Your SlideShare is downloading. ×
0
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Hdf5 intro
Upcoming SlideShare
Loading in...5
×

Thanks for flagging this SlideShare!

Oops! An error has occurred.

×
Saving this for later? Get the SlideShare app to save on your phone or tablet. Read anywhere, anytime – even offline.
Text the download link to your phone
Standard text messaging rates apply

Hdf5 intro

3,271

Published on

Introduction to HDF5

Introduction to HDF5

0 Comments
3 Likes
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total Views
3,271
On Slideshare
0
From Embeds
0
Number of Embeds
3
Actions
Shares
0
Downloads
46
Comments
0
Likes
3
Embeds 0
No embeds

Report content
Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
No notes for slide
  • 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.
  • Transcript

    • 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 November 3-5, 2009 8HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 9HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 14HDF/HDF-EOS Workshop XIII
    • 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 •November 3-5, 2009 15HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 16HDF/HDF-EOS Workshop XIII
    • 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) November 3-5, 2009 17HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 20HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 22HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 23HDF/HDF-EOS Workshop XIII
    • 23. www.hdfgroup.org The HDF Group HDF5 Software November 3-5, 2009 24HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 25HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 27HDF/HDF-EOS Workshop XIII
    • 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/ November 3-5, 2009 28HDF/HDF-EOS Workshop XIII
    • 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. November 3-5, 2009 29HDF/HDF-EOS Workshop XIII
    • 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’ November 3-5, 2009 30HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 31HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 33HDF/HDF-EOS Workshop XIII
    • 33. www.hdfgroup.org HDFView Structure of FileStructure of File Contents of Dataset Contents of Dataset November 3-5, 2009 34HDF/HDF-EOS Workshop XIII
    • 34. www.hdfgroup.org HDFView File Menu November 3-5, 2009 35HDF/HDF-EOS Workshop XIII
    • 35. www.hdfgroup.org HDF-EOS5 File in HDFView November 3-5, 2009 36HDF/HDF-EOS Workshop XIII
    • 36. www.hdfgroup.org Introduction to HDF5 Programming Model and APIs November 3-5, 2009 37HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 38HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 39HDF/HDF-EOS Workshop XIII
    • 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. November 3-5, 2009 40HDF/HDF-EOS Workshop XIII
    • 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. November 3-5, 2009 42HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 45HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 46HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 48HDF/HDF-EOS Workshop XIII
    • 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) November 3-5, 2009 49HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 50HDF/HDF-EOS Workshop XIII
    • 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) November 3-5, 2009 51HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 52HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 53HDF/HDF-EOS Workshop XIII
    • 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. November 3-5, 2009 54HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 58HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 59HDF/HDF-EOS Workshop XIII
    • 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 November 3-5, 2009 60HDF/HDF-EOS Workshop XIII
    • 58. www.hdfgroup.org Example Code - H5Dwrite status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL,H5S_ALL, H5P_DEFAULT, wdata); Dataset ID from H5Dcreate/H5Dopen Memory Datatype November 3-5, 2009 61HDF/HDF-EOS Workshop XIII
    • 59. www.hdfgroup.org 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,…) November 3-5, 2009 63HDF/HDF-EOS Workshop XIII
    • 61. www.hdfgroup.org Example Code – H5Dread status = H5Dread (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata); November 3-5, 2009 64HDF/HDF-EOS Workshop XIII
    • 62. www.hdfgroup.org 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. November 3-5, 2009 67HDF/HDF-EOS Workshop XIII
    • 64. www.hdfgroup.org Example: Create a Group A B “/” (root) 4x6 array of integers file.h5 November 3-5, 2009 68HDF/HDF-EOS Workshop XIII
    • 65. www.hdfgroup.org 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 70HDF/HDF-EOS Workshop XIII
    • 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/ November 3-5, 2009 71HDF/HDF-EOS Workshop XIII
    • 67. www.hdfgroup.org The HDF Group Thank You! November 3-5, 2009 72HDF/HDF-EOS Workshop XIII
    • 68. www.hdfgroup.org 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
    • 69. www.hdfgroup.org The HDF Group Questions/comments? November 3-5, 2009 74HDF/HDF-EOS Workshop XIII

    ×