayout
\li \see \ref LBExtDset
\li \see \ref LBComDset

There are many Property Lists associated with creating and accessing objects in HDF5. See the
\ref H5P Interface documentation in the HDF5 \ref RM for a list of the different
properties associated with HDF5 interfaces.

In summary:
\li Properties are features of HDF5 objects, that can be changed by use of the Property List API and function parameters.
\li Property lists provide a mechanism for adding functionality to HDF5 calls without increasing the number of arguments used for a given call.
\li The Property List API supports unusual cases when creating and accessing HDF5 objects.

\section secLBPListProg Programming Model
Default properties are specified by simply passing in #H5P_DEFAULT (C) / H5P_DEFAULT_F (F90) for
the property list parameter in those functions for which properties can be changed.

The programming model for changing a property list is as follows:
\li Create a copy or "instance" of the desired pre-defined property type, using the #H5Pcreate call. This
will return a property list identifier. Please see the \ref RM entry for #H5Pcreate, for a comprehensive
list of the property types.
\li With the property list identifier, modify the property, using the \ref H5P APIs.
\li Modify the object feature, by passing the property list identifier into the corresponding HDF5 object function.
\li Close the property list when done, using #H5Pclose.

<hr>
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@page LBDsetLayout Dataset Storage Layout
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<hr>

\section secLBDsetLayoutDesc Description of a Dataset
The Creating a Dataset tutorial topic defines a dataset as a multidimensional array of data elements together with supporting metadata, where:

\li The array of elements consists of the raw data values that a user wishes to store in HDF5.
\li The supporting metadata describes that data. The metadata is stored in the dataset (object) header of a dataset.

Datatype, dataspace, attribute, and storage layout information were introduced as part of the metadata associated with a dataset:
<table>
<tr>
<td>
\image html tutr-lodset.png
</td>
</tr>
</table>

\section secLBDsetLayout Dataset Storage Layout
The storage information, or storage layout, defines how the raw data values in the dataset are
physically stored on disk. There are three ways that a dataset can be stored:
\li contiguous
\li chunked
\li compact

See the #H5Pset_layout/#H5Pget_layout APIs for details.

\subsection subsecLBDsetLayoutCont Contiguous
If the storage layout is contiguous, then the raw data values will be stored physically adjacent
to each other in the HDF5 file (in one contiguous block). This is the default layout for a dataset.
In other words, if you do not explicitly change the storage layout for the dataset, then it will
be stored contiguously.
<table>
<tr>
<td>
\image html tutr-locons.png
</td>
</tr>
</table>

\subsection subsecLBDsetLayoutChunk Chunked
With a chunked storage layout the data is stored in equal-sized blocks or chunks of
a pre-defined size. The HDF5 library always writes and reads the entire chunk:
<table>
<tr>
<td>
\image html tutr-lochk.png
</td>
</tr>
</table>

Each chunk is stored as a separate contiguous block in the HDF5 file. There is a chunk index
which keeps track of the chunks associated with a dataset:
<table>
<tr>
<td>
\image html tutr-lochks.png
</td>
</tr>
</table>


\subsubsection susubsecLBDsetLayoutChunkWhy Why Chunking ?
Chunking is required for enabling compression and other filters, as well as for creating extendible
or unlimited dimension datasets.

It is also commonly used when subsetting very large datasets. Using the chunking layout can
greatly improve performance when subsetting large datasets, because only the chunks required
will need to be accessed. However, it is easy to use chunking without considering the consequences
of the chunk size, which can lead to strikingly poor performance.

Note that a chunk always has the same rank as the dataset and the chunk's dimensions do not need
to be factors of the dataset dimensions.

