The HDF Group

Introduction to HDF5
Barbara Jones
The HDF Group
The 13th HDF & HDF-EOS Workshop
November 3-5, 2009
Novembe...
Before We Begin …

HDF-EOS Home Page:
http://hdfeos.org/
Workshop Info:
http://hdfeos.org/workshops/ws13/workshop_thirteen...
HDF = Hierarchical Data Format
HDF5 is the second HDF format
• Development started in 1996
• First release was in 1998

HD...
HDF5 is like…

5

November 3-5, 2009

HDF/HDF-EOS Workshop XIII

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HDF5 is designed …
• for high volume and/or complex data
• for every size and type of system (portable)
• for flexible, ef...
HDF5 Technology

HDF5 is a data model, library and file format for
managing data.

November 3-5, 2009

HDF/HDF-EOS Worksho...
HDF5 Technology
• HDF5 (Abstract) Data Model
•
•

Defines the “building blocks” for data organization and
specification
Fi...
The HDF Group

HDF5 Abstract Data Model
a.k.a. HDF5 Logical Data Model
a.k.a. HDF5 Data Model
November 3-5, 2009

HDF/HDF-...
HDF5 File

lat | lon | temp
----|-----|----12 |eEx23 | 3.1
S pe
D ri rim
Nu
C at
15onf|e: 3a/l24ent|o 4.2
m N
ig 13 be te
...
HDF5 Groups and Links
HDF5 groups
and links
organize
data objects.

/

Experiment Notes:
Serial Number: 99378920
Date: 3/1...
HDF5 Objects
The two primary HDF5 objects are:
• HDF5 Group: A grouping structure containing
zero or more HDF5 objects
• H...
HDF5 Groups
• Used to organize collections
• Every file starts with a root group
• Similar to UNIX directories
• Path to o...
HDF5 Datasets
HDF5 Datasets organize and contain your
“raw data values”. They consist of:
• Your raw data
• Metadata descr...
HDF5 Dataset
Metadata

Data

Dataspace

Rank Dimensions
3

Datatype
Integer

Properties

Dim_1 = 4
Dim_2 = 5
Dim_3 = 7

(o...
HDF5 Dataspaces
An HDF5 Dataspace describes the logical layout
for the data elements:
• Array
• multiple elements in datas...
HDF5 Dataspaces
Two roles:
Dataspace contains spatial information (logical
layout) about a dataset
stored in a file
• Rank...
HDF5 Datatypes
The HDF5 datatype describes how to interpret
individual data elements.
HDF5 datatypes include:
− integer, f...
HDF5 Dataset
3

5

V

Datatype:

16-byte integer

Dataspace:

Rank = 2
Dimensions = 5 x 3

November 3-5, 2009

HDF/HDF-EOS...
HDF5 Properties
• Properties (also known as Property Lists)
are characteristics of HDF5 objects that can
be modified
• Def...
Storage Properties
Data elements
stored physically
adjacent to each
other

Contiguous
(default)

Better access time
for su...
HDF5 Attributes (optional)
• An HDF5 attribute has a name and a value
• Attributes typically contain user metadata
• Attri...
HDF5 Abstract Data Model Summary
• The Objects in the Data Model are the “building
blocks” for data organization and speci...
The HDF Group

HDF5 Software

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HDF/HDF-EOS Workshop XIII

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HDF5 Software Layers & Storage
API
High Level
APIs

…

Language
Interfaces
C, Fortran, C++
Internals
Virtual File
Layer

h...
HDF5 API and Applications
Applications

aClimate
Model

Domain Data
Objects

EOS
library

MATLAB

…

HDF5 Library

Storage...
HDF5 Home Page
HDF5 home page: http://hdfgroup.org/HDF5/
•

Two releases: HDF5 1.8 and HDF5 1.6

HDF5 source code:
• Writt...
Useful Tools For New Users
h5dump:
Tool to “dump” or display contents of HDF5 files
h5cc, h5c++, h5fc:
Scripts to compile ...
h5dump Utility
h5dump [options] [file]
-H, --header
-d <names>
-g <names>
-p

