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WMO ET-ADRS: 23-25 April 2008 1 WMO ET-ADRS Hierarchical Data Format (HDF) Manuel Fuentes (ECMWF) Erdem Erdi (Turkish State Meteorological Service)

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Presentation on theme: "WMO ET-ADRS: 23-25 April 2008 1 WMO ET-ADRS Hierarchical Data Format (HDF) Manuel Fuentes (ECMWF) Erdem Erdi (Turkish State Meteorological Service)"— Presentation transcript:

1 WMO ET-ADRS: 23-25 April 2008 1 WMO ET-ADRS Hierarchical Data Format (HDF) Manuel Fuentes (ECMWF) Erdem Erdi (Turkish State Meteorological Service)

2 WMO ET-ADRS: 23-25 April 2008 2 Outline Brief introduction to HDF SWOT Analysis Practical examples

3 WMO ET-ADRS: 23-25 April 2008 3 Hierarchical Data Format: HDF HDF is a file format HDF files are self-described HDF technologies at present include two data management formats (HDF4 and HDF5) and libraries, a modular data browser/editor, associated tools and utilities, and a conversion library Both HDF4 and HDF5 were designed to be a general scientific format, adaptable to virtually any scientific or engineering application, and also have been used successfully in non- technical areas HDF5 is particularly good at dealing with data where complexity and scalability are important

4 WMO ET-ADRS: 23-25 April 2008 4 Features provided by HDF5 technology Unlimited size, extensibility, and portability General data model Unlimited variety of datatypes Flexible, efficient I/O Flexible data storage Data transformation and complex subsetting

5 WMO ET-ADRS: 23-25 April 2008 5 HDF5: Unlimited size, extensibility, and portability HDF5 does not limit the size of files or the size or number of objects in a file. The HDF5 format and library are extensible and designed to evolve gracefully to satisfy new demands. HDF5 functionality and data is portable across virtually all computing platforms and is distributed with C, C++, Java, and Fortran90 programming interfaces.

6 WMO ET-ADRS: 23-25 April 2008 6 HDF5: General data model The HDF5 data model supports complex data relationships and dependencies through its grouping and linking mechanisms. HDF5 accommodates many common types of metadata and arbitrary user-defined metadata.

7 WMO ET-ADRS: 23-25 April 2008 7 HDF5: Unlimited variety of datatypes HDF5 supports a rich set of pre-defined datatypes as well as the creation of an unlimited variety of complex user-defined datatypes. Datatype definitions can be shared among objects in an HDF file, providing a powerful and efficient mechanism for describing data. Datatype definitions include information such as byte order (endian), size, and floating point representation, to fully describe how the data is stored, insuring portability to other platforms.

8 WMO ET-ADRS: 23-25 April 2008 8 Data model and datatypes

9 WMO ET-ADRS: 23-25 April 2008 9 HDF5: Flexible, efficient I/O HDF5, through its virtual file layer, offers extremely flexible storage and data transfer capabilities. Standard (Posix), Parallel, and Network I/O file drivers are provided with HDF5. Application developers can write additional file drivers to implement customized data storage or transport capabilities. The parallel I/O driver for HDF5 reduces access times on parallel systems by reading/writing multiple data streams simultaneously.

10 WMO ET-ADRS: 23-25 April 2008 10 HDF5: Flexible data storage HDF5 employs various compression, extensibility, and chunking strategies to improve access, management, and storage efficiency. HDF5 provides for external storage of raw data, allowing raw data to be shared among HDF5 files and/or applications, and often saving disk space.

11 WMO ET-ADRS: 23-25 April 2008 11 HDF5: Data transformation and complex subsetting HDF5 enables datatype and spatial transformation during I/O operations. HDF5 data I/O functions can operate on selected subsets of the data, reducing transferred data volume and improving access speed.

12 WMO ET-ADRS: 23-25 April 2008 12 Governance: The HDF Group The mission of The HDF Project is to develop, promote, deploy and support open and free technologies that facilitate scientific data exchange, access, analysis, archiving and discovery to ensure long-term availability and support for HDF technologies, and by extension, long-term accessibility of data stored using HDF technologies The HDF group currently includes 15 full time staff members and 3 to 5 students. The groups annual budget is $2.1 million, which is mostly provided by the government sector

13 WMO ET-ADRS: 23-25 April 2008 13 Copyright http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html HDF5 (Hierarchical Data Format 5) Software Library and Utilities with Copyright 2006-2008 by The HDF Group (THG). NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities with Copyright 1998-2006 by the Board of Trustees of the University of Illinois. All rights reserved.