Writing or reading a chunked dataset is transparent to the application. You would use the same
set of operations that you would use for a contiguous dataset. For example:
\code
   H5Dopen (...);
   H5Sselect_hyperslab (...);
   H5Dread (...);
\endcode

\subsubsection susubsecLBDsetLayoutChunkProb Problems Using Chunking
Issues that can cause performance problems with chunking include:
\li Chunks are too small.
If a very small chunk size is specified for a dataset it can cause the dataset to be excessively
large and it can result in degraded performance when accessing the dataset. The smaller the chunk
size the more chunks that HDF5 has to keep track of, and the more time it will take to search for a chunk.
\li Chunks are too large.
An entire chunk has to be read and uncompressed before performing an operation. There can be a
performance penalty for reading a small subset, if the chunk size is substantially larger than
the subset. Also, a dataset may be larger than expected if there are chunks that only contain a
small amount of data.
\li A chunk does not fit in the Chunk Cache.
Every chunked dataset has a chunk cache associated with it that has a default size of 1 MB. The
purpose of the chunk cache is to improve performance by keeping chunks that are accessed frequently
in memory so that they do not have to be accessed from disk. If a chunk is too large to fit in the
chunk cache, it can significantly degrade performance. However, the size of the chunk cache can be
increased by calling #H5Pset_chunk_cache.

It is a good idea to:
\li Avoid very small chunk sizes, and be aware of the 1 MB chunk cache size default.
\li Test the data with different chunk sizes to determine the optimal chunk size to use.
\li Consider the chunk size in terms of the most common access patterns that will be used once the dataset has been created.

\subsection subsecLBDsetLayoutCom Compact
A compact dataset is one in which the raw data is stored in the object header of the dataset.
This layout is for very small datasets that can easily fit in the object header.

The compact layout can improve storage and access performance for files that have many very tiny
datasets. With one I/O access both the header and data values can be read. The compact layout reduces
the size of a file, as the data is stored with the header which will always be allocated for a dataset.
However, the object header is 64 KB in size, so this layout can only be used for very small datasets.

\section secLBDsetLayoutProg Programming Model to Modify the Storage Layout
To modify the storage layout, the following steps must be done:
\li Create a Dataset Creation Property list. (See #H5Pcreate)
\li Modify the property list.
To use chunked storage layout, call: #H5Pset_chunk
To use the compact storage layout, call: #H5Pset_layout
\li Create a dataset with the modified property list. (See #H5Dcreate)
\li Close the property list. (See #H5Pclose)
For example code, see the \ref HDF5Examples page.
Specifically look at the \ref ExAPI.
There are examples for different languages.

The C example to create a chunked dataset is:
<a href="https://\SRCURL/HDF5Examples/C/H5D/h5ex_d_chunk.c">h5ex_d_chunk.c</a>
The C example to create a compact dataset is:
<a href="https://\SRCURL/HDF5Examples/C/H5D/h5ex_d_compact.c">h5ex_d_compact.c</a>

\section secLBDsetLayoutChange Changing the Layout after Dataset Creation
The dataset layout is a Dataset Creation Property List. This means that once the dataset has been
created the dataset layout cannot be changed. The h5repack utility can be used to write a file
to a new with a new layout.

\section secLBDsetLayoutSource Sources of Information
<a href="https://\DOCURL/chunking_in_hdf5.html">Chunking in HDF5</a>
(See the documentation on <a href="https://\DOCURL/advanced_topics_list.html">Advanced Topics in HDF5</a>)
\see \ref sec_plist in the HDF5 \ref UG.

<hr>
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@page LBExtDset Extendible Datasets
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<hr>

\section secLBExtDsetCreate Creating an Extendible Dataset
An extendible dataset is one whose dimensions can grow. HDF5 allows you to define a dataset to have
certain initial dimensions, then to later increase the size of any of the initial dimensions.

HDF5 requires you to use chunking to define extendible datasets. This makes it possible to extend
datasets efficiently without having to excessively reorganize storage. (To use chunking efficiently,
be sure to see the advanced topic, <a href="https://\DOCURL/chunking_in_hdf5.html">Chunking in HDF5</a>.)

The following operations are required in order to extend a dataset:
\li Declare the dataspace of the dataset to have unlimited dimensions for all dimensions that might eventually be extended.
\li Set dataset creation properties to enable chunking.
\li Create the dataset.
\li Extend the size of the dataset.

\section secLBExtDsetProg Programming Example

\subsection subsecLBExtDsetProgDesc Description
See \ref LBExamples for the examples used in the \ref LearnBasics tutorial.

The example shows how to create a 3 x 3 extendible dataset, write to that dataset, extend the dataset
to 10x3, and write to the dataset again.

