The HDF Group
Introduction to HDF5
Barbara Jones
The HDF Group
The 13th HDF & HDF-EOS Workshop
November 3-5, 2009
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Before We Begin …
HDF-EOS Home Page:
http://hdfeos.org/
Workshop Info:
http://hdfeos.org/workshops/ws13/workshop_thirteen.php
The HDF Group Page:
HDF5 Home Page:
HDF Helpdesk:
HDF Mailing Lists:
November 3-5, 2009
http://hdfgroup.org/
http://hdfgroup.org/HDF5/
help@hdfgroup.org
http://hdfgroup.org/services/support.html
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HDF = Hierarchical Data Format
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
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HDF5 is like…
5
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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
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HDF5 Technology
HDF5 is a data model, library and file format for
managing data.
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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, …
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The HDF Group
HDF5 Abstract Data Model
a.k.a. HDF5 Logical Data Model
a.k.a. HDF5 Data Model
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HDF5 File
lat | lon | temp
----|-----|----12 | 23 | 3.1
15 | 24 | 4.2
17 | 21 | 3.6
An HDF5 file is a
container that
holds data
objects.
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HDF5 Groups and Links
HDF5 groups
and links
organize
data objects.
/
Experiment Notes:
Serial Number: 99378920
Date: 3/13/09
Configuration: Standard 3
SimOut
Viz
lat | lon | temp
----|-----|----12 | 23 | 3.1
15 | 24 | 4.2
17 | 21 | 3.6
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HDF5 Objects
The two primary HDF5 objects are:
• 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.)
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HDF5 Groups
• 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 temp
“/”
A
k
B
C
l
temp
= Group
= Dataset
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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)
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HDF5 Dataset
Metadata
Data
Dataspace
Rank Dimensions
3
Datatype
Dim_1 = 4
Dim_2 = 5
Dim_3 = 7
Integer
(optional)
Attributes
Properties
Time = 32.4
Chunked
Pressure = 987
Compressed
Temp = 56
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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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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
Rank = 2
Dimensions = 4x6
Partial I/0: Dataspace describes application’s data
buffer and data elements participating in I/O
Rank = 1
Dimension = 10
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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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HDF5 Dataset
3
5
V
Datatype:
16-byte integer
Dataspace:
Rank = 2
Dimensions = 5 x 3
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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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Storage Properties
Data elements
stored physically
adjacent to each
other
Contiguous
(default)
Better access time
for subsets;
extensible
Chunked
Improves storage
efficiency,
transmission speed
Chunked &
Compressed
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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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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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The HDF Group
HDF5 Software
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HDF5 Library
Tools
HDF5 Software Layers & Storage
API
…
High Level
APIs
Language
Interfaces
C, Fortran, C++
Internals
Virtual File
Layer
h5dump
tool
h5repack
tool
Java Interface
HDF5 Data Model
Objects
Tunable Properties
Groups, Datasets, Attributes, …
Memory
Mgmt
Datatype
Conversion
Filters
Split
Files
Posix
I/O
HDFview
tool
Chunk Size, I/O Driver, …
Chunked
Storage
Version
Compatibility
and so
on…
Custom
MPI I/O
Storage
I/O Drivers
HDF5 File
Format
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File
Split
Files
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Parallel
Filesystem
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Other
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HDF5 API and Applications
Applications
aClimate
Model
Domain Data
Objects
EOS
library
MATLAB
…
HDF5 Library
Storage
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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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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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h5dump Utility
h5dump [options] [file]
-H, --header
-d <names>
-g <names>
-p
Display header only – no data
Display the specified dataset(s).
Display the specified group(s) and
all members.
Display properties.
<names> is one or more appropriate object names.
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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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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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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.
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The HDF Group
Browsing HDF5 Files with
HDFView
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HDFView
Structure of File
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Contents
of Dataset
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HDFView File Menu
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HDF-EOS5 File in HDFView
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Introduction to
HDF5 Programming Model
and APIs
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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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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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Order of Operations
• An order is imposed on operations by
argument dependencies
For Example:
A file must be opened before a dataset
-becausethe dataset open call requires a file handle
as an argument.
• Objects can be closed in any order.
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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
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HDF5 Defined Types
For portability, the HDF5 library has its own defined
types:
hid_t:
hsize_t:
herr_t:
object identifiers (native integer)
size used for dimensions (unsigned long or
unsigned long long)
function return value
hvl_t:
variable length datatype
For C, include hdf5.h in your HDF5 application.
