1.
www.hdfgroup.org
The HDF Group
Introduction to HDF5
Barbara Jones
The HDF Group
The 13th
HDF & HDF-EOS Workshop
November 3-5, 2009
November 3-5, 2009 1HDF/HDF-EOS Workshop XIII

2.
www.hdfgroup.org
Before We Begin …
HDF-EOS Home Page: http://hdfeos.org/
Workshop Info:
http://hdfeos.org/workshops/ws13/workshop_thirteen.php
The HDF Group Page: http://hdfgroup.org/
HDF5 Home Page: http://hdfgroup.org/HDF5/
HDF Helpdesk: help@hdfgroup.org
HDF Mailing Lists: http://hdfgroup.org/services/support.html
November 3-5, 2009 2HDF/HDF-EOS Workshop XIII

3.
www.hdfgroup.org
HDF5 is the second HDF format
• Development started in 1996
• First release was in 1998
HDF4 is the first HDF format
• Originally called HDF
• Development started in 1987
• Still supported by The HDF Group
HDF = Hierarchical Data Format
November 3-5, 2009 3HDF/HDF-EOS Workshop XIII

4.
www.hdfgroup.org
HDF5 is like…
5
November 3-5, 2009 4HDF/HDF-EOS Workshop XIII

5.
www.hdfgroup.org
HDF5 is designed …
• for high volume and/or complex data
• for every size and type of system (portable)
• for flexible, efficient storage and I/O
• to enable applications to evolve in their use of
HDF5 and to accommodate new models
• to support long-term data preservation
November 3-5, 2009 5HDF/HDF-EOS Workshop XIII

6.
www.hdfgroup.org
HDF5 Technology
HDF5 is a data model, library and file format for
managing data.
November 3-5, 2009 HDF/HDF-EOS Workshop XIII 6

7.
www.hdfgroup.org
HDF5 Technology
• HDF5 (Abstract) Data Model
• Defines the “building blocks” for data organization and
specification
• Files, Groups, Datasets, Attributes, Datatypes, Dataspaces, …
• HDF5 Library (C, Fortran 90, C++ APIs)
• Also Java Language Interface and High Level Libraries
• HDF5 Binary File Format
• Bit-level organization of HDF5 file
• Defined by HDF5 File Format Specification
• Tools For Accessing Data in HDF5 Format
• h5dump, h5repack, HDFView, …
November 3-5, 2009 7HDF/HDF-EOS Workshop XIII

8.
www.hdfgroup.org
The HDF Group
HDF5 Abstract Data Model
a.k.a. HDF5 Logical Data Model
a.k.a. HDF5 Data Model
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9.
www.hdfgroup.org
HDF5 File
lat | lon | temp
----|-----|-----
12 | 23 | 3.1
15 | 24 | 4.2
17 | 21 | 3.6An HDF5 file is a
container that
holds data
objects.
Experim
ent Notes:
Serial Number: 99378920
Date: 3/13/09
Configuration: Standard
3
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10.
www.hdfgroup.org
HDF5 Groups and Links
lat | lon | templat | lon | temp
----|-----|---------|-----|-----
12 | 23 | 3.112 | 23 | 3.1
15 | 24 | 4.215 | 24 | 4.2
17 | 21 | 3.617 | 21 | 3.6
Experiment Notes:
Serial Number: 99378920
Date: 3/13/09
Configuration: Standard 3
/
SimOutViz
HDF5 groups
and links
organize
data objects.
November 3-5, 2009 10HDF/HDF-EOS Workshop XIII

11.
www.hdfgroup.org
HDF5 Objects
• HDF5 Group: A grouping structure containing
zero or more HDF5 objects
• HDF5 Dataset: Raw data elements, together
with information that describes them
(There are other HDF5 objects that help support
Groups and Datasets.)
The two primary HDF5 objects are:
November 3-5, 2009 11HDF/HDF-EOS Workshop XIII

12.
www.hdfgroup.org
HDF5 Groups
“/”
A
B
C
k
l
temp
• Used to organize collections
• Every file starts with a root group
• Similar to UNIX directories
• Path to object defines it
• Objects can be shared:
/A/k and /B/l are the same
= Group
= Dataset
November 3-5, 2009 12HDF/HDF-EOS Workshop XIII
temp

13.
www.hdfgroup.org
HDF5 Datasets
HDF5 Datasets organize and contain your
“raw data values”. They consist of:
• Your raw data
• Metadata describing the data:
- The information to interpret the data (Datatype)
- The information to describe the logical layout of the
data elements (Dataspace)
- Characteristics of the data (Properties)
- Additional optional information that describes the
data (Attributes)
November 3-5,
2009 HDF/HDF-EOS Workshop XIII 13