14 WMO ET-ADRS: 23-25 April 2008 14 Copyright (cont.) Redistribution and use in source and binary forms, with or without modification, are permitted for any purpose (including commercial purposes) provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions, and the following disclaimer Redistributions in binary form must reproduce the above copyright notice (which is on the previous slide), this list of conditions, and the following disclaimer in the documentation and/or materials provided with the distribution In addition, redistributions of modified forms of the source or binary code must carry prominent notices stating that the original code was changed and the date of the change All publications or advertising materials mentioning features or use of this software are asked, but not required, to acknowledge that it was developed by The HDF Group and by the National Center for Supercomputing Applications at the University of Illinois at Urbana- Champaign and credit the contributors Neither the name of The HDF Group, the name of the University, nor the name of any Contributor may be used to endorse or promote products derived from this software without specific prior written permission from THG, the University, or the Contributor, respectively DISCLAIMER: THIS SOFTWARE IS PROVIDED BY THE HDF GROUP (THG) AND THE CONTRIBUTORS "AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED. In no event shall THG or the Contributors be liable for any damages suffered by the users arising out of the use of this software, even if advised of the possibility of such damage

15 WMO ET-ADRS: 23-25 April 2008 15 SWOT Analysis: Criteria Ability to present information pertinent to WMO Programmes Ability to encode textual information, such as warnings Ability for usage in operational data exchanges Ability for usage in transmission of information to users outside NMHSs Ability for usage in storage systems by NMHSs, centres or other users Compliance and status with regard to existing standards Inter-operability, translation back and forward to other DRSs Can it be used to envelope objects Available and widespread support (skills and technology)

16 WMO ET-ADRS: 23-25 April 2008 16 SWOT : Present information pertinent to WMO Ability/suitability to present information pertinent to WMO Programmes and Member needs including weather, climate, water, atmospheric constituents, oceanography, aviation and other related environmental information Any data of 2-D, 3-D meteorology, hydrology or similar science can be handled Used by satellite applications in meteorology due to suitability for large and complex data. There are not too many tools for non-satellite meteorological data Its not clear how to handle millions of bulletins: Group bulletins into a big file 1 bulletin per file (minimum HDF5 file size: 2 Kbyte)

17 WMO ET-ADRS: 23-25 April 2008 17 SWOT : Present information for pictorial display Ability/suitability to present information for pictorial display HDF can store and present graphical data with 2 or 3 dimensions, allows for raster and vectors. Tools can display information in graphical form

18 WMO ET-ADRS: 23-25 April 2008 18 SWOT : Encode textual information Ability/suitability to encode textual information, such as warnings HDF can store textual information of any length Suitable for storing metadata

19 WMO ET-ADRS: 23-25 April 2008 19 SWOT : Encode Metadata

20 WMO ET-ADRS: 23-25 April 2008 20 SWOT : Usage in operational data exchanges Ability/suitability for usage in operational data exchanges (real time or otherwise) between NMHSs and centres. Including information regarding existing usage especially with regard to extent of use EUMETSAT dissemination (EUMETCAST) supports HDF as delivery format There is no naming convention for satellite data (only TERRA & AQUA share naming convention, because the same team developed the 2 satellites). Otherwise each satellite has different naming convention and order of elements in file There are 2 attempts to standardize satellite data in HDF: KNMI-HDF5: Special library for encoding HDF-EOS: TERRA, AQUA & Petabytes more

21 WMO ET-ADRS: 23-25 April 2008 21 SWOT : Usage in operational data exchanges An important portion of the operational satellite based meteorological data and products are distributed to the meteorological community in the HDF format, in near-realtime or non-realtime (archive). Some examples are EUMETSAT SAF Products (NWC SAF, LAND SAF) EUMETSAT EPS data NASA EOS Data and products

22 WMO ET-ADRS: 23-25 April 2008 22 SWOT : Transmission of information to users outside NMHS Ability/suitability for usage in transmission of information to users outside NMHSs or centres. Including information regarding existing usage especially with regard to extent of use HDF is widely used in scientific communities: Universities, Research labs Space agencies (like NASA and EUMETSAT) HDF is mainly used for satellite data. Use of HDF in a variety of disciplines and users Encourages development of tools Makes it easy to use outside NMHSs Software publicly available with supported tools

23 WMO ET-ADRS: 23-25 April 2008 23 SWOT : Usage in storage systems Ability/suitability for usage in storage systems by NMHSs, centres or other users. Including information regarding existing usage especially with regard to extent of use Parallel I/O Machine independent Compression The HDF Group is committed to ensure the long-term accessibility of HDF-stored data EUMETSAT does not store data in HDF, but convert from raw NASA archives the Earth Observing System data in HDF Grouping of data at archiving may impose restrictions on how data can be retrieved