For details on compiling an HDF5 application:
[ \ref LBCompiling ]

\subsection subsecLBExtDsetProgRem Remarks
\li An unlimited dimension dataspace is specified with the #H5Screate_simple call, by passing in
#H5S_UNLIMITED as an element of the maxdims array.
\li The #H5Pcreate call creates a new property as an instance of a property list class. For creating
an extendible array dataset, pass in #H5P_DATASET_CREATE for the property list class.
\li The #H5Pset_chunk call modifies a Dataset Creation Property List instance to store a chunked
layout dataset and sets the size of the chunks used.
\li To extend an unlimited dimension dataset use the #H5Dset_extent call. Please be aware that
after this call, the dataset's dataspace must be refreshed with #H5Dget_space before more data can be accessed.
\li The #H5Pget_chunk call retrieves the size of chunks for the raw data of a chunked layout dataset.
\li Once there is no longer a need for a Property List instance, it should be closed with the #H5Pclose call.

<hr>
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@page LBComDset Compressed Datasets
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<hr>

\section secLBComDsetCreate Creating a Compressed Dataset
HDF5 requires you to use chunking to create a compressed dataset. (To use chunking efficiently,
be sure to see the advanced topic, <a href="https://\DOCURL/chunking_in_hdf5.html">Chunking in HDF5</a>.)

The following operations are required in order to create a compressed dataset:
\li Create a dataset creation property list.
\li Modify the dataset creation property list instance to enable chunking and to enable compression.
\li Create the dataset.
\li Close the dataset creation property list and dataset.

For more information on compression, see the FAQ question on <a href="https://confluence.hdfgroup.org/display/HDF5/Using+Compression+in+HDF5">Using Compression in HDF5</a>.

\section secLBComDsetProg Programming Example

\subsection subsecLBComDsetProgDesc Description
See \ref LBExamples for the examples used in the \ref LearnBasics tutorial.

The example creates a chunked and ZLIB compressed dataset. It also includes comments for what needs
to be done to create an SZIP compressed dataset. The example then reopens the dataset, prints the
filter information, and reads the dataset.

For details on compiling an HDF5 application:
[ \ref LBCompiling ]

\subsection subsecLBComDsetProgRem Remarks
\li The #H5Pset_chunk call modifies a Dataset Creation Property List instance to store a chunked layout
dataset and sets the size of the chunks used.
\li The #H5Pset_deflate call modifies the Dataset Creation Property List instance to use ZLIB or DEFLATE
compression. The #H5Pset_szip call modifies it to use SZIP compression. There are different compression
parameters required for each compression method.
\li SZIP compression can only be used with atomic datatypes that are integer, float, or char. It cannot be
applied to compound, array, variable-length, enumerations, or other user-defined datatypes. The call
to #H5Dcreate will fail if attempting to create an SZIP compressed dataset with a non-allowed datatype.
The conflict can only be detected when the property list is used.

<hr>
Previous Chapter \ref LBExtDset - Next Chapter \ref LBContents

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@page LBContents Discovering the Contents of an HDF5 File
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<hr>

\section secLBContents Discovering what is in an HDF5 file
HDFView and h5dump are standalone tools which cannot be called within an application, and using
#H5Dopen and #H5Dread require that you know the name of the HDF5 dataset. How would an application
that has no prior knowledge of an HDF5 file be able to determine or discover the contents of it,
much like HDFView and h5dump?

The answer is that there are ways to discover the contents of an HDF5 file, by using the
\ref H5G, \ref H5L and \ref H5O APIs:
\li The \ref H5G interface (covered earlier) consists of routines for working with groups. A group is
a structure that can be used to organize zero or more HDF5 objects, not unlike a Unix directory.
\li The \ref H5L interface consists of link routines. A link is a path between groups. The \ref H5L interface
allows objects to be accessed by use of these links.
\li The \ref H5O interface consists of routines for working with objects. Datasets, groups, and committed
datatypes are all objects in HDF5.

Interface routines that simplify the process:
\li #H5Literate traverses the links in a specified group, in the order of the specified index, using a
user-defined callback routine. (A callback function is one that will be called when a certain condition
is met, at a certain point in the future.)
\li #H5Ovisit / #H5Lvisit recursively visit all objects/links accessible from a specified object/group.