14.
www.hdfgroup.org
HDF5 Dataset
DataMetadata
Dataspace
3
RankRank
Dim_2 = 5
Dim_1 = 4
DimensionsDimensions
Time = 32.4
Pressure = 987
Temp = 56
(optional)(optional)
AttributesAttributes
Chunked
Compressed
Dim_3 = 7
PropertiesProperties
Integer
DatatypeDatatype
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15.
www.hdfgroup.org
HDF5 Dataspaces
An HDF5 Dataspace describes the logical layout
for the data elements:
• Array
• multiple elements in dataset organized in a
multi-dimensional (rectangular) array
• maximum number of elements in each
dimension may be fixed or unlimited
• NULL
• no elements in dataset
• Scalar
• single element in dataset
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16.
www.hdfgroup.org
HDF5 Dataspaces
Two roles:
Dataspace contains spatial information (logical
layout) about a dataset
stored in a file
• Rank and dimensions
• Permanent part of dataset
definition
Partial I/0: Dataspace describes application’s data
buffer and data elements participating in I/O
Rank = 2Rank = 2
Dimensions = 4x6Dimensions = 4x6
Rank = 1Rank = 1
Dimension = 10Dimension = 10
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17.
www.hdfgroup.org
HDF5 Datatypes
The HDF5 datatype describes how to interpret
individual data elements.
HDF5 datatypes include:
− integer, float, unsigned, bitfield, …
− user-definable (e.g., 13-bit integer)
− variable length types (e.g., strings)
− references to objects/dataset regions
− enumerations - names mapped to integers
− opaque
− compound (similar to C structs)
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18.
www.hdfgroup.org
HDF5 Dataset
Dataspace: Rank = 2
Dimensions = 5 x 3
November 3-5, 2009 19HDF/HDF-EOS Workshop XIII
Datatype: 16-byte integer
3
5
V

19.
www.hdfgroup.org
HDF5 Properties
• Properties (also known as Property Lists)
are characteristics of HDF5 objects that can
be modified
• Default properties handle most needs
• By changing properties one can take
advantage of the more powerful features in
HDF5
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20.
www.hdfgroup.org
Storage Properties
November 3-5, 2009 HDF/HDF-EOS Workshop XIII 21
ChunkedChunked
Chunked &Chunked &
CompressedCompressed
Better access time
for subsets;
extensible
Improves storage
efficiency,
transmission speed
ContiguousContiguous
(default)(default)
Data elements
stored physically
adjacent to each
other

21.
www.hdfgroup.org
HDF5 Attributes (optional)
• An HDF5 attribute has a name and a value
• Attributes typically contain user metadata
• Attributes may be associated with
- HDF5 groups
- HDF5 datasets
- HDF5 named datatypes
• An attribute’s value is described by a datatype and a
dataspace
• Attributes are analogous to datasets except…
- they are NOT extensible
- they do NOT support compression or partial I/O
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22.
www.hdfgroup.org
HDF5 Abstract Data Model Summary
• The Objects in the Data Model are the “building
blocks” for data organization and specification
• Files, Groups, Links, Datasets, Datatypes,
Dataspaces, Attributes, …
• Projects using HDF5 “map” their data concepts to
these HDF5 Objects
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23.
www.hdfgroup.org
The HDF Group
HDF5 Software
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24.
www.hdfgroup.org
HDF5 Software Layers & Storage
HDF5 File
Format File Split
Files
File on
Parallel
Filesystem
Other
I/O Drivers
Virtual File
Layer Posix
I/O
Split
Files MPI I/O Custom
Internals
Memory
Mgmt
Datatype
Conversion
Filters
Chunked
Storage
Version
Compatibility
and so
on…
Language
Interfaces
C, Fortran, C++
HDF5 Data Model
Objects
Groups, Datasets, Attributes, …
Tunable Properties
Chunk Size, I/O Driver, …
h5dump
toolHigh Level
APIs
HDFview
tool
h5repack
tool
Java Interface
…
API
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25.
www.hdfgroup.org
HDF5 API and Applications
…
Storage
Domain Data
Objects
EOS
library
Applications
aClimate
Model
MATLAB
November 3-5, 2009 26HDF/HDF-EOS Workshop XIII
HDF5 Library