Display header only – no data
Display the sp...
Example of h5dump Output
HDF5 "dset.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 4, ...
HDF5 Compile Scripts
• h5cc – HDF5 C compiler command
• h5fc – HDF5 F90 compiler command
• h5c++ – HDF5 C++ compiler comma...
Compile option: -show
-show: displays the compiler commands and options
without executing them
% h5cc –show Sample_c.c

Wi...
The HDF Group

Browsing HDF5 Files with
HDFView

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HDFView

Structure of File

November 3-5, 2009

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 an...
General Programming Paradigm
• Properties of object are optionally defined
Creation properties
Access properties

• Obje...
Order of Operations
• An order is imposed on operations by
argument dependencies
For Example:
A file must be opened before...
The General HDF5 API
• Currently C, Fortran 90, Java, and C++
bindings.
• C routines begin with prefix H5?
? is a characte...
HDF5 Defined Types
For portability, the HDF5 library has its own defined
types:
hid_t:
hsize_t:
herr_t:

object identifier...
The HDF5 API
• For flexibility, the API is extensive

Victronix
Swiss Army
Cybertool 34

 300+ functions

• This can be d...
Basic Functions
H5Fcreate (H5Fopen)

create (open) File

H5Screate_simple/H5Screate create dataSpace
H5Dcreate (H5Dopen)
H...
Other Common Functions
DataSpaces:

H5Sselect_hyperslab (Partial I/O)
H5Sselect_elements (Partial I/O)
H5Dget_space

Group...
High Level APIs
• Included along with the HDF5 library
• Simplify steps for creating, writing, and
reading objects.
• Do n...
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 properti...
Code: Create a File

hid_t
herr_t

file_id;
status;

file_id = H5Fcreate("file.h5", H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAUL...
Dataset Components

Data

Metadata
Dataspace

Rank Dimensions
3

Dim_1 = 4
Dim_2 = 5
Dim_3 = 7

Datatype
Integer

Properti...
Steps to Create a Dataset
1. Define dataset characteristics
a) Datatype – integer
b) Dataspace - 4x6
c) Properties if need...
HDF5 Pre-defined Datatype Identifiers
HDF5 defines* set of Datatype Identifiers per HDF5
session.
For example:
C Type

HDF...
Pre-defined File Datatype Identifiers
Examples:
H5T_IEEE_F64LE Eight-byte, little-endian, IEEE floating-point
H5T_STD_I32L...
Pre-defined Native Datatypes
Examples of predefined native types in C:
H5T_NATIVE_INT
H5T_NATIVE_FLOAT
H5T_NATIVE_UINT
H5T...
Storage Properties
Data elements
stored physically
adjacent to each
other

Contiguous
(default)

Better access time
for su...
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_...
Code: Create a Dataset
1
.
.
.
.
.
.
.
8

hid_t
hsize_t
herr_t

file_id, dataset_id, dataspace_id;
dims[2];
status;

file_...
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 = H5Fc...
Example Code - H5Dwrite
Dataset ID from
H5Dcreate/H5Dopen

Memory Datatype

status = H5Dwrite (dataset_id, H5T_NATIVE_INT,...
Partial I/O
status = H5Dwrite (dataset_id, H5T_NATIVE_INT,
H5S_ALL, H5S_ALL, H5P_DEFAULT,wdata);
Memory
Dataspace

H5S_ALL...
Example Code – H5Dwrite

status = H5Dwrite (dataset_id, H5T_NATIVE_INT,
H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);

Data Trans...
Example Code – H5Dread

status = H5Dread (dataset_id, H5T_NATIVE_INT,
H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);

November 3-5...
High Level APIs: HDF5 Lite (H5LT)
#include “hdf5_hl.h“
.
.
file_id = H5Fcreate(“file.h5",H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_D...
Steps to Create a Group
1. Decide where to put it – “root group”
•