\section secLBContentsProg Programming Example

\subsection subsecLBContentsProgUsing Using H5Literate, H5Lvisit and H5Ovisit
For example code, see the \ref HDF5Examples page.
Specifically look at the \ref ExAPI.
There are examples for different languages, where examples of using #H5Literate and #H5Ovisit/#H5Lvisit are included.

The h5ex_g_traverse example traverses a file using H5Literate:
\li C: <a href="https://\SRCURL/HDF5Examples/C/H5G/h5ex_g_traverse.c">h5ex_g_traverse.c</a>
\li F90: <a href="https://\SRCURL/HDF5Examples/FORTRAN/H5G/h5ex_g_traverse.F90">h5ex_g_traverse_F03.f90</a>

The h5ex_g_visit example traverses a file using H5Ovisit and H5Lvisit:
\li C: <a href="https://\SRCURL/HDF5Examples/C/H5G/h5ex_g_visit.c">h5ex_g_visit.c</a>
\li F90:  <a href="https://\SRCURL/HDF5Examples/FORTRAN/H5G/h5ex_g_visit.F90">h5ex_g_visit_F03.f90</a>

<hr>
Previous Chapter \ref LBComDset - Next Chapter \ref LBQuiz

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@page LBQuiz Learning the basics QUIZ
Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
<hr>

\ref LBFileOrg
<ol>
<li>Name and describe the two primary objects that can be stored in an HDF5 file.
</li>
<li>What is an attribute?
</li>
<li>Give the path name for an object called <code style="background-color:whitesmoke;">harry</code> that is a member of a group called <code style="background-color:whitesmoke;">dick</code>, which, in turn, is a member of the root group.
</li>
</ol>

\ref LBAPI
<ol>
<li>Describe the purpose of each of the following HDF5 APIs:
\code
       H5A, H5D, H5E, H5F, H5G, H5T, H5Z 
\endcode
</li>
</ol>

\ref LBFileCreate
<ol>
<li>What two HDF5 routines must be called to create an HDF5 file?
</li>
<li>What include file must be included in any file that uses the HDF5 library?
</li>
<li>An HDF5 file is never completely empty because as soon as it is created, it automatically contains a certain primary object. What is that object?
</li>
</ol>

\ref LBDsetCreate
<ol>
<li>Name and describe two major datatype categories.
</li>
<li>List the HDF5 atomic datatypes. Give an example of a predefined datatype. How would you create a string dataset?
</li>
<li>What does the dataspace describe? What are the major characteristics of the simple dataspace?
</li>
<li>What information needs to be passed to the #H5Dcreate function, i.e., what information is needed to describe a dataset at creation time?
</li>
</ol>


\ref LBDsetRW
<ol>
<li>What are six pieces of information which need to be specified for reading and writing a dataset?
</li>
<li>Why are both the memory dataspace and file dataspace needed for read/write operations, while only the memory datatype is required?
</li>
<li>In Figure 6.1, what does this line mean?
\code
DATASPACE { SIMPLE (4 , 6 ) / ( 4 , 6 ) }
\endcode
</li>
</ol>


\ref LBAttrCreate
<ol>
<li>What is an attribute?
</li>
<li>Can partial I/O operations be performed on attributes?
</li>
</ol>


\ref LBGrpCreate
<ol>
<li>What are the two primary objects that can be included in a group?
</li>
</ol>


\ref LBGrpCreateNames
<ol>
<li>Group names can be specified in two ways. What are these two types of group names?
</li>
<li>You have a dataset named <code style="background-color:whitesmoke;">moo</code> in the group <code style="background-color:whitesmoke;">boo</code>, which is in the group <code style="background-color:whitesmoke;">foo</code>, which, in turn,
is in the <code style="background-color:whitesmoke;">root</code> group. How would you specify an absolute name to access this dataset?
</li>
</ol>


\ref LBGrpDset
<ol>
<li>Describe a way to access the dataset moo described in the previous section
(question 2) using a relative name. Describe a way to access the same dataset using an absolute name.
</li>
</ol>

<hr>
Previous Chapter \ref LBContents - Next Chapter \ref LBQuizAnswers

Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics

@page LBQuizAnswers Learning the basics QUIZ with Answers
Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
<hr>