26.
www.hdfgroup.org
HDF5 Home Page
HDF5 home page: http://hdfgroup.org/HDF5/
• Two releases: HDF5 1.8 and HDF5 1.6
HDF5 source code:
• Written in C, and includes optional C++, Fortran 90 APIs,
and High Level APIs
• Contains command-line utilities (h5dump, h5repack,
h5diff, ..) and compile scripts
HDF pre-built binaries:
• When possible, include C, C++, F90, and High Level
libraries. Check ./lib/libhdf5.settings file.
• Built with and require the SZIP and ZLIB external libraries
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27.
www.hdfgroup.org
Useful Tools For New Users
h5dump:
Tool to “dump” or display contents of HDF5 files
h5cc, h5c++, h5fc:
Scripts to compile applications
HDFView:
Java browser to view HDF4 and HDF5 files
http://www.hdfgroup.org/hdf-java-html/hdfview/
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28.
www.hdfgroup.org
h5dump Utility
h5dump [options] [file]
-H, --header Display header only – no data
-d <names> Display the specified dataset(s).
-g <names> Display the specified group(s) and
all members.
-p Display properties.
<names> is one or more appropriate object names.
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29.
www.hdfgroup.org
Example of h5dump Output
HDF5 "dset.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 4, 6 ) / ( 4, 6 ) }
DATA {
1, 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24
}
}
}
}
“/”
‘dset’
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30.
www.hdfgroup.org
HDF5 Compile Scripts
• h5cc – HDF5 C compiler command
• h5fc – HDF5 F90 compiler command
• h5c++ – HDF5 C++ compiler command
To compile:
% h5cc h5prog.c
% h5fc h5prog.f90
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31.
www.hdfgroup.org
Compile option: -show
-show: displays the compiler commands and options
without executing them
% h5cc –show Sample_c.c
Will show the correct paths and libraries used by
the installed HDF5 library.
Will show the correct flags to specify when
building an application with that HDF5 library.
November 3-5, 2009 32HDF/HDF-EOS Workshop XIII

32.
www.hdfgroup.org
The HDF Group
Browsing HDF5 Files with
HDFView
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33.
www.hdfgroup.org
HDFView
Structure of FileStructure of File Contents
of Dataset
Contents
of Dataset
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34.
www.hdfgroup.org
HDFView File Menu
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35.
www.hdfgroup.org
HDF-EOS5 File in HDFView
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36.
www.hdfgroup.org
Introduction to
HDF5 Programming Model
and APIs
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37.
www.hdfgroup.org
Operations Supported by the API
• Create objects (groups, datasets, attributes, complex data
types, …)
• Assign storage and I/O properties to objects
• Perform complex subsetting during read/write
• Use variety of I/O “devices” (parallel, remote, etc.)
• Transform data during I/O
• Make inquiries on file and object structure, content,
properties
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38.
www.hdfgroup.org
General Programming Paradigm
• Properties of object are optionally defined
Creation properties
Access properties
• Object is opened or created
• Object is accessed, possibly many times
• Object is closed
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39.
www.hdfgroup.org
Order of Operations
• An order is imposed on operations by
argument dependencies
For Example:
A file must be opened before a dataset
-because-
the dataset open call requires a file handle
as an argument.
• Objects can be closed in any order.
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40.
www.hdfgroup.org
The General HDF5 API
• Currently C, Fortran 90, Java, and C++
bindings.
• C routines begin with prefix H5?
? is a character corresponding to the type of
object the function acts on
Example Functions:
H5D : Dataset interface e.g., H5Dread
H5F : File interface e.g., H5Fopen
H5S : dataSpace interface e.g., H5Sclose
November 3-5, 2009 41HDF/HDF-EOS Workshop XIII

41.
www.hdfgroup.org
HDF5 Defined Types
For portability, the HDF5 library has its own defined
types:
hid_t: object identifiers (native integer)
hsize_t: size used for dimensions (unsigned long or
unsigned long long)
herr_t: function return value
hvl_t: variable length datatype
For C, include hdf5.h in your HDF5 application.
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42.
www.hdfgroup.org
The HDF5 API
• For flexibility, the API is extensive
 300+ functions
• This can be daunting… but there is hope
A few functions can do a lot
Start simple
Build up knowledge as more features are
needed
Victronix
Swiss Army
Cybertool 34
November 3-5, 2009 43HDF/HDF-EOS Workshop XIII

43.
www.hdfgroup.org
Basic Functions
H5Fcreate (H5Fopen) create (open) File
H5Screate_simple/H5Screate create dataSpace
H5Dcreate (H5Dopen) create (open) Dataset
H5Dread, H5Dwrite access Dataset
H5Dclose close Dataset
H5Sclose close dataSpace
H5Fclose close File
November 3-5, 2009 44HDF/HDF-EOS Workshop XIII
NOTE: The order specified above is not required.