Obtain location ID

1. Define properties or use H5P_DE...
Example: Create a Group
“/” (root)
A

B

4x6 array of
integers

file.h5

November 3-5, 2009

HDF/HDF-EOS Workshop XIII

68...
Code: Create a Group
hid_t file_id, group_id;
...
/* Open “file.h5” */
file_id = H5Fopen (“file.h5”, H5F_ACC_RDWR,
H5P_DEF...
HDF5 Tutorial and Examples
HDF5 Tutorial:
http://www.hdfgroup.org/HDF5/Tutor/

HDF5 Example Code:
http://www.hdfgroup.org/...
The HDF Group

Thank You!

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Acknowledgements
This work was supported by cooperative agreement
number NNX08AO77A from the National
Aeronautics and Spac...
The HDF Group

Questions/comments?

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Introduction to HDF5

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This 2009 tutorial slide will cover basic HDF5 Data Model objects and their properties. It will include an overview of the HDF5 Libraries and APIs, and describe the HDF5 programming model. Simple programming examples and the HDFView data browser will be used to illustrate HDF5 concepts and start developing your own HDF5 based applications.

This tutorial is for new HDF5 users.

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  • Data Array is an ordered collection of identically typed data items distinguished by their indices
    Metadata:
    Dataspace – Rank, dimensions; spatial info about dataset
    Datatype – Information on how to interpret your data
    Storage Properties – How array is organized
    Attributes – User-defined metadata (optional)
  • To create this file, we would start by creating the file itself. When you create a file, the root group gets created with it. So every file has at least that one group.
  • Introduction to HDF5