\ref LBFileOrg
<ol>
<li>Name and describe the two primary objects that can be stored in an HDF5 file.
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>Group: A grouping structure containing zero or more HDF5 objects, together with supporting metadata.<br />
Dataset: A multidimensional array of data elements, together with supporting metadata.
</td>
</tr>
</table>
</li>
<li>What is an attribute?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>An HDF5 attribute is a user-defined HDF5 structure that provides extra information about an HDF5 object.
</td>
</tr>
</table>
</li>
<li>Give the path name for an object called <code style="background-color:whitesmoke;">harry</code> that is a member of a group called <code style="background-color:whitesmoke;">dick</code>, which, in turn, is a member of the root group.
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>/dick/harry
</td>
</tr>
</table>
</li>
</ol>

\ref LBAPI
<ol>
<li>Describe the purpose of each of the following HDF5 APIs:
\code
       H5A, H5D, H5E, H5F, H5G, H5T, H5Z 
\endcode
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>H5A: Attribute access and manipulation routines
<br />
H5D: Dataset access and manipulation routines
<br />
H5E: Error handling routines H5F: File access routines
<br />
H5G: Routines for creating and operating on groups
<br />
H5T: Routines for creating and manipulating the datatypes of dataset elements
<br />
H5Z: Data compression routines
</td>
</tr>
</table>
</li>
</ol>

\ref LBFileCreate
<ol>
<li>What two HDF5 routines must be called to create an HDF5 file?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>#H5Fcreate and #H5Fclose.
</td>
</tr>
</table>
</li>
<li>What include file must be included in any file that uses the HDF5 library?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>hdf5.h must be included because it contains definitions and declarations used by the library.
</td>
</tr>
</table>
</li>
<li>An HDF5 file is never completely empty because as soon as it is created, it automatically contains a certain primary object. What is that object?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>The root group.
</td>
</tr>
</table>
</li>
</ol>

\ref LBDsetCreate
<ol>
<li>Name and describe two major datatype categories.
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>Atomic datatype: An atomic datatype cannot be decomposed into smaller units at the API level.
<br />
Compound datatype: A compound datatype is a collection of atomic and compound datatypes, or small arrays of such types.
</td>
</tr>
</table>
</li>
<li>List the HDF5 atomic datatypes. Give an example of a predefined datatype. How would you create a string dataset?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>There are six HDF5 atomic datatypes: integer, floating point, date and time, character string, bit field, and opaque.
<br />
Examples of predefined datatypes include the following:<br />
\li #H5T_IEEE_F32LE - 4-byte little-endian, IEEE floating point
\li #H5T_NATIVE_INT - native integer

You would create a string dataset with the #H5T_C_S1 datatype, and set the size of the string with the #H5Tset_size call.
</td>
</tr>
</table>
</li>
<li>What does the dataspace describe? What are the major characteristics of the simple dataspace?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>The dataspace describes the dimensionality of the dataset. A simple dataspace is characterized by its rank and dimension sizes.
</td>
</tr>
</table>
</li>
<li>What information needs to be passed to the #H5Dcreate function, i.e., what information is needed to describe a dataset at creation time?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>The dataset location, name, dataspace, datatype, and dataset creation property list.
</td>
</tr>
</table>
</li>
</ol>


\ref LBDsetRW
<ol>
<li>What are six pieces of information which need to be specified for reading and writing a dataset?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>The dataset identifier, the dataset's datatype and dataspace in memory, the dataspace in the file,
the dataset transfer property list, and a data buffer.
</td>
</tr>
</table>
</li>
<li>Why are both the memory dataspace and file dataspace needed for read/write operations, while only the memory datatype is required?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>A dataset's file datatype is not required for a read/write operation because the file datatype is specified
when the dataset is created and cannot be changed. Both file and memory dataspaces are required for dataset
subsetting and for performing partial I/O operations.
</td>
</tr>
</table>
</li>
<li>In Figure 6.1, what does this line mean?
\code
DATASPACE { SIMPLE (4 , 6 ) / ( 4 , 6 ) }
\endcode
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>It means that the dataset dset has a simple dataspace with the current dimensions (4,6) and the maximum size of the dimensions (4,6).
</td>
</tr>
</table>
</li>
</ol>