44.
www.hdfgroup.org
Other Common Functions
DataSpaces: H5Sselect_hyperslab (Partial I/O)
H5Sselect_elements (Partial I/O)
H5Dget_space
Groups: H5Gcreate, H5Gopen, H5Gclose
Attributes: H5Acreate, H5Aopen_name,
H5Aclose, H5Aread, H5Awrite
Property lists: H5Pcreate, H5Pclose
H5Pset_chunk, H5Pset_deflate
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45.
www.hdfgroup.org
High Level APIs
• Included along with the HDF5 library
• Simplify steps for creating, writing, and
reading objects.
• Do not entirely ‘wrap’ HDF5 library
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46.
www.hdfgroup.org
The HDF Group
Example HDF5 Code
November 3-5, 2009 47HDF/HDF-EOS Workshop XIII

47.
www.hdfgroup.org
Steps to Create a File
1. Decide on properties the file should have and
create them if necessary:
• Creation properties, like size of user block
• Access properties (improve performance)
• Use default properties (H5P_DEFAULT)
2. Create the file
3. Close the file and the property lists, as needed
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48.
www.hdfgroup.org
Code: Create a File
hid_t file_id;
herr_t status;
file_id = H5Fcreate("file.h5", H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT);
status = H5Fclose (file_id);
Note: Return codes not checked for errors in code samples.
“/” (root)“/” (root)
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49.
www.hdfgroup.org
Dataset Components
DataMetadata
Dataspace
3
RankRank
Dim_2 = 5
Dim_1 = 4
DimensionsDimensions
Chunked
Compressed
Dim_3 = 7
PropertiesProperties
Integer
DatatypeDatatype
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50.
www.hdfgroup.org
Steps to Create a Dataset
1. Define dataset characteristics
a) Datatype – integer
b) Dataspace - 4x6
c) Properties if needed, or use H5P_DEFAULT
2. Decide where to put it
• Obtain location ID:
- Group ID puts it in a Group
- File ID puts it in Root Group
3. Create dataset in file
4. Close everything
A
“/” (root)
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51.
www.hdfgroup.org
HDF5 Pre-defined Datatype Identifiers
HDF5 defines* set of Datatype Identifiers per HDF5
session.
For example:
C Type HDF5 File Type HDF5 Memory Type
int H5T_STD_I32BE H5T_NATIVE_INT
H5T_STD_I32LE
float H5T_IEEE_F32BE H5T_NATIVE_FLOAT
H5T_IEEE_F32LE
double H5T_IEEE_F64BE H5T_NATIVE_DOUBLE
H5T_IEEE_F64LE
* Value of datatype is NOT fixed
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52.
www.hdfgroup.org
Pre-defined File Datatype Identifiers
Examples:
H5T_IEEE_F64LE Eight-byte, little-endian, IEEE floating-point
H5T_STD_I32LE Four-byte, little-endian, signed two's
complement integer
NOTE: What you see in the file. Name is the same everywhere and
explicitly defines a datatype.
*STD= “An architecture with a semi-standard type like 2’s complement integer, unsigned integer…”
Architecture*
Programming
Type
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53.
www.hdfgroup.org
Pre-defined Native Datatypes
Examples of predefined native types in C:
H5T_NATIVE_INT (int)
H5T_NATIVE_FLOAT (float )
H5T_NATIVE_UINT (unsigned int)
H5T_NATIVE_LONG (long )
H5T_NATIVE_CHAR (char )
NOTE: Memory types.
Different for each machine.
Used for reading/writing.
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54.
www.hdfgroup.org
Storage Properties
November 3-5, 2009 HDF/HDF-EOS Workshop XIII 55
ChunkedChunked
Chunked &Chunked &
CompressedCompressed
Better access time
for subsets;
extensible
Improves storage
efficiency,
transmission speed
ContiguousContiguous
(default)(default)
Data elements
stored physically
adjacent to each
other

