HDF - 1 - Mike Folk National Center for Supercomputing Applications HDF and HDF-EOS Workshop VI...
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Transcript of HDF - 1 - Mike Folk National Center for Supercomputing Applications HDF and HDF-EOS Workshop VI...
- 1 - HDFHDF
Mike Folk
National Center for Supercomputing Applications
HDF and HDF-EOS Workshop VI
December 4-5, 2002
HDF UpdateHDF Update
HDFHDF
- 2 - HDFHDF
TopicsTopics
• Who is supporting HDF
• HDF software in 2002
• Other activities of interest
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Who is supporting HDF?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
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HDF software in 2002HDF software in 2002
• Library releases
• Java Products
• Tools
• Compression
• Investigations of Web technologies
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HDF4 libraryHDF4 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
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1.4.3
1.4.4
1.4.5
HDF5 tables
High level
APIsHigh level library
HDF5 software milestones in 2002HDF5 software milestones in 2002Q1 ‘02 Q2 ‘02 Q3 ‘02 Q4 ‘02
H5im
port
H4-H5
conversion
library
Base library
Java products
Other tools
Java
products
1.0
Java
products
1.1
Java
prods 1.2
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HDF5 library in 2002HDF5 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
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Parallel HDF5Parallel 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
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Next major release -- HDF5 1.6Next 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
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Next major release -- HDF5 1.6Next 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
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High level APIsHigh 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
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High level APIsHigh 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/
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HDF Java Products – 2002HDF 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/
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HDFView releases in 2002HDFView releases in 2002
Version 1.0Browser for both HDF4 and HDF5
Version 1.1
Editor for both HDF4 and HDF5
Version 1.2
All features of old Java tools.Some new features.
Q2 Q3 Q4
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/
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H4toH5 Conversion ToolkitH4toH5 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
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Other tools workOther 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
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Other tools workOther 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
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CompressionCompression
• 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
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HDF5 XMLHDF5 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
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XML, Java Server Pages, etc.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/
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CORBA ExperimentsCORBA 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
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NPOESSNPOESS
• 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
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Neutron Research CommunityNeutron 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/
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National Archives and National Archives and Records AdministrationRecords 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
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Atmospheric and Ocean ModelsAtmospheric 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
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HDF5 Mesh API prototypeHDF5 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
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HDF5 Wins 2002 R&D Magazine AwardHDF5 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
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Thank you!Thank you!
• HDF website– http://hdf.ncsa.uiuc.edu/
• HDF5 Information Center– http://hdf.ncsa.uiuc.edu/HDF5/
• HDF Helpdesk– [email protected]
• HDF users mailing list– [email protected]
HDFHDF
55
Information SourcesInformation Sources
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HDF5 funding sourcesHDF5 funding sourcesDOE
SciDAC 4%
Other4%
State of IL10%
NSF14%
ASCI31%
NASA37%
NASA ASCI NSF State of IL DOE SciD Other$588,000 $495,000 $225,553 $162,750 $70,000 $60,000
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HDF5 User CommunityHDF5 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)
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Technical fields that use HDF5Technical fields that use HDF5
• 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
• 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
- 38 - HDFHDF
Next major release -- HDF5 1.6Next 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
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Next major release -- HDF5 1.6Next 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
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HDF5 High Level APIs – HDF5 High Level APIs – HDF5 ImageHDF5 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”
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HDF5 High Level APIs – HDF5 TableHDF5 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 - HDFHDF
HDF5 High Level APIs – HDF5 TableHDF5 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
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HDF5 High Level API – FutureHDF5 High Level API – Future
• Dimension scales– Similar to HDF4– In progress
• More table operations– sort and search
• Unstructured grids– E.g. triangle mesh
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Szip Compression SoftwareSzip 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
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Performance study – BZIP2 compressionPerformance 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/
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New HDFView featuresNew HDFView features
• 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
- 47 - HDFHDF
Java Native
Interface
HDF Libraryand File
H5view,etc
C
Java
Java
C
Applet
Java
CORBAServer
OtherApp. Other
App.
C++
Any
Any
Client/Remote Server/Local
Java Server
Platform
Webbrowser
HTML
XML
Java
Any
Java Native
Interface
Java C
Distributed Product
Demonstrated in Research
Should work, but not demonstrated
CORBA, XML etc. permutationsCORBA, XML etc. permutations
- 48 - HDFHDF
Local Equatorial
Crossing Time
05301330
0930
METOP
NPOESS
NPOESSLite
NPOESS
Local Equatorial
Crossing Time
METOP
0530
08301330
0930
DMSP
DMSP
POES
National Polar-orbiting Operational Environmental National Polar-orbiting Operational Environmental Satellite System (NPOESS)Satellite System (NPOESS)
Today• 4-Orbit System
– 2 US Military– 2 US Civilian
U.S. civil and defense programs to combine weather data collection, U.S. civil and defense programs to combine weather data collection, expanding to global coverage and long-term continuity of observations at expanding to global coverage and long-term continuity of observations at
less cost!less cost!
Local Equatorial
Crossing Time
0530
07301330
0830
DMSP
DMSP
POES
POES
Distribute in HDF5Distribute in HDF5
Tomorrow (2005)2 US Military1 US Civilian1 EUMETSAT/METOP
Future (2013)2 US Converged1 US “Lite”1 EUMETSAT/METOPSpecialized Satellites