24 WMO ET-ADRS: 23-25 April 2008 24 SWOT : Standards Compliance and status with regard to with existing standards. Are they open standards? Which body overseas them. Is there any proprietary nature to them. Are they flexible enough to accommodate our current and foreseen needs. How are they updated, is it a straight forward process HDF format is very suitable for GIS (as it can handle both data and metadata in the same file). However, it is not widely used for GIS because of the lack of a convention (schema) It is governed by The HDF Group Compression: SZIP method is proprietary, ZLIB is open HDF licence seems flexible The library is updated regularly in a straight forward manner

25 WMO ET-ADRS: 23-25 April 2008 25 SWOT : Interoperability How suitable is the DRS to the WIS and to developing the appropriate metadata? Is existing documentation good? How much variance is there in current implementations? Are the existing flavours inter-operable? HDF can meet the requirements regarding metadata required for the WIS Documentation is good with lots of examples There are 2 implementations: Tools to convert from HDF4 to HDF5 No direct inter-operability between the 2 implementations

26 WMO ET-ADRS: 23-25 April 2008 26 SWOT : Conversion to/from other DRS What are the issues for translating back and forward to other DRSs? Translation could be loss-less when using same encoding method (not standard) Encoding: Offset and scale factor. Tools are not aware of encoding Compression can be used instead of encoding in order to avoid larger files Compression is transparent for users Native data types are 1, 2, 4, 8 bytes

27 WMO ET-ADRS: 23-25 April 2008 27 SWOT : Envelope objects Can they be used to envelope objects or act as a pseudo-carrier for other data formats? HDF can handle/envelope any kind of data format either binary or ASCII HDF can handle BLOBs (stream of bytes)

28 WMO ET-ADRS: 23-25 April 2008 28 SWOT: Support, skills and technology Available and widespread support for the DRS (skills and technology) The HDF Groups commitment to: Support HDF Ensure long-term accessibility of the data Established user community

29 WMO ET-ADRS: 23-25 April 2008 29 SWOT Summary: Strengths HDF5 can store and present 2-D or 3-D data (gridded fields), together with metadata Rich set of predefined datatypes and data relationships High performance features: Parallel I/O Unlimited dimensions Compression Unlimited size and amount of data I/O functions can operate on subsets of data Open data format and free software (libraries and tools) Operational services (EUMETCAST) support HDF

30 WMO ET-ADRS: 23-25 April 2008 30 SWOT Summary: Weaknesses HDF is a file format, as opposed to a message/bulletin format (like GRIB or BUFR) There is no convention: Names to use Order in which to store elements May not handle well point observation data There arent many tools for meteorological data Comparison with NetCDF: HDF5s general data model makes writing data more difficult than NetCDF HDF5 will be the storage format for NetCDF4

31 WMO ET-ADRS: 23-25 April 2008 31 SWOT Summary: Opportunities Using HDF5 may improve inter-operability with other disciplines Using HDF5 may improve usability of meteorological data outside NMHSs Software publicly available, with numerous (general) tools and programming languages

32 WMO ET-ADRS: 23-25 April 2008 32 SWOT Summary: Threats The HDF format is developed and maintained by a single group (The HDF Group). Any problem with funding could jeopardise the existence of the format or its support Meteorology would be very small community compared to other users of HDF. Requirements of the Meteorological community may not be so important for the HDF community

33 WMO ET-ADRS: 23-25 April 2008 33 Practical Examples Data received at ECMWF, converted to BUFR, then used by Forecasting System: HDF4 Microwave Brightness Temperature from Tropical Rainfall Measuring Mission (trmm) Rainfall from Tropical Rainfall Measuring Mission (trmm) HDF5 METOP GOME-2 total column ozone data Aura OMI ozone data Each data stream has its own conversion tool HDF to BUFR

34 WMO ET-ADRS: 23-25 April 2008 34 Practical Examples Eumetsat HDF-EOS HDF-KNMI We havent found any examples of field observations (SYNOP, METAR, radiosondes..)

35 WMO ET-ADRS: 23-25 April 2008 35 Practical Example: MODIS swath data from channel 3

36 WMO ET-ADRS: 23-25 April 2008 36 Practical Example: 3-D data Schwarzschild metric (spatial components only)

37 WMO ET-ADRS: 23-25 April 2008 37 Practical Example: MSG total precipitable water

38 WMO ET-ADRS: 23-25 April 2008 38 Practical Example: SAF cloudtype product

39 WMO ET-ADRS: 23-25 April 2008 39 Conclusion HDF5 is going to be the base for NetCDF4. It makes more sense to focus on NetCDF4 than HDF5 Support for subsetting Parallel I/O Unlimited dimensions Compression Remove current limitations on file size HDF is a file format as opposed to GRIB/BUFR which are message (or bulletin) formats HDF might not be suitable for operational exchange of meteorological data between NMHSs, but to present meteorological information to other users/disciplines


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