55.
www.hdfgroup.org
Code: Create a Dataset
1 hid_t file_id, dataset_id, dataspace_id;
2 hsize_t dims[2];
. herr_t status;
.
. file_id = H5Fcreate (”file.h5", H5F_ACC_TRUNC,
. H5P_DEFAULT, H5P_DEFAULT);
5 dims[0] = 4;
6 dims[1] = 6;
7 dataspace_id = H5Screate_simple (2, dims, NULL);
8 dataset_id = H5Dcreate (file_id,”A",H5T_STD_I32BE,
dataspace_id, H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);
9 status = H5Dclose (dataset_id);
10 status = H5Sclose (dataspace_id);
11 status = H5Fclose (file_id);
Define a
dataspace
rank current dims
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56.
www.hdfgroup.org
Code: Create a Dataset
1 hid_t file_id, dataset_id, dataspace_id;
. hsize_t dims[2];
. herr_t status;
.
. file_id = H5Fcreate (”file.h5", H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT);
. dims[0] = 4;
. dims[1] = 6;
. dataspace_id = H5Screate_simple (2, dims, NULL);
8 dataset_id = H5Dcreate (file_id,”A",H5T_STD_I32BE,
dataspace_id, H5P_DEFAULT,H5P_DEFAULT,
H5P_DEFAULT);
Datatype
Properties
(Link Creation,
Dataset Creation and
Access)
Where to put
it
Size &
shape
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57.
www.hdfgroup.org
Code: Create a Dataset
1 hid_t file_id, dataset_id, dataspace_id;
2 hsize_t dims[2];
3 herr_t status;
4 file_id = H5Fcreate (”file.h5", H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT);
5 dims[0] = 4;
6 dims[1] = 6;
7 dataspace_id = H5Screate_simple (2, dims, NULL);
8 dataset_id = H5Dcreate (file_id,”A",H5T_STD_I32BE,
dataspace_id, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
9 status = H5Dclose (dataset_id);
10 status = H5Sclose (dataspace_id);
11 status = H5Fclose (file_id);
Terminate access to
dataspace, dataset,
file
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58.
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Example Code - H5Dwrite
status = H5Dwrite (dataset_id, H5T_NATIVE_INT,
H5S_ALL,H5S_ALL, H5P_DEFAULT, wdata);
Dataset ID from
H5Dcreate/H5Dopen Memory Datatype
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59.
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Partial I/O
File Dataspace (disk)H5S_ALL H5S_ALL
To Modify Dataspace:
H5Sselect_hyperslab
H5Sselect_elements
November 3-5, 2009 62HDF/HDF-EOS Workshop XIII
Memory
Dataspace
status = H5Dwrite (dataset_id, H5T_NATIVE_INT,
H5S_ALL, H5S_ALL, H5P_DEFAULT,wdata);

60.
www.hdfgroup.org
Example Code – H5Dwrite
status = H5Dwrite (dataset_id, H5T_NATIVE_INT,
H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
Data Transfer Property List
(MPI I/O, Transformations,…)
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61.
www.hdfgroup.org
Example Code – H5Dread
status = H5Dread (dataset_id, H5T_NATIVE_INT,
H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
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62.
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High Level APIs: HDF5 Lite (H5LT)
#include “hdf5_hl.h“
.
.
file_id = H5Fcreate(“file.h5",H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT);
status = H5LTmake_dataset (file_id,“A",2,dims,
H5T_STD_I32BE, data);
status = H5Fclose (file_id);
November 3-5, 2009 65HDF/HDF-EOS Workshop XIII

63.
www.hdfgroup.org
Steps to Create a Group
1. Decide where to put it – “root group”
• Obtain location ID
1. Define properties or use H5P_DEFAULT
3. Create group in file.
4. Close the group.
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64.
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Example: Create a Group
A B
“/” (root)
4x6 array of
integers
file.h5
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65.
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Code: Create a Group
hid_t file_id, group_id;
...
/* Open “file.h5” */
file_id = H5Fopen (“file.h5”, H5F_ACC_RDWR,
H5P_DEFAULT);
/* Create group "/B" in file. */
group_id = H5Gcreate (file_id,"B", H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
/* Close group and file. */
status = H5Gclose (group_id);
status = H5Fclose (file_id);
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66.
www.hdfgroup.org
HDF5 Tutorial and Examples
HDF5 Tutorial:
http://www.hdfgroup.org/HDF5/Tutor/
HDF5 Example Code:
http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/
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67.
www.hdfgroup.org
The HDF Group
Thank You!
November 3-5, 2009 72HDF/HDF-EOS Workshop XIII

68.
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Acknowledgements
This work was supported by cooperative agreement
number NNX08AO77A from the National
Aeronautics and Space Administration (NASA).
Any opinions, findings, conclusions, or
recommendations expressed in this material are
those of the author[s] and do not necessarily reflect
the views of the National Aeronautics and Space
Administration.
November 3-5, 2009 HDF/HDF-EOS Workshop XIII 73

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The HDF Group
Questions/comments?
November 3-5, 2009 74HDF/HDF-EOS Workshop XIII