\ref LBAttrCreate
<ol>
<li>What is an attribute?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>An attribute is a dataset attached to an object. It describes the nature and/or the intended usage of the object.
</td>
</tr>
</table>
</li>
<li>Can partial I/O operations be performed on attributes?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>No.
</td>
</tr>
</table>
</li>
</ol>


\ref LBGrpCreate
<ol>
<li>What are the two primary objects that can be included in a group?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>A group and a dataset.
</td>
</tr>
</table>
</li>
</ol>


\ref LBGrpCreateNames
<ol>
<li>Group names can be specified in two ways. What are these two types of group names?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>Relative and absolute.
</td>
</tr>
</table>
</li>
<li>You have a dataset named <code style="background-color:whitesmoke;">moo</code> in the group <code style="background-color:whitesmoke;">boo</code>, which is in the group <code style="background-color:whitesmoke;">foo</code>, which, in turn,
is in the <code style="background-color:whitesmoke;">root</code> group. How would you specify an absolute name to access this dataset?
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>/foo/boo/moo
</td>
</tr>
</table>
</li>
</ol>


\ref LBGrpDset
<ol>
<li>Describe a way to access the dataset moo described in the previous section
(question 2) using a relative name. Describe a way to access the same dataset using an absolute name.
<table>
<tr>
<th><strong>Answer</strong>
</th>
<td>Access the group /foo and get the group ID. Access the group boo using the group ID obtained in Step 1.
Access the dataset moo using the group ID obtained in Step 2.
\code
gid = H5Gopen (file_id, "/foo", 0); /* absolute path */ 
gid1 = H5Gopen (gid, "boo", 0); /* relative path */ 
did = H5Dopen (gid1, "moo"); /* relative path */ 
\endcode
Access the group /foo and get the group ID. Access the dataset boo/moo with the group ID just obtained.
\code
gid = H5Gopen (file_id, "/foo", 0); /* absolute path */ 
did = H5Dopen (gid, "boo/moo"); /* relative path */ 
\endcode
Access the dataset with an absolute path.
\code
did = H5Dopen (file_id, "/foo/boo/moo"); /* absolute path */
\endcode
</td>
</tr>
</table>
</li>
</ol>

<hr>
Previous Chapter \ref LBQuiz - Next Chapter \ref LBCompiling

Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics

/** @page LBCompiling Compiling HDF5 Applications
Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
<hr>

\section secLBCompiling Tools and Instructions on Compiling
Compiling applications to use the HDF5 Library can be as simple as executing:
\code
h5cc -o myprog myprog.c
\endcode

As an application's file base evolves, there are better solutions using autotools and makefiles or
CMake and CMakeLists.txt files. Many tutorials and references can be found with a simple search.

This tutorial section will discuss the use of compile scripts on Linux.
See the \ref secLBCompilingVS section for compiling with Visual Studio.

\section secLBCompilingLinux Compile Scripts
When the library is built, the following compile scripts are included:
\li h5cc:  compile script for HDF5 C programs
\li h5fc:  compile script for HDF5 F90 programs
\li h5c++: compile script for HDF5 C++ programs

These scripts are easily used to compile single file applications, such as those included in the tutorial.
<table>
<tr>
<th><strong>Warning</strong>
</th>
<td>The h5cc/h5fc/h5c++ compile scripts are included when building with configure. Versions of
these compile scripts have also been added to CMake for Linux ONLY. The CMake versions rely on pkgconfig files.
</td>
</tr>
</table>

<h4>Examples of Using the Unix Compile Scripts:</h4>
Following are examples of compiling and running an application with the Unix compile scripts:
\code
   h5fc myprog.f90
   ./a.out

   h5cc -o myprog myprog.c
   ./myprog 
\endcode

To see how the libraries linked in with a compile script were configured and built, use the
-showconfig option. For example, if using h5cc type:
\code
   h5cc -showconfig
\endcode

<h4>Detailed Description of Unix Compile Scripts:</h4>
The h5cc, h5c++, and h5fc compile scripts come with the HDF5 binary distributions (include files,
libraries, and utilities) for the platforms we support. The h5c++ and h5fc utilities are ONLY present
if the library was built with C++ and Fortran.