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The HDF5 API
• For flexibility, the API is extensive
Victronix
Swiss Army
Cybertool
34
 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
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Basic Functions
H5Fcreate (H5Fopen)
create (open) File
H5Screate_simple/H5Screate create dataSpace
H5Dcreate (H5Dopen)
H5Dread, H5Dwrite
H5Dclose
H5Sclose
H5Fclose
create (open) Dataset
access Dataset
close Dataset
close dataSpace
close File
NOTE: The order specified above is not required.
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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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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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The HDF Group
Example HDF5 Code
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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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Code: Create a File
hid_t
herr_t
file_id;
status;
file_id = H5Fcreate("file.h5", H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT);
status = H5Fclose (file_id);
“/” (root)
Note: Return codes not checked for errors in code samples.
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Dataset Components
Metadata
Data
Dataspace
Rank Dimensions
3
Dim_1 = 4
Dim_2 = 5
Dim_3 = 7
Datatype
Integer
Properties
Chunked
Compressed
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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
•
“/” (root)
Obtain location ID:
- Group ID puts it in a Group
- File ID puts it in Root Group
A
3. Create dataset in file
4. Close everything
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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_STD_I32LE
H5T_NATIVE_INT
float
H5T_IEEE_F32BE
H5T_IEEE_F32LE
H5T_NATIVE_FLOAT
double
H5T_IEEE_F64BE
H5T_IEEE_F64LE
H5T_NATIVE_DOUBLE
* Value of datatype is NOT fixed
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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
Architecture*
Programming
Type
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…”
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Pre-defined Native Datatypes
Examples of predefined native types in C:
H5T_NATIVE_INT
H5T_NATIVE_FLOAT
H5T_NATIVE_UINT
H5T_NATIVE_LONG
H5T_NATIVE_CHAR
(int)
(float )
(unsigned int)
(long )
(char )
NOTE: Memory types.
Different for each machine.
Used for reading/writing.
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Storage Properties
Data elements
stored physically
adjacent to each
other
Contiguous
(default)
Better access time
for subsets;
extensible
Chunked
Improves storage
efficiency,
transmission speed
Chunked &
Compressed
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Code: Create a Dataset
1
2
.
.
.
.
5
6
7
hid_t
hsize_t
herr_t
file_id, dataset_id, dataspace_id;
dims[2];
status;
file_id = H5Fcreate (”file.h5",
H5F_ACC_TRUNC,
Define a
dataspace
H5P_DEFAULT, H5P_DEFAULT);
dims[0] = 4;
current dims
rank
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);
9 status = H5Dclose (dataset_id);
10 status = H5Sclose (dataspace_id);
11 status = H5Fclose (file_id);
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Code: Create a Dataset
1
.
.
.
.
.
.
.
8
hid_t
hsize_t
herr_t
file_id, dataset_id, dataspace_id;
dims[2];
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);
Where to put it
Datatype
dataset_id = H5Dcreate (file_id,”A",H5T_STD_I32BE,
dataspace_id, H5P_DEFAULT,H5P_DEFAULT,
H5P_DEFAULT);
Size & shape
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Properties
(Link Creation, Dataset
Creation and Access)
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Code: Create a Dataset
1
2
3
hid_t
hsize_t
herr_t
file_id, dataset_id, dataspace_id;
dims[2];
status;
4
file_id = H5Fcreate (”file.h5", H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT);
5
6
7
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);
Terminate access to
9 status = H5Dclose (dataset_id);
10 status = H5Sclose (dataspace_id);
11 status = H5Fclose (file_id);
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Example Code - H5Dwrite
Dataset ID from
H5Dcreate/H5Dopen
Memory Datatype
status = H5Dwrite (dataset_id, H5T_NATIVE_INT,
H5S_ALL,H5S_ALL, H5P_DEFAULT, wdata);
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Partial I/O
status = H5Dwrite (dataset_id, H5T_NATIVE_INT,
H5S_ALL, H5S_ALL, H5P_DEFAULT,wdata);
Memory
Dataspace
H5S_ALL
H5S_ALL
File Dataspace (disk)
To Modify Dataspace:
H5Sselect_hyperslab
H5Sselect_elements
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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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Example Code – H5Dread
status = H5Dread (dataset_id, H5T_NATIVE_INT,
H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
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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);
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Steps to Create a Group
1. Decide where to put it – “root group”
•
Obtain location ID
2. Define properties or use H5P_DEFAULT
3. Create group in file.
4. Close the group.
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Example: Create a Group
“/” (root)
A
B
4x6 array of
integers
file.h5
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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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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/
November 3-5, 2009
HDF/HDF-EOS Workshop XIII
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The HDF Group
Thank You!
November 3-5, 2009
HDF/HDF-EOS Workshop XIII
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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
HDF/HDF-EOS Workshop XIII
74
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