    1. 1. 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 HDF/HDF-EOS Workshop XIII 1 www.hdfgroup.org
    2. 2. 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 HDF/HDF-EOS Workshop XIII 2 www.hdfgroup.org
    3. 3. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 3 www.hdfgroup.org
    4. 4. HDF5 is like… 5 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 4 www.hdfgroup.org
    5. 5. 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 HDF/HDF-EOS Workshop XIII 5 www.hdfgroup.org
    6. 6. HDF5 Technology HDF5 is a data model, library and file format for managing data. November 3-5, 2009 HDF/HDF-EOS Workshop XIII 6 www.hdfgroup.org
    7. 7. 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 HDF/HDF-EOS Workshop XIII 7 www.hdfgroup.org
    8. 8. The HDF Group HDF5 Abstract Data Model a.k.a. HDF5 Logical Data Model a.k.a. HDF5 Data Model November 3-5, 2009 HDF/HDF-EOS Workshop XIII 8 www.hdfgroup.org
    9. 9. HDF5 File lat | lon | temp ----|-----|----12 |eEx23 | 3.1 S pe D ri rim Nu C at 15onf|e: 3a/l24ent|o 4.2 m N ig 13 be te ur /0 r: s: 9 17 | ati21 |99373.6 on An HDF5 file is a container that holds data objects. November 3-5, 2009 :S HDF/HDF-EOS Workshop XIII 89 ta 20 nd ar d 3 9 www.hdfgroup.org
    10. 10. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 10 www.hdfgroup.org
    11. 11. 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.) November 3-5, 2009 HDF/HDF-EOS Workshop XIII 11 www.hdfgroup.org
    12. 12. 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 l C temp = Group = Dataset November 3-5, 2009 HDF/HDF-EOS Workshop XIII 12 www.hdfgroup.org
    13. 13. 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 www.hdfgroup.org
    14. 14. HDF5 Dataset Metadata Data Dataspace Rank Dimensions 3 Datatype Integer Properties Dim_1 = 4 Dim_2 = 5 Dim_3 = 7 (optional) Attributes Time = 32.4 Chunked Pressure = 987 Compressed Temp = 56 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 14 www.hdfgroup.org
    15. 15. 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 • November 3-5, 2009 HDF/HDF-EOS Workshop XIII 15 www.hdfgroup.org
    16. 16. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 16 www.hdfgroup.org
    17. 17. 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) November 3-5, 2009 HDF/HDF-EOS Workshop XIII 17 www.hdfgroup.org
    18. 18. HDF5 Dataset 3 5 V Datatype: 16-byte integer Dataspace: Rank = 2 Dimensions = 5 x 3 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 19 www.hdfgroup.org
    19. 19. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 20 www.hdfgroup.org
    20. 20. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 21 www.hdfgroup.org
    21. 21. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 22 www.hdfgroup.org
    22. 22. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 23 www.hdfgroup.org
    23. 23. The HDF Group HDF5 Software November 3-5, 2009 HDF/HDF-EOS Workshop XIII 24 www.hdfgroup.org
    24. 24. HDF5 Software Layers & Storage API High Level APIs … Language Interfaces C, Fortran, C++ Internals Virtual File Layer h5dump tool h5repack tool HDF5 Data Model Objects Datatype Conversion Filters Split Files Posix I/O Java Interface Tunable Properties Groups, Datasets, Attributes, … Memory Mgmt HDFview tool Chunk Size, I/O Driver, … Chunked Storage Version Compatibility and so on… Custom MPI I/O I/O Drivers HDF5 File Format November 3-5, 2009 File Split Files HDF/HDF-EOS Workshop XIII File on Parallel Filesystem 25 Other www.hdfgroup.org
    25. 25. HDF5 API and Applications Applications aClimate Model Domain Data Objects EOS library MATLAB … HDF5 Library Storage November 3-5, 2009 HDF/HDF-EOS Workshop XIII 26 www.hdfgroup.org
    26. 26. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 27 www.hdfgroup.org
    27. 27. 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/ November 3-5, 2009 HDF/HDF-EOS Workshop XIII 28 www.hdfgroup.org
    28. 28. 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. November 3-5, 2009 HDF/HDF-EOS Workshop XIII 29 www.hdfgroup.org
    29. 29. 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’ } } November 3-5, 2009 HDF/HDF-EOS Workshop XIII 30 www.hdfgroup.org
    30. 30. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 31 www.hdfgroup.org
    31. 31. 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 HDF/HDF-EOS Workshop XIII 32 www.hdfgroup.org
    32. 32. The HDF Group Browsing HDF5 Files with HDFView November 3-5, 2009 HDF/HDF-EOS Workshop XIII 33 www.hdfgroup.org
    33. 33. HDFView Structure of File November 3-5, 2009 Contents of Dataset HDF/HDF-EOS Workshop XIII 34 www.hdfgroup.org
    34. 34. HDFView File Menu November 3-5, 2009 HDF/HDF-EOS Workshop XIII 35 www.hdfgroup.org
    35. 35. HDF-EOS5 File in HDFView November 3-5, 2009 HDF/HDF-EOS Workshop XIII 36 www.hdfgroup.org
