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HDF Update

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  1. HDF HDF Update Mike Folk National Center for Supercomputing Applications HDF and HDF-EOS Workshop VI December 4-5, 2002

  2. Topics • Who is supporting HDF • HDF software in 2002 • Other activities of interest

  3. Who is supporting HDF? • NASA/ESDIS • Earth science applications, instrument data • DOE/ASCI (Accelerated Strategic Computing Init.) • Simulations on massively parallel machines • NCSA/NSF/State of Illinois • HPC and Grid data intensive apps, Visualization, user support • Atmospheric and ocean modeling environments • DOE Scientific Data Analysis & Computation Program • High performance I/O R & D • National Archives and Records Administration • Small grant to consider HDF5 as an archive format

  4. HDF software in 2002 • Library releases • Java Products • Tools • Compression • Investigations of Web technologies

  5. HDF4 library • No releases in 2002. • Release 1.6 planned for May, 2003 • Bug fixes • New compilers • Intel • Portland Group • New OS • Mac OS X • AIX 5.1 64-bit

  6. HDF5 software milestones in 2002 1.4.3 1.4.4 1.4.5  HDF5 tables   High level APIs  Java products 1.1  Java products 1.0  Java prods 1.2  H4-H5 conversion library  H5import Q1 ‘02 Q2 ‘02 Q3 ‘02 Q4 ‘02 Base library High level library Java products Other tools

  7. HDF5 library in 2002 • Compilers, configuration, etc. • “h5cc” script to simplify compilation of HDF5 programs • F90 shared library and C++ supported on Windows • Intel C, F90 and C++ on Linux, IA32/64 and Windows • Support for zlib 1.1.4 • Performance • Added library performance tests • Performance improvements • hyperslabs, data conversions. chunking • Fewer and larger I/O requests when accessing a file • Parallel I/O performance improvements

  8. Parallel HDF5 • Parallel I/O performance benchmark suite • Compares raw I/O, MPI-I/O, and HDF5 I/O • Distributed with HDF5 • http://hdf/RFC/PIO_Perf/PHDF5_performance.html • Parallel HDF5 tutorial • http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/ • “Flexible parallel HDF5” programming model • More flexible model for parallel HDF5 • Performance studies and tuning activities

  9. Next major release -- HDF5 1.6 • Release date: Spring 2003 • New format and library features include • Compression enhancements, including szip • Generic Properties • Checksum • Dimension scale support (tentative) • Performance improvements include • Chunking & compression • Parallel I/O performance benchmark suite

  10. Next major release -- HDF5 1.6 • Flexible parallel HDF5 • Special platforms • Large Compaq cluster (Pittsburgh SC) • Crays • Windows XP • Mac • Several new compilers (e.g. Intel, Portland Group) • Documentation • New User’s Guide-good draft, first version

  11. High level APIs • Make HDF5 easier to use • More operations per call than the normal HDF5 API • Encourage standard ways to store objects • Enforce standard representation of objects in HDF5

  12. High level APIs • Lite – done • Same as HDF5, but simpler • Image – done • Interprets dataset as image/palette • 2-D raster data like HDF4 raster images • Table – partly done • Interprets dataset as “tables” – collections of records • Insert, delete records or fields • Future: sort and search • Dimension scale – in the works • Unstructured grids – in the works • http://hdf.ncsa.uiuc.edu/HDF5/hdf5_hl/doc/

  13. HDF5 tools activities

  14. HDF Java Products – 2002 • Goal: replace older tools with single viewer/editor • HDF Java Products • Java HDF Interface (JHI) – to access the HDF4 library. • Java HDF5 Interface (JHI5) – to access the HDF5 library. • New hdf-object package – understands HDF4 and HDF5. • HDFView – tool for browsing/editing HDF4 and HDF5 • See demo, brochure, CD, web page • http://hdf.ncsa.uiuc.edu/hdf-java-html/

  15. HDFView releases in 2002 Q2 Q3 Q4 Version 1.0 Browser for both HDF4 and HDF5 Version 1.1Editor for both HDF4 and HDF5 • Version 1.2All features of old Java tools. • Some new features. HDFView can do as much as JHV and H5View and also includes many new editing features http://hdf.ncsa.uiuc.edu/hdf-java-html/hdfview/

  16. H4toH5 Conversion Toolkit • Goal: support transition from HDF4 to HDF5 • Version 1.0 released in July 2002 • Includes • h4toh5 converter • h5toh4 converter • library of functions for converting HDF4 objects into HDF5 objects • Download from: • http://hdf.ncsa.uiuc.edu/h4toh5/libh4toh5.html • Mapping specification and FAQ • http://hdf.ncsa.uiuc.edu/HDF5/doc/ADGuide/H4toH5Mapping.pdf

  17. Other tools work • H5import - convert flat files to HDF5 datasets • ASCII text file with numeric data (float or integer) • Binary file with native floating point data • Binary file with native integer data • hdf4import – souped up version of the old fptohdf • Available in hdf4r1.6 • HDF5-to-GIF and GIF-to-HDF5 converters • H5dump improvements • Subsetting • Support variable length datatypes including strings