<h4>USING_HDF5_CMake.txt:</h4>
\verbinclude USING_HDF5_CMake.txt

\section secLBCompilingVS Using Visual Studio

   1. If you are building on 64-bit Windows, find the "Platform" dropdown
      and select "x64". Also select the correct Configuration (Debug, Release, RelWithDebInfo, etc)

   2. Set up path for external headers

      The HDF5 install path settings will need to be in the project property sheets per project.
      Go to "Project" and select "Properties", find "Configuration Properties",
      and then "C/C++".

      2.1 Add the header path to the "Additional Include Directories" setting. Under "C/C++"
          find "General" and select "Additional Include Directories". Select "Edit" from the dropdown
          and add the HDF5 install/include path to the list.
          (Ex: "C:\Program Files\HDF_Group\HDF5\1.10.9\include")

      2.2 Building applications with the dynamic/shared hdf5 libraries requires
          that the "H5_BUILT_AS_DYNAMIC_LIB" compile definition be used. Under "C/C++"
          find "Preprocessor" and select "Preprocessor Definitions". Select "Edit" from the dropdown
          and add "H5_BUILT_AS_DYNAMIC_LIB" to the list.

   3. Set up path for external libraries

      The HDF5 install path/lib settings will need to be in the project property sheets per project.
      Go to "Project" and select "Properties", find "Configuration Properties",
      and then "Linker".

      3.1 Add the libraries to the "Additional Dependencies" setting. Under "Linker"
          find "Input" and select "Additional Dependencies". Select "Edit" from the dropdown
          and add the required HDF5 install/lib path to the list.
          (Ex: "C:\Program Files\HDF_Group\HDF5\1.10.9\lib\hdf5.lib")

      3.2 For static builds, the external libraries should be added.
          For example, to compile a C++ application, enter:
          libhdf5_cpp.lib libhdf5.lib libz.lib libszaec.lib libaec.lib

\section secLBCompilingLibs HDF5 Libraries
Following are the libraries included with HDF5. Whether you are using the Unix compile scripts or
Makefiles, or are compiling on Windows, these libraries are or may need to be specified. The order
they are specified is important on Linux:

<table>
<caption>HDF5 Static Libraries</caption>
<tr>
<th>Library</th>
<th>Linux Name</th>
<th>Mac Name</th>
<th>Windows Name</th>
</tr>
<tr>
<td>
\code
HDF5 High Level C++ APIs 
HDF5 C++ Library  
HDF5 High Level Fortran APIs
HDF5 Fortran Library
HDF5 High Level C APIs
HDF5 C Library
\endcode
</td>
<td>
\code
libhdf5_hl_cpp.a
libhdf5_cpp.a
libhdf5_hl_fortran.a
libhdf5_fortran.a
libhdf5_hl.a
libhdf5.a
\endcode
</td>
<td>
\code
libhdf5_hl_cpp.a
libhdf5_cpp.a
libhdf5_hl_fortran.a
libhdf5_fortran.a
libhdf5_hl.a
libhdf5.a
\endcode
</td>
<td>
<em>Windows</em>
\code
libhdf5_hl_cpp.lib
libhdf5_cpp.lib
libhdf5_hl_fortran.lib
libhdf5_fortran.lib
libhdf5_hl.lib
libhdf5.lib
\endcode
</tr>
</table>

<table>
<caption>HDF5 Shared Libraries</caption>
<tr>
<th>Library</th>
<th>Linux Name</th>
<th>Mac Name</th>
<th>Windows Name</th>
</tr>
<tr>
<td>
\code
HDF5 High Level C++ APIs 
HDF5 C++ Library  
HDF5 High Level Fortran APIs
HDF5 Fortran Library
HDF5 High Level C APIs
HDF5 C Library
\endcode
</td>
<td>
\code
libhdf5_hl_cpp.so
libhdf5_cpp.so
libhdf5_hl_fortran.so
libhdf5_fortran.so
libhdf5_hl.so
libhdf5.so
\endcode
</td>
<td>
\code
libhdf5_hl_cpp.dylib
libhdf5_cpp.dylib
libhdf5_hl_fortran.dylib
libhdf5_fortran.dylib
libhdf5_hl.dylib
libhdf5.dylib
\endcode
</td>
<td>
\code
hdf5_hl_cpp.lib
hdf5_cpp.lib
hdf5_hl_fortran.lib
hdf5_fortran.lib
hdf5_hl.lib
hdf5.lib
\endcode
</tr>
</table>

