HDF Update

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

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

-2-

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

-3-

HDF

HDF software in 2002
•
•
•
•
•

Library releases
Java Products
Tools
Compression
Investigations of Web technologies

-4-

HDF

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

-5-

HDF

HDF5 software milestones in 2002
Q1 ‘02
Base
library
High level
library
Java
products
Other
tools





Q2 ‘02

Q3 ‘02

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

HDF

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
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HDF

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
-8-

HDF

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

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HDF

• 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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HDF

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

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HDF

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/
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HDF

HDF5 tools activities

- 13 -

HDF

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/

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HDF

HDFView releases in 2002
Q2
Version 1.0
Browser for
both HDF4
and HDF5

Q3
Version 1.1
Editor for
both HDF4
and HDF5

Q4
Version 1.2
All 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/
- 15 -

HDF

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

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HDF

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
- 17 -

HDF

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

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HDF

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

- 19 -

HDF

Investigations of Web technologies

- 20 -

HDF

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
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HDF

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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HDF

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

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HDF

Other Activities of Interest

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HDF

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
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HDF

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, postprocess 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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HDF

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

- 27 -

HDF

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
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HDF

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
- 29 -

HDF

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

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HDF

Thank you!
Information Sources
HDF • HDF website
– http://hdf.ncsa.uiuc.edu/

5 • HDF5 Information Center

– http://hdf.ncsa.uiuc.edu/HDF5/

• HDF Helpdesk
– hdfhelp@ncsa.uiuc.edu

• HDF users mailing list
– hdfnews@ncsa.uiuc.edu
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HDF

HDF5 funding sources
Other
DOE 4%
SciDAC
4%
State of IL
10%

NASA
37%

NSF
14%
ASCI
31%

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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HDF

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)

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HDF

Technical fields that use HDF5
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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

•
•
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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

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•
•
•
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•
•
•
•
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•
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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

HDF

Users of HDF5 – 66 countries

- 36 -

HDF


- 37 -

HDF

• 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
- 38 -

HDF

• 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

- 39 -

HDF

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”

- 40 -

HDF

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:
- 41 -

HDF

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

- 42 -

HDF

HDF5 High Level API – Future
• Dimension scales
– Similar to HDF4
– In progress

• More table operations
– sort and search

• Unstructured grids
– E.g. triangle mesh

- 43 -

HDF

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
- 44 -

HDF

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/

- 45 -

HDF

New 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

- 46 -

•
•
•
•
•
•
•

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

HDF

CORBA, XML etc. permutations
Java

HTML

Java C

Java
Java
Server
Native
Platform Interface

Web
browser

HDF
Library
and File

C

XML

Any

CORBA
Server

Applet

C++

Java
Native
Interface

C
Java

Java

Other
App.

Other
App.

Any

H5view,
etc

Java

Any
Client/Remote

Server/Local

Distributed Product
Demonstrated in Research
Should work, but not demonstrated

- 47 -

HDF

National Polar-orbiting Operational Environmental
Satellite System (NPOESS)
U.S. civil and defense programs to combine weather data collection, expanding to
global coverage and long-term continuity of observations at lessMETOP
cost!
POES

METOP
DMSP

0730

1330
0830

0530

0830
0530

1330

DMSP

Today
• 4-Orbit System
– 2 US Military
– 2 US Civilian

NPOESS

0530

0930

0930

1330

POES

POES

Local Equatorial
Crossing Time

NPOESS

DMSP

Local Equatorial
Crossing Time

DMSP

Tomorrow (2005)
2 US Military
1 US Civilian
1 EUMETSAT/METOP

- 48 - Distribute

Local Equatorial
Crossing Time

NPOESS
Lite

Future (2013)
2 US Converged
1 US “Lite”
1 EUMETSAT/METOP
Specialized Satellites

in HDF5 HDF

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