  18. Other tools work • H5diff • compare the structure and contents of two HDF5 files, and report differences • Command line utility like Unix ‘diff’ and older ‘hdiff’ • Report missing objects, inconsistent size, datatype, etc. • Compare values of numeric datasets • First beta available January 2003 • RFC: http://hdf.ncsa.uiuc.edu/RFC/H5diff/h5diff.html

  19. Compression • Szip - fast compression method for EOS data • Expect to include in next releases of HDF4 and HDF5 • Shuffling – reorder bytes before compressing • Can improve compression ratio • Performance study – BZIP2 vs gzip compression • Study: whether or not to support bzip2 compression • Result: BZIP2 not significantly better than gzip • So not currently supported in the release • But BZIP2 can be used with HDF5

  20. Investigations of Web technologies

  21. HDF5 XML • Great interest in XML, interoperation of XML and binary formats • Results • HDF5 DTD • h5dump –XML • H5View reads XML and writes HDF5 • Studies, design notes, other info • http://hdf.ncsa.uiuc.edu/HDF5/XML/ • Possible future activity: • XML schema • Update tools • HDF4 schema, tools • Format translation via XSLT

  22. XML, Java Server Pages, etc. • How to use HDF5 data in Web environment • Experiments with XML, Java Server Pages (JSP), etc. • JSP server • Access HDF5 files on Web server using Web browser, or Java applet, or Java application • Several variations demonstrated • Is not a product! • http://hdf.ncsa.uiuc.edu/HDF5/XML/

  23. CORBA Experiments • HDF5 with CORBA on distributed systems • Prototype CORBA server to wrap HDF5 library and datasets (C++) • Remote access via C++, Java, Web • Might be valuable as replacement for Java Native Interface • Successful demonstration, but many open issues • Is not a product! http://hdf.ncsa.uiuc.edu/HDF5/XML/JSPExperiments/index.html

  24. Other Activities of Interest

  25. NPOESS • National Polar-orbiting Operational Environmental Satellite System • Combine satellite systems of civil and defense programs • HDF5 to be used to distribute data to users • First implementation in 2006 • Support the NPOESS Preparatory Program • Later full implementation by 2013 • Converged system provides global coverage • http://www.ipo.noaa.gov

  26. Neutron Research Community • Worldwide research community • England, France, Germany, Japan, Italy, Switzerland, Russia • US centers at Argonne, NIST, Los Alamos • Neutron and X-ray scattering experiments and simulations • Common software and formats to gather, share, archive, post-process data • NeXus data format • Enforces standardization of metadata and data structures • Based on HDF4 for many years • Now switching to HDF5 • http://www.neutron.anl.gov/nexus/

  27. National Archives and Records Administration • Pilot project for HDF5 • Explore scientific data format requirements for long term archiving of electronic records • Identify record types for which HDF5 is suited

  28. Atmospheric and Ocean Models • Modeling Environment for Atmospheric Discovery (MEAD) • HDF5 for high performance I/O for atmospheric and ocean modeling • Weather Research and Forecasting (WRF) model • Regional Ocean Modeling System (ROMS) • Coupling of WRF and ROMS • UAH ESML & data mining also involved

  29. HDF5 Mesh API prototype • Support for structured and unstructured “mesh” data • For applications such as computational fluid dynamics, finite element analysis, and visualization. • A higher-level API • Format • HDF5 groups and datasets to organize the data • Collaboration involving NCSA, CEI and others • Documentation still pretty sketchy, but see • ftp://ftp.ensight.com/pub/HDF_RW/hdf_rw.tgz • Discussion list in the works

  30. HDF5 Wins 2002 R&D Magazine Award “The 100 products and processes that are the most ‘technologically significant’ and can change people's lives for the better” http://www.ncsa.uiuc.edu/News/Access/Releases/020722.HDF5.html

  31. Thank you! HDF 5 Information Sources • HDF website • http://hdf.ncsa.uiuc.edu/ • HDF5 Information Center • http://hdf.ncsa.uiuc.edu/HDF5/ • HDF Helpdesk • hdfhelp@ncsa.uiuc.edu • HDF users mailing list • hdfnews@ncsa.uiuc.edu

  32. Backup slides

  33. HDF5 funding sources

  34. HDF5 User Community • Worldwide use in government, academia, industry • How many users? • 450 organizations or individuals have filled in “user” form in the past year • There are many times this many anonymous users • And some organizations have thousands of users (e.g. the Earth Observing System) • Public applications • More than 25 publicly available applications • Four vendors so far • LabVIEW • IDL • EarthScan Network • HDF Explorer • Others in the works (e.g. Matlab)