<table>
<caption>External Libraries</caption>
<tr>
<th>Library</th>
<th>Linux Name</th>
<th>Mac Name</th>
<th>Windows Name</th>
</tr>
<tr>
<td>
\code
SZIP Compression Library
SZIP Compression Library
ZLIB or DEFLATE Compression Library
\endcode
</td>
<td>
\code
libszaec.a
libaec.a
libz.a
\endcode
</td>
<td>
\code
libszaec.a
libaec.a
libz.a
\endcode
</td>
<td>
\code
libszaec.lib
libaec.lib
libz.lib
\endcode
</td>
</tr>
</table>

The pre-compiled binaries, in particular, are built (if at all possible) with these libraries as well as with
SZIP and ZLIB. If using shared libraries you may need to add the path to the library to LD_LIBRARY_PATH on Linux
or on WINDOWS you may need to add the path to the bin folder to PATH.

\section secLBCompilingCMake Compiling an Application with CMake

\subsection subsecLBCompilingCMakeScripts CMake Scripts for Building Applications
Simple scripts are provided for building applications with different languages and options.
See <a href="https://confluence.hdfgroup.org/display/support/CMake+Scripts+for+Building+Applications">CMake Scripts for Building Applications</a>.

For a more complete script (and to help resolve issues) see the script provided with the HDF5 Examples project.

\subsection subsecLBCompilingCMakeExamples HDF5 Examples
The installed HDF5 can be verified by compiling the HDF5 Examples project, included with the CMake built HDF5 binaries
in the share folder or you can go to the <a href="https://github.com/HDFGroup/hdf5-examples">HDF5 Examples</a> github repository.

Go into the share directory and follow the instructions in USING_CMake_examples.txt to build the examples.

In general, users must first set the HDF5_ROOT environment variable to the installed location of the CMake
configuration files for HDF5. For example, on Windows the following path might be set:

\code
   HDF5_ROOT=C:/Program Files/HDF_Group/HDF5/1.N.N
\endcode

\subsection subsecLBCompilingCMakeTroubless Troubleshooting CMake
<h4>How do you use find_package with HDF5?</h4>
To use find_package you will first need to make sure that HDF5_ROOT is set correctly. For setting this
environment variable see the Preconditions in the USING_HDF5_CMake.txt file in the share directory.

See the CMakeLists.txt file provided with these examples for how to use find_package with HDF5.

Please note that the find_package invocation changed to require "shared" or "static":
\code
      FIND_PACKAGE(HDF5 COMPONENTS C HL NO_MODULE REQUIRED shared)
      FIND_PACKAGE(HDF5 COMPONENTS C HL NO_MODULE REQUIRED static)  
\endcode

Previously, the find_package invocation was: 
\code
      FIND_PACKAGE(HDF5 COMPONENTS C HL NO_MODULE REQUIRED)
\endcode

<h4>My platform/compiler is not included. Can I still use the configuration files?</h4>
Yes, you can but you will have to edit the HDF5_Examples.cmake file and update the variable:
\code
   CTEST_CMAKE_GENERATOR  
\endcode

The generators for your platform can be seen by typing:
\code
   cmake --help
\endcode

<h4>What do I do if the build fails?</h4>
I received an error during the build and the application binary is not in the
build directory as I expected. How do I determine what the problem is?

If the error is not clear, then the first thing you may want to do is replace the -V (Dash Uppercase Vee)
option for ctest in the build script to -VV (Dash Uppercase Vee Uppercase Vee). Then remove the build
directory and re-run the build script. The output should be more verbose.

If the error is still not clear, then check the log files. You will find those in the build directory.
For example, on Unix the log files will be in:
\code
   build/Testing/Temporary/  
\endcode
There are log files for the configure, test, and build. 

<hr>
Previous Chapter \ref LBQuizAnswers - Next Chapter \ref LBTraining

Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics

*/

/ref LBTraining

<hr>
Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics

*/