    36. 36. Introduction to HDF5 Programming Model and APIs November 3-5, 2009 HDF/HDF-EOS Workshop XIII 37 www.hdfgroup.org
    37. 37. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 38 www.hdfgroup.org
    38. 38. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 39 www.hdfgroup.org
    39. 39. 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. November 3-5, 2009 HDF/HDF-EOS Workshop XIII 40 www.hdfgroup.org
    40. 40. 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 H5F : File interface e.g., H5Dread e.g., H5Fopen H5S : dataSpace interface e.g., H5Sclose November 3-5, 2009 HDF/HDF-EOS Workshop XIII 41 www.hdfgroup.org
    41. 41. 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. November 3-5, 2009 HDF/HDF-EOS Workshop XIII 42 www.hdfgroup.org
    42. 42. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 43 www.hdfgroup.org
    43. 43. 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. November 3-5, 2009 HDF/HDF-EOS Workshop XIII 44 www.hdfgroup.org
    44. 44. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 45 www.hdfgroup.org
    45. 45. High Level APIs • Included along with the HDF5 library • Simplify steps for creating, writing, and reading objects. • Do not entirely ‘wrap’ HDF5 library November 3-5, 2009 HDF/HDF-EOS Workshop XIII 46 www.hdfgroup.org
    46. 46. The HDF Group Example HDF5 Code November 3-5, 2009 HDF/HDF-EOS Workshop XIII 47 www.hdfgroup.org
    47. 47. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 48 www.hdfgroup.org
    48. 48. 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. November 3-5, 2009 HDF/HDF-EOS Workshop XIII 49 www.hdfgroup.org
    49. 49. Dataset Components Data Metadata Dataspace Rank Dimensions 3 Dim_1 = 4 Dim_2 = 5 Dim_3 = 7 Datatype Integer Properties Chunked Compressed November 3-5, 2009 HDF/HDF-EOS Workshop XIII 50 www.hdfgroup.org
    50. 50. 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 “/” (root) A 3. Create dataset in file 4. Close everything November 3-5, 2009 HDF/HDF-EOS Workshop XIII 51 www.hdfgroup.org
    51. 51. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 52 www.hdfgroup.org
    52. 52. 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…” November 3-5, 2009 HDF/HDF-EOS Workshop XIII 53 www.hdfgroup.org
    53. 53. 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. November 3-5, 2009 HDF/HDF-EOS Workshop XIII 54 www.hdfgroup.org
    54. 54. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 55 www.hdfgroup.org
    55. 55. 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 H5P_DEFAULT, H5P_DEFAULT); dataspace 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); November 3-5, 2009 HDF/HDF-EOS Workshop XIII 58 www.hdfgroup.org
    56. 56. 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 Datatype it dataset_id = H5Dcreate (file_id,”A",H5T_STD_I32BE, dataspace_id, H5P_DEFAULT,H5P_DEFAULT, H5P_DEFAULT); Size & shape November 3-5, 2009 HDF/HDF-EOS Workshop XIII Properties (Link Creation, Dataset Creation and Access) 59 www.hdfgroup.org
    57. 57. 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 dataspace, dataset, 9 status = H5Dclose (dataset_id); file 10 status = H5Sclose (dataspace_id); 11 status = H5Fclose (file_id); November 3-5, 2009 HDF/HDF-EOS Workshop XIII 60 www.hdfgroup.org
    58. 58. Example Code - H5Dwrite Dataset ID from H5Dcreate/H5Dopen Memory Datatype status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL,H5S_ALL, H5P_DEFAULT, wdata); November 3-5, 2009 HDF/HDF-EOS Workshop XIII 61 www.hdfgroup.org
    59. 59. 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 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 62 www.hdfgroup.org
    60. 60. 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,…) November 3-5, 2009 HDF/HDF-EOS Workshop XIII 63 www.hdfgroup.org
    61. 61. Example Code – H5Dread status = H5Dread (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata); November 3-5, 2009 HDF/HDF-EOS Workshop XIII 64 www.hdfgroup.org
    62. 62. 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 HDF/HDF-EOS Workshop XIII 65 www.hdfgroup.org
    63. 63. 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. November 3-5, 2009 HDF/HDF-EOS Workshop XIII 67 www.hdfgroup.org
    64. 64. Example: Create a Group “/” (root) A B 4x6 array of integers file.h5 November 3-5, 2009 HDF/HDF-EOS Workshop XIII 68 www.hdfgroup.org
    65. 65. 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); November 3-5, 2009 HDF/HDF-EOS Workshop XIII 70 www.hdfgroup.org
    66. 66. 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 71 www.hdfgroup.org
    67. 67. The HDF Group Thank You! November 3-5, 2009 HDF/HDF-EOS Workshop XIII 72 www.hdfgroup.org
    68. 68. 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 www.hdfgroup.org
    69. 69. The HDF Group Questions/comments? November 3-5, 2009 HDF/HDF-EOS Workshop XIII 74 www.hdfgroup.org

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