  35. Aerospace Agricultural research Air traffic control Aircraft emissions database Applied mathematics Astrophysics Astrophysics / supernovae Atmospheric chemistry Atmospheric physics Bioengineering CEM Simulation Climatology / hydrology Computational fluid dynamics Computational physics Computational physics / education Computational physics and computational astrophysics Computer modeling Computer science Data processing Earth observation / atmospheric science Earth science Photonic band gap studies Photonic crystals Photonics Post-fire erosion analysis Protein crystallography, molecular modeling Protostellar accretion discs Remote sensing SAR processing Satellite / weather radar remote sensing Satellite oceanography Semiconductor process simulation Software engineering, distributed systems Space geodesy Space physics Surface water flow and sediment transport Theoretical chemistry Visualization Volcanology Water resources management X-ray physics Technical fields that use HDF5 • Environmental science • Fast searching, sorting and retrieval • Film making special effects • Fluid mechanics • GIS • Geodetic Science • Geology • Gravitational physics • Hydrology • Information technology • Magnetic mass spectrometer development • Marine biology / ecology • Materials science • Meteorological data products • Meteorology • Microscopy • Molecular biology • Nano device simulation • Neutron scattering • Ocean color • Ocean remote sensing • Optics / optoelectronics • Petroleum engineering

  36. Users of HDF5 – 66 countries

  37. Next major release -- HDF5 1.6

  38. Next major release -- HDF5 1.6 • Performance improvements • Chunking • Compression (several) • Parallel I/O • Metadata I/O • Compact dataset storage • Other parallel • Parallel I/O performance benchmark suite • Flexible parallel HDF5 • Portland group C, Fortran 90 and C++ compilers • Quite a bit of Fortran work

  39. Next major release -- HDF5 1.6 • Testing (several) • Special platforms • PSC cluster • Cray • Windows XP • Mac • Several new compilers (e.g. Intel, Portland Group) • Documentation • New User’s Guide-good draft, first version

  40. HDF5 High Level APIs – HDF5 Image • For datasets to be interpreted as images/palettes • 2-D raster data like HDF4 raster images • Image operations • Create, write, read, query • Based on “HDF5 Image & Palette Specification”

  41. HDF5 High Level APIs – HDF5 Table • For datasets to be interpreted as “tables” • A collection of records • All records have the same structure • Like Vdatas in HDF4, but more operations • Table operations • Create, write, read, query • Insert, delete records or fields • Future: sort and search • Includes the following new Table functions:

  42. HDF5 High Level APIs – HDF5 Table • For datasets to be interpreted as “tables” • A collection of records • All records have the same structure • Like Vdatas in HDF4, but more operations • Table operations • Create, write, read, query • Insert, delete records or fields • Later: sort and search

  43. HDF5 High Level API – Future • Dimension scales • Similar to HDF4 • In progress • More table operations • sort and search • Unstructured grids • E.g. triangle mesh

  44. Szip Compression Software • Implements CCSDS lossless compression algorithm • Fast compression method for EOS data • Expect to include in next releases of HDF4 and HDF5 • HDF4: compress SDS and image • HDF5: compress datasets • Intellectual property issues • Owned by U of Idaho (formerly U of New Mexico) • Open source • No commercial of encoder use without license • Decoder free for everyone

  45. Performance study – BZIP2 compression • Goal: decide whether or not to support bzip2 compression • Compared bzip2 and gzip • Observations • Bzip2 always better than gzip in compression ratio • But the difference was just a few percentage points • And bzip2 always takes more processing time, especially for decoding • Result • Not currently supported in the release • But BZIP2 can be used with HDF5 (checked with HDF5-1.4.4) • http://hdf.ncsa.uiuc.edu/HDF5/papers/bzip2/

  46. Display palette in graph as separate RGB lines. Open file as read-only option Create new array from old array Import data from text file Save to HDF4, HDF5 or binary Create new image from subset of existing image Modify string-type dataset content Convert jpeg to HDF image Convert HDF to jpeg image More user options and well organized GUI Select vdata or compound datatype by field Select subset from preview image and using mouse Support unlimited dimension when creating new HDF4 dataset. Enable application of simple math calculations to data Support multiple palettes/image Create new image with default attributes Modify image palette or select predefined palette New HDFView features

  47. CORBA, XML etc. permutations HTML Java Java C HDF Library and File Web browser Java Server Platform Java Native Interface XML C Any CORBA Server Applet Java Native Interface C C++ Java Java Other App. H5view, etc Other App. Java Any Any The Net Client/Remote Server/Local Distributed Product Demonstrated in Research Should work, but not demonstrated

  48. National Polar-orbiting Operational Environmental Satellite System (NPOESS) METOP NPOESS 0530 1330 0930 Local Equatorial Crossing Time NPOESS Lite • Tomorrow (2005) • 2 US Military • 1 US Civilian • 1 EUMETSAT/METOP • Future (2013) • 2 US Converged • 1 US “Lite” • 1 EUMETSAT/METOP • Specialized Satellites U.S. civil and defense programs to combine weather data collection, expanding to global coverage and long-term continuity of observations at less cost! Today • 4-Orbit System • 2 US Military • 2 US Civilian POES METOP NPOESS DMSP DMSP 0830 0730 1330 1330 0930 0530 0830 0530 POES POES Local Equatorial Crossing Time Local Equatorial Crossing Time DMSP DMSP Distribute in HDF5