Introduction to HDF5
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Transcript of Introduction to HDF5
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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
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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: http://hdfgroup.org/
HDF5 Home Page: http://hdfgroup.org/HDF5/
HDF Helpdesk: [email protected]
HDF Mailing Lists:http://hdfgroup.org/services/support.html
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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
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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 | 3.6An HDF5 file is a
container that holds data objects.
Experiment Notes:
Serial Number: 99378920
Date: 3/13/09
Configuration: Standard 3
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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: 99378920Date: 3/13/09Configuration: Standard 3
/
SimOutViz
HDF5 groups and links organize data objects.
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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:
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HDF5 Groups
“/”A B
C
k ltemp
• 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
• 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
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temp
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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
DataMetadataDataspace
3
RankRank
Dim_2 = 5Dim_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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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 15HDF/HDF-EOS Workshop XIII
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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
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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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
Dataspace: Rank = 2 Dimensions = 5 x 3
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Datatype: 16-byte integer
3
5
V
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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
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ChunkedChunked
Chunked & Chunked & CompressedCompressed
Better access time for subsets; extensible
Improves storage efficiency, transmission speed
ContiguousContiguous(default)(default)ContiguousContiguous(default)(default)
Data elements stored physically adjacent to each other
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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/ONovember 3-5, 2009 22HDF/HDF-EOS Workshop XIII
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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 Software Layers & Storage
HDF5 File Format File Split
Files
File on Parallel Filesystem
Other
I/O Drivers
Virtual File Layer Posix
I/OSplit Files MPI I/O Custom
Internals Memory Mgmt
Datatype Conversion
FiltersChunked Storage
Version Compatibility
and so on…
LanguageInterfaces
C, Fortran, C++
HDF5 Data Model Objects
Groups, Datasets, Attributes, …
Tunable PropertiesChunk Size, I/O Driver, …
h5dumptoolHigh Level
APIs
HDFview tool
h5repack tool
Java Interface…
API
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HDF5 API and Applications
…
Storage
Domain DataObjects
EOSlibrary
ApplicationsaClimate
ModelMATLAB
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HDF5 Library
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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/
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 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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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’‘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 FileStructure of File Contents of DatasetContents 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 propertiesAccess 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 -because-
the dataset open call requires a file handle
as an argument.
• Objects can be closed in any order.November 3-5, 2009 40HDF/HDF-EOS Workshop XIII
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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: 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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The HDF5 API
• For flexibility, the API is extensive 300+ functions
• This can be daunting… but there is hopeA few functions can do a lotStart simple Build up knowledge as more features are
needed
Victronix Swiss Army Cybertool 34
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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
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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 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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Dataset Components
DataMetadataDataspace
3
RankRank
Dim_2 = 5Dim_1 = 4
DimensionsDimensions
Chunked
Compressed
Dim_3 = 7
PropertiesProperties
Integer DatatypeDatatype
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Steps to Create a Dataset
1. Define dataset characteristicsa) 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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HDF5 Pre-defined Datatype Identifiers
HDF5 defines* set of Datatype Identifiers per HDF5 session.
For example:
C Type HDF5 File Type HDF5 Memory Typeint 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_DOUBLEH5T_IEEE_F64LE
* 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-pointH5T_STD_I32LE Four-byte, little-endian, signed two's
complement integer
NOTE: What you see in the file. Name is the same everywhere andexplicitly defines a datatype.
*STD= “An architecture with a semi-standard type like 2’s complement integer, unsigned integer…”
Architecture*ProgrammingType
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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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Storage Properties
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ChunkedChunked
Chunked & Chunked & CompressedCompressed
Better access time for subsets; extensible
Improves storage efficiency, transmission speed
ContiguousContiguous(default)(default)ContiguousContiguous(default)(default)
Data elements stored physically adjacent to each other
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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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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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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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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Partial I/O
File Dataspace (disk)H5S_ALLH5S_ALL H5S_ALLH5S_ALL
To Modify Dataspace: H5Sselect_hyperslab H5Sselect_elements
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Memory Dataspace
status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,wdata);
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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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
A B“/” (root)
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/
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The HDF Group
Thank You!
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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.
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The HDF Group
Questions/comments?
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